Merge branch 'develop' of https://github.com/LLNL/spack into features/install_with_phases_rebase

Conflicts:
	lib/spack/spack/cmd/setup.py
	lib/spack/spack/package.py
	var/spack/repos/builtin/packages/gmp/package.py

211 files changed, 5596 insertions, 1240 deletions

diff --git a/.gitignore b/.gitignore
index b1215f0c7e..e6200a0676 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,4 @@
+/db
 /var/spack/stage
 /var/spack/cache
 /var/spack/repos/*/index.yaml
@@ -12,6 +13,7 @@
 /etc/spackconfig
 /share/spack/dotkit
 /share/spack/modules
+/share/spack/lmod
 /TAGS
 /htmlcov
 .coverage
diff --git a/README.md b/README.md
index 0b6127c541..ec2da3934e 100644
--- a/README.md
+++ b/README.md
@@ -20,7 +20,7 @@ written in pure Python, and specs allow package authors to write a
 single build script for many different builds of the same package.
 
 See the
-[Feature Overview](http://spack.readthedocs.io/latest/features.html)
+[Feature Overview](http://spack.readthedocs.io/en/latest/features.html)
 for examples and highlights.
 
 To install spack and install your first package:
diff --git a/bin/sbang b/bin/sbang
index 1ea5f06592..e71074b330 100755
--- a/bin/sbang
+++ b/bin/sbang
@@ -111,8 +111,12 @@ while read line && ((lines < 2)) ; do
 done < "$script"
 
 # Invoke any interpreter found, or raise an error if none was found.
-if [ -n "$interpreter" ]; then
-    exec $interpreter "$@"
+if [[ -n "$interpreter" ]]; then
+    if [[ "${interpreter##*/}" = "perl" ]]; then
+        exec $interpreter -x "$@"
+    else
+        exec $interpreter "$@"
+    fi
 else
     echo "error: sbang found no interpreter in $script"
     exit 1
diff --git a/bin/spack b/bin/spack
index 17586cc1f6..dcc25c5c83 100755
--- a/bin/spack
+++ b/bin/spack
@@ -25,9 +25,9 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import sys
-if not sys.version_info[:2] >= (2, 6):
+if (sys.version_info[0] > 2) or (sys.version_info[:2] < (2, 6)):
     v_info = sys.version_info[:3]
-    sys.exit("Spack requires Python 2.6 or higher. "
+    sys.exit("Spack requires Python 2.6 or 2.7. "
              "This is Python %d.%d.%d." % v_info)
 
 import os
diff --git a/etc/spack/defaults/packages.yaml b/etc/spack/defaults/packages.yaml
index 83f9eb7ece..a6b361d908 100644
--- a/etc/spack/defaults/packages.yaml
+++ b/etc/spack/defaults/packages.yaml
@@ -19,3 +19,4 @@ packages:
       mpi: [openmpi, mpich]
       blas: [openblas]
       lapack: [openblas]
+      pil: [py-pillow]
diff --git a/lib/spack/docs/Makefile b/lib/spack/docs/Makefile
index 95d26041b7..1b56959aad 100644
--- a/lib/spack/docs/Makefile
+++ b/lib/spack/docs/Makefile
@@ -2,12 +2,12 @@
 #
 
 # You can set these variables from the command line.
-SPHINXOPTS    =
+SPHINXOPTS    = -E
 SPHINXBUILD   = sphinx-build
 PAPER         =
 BUILDDIR      = _build
 
-export PYTHONPATH = ../../spack
+export PYTHONPATH := ../../spack:$(PYTHONPATH)
 APIDOC_FILES  = spack*.rst
 
 # Internal variables.
diff --git a/lib/spack/docs/command_index.in b/lib/spack/docs/command_index.in
index 94cdf38109..8c5c97dd9c 100644
--- a/lib/spack/docs/command_index.in
+++ b/lib/spack/docs/command_index.in
@@ -1,5 +1,4 @@
-.. _command_index:
-
+=================
 Command index
 =================
 
diff --git a/lib/spack/docs/conf.py b/lib/spack/docs/conf.py
index 43d37f1526..57469964ee 100644
--- a/lib/spack/docs/conf.py
+++ b/lib/spack/docs/conf.py
@@ -1,10 +1,7 @@
 # flake8: noqa
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
@@ -65,14 +62,15 @@ spack_version =  subprocess.Popen(
 
 # Set an environment variable so that colify will print output like it would to
 # a terminal.
-os.environ['COLIFY_SIZE'] = '25x80'
+os.environ['COLIFY_SIZE'] = '25x120'
 
 #
 # Generate package list using spack command
 #
-with open('package_list.rst', 'w') as plist_file:
-    subprocess.Popen(
-        [spack_root + '/bin/spack', 'package-list'], stdout=plist_file)
+if not os.path.exists('package_list.rst'):
+    with open('package_list.rst', 'w') as plist_file:
+        subprocess.Popen(
+            [spack_root + '/bin/spack', 'package-list'], stdout=plist_file)
 
 #
 # Find all the `spack-*` references and add them to a command index
@@ -85,11 +83,12 @@ for filename in glob('*rst'):
             if match:
                 command_names.append(match.group(1).strip())
 
-shutil.copy('command_index.in', 'command_index.rst')
-with open('command_index.rst', 'a') as index:
-    index.write('\n')
-    for cmd in sorted(command_names):
-        index.write('   * :ref:`%s`\n' % cmd)
+if not os.path.exists('command_index.rst'):
+    shutil.copy('command_index.in', 'command_index.rst')
+    with open('command_index.rst', 'a') as index:
+        index.write('\n')
+        for cmd in sorted(command_names):
+            index.write('   * :ref:`%s`\n' % cmd)
 
 
 # Run sphinx-apidoc
diff --git a/lib/spack/docs/configuration.rst b/lib/spack/docs/configuration.rst
index ba534d1e62..6de823c845 100644
--- a/lib/spack/docs/configuration.rst
+++ b/lib/spack/docs/configuration.rst
@@ -207,7 +207,7 @@ supply ``-p`` to Spack on the command line, before any subcommands.
 
 ``spack --profile`` output looks like this:
 
-.. command-output:: spack --profile graph dyninst
+.. command-output:: spack --profile graph --deptype=nobuild dyninst
    :ellipsis: 25
 
 The bottom of the output shows the top most time consuming functions,
diff --git a/lib/spack/docs/packaging_guide.rst b/lib/spack/docs/packaging_guide.rst
index 6936b5e423..70cd58f6c1 100644
--- a/lib/spack/docs/packaging_guide.rst
+++ b/lib/spack/docs/packaging_guide.rst
@@ -2090,12 +2090,11 @@ Blas and Lapack libraries
 
 Different packages provide implementation of ``Blas`` and ``Lapack`` routines.
 The names of the resulting static and/or shared libraries differ from package
-to package. In order to make the ``install()`` method indifferent to the
+to package. In order to make the ``install()`` method independent of the
 choice of ``Blas`` implementation, each package which provides it
-sets up ``self.spec.blas_shared_lib`` and ``self.spec.blas_static_lib`` to
-point to the shared and static ``Blas`` libraries, respectively. The same
-applies to packages which provide ``Lapack``. Package developers are advised to
-use these variables, for example ``spec['blas'].blas_shared_lib`` instead of
+sets up ``self.spec.blas_libs`` to point to the correct ``Blas`` libraries.
+The same applies to packages which provide ``Lapack``. Package developers are advised to
+use these variables, for example ``spec['blas'].blas_libs.joined()`` instead of
 hard-coding ``join_path(spec['blas'].prefix.lib, 'libopenblas.so')``.
 
 ^^^^^^^^^^^^^^^^^^^^^
@@ -2889,9 +2888,22 @@ dependency graph.  For example:
 
 .. command-output:: spack graph mpileaks
 
-At the top is the root package in the DAG, with dependency edges
-emerging from it.  On a color terminal, the edges are colored by which
-dependency they lead to.
+At the top is the root package in the DAG, with dependency edges emerging
+from it.  On a color terminal, the edges are colored by which dependency
+they lead to.
+
+.. command-output:: spack graph --deptype=all mpileaks
+
+The ``deptype`` argument tells Spack what types of dependencies to graph.
+By default it includes link and run dependencies but not build
+dependencies.  Supplying ``--deptype=all`` will show the build
+dependencies as well.  This is equivalent to
+``--deptype=build,link,run``.  Options for ``deptype`` include:
+
+* Any combination of ``build``, ``link``, and ``run`` separated by
+  commas.
+* ``nobuild``, ``nolink``, ``norun`` to omit one type.
+* ``all`` or ``alldeps`` for all types of dependencies.
 
 You can also use ``spack graph`` to generate graphs in the widely used
 `Dot <http://www.graphviz.org/doc/info/lang.html>`_ format.  For
diff --git a/lib/spack/env/cc b/lib/spack/env/cc
index c6bb50d261..4b8922178a 100755
--- a/lib/spack/env/cc
+++ b/lib/spack/env/cc
@@ -266,22 +266,38 @@ for dep in "${deps[@]}"; do
     # Prepend lib and RPATH directories
     if [[ -d $dep/lib ]]; then
         if [[ $mode == ccld ]]; then
-            $add_rpaths && args=("$rpath$dep/lib" "${args[@]}")
-            args=("-L$dep/lib" "${args[@]}")
+            if [[ $SPACK_RPATH_DEPS == *$dep* ]]; then
+                $add_rpaths && args=("$rpath$dep/lib" "${args[@]}")
+            fi
+            if [[ $SPACK_LINK_DEPS == *$dep* ]]; then
+                args=("-L$dep/lib" "${args[@]}")
+            fi
         elif [[ $mode == ld ]]; then
-            $add_rpaths && args=("-rpath" "$dep/lib" "${args[@]}")
-            args=("-L$dep/lib" "${args[@]}")
+            if [[ $SPACK_RPATH_DEPS == *$dep* ]]; then
+                $add_rpaths && args=("-rpath" "$dep/lib" "${args[@]}")
+            fi
+            if [[ $SPACK_LINK_DEPS == *$dep* ]]; then
+                args=("-L$dep/lib" "${args[@]}")
+            fi
         fi
     fi
 
     # Prepend lib64 and RPATH directories
     if [[ -d $dep/lib64 ]]; then
         if [[ $mode == ccld ]]; then
-            $add_rpaths && args=("$rpath$dep/lib64" "${args[@]}")
-            args=("-L$dep/lib64" "${args[@]}")
+            if [[ $SPACK_RPATH_DEPS == *$dep* ]]; then
+                $add_rpaths && args=("$rpath$dep/lib64" "${args[@]}")
+            fi
+            if [[ $SPACK_LINK_DEPS == *$dep* ]]; then
+                args=("-L$dep/lib64" "${args[@]}")
+            fi
         elif [[ $mode == ld ]]; then
-            $add_rpaths && args=("-rpath" "$dep/lib64" "${args[@]}")
-            args=("-L$dep/lib64" "${args[@]}")
+            if [[ $SPACK_RPATH_DEPS == *$dep* ]]; then
+                $add_rpaths && args=("-rpath" "$dep/lib64" "${args[@]}")
+            fi
+            if [[ $SPACK_LINK_DEPS == *$dep* ]]; then
+                args=("-L$dep/lib64" "${args[@]}")
+            fi
         fi
     fi
 done
diff --git a/lib/spack/llnl/util/filesystem.py b/lib/spack/llnl/util/filesystem.py
index 22ca85abf9..c3ecfde4f4 100644
--- a/lib/spack/llnl/util/filesystem.py
+++ b/lib/spack/llnl/util/filesystem.py
@@ -22,18 +22,22 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import os
+import collections
+import errno
+import fileinput
+import getpass
 import glob
+import numbers
+import os
 import re
 import shutil
 import stat
-import errno
-import getpass
-from contextlib import contextmanager
 import subprocess
-import fileinput
+import sys
+from contextlib import contextmanager
 
 import llnl.util.tty as tty
+from llnl.util.lang import dedupe
 
 __all__ = ['set_install_permissions', 'install', 'install_tree',
            'traverse_tree',
@@ -42,8 +46,8 @@ __all__ = ['set_install_permissions', 'install', 'install_tree',
            'filter_file',
            'FileFilter', 'change_sed_delimiter', 'is_exe', 'force_symlink',
            'set_executable', 'copy_mode', 'unset_executable_mode',
-           'remove_dead_links', 'remove_linked_tree', 'find_library_path',
-           'fix_darwin_install_name', 'to_link_flags', 'to_lib_name']
+           'remove_dead_links', 'remove_linked_tree',
+           'fix_darwin_install_name', 'find_libraries', 'LibraryList']
 
 
 def filter_file(regex, repl, *filenames, **kwargs):
@@ -326,7 +330,7 @@ def traverse_tree(source_root, dest_root, rel_path='', **kwargs):
     follow_links = kwargs.get('follow_link', False)
 
     # Yield in pre or post order?
-    order  = kwargs.get('order', 'pre')
+    order = kwargs.get('order', 'pre')
     if order not in ('pre', 'post'):
         raise ValueError("Order must be 'pre' or 'post'.")
 
@@ -338,7 +342,7 @@ def traverse_tree(source_root, dest_root, rel_path='', **kwargs):
         return
 
     source_path = os.path.join(source_root, rel_path)
-    dest_path   = os.path.join(dest_root, rel_path)
+    dest_path = os.path.join(dest_root, rel_path)
 
     # preorder yields directories before children
     if order == 'pre':
@@ -346,8 +350,8 @@ def traverse_tree(source_root, dest_root, rel_path='', **kwargs):
 
     for f in os.listdir(source_path):
         source_child = os.path.join(source_path, f)
-        dest_child   = os.path.join(dest_path, f)
-        rel_child    = os.path.join(rel_path, f)
+        dest_child = os.path.join(dest_path, f)
+        rel_child = os.path.join(rel_path, f)
 
         # Treat as a directory
         if os.path.isdir(source_child) and (
@@ -440,35 +444,162 @@ def fix_darwin_install_name(path):
                         stdout=subprocess.PIPE).communicate()[0]
                     break
 
+# Utilities for libraries
+
 
-def to_lib_name(library):
-    """Transforms a path to the library /path/to/lib<name>.xyz into <name>
+class LibraryList(collections.Sequence):
+    """Sequence of absolute paths to libraries
+
+    Provides a few convenience methods to manipulate library paths and get
+    commonly used compiler flags or names
     """
-    # Assume libXYZ.suffix
-    return os.path.basename(library)[3:].split(".")[0]
 
+    def __init__(self, libraries):
+        self.libraries = list(libraries)
 
-def to_link_flags(library):
-    """Transforms a path to a <library> into linking flags -L<dir> -l<name>.
+    @property
+    def directories(self):
+        """Stable de-duplication of the directories where the libraries
+        reside
 
-    Return:
-      A string of linking flags.
-    """
-    dir  = os.path.dirname(library)
-    name = to_lib_name(library)
-    res = '-L%s -l%s' % (dir, name)
-    return res
+        >>> l = LibraryList(['/dir1/liba.a', '/dir2/libb.a', '/dir1/libc.a'])
+        >>> assert l.directories == ['/dir1', '/dir2']
+        """
+        return list(dedupe(
+            os.path.dirname(x) for x in self.libraries if os.path.dirname(x)
+        ))
+
+    @property
+    def basenames(self):
+        """Stable de-duplication of the base-names in the list
+
+        >>> l = LibraryList(['/dir1/liba.a', '/dir2/libb.a', '/dir3/liba.a'])
+        >>> assert l.basenames == ['liba.a', 'libb.a']
+        """
+        return list(dedupe(os.path.basename(x) for x in self.libraries))
+
+    @property
+    def names(self):
+        """Stable de-duplication of library names in the list
+
+        >>> l = LibraryList(['/dir1/liba.a', '/dir2/libb.a', '/dir3/liba.so'])
+        >>> assert l.names == ['a', 'b']
+        """
+        return list(dedupe(x.split('.')[0][3:] for x in self.basenames))
+
+    @property
+    def search_flags(self):
+        """Search flags for the libraries
+
+        >>> l = LibraryList(['/dir1/liba.a', '/dir2/libb.a', '/dir1/liba.so'])
+        >>> assert l.search_flags == '-L/dir1 -L/dir2'
+        """
+        return ' '.join(['-L' + x for x in self.directories])
+
+    @property
+    def link_flags(self):
+        """Link flags for the libraries
+
+        >>> l = LibraryList(['/dir1/liba.a', '/dir2/libb.a', '/dir1/liba.so'])
+        >>> assert l.search_flags == '-la -lb'
+        """
+        return ' '.join(['-l' + name for name in self.names])
 
+    @property
+    def ld_flags(self):
+        """Search flags + link flags
 
-def find_library_path(libname, *paths):
-    """Searches for a file called <libname> in each path.
+        >>> l = LibraryList(['/dir1/liba.a', '/dir2/libb.a', '/dir1/liba.so'])
+        >>> assert l.search_flags == '-L/dir1 -L/dir2 -la -lb'
+        """
+        return self.search_flags + ' ' + self.link_flags
 
-    Return:
-      directory where the library was found, if found.  None otherwise.
+    def __getitem__(self, item):
+        cls = type(self)
+        if isinstance(item, numbers.Integral):
+            return self.libraries[item]
+        return cls(self.libraries[item])
 
+    def __add__(self, other):
+        return LibraryList(dedupe(self.libraries + list(other)))
+
+    def __radd__(self, other):
+        return self.__add__(other)
+
+    def __eq__(self, other):
+        return self.libraries == other.libraries
+
+    def __len__(self):
+        return len(self.libraries)
+
+    def joined(self, separator=' '):
+        return separator.join(self.libraries)
+
+    def __repr__(self):
+        return self.__class__.__name__ + '(' + repr(self.libraries) + ')'
+
+    def __str__(self):
+        return self.joined()
+
+
+def find_libraries(args, root, shared=True, recurse=False):
+    """Returns an iterable object containing a list of full paths to
+    libraries if found.
+
+    Args:
+        args: iterable object containing a list of library names to \
+            search for (e.g. 'libhdf5')
+        root: root folder where to start searching
+        shared: if True searches for shared libraries, otherwise for static
+        recurse: if False search only root folder, if True descends top-down \
+            from the root
+
+    Returns:
+        list of full paths to the libraries that have been found
     """
-    for path in paths:
-        library = join_path(path, libname)
-        if os.path.exists(library):
-            return path
-    return None
+    if not isinstance(args, collections.Sequence) or isinstance(args, str):
+        message = '{0} expects a sequence of strings as first argument'
+        message += ' [got {1} instead]'
+        raise TypeError(message.format(find_libraries.__name__, type(args)))
+
+    # Construct the right suffix for the library
+    if shared is True:
+        suffix = 'dylib' if sys.platform == 'darwin' else 'so'
+    else:
+        suffix = 'a'
+    # List of libraries we are searching with suffixes
+    libraries = ['{0}.{1}'.format(lib, suffix) for lib in args]
+    # Search method
+    if recurse is False:
+        search_method = _find_libraries_non_recursive
+    else:
+        search_method = _find_libraries_recursive
+
+    return search_method(libraries, root)
+
+
+def _find_libraries_recursive(libraries, root):
+    library_dict = collections.defaultdict(list)
+    for path, _, files in os.walk(root):
+        for lib in libraries:
+            if lib in files:
+                library_dict[lib].append(
+                    join_path(path, lib)
+                )
+    answer = []
+    for lib in libraries:
+        answer.extend(library_dict[lib])
+    return LibraryList(answer)
+
+
+def _find_libraries_non_recursive(libraries, root):
+
+    def lib_or_none(lib):
+        library = join_path(root, lib)
+        if not os.path.exists(library):
+            return None
+        return library
+
+    return LibraryList(
+        [lib_or_none(lib) for lib in libraries if lib_or_none(lib) is not None]
+    )
diff --git a/lib/spack/llnl/util/lang.py b/lib/spack/llnl/util/lang.py
index df32012e2d..253334c416 100644
--- a/lib/spack/llnl/util/lang.py
+++ b/lib/spack/llnl/util/lang.py
@@ -374,6 +374,22 @@ def DictWrapper(dictionary):
     return wrapper()
 
 
+def dedupe(sequence):
+    """Yields a stable de-duplication of an hashable sequence
+
+    Args:
+        sequence: hashable sequence to be de-duplicated
+
+    Returns:
+        stable de-duplication of the sequence
+    """
+    seen = set()
+    for x in sequence:
+        if x not in seen:
+            yield x
+            seen.add(x)
+
+
 class RequiredAttributeError(ValueError):
 
     def __init__(self, message):
diff --git a/lib/spack/llnl/util/lock.py b/lib/spack/llnl/util/lock.py
index aa8272d5fe..f5f53101ae 100644
--- a/lib/spack/llnl/util/lock.py
+++ b/lib/spack/llnl/util/lock.py
@@ -69,8 +69,17 @@ class Lock(object):
         start_time = time.time()
         while (time.time() - start_time) < timeout:
             try:
+                # If this is already open read-only and we want to
+                # upgrade to an exclusive write lock, close first.
+                if self._fd is not None:
+                    flags = fcntl.fcntl(self._fd, fcntl.F_GETFL)
+                    if op == fcntl.LOCK_EX and flags | os.O_RDONLY:
+                        os.close(self._fd)
+                        self._fd = None
+
                 if self._fd is None:
-                    self._fd = os.open(self._file_path, os.O_RDWR)
+                    mode = os.O_RDWR if op == fcntl.LOCK_EX else os.O_RDONLY
+                    self._fd = os.open(self._file_path, mode)
 
                 fcntl.lockf(self._fd, op | fcntl.LOCK_NB)
                 if op == fcntl.LOCK_EX:
diff --git a/lib/spack/spack/abi.py b/lib/spack/spack/abi.py
index 064abb9782..7a6f9c3f40 100644
--- a/lib/spack/spack/abi.py
+++ b/lib/spack/spack/abi.py
@@ -54,10 +54,10 @@ class ABI(object):
         output = None
         if compiler.cxx:
             rungcc = Executable(compiler.cxx)
-            libname = "libstdc++.so"
+            libname = "libstdc++." + dso_suffix
         elif compiler.cc:
             rungcc = Executable(compiler.cc)
-            libname = "libgcc_s.so"
+            libname = "libgcc_s." + dso_suffix
         else:
             return None
         try:
diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py
index 9f7cf0bb1b..c7cfcf9328 100644
--- a/lib/spack/spack/build_environment.py
+++ b/lib/spack/spack/build_environment.py
@@ -75,6 +75,8 @@ SPACK_NO_PARALLEL_MAKE = 'SPACK_NO_PARALLEL_MAKE'
 #
 SPACK_ENV_PATH = 'SPACK_ENV_PATH'
 SPACK_DEPENDENCIES = 'SPACK_DEPENDENCIES'
+SPACK_RPATH_DEPS = 'SPACK_RPATH_DEPS'
+SPACK_LINK_DEPS = 'SPACK_LINK_DEPS'
 SPACK_PREFIX = 'SPACK_PREFIX'
 SPACK_INSTALL = 'SPACK_INSTALL'
 SPACK_DEBUG = 'SPACK_DEBUG'
@@ -252,9 +254,15 @@ def set_build_environment_variables(pkg, env, dirty=False):
     env.set_path(SPACK_ENV_PATH, env_paths)
 
     # Prefixes of all of the package's dependencies go in SPACK_DEPENDENCIES
-    dep_prefixes = [d.prefix
-                    for d in pkg.spec.traverse(root=False, deptype='build')]
+    dep_prefixes = [d.prefix for d in
+                    pkg.spec.traverse(root=False, deptype=('build', 'link'))]
     env.set_path(SPACK_DEPENDENCIES, dep_prefixes)
+
+    # These variables control compiler wrapper behavior
+    env.set_path(SPACK_RPATH_DEPS, [d.prefix for d in get_rpath_deps(pkg)])
+    env.set_path(SPACK_LINK_DEPS, [
+        d.prefix for d in pkg.spec.traverse(root=False, deptype=('link'))])
+
     # Add dependencies to CMAKE_PREFIX_PATH
     env.set_path('CMAKE_PREFIX_PATH', dep_prefixes)
 
@@ -286,8 +294,8 @@ def set_build_environment_variables(pkg, env, dirty=False):
                 env.remove_path('PATH', p)
 
     # Add bin directories from dependencies to the PATH for the build.
-    bin_dirs = reversed(
-        filter(os.path.isdir, ['%s/bin' % prefix for prefix in dep_prefixes]))
+    bin_dirs = reversed(filter(os.path.isdir, [
+        '%s/bin' % d.prefix for d in pkg.spec.dependencies(deptype='build')]))
     for item in bin_dirs:
         env.prepend_path('PATH', item)
 
@@ -372,10 +380,15 @@ def set_module_variables_for_package(pkg, module):
     m.dso_suffix = dso_suffix
 
 
+def get_rpath_deps(pkg):
+    """We only need to RPATH immediate dependencies."""
+    return pkg.spec.dependencies(deptype='link')
+
+
 def get_rpaths(pkg):
     """Get a list of all the rpaths for a package."""
     rpaths = [pkg.prefix.lib, pkg.prefix.lib64]
-    deps = pkg.spec.dependencies(deptype='link')
+    deps = get_rpath_deps(pkg)
     rpaths.extend(d.prefix.lib for d in deps
                   if os.path.isdir(d.prefix.lib))
     rpaths.extend(d.prefix.lib64 for d in deps
diff --git a/lib/spack/spack/cmd/__init__.py b/lib/spack/spack/cmd/__init__.py
index f69f434afd..6b1561b7fc 100644
--- a/lib/spack/spack/cmd/__init__.py
+++ b/lib/spack/spack/cmd/__init__.py
@@ -69,17 +69,17 @@ def get_cmd_function_name(name):
 def get_module(name):
     """Imports the module for a particular command name and returns it."""
     module_name = "%s.%s" % (__name__, name)
-    module = __import__(
-        module_name, fromlist=[name, SETUP_PARSER, DESCRIPTION],
-        level=0)
+    module = __import__(module_name,
+                        fromlist=[name, SETUP_PARSER, DESCRIPTION],
+                        level=0)
 
     attr_setdefault(module, SETUP_PARSER, lambda *args: None)  # null-op
     attr_setdefault(module, DESCRIPTION, "")
 
     fn_name = get_cmd_function_name(name)
     if not hasattr(module, fn_name):
-        tty.die("Command module %s (%s) must define function '%s'."
-                % (module.__name__, module.__file__, fn_name))
+        tty.die("Command module %s (%s) must define function '%s'." %
+                (module.__name__, module.__file__, fn_name))
 
     return module
 
diff --git a/lib/spack/spack/cmd/checksum.py b/lib/spack/spack/cmd/checksum.py
index aedb0fd99c..2e24d0527e 100644
--- a/lib/spack/spack/cmd/checksum.py
+++ b/lib/spack/spack/cmd/checksum.py
@@ -113,6 +113,6 @@ def checksum(parser, args):
         tty.die("Could not fetch any versions for %s" % pkg.name)
 
     version_lines = [
-        "    version('%s', '%s')" % (v, h) for v, h in version_hashes
+        "  version('%s', '%s')" % (v, h) for v, h in version_hashes
     ]
     tty.msg("Checksummed new versions of %s:" % pkg.name, *version_lines)
diff --git a/lib/spack/spack/cmd/debug.py b/lib/spack/spack/cmd/debug.py
new file mode 100644
index 0000000000..958eb829b4
--- /dev/null
+++ b/lib/spack/spack/cmd/debug.py
@@ -0,0 +1,84 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+import os
+from datetime import datetime
+from glob import glob
+
+import llnl.util.tty as tty
+from llnl.util.filesystem import working_dir
+
+import spack
+from spack.util.executable import which
+
+description = "Debugging commands for troubleshooting Spack."
+
+
+def setup_parser(subparser):
+    sp = subparser.add_subparsers(metavar='SUBCOMMAND', dest='debug_command')
+    sp.add_parser('create-db-tarball',
+                  help="Create a tarball of Spack's installation metadata.")
+
+
+def _debug_tarball_suffix():
+    now = datetime.now()
+    suffix = now.strftime('%Y-%m-%d-%H%M%S')
+
+    git = which('git')
+    if not git:
+        return 'nobranch-nogit-%s' % suffix
+
+    with working_dir(spack.spack_root):
+        if not os.path.isdir('.git'):
+            return 'nobranch.nogit.%s' % suffix
+
+        symbolic = git(
+            'rev-parse', '--abbrev-ref', '--short', 'HEAD', output=str).strip()
+        commit = git(
+            'rev-parse', '--short', 'HEAD', output=str).strip()
+
+        if symbolic == commit:
+            return "nobranch.%s.%s" % (commit, suffix)
+        else:
+            return "%s.%s.%s" % (symbolic, commit, suffix)
+
+
+def create_db_tarball(args):
+    tar = which('tar')
+    tarball_name = "spack-db.%s.tar.gz" % _debug_tarball_suffix()
+    tarball_path = os.path.abspath(tarball_name)
+
+    with working_dir(spack.spack_root):
+        files = [spack.installed_db._index_path]
+        files += glob('%s/*/*/*/.spack/spec.yaml' % spack.install_path)
+        files = [os.path.relpath(f) for f in files]
+
+        tar('-czf', tarball_path, *files)
+
+    tty.msg('Created %s' % tarball_name)
+
+
+def debug(parser, args):
+    action = {'create-db-tarball': create_db_tarball}
+    action[args.debug_command](args)
diff --git a/lib/spack/spack/cmd/diy.py b/lib/spack/spack/cmd/diy.py
index 487654d261..9833e8cdce 100644
--- a/lib/spack/spack/cmd/diy.py
+++ b/lib/spack/spack/cmd/diy.py
@@ -52,6 +52,9 @@ def setup_parser(subparser):
     subparser.add_argument(
         'spec', nargs=argparse.REMAINDER,
         help="specs to use for install.  Must contain package AND version.")
+    subparser.add_argument(
+        '--dirty', action='store_true', dest='dirty',
+        help="Install a package *without* cleaning the environment.")
 
 
 def diy(self, args):
@@ -100,4 +103,5 @@ def diy(self, args):
             keep_prefix=args.keep_prefix,
             ignore_deps=args.ignore_deps,
             verbose=not args.quiet,
-            keep_stage=True)   # don't remove source dir for DIY.
+            keep_stage=True,   # don't remove source dir for DIY.
+            dirty=args.dirty)
diff --git a/lib/spack/spack/cmd/graph.py b/lib/spack/spack/cmd/graph.py
index 8faabfbb7b..ed3aed1946 100644
--- a/lib/spack/spack/cmd/graph.py
+++ b/lib/spack/spack/cmd/graph.py
@@ -24,8 +24,11 @@
 ##############################################################################
 import argparse
 
+import llnl.util.tty as tty
+
 import spack
 import spack.cmd
+from spack.spec import *
 from spack.graph import *
 
 description = "Generate graphs of package dependency relationships."
@@ -36,15 +39,28 @@ def setup_parser(subparser):
 
     method = subparser.add_mutually_exclusive_group()
     method.add_argument(
-        '--ascii', action='store_true',
+        '-a', '--ascii', action='store_true',
         help="Draw graph as ascii to stdout (default).")
     method.add_argument(
-        '--dot', action='store_true',
+        '-d', '--dot', action='store_true',
         help="Generate graph in dot format and print to stdout.")
 
     subparser.add_argument(
-        '--concretize', action='store_true',
-        help="Concretize specs before graphing.")
+        '-n', '--normalize', action='store_true',
+        help="Skip concretization; only print normalized spec.")
+
+    subparser.add_argument(
+        '-s', '--static', action='store_true',
+        help="Use static information from packages, not dynamic spec info.")
+
+    subparser.add_argument(
+        '-i', '--installed', action='store_true',
+        help="Graph all installed specs in dot format (implies --dot).")
+
+    subparser.add_argument(
+        '-t', '--deptype', action='store',
+        help="Comma-separated list of deptypes to traverse. default=%s."
+        % ','.join(alldeps))
 
     subparser.add_argument(
         'specs', nargs=argparse.REMAINDER,
@@ -52,18 +68,32 @@ def setup_parser(subparser):
 
 
 def graph(parser, args):
-    specs = spack.cmd.parse_specs(
-        args.specs, normalize=True, concretize=args.concretize)
+    concretize = not args.normalize
+    if args.installed:
+        if args.specs:
+            tty.die("Can't specify specs with --installed")
+        args.dot = True
+        specs = spack.installed_db.query()
+
+    else:
+        specs = spack.cmd.parse_specs(
+            args.specs, normalize=True, concretize=concretize)
 
     if not specs:
         setup_parser.parser.print_help()
         return 1
 
+    deptype = nobuild
+    if args.deptype:
+        deptype = tuple(args.deptype.split(','))
+        validate_deptype(deptype)
+        deptype = canonical_deptype(deptype)
+
     if args.dot:  # Dot graph only if asked for.
-        graph_dot(*specs)
+        graph_dot(specs, static=args.static, deptype=deptype)
 
     elif specs:  # ascii is default: user doesn't need to provide it explicitly
-        graph_ascii(specs[0], debug=spack.debug)
+        graph_ascii(specs[0], debug=spack.debug, deptype=deptype)
         for spec in specs[1:]:
             print  # extra line bt/w independent graphs
             graph_ascii(spec, debug=spack.debug)
diff --git a/lib/spack/spack/cmd/location.py b/lib/spack/spack/cmd/location.py
index b9c8b5c330..54f7185707 100644
--- a/lib/spack/spack/cmd/location.py
+++ b/lib/spack/spack/cmd/location.py
@@ -25,7 +25,6 @@
 import argparse
 
 import llnl.util.tty as tty
-from llnl.util.filesystem import join_path
 
 import spack
 import spack.cmd
@@ -77,7 +76,7 @@ def location(parser, args):
         print spack.prefix
 
     elif args.packages:
-        print spack.repo.root
+        print spack.repo.first_repo().root
 
     elif args.stages:
         print spack.stage_path
@@ -99,7 +98,7 @@ def location(parser, args):
 
             if args.package_dir:
                 # This one just needs the spec name.
-                print join_path(spack.repo.root, spec.name)
+                print spack.repo.dirname_for_package_name(spec.name)
 
             else:
                 # These versions need concretized specs.
diff --git a/lib/spack/spack/cmd/module.py b/lib/spack/spack/cmd/module.py
index 2d0b83fe00..c6fa84109e 100644
--- a/lib/spack/spack/cmd/module.py
+++ b/lib/spack/spack/cmd/module.py
@@ -29,10 +29,10 @@ import os
 import shutil
 import sys
 
+import llnl.util.filesystem as filesystem
 import llnl.util.tty as tty
 import spack.cmd
 import spack.cmd.common.arguments as arguments
-import llnl.util.filesystem as filesystem
 from spack.modules import module_types
 
 description = "Manipulate module files"
diff --git a/lib/spack/spack/cmd/setup.py b/lib/spack/spack/cmd/setup.py
index 652c08354f..f39a827a8d 100644
--- a/lib/spack/spack/cmd/setup.py
+++ b/lib/spack/spack/cmd/setup.py
@@ -48,6 +48,9 @@ def setup_parser(subparser):
     subparser.add_argument(
         'spec', nargs=argparse.REMAINDER,
         help="specs to use for install.  Must contain package AND version.")
+    subparser.add_argument(
+        '--dirty', action='store_true', dest='dirty',
+        help="Install a package *without* cleaning the environment.")
 
 
 def spack_transitive_include_path():
diff --git a/lib/spack/spack/cmd/test.py b/lib/spack/spack/cmd/test.py
index bf7342f606..52c2a06778 100644
--- a/lib/spack/spack/cmd/test.py
+++ b/lib/spack/spack/cmd/test.py
@@ -56,7 +56,7 @@ class MockCache(object):
     def store(self, copyCmd, relativeDst):
         pass
 
-    def fetcher(self, targetPath, digest):
+    def fetcher(self, targetPath, digest, **kwargs):
         return MockCacheFetcher()
 
 
diff --git a/lib/spack/spack/database.py b/lib/spack/spack/database.py
index e450b4d424..f73d3765c8 100644
--- a/lib/spack/spack/database.py
+++ b/lib/spack/spack/database.py
@@ -49,8 +49,9 @@ from llnl.util.filesystem import *
 from llnl.util.lock import *
 
 import spack.spec
+from spack.directory_layout import DirectoryLayoutError
 from spack.version import Version
-from spack.spec import Spec
+from spack.spec import *
 from spack.error import SpackError
 from spack.repository import UnknownPackageError
 import spack.util.spack_yaml as syaml
@@ -64,6 +65,9 @@ _db_version = Version('0.9.2')
 # Default timeout for spack database locks is 5 min.
 _db_lock_timeout = 60
 
+# Types of dependencies tracked by the database
+_tracked_deps = nobuild
+
 
 def _autospec(function):
     """Decorator that automatically converts the argument of a single-arg
@@ -232,8 +236,6 @@ class Database(object):
                                  spec.format('$_$#'), dname, dhash[:7]))
                     continue
 
-                # defensive copy (not sure everything handles extra
-                # parent links yet)
                 child = data[dhash].spec
                 spec._add_dependency(child, dtypes)
 
@@ -328,7 +330,7 @@ class Database(object):
         self._data = data
 
     def reindex(self, directory_layout):
-        """Build database index from scratch based from a directory layout.
+        """Build database index from scratch based on a directory layout.
 
         Locks the DB if it isn't locked already.
 
@@ -359,9 +361,6 @@ class Database(object):
 
                 # Ask the directory layout to traverse the filesystem.
                 for spec in directory_layout.all_specs():
-                    # Create a spec for each known package and add it.
-                    path = directory_layout.path_for_spec(spec)
-
                     # Try to recover explicit value from old DB, but
                     # default it to False if DB was corrupt.
                     explicit = False
@@ -370,7 +369,7 @@ class Database(object):
                         if old_info is not None:
                             explicit = old_info.explicit
 
-                    self._add(spec, path, directory_layout, explicit=explicit)
+                    self._add(spec, directory_layout, explicit=explicit)
 
                 self._check_ref_counts()
 
@@ -389,10 +388,7 @@ class Database(object):
         counts = {}
         for key, rec in self._data.items():
             counts.setdefault(key, 0)
-            # XXX(deptype): This checks all dependencies, but build
-            #               dependencies might be able to be dropped in the
-            #               future.
-            for dep in rec.spec.dependencies():
+            for dep in rec.spec.dependencies(_tracked_deps):
                 dep_key = dep.dag_hash()
                 counts.setdefault(dep_key, 0)
                 counts[dep_key] += 1
@@ -450,52 +446,62 @@ class Database(object):
             # reindex() takes its own write lock, so no lock here.
             self.reindex(spack.install_layout)
 
-    def _add(self, spec, path, directory_layout=None, explicit=False):
-        """Add an install record for spec at path to the database.
+    def _add(self, spec, directory_layout=None, explicit=False):
+        """Add an install record for this spec to the database.
 
-        This assumes that the spec is not already installed. It
-        updates the ref counts on dependencies of the spec in the DB.
+        Assumes spec is installed in ``layout.path_for_spec(spec)``.
 
-        This operation is in-memory, and does not lock the DB.
+        Also ensures dependencies are present and updated in the DB as
+        either intsalled or missing.
 
         """
-        key = spec.dag_hash()
-        if key in self._data:
-            rec = self._data[key]
-            rec.installed = True
+        if not spec.concrete:
+            raise NonConcreteSpecAddError(
+                "Specs added to DB must be concrete.")
 
-            # TODO: this overwrites a previous install path (when path !=
-            # self._data[key].path), and the old path still has a
-            # dependent in the DB. We could consider re-RPATH-ing the
-            # dependents.  This case is probably infrequent and may not be
-            # worth fixing, but this is where we can discover it.
-            rec.path = path
-
-        else:
-            self._data[key] = InstallRecord(spec, path, True,
-                                            explicit=explicit)
-            for dep in spec.dependencies(('link', 'run')):
-                self._increment_ref_count(dep, directory_layout)
+        for dep in spec.dependencies(_tracked_deps):
+            dkey = dep.dag_hash()
+            if dkey not in self._data:
+                self._add(dep, directory_layout, explicit=False)
 
-    def _increment_ref_count(self, spec, directory_layout=None):
-        """Recursively examine dependencies and update their DB entries."""
         key = spec.dag_hash()
         if key not in self._data:
             installed = False
             path = None
             if directory_layout:
                 path = directory_layout.path_for_spec(spec)
-                installed = os.path.isdir(path)
+                try:
+                    directory_layout.check_installed(spec)
+                    installed = True
+                except DirectoryLayoutError as e:
+                    tty.warn(
+                        'Dependency missing due to corrupt install directory:',
+                        path, str(e))
+
+            # Create a new install record with no deps initially.
+            new_spec = spec.copy(deps=False)
+            self._data[key] = InstallRecord(
+                new_spec, path, installed, ref_count=0, explicit=explicit)
+
+            # Connect dependencies from the DB to the new copy.
+            for name, dep in spec.dependencies_dict(_tracked_deps).iteritems():
+                dkey = dep.spec.dag_hash()
+                new_spec._add_dependency(self._data[dkey].spec, dep.deptypes)
+                self._data[dkey].ref_count += 1
+
+            # Mark concrete once everything is built, and preserve
+            # the original hash of concrete specs.
+            new_spec._mark_concrete()
+            new_spec._hash = key
 
-            self._data[key] = InstallRecord(spec.copy(), path, installed)
-
-            for dep in spec.dependencies(('link', 'run')):
-                self._increment_ref_count(dep)
+        else:
+            # If it is already there, mark it as installed.
+            self._data[key].installed = True
 
-        self._data[key].ref_count += 1
+        self._data[key].explicit = explicit
 
     @_autospec
-    def add(self, spec, path, explicit=False):
+    def add(self, spec, directory_layout, explicit=False):
         """Add spec at path to database, locking and reading DB to sync.
 
         ``add()`` will lock and read from the DB on disk.
@@ -504,7 +510,7 @@ class Database(object):
         # TODO: ensure that spec is concrete?
         # Entire add is transactional.
         with self.write_transaction():
-            self._add(spec, path, explicit=explicit)
+            self._add(spec, directory_layout, explicit=explicit)
 
     def _get_matching_spec_key(self, spec, **kwargs):
         """Get the exact spec OR get a single spec that matches."""
@@ -534,7 +540,7 @@ class Database(object):
 
         if rec.ref_count == 0 and not rec.installed:
             del self._data[key]
-            for dep in spec.dependencies('link'):
+            for dep in spec.dependencies(_tracked_deps):
                 self._decrement_ref_count(dep)
 
     def _remove(self, spec):
@@ -548,7 +554,7 @@ class Database(object):
             return rec.spec
 
         del self._data[key]
-        for dep in rec.spec.dependencies('link'):
+        for dep in rec.spec.dependencies(_tracked_deps):
             self._decrement_ref_count(dep)
 
         # Returns the concrete spec so we know it in the case where a
@@ -657,6 +663,10 @@ class CorruptDatabaseError(SpackError):
     """Raised when errors are found while reading the database."""
 
 
+class NonConcreteSpecAddError(SpackError):
+    """Raised when attemptint to add non-concrete spec to DB."""
+
+
 class InvalidDatabaseVersionError(SpackError):
 
     def __init__(self, expected, found):
diff --git a/lib/spack/spack/directory_layout.py b/lib/spack/spack/directory_layout.py
index 73286483ef..8ef7d3c480 100644
--- a/lib/spack/spack/directory_layout.py
+++ b/lib/spack/spack/directory_layout.py
@@ -423,7 +423,7 @@ class RemoveFailedError(DirectoryLayoutError):
     def __init__(self, installed_spec, prefix, error):
         super(RemoveFailedError, self).__init__(
             'Could not remove prefix %s for %s : %s'
-            % prefix, installed_spec.short_spec, error)
+            % (prefix, installed_spec.short_spec, error))
         self.cause = error
 
 
diff --git a/lib/spack/spack/fetch_strategy.py b/lib/spack/spack/fetch_strategy.py
index c69a23033c..21802c4556 100644
--- a/lib/spack/spack/fetch_strategy.py
+++ b/lib/spack/spack/fetch_strategy.py
@@ -170,12 +170,11 @@ class URLFetchStrategy(FetchStrategy):
             tty.msg("Already downloaded %s" % self.archive_file)
             return
 
-        possible_files = self.stage.expected_archive_files
         save_file = None
         partial_file = None
-        if possible_files:
-            save_file = self.stage.expected_archive_files[0]
-            partial_file = self.stage.expected_archive_files[0] + '.part'
+        if self.stage.save_filename:
+            save_file = self.stage.save_filename
+            partial_file = self.stage.save_filename + '.part'
 
         tty.msg("Trying to fetch from %s" % self.url)
 
@@ -307,7 +306,7 @@ class URLFetchStrategy(FetchStrategy):
         if not self.archive_file:
             raise NoArchiveFileError("Cannot call archive() before fetching.")
 
-        shutil.copy(self.archive_file, destination)
+        shutil.copyfile(self.archive_file, destination)
 
     @_needs_stage
     def check(self):
@@ -858,9 +857,9 @@ class FsCache(object):
         mkdirp(os.path.dirname(dst))
         fetcher.archive(dst)
 
-    def fetcher(self, targetPath, digest):
+    def fetcher(self, targetPath, digest, **kwargs):
         url = "file://" + join_path(self.root, targetPath)
-        return CacheURLFetchStrategy(url, digest)
+        return CacheURLFetchStrategy(url, digest, **kwargs)
 
     def destroy(self):
         shutil.rmtree(self.root, ignore_errors=True)
diff --git a/lib/spack/spack/graph.py b/lib/spack/spack/graph.py
index b875e9da99..9753741c61 100644
--- a/lib/spack/spack/graph.py
+++ b/lib/spack/spack/graph.py
@@ -67,22 +67,20 @@ from heapq import *
 from llnl.util.lang import *
 from llnl.util.tty.color import *
 
-import spack
-from spack.spec import Spec
+from spack.spec import *
 
 __all__ = ['topological_sort', 'graph_ascii', 'AsciiGraph', 'graph_dot']
 
 
-def topological_sort(spec, **kwargs):
+def topological_sort(spec, reverse=False, deptype=None):
     """Topological sort for specs.
 
     Return a list of dependency specs sorted topologically.  The spec
     argument is not modified in the process.
 
     """
-    reverse = kwargs.get('reverse', False)
-    # XXX(deptype): iterate over a certain kind of dependency. Maybe color
-    #               edges based on the type of dependency?
+    deptype = canonical_deptype(deptype)
+
     if not reverse:
         parents = lambda s: s.dependents()
         children = lambda s: s.dependencies()
@@ -91,7 +89,7 @@ def topological_sort(spec, **kwargs):
         children = lambda s: s.dependents()
 
     # Work on a copy so this is nondestructive.
-    spec = spec.copy()
+    spec = spec.copy(deps=deptype)
     nodes = spec.index()
 
     topo_order = []
@@ -129,7 +127,7 @@ def find(seq, predicate):
     return -1
 
 
-# Names of different graph line states.  We Record previous line
+# Names of different graph line states.  We record previous line
 # states so that we can easily determine what to do when connecting.
 states = ('node', 'collapse', 'merge-right', 'expand-right', 'back-edge')
 NODE, COLLAPSE, MERGE_RIGHT, EXPAND_RIGHT, BACK_EDGE = states
@@ -143,6 +141,7 @@ class AsciiGraph(object):
         self.node_character = '*'
         self.debug = False
         self.indent = 0
+        self.deptype = alldeps
 
         # These are colors in the order they'll be used for edges.
         # See llnl.util.tty.color for details on color characters.
@@ -162,6 +161,9 @@ class AsciiGraph(object):
 
     def _write_edge(self, string, index, sub=0):
         """Write a colored edge to the output stream."""
+        # Ignore empty frontier entries (they're just collapsed)
+        if not self._frontier[index]:
+            return
         name = self._frontier[index][sub]
         edge = "@%s{%s}" % (self._name_to_color[name], string)
         self._out.write(edge)
@@ -386,7 +388,7 @@ class AsciiGraph(object):
         self._out = ColorStream(sys.stdout, color=color)
 
         # We'll traverse the spec in topo order as we graph it.
-        topo_order = topological_sort(spec, reverse=True)
+        topo_order = topological_sort(spec, reverse=True, deptype=self.deptype)
 
         # Work on a copy to be nondestructive
         spec = spec.copy()
@@ -420,20 +422,26 @@ class AsciiGraph(object):
                 if back:
                     back.sort()
                     prev_ends = []
+                    collapse_l1 = False
                     for j, (b, d) in enumerate(back):
                         self._frontier[i].remove(d)
                         if i - b > 1:
-                            self._back_edge_line(prev_ends, b, i, False,
-                                                 'left-1')
+                            collapse_l1 = any(not e for e in self._frontier)
+                            self._back_edge_line(
+                                prev_ends, b, i, collapse_l1, 'left-1')
                             del prev_ends[:]
                         prev_ends.append(b)
 
                     # Check whether we did ALL the deps as back edges,
                     # in which case we're done.
-                    collapse = not self._frontier[i]
-                    if collapse:
+                    pop = not self._frontier[i]
+                    collapse_l2 = pop
+                    if collapse_l1:
+                        collapse_l2 = False
+                    if pop:
                         self._frontier.pop(i)
-                    self._back_edge_line(prev_ends, -1, -1, collapse, 'left-2')
+                    self._back_edge_line(
+                        prev_ends, -1, -1, collapse_l2, 'left-2')
 
                 elif len(self._frontier[i]) > 1:
                     # Expand forward after doing all back connections
@@ -476,32 +484,28 @@ class AsciiGraph(object):
 
                 # Replace node with its dependencies
                 self._frontier.pop(i)
-                if node.dependencies():
-                    deps = sorted((d.name for d in node.dependencies()),
-                                  reverse=True)
+                deps = node.dependencies(self.deptype)
+                if deps:
+                    deps = sorted((d.name for d in deps), reverse=True)
                     self._connect_deps(i, deps, "new-deps")  # anywhere.
 
                 elif self._frontier:
                     self._collapse_line(i)
 
 
-def graph_ascii(spec, **kwargs):
-    node_character = kwargs.get('node', 'o')
-    out            = kwargs.pop('out', None)
-    debug          = kwargs.pop('debug', False)
-    indent         = kwargs.pop('indent', 0)
-    color          = kwargs.pop('color', None)
-    check_kwargs(kwargs, graph_ascii)
-
+def graph_ascii(spec, node='o', out=None, debug=False,
+                indent=0, color=None, deptype=None):
     graph = AsciiGraph()
     graph.debug = debug
     graph.indent = indent
-    graph.node_character = node_character
+    graph.node_character = node
+    if deptype:
+        graph.deptype = canonical_deptype(deptype)
 
     graph.write(spec, color=color, out=out)
 
 
-def graph_dot(*specs, **kwargs):
+def graph_dot(specs, deptype=None, static=False, out=None):
     """Generate a graph in dot format of all provided specs.
 
     Print out a dot formatted graph of all the dependencies between
@@ -510,42 +514,73 @@ def graph_dot(*specs, **kwargs):
         spack graph --dot qt | dot -Tpdf > spack-graph.pdf
 
     """
-    out = kwargs.pop('out', sys.stdout)
-    check_kwargs(kwargs, graph_dot)
+    if out is None:
+        out = sys.stdout
+
+    if deptype is None:
+        deptype = alldeps
 
     out.write('digraph G {\n')
-    out.write('  label = "Spack Dependencies"\n')
     out.write('  labelloc = "b"\n')
-    out.write('  rankdir = "LR"\n')
+    out.write('  rankdir = "TB"\n')
     out.write('  ranksep = "5"\n')
+    out.write('node[\n')
+    out.write('     fontname=Monaco,\n')
+    out.write('     penwidth=2,\n')
+    out.write('     fontsize=12,\n')
+    out.write('     margin=.1,\n')
+    out.write('     shape=box,\n')
+    out.write('     fillcolor=lightblue,\n')
+    out.write('     style="rounded,filled"]\n')
+
     out.write('\n')
 
-    def quote(string):
+    def q(string):
         return '"%s"' % string
 
     if not specs:
-        specs = [p.name for p in spack.repo.all_packages()]
-    else:
-        roots = specs
-        specs = set()
-        for spec in roots:
-            specs.update(Spec(s.name) for s in spec.normalized().traverse())
+        raise ValueError("Must provide specs ot graph_dot")
+
+    # Static graph includes anything a package COULD depend on.
+    if static:
+        names = set.union(*[s.package.possible_dependencies() for s in specs])
+        specs = [Spec(name) for name in names]
 
-    deps = []
+    labeled = set()
+
+    def label(key, label):
+        if key not in labeled:
+            out.write('  "%s" [label="%s"]\n' % (key, label))
+            labeled.add(key)
+
+    deps = set()
     for spec in specs:
-        out.write('  %-30s [label="%s"]\n' % (quote(spec.name), spec.name))
+        if static:
+            out.write('  "%s" [label="%s"]\n' % (spec.name, spec.name))
+
+            # Skip virtual specs (we'll find out about them from concrete ones.
+            if spec.virtual:
+                continue
 
-        # Skip virtual specs (we'll find out about them from concrete ones.
-        if spec.virtual:
-            continue
+            # Add edges for each depends_on in the package.
+            for dep_name, dep in spec.package.dependencies.iteritems():
+                deps.add((spec.name, dep_name))
+
+            # If the package provides something, add an edge for that.
+            for provider in set(s.name for s in spec.package.provided):
+                deps.add((provider, spec.name))
+
+        else:
+            def key_label(s):
+                return s.dag_hash(), "%s-%s" % (s.name, s.dag_hash(7))
 
-        # Add edges for each depends_on in the package.
-        for dep_name, dep in spec.package.dependencies.iteritems():
-            deps.append((spec.name, dep_name))
+            for s in spec.traverse(deptype=deptype):
+                skey, slabel = key_label(s)
+                out.write('  "%s" [label="%s"]\n' % (skey, slabel))
 
-        # If the package provides something, add an edge for that.
-        for provider in set(s.name for s in spec.package.provided):
-            deps.append((provider, spec.name))
+                for d in s.dependencies(deptype=deptype):
+                    dkey, _ = key_label(d)
+                    deps.add((skey, dkey))
 
     out.write('\n')
 
diff --git a/lib/spack/spack/hooks/__init__.py b/lib/spack/spack/hooks/__init__.py
index c7c84defa0..ff4ebc2e57 100644
--- a/lib/spack/spack/hooks/__init__.py
+++ b/lib/spack/spack/hooks/__init__.py
@@ -24,7 +24,7 @@
 ##############################################################################
 """This package contains modules with hooks for various stages in the
    Spack install process.  You can add modules here and they'll be
-   executaed by package at various times during the package lifecycle.
+   executed by package at various times during the package lifecycle.
 
    Each hook is just a function that takes a package as a parameter.
    Hooks are not executed in any particular order.
@@ -41,9 +41,10 @@
    features.
 """
 import imp
-from llnl.util.lang import memoized, list_modules
-from llnl.util.filesystem import join_path
+
 import spack
+from llnl.util.filesystem import join_path
+from llnl.util.lang import memoized, list_modules
 
 
 @memoized
@@ -70,12 +71,11 @@ class HookRunner(object):
                 if hasattr(hook, '__call__'):
                     hook(pkg)
 
-
 #
 # Define some functions that can be called to fire off hooks.
 #
-pre_install    = HookRunner('pre_install')
-post_install   = HookRunner('post_install')
+pre_install = HookRunner('pre_install')
+post_install = HookRunner('post_install')
 
-pre_uninstall  = HookRunner('pre_uninstall')
+pre_uninstall = HookRunner('pre_uninstall')
 post_uninstall = HookRunner('post_uninstall')
diff --git a/lib/spack/spack/hooks/lmodmodule.py b/lib/spack/spack/hooks/lmodmodule.py
new file mode 100644
index 0000000000..6b4318b1d0
--- /dev/null
+++ b/lib/spack/spack/hooks/lmodmodule.py
@@ -0,0 +1,35 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://scalability-llnl.github.io/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License (as published by
+# the Free Software Foundation) version 2.1 dated February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program; if not, write to the Free Software Foundation,
+# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+import spack.modules
+
+
+def post_install(pkg):
+    dk = spack.modules.LmodModule(pkg.spec)
+    dk.write()
+
+
+def post_uninstall(pkg):
+    dk = spack.modules.LmodModule(pkg.spec)
+    dk.remove()
diff --git a/lib/spack/spack/hooks/sbang.py b/lib/spack/spack/hooks/sbang.py
index 02c1ce3816..6f9736a018 100644
--- a/lib/spack/spack/hooks/sbang.py
+++ b/lib/spack/spack/hooks/sbang.py
@@ -81,8 +81,10 @@ def filter_shebang(path):
     tty.warn("Patched overlong shebang in %s" % path)
 
 
-def filter_shebangs_in_directory(directory):
-    for file in os.listdir(directory):
+def filter_shebangs_in_directory(directory, filenames=None):
+    if filenames is None:
+        filenames = os.listdir(directory)
+    for file in filenames:
         path = os.path.join(directory, file)
 
         # only handle files
@@ -104,6 +106,6 @@ def post_install(pkg):
     """This hook edits scripts so that they call /bin/bash
        $spack_prefix/bin/sbang instead of something longer than the
        shebang limit."""
-    if not os.path.isdir(pkg.prefix.bin):
-        return
-    filter_shebangs_in_directory(pkg.prefix.bin)
+
+    for directory, _, filenames in os.walk(pkg.prefix):
+        filter_shebangs_in_directory(directory, filenames)
diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index 70c3c35d8c..aa3ad5843f 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -40,6 +40,7 @@ module file.
 """
 import copy
 import datetime
+import itertools
 import os
 import os.path
 import re
@@ -48,6 +49,7 @@ import textwrap
 
 import llnl.util.tty as tty
 import spack
+import spack.compilers  # Needed by LmodModules
 import spack.config
 from llnl.util.filesystem import join_path, mkdirp
 from spack.build_environment import parent_class_modules
@@ -56,7 +58,8 @@ from spack.environment import *
 
 __all__ = ['EnvModule', 'Dotkit', 'TclModule']
 
-# Registry of all types of modules.  Entries created by EnvModule's metaclass
+"""Registry of all types of modules.  Entries created by EnvModule's
+   metaclass."""
 module_types = {}
 
 CONFIGURATION = spack.config.get_config('modules')
@@ -120,7 +123,7 @@ def dependencies(spec, request='all'):
         return []
 
     if request == 'direct':
-        return spec.dependencies()
+        return spec.dependencies(deptype=('link', 'run'))
 
     # FIXME : during module file creation nodes seem to be visited multiple
     # FIXME : times even if cover='nodes' is given. This work around permits
@@ -133,6 +136,7 @@ def dependencies(spec, request='all'):
              spec.traverse(order='post',
                            depth=True,
                            cover='nodes',
+                           deptype=('link', 'run'),
                            root=False),
              reverse=True)]
     return [xx for ii, xx in l if not (xx in seen or seen_add(xx))]
@@ -388,6 +392,7 @@ class EnvModule(object):
             for mod in modules:
                 set_module_variables_for_package(package, mod)
             set_module_variables_for_package(package, package.module)
+            package.setup_environment(spack_env, env)
             package.setup_dependent_package(self.pkg.module, self.spec)
             package.setup_dependent_environment(spack_env, env, self.spec)
 
@@ -632,3 +637,237 @@ class TclModule(EnvModule):
                         raise SystemExit('Module generation aborted.')
                 line = line.format(**naming_tokens)
             yield line
+
+# To construct an arbitrary hierarchy of module files:
+# 1. Parse the configuration file and check that all the items in
+#    hierarchical_scheme are indeed virtual packages
+#    This needs to be done only once at start-up
+# 2. Order the stack as `hierarchical_scheme + ['mpi, 'compiler']
+# 3. Check which of the services are provided by the package
+#    -> may be more than one
+# 4. Check which of the services are needed by the package
+#    -> this determines where to write the module file
+# 5. For each combination of services in which we have at least one provider
+#    here add the appropriate conditional MODULEPATH modifications
+
+
+class LmodModule(EnvModule):
+    name = 'lmod'
+    path = join_path(spack.share_path, "lmod")
+
+    environment_modifications_formats = {
+        PrependPath: 'prepend_path("{name}", "{value}")\n',
+        AppendPath: 'append_path("{name}", "{value}")\n',
+        RemovePath: 'remove_path("{name}", "{value}")\n',
+        SetEnv: 'setenv("{name}", "{value}")\n',
+        UnsetEnv: 'unsetenv("{name}")\n'
+    }
+
+    autoload_format = ('if not isloaded("{module_file}") then\n'
+                       '    LmodMessage("Autoloading {module_file}")\n'
+                       '    load("{module_file}")\n'
+                       'end\n\n')
+
+    prerequisite_format = 'prereq("{module_file}")\n'
+
+    family_format = 'family("{family}")\n'
+
+    path_part_with_hash = join_path('{token.name}', '{token.version}-{token.hash}')  # NOQA: ignore=E501
+    path_part_without_hash = join_path('{token.name}', '{token.version}')
+
+    # TODO : Check that extra tokens specified in configuration file
+    # TODO : are actually virtual dependencies
+    configuration = CONFIGURATION.get('lmod', {})
+    hierarchy_tokens = configuration.get('hierarchical_scheme', [])
+    hierarchy_tokens = hierarchy_tokens + ['mpi', 'compiler']
+
+    def __init__(self, spec=None):
+        super(LmodModule, self).__init__(spec)
+        # Sets the root directory for this architecture
+        self.modules_root = join_path(LmodModule.path, self.spec.architecture)
+        # Retrieve core compilers
+        self.core_compilers = self.configuration.get('core_compilers', [])
+        # Keep track of the requirements that this package has in terms
+        # of virtual packages
+        # that participate in the hierarchical structure
+        self.requires = {'compiler': self.spec.compiler}
+        # For each virtual dependency in the hierarchy
+        for x in self.hierarchy_tokens:
+            if x in self.spec and not self.spec.package.provides(
+                    x):  # if I depend on it
+                self.requires[x] = self.spec[x]  # record the actual provider
+        # Check what are the services I need (this will determine where the
+        # module file will be written)
+        self.substitutions = {}
+        self.substitutions.update(self.requires)
+        # TODO : complete substitutions
+        # Check what service I provide to others
+        self.provides = {}
+        # If it is in the list of supported compilers family -> compiler
+        if self.spec.name in spack.compilers.supported_compilers():
+            self.provides['compiler'] = spack.spec.CompilerSpec(str(self.spec))
+        # Special case for llvm
+        if self.spec.name == 'llvm':
+            self.provides['compiler'] = spack.spec.CompilerSpec(str(self.spec))
+            self.provides['compiler'].name = 'clang'
+
+        for x in self.hierarchy_tokens:
+            if self.spec.package.provides(x):
+                self.provides[x] = self.spec[x]
+
+    def _hierarchy_token_combinations(self):
+        """
+        Yields all the relevant combinations that could appear in the hierarchy
+        """
+        for ii in range(len(self.hierarchy_tokens) + 1):
+            for item in itertools.combinations(self.hierarchy_tokens, ii):
+                if 'compiler' in item:
+                    yield item
+
+    def _hierarchy_to_be_provided(self):
+        """
+        Filters a list of hierarchy tokens and yields only the one that we
+        need to provide
+        """
+        for item in self._hierarchy_token_combinations():
+            if any(x in self.provides for x in item):
+                yield item
+
+    def token_to_path(self, name, value):
+        # If we are dealing with a core compiler, return 'Core'
+        if name == 'compiler' and str(value) in self.core_compilers:
+            return 'Core'
+        # CompilerSpec does not have an hash
+        if name == 'compiler':
+            return self.path_part_without_hash.format(token=value)
+        # For virtual providers add a small part of the hash
+        # to distinguish among different variants in a directory hierarchy
+        value.hash = value.dag_hash(length=6)
+        return self.path_part_with_hash.format(token=value)
+
+    @property
+    def file_name(self):
+        parts = [self.token_to_path(x, self.requires[x])
+                 for x in self.hierarchy_tokens if x in self.requires]
+        hierarchy_name = join_path(*parts)
+        fullname = join_path(self.modules_root, hierarchy_name,
+                             self.use_name + '.lua')
+        return fullname
+
+    @property
+    def use_name(self):
+        return self.token_to_path('', self.spec)
+
+    def modulepath_modifications(self):
+        # What is available is what we require plus what we provide
+        entry = ''
+        available = {}
+        available.update(self.requires)
+        available.update(self.provides)
+        available_parts = [self.token_to_path(x, available[x])
+                           for x in self.hierarchy_tokens if x in available]
+        # Missing parts
+        missing = [x for x in self.hierarchy_tokens if x not in available]
+        # Direct path we provide on top of compilers
+        modulepath = join_path(self.modules_root, *available_parts)
+        env = EnvironmentModifications()
+        env.prepend_path('MODULEPATH', modulepath)
+        for line in self.process_environment_command(env):
+            entry += line
+
+        def local_variable(x):
+            lower, upper = x.lower(), x.upper()
+            fmt = 'local {lower}_name = os.getenv("LMOD_{upper}_NAME")\n'
+            fmt += 'local {lower}_version = os.getenv("LMOD_{upper}_VERSION")\n'  # NOQA: ignore=501
+            return fmt.format(lower=lower, upper=upper)
+
+        def set_variables_for_service(env, x):
+            upper = x.upper()
+            s = self.provides[x]
+            name, version = os.path.split(self.token_to_path(x, s))
+
+            env.set('LMOD_{upper}_NAME'.format(upper=upper), name)
+            env.set('LMOD_{upper}_VERSION'.format(upper=upper), version)
+
+        def conditional_modulepath_modifications(item):
+            entry = 'if '
+            needed = []
+            for x in self.hierarchy_tokens:
+                if x in missing:
+                    needed.append('{x}_name '.format(x=x))
+            entry += 'and '.join(needed) + 'then\n'
+            entry += '  local t = pathJoin("{root}"'.format(
+                root=self.modules_root)
+            for x in item:
+                if x in missing:
+                    entry += ', {lower}_name, {lower}_version'.format(
+                        lower=x.lower())
+                else:
+                    entry += ', "{x}"'.format(
+                        x=self.token_to_path(x, available[x]))
+            entry += ')\n'
+            entry += '  prepend_path("MODULEPATH", t)\n'
+            entry += 'end\n\n'
+            return entry
+
+        if 'compiler' not in self.provides:
+            # Retrieve variables
+            entry += '\n'
+            for x in missing:
+                entry += local_variable(x)
+            entry += '\n'
+            # Conditional modifications
+            conditionals = [x
+                            for x in self._hierarchy_to_be_provided()
+                            if any(t in missing for t in x)]
+            for item in conditionals:
+                entry += conditional_modulepath_modifications(item)
+
+            # Set environment variables for the services we provide
+            env = EnvironmentModifications()
+            for x in self.provides:
+                set_variables_for_service(env, x)
+            for line in self.process_environment_command(env):
+                entry += line
+
+        return entry
+
+    @property
+    def header(self):
+        timestamp = datetime.datetime.now()
+        # Header as in
+        # https://www.tacc.utexas.edu/research-development/tacc-projects/lmod/advanced-user-guide/more-about-writing-module-files
+        header = "-- -*- lua -*-\n"
+        header += '-- Module file created by spack (https://github.com/LLNL/spack) on %s\n' % timestamp  # NOQA: ignore=E501
+        header += '--\n'
+        header += '-- %s\n' % self.spec.short_spec
+        header += '--\n'
+
+        # Short description -> whatis()
+        if self.short_description:
+            header += "whatis([[Name : {name}]])\n".format(name=self.spec.name)
+            header += "whatis([[Version : {version}]])\n".format(
+                version=self.spec.version)
+
+        # Long description -> help()
+        if self.long_description:
+            doc = re.sub(r'"', '\"', self.long_description)
+            header += "help([[{documentation}]])\n".format(documentation=doc)
+
+        # Certain things need to be done only if we provide a service
+        if self.provides:
+            # Add family directives
+            header += '\n'
+            for x in self.provides:
+                header += self.family_format.format(family=x)
+            header += '\n'
+            header += '-- MODULEPATH modifications\n'
+            header += '\n'
+            # Modify MODULEPATH
+            header += self.modulepath_modifications()
+            # Set environment variables for services we provide
+            header += '\n'
+            header += '-- END MODULEPATH modifications\n'
+            header += '\n'
+
+        return header
diff --git a/lib/spack/spack/operating_systems/mac_os.py b/lib/spack/spack/operating_systems/mac_os.py
index 3e5ab9b2e9..dafb5c1d41 100644
--- a/lib/spack/spack/operating_systems/mac_os.py
+++ b/lib/spack/spack/operating_systems/mac_os.py
@@ -22,7 +22,7 @@ class MacOs(OperatingSystem):
                         "10.11": "elcapitan",
                         "10.12": "sierra"}
 
-        mac_ver = py_platform.mac_ver()[0][:-2]
+        mac_ver = '.'.join(py_platform.mac_ver()[0].split('.')[:2])
         name = mac_releases.get(mac_ver, "macos")
         super(MacOs, self).__init__(name, mac_ver)
 
diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index dcdcee293d..498f3d4a6d 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -575,6 +575,20 @@ class PackageBase(object):
 
         self.extra_args = {}
 
+    def possible_dependencies(self, visited=None):
+        """Return set of possible transitive dependencies of this package."""
+        if visited is None:
+            visited = set()
+
+        visited.add(self.name)
+        for name in self.dependencies:
+            if name not in visited and not spack.spec.Spec(name).virtual:
+                pkg = spack.repo.get(name)
+                for name in pkg.possible_dependencies(visited):
+                    visited.add(name)
+
+        return visited
+
     @property
     def package_dir(self):
         """Return the directory where the package.py file lives."""
@@ -886,7 +900,7 @@ class PackageBase(object):
 
             if not ignore_checksum:
                 raise FetchError("Will not fetch %s" %
-                                 self.spec.format('$_$@'), checksum_msg)
+                                 self.spec.format('$_$@'), ck_msg)
 
         self.stage.fetch(mirror_only)
 
@@ -1080,7 +1094,8 @@ class PackageBase(object):
                                          skip_patch=skip_patch,
                                          verbose=verbose,
                                          make_jobs=make_jobs,
-                                         run_tests=run_tests)
+                                         run_tests=run_tests,
+                                         dirty=dirty)
 
         # Set run_tests flag before starting build.
         self.run_tests = run_tests
@@ -1171,7 +1186,9 @@ class PackageBase(object):
             keep_prefix = True if self.last_phase is None else keep_prefix
             # note: PARENT of the build process adds the new package to
             # the database, so that we don't need to re-read from file.
-            spack.installed_db.add(self.spec, self.prefix, explicit=explicit)
+            spack.installed_db.add(
+                self.spec, spack.install_layout, explicit=explicit
+            )
         except directory_layout.InstallDirectoryAlreadyExistsError:
             # Abort install if install directory exists.
             # But do NOT remove it (you'd be overwriting someone else's stuff)
diff --git a/lib/spack/spack/platforms/cray.py b/lib/spack/spack/platforms/cray.py
index 0059b49ff1..9138ad7afe 100644
--- a/lib/spack/spack/platforms/cray.py
+++ b/lib/spack/spack/platforms/cray.py
@@ -8,37 +8,21 @@ from spack.operating_systems.linux_distro import LinuxDistro
 from spack.operating_systems.cnl import Cnl
 from llnl.util.filesystem import join_path
 
-# Craype- module prefixes that are not valid CPU targets.
-NON_TARGETS = ('hugepages', 'network', 'target', 'accel', 'xtpe')
-
-
-def _target_from_clean_env(name):
-    '''Return the default back_end target as loaded in a clean login session.
-
-    A bash subshell is launched with a wiped environment and the list of loaded
-    modules is parsed for the first acceptable CrayPE target.
-    '''
-    # Based on the incantation:
-    # echo "$(env - USER=$USER /bin/bash -l -c 'module list -lt')"
-    targets = []
-    if name != 'front_end':
-        env = which('env')
-        env.add_default_arg('-')
-        # CAUTION - $USER is generally needed to initialize the environment.
-        # There may be other variables needed for general success.
-        output = env('USER=%s' % os.environ['USER'],
-                     '/bin/bash', '--noprofile', '--norc', '-c',
-                     '. /etc/profile; module list -lt',
-                     output=str, error=str)
-        default_modules = [i for i in output.splitlines()
-                           if len(i.split()) == 1]
-        tty.debug("Found default modules:",
-                  *["      " + mod for mod in default_modules])
-        pattern = 'craype-(?!{0})(\S*)'.format('|'.join(NON_TARGETS))
-        for mod in default_modules:
-            if 'craype-' in mod:
-                targets.extend(re.findall(pattern, mod))
-    return targets[0] if targets else None
+
+def _get_modules_in_modulecmd_output(output):
+    '''Return list of valid modules parsed from modulecmd output string.'''
+    return [i for i in output.splitlines()
+            if len(i.split()) == 1]
+
+
+def _fill_craype_targets_from_modules(targets, modules):
+    '''Extend CrayPE CPU targets list with those found in list of modules.'''
+    # Craype- module prefixes that are not valid CPU targets.
+    non_targets = ('hugepages', 'network', 'target', 'accel', 'xtpe')
+    pattern = r'craype-(?!{0})(\S*)'.format('|'.join(non_targets))
+    for mod in modules:
+        if 'craype-' in mod:
+            targets.extend(re.findall(pattern, mod))
 
 
 class Cray(Platform):
@@ -56,7 +40,12 @@ class Cray(Platform):
         '''
         super(Cray, self).__init__('cray')
 
-        # Get targets from config or make best guess from environment:
+        # Make all craype targets available.
+        for target in self._avail_targets():
+            name = target.replace('-', '_')
+            self.add_target(name, Target(name, 'craype-%s' % target))
+
+        # Get aliased targets from config or best guess from environment:
         conf = spack.config.get_config('targets')
         for name in ('front_end', 'back_end'):
             _target = getattr(self, name, None)
@@ -64,18 +53,16 @@ class Cray(Platform):
                 _target = os.environ.get('SPACK_' + name.upper())
             if _target is None:
                 _target = conf.get(name)
-            if _target is None:
-                _target = _target_from_clean_env(name)
-            setattr(self, name, _target)
-
+            if _target is None and name == 'back_end':
+                _target = self._default_target_from_env()
             if _target is not None:
-                self.add_target(name, Target(_target, 'craype-' + _target))
-                self.add_target(_target, Target(_target, 'craype-' + _target))
+                safe_name = _target.replace('-', '_')
+                setattr(self, name, safe_name)
+                self.add_target(name, self.targets[safe_name])
 
         if self.back_end is not None:
             self.default = self.back_end
-            self.add_target(
-                'default', Target(self.default, 'craype-' + self.default))
+            self.add_target('default', self.targets[self.back_end])
         else:
             raise NoPlatformError()
 
@@ -90,7 +77,7 @@ class Cray(Platform):
         self.add_operating_system(self.front_os, front_distro)
 
     @classmethod
-    def setup_platform_environment(self, pkg, env):
+    def setup_platform_environment(cls, pkg, env):
         """ Change the linker to default dynamic to be more
             similar to linux/standard linker behavior
         """
@@ -101,5 +88,43 @@ class Cray(Platform):
             env.prepend_path('SPACK_ENV_PATH', cray_wrapper_names)
 
     @classmethod
-    def detect(self):
+    def detect(cls):
         return os.environ.get('CRAYPE_VERSION') is not None
+
+    def _default_target_from_env(self):
+        '''Set and return the default CrayPE target loaded in a clean login
+        session.
+
+        A bash subshell is launched with a wiped environment and the list of
+        loaded modules is parsed for the first acceptable CrayPE target.
+        '''
+        # Based on the incantation:
+        # echo "$(env - USER=$USER /bin/bash -l -c 'module list -lt')"
+        if getattr(self, 'default', None) is None:
+            env = which('env')
+            env.add_default_arg('-')
+            # CAUTION - $USER is generally needed in the sub-environment.
+            # There may be other variables needed for general success.
+            output = env('USER=%s' % os.environ['USER'],
+                         'HOME=%s' % os.environ['HOME'],
+                         '/bin/bash', '--noprofile', '--norc', '-c',
+                         '. /etc/profile; module list -lt',
+                         output=str, error=str)
+            self._defmods = _get_modules_in_modulecmd_output(output)
+            targets = []
+            _fill_craype_targets_from_modules(targets, self._defmods)
+            self.default = targets[0] if targets else None
+            tty.debug("Found default modules:",
+                      *["     %s" % mod for mod in self._defmods])
+        return self.default
+
+    def _avail_targets(self):
+        '''Return a list of available CrayPE CPU targets.'''
+        if getattr(self, '_craype_targets', None) is None:
+            module = which('modulecmd', required=True)
+            module.add_default_arg('python')
+            output = module('avail', '-t', 'craype-', output=str, error=str)
+            craype_modules = _get_modules_in_modulecmd_output(output)
+            self._craype_targets = targets = []
+            _fill_craype_targets_from_modules(targets, craype_modules)
+        return self._craype_targets
diff --git a/lib/spack/spack/schema/modules.py b/lib/spack/spack/schema/modules.py
index f8066919f1..bdc70c9ef1 100644
--- a/lib/spack/spack/schema/modules.py
+++ b/lib/spack/spack/schema/modules.py
@@ -139,7 +139,20 @@ schema = {
                     'default': [],
                     'items': {
                         'type': 'string',
-                        'enum': ['tcl', 'dotkit']}},
+                        'enum': ['tcl', 'dotkit', 'lmod']}},
+                'lmod': {
+                    'allOf': [
+                        # Base configuration
+                        {'$ref': '#/definitions/module_type_configuration'},
+                        {
+                            'core_compilers': {
+                                '$ref': '#/definitions/array_of_strings'
+                            },
+                            'hierarchical_scheme': {
+                                '$ref': '#/definitions/array_of_strings'
+                            }
+                        }  # Specific lmod extensions
+                    ]},
                 'tcl': {
                     'allOf': [
                         # Base configuration
diff --git a/lib/spack/spack/spec.py b/lib/spack/spack/spec.py
index 8b0486c4da..ba9cea876d 100644
--- a/lib/spack/spack/spec.py
+++ b/lib/spack/spack/spec.py
@@ -123,6 +123,39 @@ from spack.util.spack_yaml import syaml_dict
 from spack.version import *
 from spack.provider_index import ProviderIndex
 
+__all__ = [
+    'Spec',
+    'alldeps',
+    'nolink',
+    'nobuild',
+    'canonical_deptype',
+    'validate_deptype',
+    'parse',
+    'parse_anonymous_spec',
+    'SpecError',
+    'SpecParseError',
+    'DuplicateDependencyError',
+    'DuplicateVariantError',
+    'DuplicateCompilerSpecError',
+    'UnsupportedCompilerError',
+    'UnknownVariantError',
+    'DuplicateArchitectureError',
+    'InconsistentSpecError',
+    'InvalidDependencyError',
+    'InvalidDependencyTypeError',
+    'NoProviderError',
+    'MultipleProviderError',
+    'UnsatisfiableSpecError',
+    'UnsatisfiableSpecNameError',
+    'UnsatisfiableVersionSpecError',
+    'UnsatisfiableCompilerSpecError',
+    'UnsatisfiableVariantSpecError',
+    'UnsatisfiableCompilerFlagSpecError',
+    'UnsatisfiableArchitectureSpecError',
+    'UnsatisfiableProviderSpecError',
+    'UnsatisfiableDependencySpecError',
+    'SpackYAMLError',
+    'AmbiguousHashError']
 
 # Valid pattern for an identifier in Spack
 identifier_re = r'\w[\w-]*'
@@ -156,12 +189,46 @@ _any_version = VersionList([':'])
 
 # Special types of dependencies.
 alldeps = ('build', 'link', 'run')
-nolink = ('build', 'run')
+nolink  = ('build', 'run')
+nobuild = ('link', 'run')
+norun   = ('link', 'build')
 special_types = {
     'alldeps': alldeps,
+    'all': alldeps,  # allow "all" as string but not symbol.
     'nolink': nolink,
+    'nobuild': nobuild,
+    'norun': norun,
 }
 
+legal_deps = tuple(special_types) + alldeps
+
+
+def validate_deptype(deptype):
+    if isinstance(deptype, str):
+        if deptype not in legal_deps:
+            raise InvalidDependencyTypeError(
+                "Invalid dependency type: %s" % deptype)
+
+    elif isinstance(deptype, (list, tuple)):
+        for t in deptype:
+            validate_deptype(t)
+
+    elif deptype is None:
+        raise InvalidDependencyTypeError("deptype cannot be None!")
+
+
+def canonical_deptype(deptype):
+    if deptype is None:
+        return alldeps
+
+    elif isinstance(deptype, str):
+        return special_types.get(deptype, (deptype,))
+
+    elif isinstance(deptype, (tuple, list)):
+        return (sum((canonical_deptype(d) for d in deptype), ()))
+
+    return deptype
+
 
 def colorize_spec(spec):
     """Returns a spec colorized according to the colors specified in
@@ -527,6 +594,14 @@ class Spec(object):
             # XXX(deptype): default deptypes
             self._add_dependency(spec, ('build', 'link'))
 
+    def __getattr__(self, item):
+        """Delegate to self.package if the attribute is not in the spec"""
+        # This line is to avoid infinite recursion in case package is
+        # not present among self attributes
+        if item.endswith('libs'):
+            return getattr(self.package, item)
+        raise AttributeError()
+
     def get_dependency(self, name):
         dep = self._dependencies.get(name)
         if dep is not None:
@@ -534,17 +609,8 @@ class Spec(object):
         raise InvalidDependencyException(
             self.name + " does not depend on " + comma_or(name))
 
-    def _deptype_norm(self, deptype):
-        if deptype is None:
-            return alldeps
-        # Force deptype to be a set object so that we can do set intersections.
-        if isinstance(deptype, str):
-            # Support special deptypes.
-            return special_types.get(deptype, (deptype,))
-        return deptype
-
     def _find_deps(self, where, deptype):
-        deptype = self._deptype_norm(deptype)
+        deptype = canonical_deptype(deptype)
 
         return [dep.spec
                 for dep in where.values()
@@ -557,7 +623,7 @@ class Spec(object):
         return self._find_deps(self._dependents, deptype)
 
     def _find_deps_dict(self, where, deptype):
-        deptype = self._deptype_norm(deptype)
+        deptype = canonical_deptype(deptype)
 
         return dict((dep.spec.name, dep)
                     for dep in where.values()
@@ -1353,12 +1419,11 @@ class Spec(object):
             # parser doesn't allow it. Spack must be broken!
             raise InconsistentSpecError("Invalid Spec DAG: %s" % e.message)
 
-    def index(self):
+    def index(self, deptype=None):
         """Return DependencyMap that points to all the dependencies in this
            spec."""
         dm = DependencyMap()
-        # XXX(deptype): use a deptype kwarg.
-        for spec in self.traverse():
+        for spec in self.traverse(deptype=deptype):
             dm[spec.name] = spec
         return dm
 
@@ -1561,7 +1626,7 @@ class Spec(object):
         # actually deps of this package.  Raise an error.
         extra = set(spec_deps.keys()).difference(visited)
         if extra:
-            raise InvalidDependencyException(
+            raise InvalidDependencyError(
                 self.name + " does not depend on " + comma_or(extra))
 
         # Mark the spec as normal once done.
@@ -2659,17 +2724,11 @@ def parse_anonymous_spec(spec_like, pkg_name):
 
 
 class SpecError(spack.error.SpackError):
-
     """Superclass for all errors that occur while constructing specs."""
 
-    def __init__(self, message):
-        super(SpecError, self).__init__(message)
-
 
 class SpecParseError(SpecError):
-
     """Wrapper for ParseError for when we're parsing specs."""
-
     def __init__(self, parse_error):
         super(SpecParseError, self).__init__(parse_error.message)
         self.string = parse_error.string
@@ -2677,79 +2736,53 @@ class SpecParseError(SpecError):
 
 
 class DuplicateDependencyError(SpecError):
-
     """Raised when the same dependency occurs in a spec twice."""
 
-    def __init__(self, message):
-        super(DuplicateDependencyError, self).__init__(message)
-
 
 class DuplicateVariantError(SpecError):
-
     """Raised when the same variant occurs in a spec twice."""
 
-    def __init__(self, message):
-        super(DuplicateVariantError, self).__init__(message)
-
 
 class DuplicateCompilerSpecError(SpecError):
-
     """Raised when the same compiler occurs in a spec twice."""
 
-    def __init__(self, message):
-        super(DuplicateCompilerSpecError, self).__init__(message)
-
 
 class UnsupportedCompilerError(SpecError):
-
     """Raised when the user asks for a compiler spack doesn't know about."""
-
     def __init__(self, compiler_name):
         super(UnsupportedCompilerError, self).__init__(
             "The '%s' compiler is not yet supported." % compiler_name)
 
 
 class UnknownVariantError(SpecError):
-
     """Raised when the same variant occurs in a spec twice."""
-
     def __init__(self, pkg, variant):
         super(UnknownVariantError, self).__init__(
             "Package %s has no variant %s!" % (pkg, variant))
 
 
 class DuplicateArchitectureError(SpecError):
-
     """Raised when the same architecture occurs in a spec twice."""
 
-    def __init__(self, message):
-        super(DuplicateArchitectureError, self).__init__(message)
-
 
 class InconsistentSpecError(SpecError):
-
     """Raised when two nodes in the same spec DAG have inconsistent
        constraints."""
 
-    def __init__(self, message):
-        super(InconsistentSpecError, self).__init__(message)
-
-
-class InvalidDependencyException(SpecError):
 
+class InvalidDependencyError(SpecError):
     """Raised when a dependency in a spec is not actually a dependency
        of the package."""
 
-    def __init__(self, message):
-        super(InvalidDependencyException, self).__init__(message)
 
+class InvalidDependencyTypeError(SpecError):
+    """Raised when a dependency type is not a legal Spack dep type."""
 
-class NoProviderError(SpecError):
 
+class NoProviderError(SpecError):
     """Raised when there is no package that provides a particular
        virtual dependency.
     """
-
     def __init__(self, vpkg):
         super(NoProviderError, self).__init__(
             "No providers found for virtual package: '%s'" % vpkg)
@@ -2757,11 +2790,9 @@ class NoProviderError(SpecError):
 
 
 class MultipleProviderError(SpecError):
-
     """Raised when there is no package that provides a particular
        virtual dependency.
     """
-
     def __init__(self, vpkg, providers):
         """Takes the name of the vpkg"""
         super(MultipleProviderError, self).__init__(
@@ -2772,10 +2803,8 @@ class MultipleProviderError(SpecError):
 
 
 class UnsatisfiableSpecError(SpecError):
-
     """Raised when a spec conflicts with package constraints.
        Provide the requirement that was violated when raising."""
-
     def __init__(self, provided, required, constraint_type):
         super(UnsatisfiableSpecError, self).__init__(
             "%s does not satisfy %s" % (provided, required))
@@ -2785,89 +2814,70 @@ class UnsatisfiableSpecError(SpecError):
 
 
 class UnsatisfiableSpecNameError(UnsatisfiableSpecError):
-
     """Raised when two specs aren't even for the same package."""
-
     def __init__(self, provided, required):
         super(UnsatisfiableSpecNameError, self).__init__(
             provided, required, "name")
 
 
 class UnsatisfiableVersionSpecError(UnsatisfiableSpecError):
-
     """Raised when a spec version conflicts with package constraints."""
-
     def __init__(self, provided, required):
         super(UnsatisfiableVersionSpecError, self).__init__(
             provided, required, "version")
 
 
 class UnsatisfiableCompilerSpecError(UnsatisfiableSpecError):
-
     """Raised when a spec comiler conflicts with package constraints."""
-
     def __init__(self, provided, required):
         super(UnsatisfiableCompilerSpecError, self).__init__(
             provided, required, "compiler")
 
 
 class UnsatisfiableVariantSpecError(UnsatisfiableSpecError):
-
     """Raised when a spec variant conflicts with package constraints."""
-
     def __init__(self, provided, required):
         super(UnsatisfiableVariantSpecError, self).__init__(
             provided, required, "variant")
 
 
 class UnsatisfiableCompilerFlagSpecError(UnsatisfiableSpecError):
-
     """Raised when a spec variant conflicts with package constraints."""
-
     def __init__(self, provided, required):
         super(UnsatisfiableCompilerFlagSpecError, self).__init__(
             provided, required, "compiler_flags")
 
 
 class UnsatisfiableArchitectureSpecError(UnsatisfiableSpecError):
-
     """Raised when a spec architecture conflicts with package constraints."""
-
     def __init__(self, provided, required):
         super(UnsatisfiableArchitectureSpecError, self).__init__(
             provided, required, "architecture")
 
 
 class UnsatisfiableProviderSpecError(UnsatisfiableSpecError):
-
     """Raised when a provider is supplied but constraints don't match
        a vpkg requirement"""
-
     def __init__(self, provided, required):
         super(UnsatisfiableProviderSpecError, self).__init__(
             provided, required, "provider")
 
+
 # TODO: get rid of this and be more specific about particular incompatible
 # dep constraints
-
-
 class UnsatisfiableDependencySpecError(UnsatisfiableSpecError):
-
     """Raised when some dependency of constrained specs are incompatible"""
-
     def __init__(self, provided, required):
         super(UnsatisfiableDependencySpecError, self).__init__(
             provided, required, "dependency")
 
 
 class SpackYAMLError(spack.error.SpackError):
-
     def __init__(self, msg, yaml_error):
         super(SpackYAMLError, self).__init__(msg, str(yaml_error))
 
 
 class AmbiguousHashError(SpecError):
-
     def __init__(self, msg, *specs):
         super(AmbiguousHashError, self).__init__(msg)
         for spec in specs:
diff --git a/lib/spack/spack/stage.py b/lib/spack/spack/stage.py
index c0705a89c8..b659cfb2fb 100644
--- a/lib/spack/spack/stage.py
+++ b/lib/spack/spack/stage.py
@@ -216,9 +216,9 @@ class Stage(object):
     def expected_archive_files(self):
         """Possible archive file paths."""
         paths = []
-        if isinstance(self.fetcher, fs.URLFetchStrategy):
+        if isinstance(self.default_fetcher, fs.URLFetchStrategy):
             paths.append(os.path.join(
-                self.path, os.path.basename(self.fetcher.url)))
+                self.path, os.path.basename(self.default_fetcher.url)))
 
         if self.mirror_path:
             paths.append(os.path.join(
@@ -227,18 +227,18 @@ class Stage(object):
         return paths
 
     @property
+    def save_filename(self):
+        possible_filenames = self.expected_archive_files
+        if possible_filenames:
+            # This prefers using the URL associated with the default fetcher if
+            # available, so that the fetched resource name matches the remote
+            # name
+            return possible_filenames[0]
+
+    @property
     def archive_file(self):
         """Path to the source archive within this stage directory."""
-        paths = []
-        if isinstance(self.fetcher, fs.URLFetchStrategy):
-            paths.append(os.path.join(
-                self.path, os.path.basename(self.fetcher.url)))
-
-        if self.mirror_path:
-            paths.append(os.path.join(
-                self.path, os.path.basename(self.mirror_path)))
-
-        for path in paths:
+        for path in self.expected_archive_files:
             if os.path.exists(path):
                 return path
         else:
@@ -301,8 +301,10 @@ class Stage(object):
             # then use the same digest.  `spack mirror` ensures that
             # the checksum will be the same.
             digest = None
+            expand = True
             if isinstance(self.default_fetcher, fs.URLFetchStrategy):
                 digest = self.default_fetcher.digest
+                expand = self.default_fetcher.expand_archive
 
             # Have to skip the checksum for things archived from
             # repositories.  How can this be made safer?
@@ -310,9 +312,11 @@ class Stage(object):
 
             # Add URL strategies for all the mirrors with the digest
             for url in urls:
-                fetchers.insert(0, fs.URLFetchStrategy(url, digest))
-            fetchers.insert(0, spack.fetch_cache.fetcher(self.mirror_path,
-                                                         digest))
+                fetchers.insert(
+                    0, fs.URLFetchStrategy(url, digest, expand=expand))
+            fetchers.insert(
+                0, spack.fetch_cache.fetcher(
+                    self.mirror_path, digest, expand=expand))
 
             # Look for the archive in list_url
             package_name = os.path.dirname(self.mirror_path)
diff --git a/lib/spack/spack/test/__init__.py b/lib/spack/spack/test/__init__.py
index db683917b5..0a946ff2ff 100644
--- a/lib/spack/spack/test/__init__.py
+++ b/lib/spack/spack/test/__init__.py
@@ -53,6 +53,7 @@ test_names = [
     'git_fetch',
     'hg_fetch',
     'install',
+    'library_list',
     'link_tree',
     'lock',
     'make_executable',
diff --git a/lib/spack/spack/test/cc.py b/lib/spack/spack/test/cc.py
index f3e4bb31d2..73c711724c 100644
--- a/lib/spack/spack/test/cc.py
+++ b/lib/spack/spack/test/cc.py
@@ -223,6 +223,8 @@ class CompilerTest(unittest.TestCase):
     def test_dep_include(self):
         """Ensure a single dependency include directory is added."""
         os.environ['SPACK_DEPENDENCIES'] = self.dep4
+        os.environ['SPACK_RPATH_DEPS'] = os.environ['SPACK_DEPENDENCIES']
+        os.environ['SPACK_LINK_DEPS'] = os.environ['SPACK_DEPENDENCIES']
         self.check_cc('dump-args', test_command,
                       self.realcc + ' ' +
                       '-Wl,-rpath,' + self.prefix + '/lib ' +
@@ -233,6 +235,8 @@ class CompilerTest(unittest.TestCase):
     def test_dep_lib(self):
         """Ensure a single dependency RPATH is added."""
         os.environ['SPACK_DEPENDENCIES'] = self.dep2
+        os.environ['SPACK_RPATH_DEPS'] = os.environ['SPACK_DEPENDENCIES']
+        os.environ['SPACK_LINK_DEPS'] = os.environ['SPACK_DEPENDENCIES']
         self.check_cc('dump-args', test_command,
                       self.realcc + ' ' +
                       '-Wl,-rpath,' + self.prefix + '/lib ' +
@@ -241,10 +245,34 @@ class CompilerTest(unittest.TestCase):
                       '-Wl,-rpath,' + self.dep2 + '/lib64 ' +
                       ' '.join(test_command))
 
+    def test_dep_lib_no_rpath(self):
+        """Ensure a single dependency link flag is added with no dep RPATH."""
+        os.environ['SPACK_DEPENDENCIES'] = self.dep2
+        os.environ['SPACK_LINK_DEPS'] = os.environ['SPACK_DEPENDENCIES']
+        self.check_cc('dump-args', test_command,
+                      self.realcc + ' ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib64 ' +
+                      '-L' + self.dep2 + '/lib64 ' +
+                      ' '.join(test_command))
+
+    def test_dep_lib_no_lib(self):
+        """Ensure a single dependency RPATH is added with no -L."""
+        os.environ['SPACK_DEPENDENCIES'] = self.dep2
+        os.environ['SPACK_RPATH_DEPS'] = os.environ['SPACK_DEPENDENCIES']
+        self.check_cc('dump-args', test_command,
+                      self.realcc + ' ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib64 ' +
+                      '-Wl,-rpath,' + self.dep2 + '/lib64 ' +
+                      ' '.join(test_command))
+
     def test_all_deps(self):
         """Ensure includes and RPATHs for all deps are added. """
         os.environ['SPACK_DEPENDENCIES'] = ':'.join([
             self.dep1, self.dep2, self.dep3, self.dep4])
+        os.environ['SPACK_RPATH_DEPS'] = os.environ['SPACK_DEPENDENCIES']
+        os.environ['SPACK_LINK_DEPS'] = os.environ['SPACK_DEPENDENCIES']
 
         # This is probably more constrained than it needs to be; it
         # checks order within prepended args and doesn't strictly have
@@ -273,6 +301,8 @@ class CompilerTest(unittest.TestCase):
         """Ensure no (extra) -I args or -Wl, are passed in ld mode."""
         os.environ['SPACK_DEPENDENCIES'] = ':'.join([
             self.dep1, self.dep2, self.dep3, self.dep4])
+        os.environ['SPACK_RPATH_DEPS'] = os.environ['SPACK_DEPENDENCIES']
+        os.environ['SPACK_LINK_DEPS'] = os.environ['SPACK_DEPENDENCIES']
 
         self.check_ld('dump-args', test_command,
                       'ld ' +
@@ -290,10 +320,46 @@ class CompilerTest(unittest.TestCase):
 
                       ' '.join(test_command))
 
+    def test_ld_deps_no_rpath(self):
+        """Ensure SPACK_RPATH_DEPS controls RPATHs for ld."""
+        os.environ['SPACK_DEPENDENCIES'] = ':'.join([
+            self.dep1, self.dep2, self.dep3, self.dep4])
+        os.environ['SPACK_LINK_DEPS'] = os.environ['SPACK_DEPENDENCIES']
+
+        self.check_ld('dump-args', test_command,
+                      'ld ' +
+                      '-rpath ' + self.prefix + '/lib ' +
+                      '-rpath ' + self.prefix + '/lib64 ' +
+
+                      '-L' + self.dep3 + '/lib64 ' +
+                      '-L' + self.dep2 + '/lib64 ' +
+                      '-L' + self.dep1 + '/lib ' +
+
+                      ' '.join(test_command))
+
+    def test_ld_deps_no_link(self):
+        """Ensure SPACK_LINK_DEPS controls -L for ld."""
+        os.environ['SPACK_DEPENDENCIES'] = ':'.join([
+            self.dep1, self.dep2, self.dep3, self.dep4])
+        os.environ['SPACK_RPATH_DEPS'] = os.environ['SPACK_DEPENDENCIES']
+
+        self.check_ld('dump-args', test_command,
+                      'ld ' +
+                      '-rpath ' + self.prefix + '/lib ' +
+                      '-rpath ' + self.prefix + '/lib64 ' +
+
+                      '-rpath ' + self.dep3 + '/lib64 ' +
+                      '-rpath ' + self.dep2 + '/lib64 ' +
+                      '-rpath ' + self.dep1 + '/lib ' +
+
+                      ' '.join(test_command))
+
     def test_ld_deps_reentrant(self):
         """Make sure ld -r is handled correctly on OS's where it doesn't
            support rpaths."""
         os.environ['SPACK_DEPENDENCIES'] = ':'.join([self.dep1])
+        os.environ['SPACK_RPATH_DEPS'] = os.environ['SPACK_DEPENDENCIES']
+        os.environ['SPACK_LINK_DEPS'] = os.environ['SPACK_DEPENDENCIES']
 
         os.environ['SPACK_SHORT_SPEC'] = "foo@1.2=linux-x86_64"
         reentrant_test_command = ['-r'] + test_command
diff --git a/lib/spack/spack/test/database.py b/lib/spack/spack/test/database.py
index 22b1f17890..4395f17f97 100644
--- a/lib/spack/spack/test/database.py
+++ b/lib/spack/spack/test/database.py
@@ -26,8 +26,8 @@
 These tests check the database is functioning properly,
 both in memory and in its file
 """
-import os.path
 import multiprocessing
+import os.path
 
 import spack
 from llnl.util.filesystem import join_path
@@ -88,16 +88,16 @@ class DatabaseTest(MockDatabase):
         # query specs with multiple configurations
         mpileaks_specs = [s for s in all_specs if s.satisfies('mpileaks')]
         callpath_specs = [s for s in all_specs if s.satisfies('callpath')]
-        mpi_specs      = [s for s in all_specs if s.satisfies('mpi')]
+        mpi_specs = [s for s in all_specs if s.satisfies('mpi')]
 
         self.assertEqual(len(mpileaks_specs), 3)
         self.assertEqual(len(callpath_specs), 3)
         self.assertEqual(len(mpi_specs),      3)
 
         # query specs with single configurations
-        dyninst_specs  = [s for s in all_specs if s.satisfies('dyninst')]
+        dyninst_specs = [s for s in all_specs if s.satisfies('dyninst')]
         libdwarf_specs = [s for s in all_specs if s.satisfies('libdwarf')]
-        libelf_specs   = [s for s in all_specs if s.satisfies('libelf')]
+        libelf_specs = [s for s in all_specs if s.satisfies('libelf')]
 
         self.assertEqual(len(dyninst_specs),  1)
         self.assertEqual(len(libdwarf_specs), 1)
@@ -124,6 +124,19 @@ class DatabaseTest(MockDatabase):
             self.assertEqual(new_rec.path,      rec.path)
             self.assertEqual(new_rec.installed, rec.installed)
 
+    def _check_merkleiness(self):
+        """Ensure the spack database is a valid merkle graph."""
+        all_specs = spack.installed_db.query(installed=any)
+
+        seen = {}
+        for spec in all_specs:
+            for dep in spec.dependencies():
+                hash_key = dep.dag_hash()
+                if hash_key not in seen:
+                    seen[hash_key] = id(dep)
+                else:
+                    self.assertEqual(seen[hash_key], id(dep))
+
     def _check_db_sanity(self):
         """Utiilty function to check db against install layout."""
         expected = sorted(spack.install_layout.all_specs())
@@ -133,10 +146,17 @@ class DatabaseTest(MockDatabase):
         for e, a in zip(expected, actual):
             self.assertEqual(e, a)
 
+        self._check_merkleiness()
+
     def test_020_db_sanity(self):
         """Make sure query() returns what's actually in the db."""
         self._check_db_sanity()
 
+    def test_025_reindex(self):
+        """Make sure reindex works and ref counts are valid."""
+        spack.installed_db.reindex(spack.install_layout)
+        self._check_db_sanity()
+
     def test_030_db_sanity_from_another_process(self):
         def read_and_modify():
             self._check_db_sanity()  # check that other process can read DB
@@ -163,16 +183,16 @@ class DatabaseTest(MockDatabase):
         # query specs with multiple configurations
         mpileaks_specs = self.installed_db.query('mpileaks')
         callpath_specs = self.installed_db.query('callpath')
-        mpi_specs      = self.installed_db.query('mpi')
+        mpi_specs = self.installed_db.query('mpi')
 
         self.assertEqual(len(mpileaks_specs), 3)
         self.assertEqual(len(callpath_specs), 3)
         self.assertEqual(len(mpi_specs),      3)
 
         # query specs with single configurations
-        dyninst_specs  = self.installed_db.query('dyninst')
+        dyninst_specs = self.installed_db.query('dyninst')
         libdwarf_specs = self.installed_db.query('libdwarf')
-        libelf_specs   = self.installed_db.query('libelf')
+        libelf_specs = self.installed_db.query('libelf')
 
         self.assertEqual(len(dyninst_specs),  1)
         self.assertEqual(len(libdwarf_specs), 1)
@@ -203,9 +223,10 @@ class DatabaseTest(MockDatabase):
         self.assertTrue(concrete_spec not in remaining)
 
         # add it back and make sure everything is ok.
-        self.installed_db.add(concrete_spec, "")
+        self.installed_db.add(concrete_spec, spack.install_layout)
         installed = self.installed_db.query()
-        self.assertEqual(len(installed), len(original))
+        self.assertTrue(concrete_spec in installed)
+        self.assertEqual(installed, original)
 
         # sanity check against direcory layout and check ref counts.
         self._check_db_sanity()
@@ -233,7 +254,7 @@ class DatabaseTest(MockDatabase):
         self.assertEqual(self.installed_db.get_record('mpich').ref_count, 1)
 
         # Put the spec back
-        self.installed_db.add(rec.spec, rec.path)
+        self.installed_db.add(rec.spec, spack.install_layout)
 
         # record is present again
         self.assertEqual(
diff --git a/lib/spack/spack/test/library_list.py b/lib/spack/spack/test/library_list.py
new file mode 100644
index 0000000000..7fc2fd222f
--- /dev/null
+++ b/lib/spack/spack/test/library_list.py
@@ -0,0 +1,111 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+
+import unittest
+
+from llnl.util.filesystem import LibraryList
+
+
+class LibraryListTest(unittest.TestCase):
+    def setUp(self):
+        l = [
+            '/dir1/liblapack.a',
+            '/dir2/libfoo.dylib',
+            '/dir1/libblas.a',
+            '/dir3/libbar.so',
+            'libbaz.so'
+        ]
+        self.liblist = LibraryList(l)
+
+    def test_repr(self):
+        x = eval(repr(self.liblist))
+        self.assertEqual(self.liblist, x)
+
+    def test_joined_and_str(self):
+        s1 = self.liblist.joined()
+        self.assertEqual(
+            s1,
+            '/dir1/liblapack.a /dir2/libfoo.dylib /dir1/libblas.a /dir3/libbar.so libbaz.so'  # NOQA: ignore=E501
+        )
+        s2 = str(self.liblist)
+        self.assertEqual(s1, s2)
+        s3 = self.liblist.joined(';')
+        self.assertEqual(
+            s3,
+            '/dir1/liblapack.a;/dir2/libfoo.dylib;/dir1/libblas.a;/dir3/libbar.so;libbaz.so'  # NOQA: ignore=E501
+        )
+
+    def test_flags(self):
+        search_flags = self.liblist.search_flags
+        self.assertTrue('-L/dir1' in search_flags)
+        self.assertTrue('-L/dir2' in search_flags)
+        self.assertTrue('-L/dir3' in search_flags)
+        self.assertTrue(isinstance(search_flags, str))
+
+        link_flags = self.liblist.link_flags
+        self.assertEqual(
+            link_flags,
+            '-llapack -lfoo -lblas -lbar -lbaz'
+        )
+
+        ld_flags = self.liblist.ld_flags
+        self.assertEqual(ld_flags, search_flags + ' ' + link_flags)
+
+    def test_paths_manipulation(self):
+        names = self.liblist.names
+        self.assertEqual(names, ['lapack', 'foo', 'blas', 'bar', 'baz'])
+
+        directories = self.liblist.directories
+        self.assertEqual(directories, ['/dir1', '/dir2', '/dir3'])
+
+    def test_get_item(self):
+        a = self.liblist[0]
+        self.assertEqual(a, '/dir1/liblapack.a')
+
+        b = self.liblist[:]
+        self.assertEqual(type(b), type(self.liblist))
+        self.assertEqual(self.liblist, b)
+        self.assertTrue(self.liblist is not b)
+
+    def test_add(self):
+        pylist = [
+            '/dir1/liblapack.a',  # removed from the final list
+            '/dir2/libbaz.so',
+            '/dir4/libnew.a'
+        ]
+        another = LibraryList(pylist)
+        l = self.liblist + another
+        self.assertEqual(len(l), 7)
+        # Invariant : l == l + l
+        self.assertEqual(l, l + l)
+        # Always produce an instance of LibraryList
+        self.assertEqual(
+            type(self.liblist),
+            type(self.liblist + pylist)
+        )
+        self.assertEqual(
+            type(pylist + self.liblist),
+            type(self.liblist)
+        )
diff --git a/lib/spack/spack/test/lock.py b/lib/spack/spack/test/lock.py
index fb96539897..32cbe13ce1 100644
--- a/lib/spack/spack/test/lock.py
+++ b/lib/spack/spack/test/lock.py
@@ -158,6 +158,35 @@ class LockTest(unittest.TestCase):
             self.timeout_write, self.timeout_write)
 
     #
+    # Test that read can be upgraded to write.
+    #
+    def test_upgrade_read_to_write(self):
+        # ensure lock file exists the first time, so we open it read-only
+        # to begin wtih.
+        touch(self.lock_path)
+
+        lock = Lock(self.lock_path)
+        self.assertTrue(lock._reads == 0)
+        self.assertTrue(lock._writes == 0)
+
+        lock.acquire_read()
+        self.assertTrue(lock._reads == 1)
+        self.assertTrue(lock._writes == 0)
+
+        lock.acquire_write()
+        self.assertTrue(lock._reads == 1)
+        self.assertTrue(lock._writes == 1)
+
+        lock.release_write()
+        self.assertTrue(lock._reads == 1)
+        self.assertTrue(lock._writes == 0)
+
+        lock.release_read()
+        self.assertTrue(lock._reads == 0)
+        self.assertTrue(lock._writes == 0)
+        self.assertTrue(lock._fd is None)
+
+    #
     # Longer test case that ensures locks are reusable. Ordering is
     # enforced by barriers throughout -- steps are shown with numbers.
     #
diff --git a/lib/spack/spack/test/modules.py b/lib/spack/spack/test/modules.py
index 5e280d8e43..c4cf2865bb 100644
--- a/lib/spack/spack/test/modules.py
+++ b/lib/spack/spack/test/modules.py
@@ -49,105 +49,10 @@ def mock_open(filename, mode):
         handle.close()
 
 
-configuration_autoload_direct = {
-    'enable': ['tcl'],
-    'tcl': {
-        'all': {
-            'autoload': 'direct'
-        }
-    }
-}
-
-configuration_autoload_all = {
-    'enable': ['tcl'],
-    'tcl': {
-        'all': {
-            'autoload': 'all'
-        }
-    }
-}
-
-configuration_prerequisites_direct = {
-    'enable': ['tcl'],
-    'tcl': {
-        'all': {
-            'prerequisites': 'direct'
-        }
-    }
-}
-
-configuration_prerequisites_all = {
-    'enable': ['tcl'],
-    'tcl': {
-        'all': {
-            'prerequisites': 'all'
-        }
-    }
-}
-
-configuration_alter_environment = {
-    'enable': ['tcl'],
-    'tcl': {
-        'all': {
-            'filter': {'environment_blacklist': ['CMAKE_PREFIX_PATH']},
-            'environment': {
-                'set': {'{name}_ROOT': '{prefix}'}
-            }
-        },
-        'platform=test target=x86_64': {
-            'environment': {
-                'set': {'FOO': 'foo'},
-                'unset': ['BAR']
-            }
-        },
-        'platform=test target=x86_32': {
-            'load': ['foo/bar']
-        }
-    }
-}
-
-configuration_blacklist = {
-    'enable': ['tcl'],
-    'tcl': {
-        'whitelist': ['zmpi'],
-        'blacklist': ['callpath', 'mpi'],
-        'all': {
-            'autoload': 'direct'
-        }
-    }
-}
-
-configuration_conflicts = {
-    'enable': ['tcl'],
-    'tcl': {
-        'naming_scheme': '{name}/{version}-{compiler.name}',
-        'all': {
-            'conflict': ['{name}', 'intel/14.0.1']
-        }
-    }
-}
-
-configuration_wrong_conflicts = {
-    'enable': ['tcl'],
-    'tcl': {
-        'naming_scheme': '{name}/{version}-{compiler.name}',
-        'all': {
-            'conflict': ['{name}/{compiler.name}']
-        }
-    }
-}
-
-configuration_suffix = {
-    'enable': ['tcl'],
-    'tcl': {
-        'mpileaks': {
-            'suffixes': {
-                '+debug': 'foo',
-                '~debug': 'bar'
-            }
-        }
-    }
-}
+# Spec strings that will be used throughout the tests
+mpich_spec_string = 'mpich@3.0.4'
+mpileaks_spec_string = 'mpileaks'
+libdwarf_spec_string = 'libdwarf arch=x64-linux'
 
 
 class HelperFunctionsTests(MockPackagesTest):
@@ -187,61 +92,195 @@ class HelperFunctionsTests(MockPackagesTest):
         self.assertTrue('CPATH' in names)
 
 
-class TclTests(MockPackagesTest):
+class ModuleFileGeneratorTests(MockPackagesTest):
+    """
+    Base class to test module file generators. Relies on child having defined
+    a 'factory' attribute to create an instance of the generator to be tested.
+    """
 
     def setUp(self):
-        super(TclTests, self).setUp()
-        self.configuration_obj = spack.modules.CONFIGURATION
+        super(ModuleFileGeneratorTests, self).setUp()
+        self.configuration_instance = spack.modules.CONFIGURATION
+        self.module_types_instance = spack.modules.module_types
         spack.modules.open = mock_open
         # Make sure that a non-mocked configuration will trigger an error
         spack.modules.CONFIGURATION = None
+        spack.modules.module_types = {self.factory.name: self.factory}
 
     def tearDown(self):
         del spack.modules.open
-        spack.modules.CONFIGURATION = self.configuration_obj
-        super(TclTests, self).tearDown()
+        spack.modules.module_types = self.module_types_instance
+        spack.modules.CONFIGURATION = self.configuration_instance
+        super(ModuleFileGeneratorTests, self).tearDown()
 
     def get_modulefile_content(self, spec):
         spec.concretize()
-        generator = spack.modules.TclModule(spec)
+        generator = self.factory(spec)
         generator.write()
         content = FILE_REGISTRY[generator.file_name].split('\n')
         return content
 
+
+class TclTests(ModuleFileGeneratorTests):
+
+    factory = spack.modules.TclModule
+
+    configuration_autoload_direct = {
+        'enable': ['tcl'],
+        'tcl': {
+            'all': {
+                'autoload': 'direct'
+            }
+        }
+    }
+
+    configuration_autoload_all = {
+        'enable': ['tcl'],
+        'tcl': {
+            'all': {
+                'autoload': 'all'
+            }
+        }
+    }
+
+    configuration_prerequisites_direct = {
+        'enable': ['tcl'],
+        'tcl': {
+            'all': {
+                'prerequisites': 'direct'
+            }
+        }
+    }
+
+    configuration_prerequisites_all = {
+        'enable': ['tcl'],
+        'tcl': {
+            'all': {
+                'prerequisites': 'all'
+            }
+        }
+    }
+
+    configuration_alter_environment = {
+        'enable': ['tcl'],
+        'tcl': {
+            'all': {
+                'filter': {'environment_blacklist': ['CMAKE_PREFIX_PATH']},
+                'environment': {
+                    'set': {'{name}_ROOT': '{prefix}'}
+                }
+            },
+            'platform=test target=x86_64': {
+                'environment': {
+                    'set': {'FOO': 'foo'},
+                    'unset': ['BAR']
+                }
+            },
+            'platform=test target=x86_32': {
+                'load': ['foo/bar']
+            }
+        }
+    }
+
+    configuration_blacklist = {
+        'enable': ['tcl'],
+        'tcl': {
+            'whitelist': ['zmpi'],
+            'blacklist': ['callpath', 'mpi'],
+            'all': {
+                'autoload': 'direct'
+            }
+        }
+    }
+
+    configuration_conflicts = {
+        'enable': ['tcl'],
+        'tcl': {
+            'naming_scheme': '{name}/{version}-{compiler.name}',
+            'all': {
+                'conflict': ['{name}', 'intel/14.0.1']
+            }
+        }
+    }
+
+    configuration_wrong_conflicts = {
+        'enable': ['tcl'],
+        'tcl': {
+            'naming_scheme': '{name}/{version}-{compiler.name}',
+            'all': {
+                'conflict': ['{name}/{compiler.name}']
+            }
+        }
+    }
+
+    configuration_suffix = {
+        'enable': ['tcl'],
+        'tcl': {
+            'mpileaks': {
+                'suffixes': {
+                    '+debug': 'foo',
+                    '~debug': 'bar'
+                }
+            }
+        }
+    }
+
     def test_simple_case(self):
-        spack.modules.CONFIGURATION = configuration_autoload_direct
-        spec = spack.spec.Spec('mpich@3.0.4')
+        spack.modules.CONFIGURATION = self.configuration_autoload_direct
+        spec = spack.spec.Spec(mpich_spec_string)
         content = self.get_modulefile_content(spec)
         self.assertTrue('module-whatis "mpich @3.0.4"' in content)
         self.assertRaises(TypeError, spack.modules.dependencies,
                           spec, 'non-existing-tag')
 
     def test_autoload(self):
-        spack.modules.CONFIGURATION = configuration_autoload_direct
-        spec = spack.spec.Spec('mpileaks')
+        spack.modules.CONFIGURATION = self.configuration_autoload_direct
+        spec = spack.spec.Spec(mpileaks_spec_string)
         content = self.get_modulefile_content(spec)
         self.assertEqual(len([x for x in content if 'is-loaded' in x]), 2)
         self.assertEqual(len([x for x in content if 'module load ' in x]), 2)
 
-        spack.modules.CONFIGURATION = configuration_autoload_all
-        spec = spack.spec.Spec('mpileaks')
+        spack.modules.CONFIGURATION = self.configuration_autoload_all
+        spec = spack.spec.Spec(mpileaks_spec_string)
         content = self.get_modulefile_content(spec)
         self.assertEqual(len([x for x in content if 'is-loaded' in x]), 5)
         self.assertEqual(len([x for x in content if 'module load ' in x]), 5)
 
+        # dtbuild1 has
+        # - 1 ('run',) dependency
+        # - 1 ('build','link') dependency
+        # - 1 ('build',) dependency
+        # Just make sure the 'build' dependency is not there
+        spack.modules.CONFIGURATION = self.configuration_autoload_direct
+        spec = spack.spec.Spec('dtbuild1')
+        content = self.get_modulefile_content(spec)
+        self.assertEqual(len([x for x in content if 'is-loaded' in x]), 2)
+        self.assertEqual(len([x for x in content if 'module load ' in x]), 2)
+
+        # dtbuild1 has
+        # - 1 ('run',) dependency
+        # - 1 ('build','link') dependency
+        # - 1 ('build',) dependency
+        # Just make sure the 'build' dependency is not there
+        spack.modules.CONFIGURATION = self.configuration_autoload_all
+        spec = spack.spec.Spec('dtbuild1')
+        content = self.get_modulefile_content(spec)
+        self.assertEqual(len([x for x in content if 'is-loaded' in x]), 2)
+        self.assertEqual(len([x for x in content if 'module load ' in x]), 2)
+
     def test_prerequisites(self):
-        spack.modules.CONFIGURATION = configuration_prerequisites_direct
+        spack.modules.CONFIGURATION = self.configuration_prerequisites_direct
         spec = spack.spec.Spec('mpileaks arch=x86-linux')
         content = self.get_modulefile_content(spec)
         self.assertEqual(len([x for x in content if 'prereq' in x]), 2)
 
-        spack.modules.CONFIGURATION = configuration_prerequisites_all
+        spack.modules.CONFIGURATION = self.configuration_prerequisites_all
         spec = spack.spec.Spec('mpileaks arch=x86-linux')
         content = self.get_modulefile_content(spec)
         self.assertEqual(len([x for x in content if 'prereq' in x]), 5)
 
     def test_alter_environment(self):
-        spack.modules.CONFIGURATION = configuration_alter_environment
+        spack.modules.CONFIGURATION = self.configuration_alter_environment
         spec = spack.spec.Spec('mpileaks platform=test target=x86_64')
         content = self.get_modulefile_content(spec)
         self.assertEqual(
@@ -271,7 +310,7 @@ class TclTests(MockPackagesTest):
             len([x for x in content if 'setenv LIBDWARF_ROOT' in x]), 1)
 
     def test_blacklist(self):
-        spack.modules.CONFIGURATION = configuration_blacklist
+        spack.modules.CONFIGURATION = self.configuration_blacklist
         spec = spack.spec.Spec('mpileaks ^zmpi')
         content = self.get_modulefile_content(spec)
         self.assertEqual(len([x for x in content if 'is-loaded' in x]), 1)
@@ -285,7 +324,7 @@ class TclTests(MockPackagesTest):
         self.assertEqual(len([x for x in content if 'module load ' in x]), 1)
 
     def test_conflicts(self):
-        spack.modules.CONFIGURATION = configuration_conflicts
+        spack.modules.CONFIGURATION = self.configuration_conflicts
         spec = spack.spec.Spec('mpileaks')
         content = self.get_modulefile_content(spec)
         self.assertEqual(
@@ -295,11 +334,11 @@ class TclTests(MockPackagesTest):
         self.assertEqual(
             len([x for x in content if x == 'conflict intel/14.0.1']), 1)
 
-        spack.modules.CONFIGURATION = configuration_wrong_conflicts
+        spack.modules.CONFIGURATION = self.configuration_wrong_conflicts
         self.assertRaises(SystemExit, self.get_modulefile_content, spec)
 
     def test_suffixes(self):
-        spack.modules.CONFIGURATION = configuration_suffix
+        spack.modules.CONFIGURATION = self.configuration_suffix
         spec = spack.spec.Spec('mpileaks+debug arch=x86-linux')
         spec.concretize()
         generator = spack.modules.TclModule(spec)
@@ -311,18 +350,123 @@ class TclTests(MockPackagesTest):
         self.assertTrue('bar' in generator.use_name)
 
 
-configuration_dotkit = {
-    'enable': ['dotkit'],
-    'dotkit': {
-        'all': {
-            'prerequisites': 'direct'
+class LmodTests(ModuleFileGeneratorTests):
+    factory = spack.modules.LmodModule
+
+    configuration_autoload_direct = {
+        'enable': ['lmod'],
+        'lmod': {
+            'all': {
+                'autoload': 'direct'
+            }
+        }
+    }
+
+    configuration_autoload_all = {
+        'enable': ['lmod'],
+        'lmod': {
+            'all': {
+                'autoload': 'all'
+            }
+        }
+    }
+
+    configuration_alter_environment = {
+        'enable': ['lmod'],
+        'lmod': {
+            'all': {
+                'filter': {'environment_blacklist': ['CMAKE_PREFIX_PATH']}
+            },
+            'platform=test target=x86_64': {
+                'environment': {
+                    'set': {'FOO': 'foo'},
+                    'unset': ['BAR']
+                }
+            },
+            'platform=test target=x86_32': {
+                'load': ['foo/bar']
+            }
+        }
+    }
+
+    configuration_blacklist = {
+        'enable': ['lmod'],
+        'lmod': {
+            'blacklist': ['callpath'],
+            'all': {
+                'autoload': 'direct'
+            }
         }
     }
-}
+
+    def test_simple_case(self):
+        spack.modules.CONFIGURATION = self.configuration_autoload_direct
+        spec = spack.spec.Spec(mpich_spec_string)
+        content = self.get_modulefile_content(spec)
+        self.assertTrue('-- -*- lua -*-' in content)
+        self.assertTrue('whatis([[Name : mpich]])' in content)
+        self.assertTrue('whatis([[Version : 3.0.4]])' in content)
+
+    def test_autoload(self):
+        spack.modules.CONFIGURATION = self.configuration_autoload_direct
+        spec = spack.spec.Spec(mpileaks_spec_string)
+        content = self.get_modulefile_content(spec)
+        self.assertEqual(
+            len([x for x in content if 'if not isloaded(' in x]), 2)
+        self.assertEqual(len([x for x in content if 'load(' in x]), 2)
+
+        spack.modules.CONFIGURATION = self.configuration_autoload_all
+        spec = spack.spec.Spec(mpileaks_spec_string)
+        content = self.get_modulefile_content(spec)
+        self.assertEqual(
+            len([x for x in content if 'if not isloaded(' in x]), 5)
+        self.assertEqual(len([x for x in content if 'load(' in x]), 5)
+
+    def test_alter_environment(self):
+        spack.modules.CONFIGURATION = self.configuration_alter_environment
+        spec = spack.spec.Spec('mpileaks platform=test target=x86_64')
+        content = self.get_modulefile_content(spec)
+        self.assertEqual(
+            len([x
+                 for x in content
+                 if x.startswith('prepend_path("CMAKE_PREFIX_PATH"')]), 0)
+        self.assertEqual(
+            len([x for x in content if 'setenv("FOO", "foo")' in x]), 1)
+        self.assertEqual(
+            len([x for x in content if 'unsetenv("BAR")' in x]), 1)
+
+        spec = spack.spec.Spec('libdwarf %clang platform=test target=x86_32')
+        content = self.get_modulefile_content(spec)
+        print('\n'.join(content))
+        self.assertEqual(
+            len([x
+                 for x in content
+                 if x.startswith('prepend-path("CMAKE_PREFIX_PATH"')]), 0)
+        self.assertEqual(
+            len([x for x in content if 'setenv("FOO", "foo")' in x]), 0)
+        self.assertEqual(
+            len([x for x in content if 'unsetenv("BAR")' in x]), 0)
+
+    def test_blacklist(self):
+        spack.modules.CONFIGURATION = self.configuration_blacklist
+        spec = spack.spec.Spec(mpileaks_spec_string)
+        content = self.get_modulefile_content(spec)
+        self.assertEqual(
+            len([x for x in content if 'if not isloaded(' in x]), 1)
+        self.assertEqual(len([x for x in content if 'load(' in x]), 1)
 
 
 class DotkitTests(MockPackagesTest):
 
+    configuration_dotkit = {
+        'enable': ['dotkit'],
+        'dotkit': {
+            'all': {
+                'prerequisites': 'direct'
+            }
+        }
+    }
+
     def setUp(self):
         super(DotkitTests, self).setUp()
         self.configuration_obj = spack.modules.CONFIGURATION
@@ -343,7 +487,7 @@ class DotkitTests(MockPackagesTest):
         return content
 
     def test_dotkit(self):
-        spack.modules.CONFIGURATION = configuration_dotkit
+        spack.modules.CONFIGURATION = self.configuration_dotkit
         spec = spack.spec.Spec('mpileaks arch=x86-linux')
         content = self.get_modulefile_content(spec)
         self.assertTrue('#c spack' in content)
diff --git a/lib/spack/spack/test/spec_dag.py b/lib/spack/spack/test/spec_dag.py
index 5c2731041c..40cdb02966 100644
--- a/lib/spack/spack/test/spec_dag.py
+++ b/lib/spack/spack/test/spec_dag.py
@@ -241,15 +241,15 @@ class SpecDagTest(MockPackagesTest):
 
     def test_invalid_dep(self):
         spec = Spec('libelf ^mpich')
-        self.assertRaises(spack.spec.InvalidDependencyException,
+        self.assertRaises(spack.spec.InvalidDependencyError,
                           spec.normalize)
 
         spec = Spec('libelf ^libdwarf')
-        self.assertRaises(spack.spec.InvalidDependencyException,
+        self.assertRaises(spack.spec.InvalidDependencyError,
                           spec.normalize)
 
         spec = Spec('mpich ^dyninst ^libelf')
-        self.assertRaises(spack.spec.InvalidDependencyException,
+        self.assertRaises(spack.spec.InvalidDependencyError,
                           spec.normalize)
 
     def test_equal(self):
diff --git a/lib/spack/spack/test/spec_syntax.py b/lib/spack/spack/test/spec_syntax.py
index 3079288c77..d4eb9e057f 100644
--- a/lib/spack/spack/test/spec_syntax.py
+++ b/lib/spack/spack/test/spec_syntax.py
@@ -24,34 +24,34 @@
 ##############################################################################
 import unittest
 
-import spack.spec
+import spack.spec as sp
 from spack.parse import Token
 from spack.spec import *
 
 # Sample output for a complex lexing.
-complex_lex = [Token(ID, 'mvapich_foo'),
-               Token(DEP),
-               Token(ID, '_openmpi'),
-               Token(AT),
-               Token(ID, '1.2'),
-               Token(COLON),
-               Token(ID, '1.4'),
-               Token(COMMA),
-               Token(ID, '1.6'),
-               Token(PCT),
-               Token(ID, 'intel'),
-               Token(AT),
-               Token(ID, '12.1'),
-               Token(COLON),
-               Token(ID, '12.6'),
-               Token(ON),
-               Token(ID, 'debug'),
-               Token(OFF),
-               Token(ID, 'qt_4'),
-               Token(DEP),
-               Token(ID, 'stackwalker'),
-               Token(AT),
-               Token(ID, '8.1_1e')]
+complex_lex = [Token(sp.ID, 'mvapich_foo'),
+               Token(sp.DEP),
+               Token(sp.ID, '_openmpi'),
+               Token(sp.AT),
+               Token(sp.ID, '1.2'),
+               Token(sp.COLON),
+               Token(sp.ID, '1.4'),
+               Token(sp.COMMA),
+               Token(sp.ID, '1.6'),
+               Token(sp.PCT),
+               Token(sp.ID, 'intel'),
+               Token(sp.AT),
+               Token(sp.ID, '12.1'),
+               Token(sp.COLON),
+               Token(sp.ID, '12.6'),
+               Token(sp.ON),
+               Token(sp.ID, 'debug'),
+               Token(sp.OFF),
+               Token(sp.ID, 'qt_4'),
+               Token(sp.DEP),
+               Token(sp.ID, 'stackwalker'),
+               Token(sp.AT),
+               Token(sp.ID, '8.1_1e')]
 
 
 class SpecSyntaxTest(unittest.TestCase):
@@ -74,16 +74,16 @@ class SpecSyntaxTest(unittest.TestCase):
         """
         if spec is None:
             spec = expected
-        output = spack.spec.parse(spec)
+        output = sp.parse(spec)
 
         parsed = (" ".join(str(spec) for spec in output))
         self.assertEqual(expected, parsed)
 
     def check_lex(self, tokens, spec):
         """Check that the provided spec parses to the provided token list."""
-        lex_output = SpecLexer().lex(spec)
+        lex_output = sp.SpecLexer().lex(spec)
         for tok, spec_tok in zip(tokens, lex_output):
-            if tok.type == ID:
+            if tok.type == sp.ID:
                 self.assertEqual(tok, spec_tok)
             else:
                 # Only check the type for non-identifiers.
diff --git a/share/spack/qa/changed_files b/share/spack/qa/changed_files
index 9c60b3b20b..c1fa55c053 100755
--- a/share/spack/qa/changed_files
+++ b/share/spack/qa/changed_files
@@ -18,11 +18,11 @@ SPACK_ROOT="$(dirname "$0")/../../.."
 cd "$SPACK_ROOT"
 
 # Add changed files that have been committed since branching off of develop
-changed=($(git diff --name-only --find-renames develop... -- "$@"))
+changed=($(git diff --name-only --diff-filter=ACMR develop... -- "$@"))
 # Add changed files that have been staged but not yet committed
-changed+=($(git diff --name-only --find-renames --cached -- "$@"))
+changed+=($(git diff --name-only --diff-filter=ACMR --cached -- "$@"))
 # Add changed files that are unstaged
-changed+=($(git diff --name-only --find-renames -- "$@"))
+changed+=($(git diff --name-only --diff-filter=ACMR -- "$@"))
 # Add new files that are untracked
 changed+=($(git ls-files --exclude-standard --other -- "$@"))
 
diff --git a/share/spack/qa/check_dependencies b/share/spack/qa/check_dependencies
index 08fad9cdc9..cf3d204f48 100755
--- a/share/spack/qa/check_dependencies
+++ b/share/spack/qa/check_dependencies
@@ -27,6 +27,9 @@ for dep in "$@"; do
                 spack_package=py-flake8
                 pip_package=flake8
                 ;;
+            dot)
+                spack_package=graphviz
+                ;;
             git)
                 spack_package=git
                 ;;
diff --git a/share/spack/qa/run-doc-tests b/share/spack/qa/run-doc-tests
index 96b76a216e..dbf46c71aa 100755
--- a/share/spack/qa/run-doc-tests
+++ b/share/spack/qa/run-doc-tests
@@ -9,7 +9,7 @@
 #     run-doc-tests
 #
 # Notes:
-#     Requires sphinx, git, mercurial, and subversion.
+#     Requires sphinx, graphviz, git, mercurial, and subversion.
 #
 
 QA_DIR="$(dirname "$0")"
@@ -20,6 +20,7 @@ DOC_DIR="$SPACK_ROOT/lib/spack/docs"
 deps=(
     sphinx-apidoc
     sphinx-build
+    dot
     git
     hg
     svn
@@ -35,9 +36,7 @@ export PATH="$SPACK_ROOT/bin:$PATH"
 # Allows script to be run from anywhere
 cd "$DOC_DIR"
 
-# Cleanup temporary files upon exit or when script is killed
-trap 'make clean --silent' EXIT SIGINT SIGTERM
-
 # Treat warnings as fatal errors
+make clean --silent
 make SPHINXOPTS=-W
 
diff --git a/var/spack/repos/builtin/packages/R/package.py b/var/spack/repos/builtin/packages/R/package.py
index e880a3aa66..a0899084d0 100644
--- a/var/spack/repos/builtin/packages/R/package.py
+++ b/var/spack/repos/builtin/packages/R/package.py
@@ -58,7 +58,7 @@ class R(Package):
     # Concrete dependencies
     depends_on('readline')
     depends_on('ncurses')
-    depends_on('icu')
+    depends_on('icu4c')
     depends_on('glib')
     depends_on('zlib')
     depends_on('bzip2')
diff --git a/var/spack/repos/builtin/packages/adios/adios_1100.patch b/var/spack/repos/builtin/packages/adios/adios_1100.patch
new file mode 100644
index 0000000000..7a9f857c32
--- /dev/null
+++ b/var/spack/repos/builtin/packages/adios/adios_1100.patch
@@ -0,0 +1,29 @@
+From 3b21a8a4150962c6938baeceacd04f619cea2fbc Mon Sep 17 00:00:00 2001
+From: Norbert Podhorszki <pnorbert@ornl.gov>
+Date: Thu, 1 Sep 2016 16:26:23 -0400
+Subject: [PATCH] ifdef around 'bool' type. hdf5 1.10 defines bool and breaks
+ compiling bp2h5.c
+
+---
+ utils/bp2h5/bp2h5.c | 8 +++++---
+ 1 file changed, 5 insertions(+), 3 deletions(-)
+
+diff --git a/utils/bp2h5/bp2h5.c b/utils/bp2h5/bp2h5.c
+index 9c500c7..fa746bd 100644
+--- a/utils/bp2h5/bp2h5.c
++++ b/utils/bp2h5/bp2h5.c
+@@ -43,9 +43,11 @@
+ #include "dmalloc.h"
+ #endif
+ 
+-typedef int bool;
+-#define false 0
+-#define true  1
++#ifndef bool
++    typedef int bool;
++#   define false 0
++#   define true  1
++#endif
+ 
+ bool noindex = false;              // do no print array indices with data
+ bool printByteAsChar = false;      // print 8 bit integer arrays as string
diff --git a/var/spack/repos/builtin/packages/adios/package.py b/var/spack/repos/builtin/packages/adios/package.py
index 01834383b8..e240ce0858 100644
--- a/var/spack/repos/builtin/packages/adios/package.py
+++ b/var/spack/repos/builtin/packages/adios/package.py
@@ -36,6 +36,8 @@ class Adios(Package):
     homepage = "http://www.olcf.ornl.gov/center-projects/adios/"
     url      = "https://github.com/ornladios/ADIOS/archive/v1.10.0.tar.gz"
 
+    version('develop', git='https://github.com/ornladios/ADIOS.git',
+            branch='master')
     version('1.10.0', 'eff450a4c0130479417cfd63186957f3')
     version('1.9.0', '310ff02388bbaa2b1c1710ee970b5678')
 
@@ -48,14 +50,14 @@ class Adios(Package):
     variant('mpi', default=True, description='Enable MPI support')
     variant('infiniband', default=False, description='Enable infiniband support')
 
+    # transforms
     variant('zlib', default=True, description='Enable szip transform support')
     variant('szip', default=False, description='Enable szip transform support')
-    variant('hdf5', default=False, description='Enable HDF5 transport support')
-    variant('netcdf', default=False, description='Enable NetCDF transport support')
+    # transports and serial file converters
+    variant('hdf5', default=False, description='Enable parallel HDF5 transport and serial bp2h5 converter')
 
     # Lots of setting up here for this package
     # module swap PrgEnv-intel PrgEnv-$COMP
-    # module load cray-netcdf/4.3.3.1
     # module load cray-hdf5/1.8.14
     # module load python/2.7.10
 
@@ -69,9 +71,13 @@ class Adios(Package):
     # optional transformations
     depends_on('zlib', when='+zlib')
     depends_on('szip', when='+szip')
-    # optional transports
-    depends_on('hdf5', when='+hdf5')
-    depends_on('netcdf', when='+netcdf')
+    # optional transports & file converters
+    depends_on('hdf5@1.8:+mpi', when='+hdf5')
+
+    # Fix ADIOS <=1.10.0 compile error on HDF5 1.10+
+    #   https://github.com/ornladios/ADIOS/commit/3b21a8a41509
+    #   https://github.com/LLNL/spack/issues/1683
+    patch('adios_1100.patch', when='@:1.10.0^hdf5@1.10:')
 
     def validate(self, spec):
         """
@@ -114,9 +120,7 @@ class Adios(Package):
         if '+szip' in spec:
             extra_args.append('--with-szip=%s' % spec['szip'].prefix)
         if '+hdf5' in spec:
-            extra_args.append('--with-hdf5=%s' % spec['hdf5'].prefix)
-        if '+netcdf' in spec:
-            extra_args.append('--with-netcdf=%s' % spec['netcdf'].prefix)
+            extra_args.append('--with-phdf5=%s' % spec['hdf5'].prefix)
 
         sh = which('sh')
         sh('./autogen.sh')
diff --git a/var/spack/repos/builtin/packages/armadillo/package.py b/var/spack/repos/builtin/packages/armadillo/package.py
index 4356f60aca..fdd682f5e5 100644
--- a/var/spack/repos/builtin/packages/armadillo/package.py
+++ b/var/spack/repos/builtin/packages/armadillo/package.py
@@ -46,18 +46,20 @@ class Armadillo(Package):
     depends_on('hdf5', when='+hdf5')
 
     def install(self, spec, prefix):
+        arpack = find_libraries(['libarpack'], root=spec[
+                                'arpack-ng'].prefix.lib, shared=True)
+        superlu = find_libraries(['libsuperlu'], root=spec[
+                                 'superlu'].prefix, shared=False, recurse=True)
         cmake_args = [
             # ARPACK support
-            '-DARPACK_LIBRARY={0}/libarpack.{1}'.format(
-                spec['arpack-ng'].prefix.lib, dso_suffix),
+            '-DARPACK_LIBRARY={0}'.format(arpack.joined()),
             # BLAS support
-            '-DBLAS_LIBRARY={0}'.format(spec['blas'].blas_shared_lib),
+            '-DBLAS_LIBRARY={0}'.format(spec['blas'].blas_libs.joined()),
             # LAPACK support
-            '-DLAPACK_LIBRARY={0}'.format(spec['lapack'].lapack_shared_lib),
+            '-DLAPACK_LIBRARY={0}'.format(spec['lapack'].lapack_libs.joined()),
             # SuperLU support
             '-DSuperLU_INCLUDE_DIR={0}'.format(spec['superlu'].prefix.include),
-            '-DSuperLU_LIBRARY={0}/libsuperlu.a'.format(
-                spec['superlu'].prefix.lib64),
+            '-DSuperLU_LIBRARY={0}'.format(superlu.joined()),
             # HDF5 support
             '-DDETECT_HDF5={0}'.format('ON' if '+hdf5' in spec else 'OFF')
         ]
diff --git a/var/spack/repos/builtin/packages/arpack-ng/package.py b/var/spack/repos/builtin/packages/arpack-ng/package.py
index 0e71125d41..87ab2bbaac 100644
--- a/var/spack/repos/builtin/packages/arpack-ng/package.py
+++ b/var/spack/repos/builtin/packages/arpack-ng/package.py
@@ -88,17 +88,16 @@ class ArpackNg(Package):
         options.append('-DCMAKE_INSTALL_NAME_DIR:PATH=%s/lib' % prefix)
 
         # Make sure we use Spack's blas/lapack:
+        lapack_libs = spec['lapack'].lapack_libs.joined(';')
+        blas_libs = spec['blas'].blas_libs.joined(';')
+
         options.extend([
             '-DLAPACK_FOUND=true',
-            '-DLAPACK_INCLUDE_DIRS=%s' % spec['lapack'].prefix.include,
-            '-DLAPACK_LIBRARIES=%s' % (
-                spec['lapack'].lapack_shared_lib if '+shared' in spec else
-                spec['lapack'].lapack_static_lib),
+            '-DLAPACK_INCLUDE_DIRS={0}'.format(spec['lapack'].prefix.include),
+            '-DLAPACK_LIBRARIES={0}'.format(lapack_libs),
             '-DBLAS_FOUND=true',
-            '-DBLAS_INCLUDE_DIRS=%s' % spec['blas'].prefix.include,
-            '-DBLAS_LIBRARIES=%s' % (
-                spec['blas'].blas_shared_lib if '+shared' in spec else
-                spec['blas'].blas_static_lib)
+            '-DBLAS_INCLUDE_DIRS={0}'.format(spec['blas'].prefix.include),
+            '-DBLAS_LIBRARIES={0}'.format(blas_libs)
         ])
 
         if '+mpi' in spec:
@@ -129,19 +128,12 @@ class ArpackNg(Package):
                 'F77=%s' % spec['mpi'].mpif77
             ])
 
-        if '+shared' in spec:
-            options.extend([
-                '--with-blas=%s' % to_link_flags(
-                    spec['blas'].blas_shared_lib),
-                '--with-lapack=%s' % to_link_flags(
-                    spec['lapack'].lapack_shared_lib)
-            ])
-        else:
-            options.extend([
-                '--with-blas=%s' % spec['blas'].blas_static_lib,
-                '--with-lapack=%s' % spec['lapack'].lapack_static_lib,
-                '--enable-shared=no'
-            ])
+        options.extend([
+            '--with-blas={0}'.format(spec['blas'].blas_libs.ld_flags),
+            '--with-lapack={0}'.format(spec['lapack'].lapack_libs.ld_flags)
+        ])
+        if '+shared' not in spec:
+            options.append('--enable-shared=no')
 
         bootstrap()
         configure(*options)
diff --git a/var/spack/repos/builtin/packages/atlas/package.py b/var/spack/repos/builtin/packages/atlas/package.py
index f9d5da6166..b31e365336 100644
--- a/var/spack/repos/builtin/packages/atlas/package.py
+++ b/var/spack/repos/builtin/packages/atlas/package.py
@@ -51,6 +51,7 @@ class Atlas(Package):
             url='http://sourceforge.net/projects/math-atlas/files/Developer%20%28unstable%29/3.11.34/atlas3.11.34.tar.bz2')
 
     variant('shared', default=True, description='Builds shared library')
+    variant('pthread', default=False, description='Use multithreaded libraries')
 
     provides('blas')
     provides('lapack')
@@ -107,18 +108,32 @@ class Atlas(Package):
             make("install")
             self.install_test()
 
-    def setup_dependent_package(self, module, dspec):
+    @property
+    def blas_libs(self):
         # libsatlas.[so,dylib,dll ] contains all serial APIs (serial lapack,
         # serial BLAS), and all ATLAS symbols needed to support them. Whereas
         # libtatlas.[so,dylib,dll ] is parallel (multithreaded) version.
-        name = 'libsatlas.%s' % dso_suffix
-        libdir = find_library_path(name,
-                                   self.prefix.lib64,
-                                   self.prefix.lib)
-
+        is_threaded = '+pthread' in self.spec
         if '+shared' in self.spec:
-            self.spec.blas_shared_lib   = join_path(libdir, name)
-            self.spec.lapack_shared_lib = self.spec.blas_shared_lib
+            to_find = ['libtatlas'] if is_threaded else ['libsatlas']
+            shared = True
+        else:
+            interfaces = [
+                'libptcblas',
+                'libptf77blas'
+            ] if is_threaded else [
+                'libcblas',
+                'libf77blas'
+            ]
+            to_find = ['liblapack'] + interfaces + ['libatlas']
+            shared = False
+        return find_libraries(
+            to_find, root=self.prefix, shared=shared, recurse=True
+        )
+
+    @property
+    def lapack_libs(self):
+        return self.blas_libs
 
     def install_test(self):
         source_file = join_path(os.path.dirname(self.module.__file__),
@@ -126,9 +141,8 @@ class Atlas(Package):
         blessed_file = join_path(os.path.dirname(self.module.__file__),
                                  'test_cblas_dgemm.output')
 
-        include_flags = ["-I%s" % join_path(self.spec.prefix, "include")]
-        link_flags = ["-L%s" % join_path(self.spec.prefix, "lib"),
-                      "-lsatlas"]
+        include_flags = ["-I%s" % self.spec.prefix.include]
+        link_flags = self.lapack_libs.ld_flags.split()
 
         output = compile_c_and_execute(source_file, include_flags, link_flags)
         compare_output_file(output, blessed_file)
diff --git a/var/spack/repos/builtin/packages/bamtools/package.py b/var/spack/repos/builtin/packages/bamtools/package.py
new file mode 100644
index 0000000000..7bb1985003
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bamtools/package.py
@@ -0,0 +1,45 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Bamtools(Package):
+    """C++ API & command-line toolkit for working with BAM data."""
+
+    homepage = "https://github.com/pezmaster31/bamtools"
+    url      = "https://github.com/pezmaster31/bamtools/archive/v2.4.0.tar.gz"
+
+    version('2.4.0', '6139d00c1b1fe88fe15d094d8a74d8b9')
+    version('2.3.0', 'd327df4ba037d6eb8beef65d7da75ebc')
+    version('2.2.3', '6eccd3e45e4ba12a68daa3298998e76d')
+
+    depends_on('cmake', type='build')
+
+    def install(self, spec, prefix):
+        with working_dir('spack-build', create=True):
+            cmake('..', *std_cmake_args)
+
+            make()
+            make('install')
diff --git a/var/spack/repos/builtin/packages/bash-completion/package.py b/var/spack/repos/builtin/packages/bash-completion/package.py
new file mode 100644
index 0000000000..666a1bef13
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bash-completion/package.py
@@ -0,0 +1,64 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class BashCompletion(Package):
+    """Programmable completion functions for bash."""
+    homepage = "https://github.com/scop/bash-completion"
+    url      = "https://github.com/scop/bash-completion/archive/2.3.tar.gz"
+
+    version('2.3', '67e50f5f3c804350b43f2b664c33dde811d24292')
+    version('develop',  git='https://github.com/scop/bash-completion.git')
+
+    # Build dependencies
+    depends_on('automake', type='build')
+    depends_on('autoconf', type='build')
+    depends_on('libtool',  type='build')
+
+    # Other dependencies
+    depends_on('bash@4.1:', type='run')
+
+    def install(self, spec, prefix):
+        make_args = ['--prefix=%s' % prefix]
+
+        autoreconf('-i')
+        configure(*make_args)
+        make()
+        # make("check") # optional, requires dejagnu and tcllib
+        make("install",
+             parallel=False)
+
+        # Guidelines for individual user as provided by the author at
+        # https://github.com/scop/bash-completion
+        print('=====================================================')
+        print('Bash completion has been installed. To use it, please')
+        print('include the following lines in your ~/.bash_profile :')
+        print('')
+        print('# Use bash-completion, if available')
+        print('[[ $PS1 && -f %s/share/bash-completion/bash_completion ]] && \ ' % prefix)  # NOQA: ignore=E501
+        print('    . %s/share/bash-completion/bash_completion'  % prefix)
+        print('')
+        print('=====================================================')
diff --git a/var/spack/repos/builtin/packages/bedtools2/package.py b/var/spack/repos/builtin/packages/bedtools2/package.py
new file mode 100644
index 0000000000..46f3185154
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bedtools2/package.py
@@ -0,0 +1,43 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Bedtools2(Package):
+    """Collectively, the bedtools utilities are a swiss-army knife of
+       tools for a wide-range of genomics analysis tasks. The most
+       widely-used tools enable genome arithmetic: that is, set theory
+       on the genome."""
+
+    homepage = "https://github.com/arq5x/bedtools2"
+    url      = "https://github.com/arq5x/bedtools2/archive/v2.26.0.tar.gz"
+
+    version('2.26.0', '52227e7efa6627f0f95d7d734973233d')
+    version('2.25.0', '534fb4a7bf0d0c3f05be52a0160d8e3d')
+
+    depends_on('zlib')
+
+    def install(self, spec, prefix):
+        make("prefix=%s" % prefix, "install")
diff --git a/var/spack/repos/builtin/packages/binutils/package.py b/var/spack/repos/builtin/packages/binutils/package.py
index e329e6fd7a..bf49ca9405 100644
--- a/var/spack/repos/builtin/packages/binutils/package.py
+++ b/var/spack/repos/builtin/packages/binutils/package.py
@@ -31,9 +31,9 @@ class Binutils(Package):
     homepage = "http://www.gnu.org/software/binutils/"
     url      = "https://ftp.gnu.org/gnu/binutils/binutils-2.25.tar.bz2"
 
-    # 2.26 is incompatible with py-pillow build for some reason.
+    version('2.27', '2869c9bf3e60ee97c74ac2a6bf4e9d68')
     version('2.26', '64146a0faa3b411ba774f47d41de239f')
-    version('2.25', 'd9f3303f802a5b6b0bb73a335ab89d66', preferred=True)
+    version('2.25', 'd9f3303f802a5b6b0bb73a335ab89d66')
     version('2.24', 'e0f71a7b2ddab0f8612336ac81d9636b')
     version('2.23.2', '4f8fa651e35ef262edc01d60fb45702e')
     version('2.20.1', '2b9dc8f2b7dbd5ec5992c6e29de0b764')
diff --git a/var/spack/repos/builtin/packages/boost/package.py b/var/spack/repos/builtin/packages/boost/package.py
index 0d4ccc7ea3..22351a2c3a 100644
--- a/var/spack/repos/builtin/packages/boost/package.py
+++ b/var/spack/repos/builtin/packages/boost/package.py
@@ -41,6 +41,7 @@ class Boost(Package):
     list_url = "http://sourceforge.net/projects/boost/files/boost/"
     list_depth = 2
 
+    version('1.62.0', '5fb94629535c19e48703bdb2b2e9490f')
     version('1.61.0', '6095876341956f65f9d35939ccea1a9f')
     version('1.60.0', '65a840e1a0b13a558ff19eeb2c4f0cbe')
     version('1.59.0', '6aa9a5c6a4ca1016edd0ed1178e3cb87')
@@ -111,12 +112,12 @@ class Boost(Package):
             description="Build multi-threaded versions of libraries")
     variant('singlethreaded', default=True,
             description="Build single-threaded versions of libraries")
-    variant('icu_support', default=False,
-            description="Include ICU support (for regex/locale libraries)")
+    variant('icu', default=False,
+            description="Build with Unicode and ICU suport")
     variant('graph', default=False,
             description="Build the Boost Graph library")
 
-    depends_on('icu', when='+icu_support')
+    depends_on('icu4c', when='+icu')
     depends_on('python', when='+python')
     depends_on('mpi', when='+mpi')
     depends_on('bzip2', when='+iostreams')
@@ -138,15 +139,13 @@ class Boost(Package):
     def determine_toolset(self, spec):
         if spec.satisfies("platform=darwin"):
             return 'darwin'
-        else:
-            platform = 'linux'
 
         toolsets = {'g++': 'gcc',
                     'icpc': 'intel',
                     'clang++': 'clang'}
 
         if spec.satisfies('@1.47:'):
-            toolsets['icpc'] += '-' + platform
+            toolsets['icpc'] += '-linux'
         for cc, toolset in toolsets.iteritems():
             if cc in self.compiler.cxx_names:
                 return toolset
@@ -164,6 +163,16 @@ class Boost(Package):
                            join_path(spec['python'].prefix.bin, 'python'))
 
         with open('user-config.jam', 'w') as f:
+            # Boost may end up using gcc even though clang+gfortran is set in
+            # compilers.yaml. Make sure this does not happen:
+            if not spec.satisfies('%intel'):
+                # using intel-linux : : spack_cxx in user-config.jam leads to
+                # error: at project-config.jam:12
+                # error: duplicate initialization of intel-linux with the following parameters:  # noqa
+                # error: version = <unspecified>
+                # error: previous initialization at ./user-config.jam:1
+                f.write("using {0} : : {1} ;\n".format(boostToolsetId,
+                                                       spack_cxx))
 
             if '+mpi' in spec:
                 f.write('using mpi : %s ;\n' %
@@ -204,7 +213,13 @@ class Boost(Package):
 
         options.extend([
             'link=%s' % ','.join(linkTypes),
-            '--layout=tagged'])
+            '--layout=tagged'
+        ])
+
+        if not spec.satisfies('%intel'):
+            options.extend([
+                'toolset=%s' % self.determine_toolset(spec)
+            ])
 
         return threadingOpts
 
diff --git a/var/spack/repos/builtin/packages/bpp-suite/package.py b/var/spack/repos/builtin/packages/bpp-suite/package.py
index ef7f25a7ce..d15030622e 100644
--- a/var/spack/repos/builtin/packages/bpp-suite/package.py
+++ b/var/spack/repos/builtin/packages/bpp-suite/package.py
@@ -34,7 +34,6 @@ class BppSuite(Package):
 
     version('2.2.0', 'd8b29ad7ccf5bd3a7beb701350c9e2a4')
 
-    # FIXME: Add dependencies if required.
     depends_on('cmake', type='build')
     depends_on('texinfo', type='build')
     depends_on('bpp-core')
diff --git a/var/spack/repos/builtin/packages/cantera/package.py b/var/spack/repos/builtin/packages/cantera/package.py
index 9c9c035325..9a9bc5bdbd 100644
--- a/var/spack/repos/builtin/packages/cantera/package.py
+++ b/var/spack/repos/builtin/packages/cantera/package.py
@@ -85,8 +85,9 @@ class Cantera(Package):
 
         # BLAS/LAPACK support
         if '+lapack' in spec:
+            lapack_blas = spec['lapack'].lapack_libs + spec['blas'].blas_libs
             options.extend([
-                'blas_lapack_libs=lapack,blas',
+                'blas_lapack_libs={0}'.format(','.join(lapack_blas.names)),
                 'blas_lapack_dir={0}'.format(spec['lapack'].prefix.lib)
             ])
 
diff --git a/var/spack/repos/builtin/packages/cdo/package.py b/var/spack/repos/builtin/packages/cdo/package.py
index a2f04e5b35..775dc31cf3 100644
--- a/var/spack/repos/builtin/packages/cdo/package.py
+++ b/var/spack/repos/builtin/packages/cdo/package.py
@@ -30,17 +30,88 @@ class Cdo(Package):
     Climate and NWP model Data. """
 
     homepage = "https://code.zmaw.de/projects/cdo"
-    url      = "https://code.zmaw.de/attachments/download/10198/cdo-1.6.9.tar.gz"
 
-    version('1.6.9', 'bf0997bf20e812f35e10188a930e24e2')
+    version('1.7.2', 'f08e4ce8739a4f2b63fc81a24db3ee31', url='https://code.zmaw.de/attachments/download/12760/cdo-1.7.2.tar.gz')
+    version('1.6.9', 'bf0997bf20e812f35e10188a930e24e2', url='https://code.zmaw.de/attachments/download/10198/cdo-1.6.9.tar.gz')
 
-    variant('mpi', default=True)
+    variant('szip', default=True, description='Enable szip compression for GRIB1')
+    variant('hdf5', default=False, description='Enable HDF5 support')
+    variant('netcdf', default=True, description='Enable NetCDF support')
+    variant('udunits2', default=True, description='Enable UDUNITS2 support')
+    variant('grib', default=True, description='Enable GRIB_API support')
+    variant('libxml2', default=True, description='Enable libxml2 support')
+    variant('proj', default=True, description='Enable PROJ library for cartographic projections')
+    variant('curl', default=True, description='Enable curl support')
+    variant('fftw', default=True, description='Enable support for fftw3')
+    variant('magics', default=True, description='Enable Magics library support')
 
-    depends_on('netcdf')
-    depends_on('netcdf+mpi', when='+mpi')
-    depends_on('netcdf~mpi', when='~mpi')
+    depends_on('szip', when='+szip')
+    depends_on('netcdf', when='+netcdf')
+    depends_on('hdf5+threadsafe', when='+hdf5')
+    depends_on('udunits2', when='+udunits2')
+    depends_on('grib-api', when='+grib')
+    depends_on('libxml2', when='+libxml2')
+    depends_on('proj', when='+proj')
+    depends_on('curl', when='+curl')
+    depends_on('fftw', when='+fftw')
+    depends_on('magics', when='+magics') 
 
     def install(self, spec, prefix):
-        configure('--prefix={0}'.format(prefix))
+        config_args = ["--prefix=" + prefix,
+                       "--enable-shared",
+                       "--enable-static"]
+
+        if '+szip' in spec:
+            config_args.append('--with-szlib=' + spec['szip'].prefix)
+        else:
+            config_args.append('--without-szlib')
+
+        if '+hdf5' in spec:
+            config_args.append('--with-hdf5=' + spec['hdf5'].prefix)
+        else:
+            config_args.append('--without-hdf5')
+
+        if '+netcdf' in spec:
+            config_args.append('--with-netcdf=' + spec['netcdf'].prefix)
+        else:
+            config_args.append('--without-netcdf')
+
+        if '+udunits2' in spec:
+            config_args.append('--with-udunits2=' + spec['udunits2'].prefix)
+        else:
+            config_args.append('--without-udunits2')
+
+        if '+grib' in spec:
+            config_args.append('--with-grib_api=' + spec['grib-api'].prefix)
+        else:
+            config_args.append('--without-grib_api')
+
+        if '+libxml2' in spec:
+            config_args.append('--with-libxml2=' + spec['libxml2'].prefix)
+        else:
+            config_args.append('--without-libxml2')
+
+        if '+proj' in spec:
+            config_args.append('--with-proj=' + spec['proj'].prefix)
+        else:
+            config_args.append('--without-proj')
+
+        if '+curl' in spec:
+            config_args.append('--with-curl=' + spec['curl'].prefix)
+        else:
+            config_args.append('--without-curl')
+
+        if '+fftw' in spec:
+            config_args.append('--with-fftw3')
+        else:
+            config_args.append('--without-fftw3')
+
+        if '+magics' in spec:
+            config_args.append('--with-magics=' + spec['magics'].prefix)
+        else:
+            config_args.append('--without-magics')
+
+        configure(*config_args)
+
         make()
         make('install')
diff --git a/var/spack/repos/builtin/packages/cereal/package.py b/var/spack/repos/builtin/packages/cereal/package.py
index 716e0103d1..0ce6ec593c 100644
--- a/var/spack/repos/builtin/packages/cereal/package.py
+++ b/var/spack/repos/builtin/packages/cereal/package.py
@@ -39,6 +39,7 @@ class Cereal(Package):
     homepage = "http://uscilab.github.io/cereal/"
     url      = "https://github.com/USCiLab/cereal/archive/v1.1.2.tar.gz"
 
+    version('1.2.1', '64476ed74c19068ee543b53ad3992261')
     version('1.2.0', 'e372c9814696481dbdb7d500e1410d2b')
     version('1.1.2', '34d4ad174acbff005c36d4d10e48cbb9')
     version('1.1.1', '0ceff308c38f37d5b5f6df3927451c27')
diff --git a/var/spack/repos/builtin/packages/cgal/package.py b/var/spack/repos/builtin/packages/cgal/package.py
index e522b4a5a0..d986f77487 100644
--- a/var/spack/repos/builtin/packages/cgal/package.py
+++ b/var/spack/repos/builtin/packages/cgal/package.py
@@ -22,44 +22,57 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-
 from spack import *
 
 
 class Cgal(Package):
-    """CGAL is a software project that provides easy access to efficient and
-       reliable geometric algorithms in the form of a C++ library. CGAL
-       is used in various areas needing geometric computation, such as
-       geographic information systems, computer aided design, molecular
-       biology, medical imaging, computer graphics, and robotics.
-
+    """The Computational Geometry Algorithms Library (CGAL) is a C++ library
+    that aims to provide easy access to efficient and reliable algorithms in
+    computational geometry. CGAL is used in various areas needing geometric
+    computation, such as geographic information systems, computer aided design,
+    molecular biology, medical imaging, computer graphics, and robotics.
     """
     homepage = 'http://www.cgal.org/'
     url = 'https://github.com/CGAL/cgal/archive/releases/CGAL-4.7.tar.gz'
 
+    version('4.9', '7b628db3e5614347f776c046b7666089')
     version('4.7', '4826714810f3b4c65cac96b90fb03b67')
     version('4.6.3', 'e8ee2ecc8d2b09b94a121c09257b576d')
 
-    # Installation instructions :
-    # http://doc.cgal.org/latest/Manual/installation.html
     variant('shared', default=True,
             description='Enables the build of shared libraries')
     variant('debug', default=False,
             description='Builds a debug version of the libraries')
 
+    # Essential Third Party Libraries
     depends_on('boost')
-    depends_on('mpfr')
     depends_on('gmp')
+    depends_on('mpfr')
     depends_on('zlib')
-    depends_on('cmake', type='build')
+    # depends_on('opengl')
+    depends_on('qt@5:')
 
-    # FIXME : Qt5 dependency missing (needs Qt5 and OpenGL)
-    # FIXME : Optional third party libraries missing
+    # Optional Third Party Libraries
+    # depends_on('leda')
+    # depends_on('mpfi')
+    # depends_on('rs')
+    # depends_on('rs3')
+    # depends_on('ntl')
+    # depends_on('eigen')
+    # depends_on('libqglviewer')
+    # depends_on('esbtl')
+    # depends_on('intel-tbb')
+
+    # Build dependencies
+    depends_on('cmake', type='build')
 
     def install(self, spec, prefix):
+        # Installation instructions:
+        # http://doc.cgal.org/latest/Manual/installation.html
 
         options = []
         options.extend(std_cmake_args)
+
         # CGAL supports only Release and Debug build type. Any other build type
         # will raise an error at configure time
         if '+debug' in spec:
@@ -72,9 +85,7 @@ class Cgal(Package):
         else:
             options.append('-DBUILD_SHARED_LIBS:BOOL=OFF')
 
-        build_directory = join_path(self.stage.path, 'spack-build')
-        source_directory = self.stage.source_path
-        with working_dir(build_directory, create=True):
-            cmake(source_directory, *options)
-            make()
-            make("install")
+        cmake('.', *options)
+
+        make()
+        make('install')
diff --git a/var/spack/repos/builtin/packages/charm/mpi.patch b/var/spack/repos/builtin/packages/charm/mpi.patch
new file mode 100644
index 0000000000..e909d5f876
--- /dev/null
+++ b/var/spack/repos/builtin/packages/charm/mpi.patch
@@ -0,0 +1,19 @@
+--- old/src/scripts/configure
++++ new/src/scripts/configure
+@@ -3293,10 +3293,16 @@
+         test_link "whether -lmpi" "ok" "no" "-lmpi"
+         if test $pass -eq 1
+         then
+                 add_flag CMK_SYSLIBS='"$CMK_SYSLIBS -lmpi"' "mpi lib"
+         else
++          test_link "whether -lmpi -lmpi_cxx" "ok" "no" "-lmpi -lmpi_cxx"
++          if test $pass -eq 1
++          then
++            add_flag CMK_SYSLIBS='"$CMK_SYSLIBS -lmpi -lmpi_cxx"' "mpi lib"
++          else
+                 echo "Error: can not find mpi library"
+                 test_finish 1
++          fi
+         fi
+       fi
+     else
diff --git a/var/spack/repos/builtin/packages/charm/package.py b/var/spack/repos/builtin/packages/charm/package.py
new file mode 100644
index 0000000000..d67ac80de1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/charm/package.py
@@ -0,0 +1,172 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+
+import platform
+import shutil
+import sys
+from spack import *
+
+
+class Charm(Package):
+    """Charm++ is a parallel programming framework in C++ supported by
+    an adaptive runtime system, which enhances user productivity and
+    allows programs to run portably from small multicore computers
+    (your laptop) to the largest supercomputers."""
+
+    homepage = "http://charmplusplus.org"
+    url      = "http://charm.cs.illinois.edu/distrib/charm-6.7.1.tar.gz"
+
+    version("6.7.1", "a8e20cf85e9c8721158f5bbd0ade48d9")
+    version("6.7.0", "35a39a7975f1954a7db2d76736158231")
+    version("6.6.1", "9554230f741e2599deaaac4d9d93d7ab")
+    version("6.6.0", "31e95901b3f7324d52107e6ad000fcc8")
+    version("6.5.1", "034d99458474a3ab96d8bede8a691a5d")
+
+    # Support OpenMPI; see
+    # <https://charm.cs.illinois.edu/redmine/issues/1206>
+    patch("mpi.patch")
+
+    # Communication mechanisms (choose exactly one)
+    # TODO: Support Blue Gene/Q PAMI, Cray GNI, Cray shmem, CUDA
+    variant("mpi", default=False,
+            description="Use MPI as communication mechanism")
+    variant("multicore", default=False,
+            description="Disable inter-node communication")
+    variant("net", default=False,
+            description="Use net communication mechanism")
+    variant("netlrts", default=True,
+            description="Use netlrts communication mechanism")
+    variant("verbs", default=False,
+            description="Use Infiniband as communication mechanism")
+
+    # Other options
+    # Something is off with PAPI -- there are build errors. Maybe
+    # Charm++ expects a particular version?
+    variant("papi", default=False, description="Enable PAPI integration")
+    variant("smp", default=True,
+            description=(
+                "Enable SMP parallelism (does not work with +multicore)"))
+    variant("tcp", default=False,
+            description="Use TCP as transport mechanism (requires +net)")
+
+    # Note: We could add variants for AMPI, LIBS, bigemulator, msa, Tau
+    # Note: We could support shared libraries
+
+    depends_on("mpi", when="+mpi")
+    depends_on("papi", when="+papi")
+
+    def install(self, spec, prefix):
+        target = "charm++"
+
+        # Note: Turn this into a multi-valued variant, once these
+        # exist in Spack
+        if sum(["+mpi" in spec,
+                "+multicore" in spec,
+                "+net" in spec,
+                "+netlrts" in spec,
+                "+verbs" in spec]) != 1:
+            raise InstallError(
+                "Exactly one communication mechanism "
+                "(+mpi, +multicore, +net, +netlrts, or +verbs) "
+                "must be enabled")
+        if "+mpi" in spec:
+            comm = "mpi"
+        if "+multicore" in spec:
+            comm = "multicore"
+        if "+net" in spec:
+            comm = "net"
+        if "+netlrts" in spec:
+            comm = "netlrts"
+        if "+verbs" in spec:
+            comm = "verbs"
+
+        plat = sys.platform
+        if plat.startswith("linux"):
+            plat = "linux"
+        mach = platform.machine()
+
+        # Define Charm++ version names for various (plat, mach, comm)
+        # combinations. Note that not all combinations are supported.
+        versions = {
+            ("darwin", "i386", "multicore"): "multicore-darwin-x86",
+            ("darwin", "i386", "net"): "net-darwin-x86",
+            ("darwin", "x86_64", "mpi"): "mpi-darwin-x86_64",
+            ("darwin", "x86_64", "multicore"): "multicore-darwin-x86_64",
+            ("darwin", "x86_64", "net"): "net-darwin-x86_64",
+            ("darwin", "x86_64", "netlrts"): "netlrts-darwin-x86_64",
+            ("linux", "i386", "mpi"): "mpi-linux",
+            ("linux", "i386", "multicore"): "multicore-linux32",
+            ("linux", "i386", "net"): "net-linux",
+            ("linux", "i386", "netlrts"): "netlrts-linux",
+            ("linux", "x86_64", "mpi"): "mpi-linux-x86_64",
+            ("linux", "x86_64", "multicore"): "multicore-linux64",
+            ("linux", "x86_64", "net"): "net-linux-x86_64",
+            ("linux", "x86_64", "netlrts"): "netlrts-linux-x86_64",
+            ("linux", "x86_64", "verbs"): "verbs-linux-x86_64",
+        }
+        if (plat, mach, comm) not in versions:
+            raise InstallError(
+                "The communication mechanism %s is not supported "
+                "on a %s platform with a %s CPU" %
+                (comm, plat, mach))
+        version = versions[(plat, mach, comm)]
+
+        # We assume that Spack's compiler wrappers make this work. If
+        # not, then we need to query the compiler vendor from Spack
+        # here.
+        compiler = "gcc"
+
+        options = [compiler,
+                   "--with-production",   # Note: turn this into a variant
+                   "-j%d" % make_jobs,
+                   "--destination=%s" % prefix]
+        if "+mpi" in spec:
+            options.append("--basedir=%s" % spec["mpi"].prefix)
+        if "+papi" in spec:
+            options.extend(["papi", "--basedir=%s" % spec["papi"].prefix])
+        if "+smp" in spec:
+            if "+multicore" in spec:
+                # This is a Charm++ limitation; it would lead to a
+                # build error
+                raise InstallError("Cannot combine +smp with +multicore")
+            options.append("smp")
+        if "+tcp" in spec:
+            if "+net" not in spec:
+                # This is a Charm++ limitation; it would lead to a
+                # build error
+                raise InstallError(
+                    "The +tcp variant requires "
+                    "the +net communication mechanism")
+            options.append("tcp")
+
+        # Call "make" via the build script
+        # Note: This builds Charm++ in the "tmp" subdirectory of the
+        # install directory. Maybe we could set up a symbolic link
+        # back to the build tree to prevent this? Alternatively, we
+        # could dissect the build script; the build instructions say
+        # this wouldn't be difficult.
+        build = Executable(join_path(".", "build"))
+        build(target, version, *options)
+        shutil.rmtree(join_path(prefix, "tmp"))
diff --git a/var/spack/repos/builtin/packages/clhep/darwin/CLHEP.patch b/var/spack/repos/builtin/packages/clhep/darwin/CLHEP.patch
new file mode 100644
index 0000000000..ca1d96574a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/clhep/darwin/CLHEP.patch
@@ -0,0 +1,11 @@
+--- CLHEP/CMakeLists.txt	2016-06-20 14:41:12.000000000 -0500
++++ CLHEP/CMakeLists.txt	2016-06-20 14:40:57.000000000 -0500
+@@ -37,7 +37,7 @@
+ # If Policy CMP0042 exists, use OLD to prefer the use of install names
+ # instead of the new @rpath default. 
+ if(POLICY CMP0042)
+-  cmake_policy(SET CMP0042 NEW)
++  cmake_policy(SET CMP0042 OLD)
+ endif()
+ 
+ set(CMAKE_MODULE_PATH 
diff --git a/var/spack/repos/builtin/packages/clhep/package.py b/var/spack/repos/builtin/packages/clhep/package.py
new file mode 100644
index 0000000000..02a9da9e27
--- /dev/null
+++ b/var/spack/repos/builtin/packages/clhep/package.py
@@ -0,0 +1,81 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+
+from spack import *
+
+
+class Clhep(Package):
+    """CLHEP is a C++ Class Library for High Energy Physics. """
+    homepage = "http://proj-clhep.web.cern.ch/proj-clhep/"
+    url      = "http://proj-clhep.web.cern.ch/proj-clhep/DISTRIBUTION/tarFiles/clhep-2.2.0.5.tgz"
+    list_url = "https://proj-clhep.web.cern.ch/proj-clhep/DISTRIBUTION/"
+
+    version('2.3.2.2', '567b304b0fa017e1e9fbf199f456ebe9')
+    version('2.3.1.1', '16efca7641bc118c9d217cc96fe90bf5')
+    version('2.3.1.0', 'b084934fc26a4182a08c09c292e19161')
+    version('2.3.0.0', 'a00399a2ca867f2be902c22fc71d7e2e')
+    version('2.2.0.8', '5a23ed3af785ac100a25f6cb791846af')
+    version('2.2.0.5', '1584e8ce6ebf395821aed377df315c7c')
+    version('2.2.0.4', '71d2c7c2e39d86a0262e555148de01c1')
+
+    variant('debug', default=False, description="Switch to the debug version of CLHEP.")
+    variant('cxx11', default=True, description="Compile using c++11 dialect.")
+    variant('cxx14', default=False, description="Compile using c++14 dialect.")
+
+    depends_on('cmake@2.8.12.2:', when='@2.2.0.4:2.3.0.0', type='build')
+    depends_on('cmake@3.2:', when='@2.3.0.1:', type='build')
+
+    def patch(self):
+        filter_file('SET CMP0042 OLD',
+                    'SET CMP0042 NEW',
+                    '%s/%s/CLHEP/CMakeLists.txt'
+                    % (self.stage.path, self.spec.version))
+
+    def install(self, spec, prefix):
+        # Handle debug
+        # Pull out the BUILD_TYPE so we can change it (Release is default)
+        cmake_args = [arg for arg in std_cmake_args if 'BUILD_TYPE' not in arg]
+        build_type = 'Debug' if '+debug' in spec else 'MinSizeRel'
+        cmake_args.extend(['-DCMAKE_BUILD_TYPE=' + build_type])
+
+        if '+cxx11' in spec:
+            env['CXXFLAGS'] = self.compiler.cxx11_flag
+            cmake_args.append('-DCLHEP_BUILD_CXXSTD=' +
+                              self.compiler.cxx11_flag)
+
+        if '+cxx14' in spec:
+            env['CXXFLAGS'] = self.compiler.cxx14_flag
+            cmake_args.append('-DCLHEP_BUILD_CXXSTD=' +
+                              self.compiler.cxx14_flag)
+
+        # Note that the tar file is unusual in that there's a
+        # CLHEP directory (addtional layer)
+        cmake_args.append("../CLHEP")
+
+        # Run cmake in a build directory
+        with working_dir('build', create=True):
+            cmake(*cmake_args)
+            make()
+            make("install")
diff --git a/var/spack/repos/builtin/packages/cmake/package.py b/var/spack/repos/builtin/packages/cmake/package.py
index 0c16adcef7..83a68fda07 100644
--- a/var/spack/repos/builtin/packages/cmake/package.py
+++ b/var/spack/repos/builtin/packages/cmake/package.py
@@ -88,11 +88,13 @@ class Cmake(Package):
 
         options = [
             '--prefix={0}'.format(prefix),
-            '--parallel={0}'.format(make_jobs),
-            # jsoncpp requires CMake to build
-            # use CMake-provided library to avoid circular dependency
-            '--no-system-jsoncpp'
-        ]
+            '--parallel={0}'.format(make_jobs)]
+        if spec.satisfies("@3:"):
+            options.append(
+                # jsoncpp requires CMake to build
+                # use CMake-provided library to avoid circular dependency
+                '--no-system-jsoncpp'
+            )
 
         if '+ownlibs' in spec:
             # Build and link to the CMake-provided third-party libraries
diff --git a/var/spack/repos/builtin/packages/cp2k/package.py b/var/spack/repos/builtin/packages/cp2k/package.py
index 052c7a971c..3a175ea1a2 100644
--- a/var/spack/repos/builtin/packages/cp2k/package.py
+++ b/var/spack/repos/builtin/packages/cp2k/package.py
@@ -47,19 +47,18 @@ class Cp2k(Package):
     depends_on('lapack')
     depends_on('blas')
     depends_on('fftw')
+    depends_on('libint@:1.2', when='@3.0')
 
     depends_on('mpi', when='+mpi')
     depends_on('scalapack', when='+mpi')
     depends_on('plumed+shared+mpi', when='+plumed+mpi')
     depends_on('plumed+shared~mpi', when='+plumed~mpi')
     depends_on('pexsi', when='+mpi')
+    depends_on('wannier90', when='+mpi')
+    depends_on('elpa', when='+mpi')
 
-    # TODO : add dependency on libint
     # TODO : add dependency on libsmm, libxsmm
-    # TODO : add dependency on elpa
     # TODO : add dependency on CUDA
-    # TODO : add dependency on QUIP
-    # TODO : add dependency on libwannier90
 
     parallel = False
 
@@ -88,15 +87,20 @@ class Cp2k(Package):
             }
             cppflags = [
                 '-D__FFTW3',
-                '-D__LIBPEXSI',
+                '-D__LIBINT',
                 '-I' + spec['fftw'].prefix.include
             ]
             fcflags = copy.deepcopy(optflags[self.spec.compiler.name])
             fcflags.extend([
                 '-I' + spec['fftw'].prefix.include
             ])
-            ldflags = ['-L' + spec['fftw'].prefix.lib]
-            libs = []
+            fftw = find_libraries(['libfftw3'], root=spec['fftw'].prefix.lib)
+            ldflags = [fftw.search_flags]
+            libs = [
+                join_path(spec['libint'].prefix.lib, 'libint.so'),
+                join_path(spec['libint'].prefix.lib, 'libderiv.so'),
+                join_path(spec['libint'].prefix.lib, 'libr12.so')
+            ]
             if '+plumed' in self.spec:
                 # Include Plumed.inc in the Makefile
                 mkf.write('include {0}\n'.format(
@@ -109,7 +113,8 @@ class Cp2k(Package):
                 # Add required macro
                 cppflags.extend(['-D__PLUMED2'])
                 libs.extend([
-                    join_path(self.spec['plumed'].prefix.lib, 'libplumed.so')
+                    join_path(self.spec['plumed'].prefix.lib,
+                              'libplumed.{0}'.format(dso_suffix))
                 ])
 
             mkf.write('CC = {0.compiler.cc}\n'.format(self))
@@ -143,15 +148,26 @@ class Cp2k(Package):
             if '+mpi' in self.spec:
                 cppflags.extend([
                     '-D__parallel',
+                    '-D__LIBPEXSI',
+                    '-D__WANNIER90',
+                    '-D__ELPA3',
                     '-D__SCALAPACK'
                 ])
                 fcflags.extend([
+                    '-I' + join_path(
+                        spec['elpa'].prefix,
+                        'include',
+                        'elpa-{0}'.format(str(spec['elpa'].version)),
+                        'modules'
+                    ),
                     '-I' + join_path(spec['pexsi'].prefix, 'fortran')
                 ])
-                ldflags.extend([
-                    '-L' + spec['scalapack'].prefix.lib
-                ])
+                scalapack = spec['scalapack'].scalapack_libs
+                ldflags.append(scalapack.search_flags)
                 libs.extend([
+                    join_path(spec['elpa'].prefix.lib,
+                              'libelpa.{0}'.format(dso_suffix)),
+                    join_path(spec['wannier90'].prefix.lib, 'libwannier.a'),
                     join_path(spec['pexsi'].prefix.lib, 'libpexsi.a'),
                     join_path(spec['superlu-dist'].prefix.lib,
                               'libsuperlu_dist.a'),
@@ -164,19 +180,15 @@ class Cp2k(Package):
                         'libmetis.{0}'.format(dso_suffix)
                     ),
                 ])
-                libs.extend(spec['scalapack'].scalapack_shared_libs)
+                libs.extend(scalapack)
                 libs.extend(self.spec['mpi'].mpicxx_shared_libs)
                 libs.extend(self.compiler.stdcxx_libs)
             # LAPACK / BLAS
-            ldflags.extend([
-                '-L' + spec['lapack'].prefix.lib,
-                '-L' + spec['blas'].prefix.lib
-            ])
-            libs.extend([
-                join_path(spec['fftw'].prefix.lib, 'libfftw3.so'),
-                spec['lapack'].lapack_shared_lib,
-                spec['blas'].blas_shared_lib
-            ])
+            lapack = spec['lapack'].lapack_libs
+            blas = spec['blas'].blas_libs
+
+            ldflags.append((lapack + blas).search_flags)
+            libs.extend([str(x) for x in (fftw, lapack, blas)])
 
             # Write compiler flags to file
             mkf.write('CPPFLAGS = {0}\n'.format(' '.join(cppflags)))
diff --git a/var/spack/repos/builtin/packages/cube/package.py b/var/spack/repos/builtin/packages/cube/package.py
index 8c835b3886..9cea3c40e8 100644
--- a/var/spack/repos/builtin/packages/cube/package.py
+++ b/var/spack/repos/builtin/packages/cube/package.py
@@ -43,14 +43,19 @@ class Cube(Package):
     version('4.2.3', '8f95b9531f5a8f8134f279c2767c9b20',
             url="http://apps.fz-juelich.de/scalasca/releases/cube/4.2/dist/cube-4.2.3.tar.gz")
 
-    # TODO : add variant that builds GUI on top of Qt
+    variant('gui', default=False, description='Build CUBE GUI')
 
     depends_on('zlib')
+    depends_on('qt@4.6:', when='+gui')
 
     def install(self, spec, prefix):
         configure_args = ["--prefix=%s" % prefix,
-                          "--without-paraver",
-                          "--without-gui"]
+                          "--without-paraver"]
+
+        # TODO : need to handle cross compiling build
+        if '+gui' not in spec:
+            configure_args.append('--without-gui')
+
         configure(*configure_args)
-        make(parallel=False)
+        make()
         make("install", parallel=False)
diff --git a/var/spack/repos/builtin/packages/cuda/package.py b/var/spack/repos/builtin/packages/cuda/package.py
index 558535bec6..36cf3058d7 100644
--- a/var/spack/repos/builtin/packages/cuda/package.py
+++ b/var/spack/repos/builtin/packages/cuda/package.py
@@ -39,7 +39,7 @@ class Cuda(Package):
     Type, select runfile and click Download. Spack will search your
     current directory for this file. Alternatively, add this file to a
     mirror so that Spack can find it. For instructions on how to set up a
-    mirror, see http://software.llnl.gov/spack/mirrors.html
+    mirror, see http://spack.readthedocs.io/en/latest/mirrors.html.
 
     Note: This package does not currently install the drivers necessary
     to run CUDA. These will need to be installed manually. See:
diff --git a/var/spack/repos/builtin/packages/curl/package.py b/var/spack/repos/builtin/packages/curl/package.py
index 4954e435c0..a22ac52714 100644
--- a/var/spack/repos/builtin/packages/curl/package.py
+++ b/var/spack/repos/builtin/packages/curl/package.py
@@ -32,6 +32,8 @@ class Curl(Package):
     homepage = "http://curl.haxx.se"
     url      = "http://curl.haxx.se/download/curl-7.46.0.tar.bz2"
 
+    version('7.50.3', 'bd177fd6deecce00cfa7b5916d831c5e')
+    version('7.50.2', '6e161179f7af4b9f8b6ea21420132719')
     version('7.50.1', '015f6a0217ca6f2c5442ca406476920b')
     version('7.49.1', '6bb1f7af5b58b30e4e6414b8c1abccab')
     version('7.47.1', '9ea3123449439bbd960cd25cf98796fb')
diff --git a/var/spack/repos/builtin/packages/daal/package.py b/var/spack/repos/builtin/packages/daal/package.py
index e13dd80e19..35cb6cbce8 100644
--- a/var/spack/repos/builtin/packages/daal/package.py
+++ b/var/spack/repos/builtin/packages/daal/package.py
@@ -9,7 +9,7 @@ class Daal(IntelInstaller):
 
     Note: You will have to add the download file to a
     mirror so that Spack can find it. For instructions on how to set up a
-    mirror, see http://software.llnl.gov/spack/mirrors.html"""
+    mirror, see http://spack.readthedocs.io/en/latest/mirrors.html"""
 
     homepage = "https://software.intel.com/en-us/daal"
 
diff --git a/var/spack/repos/builtin/packages/darshan-runtime/package.py b/var/spack/repos/builtin/packages/darshan-runtime/package.py
new file mode 100644
index 0000000000..640573fdc1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/darshan-runtime/package.py
@@ -0,0 +1,65 @@
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+import os
+
+
+class DarshanRuntime(Package):
+    """Darshan (runtime) is a scalable HPC I/O characterization tool
+    designed to capture an accurate picture of application I/O behavior,
+    including properties such as patterns of access within files, with
+    minimum overhead. DarshanRuntime package should be installed on
+    systems where you intend to instrument MPI applications."""
+
+    homepage = "http://www.mcs.anl.gov/research/projects/darshan/"
+    url = "ftp://ftp.mcs.anl.gov/pub/darshan/releases/darshan-3.1.0.tar.gz"
+
+    version('3.1.0', '439d717323e6265b2612ed127886ae52')
+    version('3.0.0', '732577fe94238936268d74d7d74ebd08')
+
+    depends_on('mpi')
+    depends_on('zlib')
+
+    variant('slurm', default=False, description='Use Slurm Job ID')
+    variant('cobalt', default=False, description='Use Coblat Job Id')
+    variant('pbs', default=False, description='Use PBS Job Id')
+
+    def install(self, spec, prefix):
+
+        job_id = 'NONE'
+        if '+slurm' in spec:
+            job_id = 'SLURM_JOBID'
+        if '+cobalt' in spec:
+            job_id = 'COBALT_JOBID'
+        if '+pbs' in spec:
+            job_id = 'PBS_JOBID'
+
+        # TODO: BG-Q and other platform configure options
+        options = ['CC=%s' % spec['mpi'].mpicc,
+                   '--with-mem-align=8',
+                   '--with-log-path-by-env=DARSHAN_LOG_DIR_PATH',
+                   '--with-jobid-env=%s' % job_id,
+                   '--with-zlib=%s' % spec['zlib'].prefix]
+
+        with working_dir('spack-build', create=True):
+            configure = Executable('../darshan-runtime/configure')
+            configure('--prefix=%s' % prefix, *options)
+            make()
+            make('install')
+
+    def setup_environment(self, spack_env, run_env):
+        # default path for log file, could be user or site specific setting
+        darshan_log_dir = '%s' % os.environ['HOME']
+        run_env.set('DARSHAN_LOG_DIR_PATH', darshan_log_dir)
diff --git a/var/spack/repos/builtin/packages/darshan-util/package.py b/var/spack/repos/builtin/packages/darshan-util/package.py
new file mode 100644
index 0000000000..3446104a83
--- /dev/null
+++ b/var/spack/repos/builtin/packages/darshan-util/package.py
@@ -0,0 +1,41 @@
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class DarshanUtil(Package):
+    """Darshan (util) is collection of tools for parsing and summarizing log
+    files produced by Darshan (runtime) instrumentation. This package is
+    typically installed on systems (front-end) where you intend to analyze
+    log files produced by Darshan (runtime)."""
+
+    homepage = "http://www.mcs.anl.gov/research/projects/darshan/"
+    url = "ftp://ftp.mcs.anl.gov/pub/darshan/releases/darshan-3.1.0.tar.gz"
+
+    version('3.1.0', '439d717323e6265b2612ed127886ae52')
+    version('3.0.0', '732577fe94238936268d74d7d74ebd08')
+
+    depends_on('zlib')
+
+    def install(self, spec, prefix):
+
+        options = ['CC=%s' % self.compiler.cc,
+                   '--with-zlib=%s' % spec['zlib'].prefix]
+
+        with working_dir('spack-build', create=True):
+            configure = Executable('../darshan-util/configure')
+            configure('--prefix=%s' % prefix, *options)
+            make()
+            make('install')
diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py
index 939d8fc013..0d293e5d92 100644
--- a/var/spack/repos/builtin/packages/dealii/package.py
+++ b/var/spack/repos/builtin/packages/dealii/package.py
@@ -32,6 +32,7 @@ class Dealii(Package):
     homepage = "https://www.dealii.org"
     url      = "https://github.com/dealii/dealii/releases/download/v8.4.1/dealii-8.4.1.tar.gz"
 
+    version('8.4.2', '84c6bd3f250d3e0681b645d24cb987a7')
     version('8.4.1', 'efbaf16f9ad59cfccad62302f36c3c1d')
     version('8.4.0', 'ac5dbf676096ff61e092ce98c80c2b00')
     version('8.3.0', 'fc6cdcb16309ef4bea338a4f014de6fa')
@@ -67,11 +68,11 @@ class Dealii(Package):
     # Boost 1.58 is blacklisted, see
     # https://github.com/dealii/dealii/issues/1591
     # Require at least 1.59
-    # +python won't affect @:8.4.1
+    # +python won't affect @:8.4.2
     depends_on("boost@1.59.0:+thread+system+serialization+iostreams",
-               when='@:8.4.1~mpi')
+               when='@:8.4.2~mpi')
     depends_on("boost@1.59.0:+thread+system+serialization+iostreams+mpi",
-               when='@:8.4.1+mpi')
+               when='@:8.4.2+mpi')
     # since @8.5.0: (and @develop) python bindings are introduced:
     depends_on("boost@1.59.0:+thread+system+serialization+iostreams",
                when='@8.5.0:~mpi~python')
@@ -102,8 +103,9 @@ class Dealii(Package):
     depends_on("netcdf-cxx",       when='+netcdf+mpi')
     depends_on("oce",              when='+oce')
     depends_on("p4est",            when='+p4est+mpi')
-    depends_on("petsc+mpi",        when='@8.5.0:+petsc+mpi')
-    depends_on("slepc",            when='@8.5.0:+slepc+petsc+mpi')
+    depends_on("petsc+mpi",        when='@8.4.2:+petsc+mpi')
+    depends_on('python',           when='@8.5.0:+python')
+    depends_on("slepc",            when='@8.4.2:+slepc+petsc+mpi')
     depends_on("petsc@:3.6.4+mpi", when='@:8.4.1+petsc+mpi')
     depends_on("slepc@:3.6.3",     when='@:8.4.1+slepc+petsc+mpi')
     depends_on("trilinos",         when='+trilinos+mpi')
@@ -122,6 +124,7 @@ class Dealii(Package):
                 options.remove(word)
 
         dsuf = 'dylib' if sys.platform == 'darwin' else 'so'
+        lapack_blas = spec['lapack'].lapack_libs + spec['blas'].blas_libs
         options.extend([
             '-DCMAKE_BUILD_TYPE=DebugRelease',
             '-DDEAL_II_COMPONENT_EXAMPLES=ON',
@@ -134,9 +137,7 @@ class Dealii(Package):
             '-DLAPACK_FOUND=true',
             '-DLAPACK_INCLUDE_DIRS=%s;%s' % (
                 spec['lapack'].prefix.include, spec['blas'].prefix.include),
-            '-DLAPACK_LIBRARIES=%s;%s' % (
-                spec['lapack'].lapack_shared_lib,
-                spec['blas'].blas_shared_lib),
+            '-DLAPACK_LIBRARIES=%s' % lapack_blas.joined(';'),
             '-DMUPARSER_DIR=%s' % spec['muparser'].prefix,
             '-DUMFPACK_DIR=%s' % spec['suite-sparse'].prefix,
             '-DTBB_DIR=%s' % spec['tbb'].prefix,
diff --git a/var/spack/repos/builtin/packages/elk/package.py b/var/spack/repos/builtin/packages/elk/package.py
index b089e585dd..acaf863935 100644
--- a/var/spack/repos/builtin/packages/elk/package.py
+++ b/var/spack/repos/builtin/packages/elk/package.py
@@ -87,12 +87,12 @@ class Elk(Package):
         # BLAS/LAPACK support
         # Note: BLAS/LAPACK must be compiled with OpenMP support
         # if the +openmp variant is chosen
-        blas   = 'blas.a'
+        blas = 'blas.a'
         lapack = 'lapack.a'
         if '+blas' in spec:
-            blas   = spec['blas'].blas_shared_lib
+            blas = spec['blas'].blas_libs.joined()
         if '+lapack' in spec:
-            lapack = spec['lapack'].lapack_shared_lib
+            lapack = spec['lapack'].lapack_libs.joined()
         # lapack must come before blas
         config['LIB_LPK'] = ' '.join([lapack, blas])
 
diff --git a/var/spack/repos/builtin/packages/elpa/package.py b/var/spack/repos/builtin/packages/elpa/package.py
index f28d63f6c3..b433bf40b0 100644
--- a/var/spack/repos/builtin/packages/elpa/package.py
+++ b/var/spack/repos/builtin/packages/elpa/package.py
@@ -34,8 +34,16 @@ class Elpa(Package):
     homepage = 'http://elpa.mpcdf.mpg.de/'
     url = 'http://elpa.mpcdf.mpg.de/elpa-2015.11.001.tar.gz'
 
-    version('2015.11.001', 'de0f35b7ee7c971fd0dca35c900b87e6',
-            url='http://elpa.mpcdf.mpg.de/elpa-2015.11.001.tar.gz')
+    version(
+        '2016.05.003',
+        '88a9f3f3bfb63e16509dd1be089dcf2c',
+        url='http://elpa.mpcdf.mpg.de/html/Releases/2016.05.003/elpa-2016.05.003.tar.gz'
+    )
+    version(
+        '2015.11.001',
+        'de0f35b7ee7c971fd0dca35c900b87e6',
+        url='http://elpa.mpcdf.mpg.de/elpa-2015.11.001.tar.gz'
+    )
 
     variant('openmp', default=False, description='Activates OpenMP support')
 
@@ -46,7 +54,24 @@ class Elpa(Package):
 
     def install(self, spec, prefix):
 
-        options = ["--prefix=%s" % prefix]
+        options = [
+            'CC={0}'.format(self.spec['mpi'].mpicc),
+            'FC={0}'.format(self.spec['mpi'].mpifc),
+            'CXX={0}'.format(self.spec['mpi'].mpicxx),
+            'FCFLAGS={0}'.format(
+                spec['lapack'].lapack_libs.joined()
+            ),
+            'LDFLAGS={0}'.format(
+                spec['lapack'].lapack_libs.joined()
+            ),
+            'SCALAPACK_FCFLAGS={0}'.format(
+                spec['scalapack'].scalapack_libs.joined()
+            ),
+            'SCALAPACK_LDFLAGS={0}'.format(
+                spec['scalapack'].scalapack_libs.joined()
+            ),
+            '--prefix={0}'.format(self.prefix)
+        ]
 
         if '+openmp' in spec:
             options.append("--enable-openmp")
diff --git a/var/spack/repos/builtin/packages/espresso/package.py b/var/spack/repos/builtin/packages/espresso/package.py
index 3dca1ba187..d2c825513c 100644
--- a/var/spack/repos/builtin/packages/espresso/package.py
+++ b/var/spack/repos/builtin/packages/espresso/package.py
@@ -88,7 +88,7 @@ class Espresso(Package):
 
         # Add a list of directories to search
         search_list = []
-        for name, dependency_spec in spec.dependencies.iteritems():
+        for dependency_spec in spec.dependencies():
             search_list.extend([dependency_spec.prefix.lib,
                                 dependency_spec.prefix.lib64])
 
diff --git a/var/spack/repos/builtin/packages/extrae/package.py b/var/spack/repos/builtin/packages/extrae/package.py
index 72bfbe6326..cb20a8109e 100644
--- a/var/spack/repos/builtin/packages/extrae/package.py
+++ b/var/spack/repos/builtin/packages/extrae/package.py
@@ -53,8 +53,8 @@ class Extrae(Package):
        programming models either alone or in conjunction with MPI :
        OpenMP, CUDA, OpenCL, pthread, OmpSs"""
     homepage = "http://www.bsc.es/computer-sciences/extrae"
-    url      = "http://www.bsc.es/ssl/apps/performanceTools/files/extrae-3.0.1.tar.bz2"
-    version('3.0.1', 'a6a8ca96cd877723cd8cc5df6bdb922b')
+    url      = "http://www.bsc.es/ssl/apps/performanceTools/files/extrae-3.3.0.tar.bz2"
+    version('3.3.0', 'f46e3f1a6086b5b3ac41c9585b42952d')
 
     depends_on("mpi")
     depends_on("dyninst")
@@ -62,6 +62,9 @@ class Extrae(Package):
     depends_on("boost")
     depends_on("libdwarf")
     depends_on("papi")
+    depends_on("libelf")
+    depends_on("libxml2")
+    depends_on("binutils+libiberty")
 
     def install(self, spec, prefix):
         if 'openmpi' in spec:
@@ -80,6 +83,9 @@ class Extrae(Package):
                   "--with-papi=%s" % spec['papi'].prefix,
                   "--with-dyninst-headers=%s" % spec[
                       'dyninst'].prefix.include,
+                  "--with-elf=%s" % spec['libelf'].prefix,
+                  "--with-xml-prefix=%s" % spec['libxml2'].prefix,
+                  "--with-binutils=%s" % spec['binutils'].prefix,
                   "--with-dyninst-libs=%s" % spec['dyninst'].prefix.lib)
 
         make()
diff --git a/var/spack/repos/builtin/packages/fenics/hdf5~cxx-detection.patch b/var/spack/repos/builtin/packages/fenics/hdf5~cxx-detection.patch
new file mode 100644
index 0000000000..52e36ab00b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fenics/hdf5~cxx-detection.patch
@@ -0,0 +1,11 @@
+--- a/CMakeLists.txt	2016-08-16 02:30:13.466078087 +0200
++++ b/CMakeLists.txt	2016-08-16 02:30:36.879586772 +0200
+@@ -553,7 +553,7 @@
+     set(ENV{HDF5_ROOT} "$ENV{HDF5_DIR}")
+   endif()
+   set(HDF5_PREFER_PARALLEL TRUE)
+-  find_package(HDF5)
++  find_package(HDF5 COMPONENTS C)
+   set_package_properties(HDF5 PROPERTIES TYPE OPTIONAL
+     DESCRIPTION "Hierarchical Data Format 5 (HDF5)"
+     URL "https://www.hdfgroup.org/HDF5")
diff --git a/var/spack/repos/builtin/packages/fenics/package.py b/var/spack/repos/builtin/packages/fenics/package.py
index eeeefc540d..fd9a37df1b 100644
--- a/var/spack/repos/builtin/packages/fenics/package.py
+++ b/var/spack/repos/builtin/packages/fenics/package.py
@@ -62,17 +62,15 @@ class Fenics(Package):
     # variant('slepc4py',     default=True,  description='Uses SLEPc4py')
     # variant('pastix',       default=True,  description='Compile with Pastix')
 
-    patch('petsc-3.7.patch', when='^petsc@3.7:')
+    patch('petsc-3.7.patch', when='@1.6.1^petsc@3.7:')
     patch('petsc-version-detection.patch', when='@:1.6.1')
+    patch('hdf5~cxx-detection.patch')
 
     extends('python')
 
-    depends_on('py-numpy')
-    depends_on('py-ply')
-    depends_on('py-six')
-    depends_on('py-sphinx@1.0.1:', when='+doc')
-    depends_on('eigen@3.2.0:')
-    depends_on('boost')
+    depends_on('eigen@3.2.0:', type='build')
+    depends_on('boost+filesystem+program_options+system+iostreams+timer+regex+chrono')
+
     depends_on('mpi', when='+mpi')
     depends_on('hdf5', when='+hdf5')
     depends_on('parmetis@4.0.2:^metis+real64', when='+parmetis')
@@ -85,13 +83,28 @@ class Fenics(Package):
     depends_on('suite-sparse', when='+suite-sparse')
     depends_on('qt', when='+qt')
 
-    # This are the build dependencies
-    depends_on('py-setuptools')
-    depends_on('cmake@2.8.12:')
-    depends_on('swig@3.0.3:')
+    depends_on('py-ply', type=nolink)
+    depends_on('py-six', type=nolink)
+    depends_on('py-numpy', type=nolink)
+    depends_on('py-sympy', type=nolink)
+    depends_on('swig@3.0.3:', type=nolink)
+    depends_on('cmake@2.8.12:', type=nolink)
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-sphinx@1.0.1:', when='+doc', type='build')
 
     releases = [
         {
+            'version': '2016.1.0',
+            'md5': '92e8d00f6487a575987201f0b0d19173',
+            'resources': {
+                'ffc': '35457ae164e481ba5c9189ebae060a47',
+                'fiat': 'ac0c49942831ee434301228842bcc280',
+                'instant': '0e3dbb464c4d90d691f31f0fdd63d4f6',
+                'ufl': '37433336e5c9b58d1d5ab4acca9104a7',
+            }
+        },
+        {
             'version': '1.6.0',
             'md5': '35cb4baf7ab4152a40fb7310b34d5800',
             'resources': {
diff --git a/var/spack/repos/builtin/packages/fontconfig/package.py b/var/spack/repos/builtin/packages/fontconfig/package.py
index 0d7e47f228..311156378a 100644
--- a/var/spack/repos/builtin/packages/fontconfig/package.py
+++ b/var/spack/repos/builtin/packages/fontconfig/package.py
@@ -34,9 +34,12 @@ class Fontconfig(Package):
 
     depends_on('freetype')
     depends_on('libxml2')
+    depends_on('pkg-config', type='build')
 
     def install(self, spec, prefix):
-        configure("--prefix=%s" % prefix, "--enable-libxml2")
+        configure("--prefix=%s" % prefix,
+                  "--enable-libxml2",
+                  "--disable-docs")
 
         make()
         make("install")
diff --git a/var/spack/repos/builtin/packages/gcc/package.py b/var/spack/repos/builtin/packages/gcc/package.py
index 3be3948b59..d152ce61c7 100644
--- a/var/spack/repos/builtin/packages/gcc/package.py
+++ b/var/spack/repos/builtin/packages/gcc/package.py
@@ -3,6 +3,7 @@ from spack import *
 from contextlib import closing
 from glob import glob
 import sys
+from os.path import isfile
 
 
 class Gcc(Package):
@@ -68,6 +69,19 @@ class Gcc(Package):
         if spec.satisfies("@4.7.1:") and sys.platform != 'darwin':
             enabled_languages.add('go')
 
+        # Fix a standard header file for OS X Yosemite that
+        # is GCC incompatible by replacing non-GCC compliant macros
+        if 'yosemite' in spec.architecture:
+            if isfile(r'/usr/include/dispatch/object.h'):
+                new_dispatch_dir = join_path(prefix, 'include', 'dispatch')
+                mkdirp(new_dispatch_dir)
+                cp = which('cp')
+                new_header = join_path(new_dispatch_dir, 'object.h')
+                cp(r'/usr/include/dispatch/object.h', new_header)
+                filter_file(r'typedef void \(\^dispatch_block_t\)\(void\)',
+                            'typedef void* dispatch_block_t',
+                            new_header)
+
         # Generic options to compile GCC
         options = ["--prefix=%s" % prefix, "--libdir=%s/lib64" % prefix,
                    "--disable-multilib",
diff --git a/var/spack/repos/builtin/packages/gdb/package.py b/var/spack/repos/builtin/packages/gdb/package.py
index a14e166ed4..f90e4e7ff0 100644
--- a/var/spack/repos/builtin/packages/gdb/package.py
+++ b/var/spack/repos/builtin/packages/gdb/package.py
@@ -41,9 +41,18 @@ class Gdb(Package):
     version('7.9', '8f8ced422fe462a00e0135a643544f17')
     version('7.8.2', '8b0ea8b3559d3d90b3ff4952f0aeafbc')
 
+    variant('python', default=True, description='Compile with Python support')
+
+    # Required dependency
     depends_on('texinfo', type='build')
 
+    # Optional dependency
+    depends_on('python', when='+python')
+
     def install(self, spec, prefix):
-        configure('--prefix=%s' % prefix)
+        options = ['--prefix=%s' % prefix]
+        if '+python' in spec:
+            options.extend(['--with-python'])
+        configure(*options)
         make()
         make("install")
diff --git a/var/spack/repos/builtin/packages/geant4/package.py b/var/spack/repos/builtin/packages/geant4/package.py
new file mode 100644
index 0000000000..239ef6d586
--- /dev/null
+++ b/var/spack/repos/builtin/packages/geant4/package.py
@@ -0,0 +1,85 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+
+from spack import *
+
+
+class Geant4(Package):
+    """Geant4 is a toolkit for the simulation of the passage of particles
+    through matter. Its areas of application include high energy, nuclear
+    and accelerator physics, as well as studies in medical and space
+    science."""
+
+    homepage = "http://geant4.cern.ch/"
+    url      = "http://geant4.cern.ch/support/source/geant4.10.01.p03.tar.gz"
+
+    version('10.02.p01', 'b81f7082a15f6a34b720b6f15c6289cfe4ddbbbdcef0dc52719f71fac95f7f1c')
+    version('10.01.p03', '4fb4175cc0dabcd517443fbdccd97439')
+
+    variant('qt', default=False, description='Enable Qt support')
+
+    depends_on('cmake@3.5:', type='build')
+
+    depends_on("clhep@2.3.1.1~cxx11+cxx14", when="@10.02.p01")
+    depends_on("clhep@2.2.0.4~cxx11+cxx14", when="@10.01.p03")
+    depends_on("expat")
+    depends_on("zlib")
+    depends_on("xerces-c")
+    depends_on("qt@4.8:", when="+qt")
+
+    def install(self, spec, prefix):
+        cmake_args = list(std_cmake_args)
+        cmake_args.append('-DXERCESC_ROOT_DIR:STRING=%s' %
+                          spec['xerces-c'].prefix)
+        cmake_args.append('-DGEANT4_BUILD_CXXSTD=c++14')
+
+        cmake_args += ['-DGEANT4_USE_GDML=ON',
+                       '-DGEANT4_USE_SYSTEM_EXPAT=ON',
+                       '-DGEANT4_USE_SYSTEM_ZLIB=ON',
+                       '-DGEANT4_USE_SYSTEM_CLHEP=ON']
+
+        # fixme: turn off data for now and maybe each data set should
+        # go into a separate package to cut down on disk usage between
+        # different code versions using the same data versions.
+        cmake_args.append('-DGEANT4_INSTALL_DATA=OFF')
+
+        # http://geant4.web.cern.ch/geant4/UserDocumentation/UsersGuides/InstallationGuide/html/ch02s03.html
+        # fixme: likely things that need addressing:
+        # -DGEANT4_USE_OPENGL_X11=ON
+
+        if '+qt' in spec:
+            cmake_args.append('-DGEANT4_USE_QT=ON')
+
+        build_directory = join_path(self.stage.path, 'spack-build')
+        source_directory = self.stage.source_path
+
+        with working_dir(build_directory, create=True):
+            cmake(source_directory, *cmake_args)
+            make()
+            make("install")
+
+    def url_for_version(self, version):
+        """Handle Geant4's unusual version string."""
+        return "http://geant4.cern.ch/support/source/geant4.%s.tar.gz" % version
diff --git a/var/spack/repos/builtin/packages/git-lfs/package.py b/var/spack/repos/builtin/packages/git-lfs/package.py
index a080660721..25e440ff6d 100644
--- a/var/spack/repos/builtin/packages/git-lfs/package.py
+++ b/var/spack/repos/builtin/packages/git-lfs/package.py
@@ -26,17 +26,28 @@ from spack import *
 
 
 class GitLfs(Package):
-    """Tool for managing large files with Git."""
+    """Git LFS is a system for managing and versioning large files in
+       association with a Git repository.  Instead of storing the large files
+       within the Git repository as blobs, Git LFS stores special "pointer
+       files" in the repository, while storing the actual file contents on a
+       Git LFS server."""
 
     homepage = "https://git-lfs.github.com"
-    url      = "https://github.com/github/git-lfs/archive/v1.4.1.tar.gz"
+    git_url  = "https://github.com/github/git-lfs.git"
 
-    version('1.4.1', 'c62a314d96d3a30af4d98fa3305ad317')
+    version('1.4.1', git=git_url, tag='v1.4.1')
+    version('1.3.1', git=git_url, tag='v1.3.1')
+
+    # TODO: Implement this by following the instructions at this location:
+    # https://github.com/github/git-lfs/blob/master/CONTRIBUTING.md#building
+    # variant('test', default=True, description='Build and run tests as part of the build.')  # NOQA: E501
 
     depends_on('go@1.5:', type='build')
     depends_on('git@1.8.2:', type='run')
 
     def install(self, spec, prefix):
-        bootstrap = Executable('./scripts/bootstrap')
-        bootstrap()
-        install('bin/git-lfs', prefix.bin)
+        bootstrap_script = Executable(join_path('script', 'bootstrap'))
+        bootstrap_script()
+
+        mkdirp(prefix.bin)
+        install(join_path('bin', 'git-lfs'), prefix.bin)
diff --git a/var/spack/repos/builtin/packages/git/package.py b/var/spack/repos/builtin/packages/git/package.py
index ed058e0a68..ac97ad392b 100644
--- a/var/spack/repos/builtin/packages/git/package.py
+++ b/var/spack/repos/builtin/packages/git/package.py
@@ -22,6 +22,7 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
+import sys
 from spack import *
 
 
@@ -54,28 +55,33 @@ class Git(Package):
     # version('2.5.4', '3eca2390cf1fa698b48e2a233563a76b')
     # version('2.2.1', 'ff41fdb094eed1ec430aed8ee9b9849c')
 
-    depends_on("openssl")
     depends_on("autoconf", type='build')
     depends_on("curl")
     depends_on("expat")
     depends_on("gettext")
-    depends_on("zlib")
+    depends_on("libiconv")
+    depends_on("openssl")
     depends_on("pcre")
     depends_on("perl")
+    depends_on("zlib")
 
     def install(self, spec, prefix):
         env['LDFLAGS'] = "-L%s" % spec['gettext'].prefix.lib + " -lintl"
         configure_args = [
             "--prefix=%s" % prefix,
-            "--with-libpcre=%s" % spec['pcre'].prefix,
-            "--with-openssl=%s" % spec['openssl'].prefix,
-            "--with-zlib=%s" % spec['zlib'].prefix,
             "--with-curl=%s" % spec['curl'].prefix,
             "--with-expat=%s" % spec['expat'].prefix,
+            "--with-iconv=%s" % spec['libiconv'].prefix,
+            "--with-libpcre=%s" % spec['pcre'].prefix,
+            "--with-openssl=%s" % spec['openssl'].prefix,
             "--with-perl=%s" % join_path(spec['perl'].prefix.bin, 'perl'),
+            "--with-zlib=%s" % spec['zlib'].prefix,
         ]
 
         which('autoreconf')('-i')
         configure(*configure_args)
+        if sys.platform == "darwin":
+            # Don't link with -lrt; the system has no (and needs no) librt
+            filter_file(r' -lrt$', '', 'Makefile')
         make()
         make("install")
diff --git a/var/spack/repos/builtin/packages/glib/no-Werror=format-security.patch b/var/spack/repos/builtin/packages/glib/no-Werror=format-security.patch
new file mode 100644
index 0000000000..cfcfe424be
--- /dev/null
+++ b/var/spack/repos/builtin/packages/glib/no-Werror=format-security.patch
@@ -0,0 +1,16 @@
+--- a/configure.ac	2016-08-16 11:57:34.000000000 -0400
++++ b/configure.ac	2016-08-16 11:57:36.000000000 -0400
+@@ -3357,11 +3357,11 @@
+ 			      enable_compile_warnings=yes)
+ AS_IF([test "x$enable_compile_warnings" = xyes], [
+   CC_CHECK_FLAGS_APPEND([GLIB_WARN_CFLAGS], [CFLAGS], [\
+    -Wall -Wstrict-prototypes -Werror=declaration-after-statement \
+    -Werror=missing-prototypes -Werror=implicit-function-declaration \
+-   -Werror=pointer-arith -Werror=init-self -Werror=format-security \
+-   -Werror=format=2 -Werror=missing-include-dirs])
++   -Werror=pointer-arith -Werror=init-self \
++   -Werror=missing-include-dirs])
+ ])
+ AC_SUBST(GLIB_WARN_CFLAGS)
+ 
+ #
diff --git a/var/spack/repos/builtin/packages/glib/package.py b/var/spack/repos/builtin/packages/glib/package.py
index 94ef95e7ab..3e687ccd95 100644
--- a/var/spack/repos/builtin/packages/glib/package.py
+++ b/var/spack/repos/builtin/packages/glib/package.py
@@ -23,6 +23,7 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
+import os
 
 
 class Glib(Package):
@@ -38,14 +39,20 @@ class Glib(Package):
     version('2.48.1', '67bd3b75c9f6d5587b457dc01cdcd5bb')
     version('2.42.1', '89c4119e50e767d3532158605ee9121a')
 
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool', type='build')
+    depends_on('pkg-config', type='build')
     depends_on('libffi')
     depends_on('zlib')
-    depends_on('pkg-config', type='build')
     depends_on('gettext')
     depends_on('pcre+utf', when='@2.48:')
 
     # The following patch is needed for gcc-6.1
     patch('g_date_strftime.patch', when='@2.42.1')
+    # Clang doesn't seem to acknowledge the pragma lines to disable the -Werror
+    # around a legitimate usage.
+    patch('no-Werror=format-security.patch')
 
     def url_for_version(self, version):
         """Handle glib's version-based custom URLs."""
@@ -53,6 +60,16 @@ class Glib(Package):
         return url + '/%s/glib-%s.tar.xz' % (version.up_to(2), version)
 
     def install(self, spec, prefix):
+        autoreconf = which("autoreconf")
+        autoreconf("--install", "--verbose", "--force",
+                   "-I", "config",
+                   "-I", os.path.join(spec['pkg-config'].prefix,
+                                      "share", "aclocal"),
+                   "-I", os.path.join(spec['automake'].prefix,
+                                      "share", "aclocal"),
+                   "-I", os.path.join(spec['libtool'].prefix,
+                                      "share", "aclocal"),
+                   )
         configure("--prefix=%s" % prefix)
         make()
         make("install", parallel=False)
diff --git a/var/spack/repos/builtin/packages/gmake/package.py b/var/spack/repos/builtin/packages/gmake/package.py
new file mode 100644
index 0000000000..ca296350a4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gmake/package.py
@@ -0,0 +1,42 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Gmake(Package):
+    """GNU Make."""
+
+    homepage = "http://gnu.org/gnu/make"
+    url      = "ftp://ftp.gnu.org/gnu/make/make-4.0.tar.gz"
+
+    version('4.0', 'b5e558f981326d9ca1bfdb841640721a')
+
+    def install(self, spec, prefix):
+        configure('--prefix={0}'.format(prefix))
+
+        make()
+        make('install')
+        with working_dir(prefix.bin):
+            symlink('make', 'gmake')
diff --git a/var/spack/repos/builtin/packages/gmp/package.py b/var/spack/repos/builtin/packages/gmp/package.py
index bd1f653bd7..ddc2dbb935 100644
--- a/var/spack/repos/builtin/packages/gmp/package.py
+++ b/var/spack/repos/builtin/packages/gmp/package.py
@@ -37,4 +37,7 @@ class Gmp(AutotoolsPackage):
     version('6.0.0a', 'b7ff2d88cae7f8085bd5006096eed470')
     version('6.0.0',  '6ef5869ae735db9995619135bd856b84')
 
-    depends_on("m4", type='build')
+    depends_on('m4', type='build')
+
+    def configure_args(self):
+        return ['--enable-cxx']
diff --git a/var/spack/repos/builtin/packages/gmsh/package.py b/var/spack/repos/builtin/packages/gmsh/package.py
index 1d375f2186..dd142866e5 100644
--- a/var/spack/repos/builtin/packages/gmsh/package.py
+++ b/var/spack/repos/builtin/packages/gmsh/package.py
@@ -87,9 +87,9 @@ class Gmsh(Package):
         options.append('-DENABLE_OS_SPECIFIC_INSTALL=OFF')
 
         # Make sure GMSH picks up correct BlasLapack by providing linker flags
-        options.append('-DBLAS_LAPACK_LIBRARIES=%s %s' %
-                       (to_link_flags(spec['lapack'].lapack_shared_lib),
-                        to_link_flags(spec['blas'].blas_shared_lib)))
+        blas_lapack = spec['lapack'].lapack_libs + spec['blas'].blas_libs
+        options.append(
+            '-DBLAS_LAPACK_LIBRARIES={0}'.format(blas_lapack.ld_flags))
 
         # Gmsh does not have an option to compile against external metis.
         # Its own Metis, however, fails to build
diff --git a/var/spack/repos/builtin/packages/go-bootstrap/package.py b/var/spack/repos/builtin/packages/go-bootstrap/package.py
index b0e2109fd3..d48c7c9756 100644
--- a/var/spack/repos/builtin/packages/go-bootstrap/package.py
+++ b/var/spack/repos/builtin/packages/go-bootstrap/package.py
@@ -1,3 +1,27 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
 import os
 import shutil
 import glob
@@ -17,25 +41,37 @@ class GoBootstrap(Package):
 
     extendable = True
 
-    # temporary fix until tags are pulled correctly
+    # NOTE: Go@1.4.2 is the only supported bootstrapping compiler because all
+    # later versions require a Go compiler to build.
+    # See: https://golang.org/doc/install/source
     version('1.4.2', git='https://go.googlesource.com/go', tag='go1.4.2')
 
-    variant('test',
-            default=True,
-            description="Run tests as part of build, a good idea but quite"
-            " time consuming")
+    variant('test', default=True, description='Build and run tests as part of the build.')
 
     provides('golang@:1.4.2')
 
-    depends_on('git')
+    depends_on('git', type='alldeps')
+
+    # NOTE: Older versions of Go attempt to download external files that have
+    # since been moved while running the test suite.  This patch modifies the
+    # test files so that these tests don't cause false failures.
+    # See: https://github.com/golang/go/issues/15694
+    @when('@:1.4.3')
+    def patch(self):
+        test_suite_file = FileFilter(join_path('src', 'run.bash'))
+        test_suite_file.filter(
+            r'^(.*)(\$GOROOT/src/cmd/api/run.go)(.*)$',
+            r'# \1\2\3',
+        )
+
+    @when('@1.5.0:')
+    def patch(self):
+        pass
 
     def install(self, spec, prefix):
         bash = which('bash')
         with working_dir('src'):
-            if '+test' in spec:
-                bash('all.bash')
-            else:
-                bash('make.bash')
+            bash('{0}.bash'.format('all' if '+test' in spec else 'make'))
 
         try:
             os.makedirs(prefix)
diff --git a/var/spack/repos/builtin/packages/go/package.py b/var/spack/repos/builtin/packages/go/package.py
index 259498c145..5fa3017ab5 100644
--- a/var/spack/repos/builtin/packages/go/package.py
+++ b/var/spack/repos/builtin/packages/go/package.py
@@ -1,3 +1,27 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
 import os
 import shutil
 import glob
@@ -12,28 +36,39 @@ class Go(Package):
 
     extendable = True
 
-    version('1.5.4', git='https://go.googlesource.com/go', tag='go1.5.4')
     version('1.6.2', git='https://go.googlesource.com/go', tag='go1.6.2')
+    version('1.5.4', git='https://go.googlesource.com/go', tag='go1.5.4')
+    version('1.4.2', git='https://go.googlesource.com/go', tag='go1.4.2')
 
-    variant('test',
-            default=True,
-            description="Run tests as part of build, a good idea but quite"
-            " time consuming")
+    variant('test', default=True, description='Build and run tests as part of the build.')
 
     provides('golang')
 
-    # to-do, make non-c self-hosting compilers feasible without backflips
+    depends_on('git', type='alldeps')
+    # TODO: Make non-c self-hosting compilers feasible without backflips
     # should be a dep on external go compiler
     depends_on('go-bootstrap', type='build')
-    depends_on('git', type='alldeps')
+
+    # NOTE: Older versions of Go attempt to download external files that have
+    # since been moved while running the test suite.  This patch modifies the
+    # test files so that these tests don't cause false failures.
+    # See: https://github.com/golang/go/issues/15694
+    @when('@:1.4.3')
+    def patch(self):
+        test_suite_file = FileFilter(join_path('src', 'run.bash'))
+        test_suite_file.filter(
+            r'^(.*)(\$GOROOT/src/cmd/api/run.go)(.*)$',
+            r'# \1\2\3',
+        )
+
+    @when('@1.5.0:')
+    def patch(self):
+        pass
 
     def install(self, spec, prefix):
         bash = which('bash')
         with working_dir('src'):
-            if '+test' in spec:
-                bash('all.bash')
-            else:
-                bash('make.bash')
+            bash('{0}.bash'.format('all' if '+test' in spec else 'make'))
 
         try:
             os.makedirs(prefix)
diff --git a/var/spack/repos/builtin/packages/grackle/Make.mach.template b/var/spack/repos/builtin/packages/grackle/Make.mach.template
new file mode 100644
index 0000000000..83abaa26d1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/grackle/Make.mach.template
@@ -0,0 +1,71 @@
+MACH_TEXT  = Generic Linux
+MACH_VALID = 1
+MACH_FILE  = Make.mach.@ARCHITECTURE
+
+#-----------------------------------------------------------------------
+# Install paths (local variables)
+#-----------------------------------------------------------------------
+
+LOCAL_HDF5_INSTALL = @HDF5_ROOT
+
+#-----------------------------------------------------------------------
+# Compiler settings
+#-----------------------------------------------------------------------
+
+MACH_CC_NOMPI  = @CC # C compiler
+MACH_CXX_NOMPI = @CXX # C++ compiler
+MACH_FC_NOMPI  = @F77 # Fortran 77
+MACH_F90_NOMPI = @FC # Fortran 90
+MACH_LD_NOMPI  = @FC # Linker
+@LINK_VARIABLES_DEFINITION
+
+#-----------------------------------------------------------------------
+# Machine-dependent defines
+#-----------------------------------------------------------------------
+
+MACH_DEFINES   = -DLINUX -DH5_USE_16_API -fPIC
+
+#-----------------------------------------------------------------------
+# Compiler flag settings
+#-----------------------------------------------------------------------
+
+MACH_CPPFLAGS = -P -traditional
+MACH_CFLAGS   = 
+MACH_CXXFLAGS = 
+MACH_FFLAGS   = -fno-second-underscore -ffixed-line-length-132
+MACH_F90FLAGS = -fno-second-underscore
+MACH_LDFLAGS  = @STDCXX_LIB
+
+#-----------------------------------------------------------------------
+# Optimization flags
+#-----------------------------------------------------------------------
+
+MACH_OPT_WARN        = -Wall -g
+MACH_OPT_DEBUG       = -g
+MACH_OPT_HIGH        = -O2
+MACH_OPT_AGGRESSIVE  = -O3 -g
+
+#-----------------------------------------------------------------------
+# Includes
+#-----------------------------------------------------------------------
+
+LOCAL_INCLUDES_HDF5   = -I@HDF5_ROOT/include # HDF5 includes
+
+MACH_INCLUDES         = $(LOCAL_INCLUDES_HDF5)
+
+#-----------------------------------------------------------------------
+# Libraries
+#-----------------------------------------------------------------------
+
+LOCAL_LIBS_HDF5   = -L@HDF5_ROOT/lib -lhdf5 # HDF5 libraries
+LOCAL_LIBS_MACH   =  # Machine-dependent libraries
+
+MACH_LIBS         = $(LOCAL_LIBS_HDF5) $(LOCAL_LIBS_MACH)
+
+#-----------------------------------------------------------------------
+# Installation
+#-----------------------------------------------------------------------
+
+MACH_INSTALL_PREFIX = @PREFIX
+MACH_INSTALL_LIB_DIR =
+MACH_INSTALL_INCLUDE_DIR =
diff --git a/var/spack/repos/builtin/packages/grackle/package.py b/var/spack/repos/builtin/packages/grackle/package.py
new file mode 100644
index 0000000000..7e3777158f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/grackle/package.py
@@ -0,0 +1,89 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+import os.path
+import shutil
+import inspect
+
+from spack import *
+
+
+class Grackle(Package):
+    """Grackle is a chemistry and radiative cooling library for astrophysical
+    simulations with interfaces for C, C++, and Fortran codes. It is a
+    generalized and trimmed down version of the chemistry network of the Enzo
+    simulation code
+    """
+    homepage = 'http://grackle.readthedocs.io/en/grackle-2.2/'
+    url = 'https://bitbucket.org/grackle/grackle/get/grackle-2.0.1.tar.bz2'
+
+    version('2.2', 'ec49ed1db5a42db21f478285150c2ba3')
+    version('2.0.1', 'a9624ad13a60c592c1a0a4ea8e1ae86d')
+
+    depends_on('libtool', when='@2.2')
+
+    depends_on('mpi')
+    depends_on('hdf5+mpi')
+
+    parallel = False
+
+    def install(self, spec, prefix):
+        template_name = '{0.architecture}-{0.compiler.name}'
+        grackle_architecture = template_name.format(spec)
+        link_variables = 'MACH_AR = ar' if spec.version < Version(2.2) else 'MACH_LIBTOOL = libtool'  # NOQA: ignore=E501
+        substitutions = {
+            '@ARCHITECTURE': grackle_architecture,
+            '@CC': spec['mpi'].mpicc,
+            '@CXX': spec['mpi'].mpicxx,
+            '@FC': spec['mpi'].mpifc,
+            '@F77': spec['mpi'].mpif77,
+            '@STDCXX_LIB': ' '.join(self.compiler.stdcxx_libs),
+            '@HDF5_ROOT': spec['hdf5'].prefix,
+            '@PREFIX': prefix,
+            '@LINK_VARIABLES_DEFINITION': link_variables
+        }
+
+        template = join_path(
+            os.path.dirname(inspect.getmodule(self).__file__),
+            'Make.mach.template'
+        )
+        makefile = join_path(
+            self.stage.source_path,
+            'src',
+            'clib',
+            'Make.mach.{0}'.format(grackle_architecture)
+        )
+        shutil.copy(template, makefile)
+        for key, value in substitutions.items():
+            filter_file(key, value, makefile)
+
+        configure()
+        with working_dir('src/clib'):
+            make('clean')
+            make('machine-{0}'.format(grackle_architecture))
+            make('opt-high')
+            make('show-config')
+            make()
+            mkdirp(prefix.lib)
+            make('install')
diff --git a/var/spack/repos/builtin/packages/grib-api/package.py b/var/spack/repos/builtin/packages/grib-api/package.py
new file mode 100644
index 0000000000..8b81e14a27
--- /dev/null
+++ b/var/spack/repos/builtin/packages/grib-api/package.py
@@ -0,0 +1,80 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class GribApi(Package):
+    """The ECMWF GRIB API is an application program interface accessible from
+       C, FORTRAN and Python programs developed for encoding and decoding WMO
+       FM-92 GRIB edition 1 and edition 2 messages."""
+
+    homepage = "https://software.ecmwf.int/wiki/display/GRIB/Home"
+    url      = "https://software.ecmwf.int/wiki/download/attachments/3473437/grib_api-1.17.0-Source.tar.gz"
+
+    version('1.17.0', 'bca7114d2c3100501a08190a146818d2')
+    version('1.16.0', '8c7fdee03344e4379d400ae20976a460')
+
+    variant('netcdf', default=False, description='Enable netcdf encoding/decoding using netcdf library')
+    variant('jpeg', default=True, description='Enable jpeg 2000 for grib 2 decoding/encoding')
+    variant('png', default=False, description='Enable png for decoding/encoding')
+
+    depends_on('cmake', type='build')
+    depends_on('libpng', when='+png')
+    depends_on('netcdf', when='+netcdf')
+    depends_on('jasper', when='+jpeg')
+
+    def install(self, spec, prefix):
+        options = []
+        options.extend(std_cmake_args)
+        options.append('-DBUILD_SHARED_LIBS=BOTH')
+
+        # We will add python support later.
+        options.append('-DENABLE_PYTHON=OFF')
+
+        # Disable FORTRAN interface if we don't have it.
+        if (self.compiler.f77 is None) or (self.compiler.fc is None):
+            options.append('-DENABLE_FORTRAN=OFF')
+
+        if '+netcdf' in spec:
+            options.append('-DENABLE_NETCDF=ON')
+            options.append('-DNETCDF_PATH=%s' % spec['netcdf'].prefix)
+        else:
+            options.append('-DENABLE_NETCDF=OFF')
+
+        if '+jpeg' in spec:
+            options.append('-DENABLE_JPG=ON')
+            options.append('-DJASPER_PATH=%s' % spec['jasper'].prefix)
+        else:
+            options.append('-DENABLE_JPG=OFF')
+
+        if '+png' in spec:
+            options.append('-DENABLE_PNG=ON')
+        else:
+            options.append('-DENABLE_PNG=OFF')
+
+        with working_dir('spack-build', create=True):
+            cmake('..', *options)
+            make()
+            make('install')
diff --git a/var/spack/repos/builtin/packages/h5hut/package.py b/var/spack/repos/builtin/packages/h5hut/package.py
new file mode 100644
index 0000000000..1501384493
--- /dev/null
+++ b/var/spack/repos/builtin/packages/h5hut/package.py
@@ -0,0 +1,70 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+
+from spack import *
+
+
+class H5hut(Package):
+    """H5hut (HDF5 Utility Toolkit)
+    High-Performance I/O Library for Particle-based Simulations
+    """
+
+    homepage = "https://amas.psi.ch/H5hut/"
+    url      = "https://amas.psi.ch/H5hut/raw-attachment/wiki/DownloadSources/H5hut-1.99.13.tar.gz"
+
+    version("1.99.13", "2a07a449afe50534de006ac6954a421a")
+
+    variant("fortran", default=True, description="Enable Fortran support")
+    variant("mpi", default=False, description="Enable MPI support")
+
+    depends_on("autoconf @2.60:", type="build")
+    depends_on("automake", type="build")
+    depends_on("hdf5 +mpi", when="+mpi")
+    depends_on("hdf5 @1.8:")
+    # h5hut +mpi uses the obsolete function H5Pset_fapl_mpiposix:
+    depends_on("hdf5 @:1.8.12", when="+mpi")
+    depends_on("libtool", type="build")
+    depends_on("mpi", when="+mpi")
+
+    def install(self, spec, prefix):
+        autogen = Executable("./autogen.sh")
+        autogen()
+        configopts = ["--prefix={0}".format(prefix)]
+        if "+fortran" in spec:
+            if not self.compiler.fc:
+                raise RuntimeError(
+                    "Cannot build Fortran variant without a Fortran compiler")
+            configopts.append("--enable-fortran")
+        if "+mpi" in spec:
+            configopts.extend([
+                "--enable-parallel",
+                "CC=%s" % spec["mpi"].mpicc,
+                "CXX=%s" % spec["mpi"].mpicxx])
+            if "+fortran" in spec:
+                configopts.append("FC=%s" % spec["mpi"].mpifc)
+        configure(*configopts)
+
+        make()
+        make("install")
diff --git a/var/spack/repos/builtin/packages/hadoop/package.py b/var/spack/repos/builtin/packages/hadoop/package.py
new file mode 100644
index 0000000000..fdcac10335
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hadoop/package.py
@@ -0,0 +1,53 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Alfredo Gimenez, gimenez1@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+
+from spack import *
+
+
+class Hadoop(Package):
+    """The Apache Hadoop software library is a framework that
+    allows for the distributed processing of large data sets
+    across clusters of computers using simple programming models.
+    """
+
+    homepage = "http://hadoop.apache.org/"
+    url      = "http://mirrors.ocf.berkeley.edu/apache/hadoop/common/hadoop-2.6.4/hadoop-2.6.4.tar.gz"
+
+    version('2.6.4', '37019f13d7dcd819727be158440b9442')
+
+    depends_on('jdk', type='run')
+
+    def install(self, spec, prefix):
+
+        def install_dir(dirname):
+            install_tree(dirname, join_path(prefix, dirname))
+
+        install_dir('bin')
+        install_dir('etc')
+        install_dir('include')
+        install_dir('lib')
+        install_dir('libexec')
+        install_dir('sbin')
+        install_dir('share')
diff --git a/var/spack/repos/builtin/packages/harfbuzz/package.py b/var/spack/repos/builtin/packages/harfbuzz/package.py
index f8d73d651b..7c98c2a96a 100644
--- a/var/spack/repos/builtin/packages/harfbuzz/package.py
+++ b/var/spack/repos/builtin/packages/harfbuzz/package.py
@@ -32,8 +32,9 @@ class Harfbuzz(Package):
 
     version('0.9.37', 'bfe733250e34629a188d82e3b971bc1e')
 
+    depends_on("pkg-config", type="build")
     depends_on("glib")
-    depends_on("icu")
+    depends_on("icu4c")
     depends_on("freetype")
     depends_on("cairo")
     depends_on("zlib")
diff --git a/var/spack/repos/builtin/packages/hdf/package.py b/var/spack/repos/builtin/packages/hdf/package.py
index aafb345be6..9a44184256 100644
--- a/var/spack/repos/builtin/packages/hdf/package.py
+++ b/var/spack/repos/builtin/packages/hdf/package.py
@@ -38,13 +38,12 @@ class Hdf(Package):
 
     variant('szip', default=False, description="Enable szip support")
 
-    depends_on("jpeg")
-    depends_on("szip", when='+szip')
-    depends_on("zlib")
+    depends_on('jpeg')
+    depends_on('szip', when='+szip')
+    depends_on('zlib')
 
-    def url_for_version(self, version):
-        return "https://www.hdfgroup.org/ftp/HDF/releases/HDF" + str(
-            version) + "/src/hdf-" + str(version) + ".tar.gz"
+    depends_on('bison', type='build')
+    depends_on('flex',  type='build')
 
     def install(self, spec, prefix):
         config_args = [
@@ -66,4 +65,5 @@ class Hdf(Package):
         configure(*config_args)
 
         make()
-        make("install")
+        make('check')
+        make('install')
diff --git a/var/spack/repos/builtin/packages/hdf5/package.py b/var/spack/repos/builtin/packages/hdf5/package.py
index 601e3278e5..b5a7a65083 100644
--- a/var/spack/repos/builtin/packages/hdf5/package.py
+++ b/var/spack/repos/builtin/packages/hdf5/package.py
@@ -43,6 +43,7 @@ class Hdf5(AutotoolsPackage):
     version('1.8.16', 'b8ed9a36ae142317f88b0c7ef4b9c618')
     version('1.8.15', '03cccb5b33dbe975fdcd8ae9dc021f24')
     version('1.8.13', 'c03426e9e77d7766944654280b467289')
+    version('1.8.12', 'd804802feb99b87fc668a90e6fa34411')
 
     variant('debug', default=False,
             description='Builds a debug version of the library')
@@ -52,7 +53,7 @@ class Hdf5(AutotoolsPackage):
     variant('cxx', default=True, description='Enable C++ support')
     variant('fortran', default=True, description='Enable Fortran support')
 
-    variant('mpi', default=False, description='Enable MPI support')
+    variant('mpi', default=True, description='Enable MPI support')
     variant('szip', default=False, description='Enable szip support')
     variant('threadsafe', default=False,
             description='Enable thread-safe capabilities')
diff --git a/var/spack/repos/builtin/packages/hepmc/package.py b/var/spack/repos/builtin/packages/hepmc/package.py
new file mode 100644
index 0000000000..ab80dcf6ba
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hepmc/package.py
@@ -0,0 +1,55 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+
+from spack import *
+
+
+class Hepmc(Package):
+    """The HepMC package is an object oriented, C++ event record for
+       High Energy Physics Monte Carlo generators and simulation."""
+
+    homepage = "http://hepmc.web.cern.ch/hepmc/"
+    url      = "http://hepmc.web.cern.ch/hepmc/releases/hepmc2.06.09.tgz"
+
+    version('2.06.09', 'c47627ced4255b40e731b8666848b087')
+    version('2.06.08', 'a2e889114cafc4f60742029d69abd907')
+    version('2.06.07', '11d7035dccb0650b331f51520c6172e7')
+    version('2.06.06', '102e5503537a3ecd6ea6f466aa5bc4ae')
+    version('2.06.05', '2a4a2a945adf26474b8bdccf4f881d9c')
+
+    depends_on("cmake", type='build')
+
+    def install(self, spec, prefix):
+        build_directory = join_path(self.stage.path, 'spack-build')
+        source_directory = self.stage.source_path
+        options = [source_directory]
+        options.append('-Dmomentum:STRING=GEV')
+        options.append('-Dlength:STRING=MM')
+        options.extend(std_cmake_args)
+
+        with working_dir(build_directory, create=True):
+            cmake(*options)
+            make()
+            make('install')
diff --git a/var/spack/repos/builtin/packages/heppdt/package.py b/var/spack/repos/builtin/packages/heppdt/package.py
new file mode 100644
index 0000000000..54c846ae33
--- /dev/null
+++ b/var/spack/repos/builtin/packages/heppdt/package.py
@@ -0,0 +1,48 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+
+from spack import *
+
+
+class Heppdt(Package):
+    """The HepPID library contains translation methods for particle ID's
+    to and from various Monte Carlo generators and the PDG standard
+    numbering scheme. We realize that the generators adhere closely
+    to the standard, but there are occasional differences."""
+    homepage = "http://lcgapp.cern.ch/project/simu/HepPDT/"
+    url      = "http://lcgapp.cern.ch/project/simu/HepPDT/download/HepPDT-2.06.01.tar.gz"
+
+    version('3.04.01', 'a8e93c7603d844266b62d6f189f0ac7e')
+    version('3.04.00', '2d2cd7552d3e9539148febacc6287db2')
+    version('3.03.02', '0b85f1809bb8b0b28a46f23c718b2773')
+    version('3.03.01', 'd411f3bfdf9c4350d802241ba2629cc2')
+    version('3.03.00', 'cd84d0a0454be982dcd8c285e060a7b3')
+    version('2.06.01', '5688b4bdbd84b48ed5dd2545a3dc33c0')
+
+    def install(self, spec, prefix):
+        configure('--prefix=%s' % prefix)
+
+        make()
+        make("install")
diff --git a/var/spack/repos/builtin/packages/hpctoolkit-externals/package.py b/var/spack/repos/builtin/packages/hpctoolkit-externals/package.py
new file mode 100644
index 0000000000..64b5d17851
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hpctoolkit-externals/package.py
@@ -0,0 +1,39 @@
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class HpctoolkitExternals(Package):
+    """HPCToolkit performance analysis tool has many prerequisites and
+    HpctoolkitExternals package provides all these prerequisites."""
+
+    homepage = "http://hpctoolkit.org"
+
+    # Note: No precise release tags/branches provided
+    version('5.4',
+            git='https://github.com/HPCToolkit/hpctoolkit-externals.git',
+            commit='3d2953623357bb06e9a4b51eca90a4b039c2710e')
+
+    parallel = False
+
+    def install(self, spec, prefix):
+
+        options = ['CC=%s' % self.compiler.cc,
+                   'CXX=%s' % self.compiler.cxx]
+
+        with working_dir('spack-build', create=True):
+            configure = Executable('../configure')
+            configure('--prefix=%s' % prefix, *options)
+            make('install')
diff --git a/var/spack/repos/builtin/packages/hpctoolkit/package.py b/var/spack/repos/builtin/packages/hpctoolkit/package.py
new file mode 100644
index 0000000000..aac22ef829
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hpctoolkit/package.py
@@ -0,0 +1,55 @@
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Hpctoolkit(Package):
+    """HPCToolkit is an integrated suite of tools for measurement and analysis
+    of program performance on computers ranging from multicore desktop systems
+    to the nation's largest supercomputers. By using statistical sampling of
+    timers and hardware performance counters, HPCToolkit collects accurate
+    measurements of a program's work, resource consumption, and inefficiency
+    and attributes them to the full calling context in which they occur."""
+
+    homepage = "http://hpctoolkit.org"
+
+    # Note: No precise release tags/branches provided
+    version('5.4', git='https://github.com/HPCToolkit/hpctoolkit.git',
+            commit='d9ca2112762e5a06ea31b5295d793e4a83272d19')
+
+    variant('mpi', default=True, description='Enable MPI supoort')
+    variant('papi', default=True, description='Enable PAPI counter support')
+
+    depends_on('hpctoolkit-externals')
+    depends_on('papi', when='+papi')
+    depends_on('mpi', when='+mpi')
+
+    def install(self, spec, prefix):
+
+        options = ['CC=%s' % self.compiler.cc,
+                   'CXX=%s' % self.compiler.cxx,
+                   '--with-externals=%s' % spec['hpctoolkit-externals'].prefix]
+
+        if '+mpi' in spec:
+            options.extend(['MPICXX=%s' % spec['mpi'].mpicxx])
+
+        if '+papi' in spec:
+            options.extend(['--with-papi=%s' % spec['papi'].prefix])
+
+        # TODO: BG-Q configure option
+        with working_dir('spack-build', create=True):
+            configure = Executable('../configure')
+            configure('--prefix=%s' % prefix, *options)
+            make('install')
diff --git a/var/spack/repos/builtin/packages/hpl/package.py b/var/spack/repos/builtin/packages/hpl/package.py
index efd5c8bb1d..fa0013de17 100644
--- a/var/spack/repos/builtin/packages/hpl/package.py
+++ b/var/spack/repos/builtin/packages/hpl/package.py
@@ -78,7 +78,7 @@ class Hpl(Package):
             'MPlib        = -L{0}'.format(spec['mpi'].prefix.lib),
             # Linear Algebra library (BLAS or VSIPL)
             'LAinc        = {0}'.format(spec['blas'].prefix.include),
-            'LAlib        = {0}'.format(spec['blas'].blas_shared_lib),
+            'LAlib        = {0}'.format(spec['blas'].blas_libs.joined()),
             # F77 / C interface
             'F2CDEFS      = -DAdd_ -DF77_INTEGER=int -DStringSunStyle',
             # HPL includes / libraries / specifics
diff --git a/var/spack/repos/builtin/packages/hwloc/package.py b/var/spack/repos/builtin/packages/hwloc/package.py
index c163628840..111c424b22 100644
--- a/var/spack/repos/builtin/packages/hwloc/package.py
+++ b/var/spack/repos/builtin/packages/hwloc/package.py
@@ -42,6 +42,7 @@ class Hwloc(Package):
     list_url = "http://www.open-mpi.org/software/hwloc/"
     list_depth = 3
 
+    version('1.11.4', 'b6f23eb59074fd09fdd84905d50b103d')
     version('1.11.3', 'c1d36a9de6028eac1d18ea4782ef958f')
     version('1.11.2', 'e4ca55c2a5c5656da4a4e37c8fc51b23')
     version('1.11.1', 'feb4e416a1b25963ed565d8b42252fdc')
diff --git a/var/spack/repos/builtin/packages/hypre/package.py b/var/spack/repos/builtin/packages/hypre/package.py
index fdc236dcf4..f22303a864 100644
--- a/var/spack/repos/builtin/packages/hypre/package.py
+++ b/var/spack/repos/builtin/packages/hypre/package.py
@@ -54,19 +54,15 @@ class Hypre(Package):
         os.environ['CXX'] = spec['mpi'].mpicxx
         os.environ['F77'] = spec['mpi'].mpif77
 
-        # Since +shared does not build on macOS and also Atlas does not have
-        # a single static lib to build against, link against shared libs with
-        # a hope that --whole-archive linker option (or alike) was used
-        # to command the linker to include whole static libs' content into the
-        # shared lib
         # Note: --with-(lapack|blas)_libs= needs space separated list of names
+        lapack = spec['lapack'].lapack_libs
+        blas = spec['blas'].blas_libs
+
         configure_args = [
             '--prefix=%s' % prefix,
-            '--with-lapack-libs=%s' % to_lib_name(
-                spec['lapack'].lapack_shared_lib),
+            '--with-lapack-libs=%s' % ' '.join(lapack.names),
             '--with-lapack-lib-dirs=%s' % spec['lapack'].prefix.lib,
-            '--with-blas-libs=%s' % to_lib_name(
-                spec['blas'].blas_shared_lib),
+            '--with-blas-libs=%s' % ' '.join(blas.names),
             '--with-blas-lib-dirs=%s' % spec['blas'].prefix.lib
         ]
 
diff --git a/var/spack/repos/builtin/packages/icu4c/package.py b/var/spack/repos/builtin/packages/icu4c/package.py
index 2bcf86cd13..848ebfdeac 100644
--- a/var/spack/repos/builtin/packages/icu4c/package.py
+++ b/var/spack/repos/builtin/packages/icu4c/package.py
@@ -27,18 +27,23 @@ from spack import *
 
 class Icu4c(Package):
     """ICU is a mature, widely used set of C/C++ and Java libraries providing
-       Unicode and Globalization support for software applications.
-
-    """
+    Unicode and Globalization support for software applications. ICU4C is the
+    C/C++ interface."""
 
     homepage = "http://site.icu-project.org/"
-    url      = "http://downloads.sourceforge.net/project/icu/ICU4C/54.1/icu4c-54_1-src.tgz"
+    url      = "http://download.icu-project.org/files/icu4c/57.1/icu4c-57_1-src.tgz"
+
+    version('57.1', '976734806026a4ef8bdd17937c8898b9')
 
-    version('54_1', 'e844caed8f2ca24c088505b0d6271bc0')
+    def url_for_version(self, version):
+        base_url = "http://download.icu-project.org/files/icu4c"
+        return "{0}/{1}/icu4c-{2}-src.tgz".format(
+            base_url, version, version.underscored)
 
     def install(self, spec, prefix):
-        cd("source")
-        configure("--prefix=%s" % prefix)
+        with working_dir('source'):
+            configure('--prefix={0}'.format(prefix))
 
-        make()
-        make("install")
+            make()
+            make('check')
+            make('install')
diff --git a/var/spack/repos/builtin/packages/intel-parallel-studio/package.py b/var/spack/repos/builtin/packages/intel-parallel-studio/package.py
index 65db3351a1..efa30f9305 100644
--- a/var/spack/repos/builtin/packages/intel-parallel-studio/package.py
+++ b/var/spack/repos/builtin/packages/intel-parallel-studio/package.py
@@ -11,7 +11,7 @@ class IntelParallelStudio(IntelInstaller):
 
     Note: You will have to add the download file to a
     mirror so that Spack can find it. For instructions on how to set up a
-    mirror, see http://software.llnl.gov/spack/mirrors.html"""
+    mirror, see http://spack.readthedocs.io/en/latest/mirrors.html"""
 
     homepage = "https://software.intel.com/en-us/intel-parallel-studio-xe"
 
@@ -45,6 +45,10 @@ class IntelParallelStudio(IntelInstaller):
     variant('tools', default=True, description="Install the Intel Advisor, "
             "VTune Amplifier, and Inspector tools")
 
+    variant('shared', default=True, description='Builds shared library')
+    variant('ilp64', default=False, description='64 bit integers')
+    variant('openmp', default=False, description='OpenMP multithreading layer')
+
     provides('mpi', when='@cluster:+mpi')
     provides('mkl', when='+mkl')
     provides('daal', when='+daal')
@@ -55,6 +59,31 @@ class IntelParallelStudio(IntelInstaller):
     provides('lapack', when='+mkl')
     # TODO: MKL also provides implementation of Scalapack.
 
+    @property
+    def blas_libs(self):
+        shared = True if '+shared' in self.spec else False
+        suffix = dso_suffix if '+shared' in self.spec else 'a'
+        mkl_integer = ['libmkl_intel_ilp64'] if '+ilp64' in self.spec else ['libmkl_intel_lp64']  # NOQA: ignore=E501
+        mkl_threading = ['libmkl_sequential']
+        if '+openmp' in self.spec:
+            mkl_threading = ['libmkl_intel_thread', 'libiomp5'] if '%intel' in self.spec else ['libmkl_gnu_thread']  # NOQA: ignore=E501
+        # TODO: TBB threading: ['libmkl_tbb_thread', 'libtbb', 'libstdc++']
+        mkl_libs = find_libraries(
+            mkl_integer + ['libmkl_core'] + mkl_threading,
+            root=join_path(self.prefix.lib, 'intel64'),
+            shared=shared
+        )
+        system_libs = [
+            'libpthread.{0}'.format(suffix),
+            'libm.{0}'.format(suffix),
+            'libdl.{0}'.format(suffix)
+        ]
+        return mkl_libs + system_libs
+
+    @property
+    def lapack_libs(self):
+        return self.blas_libs
+
     def check_variants(self, spec):
         error_message = '\t{variant} can not be turned off if "+all" is set'
 
@@ -171,24 +200,6 @@ class IntelParallelStudio(IntelInstaller):
         os.symlink(os.path.join(self.prefix.man, "common", "man1"),
                    os.path.join(self.prefix.man, "man1"))
 
-    def setup_dependent_package(self, module, dspec):
-        # For now use Single Dynamic Library:
-        # To set the threading layer at run time, use the
-        # mkl_set_threading_layer function or set MKL_THREADING_LAYER
-        # variable to one of the following values: INTEL, SEQUENTIAL, PGI.
-        # To set interface layer at run time, use the mkl_set_interface_layer
-        # function or set the MKL_INTERFACE_LAYER variable to LP64 or ILP64.
-
-        # Otherwise one would need to specify several libraries
-        # (e.g. mkl_intel_lp64;mkl_sequential;mkl_core), which reflect
-        # different interface and threading layers.
-
-        name = 'libmkl_rt.%s' % dso_suffix
-        libdir = find_library_path(name, self.prefix.lib64, self.prefix.lib)
-
-        self.spec.blas_shared_lib   = join_path(libdir, name)
-        self.spec.lapack_shared_lib = self.spec.blas_shared_lib
-
     def setup_environment(self, spack_env, run_env):
         # TODO: Determine variables needed for the professional edition.
 
diff --git a/var/spack/repos/builtin/packages/intel/package.py b/var/spack/repos/builtin/packages/intel/package.py
index 26134a12ae..5b9c26df0e 100644
--- a/var/spack/repos/builtin/packages/intel/package.py
+++ b/var/spack/repos/builtin/packages/intel/package.py
@@ -77,7 +77,7 @@ class Intel(IntelInstaller):
 
     Note: You will have to add the download file to a
     mirror so that Spack can find it. For instructions on how to set up a
-    mirror, see http://software.llnl.gov/spack/mirrors.html"""
+    mirror, see http://spack.readthedocs.io/en/latest/mirrors.html"""
 
     homepage = "https://software.intel.com/en-us/intel-parallel-studio-xe"
 
diff --git a/var/spack/repos/builtin/packages/ipopt/package.py b/var/spack/repos/builtin/packages/ipopt/package.py
index d5981e9975..bd1e5f36ef 100644
--- a/var/spack/repos/builtin/packages/ipopt/package.py
+++ b/var/spack/repos/builtin/packages/ipopt/package.py
@@ -53,9 +53,8 @@ class Ipopt(Package):
         mumps_flags = "-ldmumps -lmumps_common -lpord -lmpiseq"
         mumps_libcmd = "-L%s " % mumps_dir.lib + mumps_flags
 
-        # By convention, spack links blas & lapack libs to libblas & liblapack
-        blas_lib = "-L%s" % blas_dir.lib + " -lblas"
-        lapack_lib = "-L%s" % lapack_dir.lib + " -llapack"
+        blas_lib = spec['blas'].blas_libs.ld_flags
+        lapack_lib = spec['lapack'].lapack_libs.ld_flags
 
         configure_args = [
             "--prefix=%s" % prefix,
diff --git a/var/spack/repos/builtin/packages/ipp/package.py b/var/spack/repos/builtin/packages/ipp/package.py
index 2bd931d5bd..93c5284695 100644
--- a/var/spack/repos/builtin/packages/ipp/package.py
+++ b/var/spack/repos/builtin/packages/ipp/package.py
@@ -9,7 +9,7 @@ class Ipp(IntelInstaller):
 
     Note: You will have to add the download file to a
     mirror so that Spack can find it. For instructions on how to set up a
-    mirror, see http://software.llnl.gov/spack/mirrors.html"""
+    mirror, see http://spack.readthedocs.io/en/latest/mirrors.html"""
 
     homepage = "https://software.intel.com/en-us/intel-ipp"
 
diff --git a/var/spack/repos/builtin/packages/itstool/package.py b/var/spack/repos/builtin/packages/itstool/package.py
new file mode 100644
index 0000000000..b8b2b4459f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/itstool/package.py
@@ -0,0 +1,44 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Itstool(Package):
+    """ITS Tool allows you to translate your XML documents with PO files, using
+       rules from the W3C Internationalization Tag Set (ITS) to determine what
+       to translate and how to separate it into PO file messages."""
+
+    homepage = "http://itstool.org/"
+    url      = "http://files.itstool.org/itstool/itstool-2.0.2.tar.bz2"
+
+    version('2.0.2', 'd472d877a7bc49899a73d442085b2f93')
+    version('2.0.1', '40935cfb08228488bd45575e5f001a34')
+    version('2.0.0', 'd8c702c3e8961db83d04182c2aa4730b')
+    version('1.2.0', 'c0925f6869e33af8e7fe56848c129152')
+
+    def install(self, spec, prefix):
+        configure("--prefix=%s" % prefix)
+        make()
+        make('install')
diff --git a/var/spack/repos/builtin/packages/jdk/package.py b/var/spack/repos/builtin/packages/jdk/package.py
index 63bf6514cb..bab0920434 100644
--- a/var/spack/repos/builtin/packages/jdk/package.py
+++ b/var/spack/repos/builtin/packages/jdk/package.py
@@ -68,3 +68,9 @@ class Jdk(Package):
 
     def install(self, spec, prefix):
         distutils.dir_util.copy_tree(".", prefix)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.set('JAVA_HOME', self.spec.prefix)
+
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        spack_env.set('JAVA_HOME', self.spec.prefix)
diff --git a/var/spack/repos/builtin/packages/jemalloc/package.py b/var/spack/repos/builtin/packages/jemalloc/package.py
index f5a983b7a9..e13d4292f8 100644
--- a/var/spack/repos/builtin/packages/jemalloc/package.py
+++ b/var/spack/repos/builtin/packages/jemalloc/package.py
@@ -31,6 +31,8 @@ class Jemalloc(Package):
     homepage = "http://www.canonware.com/jemalloc/"
     url      = "https://github.com/jemalloc/jemalloc/releases/download/4.0.4/jemalloc-4.0.4.tar.bz2"
 
+    version('4.2.1', '094b0a7b8c77c464d0dc8f0643fd3901')
+    version('4.2.0', 'e6b5d5a1ea93a04207528d274efdd144')
     version('4.1.0', 'c4e53c947905a533d5899e5cc3da1f94')
     version('4.0.4', '687c5cc53b9a7ab711ccd680351ff988')
 
diff --git a/var/spack/repos/builtin/packages/julia/package.py b/var/spack/repos/builtin/packages/julia/package.py
index 6ccaa11c90..033e27fb64 100644
--- a/var/spack/repos/builtin/packages/julia/package.py
+++ b/var/spack/repos/builtin/packages/julia/package.py
@@ -37,9 +37,11 @@ class Julia(Package):
             git='https://github.com/JuliaLang/julia.git', branch='master')
     version('release-0.5',
             git='https://github.com/JuliaLang/julia.git', branch='release-0.5')
+    version('0.5.0', 'b61385671ba74767ab452363c43131fb', preferred=True)
     version('release-0.4',
             git='https://github.com/JuliaLang/julia.git', branch='release-0.4')
-    version('0.4.6', 'd88db18c579049c23ab8ef427ccedf5d', preferred=True)
+    version('0.4.7', '75a7a7dd882b7840829d8f165e9b9078')
+    version('0.4.6', 'd88db18c579049c23ab8ef427ccedf5d')
     version('0.4.5', '69141ff5aa6cee7c0ec8c85a34aa49a6')
     version('0.4.3', '8a4a59fd335b05090dd1ebefbbe5aaac')
 
@@ -68,7 +70,8 @@ class Julia(Package):
     depends_on("binutils", when='+binutils')
     depends_on("cmake @2.8:")
     depends_on("curl")
-    depends_on("git")           # I think Julia @0.5: doesn't use git any more
+    depends_on("git", when='@:0.4')
+    depends_on("git", when='@release-0.4')
     depends_on("openssl")
     depends_on("python @2.7:2.999")
 
@@ -162,7 +165,7 @@ class Julia(Package):
         # Configure Julia
         with open(join_path(prefix, "etc", "julia", "juliarc.jl"),
                   "a") as juliarc:
-            if "@master" in spec or "@release-0.5" in spec:
+            if "@master" in spec or "@release-0.5" in spec or "@0.5:" in spec:
                 # This is required for versions @0.5:
                 juliarc.write(
                     '# Point package manager to working certificates\n')
diff --git a/var/spack/repos/builtin/packages/libemos/package.py b/var/spack/repos/builtin/packages/libemos/package.py
new file mode 100644
index 0000000000..0275c7ede9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libemos/package.py
@@ -0,0 +1,52 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Libemos(Package):
+    """The Interpolation library (EMOSLIB) includes Interpolation software and
+       BUFR & CREX encoding/decoding routines."""
+
+    homepage = "https://software.ecmwf.int/wiki/display/EMOS/Emoslib"
+    url      = "https://software.ecmwf.int/wiki/download/attachments/3473472/libemos-4.4.2-Source.tar.gz"
+
+    version('4.4.2', 'f15a9aff0f40861f3f046c9088197376')
+
+    depends_on('cmake', type='build')
+    depends_on('grib-api')
+
+    def install(self, spec, prefix):
+        options = []
+        options.extend(std_cmake_args)
+
+        options.append('-DGRIB_API_PATH=%s' % spec['grib_api'].prefix)
+
+        # To support long pathnames that spack generates
+        options.append('-DCMAKE_Fortran_FLAGS=-ffree-line-length-none')
+
+        with working_dir('spack-build', create=True):
+            cmake('..', *options)
+            make()
+            make('install')
diff --git a/var/spack/repos/builtin/packages/libgd/package.py b/var/spack/repos/builtin/packages/libgd/package.py
index acfdebb972..6329adf8f3 100644
--- a/var/spack/repos/builtin/packages/libgd/package.py
+++ b/var/spack/repos/builtin/packages/libgd/package.py
@@ -40,18 +40,33 @@ class Libgd(Package):
     homepage = "https://github.com/libgd/libgd"
     url      = "https://github.com/libgd/libgd/archive/gd-2.1.1.tar.gz"
 
+    version('2.2.3', 'a67bd15fa33d4aac0a1c7904aed19f49')
     version('2.1.1', 'e91a1a99903e460e7ba00a794e72cc1e')
 
+    # Build dependencies
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool', type='build')
+    depends_on('m4', type='build')
+    depends_on('gettext', type='build')
+    depends_on('pkg-config', type='build')
+
     depends_on('libpng')
-    depends_on('cmake', type='build')
+    depends_on('libtiff')
+    depends_on('fontconfig')
 
     def install(self, spec, prefix):
-
-        with working_dir('spack-build', create=True):
-            cmake('..',
-                  '-DENABLE_JPEG:BOOL=ON',
-                  '-DENABLE_PNG:BOOL=ON',
-                  '-DENABLE_TIFF:BOOL=ON',
-                  *std_cmake_args)
-            make()
-            make("install")
+        autoreconf("--install", "--force",
+                   "-I", "m4",
+                   "-I", join_path(spec['gettext'].prefix,
+                                   "share", "aclocal"),
+                   "-I", join_path(spec['pkg-config'].prefix,
+                                   "share", "aclocal"),
+                   "-I", join_path(spec['automake'].prefix,
+                                   "share", "aclocal"),
+                   "-I", join_path(spec['libtool'].prefix,
+                                   "share", "aclocal")
+                   )
+        configure('--prefix={0}'.format(prefix))
+        make()
+        make("install")
diff --git a/var/spack/repos/builtin/packages/libint/package.py b/var/spack/repos/builtin/packages/libint/package.py
new file mode 100644
index 0000000000..2ad5e93191
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libint/package.py
@@ -0,0 +1,104 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Libint(Package):
+    """Libint is a high-performance library for computing
+    Gaussian integrals in quantum mechanics."""
+
+    homepage = "https://github.com/evaleev/libint"
+    url      = "https://github.com/evaleev/libint/archive/v2.1.0.tar.gz"
+
+    version('2.1.0', 'd0dcb985fe32ddebc78fe571ce37e2d6')
+    version('1.1.6', '990f67b55f49ecc18f32c58da9240684')
+    version('1.1.5', '379b7d0718ff398715d6898807adf628')
+
+    # Build dependencies
+    depends_on('autoconf@2.52:', type='build')
+    depends_on('automake',       type='build')
+    depends_on('libtool',        type='build')
+
+    # Libint 2 dependencies
+    depends_on('boost', when='@2:')
+    depends_on('gmp',   when='@2:')
+
+    def url_for_version(self, version):
+        base_url = "https://github.com/evaleev/libint/archive"
+        if version == Version('1.0.0'):
+            return "{0}/LIBINT_1_00.tar.gz".format(base_url)
+        elif version < Version('2.1.0'):
+            return "{0}/release-{1}.tar.gz".format(base_url, version.dashed)
+        else:
+            return "{0}/v{1}.tar.gz".format(base_url, version)
+
+    def install(self, spec, prefix):
+        # Generate configure
+        libtoolize()
+        aclocal('-I', 'lib/autoconf')
+        autoconf()
+
+        config_args = [
+            '--prefix={0}'.format(prefix),
+            '--enable-shared'
+        ]
+
+        # Optimizations for the Intel compiler, suggested by CP2K
+        optflags = '-O2'
+        if self.compiler.name == 'intel':
+            optflags += ' -xAVX -axCORE-AVX2 -ipo'
+            if which('xiar'):
+                env['AR'] = 'xiar'
+
+        env['CFLAGS']   = optflags
+        env['CXXFLAGS'] = optflags
+
+        # Optimization flag names have changed in libint 2
+        if self.version < Version('2.0.0'):
+            config_args.extend([
+                '--with-cc-optflags={0}'.format(optflags),
+                '--with-cxx-optflags={0}'.format(optflags)
+            ])
+        else:
+            config_args.extend([
+                '--with-cxx-optflags={0}'.format(optflags),
+                '--with-cxxgen-optflags={0}'.format(optflags)
+            ])
+
+        # Options required by CP2K, removed in libint 2
+        if self.version < Version('2.0.0'):
+            config_args.extend([
+                '--with-libint-max-am=5',
+                '--with-libderiv-max-am1=4'
+            ])
+
+        configure(*config_args)
+        make()
+
+        # Testing suite was added in libint 2
+        if self.version >= Version('2.0.0'):
+            make('check')
+
+        make('install')
diff --git a/var/spack/repos/builtin/packages/libmesh/package.py b/var/spack/repos/builtin/packages/libmesh/package.py
new file mode 100644
index 0000000000..ea81f5da73
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libmesh/package.py
@@ -0,0 +1,42 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Libmesh(Package):
+    """The libMesh library provides a framework for the numerical simulation of
+       partial differential equations using arbitrary unstructured
+       discretizations on serial and parallel platforms."""
+
+    homepage = "http://libmesh.github.io/"
+    url      = "https://github.com/libMesh/libmesh/releases/download/v1.0.0/libmesh-1.0.0.tar.bz2"
+
+    version('1.0.0', 'cb464fc63ea0b71b1e69fa3f5d4f93a4')
+
+    def install(self, spec, prefix):
+        configure('--prefix={0}'.format(prefix))
+
+        make()
+        make('install')
diff --git a/var/spack/repos/builtin/packages/libpng/package.py b/var/spack/repos/builtin/packages/libpng/package.py
index 1afe4911e6..c3a595d12d 100644
--- a/var/spack/repos/builtin/packages/libpng/package.py
+++ b/var/spack/repos/builtin/packages/libpng/package.py
@@ -30,6 +30,7 @@ class Libpng(Package):
     homepage = "http://www.libpng.org/pub/png/libpng.html"
     url      = "http://download.sourceforge.net/libpng/libpng-1.6.16.tar.gz"
 
+    version('1.6.24', '65213080dd30a9b16193d9b83adc1ee9')
     version('1.6.16', '1a4ad377919ab15b54f6cb6a3ae2622d')
     version('1.6.15', '829a256f3de9307731d4f52dc071916d')
     version('1.6.14', '2101b3de1d5f348925990f9aa8405660')
@@ -37,9 +38,10 @@ class Libpng(Package):
     version('1.4.19', '89bcbc4fc8b31f4a403906cf4f662330')
     version('1.2.56', '9508fc59d10a1ffadd9aae35116c19ee')
 
-    depends_on('zlib')
+    depends_on('zlib@1.0.4:')  # 1.2.5 or later recommended
 
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
         make()
+        make("check")
         make("install")
diff --git a/var/spack/repos/builtin/packages/libquo/package.py b/var/spack/repos/builtin/packages/libquo/package.py
new file mode 100644
index 0000000000..8856913bb2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libquo/package.py
@@ -0,0 +1,68 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+import os
+
+
+class Libquo(Package):
+    """A high-level, easy to use programming interface tailored specifically
+    for MPI/MPI+X codes that may benefit from evolving process binding
+    policies during their execution. QUO allows for arbitrary process binding
+    policies to be enacted and reverted during the execution of an MPI/MPI+X
+    application as different computational phases are entered and exited,
+    respectively."""
+
+    homepage = "https://github.com/losalamos/libquo"
+    url      = "https://github.com/losalamos/libquo/archive/v1.2.9.tar.gz"
+
+    version('1.2.9', 'ca82ab33f13e2b89983f81e7c02e98c2')
+
+    depends_on('mpi')
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool', type='build')
+
+    def install(self, spec, prefix):
+        autoreconf_options = [
+            '--install',
+            '--verbose',
+            '--force',
+            '-I', 'config',
+            '-I', os.path.join(spec['automake'].prefix,
+                               'share', 'aclocal'),
+            '-I', os.path.join(spec['libtool'].prefix,
+                               'share', 'aclocal')
+        ]
+        autoreconf(*autoreconf_options)
+
+        configure_options = [
+            '--prefix={0}'.format(prefix),
+            'CC=%s' % join_path(spec['mpi'].prefix.bin, "mpicc"),
+            'FC=%s' % join_path(spec['mpi'].prefix.bin, "mpif90")
+        ]
+        configure(*configure_options)
+
+        make()
+        make('install')
diff --git a/var/spack/repos/builtin/packages/libuuid/package.py b/var/spack/repos/builtin/packages/libuuid/package.py
index 553f0dddb8..b8f6b1cc3a 100644
--- a/var/spack/repos/builtin/packages/libuuid/package.py
+++ b/var/spack/repos/builtin/packages/libuuid/package.py
@@ -27,7 +27,7 @@ from spack import *
 
 class Libuuid(Package):
     """Portable uuid C library"""
-    # FIXME: add a proper url for your package's homepage here.
+
     homepage = "http://sourceforge.net/projects/libuuid/"
     url      = "http://downloads.sourceforge.net/project/libuuid/libuuid-1.0.3.tar.gz?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Flibuuid%2F&ts=1433881396&use_mirror=iweb"
 
@@ -36,6 +36,5 @@ class Libuuid(Package):
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
 
-        # FIXME: Add logic to build and install here
         make()
         make("install")
diff --git a/var/spack/repos/builtin/packages/libxc/package.py b/var/spack/repos/builtin/packages/libxc/package.py
index 9ea4d1c326..fe82613ce2 100644
--- a/var/spack/repos/builtin/packages/libxc/package.py
+++ b/var/spack/repos/builtin/packages/libxc/package.py
@@ -32,11 +32,27 @@ class Libxc(Package):
     homepage = "http://www.tddft.org/programs/octopus/wiki/index.php/Libxc"
     url      = "http://www.tddft.org/programs/octopus/down.php?file=libxc/libxc-2.2.2.tar.gz"
 
+    version('3.0.0', '8227fa3053f8fc215bd9d7b0d36de03c')
     version('2.2.2', 'd9f90a0d6e36df6c1312b6422280f2ec')
 
     def install(self, spec, prefix):
-        configure('--prefix=%s' % prefix,
+        # Optimizations for the Intel compiler, suggested by CP2K
+        optflags = '-O2'
+        if self.compiler.name == 'intel':
+            optflags += ' -xAVX -axCORE-AVX2 -ipo'
+            if which('xiar'):
+                env['AR'] = 'xiar'
+
+        env['CFLAGS']  = optflags
+        env['FCFLAGS'] = optflags
+
+        configure('--prefix={0}'.format(prefix),
                   '--enable-shared')
 
         make()
-        make("install")
+
+        # libxc provides a testsuite, but many tests fail
+        # http://www.tddft.org/pipermail/libxc/2013-February/000032.html
+        # make('check')
+
+        make('install')
diff --git a/var/spack/repos/builtin/packages/libxstream/package.py b/var/spack/repos/builtin/packages/libxstream/package.py
new file mode 100644
index 0000000000..3201b58620
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libxstream/package.py
@@ -0,0 +1,50 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Libxstream(Package):
+    '''LIBXSTREAM is a library to work with streams, events, and code regions
+    that are able to run asynchronous while preserving the usual stream
+    conditions.'''
+
+    homepage = 'https://github.com/hfp/libxstream'
+    url      = 'https://github.com/hfp/libxstream.git'
+
+    version('0.9.0', git='https://github.com/hfp/libxstream.git')
+
+    def patch(self):
+        kwargs = {'ignore_absent': False, 'backup': True, 'string': True}
+        makefile = FileFilter('Makefile.inc')
+
+        makefile.filter('CC =',  'CC ?=',  **kwargs)
+        makefile.filter('CXX =', 'CXX ?=', **kwargs)
+        makefile.filter('FC =',  'FC ?=',  **kwargs)
+
+    def install(self, spec, prefix):
+        make()
+        install_tree('lib', prefix.lib)
+        install_tree('include', prefix.include)
+        install_tree('documentation', prefix.share + '/libxstream/doc/')
diff --git a/var/spack/repos/builtin/packages/llvm/package.py b/var/spack/repos/builtin/packages/llvm/package.py
index 61ea8daac4..06572ea312 100644
--- a/var/spack/repos/builtin/packages/llvm/package.py
+++ b/var/spack/repos/builtin/packages/llvm/package.py
@@ -22,9 +22,10 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-from spack import *
 import os
 
+from spack import *
+
 
 class Llvm(Package):
     """The LLVM Project is a collection of modular and reusable compiler and
@@ -32,11 +33,13 @@ class Llvm(Package):
        with traditional virtual machines, though it does provide helpful
        libraries that can be used to build them. The name "LLVM" itself
        is not an acronym; it is the full name of the project.
-
     """
+
     homepage = 'http://llvm.org/'
     url = 'http://llvm.org/releases/3.7.1/llvm-3.7.1.src.tar.xz'
 
+    family = 'compiler'  # Used by lmod
+
     # currently required by mesa package
     version('3.0', 'a8e5f5f1c1adebae7b4a654c376a6005',
             url='http://llvm.org/releases/3.0/llvm-3.0.tar.gz')
@@ -111,7 +114,7 @@ class Llvm(Package):
             'destination': 'projects',
             'placement': 'libcxxabi',
         },
-        'clang': {
+        'cfe': {
             'url':  base_url % {'pkg': 'cfe'},
             'destination': 'tools',
             'placement': 'clang',
@@ -141,63 +144,93 @@ class Llvm(Package):
         {
             'version': 'trunk',
             'repo': 'http://llvm.org/svn/llvm-project/llvm/trunk',
-                    'resources': {
-                        'compiler-rt': 'http://llvm.org/svn/llvm-project/compiler-rt/trunk',
-                        'openmp': 'http://llvm.org/svn/llvm-project/openmp/trunk',
-                        'polly': 'http://llvm.org/svn/llvm-project/polly/trunk',
-                        'libcxx': 'http://llvm.org/svn/llvm-project/libcxx/trunk',
-                        'libcxxabi': 'http://llvm.org/svn/llvm-project/libcxxabi/trunk',
-                        'clang': 'http://llvm.org/svn/llvm-project/cfe/trunk',
-                        'clang-tools-extra': 'http://llvm.org/svn/llvm-project/clang-tools-extra/trunk',
-                        'lldb': 'http://llvm.org/svn/llvm-project/lldb/trunk',
-                        'llvm-libunwind': 'http://llvm.org/svn/llvm-project/libunwind/trunk',
-                    }
-        },
-        {
-            'version': '3.8.0',
-            'md5': '07a7a74f3c6bd65de4702bf941b511a0',
-            'resources': {
-                'compiler-rt': 'd6fcbe14352ffb708e4d1ac2e48bb025',
-                'openmp': '8fd7cc35d48051613cf1e750e9f22e40',
-                'polly': '1b3b20f52d34a4024e21a4ea7112caa7',
-                'libcxx': 'd6e0bdbbee39f7907ad74fd56d03b88a',
-                'libcxxabi': 'bbe6b4d72c7c5978550d370af529bcf7',
-                'clang': 'cc99e7019bb74e6459e80863606250c5',
-                'clang-tools-extra': 'c2344f50e0eea0b402f0092a80ddc036',
-                'lldb': 'a5da35ed9cc8c8817ee854e3dbfba00e',
-                        'llvm-libunwind': '162ade468607f153cca12be90b5194fa',
-            }
-        },
-        {
-            'version': '3.7.1',
-            'md5': 'bf8b3a2c79e61212c5409041dfdbd319',
-            'resources': {
-                'compiler-rt': '1c6975daf30bb3b0473b53c3a1a6ff01',
-                'openmp': 'b4ad08cda4e5c22e42b66062b140438e',
-                'polly': '3a2a7367002740881637f4d47bca4dc3',
-                'libcxx': 'f9c43fa552a10e14ff53b94d04bea140',
-                'libcxxabi': '52d925afac9f97e9dcac90745255c169',
-                'clang': '0acd026b5529164197563d135a8fd83e',
-                'clang-tools-extra': '5d49ff745037f061a7c86aeb6a24c3d2',
-                'lldb': 'a106d8a0d21fc84d76953822fbaf3398',
-                        'llvm-libunwind': '814bd52c9247c5d04629658fbcb3ab8c',
-            }
-        },
-        {
-            'version': '3.7.0',
-            'md5': 'b98b9495e5655a672d6cb83e1a180f8e',
             'resources': {
-                'compiler-rt': '383c10affd513026f08936b5525523f5',
-                'openmp': 'f482c86fdead50ba246a1a2b0bbf206f',
-                'polly': '32f93ffc9cc7e042df22089761558f8b',
-                'libcxx': '46aa5175cbe1ad42d6e9c995968e56dd',
-                'libcxxabi': '5aa769e2fca79fa5335cfae8f6258772',
-                'clang': '8f9d27335e7331cf0a4711e952f21f01',
-                'clang-tools-extra': 'd5a87dacb65d981a427a536f6964642e',
-                'lldb': 'e5931740400d1dc3e7db4c7ba2ceff68',
-                        'llvm-libunwind': '9a75392eb7eb8ed5c0840007e212baf5',
-            }
-        },
+                'compiler-rt': 'http://llvm.org/svn/llvm-project/compiler-rt/trunk',
+                'openmp': 'http://llvm.org/svn/llvm-project/openmp/trunk',
+                'polly': 'http://llvm.org/svn/llvm-project/polly/trunk',
+                'libcxx': 'http://llvm.org/svn/llvm-project/libcxx/trunk',
+                'libcxxabi': 'http://llvm.org/svn/llvm-project/libcxxabi/trunk',
+                'cfe': 'http://llvm.org/svn/llvm-project/cfe/trunk',
+                'clang-tools-extra': 'http://llvm.org/svn/llvm-project/clang-tools-extra/trunk',
+                'lldb': 'http://llvm.org/svn/llvm-project/lldb/trunk',
+                'llvm-libunwind': 'http://llvm.org/svn/llvm-project/libunwind/trunk',
+                }
+            },
+            {
+                'version': '3.9.0',
+                'md5': 'f2093e98060532449eb7d2fcfd0bc6c6',
+                'resources': {
+                    'compiler-rt': 'b7ea34c9d744da16ffc0217b6990d095',
+                    'openmp': '5390164f2374e1444e82393541ecf6c7',
+                    'polly': '1cf328cbae25267749b68cfa6f113674',
+                    'libcxx': '0a11efefd864ce6f321194e441f7e569',
+                    'libcxxabi': 'd02642308e22e614af6b061b9b4fedfa',
+                    'cfe': '29e1d86bee422ab5345f5e9fb808d2dc',
+                    'clang-tools-extra': 'f4f663068c77fc742113211841e94d5e',
+                    'lldb': '968d053c3c3d7297983589164c6999e9',
+                    'llvm-libunwind': '3e5c87c723a456be599727a444b1c166',
+                    }
+                },
+            {
+                'version': '3.8.1',
+                'md5': '538467e6028bbc9259b1e6e015d25845',
+                'resources': {
+                    'compiler-rt': 'f140db073d2453f854fbe01cc46f3110',
+                    'openmp': '078b8d4c51ad437a4f8b5989f5ec4156',
+                    'polly': '8a40e697a4ba1c8b640b85d074bd6e25',
+                    'libcxx': '1bc60150302ff76a0d79d6f9db22332e',
+                    'libcxxabi': '3c63b03ba2f30a01279ca63384a67773',
+                    'cfe': '4ff2f8844a786edb0220f490f7896080',
+                    'clang-tools-extra': '6e49f285d0b366cc3cab782d8c92d382',
+                    'lldb': '9e4787b71be8e432fffd31e13ac87623',
+                    'llvm-libunwind': 'd66e2387e1d37a8a0c8fe6a0063a3bab',
+                    }
+                },
+            {
+                'version': '3.8.0',
+                'md5': '07a7a74f3c6bd65de4702bf941b511a0',
+                'resources': {
+                    'compiler-rt': 'd6fcbe14352ffb708e4d1ac2e48bb025',
+                    'openmp': '8fd7cc35d48051613cf1e750e9f22e40',
+                    'polly': '1b3b20f52d34a4024e21a4ea7112caa7',
+                    'libcxx': 'd6e0bdbbee39f7907ad74fd56d03b88a',
+                    'libcxxabi': 'bbe6b4d72c7c5978550d370af529bcf7',
+                    'cfe': 'cc99e7019bb74e6459e80863606250c5',
+                    'clang-tools-extra': 'c2344f50e0eea0b402f0092a80ddc036',
+                    'lldb': 'a5da35ed9cc8c8817ee854e3dbfba00e',
+                    'llvm-libunwind': '162ade468607f153cca12be90b5194fa',
+                    }
+                },
+            {
+                'version': '3.7.1',
+                'md5': 'bf8b3a2c79e61212c5409041dfdbd319',
+                'resources': {
+                    'compiler-rt': '1c6975daf30bb3b0473b53c3a1a6ff01',
+                    'openmp': 'b4ad08cda4e5c22e42b66062b140438e',
+                    'polly': '3a2a7367002740881637f4d47bca4dc3',
+                    'libcxx': 'f9c43fa552a10e14ff53b94d04bea140',
+                    'libcxxabi': '52d925afac9f97e9dcac90745255c169',
+                    'cfe': '0acd026b5529164197563d135a8fd83e',
+                    'clang-tools-extra': '5d49ff745037f061a7c86aeb6a24c3d2',
+                    'lldb': 'a106d8a0d21fc84d76953822fbaf3398',
+                    'llvm-libunwind': '814bd52c9247c5d04629658fbcb3ab8c',
+                    }
+                },
+            {
+                'version': '3.7.0',
+                'md5': 'b98b9495e5655a672d6cb83e1a180f8e',
+                'resources': {
+                    'compiler-rt': '383c10affd513026f08936b5525523f5',
+                    'openmp': 'f482c86fdead50ba246a1a2b0bbf206f',
+                    'polly': '32f93ffc9cc7e042df22089761558f8b',
+                    'libcxx': '46aa5175cbe1ad42d6e9c995968e56dd',
+                    'libcxxabi': '5aa769e2fca79fa5335cfae8f6258772',
+                    'cfe': '8f9d27335e7331cf0a4711e952f21f01',
+                    'clang-tools-extra': 'd5a87dacb65d981a427a536f6964642e',
+                    'lldb': 'e5931740400d1dc3e7db4c7ba2ceff68',
+                    'llvm-libunwind': '9a75392eb7eb8ed5c0840007e212baf5',
+                    }
+                },
         {
             'version': '3.6.2',
             'md5': '0c1ee3597d75280dee603bae9cbf5cc2',
@@ -206,7 +239,7 @@ class Llvm(Package):
                 'openmp': '65dd5863b9b270960a96817e9152b123',
                 'libcxx': '22214c90697636ef960a49aef7c1823a',
                 'libcxxabi': '17518e361e4e228f193dd91e8ef54ba2',
-                'clang': 'ff862793682f714bb7862325b9c06e20',
+                'cfe': 'ff862793682f714bb7862325b9c06e20',
                 'clang-tools-extra': '3ebc1dc41659fcec3db1b47d81575e06',
                 'lldb': '51e5eb552f777b950bb0ff326e60d5f0',
             }
@@ -219,7 +252,7 @@ class Llvm(Package):
                 'openmp': '121ddb10167d7fc38b1f7e4b029cf059',
                 'libcxx': '406f09b1dab529f3f7879f4d548329d2',
                 'libcxxabi': 'b22c707e8d474a99865ad3c521c3d464',
-                'clang': '93f9532f8f7e6f1d8e5c1116907051cb',
+                'cfe': '93f9532f8f7e6f1d8e5c1116907051cb',
                 'clang-tools-extra': 'f13f31ed3038acadc6fa63fef812a246',
                 'lldb': 'cc5ea8a414c62c33e760517f8929a204',
             }
diff --git a/var/spack/repos/builtin/packages/lulesh/package.py b/var/spack/repos/builtin/packages/lulesh/package.py
new file mode 100644
index 0000000000..e880d4fa14
--- /dev/null
+++ b/var/spack/repos/builtin/packages/lulesh/package.py
@@ -0,0 +1,55 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+import os
+
+
+class Lulesh(Package):
+    """Livermore Unstructured Lagrangian Explicit Shock Hydrodynamics (LULESH)
+    """
+
+    homepage = "https://codesign.llnl.gov/lulesh.php"
+    url      = "https://codesign.llnl.gov/lulesh/lulesh2.0.3.tgz"
+
+    version("2.0.3", "336644a8750f71c7c6b9d2960976e7aa")
+
+    patch("remove_defaults.patch")
+
+    variant('mpip', default=False)
+
+    depends_on("mpi", type="build")
+    depends_on("mpip", when="+mpip")
+
+    def install(self, spec, prefix):
+        if '+mpip' in spec:
+            os.environ["LDFLAGS"] = " -lmpiP -ldwarf -lelf"
+
+            if os.uname()[4] == "x86_64":
+                os.environ["LDFLAGS"] += " -lunwind"
+
+        os.environ["CXX"] = spec['mpi'].mpicxx + " -DUSE_MPI=1"
+        os.environ["PREFIX"] = prefix
+        make()
+        make("install")
diff --git a/var/spack/repos/builtin/packages/lulesh/remove_defaults.patch b/var/spack/repos/builtin/packages/lulesh/remove_defaults.patch
new file mode 100644
index 0000000000..36cce25ba1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/lulesh/remove_defaults.patch
@@ -0,0 +1,60 @@
+--- a/Makefile
++++ b/Makefile
+@@ -1,17 +1,9 @@
+ #default build suggestion of MPI + OPENMP with gcc on Livermore machines you might have to change the compiler name
+ 
+-SHELL = /bin/sh
+ .SUFFIXES: .cc .o
+ 
+ LULESH_EXEC = lulesh2.0
+ 
+-MPI_INC = /opt/local/include/openmpi
+-MPI_LIB = /opt/local/lib
+-
+-SERCXX = g++ -DUSE_MPI=0
+-MPICXX = mpig++ -DUSE_MPI=1
+-CXX = $(MPICXX)
+-
+ SOURCES2.0 = \
+ 	lulesh.cc \
+ 	lulesh-comm.cc \
+@@ -20,28 +12,6 @@
+ 	lulesh-init.cc
+ OBJECTS2.0 = $(SOURCES2.0:.cc=.o)
+ 
+-#Default build suggestions with OpenMP for g++
+-CXXFLAGS = -g -O3 -fopenmp -I. -Wall
+-LDFLAGS = -g -O3 -fopenmp
+-
+-#Below are reasonable default flags for a serial build
+-#CXXFLAGS = -g -O3 -I. -Wall
+-#LDFLAGS = -g -O3 
+-
+-#common places you might find silo on the Livermore machines.
+-#SILO_INCDIR = /opt/local/include
+-#SILO_LIBDIR = /opt/local/lib
+-#SILO_INCDIR = ./silo/4.9/1.8.10.1/include
+-#SILO_LIBDIR = ./silo/4.9/1.8.10.1/lib
+-
+-#If you do not have silo and visit you can get them at:
+-#silo:  https://wci.llnl.gov/codes/silo/downloads.html
+-#visit: https://wci.llnl.gov/codes/visit/download.html
+-
+-#below is and example of how to make with silo, hdf5 to get vizulization by default all this is turned off.  All paths are Livermore specific.
+-#CXXFLAGS = -g -DVIZ_MESH -I${SILO_INCDIR} -Wall -Wno-pragmas
+-#LDFLAGS = -g -L${SILO_LIBDIR} -Wl,-rpath -Wl,${SILO_LIBDIR} -lsiloh5 -lhdf5
+-
+ .cc.o: lulesh.h
+ 	@echo "Building $<"
+ 	$(CXX) -c $(CXXFLAGS) -o $@  $<
+@@ -56,6 +26,7 @@
+        /bin/rm -f *.o *~ $(OBJECTS) $(LULESH_EXEC)
+ 	/bin/rm -rf *.dSYM
+ 
+-tar: clean
+-	cd .. ; tar cvf lulesh-2.0.tar LULESH-2.0 ; mv lulesh-2.0.tar LULESH-2.0
+-
++install: lulesh2.0
++	@echo "Installing"
++	mkdir -p $(PREFIX)/bin
++	install --mode=755 lulesh2.0 $(PREFIX)/bin/
diff --git a/var/spack/repos/builtin/packages/m4/package.py b/var/spack/repos/builtin/packages/m4/package.py
index b3bb5e61ce..f7150727fe 100644
--- a/var/spack/repos/builtin/packages/m4/package.py
+++ b/var/spack/repos/builtin/packages/m4/package.py
@@ -23,6 +23,7 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
+import sys
 
 
 class M4(Package):
@@ -47,6 +48,11 @@ class M4(Package):
         else:
             configure_args.append('--without-libsigsegv-prefix')
 
+        # http://lists.gnu.org/archive/html/bug-m4/2016-09/msg00002.html
+        if (sys.platform == "darwin") and (spec.satisfies('%gcc')) and \
+           (spec.architecture.platform_os.version == "10.12"):
+            configure_args.append('ac_cv_type_struct_sched_param=yes')
+
         configure("--prefix=%s" % prefix, *configure_args)
         make()
         make("install")
diff --git a/var/spack/repos/builtin/packages/magics/no_hardcoded_python.patch b/var/spack/repos/builtin/packages/magics/no_hardcoded_python.patch
new file mode 100644
index 0000000000..e2e2a5d1ba
--- /dev/null
+++ b/var/spack/repos/builtin/packages/magics/no_hardcoded_python.patch
@@ -0,0 +1,5 @@
+--- a/tools/xml2mv.py	2016-06-27 17:49:27.000000000 +0200
++++ a/tools/xml2mv.py	2016-09-13 16:25:17.246960456 +0200
+@@ -1 +1 @@
+-#!/usr/bin/python
++#!/usr/bin/env python
diff --git a/var/spack/repos/builtin/packages/magics/package.py b/var/spack/repos/builtin/packages/magics/package.py
new file mode 100644
index 0000000000..cd793ae051
--- /dev/null
+++ b/var/spack/repos/builtin/packages/magics/package.py
@@ -0,0 +1,115 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Magics(Package):
+    """Magics is the latest generation of the ECMWF's Meteorological plotting
+       software MAGICS. Although completely redesigned in C++, it is intended
+       to be as backwards-compatible as possible with the Fortran interface."""
+
+    homepage = "https://software.ecmwf.int/wiki/display/MAGP/Magics"
+    url      = "https://software.ecmwf.int/wiki/download/attachments/3473464/Magics-2.29.0-Source.tar.gz"
+
+    # Maintainers of Magics do not keep tarballs of minor releases. Once the
+    # next minor released is published the previous one becomes unavailable.
+    # That is why the preferred version is the latest stable one.
+    version('2.29.4', '91c561f413316fb665b3bb563f3878d1')
+    version('2.29.0', 'db20a4d3c51a2da5657c31ae3de59709', preferred=True)
+
+    # The patch changes the hardcoded path to python in shebang to enable the
+    # usage of the first python installation that appears in $PATH
+    patch('no_hardcoded_python.patch')
+
+    # The patch reorders includes and adds namespaces where necessary to
+    # resolve ambiguity of invocations of isnan and isinf functions. The
+    # patch is not needed since the version 2.29.1
+    patch('resolve_isnan_ambiguity.patch', when='@2.29.0')
+
+    variant('bufr', default=False, description='Enable BUFR support')
+    variant('netcdf', default=False, description='Enable NetCDF support')
+    variant('cairo', default=True, description='Enable cairo support[png/jpeg]')
+    variant('metview', default=False, description='Enable metview support')
+    variant('qt', default=False, description='Enable metview support with qt')
+
+    depends_on('cmake', type='build')
+    depends_on('pkg-config', type='build')
+
+    # Currently python is only necessary to run
+    # building preprocessing scripts.
+    depends_on('python', type='build')
+    depends_on('grib-api')
+    depends_on('proj')
+    depends_on('boost')
+    depends_on('expat')
+    depends_on('pango', when='+cairo')
+    depends_on('netcdf-cxx', when='+netcdf')
+    depends_on('libemos', when='+bufr')
+    depends_on('qt', when='+metview+qt')
+
+    def install(self, spec, prefix):
+        options = []
+        options.extend(std_cmake_args)
+        options.append('-DENABLE_ODB=OFF')
+        options.append('-DENABLE_PYTHON=OFF')
+        options.append('-DBOOST_ROOT=%s' % spec['boost'].prefix)
+        options.append('-DPROJ4_PATH=%s' % spec['proj'].prefix)
+        options.append('-DGRIB_API_PATH=%s' % spec['grib-api'].prefix)
+        options.append('-DENABLE_TESTS=OFF')
+
+        if '+bufr' in spec:
+            options.append('-DENABLE_BUFR=ON')
+            options.append('-DLIBEMOS_PATH=%s' % spec['libemos'].prefix)
+        else:
+            options.append('-DENABLE_BUFR=OFF')
+
+        if '+netcdf' in spec:
+            options.append('-DENABLE_NETCDF=ON')
+            options.append('-DNETCDF_PATH=%s' % spec['netcdf-cxx'].prefix)
+        else:
+            options.append('-DENABLE_NETCDF=OFF')
+
+        if '+cairo' in spec:
+            options.append('-DENABLE_CAIRO=ON')
+        else:
+            options.append('-DENABLE_CAIRO=OFF')
+
+        if '+metview' in spec:
+            if '+qt' in spec:
+                options.append('-DENABLE_METVIEW=ON')
+                if spec['qt'].version.up_to(1) == '5':
+                    options.append('-DENABLE_QT5=ON')
+            else:
+                options.append('-DENABLE_METVIEW_NO_QT=ON')
+        else:
+            options.append('-DENABLE_METVIEW=OFF')
+
+        if (self.compiler.f77 is None) or (self.compiler.fc is None):
+            options.append('-DENABLE_FORTRAN=OFF')
+
+        with working_dir('spack-build', create=True):
+            cmake('..', *options)
+            make()
+            make('install')
diff --git a/var/spack/repos/builtin/packages/magics/resolve_isnan_ambiguity.patch b/var/spack/repos/builtin/packages/magics/resolve_isnan_ambiguity.patch
new file mode 100644
index 0000000000..54b96ae88e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/magics/resolve_isnan_ambiguity.patch
@@ -0,0 +1,73 @@
+--- a/src/common/Polyline.cc	2016-04-28 14:38:09.000000000 +0200
++++ b/src/common/Polyline.cc	2016-09-14 13:31:35.784617803 +0200
+@@ -31,2 +30,0 @@
+-#include "TeCoord2D.h"
+-#include "TeGeometryAlgorithms.h"
+--- a/src/decoders/GribRegularInterpretor.cc	2016-04-28 14:38:09.000000000 +0200
++++ b/src/decoders/GribRegularInterpretor.cc	2016-09-14 13:43:41.673614590 +0200
+@@ -2083,2 +2083,2 @@
+-                            if (isnan(val1)) {
+-                                if (isnan(val2)) {
++                            if (std::isnan(val1)) {
++                                if (std::isnan(val2)) {
+@@ -2090 +2090 @@
+-                                if (isnan(val2)) {
++                                if (std::isnan(val2)) {
+@@ -2101 +2101 @@
+-                            if (isnan(val) || isinf(val) || isinf(-val)) {
++                            if (std::isnan(val) || std::isinf(val) || std::isinf(-val)) {
+@@ -2105 +2105 @@
+-                        if (isnan(val))
++                        if (std::isnan(val))
+--- a/src/decoders/GribSatelliteInterpretor.cc	2016-04-28 14:38:09.000000000 +0200
++++ b/src/decoders/GribSatelliteInterpretor.cc	2016-09-14 13:48:55.243699910 +0200
+@@ -33,5 +32,0 @@
+-#include "TeProjection.h"
+-#include "TeDataTypes.h"
+-#include "TeRasterParams.h"
+-#include "TeDecoderMemory.h"
+-#include "TeRasterRemap.h"
+--- a/src/decoders/NetcdfGeoMatrixInterpretor.cc	2016-04-28 14:38:09.000000000 +0200
++++ b/src/decoders/NetcdfGeoMatrixInterpretor.cc	2016-09-14 13:52:37.481201085 +0200
+@@ -93 +93 @@
+-				if ( !isnan(*d) ) {
++				if ( !std::isnan(*d) ) {
+--- a/src/decoders/NetcdfOrcaInterpretor.cc	2016-04-28 14:38:09.000000000 +0200
++++ b/src/decoders/NetcdfOrcaInterpretor.cc	2016-09-14 13:51:16.248650570 +0200
+@@ -210,2 +210,2 @@
+-							if ( isnan(val1) ) {
+-								if ( isnan(val2) ) {
++							if ( std::isnan(val1) ) {
++								if ( std::isnan(val2) ) {
+@@ -218 +218 @@
+-								if ( isnan(val2) ) {
++								if ( std::isnan(val2) ) {
+@@ -226 +226 @@
+-							if (isnan(val) || isinf(val) || isinf(-val) ) {
++							if (std::isnan(val) || std::isinf(val) || std::isinf(-val) ) {
+@@ -230 +230 @@
+-						if (isnan(val) ) val = missing;
++						if (std::isnan(val) ) val = missing;
+@@ -296 +296 @@
+-           if (isnan(value) ) 
++           if (std::isnan(value) ) 
+--- a/src/terralib/kernel/TeCentroid.cpp	2016-04-28 14:38:09.000000000 +0200
++++ b/src/terralib/kernel/TeCentroid.cpp	2016-09-14 14:17:31.675996554 +0200
+@@ -23,0 +24,2 @@
++#include "TeGeometryAlgorithms.h"
++
+@@ -30 +31,0 @@
+-#include "TeGeometryAlgorithms.h"
+--- a/src/terralib/kernel/TeDatabase.h	2014-11-07 17:39:24.000000000 +0100
++++ b/src/terralib/kernel/TeDatabase.h	2016-09-14 14:20:01.041100590 +0200
+@@ -33,0 +34 @@
++#include "TeGeometry.h"
+@@ -38 +38,0 @@
+-#include "TeGeometry.h"
+--- a/src/terralib/kernel/TeOverlayUtils.h	2014-11-07 17:39:24.000000000 +0100
++++ b/src/terralib/kernel/TeOverlayUtils.h	2016-09-14 14:21:51.649920405 +0200
+@@ -37,0 +38,2 @@
++#include "TeGeometry.h"

++

+@@ -44 +45,0 @@
+-#include "TeGeometry.h"

diff --git a/var/spack/repos/builtin/packages/mbedtls/package.py b/var/spack/repos/builtin/packages/mbedtls/package.py
index e1a42c0d9a..493ea59f0b 100644
--- a/var/spack/repos/builtin/packages/mbedtls/package.py
+++ b/var/spack/repos/builtin/packages/mbedtls/package.py
@@ -35,6 +35,7 @@ class Mbedtls(Package):
     homepage = "https://tls.mbed.org"
     url      = "https://github.com/ARMmbed/mbedtls/archive/mbedtls-2.2.1.tar.gz"
 
+    version('2.3.0', '98158e1160a0825a3e8db38881a177a0')
     version('2.2.1', '73a38f96898d6d03e32f55dd9f9a67be')
     version('2.2.0', 'eaf4586c1ef93ae872e606b6c1203942')
     version('2.1.4', '40cdf67b6c6d92c9cbcfd552d39ea3ae')
diff --git a/var/spack/repos/builtin/packages/mercurial/package.py b/var/spack/repos/builtin/packages/mercurial/package.py
index e51069662f..ea77953f15 100644
--- a/var/spack/repos/builtin/packages/mercurial/package.py
+++ b/var/spack/repos/builtin/packages/mercurial/package.py
@@ -22,23 +22,48 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-
 from spack import *
+import llnl.util.tty as tty
+import os
 
 
 class Mercurial(Package):
     """Mercurial is a free, distributed source control management tool."""
+
     homepage = "https://www.mercurial-scm.org"
     url      = "https://www.mercurial-scm.org/release/mercurial-3.9.tar.gz"
 
-    version('3.9'  , 'e2b355da744e94747daae3a5339d28a0')
+    version('3.9.1', '3759dd10edb8c1a6dfb8ff0ce82658ce')
+    version('3.9',   'e2b355da744e94747daae3a5339d28a0')
     version('3.8.4', 'cec2c3db688cb87142809089c6ae13e9')
     version('3.8.3', '97aced7018614eeccc9621a3dea35fda')
     version('3.8.2', 'c38daa0cbe264fc621dc3bb05933b0b3')
     version('3.8.1', '172a8c588adca12308c2aca16608d7f4')
 
-    depends_on("python @2.6:2.7.999")
-    depends_on("py-docutils", type="build")
+    extends('python')
+    depends_on('python@2.6:2.8')
+    depends_on('py-docutils', type='build')
 
     def install(self, spec, prefix):
-        make('PREFIX=%s' % prefix, 'install')
+        make('install', 'PREFIX={0}'.format(prefix))
+
+        # Configuration of HTTPS certificate authorities
+        # https://www.mercurial-scm.org/wiki/CACertificates
+        hgrc_filename = join_path(prefix.etc, 'mercurial', 'hgrc')
+        mkdirp(os.path.dirname(hgrc_filename))
+
+        with open(hgrc_filename, 'w') as hgrc:
+            if os.path.exists('/etc/ssl/certs/ca-certificates.crt'):
+                # Debian/Ubuntu/Gentoo/Arch Linux
+                hgrc.write('[web]\ncacerts = /etc/ssl/certs/ca-certificates.crt')  # noqa
+            elif os.path.exists('/etc/pki/tls/certs/ca-bundle.crt'):
+                # Fedora/RHEL/CentOS
+                hgrc.write('[web]\ncacerts = /etc/pki/tls/certs/ca-bundle.crt')
+            elif os.path.exists('/etc/ssl/ca-bundle.pem'):
+                # openSUSE/SLE
+                hgrc.write('[web]\ncacerts = /etc/ssl/ca-bundle.pem')
+            else:
+                tty.warn('CA certificate not found. You may not be able to '
+                         'connect to an HTTPS server. If your CA certificate '
+                         'is in a non-standard location, you should add it to '
+                         '{0}'.format(hgrc_filename))
diff --git a/var/spack/repos/builtin/packages/metis/package.py b/var/spack/repos/builtin/packages/metis/package.py
index 9f8ed5c9e8..ca48a47817 100644
--- a/var/spack/repos/builtin/packages/metis/package.py
+++ b/var/spack/repos/builtin/packages/metis/package.py
@@ -43,16 +43,12 @@ class Metis(Package):
     version('5.0.2', 'acb521a4e8c2e6dd559a7f9abd0468c5')
     version('4.0.3', 'd3848b454532ef18dc83e4fb160d1e10')
 
-    variant('shared', default=True,
-            description='Enables the build of shared libraries')
-    variant('debug', default=False,
-            description='Builds the library in debug mode')
-    variant('gdb', default=False, description='Enables gdb support')
+    variant('shared', default=True, description='Enables the build of shared libraries.')
+    variant('debug', default=False, description='Builds the library in debug mode.')
+    variant('gdb', default=False, description='Enables gdb support.')
 
-    variant('idx64', default=False,
-            description='Use int64_t as default index type')
-    variant('real64', default=False,
-            description='Use double precision floating point types')
+    variant('idx64', default=False, description='Sets the bit width of METIS\'s index type to 64.')
+    variant('real64', default=False, description='Sets the bit width of METIS\'s real type to 64.')
 
     depends_on('cmake@2.8:', when='@5:', type='build')
 
@@ -63,12 +59,37 @@ class Metis(Package):
         return '%s/%smetis-%s.tar.gz' % (Metis.base_url, verdir, version)
 
     @when('@:4')
+    def patch(self):
+        pass
+
+    @when('@5:')
+    def patch(self):
+        source_path = self.stage.source_path
+        metis_header = FileFilter(join_path(source_path, 'include', 'metis.h'))
+
+        metis_header.filter(
+            r'(\b)(IDXTYPEWIDTH )(\d+)(\b)',
+            r'\1\2{0}\4'.format('64' if '+idx64' in self.spec else '32'),
+        )
+        metis_header.filter(
+            r'(\b)(REALTYPEWIDTH )(\d+)(\b)',
+            r'\1\2{0}\4'.format('64' if '+real64' in self.spec else '32'),
+        )
+
+        # Make clang 7.3 happy.
+        # Prevents "ld: section __DATA/__thread_bss extends beyond end of file"
+        # See upstream LLVM issue https://llvm.org/bugs/show_bug.cgi?id=27059
+        # and https://github.com/Homebrew/homebrew-science/blob/master/metis.rb
+        if self.spec.satisfies('%clang@7.3.0'):
+            filter_file('#define MAX_JBUFS 128', '#define MAX_JBUFS 24',
+                        join_path(source_path, 'GKlib', 'error.c'))
+
+    @when('@:4')
     def install(self, spec, prefix):
         # Process library spec and options
-        unsupp_vars = [v for v in ('+gdb', '+idx64', '+real64') if v in spec]
-        if unsupp_vars:
-            msg = 'Given variants %s are unsupported by METIS 4!' % unsupp_vars
-            raise InstallError(msg)
+        if any('+{0}'.format(v) in spec for v in ['gdb', 'idx64', 'real64']):
+            raise InstallError('METIS@:4 does not support the following '
+                               'variants: gdb, idx64, real64.')
 
         options = ['COPTIONS=-fPIC']
         if '+debug' in spec:
@@ -118,49 +139,48 @@ class Metis(Package):
                  join_path('Programs', 'io.o'), join_path('Test', 'mtest.c'),
                  '-o', '%s/mtest' % prefix.bin, '-lmetis', '-lm')
 
-        test_bin = lambda testname: join_path(prefix.bin, testname)
-        test_graph = lambda graphname: join_path(prefix.share, graphname)
-
-        graph = test_graph('4elt.graph')
-        os.system('%s %s' % (test_bin('mtest'), graph))
-        os.system('%s %s 40' % (test_bin('kmetis'), graph))
-        os.system('%s %s' % (test_bin('onmetis'), graph))
-        graph = test_graph('test.mgraph')
-        os.system('%s %s 2' % (test_bin('pmetis'), graph))
-        os.system('%s %s 2' % (test_bin('kmetis'), graph))
-        os.system('%s %s 5' % (test_bin('kmetis'), graph))
-        graph = test_graph('metis.mesh')
-        os.system('%s %s 10' % (test_bin('partnmesh'), graph))
-        os.system('%s %s 10' % (test_bin('partdmesh'), graph))
-        os.system('%s %s' % (test_bin('mesh2dual'), graph))
-
-        # FIXME: The following code should replace the testing code in the
-        # block above since it causes installs to fail when one or more of the
-        # Metis tests fail, but it currently doesn't work because the 'mtest',
-        # 'onmetis', and 'partnmesh' tests return error codes that trigger
-        # false positives for failure.
-        """
-        Executable(test_bin('mtest'))(test_graph('4elt.graph'))
-        Executable(test_bin('kmetis'))(test_graph('4elt.graph'), '40')
-        Executable(test_bin('onmetis'))(test_graph('4elt.graph'))
-
-        Executable(test_bin('pmetis'))(test_graph('test.mgraph'), '2')
-        Executable(test_bin('kmetis'))(test_graph('test.mgraph'), '2')
-        Executable(test_bin('kmetis'))(test_graph('test.mgraph'), '5')
-
-        Executable(test_bin('partnmesh'))(test_graph('metis.mesh'), '10')
-        Executable(test_bin('partdmesh'))(test_graph('metis.mesh'), '10')
-        Executable(test_bin('mesh2dual'))(test_graph('metis.mesh'))
-        """
+        if self.run_tests:
+            test_bin = lambda testname: join_path(prefix.bin, testname)
+            test_graph = lambda graphname: join_path(prefix.share, graphname)
+
+            graph = test_graph('4elt.graph')
+            os.system('%s %s' % (test_bin('mtest'), graph))
+            os.system('%s %s 40' % (test_bin('kmetis'), graph))
+            os.system('%s %s' % (test_bin('onmetis'), graph))
+            graph = test_graph('test.mgraph')
+            os.system('%s %s 2' % (test_bin('pmetis'), graph))
+            os.system('%s %s 2' % (test_bin('kmetis'), graph))
+            os.system('%s %s 5' % (test_bin('kmetis'), graph))
+            graph = test_graph('metis.mesh')
+            os.system('%s %s 10' % (test_bin('partnmesh'), graph))
+            os.system('%s %s 10' % (test_bin('partdmesh'), graph))
+            os.system('%s %s' % (test_bin('mesh2dual'), graph))
+
+            # FIXME: The following code should replace the testing code in the
+            # block above since it causes installs to fail when one or more of
+            # the Metis tests fail, but it currently doesn't work because the
+            # 'mtest', 'onmetis', and 'partnmesh' tests return error codes that
+            # trigger false positives for failure.
+            """
+            Executable(test_bin('mtest'))(test_graph('4elt.graph'))
+            Executable(test_bin('kmetis'))(test_graph('4elt.graph'), '40')
+            Executable(test_bin('onmetis'))(test_graph('4elt.graph'))
+
+            Executable(test_bin('pmetis'))(test_graph('test.mgraph'), '2')
+            Executable(test_bin('kmetis'))(test_graph('test.mgraph'), '2')
+            Executable(test_bin('kmetis'))(test_graph('test.mgraph'), '5')
+
+            Executable(test_bin('partnmesh'))(test_graph('metis.mesh'), '10')
+            Executable(test_bin('partdmesh'))(test_graph('metis.mesh'), '10')
+            Executable(test_bin('mesh2dual'))(test_graph('metis.mesh'))
+            """
 
     @when('@5:')
     def install(self, spec, prefix):
-        options = []
-        options.extend(std_cmake_args)
-
-        build_directory = join_path(self.stage.path, 'spack-build')
         source_directory = self.stage.source_path
+        build_directory = join_path(source_directory, 'build')
 
+        options = std_cmake_args[:]
         options.append('-DGKLIB_PATH:PATH=%s/GKlib' % source_directory)
         options.append('-DCMAKE_INSTALL_NAME_DIR:PATH=%s/lib' % prefix)
 
@@ -172,26 +192,24 @@ class Metis(Package):
         if '+gdb' in spec:
             options.append('-DGDB:BOOL=ON')
 
-        metis_header = join_path(source_directory, 'include', 'metis.h')
-        if '+idx64' in spec:
-            filter_file('IDXTYPEWIDTH 32', 'IDXTYPEWIDTH 64', metis_header)
-        if '+real64' in spec:
-            filter_file('REALTYPEWIDTH 32', 'REALTYPEWIDTH 64', metis_header)
-
-        # Make clang 7.3 happy.
-        # Prevents "ld: section __DATA/__thread_bss extends beyond end of file"
-        # See upstream LLVM issue https://llvm.org/bugs/show_bug.cgi?id=27059
-        # and https://github.com/Homebrew/homebrew-science/blob/master/metis.rb
-        if spec.satisfies('%clang@7.3.0'):
-            filter_file('#define MAX_JBUFS 128', '#define MAX_JBUFS 24',
-                        join_path(source_directory, 'GKlib', 'error.c'))
-
         with working_dir(build_directory, create=True):
             cmake(source_directory, *options)
             make()
             make('install')
 
-            # now run some tests:
+            # install GKlib headers, which will be needed for ParMETIS
+            GKlib_dist = join_path(prefix.include, 'GKlib')
+            mkdirp(GKlib_dist)
+            hfiles = glob.glob(join_path(source_directory, 'GKlib', '*.h'))
+            for hfile in hfiles:
+                install(hfile, GKlib_dist)
+
+        if self.run_tests:
+            # FIXME: On some systems, the installed binaries for METIS cannot
+            # be executed without first being read.
+            ls = which('ls')
+            ls('-a', '-l', prefix.bin)
+
             for f in ['4elt', 'copter2', 'mdual']:
                 graph = join_path(source_directory, 'graphs', '%s.graph' % f)
                 Executable(join_path(prefix.bin, 'graphchk'))(graph)
@@ -202,10 +220,3 @@ class Metis(Package):
             Executable(join_path(prefix.bin, 'gpmetis'))(graph, '2')
             graph = join_path(source_directory, 'graphs', 'metis.mesh')
             Executable(join_path(prefix.bin, 'mpmetis'))(graph, '2')
-
-            # install GKlib headers, which will be needed for ParMETIS
-            GKlib_dist = join_path(prefix.include, 'GKlib')
-            mkdirp(GKlib_dist)
-            hfiles = glob.glob(join_path(source_directory, 'GKlib', '*.h'))
-            for hfile in hfiles:
-                install(hfile, GKlib_dist)
diff --git a/var/spack/repos/builtin/packages/mfem/package.py b/var/spack/repos/builtin/packages/mfem/package.py
index fd91f705eb..cbf9059f65 100644
--- a/var/spack/repos/builtin/packages/mfem/package.py
+++ b/var/spack/repos/builtin/packages/mfem/package.py
@@ -89,8 +89,7 @@ class Mfem(Package):
         options = ['PREFIX=%s' % prefix]
 
         if '+lapack' in spec:
-            lapack_lib = '-L{0} -llapack -L{1} -lblas'.format(
-                spec['lapack'].prefix.lib, spec['blas'].prefix.lib)
+            lapack_lib = (spec['lapack'].lapack_libs + spec['blas'].blas_libs).ld_flags  # NOQA: ignore=E501
             options.extend([
                 'MFEM_USE_LAPACK=YES',
                 'LAPACK_OPT=-I%s' % spec['lapack'].prefix.include,
diff --git a/var/spack/repos/builtin/packages/mkl/package.py b/var/spack/repos/builtin/packages/mkl/package.py
index 71a233ff3e..8a31858bf5 100644
--- a/var/spack/repos/builtin/packages/mkl/package.py
+++ b/var/spack/repos/builtin/packages/mkl/package.py
@@ -9,7 +9,7 @@ class Mkl(IntelInstaller):
 
     Note: You will have to add the download file to a
     mirror so that Spack can find it. For instructions on how to set up a
-    mirror, see http://software.llnl.gov/spack/mirrors.html.
+    mirror, see http://spack.readthedocs.io/en/latest/mirrors.html.
 
     To set the threading layer at run time set MKL_THREADING_LAYER
     variable to one of the following values: INTEL (default), SEQUENTIAL, PGI.
@@ -24,13 +24,41 @@ class Mkl(IntelInstaller):
     version('11.3.3.210', 'f72546df27f5ebb0941b5d21fd804e34',
             url="file://%s/l_mkl_11.3.3.210.tgz" % os.getcwd())
 
+    variant('shared', default=True, description='Builds shared library')
+    variant('ilp64', default=False, description='64 bit integers')
+    variant('openmp', default=False, description='OpenMP multithreading layer')
+
     # virtual dependency
     provides('blas')
     provides('lapack')
     # TODO: MKL also provides implementation of Scalapack.
 
-    def install(self, spec, prefix):
+    @property
+    def blas_libs(self):
+        shared = True if '+shared' in self.spec else False
+        suffix = dso_suffix if '+shared' in self.spec else 'a'
+        mkl_integer = ['libmkl_intel_ilp64'] if '+ilp64' in self.spec else ['libmkl_intel_lp64']  # NOQA: ignore=E501
+        mkl_threading = ['libmkl_sequential']
+        if '+openmp' in self.spec:
+            mkl_threading = ['libmkl_intel_thread', 'libiomp5'] if '%intel' in self.spec else ['libmkl_gnu_thread']  # NOQA: ignore=E501
+        # TODO: TBB threading: ['libmkl_tbb_thread', 'libtbb', 'libstdc++']
+        mkl_libs = find_libraries(
+            mkl_integer + ['libmkl_core'] + mkl_threading,
+            root=join_path(self.prefix.lib, 'intel64'),
+            shared=shared
+        )
+        system_libs = [
+            'libpthread.{0}'.format(suffix),
+            'libm.{0}'.format(suffix),
+            'libdl.{0}'.format(suffix)
+        ]
+        return mkl_libs + system_libs
+
+    @property
+    def lapack_libs(self):
+        return self.blas_libs
 
+    def install(self, spec, prefix):
         self.intel_prefix = os.path.join(prefix, "pkg")
         IntelInstaller.install(self, spec, prefix)
 
@@ -45,25 +73,6 @@ class Mkl(IntelInstaller):
             os.symlink(os.path.join(mkl_lib_dir, f),
                        os.path.join(self.prefix, "lib", f))
 
-    def setup_dependent_package(self, module, dspec):
-        # For now use Single Dynamic Library:
-        # To set the threading layer at run time, use the
-        # mkl_set_threading_layer function or set MKL_THREADING_LAYER
-        # variable to one of the following values: INTEL, SEQUENTIAL, PGI.
-        # To set interface layer at run time, use the mkl_set_interface_layer
-        # function or set the MKL_INTERFACE_LAYER variable to LP64 or ILP64.
-
-        # Otherwise one would need to specify several libraries
-        # (e.g. mkl_intel_lp64;mkl_sequential;mkl_core), which reflect
-        # different interface and threading layers.
-
-        name = 'libmkl_rt.%s' % dso_suffix
-        libdir = find_library_path(name, self.prefix.lib64, self.prefix.lib)
-
-        # Now set blas/lapack libs:
-        self.spec.blas_shared_lib   = join_path(libdir, name)
-        self.spec.lapack_shared_lib = self.spec.blas_shared_lib
-
     def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
         # set up MKLROOT for everyone using MKL package
         spack_env.set('MKLROOT', self.prefix)
diff --git a/var/spack/repos/builtin/packages/moab/package.py b/var/spack/repos/builtin/packages/moab/package.py
index 893a543e97..4dfc5432d2 100644
--- a/var/spack/repos/builtin/packages/moab/package.py
+++ b/var/spack/repos/builtin/packages/moab/package.py
@@ -37,7 +37,7 @@ class Moab(Package):
     homepage = "https://bitbucket.org/fathomteam/moab"
     url      = "http://ftp.mcs.anl.gov/pub/fathom/moab-4.6.3.tar.gz"
 
-    version('4.9.1', 'bcb8bee3e58c076c7f31884db119088e')
+    version('4.9.1', '19cc2189fa266181ad9109b18d0b2ab8')
     version('4.9.0', '40695d0a159040683cfa05586ad4a7c2')
     version('4.8.2', '1dddd10f162fce3cfffaedc48f6f467d')
 
diff --git a/var/spack/repos/builtin/packages/mpip/package.py b/var/spack/repos/builtin/packages/mpip/package.py
new file mode 100644
index 0000000000..78e1dca68a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mpip/package.py
@@ -0,0 +1,44 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+import os
+
+
+class Mpip(Package):
+    """mpiP: Lightweight, Scalable MPI Profiling"""
+    homepage = "http://mpip.sourceforge.net/"
+    url      = "http://downloads.sourceforge.net/project/mpip/mpiP/mpiP-3.4.1/mpiP-3.4.1.tar.gz"
+
+    version("3.4.1", "1168adc83777ac31d6ebd385823aabbd")
+
+    depends_on("libelf", type="build")
+    depends_on("libdwarf", type="build")
+    depends_on('libunwind', when=os.uname()[4] == "x86_64", type="build")
+    depends_on("mpi", type="build")
+
+    def install(self, spec, prefix):
+        configure("--prefix=" + prefix, "--without-f77")
+        make()
+        make("install")
diff --git a/var/spack/repos/builtin/packages/mumps/package.py b/var/spack/repos/builtin/packages/mumps/package.py
index 32bc42a9c3..3466f091a0 100644
--- a/var/spack/repos/builtin/packages/mumps/package.py
+++ b/var/spack/repos/builtin/packages/mumps/package.py
@@ -75,9 +75,8 @@ class Mumps(Package):
             raise RuntimeError(
                 'You cannot use the variants parmetis or ptscotch without mpi')
 
-        makefile_conf = ["LIBBLAS = %s" % to_link_flags(
-            self.spec['blas'].blas_shared_lib)
-        ]
+        blas = self.spec['blas'].blas_libs
+        makefile_conf = ["LIBBLAS = %s" % blas.ld_flags]
 
         orderings = ['-Dpord']
 
@@ -136,11 +135,12 @@ class Mumps(Package):
                  'OPTC    = %s -O ' % fpic])
 
         if '+mpi' in self.spec:
+            scalapack = self.spec['scalapack'].scalapack_libs
             makefile_conf.extend(
                 ["CC = %s" % join_path(self.spec['mpi'].prefix.bin, 'mpicc'),
                  "FC = %s" % join_path(self.spec['mpi'].prefix.bin, 'mpif90'),
                  "FL = %s" % join_path(self.spec['mpi'].prefix.bin, 'mpif90'),
-                 "SCALAP = %s" % self.spec['scalapack'].fc_link,
+                 "SCALAP = %s" % scalapack.ld_flags,
                  "MUMPS_TYPE = par"])
         else:
             makefile_conf.extend(
diff --git a/var/spack/repos/builtin/packages/mvapich2/package.py b/var/spack/repos/builtin/packages/mvapich2/package.py
index a123830185..06678bf08b 100644
--- a/var/spack/repos/builtin/packages/mvapich2/package.py
+++ b/var/spack/repos/builtin/packages/mvapich2/package.py
@@ -28,14 +28,12 @@ from spack import *
 class Mvapich2(Package):
     """MVAPICH2 is an MPI implementation for Infiniband networks."""
     homepage = "http://mvapich.cse.ohio-state.edu/"
-    url = "http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.2rc2.tar.gz"
+    url = "http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.2.tar.gz"
 
-    version('2.2rc2', 'f9082ffc3b853ad1b908cf7f169aa878')
-    version('2.2b',   '5651e8b7a72d7c77ca68da48f3a5d108')
-    version('2.2a',   'b8ceb4fc5f5a97add9b3ff1b9cbe39d2')
-    version('2.1',    '0095ceecb19bbb7fb262131cb9c2cdd6')
-    version('2.0',    '9fbb68a4111a8b6338e476dc657388b4')
-    version('1.9',    '5dc58ed08fd3142c260b70fe297e127c')
+    version('2.2', '939b65ebe5b89a5bc822cdab0f31f96e')
+    version('2.1', '0095ceecb19bbb7fb262131cb9c2cdd6')
+    version('2.0', '9fbb68a4111a8b6338e476dc657388b4')
+    version('1.9', '5dc58ed08fd3142c260b70fe297e127c')
 
     patch('ad_lustre_rwcontig_open_source.patch', when='@1.9')
 
@@ -95,6 +93,7 @@ class Mvapich2(Package):
     ##########
 
     # FIXME : CUDA support is missing
+    depends_on('bison')
     depends_on('libpciaccess')
 
     def url_for_version(self, version):
diff --git a/var/spack/repos/builtin/packages/ncurses/package.py b/var/spack/repos/builtin/packages/ncurses/package.py
index aaacbac7b1..e4fd5bf269 100644
--- a/var/spack/repos/builtin/packages/ncurses/package.py
+++ b/var/spack/repos/builtin/packages/ncurses/package.py
@@ -50,7 +50,10 @@ class Ncurses(Package):
             "--enable-widec",
             "--enable-overwrite",
             "--disable-lib-suffixes",
-            "--without-ada"]
+            "--without-ada",
+            "--enable-pc-files",
+            "--with-pkg-config-libdir={0}/lib/pkgconfig".format(prefix)
+        ]
         configure(*opts)
         make()
         make("install")
diff --git a/var/spack/repos/builtin/packages/ncview/package.py b/var/spack/repos/builtin/packages/ncview/package.py
index f61e6984b5..4abc09deb0 100644
--- a/var/spack/repos/builtin/packages/ncview/package.py
+++ b/var/spack/repos/builtin/packages/ncview/package.py
@@ -34,6 +34,7 @@ class Ncview(Package):
 
     depends_on("netcdf")
     depends_on("udunits2")
+    depends_on("libpng")
 
     # OS Dependencies
     # Ubuntu: apt-get install libxaw7-dev
diff --git a/var/spack/repos/builtin/packages/netcdf/package.py b/var/spack/repos/builtin/packages/netcdf/package.py
index ab40c14340..5dc686c907 100644
--- a/var/spack/repos/builtin/packages/netcdf/package.py
+++ b/var/spack/repos/builtin/packages/netcdf/package.py
@@ -50,12 +50,18 @@ class Netcdf(Package):
 
     # Required for NetCDF-4 support
     depends_on("zlib")
-    depends_on('hdf5@:1.8+mpi', when='@:4.4.0+mpi')
-    depends_on('hdf5+mpi', when='@4.4.1:+mpi')
-    depends_on('hdf5@:1.8~mpi', when='@:4.4.0~mpi')
-    depends_on('hdf5~mpi', when='@4.4.1:~mpi')
+    depends_on('hdf5')
+
+    # NetCDF 4.4.0 and prior have compatibility issues with HDF5 1.10 and later
+    # https://github.com/Unidata/netcdf-c/issues/250
+    depends_on('hdf5@:1.8', when='@:4.4.0')
 
     def install(self, spec, prefix):
+        # Workaround until variant forwarding works properly
+        if '+mpi' in spec and spec.satisfies('^hdf5~mpi'):
+            raise RuntimeError('Invalid spec. Package netcdf requires '
+                               'hdf5+mpi, but spec asked for hdf5~mpi.')
+
         # Environment variables
         CPPFLAGS = []
         LDFLAGS  = []
diff --git a/var/spack/repos/builtin/packages/netlib-lapack/package.py b/var/spack/repos/builtin/packages/netlib-lapack/package.py
index 08c94a5c9b..874473ba9c 100644
--- a/var/spack/repos/builtin/packages/netlib-lapack/package.py
+++ b/var/spack/repos/builtin/packages/netlib-lapack/package.py
@@ -36,6 +36,7 @@ class NetlibLapack(Package):
     homepage = "http://www.netlib.org/lapack/"
     url = "http://www.netlib.org/lapack/lapack-3.5.0.tgz"
 
+    version('3.6.1', '421b2cb72e15f237e144428f9c460ee0')
     version('3.6.0', 'f2f6c67134e851fe189bb3ca1fbb5101')
     version('3.5.0', 'b1d3e3e425b2e44a06760ff173104bdf')
     version('3.4.2', '61bf1a8a4469d4bdb7604f5897179478')
@@ -66,6 +67,20 @@ class NetlibLapack(Package):
                 '${CMAKE_CURRENT_SOURCE_DIR}/cmake/',
                 'CBLAS/CMakeLists.txt', string=True)
 
+    @property
+    def blas_libs(self):
+        shared = True if '+shared' in self.spec else False
+        return find_libraries(
+            ['libblas'], root=self.prefix, shared=shared, recurse=True
+        )
+
+    @property
+    def lapack_libs(self):
+        shared = True if '+shared' in self.spec else False
+        return find_libraries(
+            ['liblapack'], root=self.prefix, shared=shared, recurse=True
+        )
+
     def install_one(self, spec, prefix, shared):
         cmake_args = [
             '-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if shared else 'OFF'),
@@ -76,12 +91,9 @@ class NetlibLapack(Package):
             cmake_args.extend(['-DCBLAS=ON'])  # always build CBLAS
 
         if '+external-blas' in spec:
-            # TODO : mechanism to specify the library should be more general,
-            # TODO : but this allows to have an hook to an external blas
             cmake_args.extend([
                 '-DUSE_OPTIMIZED_BLAS:BOOL=ON',
-                '-DBLAS_LIBRARIES:PATH=%s' % join_path(
-                    spec['blas'].prefix.lib, 'libblas.a')
+                '-DBLAS_LIBRARIES:PATH=%s' % spec['blas'].blas_libs.joined(';')
             ])
 
         cmake_args.extend(std_cmake_args)
@@ -99,18 +111,3 @@ class NetlibLapack(Package):
         # Build shared libraries if requested.
         if '+shared' in spec:
             self.install_one(spec, prefix, True)
-
-    def setup_dependent_package(self, module, dspec):
-        # This is WIP for a prototype interface for virtual packages.
-        # We can update this as more builds start depending on BLAS/LAPACK.
-        libdir = find_library_path(
-            'libblas.a', self.prefix.lib64, self.prefix.lib)
-
-        self.spec.blas_static_lib   = join_path(libdir, 'libblas.a')
-        self.spec.lapack_static_lib = join_path(libdir, 'liblapack.a')
-
-        if '+shared' in self.spec:
-            self.spec.blas_shared_lib   = join_path(
-                libdir, 'libblas.%s' % dso_suffix)
-            self.spec.lapack_shared_lib = join_path(
-                libdir, 'liblapack.%s' % dso_suffix)
diff --git a/var/spack/repos/builtin/packages/netlib-scalapack/package.py b/var/spack/repos/builtin/packages/netlib-scalapack/package.py
index 49b8633209..578d2d8988 100644
--- a/var/spack/repos/builtin/packages/netlib-scalapack/package.py
+++ b/var/spack/repos/builtin/packages/netlib-scalapack/package.py
@@ -28,10 +28,11 @@ import sys
 
 class NetlibScalapack(Package):
     """ScaLAPACK is a library of high-performance linear algebra routines for
-    parallel distributed memory machines"""
+    parallel distributed memory machines
+    """
 
     homepage = "http://www.netlib.org/scalapack/"
-    url      = "http://www.netlib.org/scalapack/scalapack-2.0.2.tgz"
+    url = "http://www.netlib.org/scalapack/scalapack-2.0.2.tgz"
 
     version('2.0.2', '2f75e600a2ba155ed9ce974a1c4b536f')
     version('2.0.1', '17b8cde589ea0423afe1ec43e7499161')
@@ -39,33 +40,47 @@ class NetlibScalapack(Package):
     # versions before 2.0.0 are not using cmake and requires blacs as
     # a separated package
 
-    variant('shared', default=True,
-            description='Build the shared library version')
-    variant('fpic', default=False, description="Build with -fpic compiler option")
+    variant(
+        'shared',
+        default=True,
+        description='Build the shared library version'
+    )
+    variant(
+        'fpic',
+        default=False,
+        description='Build with -fpic compiler option'
+    )
 
     provides('scalapack')
 
     depends_on('mpi')
     depends_on('lapack')
+    depends_on('blas')
     depends_on('cmake', when='@2.0.0:', type='build')
 
+    @property
+    def scalapack_libs(self):
+        shared = True if '+shared' in self.spec else False
+        return find_libraries(
+            ['libscalapack'], root=self.prefix, shared=shared, recurse=True
+        )
+
     def install(self, spec, prefix):
         options = [
             "-DBUILD_SHARED_LIBS:BOOL=%s" % ('ON' if '+shared' in spec else
                                              'OFF'),
             "-DBUILD_STATIC_LIBS:BOOL=%s" % ('OFF' if '+shared' in spec else
-                                             'ON'),
-            # forces scalapack to use find_package(LAPACK):
-            "-DUSE_OPTIMIZED_LAPACK_BLAS:BOOL=ON",
+                                             'ON')
         ]
 
         # Make sure we use Spack's Lapack:
+        blas = spec['blas'].blas_libs
+        lapack = spec['lapack'].lapack_libs
         options.extend([
             '-DLAPACK_FOUND=true',
             '-DLAPACK_INCLUDE_DIRS=%s' % spec['lapack'].prefix.include,
-            '-DLAPACK_LIBRARIES=%s' % (
-                spec['lapack'].lapack_shared_lib if '+shared' in spec else
-                spec['lapack'].lapack_static_lib),
+            '-DLAPACK_LIBRARIES=%s' % (lapack.joined(';')),
+            '-DBLAS_LIBRARIES=%s' % (blas.joined(';'))
         ])
 
         if '+fpic' in spec:
@@ -84,12 +99,3 @@ class NetlibScalapack(Package):
         # The shared libraries are not installed correctly on Darwin:
         if (sys.platform == 'darwin') and ('+shared' in spec):
             fix_darwin_install_name(prefix.lib)
-
-    def setup_dependent_package(self, module, dependent_spec):
-        spec = self.spec
-        lib_suffix = dso_suffix if '+shared' in spec else 'a'
-
-        spec.fc_link = '-L%s -lscalapack' % spec.prefix.lib
-        spec.cc_link = spec.fc_link
-        spec.libraries = [join_path(spec.prefix.lib,
-                                    'libscalapack.%s' % lib_suffix)]
diff --git a/var/spack/repos/builtin/packages/nwchem/package.py b/var/spack/repos/builtin/packages/nwchem/package.py
index 13c710a35a..b15c1c02fd 100644
--- a/var/spack/repos/builtin/packages/nwchem/package.py
+++ b/var/spack/repos/builtin/packages/nwchem/package.py
@@ -66,6 +66,9 @@ class Nwchem(Package):
     patch('Gcc6_macs_optfix.patch', when='@6.6', level=0)
 
     def install(self, spec, prefix):
+        scalapack = spec['scalapack'].scalapack_libs
+        lapack = spec['lapack'].lapack_libs
+        blas = spec['blas'].blas_libs
         # see http://www.nwchem-sw.org/index.php/Compiling_NWChem
         args = []
         args.extend([
@@ -79,13 +82,11 @@ class Nwchem(Package):
             'USE_PYTHONCONFIG=y',
             'PYTHONVERSION=%s' % spec['python'].version.up_to(2),
             'PYTHONHOME=%s' % spec['python'].prefix,
-            'BLASOPT=%s %s' % (
-                to_link_flags(spec['lapack'].lapack_shared_lib),
-                to_link_flags(spec['blas'].blas_shared_lib)),
-            'BLAS_LIB=%s' % to_link_flags(spec['blas'].blas_shared_lib),
-            'LAPACK_LIB=%s' % to_link_flags(spec['lapack'].lapack_shared_lib),
+            'BLASOPT=%s' % ((lapack + blas).ld_flags),
+            'BLAS_LIB=%s' % blas.ld_flags,
+            'LAPACK_LIB=%s' % lapack.ld_flags,
             'USE_SCALAPACK=y',
-            'SCALAPACK=%s' % spec['scalapack'].fc_link,
+            'SCALAPACK=%s' % scalapack.ld_flags,
             'NWCHEM_MODULES=all python',
             'NWCHEM_LONG_PATHS=Y'  # by default NWCHEM_TOP is 64 char max
         ])
diff --git a/var/spack/repos/builtin/packages/octopus/package.py b/var/spack/repos/builtin/packages/octopus/package.py
index ff4a106940..adb760f06d 100644
--- a/var/spack/repos/builtin/packages/octopus/package.py
+++ b/var/spack/repos/builtin/packages/octopus/package.py
@@ -46,13 +46,13 @@ class Octopus(Package):
     # FEAST, Libfm, PFFT, ISF, PNFFT
 
     def install(self, spec, prefix):
+        lapack = spec['lapack'].lapack_libs
+        blas = spec['blas'].blas_libs
         args = []
         args.extend([
             '--prefix=%s' % prefix,
-            '--with-blas=%s' % to_link_flags(
-                spec['blas'].blas_shared_lib),
-            '--with-lapack=%s' % to_link_flags(
-                spec['lapack'].lapack_shared_lib),
+            '--with-blas=%s' % blas.ld_flags,
+            '--with-lapack=%s' % lapack.ld_flags,
             '--with-gsl-prefix=%s' % spec['gsl'].prefix,
             '--with-libxc-prefix=%s' % spec['libxc'].prefix,
             'CC=%s' % spec['mpi'].mpicc,
diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py
index 37f7a7005d..1f6dd0e013 100644
--- a/var/spack/repos/builtin/packages/openblas/package.py
+++ b/var/spack/repos/builtin/packages/openblas/package.py
@@ -30,8 +30,9 @@ import os
 class Openblas(Package):
     """OpenBLAS: An optimized BLAS library"""
     homepage = "http://www.openblas.net"
-    url      = "http://github.com/xianyi/OpenBLAS/archive/v0.2.15.tar.gz"
+    url = "http://github.com/xianyi/OpenBLAS/archive/v0.2.15.tar.gz"
 
+    version('0.2.19', '28c998054fd377279741c6f0b9ea7941')
     version('0.2.18', '805e7f660877d588ea7e3792cda2ee65')
     version('0.2.17', '664a12807f2a2a7cda4781e3ab2ae0e1')
     version('0.2.16', 'fef46ab92463bdbb1479dcec594ef6dc')
@@ -50,6 +51,17 @@ class Openblas(Package):
 
     patch('make.patch')
 
+    @property
+    def blas_libs(self):
+        shared = True if '+shared' in self.spec else False
+        return find_libraries(
+            ['libopenblas'], root=self.prefix, shared=shared, recurse=True
+        )
+
+    @property
+    def lapack_libs(self):
+        return self.blas_libs
+
     def install(self, spec, prefix):
         # As of 06/2016 there is no mechanism to specify that packages which
         # depends on Blas/Lapack need C or/and Fortran symbols. For now
@@ -99,41 +111,11 @@ class Openblas(Package):
         # no quotes around prefix (spack doesn't use a shell)
         make('install', "PREFIX=%s" % prefix, *make_defs)
 
-        # Blas virtual package should provide blas.a and libblas.a
-        with working_dir(prefix.lib):
-            symlink('libopenblas.a', 'blas.a')
-            symlink('libopenblas.a', 'libblas.a')
-            if '+shared' in spec:
-                symlink('libopenblas.%s' % dso_suffix,
-                        'libblas.%s' % dso_suffix)
-
-        # Lapack virtual package should provide liblapack.a
-        with working_dir(prefix.lib):
-            symlink('libopenblas.a', 'liblapack.a')
-            if '+shared' in spec:
-                symlink('libopenblas.%s' % dso_suffix,
-                        'liblapack.%s' % dso_suffix)
-
         # Openblas may pass its own test but still fail to compile Lapack
         # symbols. To make sure we get working Blas and Lapack, do a small
         # test.
         self.check_install(spec)
 
-    def setup_dependent_package(self, module, dspec):
-        # This is WIP for a prototype interface for virtual packages.
-        # We can update this as more builds start depending on BLAS/LAPACK.
-        libdir = find_library_path('libopenblas.a',
-                                   self.prefix.lib64,
-                                   self.prefix.lib)
-
-        self.spec.blas_static_lib   = join_path(libdir, 'libopenblas.a')
-        self.spec.lapack_static_lib = self.spec.blas_static_lib
-
-        if '+shared' in self.spec:
-            self.spec.blas_shared_lib   = join_path(libdir, 'libopenblas.%s' %
-                                                    dso_suffix)
-            self.spec.lapack_shared_lib = self.spec.blas_shared_lib
-
     def check_install(self, spec):
         source_file = join_path(os.path.dirname(self.module.__file__),
                                 'test_cblas_dgemm.c')
@@ -141,10 +123,8 @@ class Openblas(Package):
                                  'test_cblas_dgemm.output')
 
         include_flags = ["-I%s" % join_path(spec.prefix, "include")]
-        link_flags = ["-L%s" % join_path(spec.prefix, "lib"),
-                      "-llapack",
-                      "-lblas",
-                      "-lpthread"]
+        link_flags = self.lapack_libs.ld_flags.split()
+        link_flags.extend(["-lpthread"])
         if '+openmp' in spec:
             link_flags.extend([self.compiler.openmp_flag])
 
diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py
index ca6bd473f1..bb356aaccc 100644
--- a/var/spack/repos/builtin/packages/openmpi/package.py
+++ b/var/spack/repos/builtin/packages/openmpi/package.py
@@ -65,6 +65,7 @@ class Openmpi(Package):
     list_url = "http://www.open-mpi.org/software/ompi/"
     list_depth = 3
 
+    version('2.0.1', '6f78155bd7203039d2448390f3b51c96')
     version('2.0.0', 'cdacc800cb4ce690c1f1273cb6366674')
     version('1.10.3', 'e2fe4513200e2aaa1500b762342c674b')
     version('1.10.2', 'b2f43d9635d2d52826e5ef9feb97fd4c')
@@ -165,6 +166,10 @@ class Openmpi(Package):
                        "--enable-shared",
                        "--enable-static"]
 
+        # for Open-MPI 2.0:, C++ bindings are disabled by default.
+        if self.spec.satisfies('@2.0:'):
+            config_args.extend(['--enable-mpi-cxx'])
+
         if getattr(self, 'config_extra', None) is not None:
             config_args.extend(self.config_extra)
 
diff --git a/var/spack/repos/builtin/packages/openssl/package.py b/var/spack/repos/builtin/packages/openssl/package.py
index 8d9049a8f7..12b5ed9c52 100644
--- a/var/spack/repos/builtin/packages/openssl/package.py
+++ b/var/spack/repos/builtin/packages/openssl/package.py
@@ -36,24 +36,21 @@ class Openssl(Package):
     homepage = "http://www.openssl.org"
     url = "ftp://openssl.org/source/openssl-1.0.1h.tar.gz"
 
-    version('1.0.1h', '8d6d684a9430d5cc98a62a5d8fbda8cf')
-    version('1.0.1r', '1abd905e079542ccae948af37e393d28')
-    version('1.0.1t', '9837746fcf8a6727d46d22ca35953da1')
-    version('1.0.2d', '38dd619b2e77cbac69b99f52a053d25a')
-    version('1.0.2e', '5262bfa25b60ed9de9f28d5d52d77fc5')
-    version('1.0.2f', 'b3bf73f507172be9292ea2a8c28b659d')
-    version('1.0.2g', 'f3c710c045cdee5fd114feb69feba7aa')
+    version('1.0.2j', '96322138f0b69e61b7212bc53d5e912b')
+    version('1.0.2i', '678374e63f8df456a697d3e5e5a931fb')
     version('1.0.2h', '9392e65072ce4b614c1392eefc1f23d0')
+    version('1.0.2g', 'f3c710c045cdee5fd114feb69feba7aa')
+    version('1.0.2f', 'b3bf73f507172be9292ea2a8c28b659d')
+    version('1.0.2e', '5262bfa25b60ed9de9f28d5d52d77fc5')
+    version('1.0.2d', '38dd619b2e77cbac69b99f52a053d25a')
+    version('1.0.1u', '130bb19745db2a5a09f22ccbbf7e69d0')
+    version('1.0.1t', '9837746fcf8a6727d46d22ca35953da1')
+    version('1.0.1r', '1abd905e079542ccae948af37e393d28')
+    version('1.0.1h', '8d6d684a9430d5cc98a62a5d8fbda8cf')
 
     depends_on("zlib")
     parallel = False
 
-    def url_for_version(self, version):
-        if '@system' in self.spec:
-            return '@system (reserved version for system openssl)'
-        else:
-            return super(Openssl, self).url_for_version(self.version)
-
     def handle_fetch_error(self, error):
         tty.warn("Fetching OpenSSL failed. This may indicate that OpenSSL has "
                  "been updated, and the version in your instance of Spack is "
diff --git a/var/spack/repos/builtin/packages/opium/package.py b/var/spack/repos/builtin/packages/opium/package.py
index 2c81d92cc0..521f917230 100644
--- a/var/spack/repos/builtin/packages/opium/package.py
+++ b/var/spack/repos/builtin/packages/opium/package.py
@@ -29,7 +29,7 @@ class Opium(Package):
     """DFT pseudopotential generation project"""
 
     homepage = "https://opium.sourceforge.net/index.html"
-    url      = "https://downloads.sourceforge.net/project/opium/opium/opium-v3.8/opium-v3.8-src.tgz"
+    url = "https://downloads.sourceforge.net/project/opium/opium/opium-v3.8/opium-v3.8-src.tgz"
 
     version('3.8', 'f710c0f869e70352b4a510c31e13bf9f')
 
@@ -37,12 +37,8 @@ class Opium(Package):
     depends_on('lapack')
 
     def install(self, spec, prefix):
-        options = [
-            'LDFLAGS=%s %s' % (
-                to_link_flags(spec['lapack'].lapack_shared_lib),
-                to_link_flags(spec['blas'].blas_shared_lib)
-            )
-        ]
+        libs = spec['lapack'].lapack_libs + spec['blas'].blas_libs
+        options = ['LDFLAGS=%s' % libs.ld_flags]
 
         configure(*options)
         with working_dir("src", create=False):
diff --git a/var/spack/repos/builtin/packages/pango/package.py b/var/spack/repos/builtin/packages/pango/package.py
index 2da20e9dc2..75c4ac807d 100644
--- a/var/spack/repos/builtin/packages/pango/package.py
+++ b/var/spack/repos/builtin/packages/pango/package.py
@@ -38,6 +38,7 @@ class Pango(Package):
     version('1.36.8', '217a9a753006275215fa9fa127760ece')
     version('1.40.1', '6fc88c6529890d6c8e03074d57a3eceb')
 
+    depends_on("pkg-config", type="build")
     depends_on("harfbuzz")
     depends_on("cairo")
 
diff --git a/var/spack/repos/builtin/packages/papi/package.py b/var/spack/repos/builtin/packages/papi/package.py
index 5c4abe1730..90a7490e75 100644
--- a/var/spack/repos/builtin/packages/papi/package.py
+++ b/var/spack/repos/builtin/packages/papi/package.py
@@ -41,6 +41,7 @@ class Papi(Package):
     homepage = "http://icl.cs.utk.edu/papi/index.html"
 
     url      = "http://icl.cs.utk.edu/projects/papi/downloads/papi-5.4.1.tar.gz"
+    version('5.5.0', '5e1244a04ca031d4cc29b46ce3dd05b5')
     version('5.4.3', '3211b5a5bb389fe692370f5cf4cc2412')
     version('5.4.1', '9134a99219c79767a11463a76b0b01a2')
     version('5.3.0', '367961dd0ab426e5ae367c2713924ffb')
diff --git a/var/spack/repos/builtin/packages/parmetis/package.py b/var/spack/repos/builtin/packages/parmetis/package.py
index 8afae91af1..74e00cc9e0 100644
--- a/var/spack/repos/builtin/packages/parmetis/package.py
+++ b/var/spack/repos/builtin/packages/parmetis/package.py
@@ -38,11 +38,9 @@ class Parmetis(Package):
     version('4.0.3', 'f69c479586bf6bb7aff6a9bc0c739628')
     version('4.0.2', '0912a953da5bb9b5e5e10542298ffdce')
 
-    variant('shared', default=True,
-            description='Enables the build of shared libraries')
-    variant('debug', default=False,
-            description='Builds the library in debug mode')
-    variant('gdb', default=False, description='Enables gdb support')
+    variant('shared', default=True, description='Enables the build of shared libraries.')
+    variant('debug', default=False, description='Builds the library in debug mode.')
+    variant('gdb', default=False, description='Enables gdb support.')
 
     depends_on('cmake@2.8:', type='build')
     depends_on('mpi')
@@ -50,9 +48,9 @@ class Parmetis(Package):
 
     patch('enable_external_metis.patch')
     # bug fixes from PETSc developers
-    # https://bitbucket.org/petsc/pkg-parmetis/commits/1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b/raw/
+    # https://bitbucket.org/petsc/pkg-parmetis/commits/1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b/raw/  # NOQA: E501
     patch('pkg-parmetis-1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b.patch')
-    # https://bitbucket.org/petsc/pkg-parmetis/commits/82409d68aa1d6cbc70740d0f35024aae17f7d5cb/raw/
+    # https://bitbucket.org/petsc/pkg-parmetis/commits/82409d68aa1d6cbc70740d0f35024aae17f7d5cb/raw/  # NOQA: E501
     patch('pkg-parmetis-82409d68aa1d6cbc70740d0f35024aae17f7d5cb.patch')
 
     def url_for_version(self, version):
@@ -60,12 +58,10 @@ class Parmetis(Package):
         return '%s/%sparmetis-%s.tar.gz' % (Parmetis.base_url, verdir, version)
 
     def install(self, spec, prefix):
-        options = []
-        options.extend(std_cmake_args)
-
-        build_directory = join_path(self.stage.path, 'spack-build')
         source_directory = self.stage.source_path
+        build_directory = join_path(source_directory, 'build')
 
+        options = std_cmake_args[:]
         options.extend([
             '-DGKLIB_PATH:PATH=%s/GKlib' % spec['metis'].prefix.include,
             '-DMETIS_PATH:PATH=%s' % spec['metis'].prefix,
diff --git a/var/spack/repos/builtin/packages/pdt/package.py b/var/spack/repos/builtin/packages/pdt/package.py
index 648b2fab98..bed01aeefb 100644
--- a/var/spack/repos/builtin/packages/pdt/package.py
+++ b/var/spack/repos/builtin/packages/pdt/package.py
@@ -35,13 +35,14 @@ class Pdt(Package):
 
     """
     homepage = "https://www.cs.uoregon.edu/research/pdt/home.php"
-    url      = "http://www.cs.uoregon.edu/research/paracomp/pdtoolkit/Download/pdt-3.22.1.tar.gz"
+    url      = "http://www.cs.uoregon.edu/research/paracomp/pdtoolkit/Download/pdtoolkit-3.22.1.tar.gz"
 
-    version('3.22.1', 'be6fac0b1edb3e3287b0cb78741a24b6')
-    version('3.22',   'e6c7879fc49ac5ff67a76ce31ef9e251')
-    version('3.21',   '8df94298b71703decf680709a4ddf68f')
-    version('3.19',   'ba5591994998771fdab216699e362228')
-    version('3.18.1', '05281b5c82a4754df936df99ad7eec0f')
+    version('3.22.1', 'b56b9b3e621161c7fd9e4908b944840d')
+    version('3.22',   '982d667617802962a1f7fe6c4c31184f')
+    version('3.21',   '3092ca0d8833b69992c17e63ae66c263')
+    version('3.20',   'c3edabe202926abe04552e33cd39672d')
+    version('3.19',   '5c5e1e6607086aa13bf4b1b9befc5864')
+    version('3.18.1', 'e401534f5c476c3e77f05b7f73b6c4f2')
 
     def install(self, spec, prefix):
         configure('-prefix=%s' % prefix)
diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py
index 73091bb182..7ee2d29f4d 100644
--- a/var/spack/repos/builtin/packages/petsc/package.py
+++ b/var/spack/repos/builtin/packages/petsc/package.py
@@ -22,7 +22,9 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
+
 import os
+import sys
 from spack import *
 
 
@@ -114,6 +116,11 @@ class Petsc(Package):
                 '--with-mpi=1',
                 '--with-mpi-dir=%s' % self.spec['mpi'].prefix,
             ]
+        if sys.platform != "darwin":
+            compiler_opts.extend([
+                '--with-cpp=cpp',
+                '--with-cxxcpp=cpp',
+            ])
         return compiler_opts
 
     def install(self, spec, prefix):
@@ -125,9 +132,15 @@ class Petsc(Package):
             '--with-scalar-type=%s' % (
                 'complex' if '+complex' in spec else 'real'),
             '--with-shared-libraries=%s' % ('1' if '+shared' in spec else '0'),
-            '--with-debugging=%s' % ('1' if '+debug' in spec else '0'),
-            '--with-blas-lapack-dir=%s' % spec['lapack'].prefix
+            '--with-debugging=%s' % ('1' if '+debug' in spec else '0')
         ])
+        # Make sure we use exactly the same Blas/Lapack libraries
+        # across the DAG. To that end list them explicitly
+        lapack_blas = spec['lapack'].lapack_libs + spec['blas'].blas_libs
+        options.extend([
+            '--with-blas-lapack-lib=%s' % lapack_blas.joined()
+        ])
+
         # Activates library support if needed
         for library in ('metis', 'boost', 'hdf5', 'hypre', 'parmetis',
                         'mumps', 'scalapack'):
diff --git a/var/spack/repos/builtin/packages/pexsi/package.py b/var/spack/repos/builtin/packages/pexsi/package.py
index e74ad6df01..9fc71d4c52 100644
--- a/var/spack/repos/builtin/packages/pexsi/package.py
+++ b/var/spack/repos/builtin/packages/pexsi/package.py
@@ -67,8 +67,8 @@ class Pexsi(Package):
             '@PARMETIS_PREFIX': self.spec['parmetis'].prefix,
             '@LAPACK_PREFIX': self.spec['lapack'].prefix,
             '@BLAS_PREFIX': self.spec['blas'].prefix,
-            '@LAPACK_LIBS': self.spec['lapack'].lapack_shared_lib,
-            '@BLAS_LIBS': self.spec['lapack'].blas_shared_lib,
+            '@LAPACK_LIBS': self.spec['lapack'].lapack_libs.joined(),
+            '@BLAS_LIBS': self.spec['lapack'].blas_libs.joined(),
             '@STDCXX_LIB': ' '.join(self.compiler.stdcxx_libs)
         }
 
diff --git a/var/spack/repos/builtin/packages/pgi/package.py b/var/spack/repos/builtin/packages/pgi/package.py
index c58d563682..6fa8457dc9 100644
--- a/var/spack/repos/builtin/packages/pgi/package.py
+++ b/var/spack/repos/builtin/packages/pgi/package.py
@@ -36,7 +36,7 @@ class Pgi(Package):
     architecture) to the format: pgi-<version>.tar.gz. Spack will search your
     current directory for a file of this format. Alternatively, add this
     file to a mirror so that Spack can find it. For instructions on how to
-    set up a mirror, see http://software.llnl.gov/spack/mirrors.html"""
+    set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html"""
 
     homepage = "http://www.pgroup.com/"
     url = "file://%s/pgi-16.3.tar.gz" % os.getcwd()
diff --git a/var/spack/repos/builtin/packages/pixman/package.py b/var/spack/repos/builtin/packages/pixman/package.py
index 39041587f5..41aad0c90a 100644
--- a/var/spack/repos/builtin/packages/pixman/package.py
+++ b/var/spack/repos/builtin/packages/pixman/package.py
@@ -39,6 +39,7 @@ class Pixman(Package):
 
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix,
+                  "--disable-mmx",
                   "--disable-gtk")
         make()
         make("install")
diff --git a/var/spack/repos/builtin/packages/plumed/package.py b/var/spack/repos/builtin/packages/plumed/package.py
index 79632abf38..60dfdf7405 100644
--- a/var/spack/repos/builtin/packages/plumed/package.py
+++ b/var/spack/repos/builtin/packages/plumed/package.py
@@ -66,6 +66,8 @@ class Plumed(Package):
     depends_on('mpi', when='+mpi')
     depends_on('gsl', when='+gsl')
 
+    depends_on('autoconf', type='build')
+
     # Dictionary mapping PLUMED versions to the patches it provides
     # interactively
     plumed_patches = {
@@ -98,6 +100,12 @@ class Plumed(Package):
         module.plumed = Executable(join_path(self.spec.prefix.bin, 'plumed'))
 
     def install(self, spec, prefix):
+        # This part is needed to avoid linking with gsl cblas
+        # interface which will mask the cblas interface
+        # provided by optimized libraries due to linking order
+        filter_file('-lgslcblas', '', 'configure.ac')
+        autoreconf('-ivf')
+
         # From plumed docs :
         # Also consider that this is different with respect to what some other
         # configure script does in that variables such as MPICXX are
diff --git a/var/spack/repos/builtin/packages/psi4/package.py b/var/spack/repos/builtin/packages/psi4/package.py
index 6296d0cee6..566aa50f44 100644
--- a/var/spack/repos/builtin/packages/psi4/package.py
+++ b/var/spack/repos/builtin/packages/psi4/package.py
@@ -32,7 +32,7 @@ class Psi4(Package):
     a variety of molecular properties."""
 
     homepage = "http://www.psicode.org/"
-    url      = "https://github.com/psi4/psi4/archive/0.5.tar.gz"
+    url = "https://github.com/psi4/psi4/archive/0.5.tar.gz"
 
     version('0.5', '53041b8a9be3958384171d0d22f9fdd0')
 
@@ -62,9 +62,10 @@ class Psi4(Package):
     def install(self, spec, prefix):
         cmake_args = [
             '-DBLAS_TYPE={0}'.format(spec['blas'].name.upper()),
-            '-DBLAS_LIBRARIES={0}'.format(spec['blas'].blas_shared_lib),
+            '-DBLAS_LIBRARIES={0}'.format(spec['blas'].blas_libs.joined()),
             '-DLAPACK_TYPE={0}'.format(spec['lapack'].name.upper()),
-            '-DLAPACK_LIBRARIES={0}'.format(spec['lapack'].lapack_shared_lib),
+            '-DLAPACK_LIBRARIES={0}'.format(
+                spec['lapack'].lapack_libs.joined()),
             '-DBOOST_INCLUDEDIR={0}'.format(spec['boost'].prefix.include),
             '-DBOOST_LIBRARYDIR={0}'.format(spec['boost'].prefix.lib),
             '-DENABLE_CHEMPS2=OFF'
@@ -90,9 +91,9 @@ class Psi4(Package):
 
         kwargs = {'ignore_absent': True, 'backup': False, 'string': True}
 
-        cc_files  = ['bin/psi4-config']
+        cc_files = ['bin/psi4-config']
         cxx_files = ['bin/psi4-config', 'include/psi4/psiconfig.h']
-        template  = 'share/psi4/plugin/Makefile.template'
+        template = 'share/psi4/plugin/Makefile.template'
 
         for filename in cc_files:
             filter_file(os.environ['CC'], self.compiler.cc,
diff --git a/var/spack/repos/builtin/packages/py-beautifulsoup4/package.py b/var/spack/repos/builtin/packages/py-beautifulsoup4/package.py
index 64368fe70d..d3a260bd7f 100644
--- a/var/spack/repos/builtin/packages/py-beautifulsoup4/package.py
+++ b/var/spack/repos/builtin/packages/py-beautifulsoup4/package.py
@@ -37,5 +37,7 @@ class PyBeautifulsoup4(Package):
 
     extends('python')
 
+    depends_on('py-setuptools', type='build')
+
     def install(self, spec, prefix):
         python('setup.py', 'install', '--prefix={0}'.format(prefix))
diff --git a/var/spack/repos/builtin/packages/py-numpy/package.py b/var/spack/repos/builtin/packages/py-numpy/package.py
index f800b5e834..0d68a892f2 100644
--- a/var/spack/repos/builtin/packages/py-numpy/package.py
+++ b/var/spack/repos/builtin/packages/py-numpy/package.py
@@ -32,9 +32,12 @@ class PyNumpy(Package):
     sophisticated (broadcasting) functions, tools for integrating C/C++ and
     Fortran code, and useful linear algebra, Fourier transform, and random
     number capabilities"""
+
     homepage = "http://www.numpy.org/"
     url      = "https://pypi.python.org/packages/source/n/numpy/numpy-1.9.1.tar.gz"
 
+    version('1.11.1', '2f44a895a8104ffac140c3a70edbd450',
+            url="https://pypi.python.org/packages/e0/4c/515d7c4ac424ff38cc919f7099bf293dd064ba9a600e1e3835b3edefdb18/numpy-1.11.1.tar.gz")
     version('1.11.0', 'bc56fb9fc2895aa4961802ffbdb31d0b')
     version('1.10.4', 'aed294de0aa1ac7bd3f9745f4f1968ad')
     version('1.9.2',  'a1ed53432dbcd256398898d35bc8e645')
@@ -44,6 +47,7 @@ class PyNumpy(Package):
     variant('lapack', default=True)
 
     extends('python')
+    depends_on('python@2.6:2.8,3.2:')
     depends_on('py-nose', type='build')
     depends_on('py-setuptools', type='build')
     depends_on('blas',   when='+blas')
@@ -79,4 +83,4 @@ class PyNumpy(Package):
                 f.write('library_dirs=%s\n' % ':'.join(library_dirs))
                 f.write('rpath=%s\n' % ':'.join(library_dirs))
 
-        python('setup.py', 'install', '--prefix=%s' % prefix)
+        setup_py('install', '--prefix={0}'.format(prefix))
diff --git a/var/spack/repos/builtin/packages/py-pil/package.py b/var/spack/repos/builtin/packages/py-pil/package.py
index 2b3cce26d3..29a86d1e85 100644
--- a/var/spack/repos/builtin/packages/py-pil/package.py
+++ b/var/spack/repos/builtin/packages/py-pil/package.py
@@ -37,7 +37,10 @@ class PyPil(Package):
 
     provides('pil')
 
+    # py-pil currently only works with Python2.
+    # If you are using Python 3, try using py-pillow instead.
     extends('python')
+    depends_on('python@1.5.2:2.8')
 
     def install(self, spec, prefix):
         python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/repos/builtin/packages/py-pillow/package.py b/var/spack/repos/builtin/packages/py-pillow/package.py
index 1d8b3faa6f..211e3b4199 100644
--- a/var/spack/repos/builtin/packages/py-pillow/package.py
+++ b/var/spack/repos/builtin/packages/py-pillow/package.py
@@ -32,7 +32,7 @@ class PyPillow(Package):
     capabilities."""
 
     homepage = "https://python-pillow.org/"
-    url      = "https://pypi.python.org/packages/source/P/Pillow/Pillow-3.0.0.tar.gz"
+    url = "https://pypi.python.org/packages/source/P/Pillow/Pillow-3.0.0.tar.gz"
 
     # TODO: This version should be deleted once the next release comes out.
     # TODO: It fixes a bug that prevented us from linking to Tk/Tcl.
diff --git a/var/spack/repos/builtin/packages/py-proj/package.py b/var/spack/repos/builtin/packages/py-proj/package.py
new file mode 100644
index 0000000000..2835bfcca8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-proj/package.py
@@ -0,0 +1,52 @@
+##############################################################################
+# Copyright (c) 2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by David Beckingsale, david@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License (as published by
+# the Free Software Foundation) version 2.1 dated February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program; if not, write to the Free Software Foundation,
+# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+
+from spack import *
+
+
+class PyProj(Package):
+    """Python interface to the PROJ.4 Library."""
+    homepage = "http://jswhit.github.io/pyproj/"
+    url      = "https://github.com/jswhit/pyproj/tarball/v1.9.5.1rel"
+
+    # This is not a tagged release of pyproj.
+    # The changes in this "version" fix some bugs, especially with Python3 use.
+    version('1.9.5.1.1', 'd035e4bc704d136db79b43ab371b27d2',
+        url='https://www.github.com/jswhit/pyproj/tarball/0be612cc9f972e38b50a90c946a9b353e2ab140f')
+
+    version('1.9.5.1', 'a4b80d7170fc82aee363d7f980279835')
+
+    extends('python')
+
+    depends_on('py-cython', type='build')
+    depends_on('py-setuptools', type='build')
+
+    # NOTE: py-proj does NOT depends_on('proj').
+    # The py-proj git repo actually includes the correct version of PROJ.4,
+    # which is built internally as part of the py-proj build.
+    # Adding depends_on('proj') will cause mysterious build errors.
+
+    def install(self, spec, prefix):
+        setup_py('install', '--prefix=%s' % prefix)
diff --git a/var/spack/repos/builtin/packages/py-py2neo/package.py b/var/spack/repos/builtin/packages/py-py2neo/package.py
index a79c2e477b..97632493af 100644
--- a/var/spack/repos/builtin/packages/py-py2neo/package.py
+++ b/var/spack/repos/builtin/packages/py-py2neo/package.py
@@ -27,9 +27,10 @@ from spack import Package
 
 
 class PyPy2neo(Package):
-    """FIXME: put a proper description of your package here."""
-    # FIXME: add a proper url for your package's homepage here.
-    homepage = "http://www.example.com"
+    """Py2neo is a client library and toolkit for working with Neo4j from
+    within Python applications and from the command line."""
+
+    homepage = "http://py2neo.org/"
     url      = "https://github.com/nigelsmall/py2neo/archive/py2neo-2.0.8.tar.gz"
 
     version('2.0.8', 'e3ec5172a9e006515ef4155688a05a55')
diff --git a/var/spack/repos/builtin/packages/py-scipy/package.py b/var/spack/repos/builtin/packages/py-scipy/package.py
index cab516e1df..abb843f8ee 100644
--- a/var/spack/repos/builtin/packages/py-scipy/package.py
+++ b/var/spack/repos/builtin/packages/py-scipy/package.py
@@ -26,17 +26,25 @@ from spack import *
 
 
 class PyScipy(Package):
-    """Scientific Library for Python."""
+    """SciPy (pronounced "Sigh Pie") is a Scientific Library for Python.
+    It provides many user-friendly and efficient numerical routines such
+    as routines for numerical integration and optimization."""
+
     homepage = "http://www.scipy.org/"
-    url      = "https://pypi.python.org/packages/source/s/scipy/scipy-0.15.0.tar.gz"
+    url = "https://pypi.python.org/packages/source/s/scipy/scipy-0.15.0.tar.gz"
 
+    version('0.18.1', '5fb5fb7ccb113ab3a039702b6c2f3327',
+            url="https://pypi.python.org/packages/22/41/b1538a75309ae4913cdbbdc8d1cc54cae6d37981d2759532c1aa37a41121/scipy-0.18.1.tar.gz")
     version('0.17.0', '5ff2971e1ce90e762c59d2cd84837224')
     version('0.15.1', 'be56cd8e60591d6332aac792a5880110')
     version('0.15.0', '639112f077f0aeb6d80718dc5019dc7a')
 
     extends('python')
+    depends_on('python@2.6:2.8,3.2:')
     depends_on('py-nose', type='build')
-    depends_on('py-numpy+blas+lapack', type=nolink)
+    # Known not to work with 2.23, 2.25
+    depends_on('binutils@2.26:', type='build')
+    depends_on('py-numpy@1.7.1:+blas+lapack', type=nolink)
 
     def install(self, spec, prefix):
         if 'atlas' in spec:
@@ -45,7 +53,7 @@ class PyScipy(Package):
             env['ATLAS'] = join_path(
                 spec['atlas'].prefix.lib, 'libatlas.' + dso_suffix)
         else:
-            env['BLAS']   = spec['blas'].blas_shared_lib
-            env['LAPACK'] = spec['lapack'].lapack_shared_lib
+            env['BLAS'] = spec['blas'].blas_libs.joined()
+            env['LAPACK'] = spec['lapack'].lapack_libs.joined()
 
-        python('setup.py', 'install', '--prefix=%s' % prefix)
+        setup_py('install', '--prefix={0}'.format(prefix))
diff --git a/var/spack/repos/builtin/packages/py-yt/package.py b/var/spack/repos/builtin/packages/py-yt/package.py
new file mode 100644
index 0000000000..646bd4db2f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-yt/package.py
@@ -0,0 +1,78 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+
+from spack import *
+
+
+class PyYt(Package):
+    """Volumetric Data Analysis
+
+       yt is a python package for analyzing and visualizing
+       volumetric, multi-resolution data from astrophysical
+       simulations, radio telescopes, and a burgeoning
+       interdisciplinary community.
+    """
+    homepage = "http://yt-project.org"
+    url = "https://bitbucket.org/yt_analysis/yt"
+
+    version("3.3.1", hg="https://bitbucket.org/yt_analysis/yt",
+            tag="yt-3.3.1", commit="9bc3d0e9b750c923d44d73c447df64fc431f5838")
+    version("3.2.3", hg="https://bitbucket.org/yt_analysis/yt",
+            tag="yt-3.2.3", commit="83d2c1e9313e7d83eb5b96888451ff2646fd8ff3")
+    version("3.1.0", hg="https://bitbucket.org/yt_analysis/yt",
+            tag="yt-3.1.0", commit="fd7cdc4836188a3badf81adb477bcc1b9632e485")
+    version("3.0.2", hg="https://bitbucket.org/yt_analysis/yt",
+            tag="yt-3.0.2", commit="511887af4c995a78fe606e58ce8162c88380ecdc")
+    version("2.6.3", hg="https://bitbucket.org/yt_analysis/yt",
+            tag="yt-2.6.3", commit="816186f16396a16853810ac9ebcde5057d8d5b1a")
+    version("development", hg="https://bitbucket.org/yt_analysis/yt",
+            branch="yt")
+
+    variant("astropy", default=True, description="enable astropy support")
+    variant("h5py", default=True, description="enable h5py support")
+    variant("scipy", default=True, description="enable scipy support")
+
+    extends("python")
+
+    depends_on("py-astropy", type="nolink", when="+astropy")
+    depends_on("py-cython", type="nolink")
+    depends_on("py-h5py", type="nolink", when="+h5py")
+    depends_on("py-ipython", type="nolink")
+    depends_on("py-matplotlib", type="nolink")
+    depends_on("py-numpy", type="nolink")
+    depends_on("py-scipy", type="nolink", when="+scipy")
+    depends_on("py-setuptools", type="build")
+    depends_on("py-sympy", type="nolink")
+    depends_on("python @2.7:2.999,3.4:")
+
+    def install(self, spec, prefix):
+        setup_py("install", "--prefix=%s" % prefix)
+        self.check_install(spec, prefix)
+
+    def check_install(self, spec, prefix):
+        # The Python interpreter path can be too long for this
+        # yt = Executable(join_path(prefix.bin, "yt"))
+        # yt("--help")
+        python(join_path(prefix.bin, "yt"), "--help")
diff --git a/var/spack/repos/builtin/packages/python/ncurses.patch b/var/spack/repos/builtin/packages/python/ncurses.patch
new file mode 100644
index 0000000000..9054c03e7b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/python/ncurses.patch
@@ -0,0 +1,11 @@
+--- a/setup.py	2016-08-30 15:39:59.334926574 -0500
++++ b/setup.py	2016-08-30 15:46:57.227946339 -0500
+@@ -745,8 +745,6 @@
+         # use the same library for the readline and curses modules.
+         if 'curses' in readline_termcap_library:
+             curses_library = readline_termcap_library
+-        elif self.compiler.find_library_file(lib_dirs, 'ncursesw'):
+-            curses_library = 'ncursesw'
+         elif self.compiler.find_library_file(lib_dirs, 'ncurses'):
+             curses_library = 'ncurses'
+         elif self.compiler.find_library_file(lib_dirs, 'curses'):
diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py
index 57783b0542..f3380cf75d 100644
--- a/var/spack/repos/builtin/packages/python/package.py
+++ b/var/spack/repos/builtin/packages/python/package.py
@@ -74,6 +74,8 @@ class Python(Package):
     depends_on("tk",  when="+tk")
     depends_on("tcl", when="+tk")
 
+    patch('ncurses.patch')
+
     @when('@2.7,3.4:')
     def patch(self):
         # NOTE: Python's default installation procedure makes it possible for a
@@ -110,6 +112,8 @@ class Python(Package):
             'CPPFLAGS=-I{0}'.format(' -I'.join(dp.include for dp in dep_pfxs)),
             'LDFLAGS=-L{0}'.format(' -L'.join(dp.lib for dp in dep_pfxs)),
         ]
+        if spec.satisfies("platform=darwin") and ('%gcc' in spec):
+            config_args.append('--disable-toolbox-glue')
 
         if '+ucs4' in spec:
             if spec.satisfies('@:2.7'):
diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py
index 436702fa4e..2dba05ce13 100644
--- a/var/spack/repos/builtin/packages/qt/package.py
+++ b/var/spack/repos/builtin/packages/qt/package.py
@@ -6,7 +6,7 @@
 # Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
-# For details, see https://github.com/llnl/spack
+# For details, see https://github.com/llnl/spack  # NOQA: ignore=E501
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
@@ -24,13 +24,14 @@
 ##############################################################################
 from spack import *
 import os
+import sys
 
 
 class Qt(Package):
     """Qt is a comprehensive cross-platform C++ application framework."""
-    homepage = 'http://qt.io'
-    url      = 'http://download.qt.io/archive/qt/5.7/5.7.0/single/qt-everywhere-opensource-src-5.7.0.tar.gz'
-    list_url = 'http://download.qt.io/archive/qt/'
+    homepage = 'http://qt.io'  # NOQA: ignore=E501
+    url      = 'http://download.qt.io/archive/qt/5.7/5.7.0/single/qt-everywhere-opensource-src-5.7.0.tar.gz'  # NOQA: ignore=E501
+    list_url = 'http://download.qt.io/archive/qt/'  # NOQA: ignore=E501
     list_depth = 4
 
     version('5.7.0',  '9a46cce61fc64c20c3ac0a0e0fa41b42')
@@ -47,19 +48,25 @@ class Qt(Package):
     variant('krellpatch', default=False, description="Build with openspeedshop based patch.")
     variant('mesa',       default=False, description="Depend on mesa.")
     variant('gtk',        default=False, description="Build with gtkplus.")
+    variant('examples',   default=False, description="Build examples.")
+    variant('dbus',       default=False, description="Build with D-Bus support.")
 
     patch('qt3krell.patch', when='@3.3.8b+krellpatch')
 
-    # https://github.com/xboxdrv/xboxdrv/issues/188
+    # https://github.com/xboxdrv/xboxdrv/issues/188  # NOQA: ignore=E501
     patch('btn_trigger_happy.patch', when='@5.7.0:')
 
+    patch('qt4-corewlan-new-osx.patch', when='@4')
+    patch('qt4-pcre-include-conflict.patch', when='@4')
+    patch('qt4-el-capitan.patch', when='@4')
+
     # Use system openssl for security.
-    # depends_on("openssl")
+    depends_on("openssl")
 
     depends_on("gtkplus", when='+gtk')
     depends_on("libxml2")
     depends_on("zlib")
-    depends_on("dbus", when='@4:')
+    depends_on("dbus", when='@4:+dbus')
     depends_on("libtiff")
     depends_on("libpng@1.2.56", when='@3')
     depends_on("libpng", when='@4:')
@@ -71,11 +78,11 @@ class Qt(Package):
     # depends_on("flex", type='build')
     # depends_on("bison", type='build')
     # depends_on("ruby", type='build')
-    # depends_on("icu4c")
+    depends_on("icu4c")
 
     # OpenGL hardware acceleration
     depends_on("mesa", when='@4:+mesa')
-    depends_on("libxcb")
+    depends_on("libxcb", when=sys.platform != 'darwin')
 
     def url_for_version(self, version):
         # URL keeps getting more complicated with every release
@@ -123,7 +130,7 @@ class Qt(Package):
                         'mkspecs/common/g++-base.conf')
 
             # Necessary to build with GCC 6 and other modern compilers
-            # http://stackoverflow.com/questions/10354371/
+            # http://stackoverflow.com/questions/10354371/  # NOQA: ignore=E501
             filter_file('(^QMAKE_CXXFLAGS .*)', r'\1 -std=gnu++98',
                         'mkspecs/common/gcc-base.conf')
 
@@ -143,7 +150,7 @@ class Qt(Package):
 
     @property
     def common_config_args(self):
-        return [
+        config_args = [
             '-prefix', self.prefix,
             '-v',
             '-opensource',
@@ -152,7 +159,6 @@ class Qt(Package):
             '-shared',
             '-confirm-license',
             '-openssl-linked',
-            '-dbus-linked',
             '-optimized-qmake',
             '-no-openvg',
             '-no-pch',
@@ -160,10 +166,53 @@ class Qt(Package):
             '-no-nis'
         ]
 
+        if '~examples' in self.spec:
+            config_args.extend(['-nomake', 'examples'])
+
+        if '@4' in self.spec:
+            config_args.append('-no-phonon')
+
+        if '+dbus' in self.spec:
+            config_args.append('-dbus-linked')
+        else:
+            config_args.append('-no-dbus')
+
+        if '@5:' in self.spec and sys.platform == 'darwin':
+            config_args.extend([
+                '-no-xinput2',
+                '-no-xcb-xlib',
+                '-no-pulseaudio',
+                '-no-alsa',
+                '-no-gtkstyle',
+            ])
+
+        if '@4' in self.spec and sys.platform == 'darwin':
+            sdkpath = which('xcrun')('--show-sdk-path',
+                                     # XXX(macos): 10.11 SDK fails to configure
+                                     '--sdk', 'macosx10.9',
+                                     output=str)
+            config_args.extend([
+                '-sdk', sdkpath.strip(),
+            ])
+            use_clang_platform = False
+            if self.spec.compiler.name == 'clang' and \
+               str(self.spec.compiler.version).endwith('-apple'):
+                use_clang_platform = True
+            # No one uses gcc-4.2.1 anymore; this is clang.
+            if self.spec.compiler.name == 'gcc' and \
+               str(self.spec.compiler.version) == '4.2.1':
+                use_clang_platform = True
+            if use_clang_platform:
+                config_args.extend([
+                    '-platform', 'unsupported/macx-clang',
+                ])
+
+        return config_args
+
     # Don't disable all the database drivers, but should
     # really get them into spack at some point.
 
-    @when('@3')
+    @when('@3')  # NOQA: ignore=F811
     def configure(self):
         # A user reported that this was necessary to link Qt3 on ubuntu
         os.environ['LD_LIBRARY_PATH'] = os.getcwd() + '/lib'
@@ -174,30 +223,36 @@ class Qt(Package):
                   '-release',
                   '-fast')
 
-    @when('@4')
+    @when('@4')  # NOQA: ignore=F811
     def configure(self):
         configure('-fast',
                   '-no-webkit',
                   '{0}-gtkstyle'.format('' if '+gtk' in self.spec else '-no'),
+                  '-arch', str(self.spec.architecture.target),
                   *self.common_config_args)
 
-    @when('@5.0:5.6')
+    @when('@5.0:5.6')  # NOQA: ignore=F811
     def configure(self):
         configure('-no-eglfs',
                   '-no-directfb',
-                  '-qt-xcb',
                   '{0}-gtkstyle'.format('' if '+gtk' in self.spec else '-no'),
                   '-skip', 'qtwebkit',
                   *self.common_config_args)
 
-    @when('@5.7:')
+    @when('@5.7:')  # NOQA: ignore=F811
     def configure(self):
+        args = self.common_config_args
+
+        if not sys.platform == 'darwin':
+            args.extend([
+                '-qt-xcb',
+            ])
+
         configure('-no-eglfs',
                   '-no-directfb',
-                  '-qt-xcb',
                   '{0}-gtk'.format('' if '+gtk' in self.spec else '-no'),
                   '-skip', 'webengine',
-                  *self.common_config_args)
+                  *args)
 
     def install(self, spec, prefix):
         self.configure()
diff --git a/var/spack/repos/builtin/packages/qt/qt4-corewlan-new-osx.patch b/var/spack/repos/builtin/packages/qt/qt4-corewlan-new-osx.patch
new file mode 100644
index 0000000000..370edf7fa5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/qt/qt4-corewlan-new-osx.patch
@@ -0,0 +1,16 @@
+diff -Nr -U5 qt-everywhere-opensource-src-4.8.6/src/plugins/bearer/corewlan/corewlan.pro qt-everywhere-opensource-src-4.8.6.corewlan-new-osx/src/plugins/bearer/corewlan/corewlan.pro
+--- qt-everywhere-opensource-src-4.8.6/src/plugins/bearer/corewlan/corewlan.pro	2014-04-10 14:37:12.000000000 -0400
++++ qt-everywhere-opensource-src-4.8.6.corewlan-new-osx/src/plugins/bearer/corewlan/corewlan.pro	2015-12-02 12:21:34.608585392 -0500
+@@ -3,11 +3,11 @@
+ 
+ QT = core network
+ LIBS += -framework Foundation -framework SystemConfiguration
+ 
+ contains(QT_CONFIG, corewlan) {
+-    isEmpty(QMAKE_MAC_SDK)|contains(QMAKE_MAC_SDK, "/Developer/SDKs/MacOSX10\.[67]\.sdk") {
++    isEmpty(QMAKE_MAC_SDK)|contains(QMAKE_MAC_SDK, ".*MacOSX10\.([6789]|1[01])\.sdk") {
+          LIBS += -framework CoreWLAN -framework Security
+     }
+ }
+ 
+ HEADERS += qcorewlanengine.h \
diff --git a/var/spack/repos/builtin/packages/qt/qt4-el-capitan.patch b/var/spack/repos/builtin/packages/qt/qt4-el-capitan.patch
new file mode 100644
index 0000000000..35f154d3b0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/qt/qt4-el-capitan.patch
@@ -0,0 +1,31 @@
+From 27aa46933bb32a88c310fe5918a49a3f34d65dfe Mon Sep 17 00:00:00 2001
+From: Mike McQuaid <mike@mikemcquaid.com>
+Date: Sun, 13 Sep 2015 11:55:59 +0100
+Subject: [PATCH] Fix El Capitan build.
+
+---
+ src/gui/painting/qpaintengine_mac.cpp | 8 +-------
+ 1 file changed, 1 insertion(+), 7 deletions(-)
+
+diff --git a/src/gui/painting/qpaintengine_mac.cpp b/src/gui/painting/qpaintengine_mac.cpp
+index 4aa0668..63b646d 100644
+--- a/src/gui/painting/qpaintengine_mac.cpp
++++ b/src/gui/painting/qpaintengine_mac.cpp
+@@ -340,13 +340,7 @@ CGColorSpaceRef QCoreGraphicsPaintEngine::macDisplayColorSpace(const QWidget *wi
+     }
+ 
+     // Get the color space from the display profile.
+-    CGColorSpaceRef colorSpace = 0;
+-    CMProfileRef displayProfile = 0;
+-    CMError err = CMGetProfileByAVID((CMDisplayIDType)displayID, &displayProfile);
+-    if (err == noErr) {
+-        colorSpace = CGColorSpaceCreateWithPlatformColorSpace(displayProfile);
+-        CMCloseProfile(displayProfile);
+-    }
++    CGColorSpaceRef colorSpace = CGDisplayCopyColorSpace(displayID);
+ 
+     // Fallback: use generic DeviceRGB
+     if (colorSpace == 0)
+-- 
+2.3.8 (Apple Git-58)
+
diff --git a/var/spack/repos/builtin/packages/qt/qt4-pcre-include-conflict.patch b/var/spack/repos/builtin/packages/qt/qt4-pcre-include-conflict.patch
new file mode 100644
index 0000000000..854e564bfb
--- /dev/null
+++ b/var/spack/repos/builtin/packages/qt/qt4-pcre-include-conflict.patch
@@ -0,0 +1,16 @@
+diff -U5 -Nru qt-everywhere-opensource-src-4.8.6/src/3rdparty/javascriptcore/JavaScriptCore/yarr/RegexJIT.h qt-everywhere-opensource-src-4.8.6.pcre/src/3rdparty/javascriptcore/JavaScriptCore/yarr/RegexJIT.h
+--- qt-everywhere-opensource-src-4.8.6/src/3rdparty/javascriptcore/JavaScriptCore/yarr/RegexJIT.h	2014-04-10 14:37:12.000000000 -0400
++++ qt-everywhere-opensource-src-4.8.6.pcre/src/3rdparty/javascriptcore/JavaScriptCore/yarr/RegexJIT.h	2016-08-29 15:30:02.216546252 -0400
+@@ -32,11 +32,11 @@
+ 
+ #include "MacroAssembler.h"
+ #include "RegexPattern.h"
+ #include <UString.h>
+ 
+-#include <pcre.h>
++#include <pcre/pcre.h>
+ struct JSRegExp; // temporary, remove when fallback is removed.
+ 
+ #if CPU(X86) && !COMPILER(MSVC)
+ #define YARR_CALL __attribute__ ((regparm (3)))
+ #else
diff --git a/var/spack/repos/builtin/packages/qthreads/ldflags.patch b/var/spack/repos/builtin/packages/qthreads/ldflags.patch
deleted file mode 100644
index 0c15eab386..0000000000
--- a/var/spack/repos/builtin/packages/qthreads/ldflags.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/configure
-+++ b/configure
-@@ -40456,7 +40456,7 @@
-   hwloc_saved_LDFLAGS="$LDFLAGS"
-   if test "x$with_hwloc" != x; then
-   CPPFLAGS="-I$with_hwloc/include $CPPFLAGS"
--		 LDFLAGS="-L$with_hwloc/lib $CPPFLAGS"
-+		 LDFLAGS="-L$with_hwloc/lib $LDFLAGS"
- fi
-   
-   
diff --git a/var/spack/repos/builtin/packages/qthreads/package.py b/var/spack/repos/builtin/packages/qthreads/package.py
index 8d5cc87062..aa2f0ac67a 100644
--- a/var/spack/repos/builtin/packages/qthreads/package.py
+++ b/var/spack/repos/builtin/packages/qthreads/package.py
@@ -38,28 +38,16 @@ class Qthreads(Package):
        attain either state."""
     homepage = "http://www.cs.sandia.gov/qthreads/"
 
-    # Google Code has stopped serving tarballs
-    # We assume the tarballs will soon be available on Github instead
-    # url = "https://qthreads.googlecode.com/files/qthread-1.10.tar.bz2"
-    # version('1.10', '5af8c8bbe88c2a6d45361643780d1671')
+    url = "https://github.com/Qthreads/qthreads/releases/download/1.10/qthread-1.10.tar.bz2"
+    version("1.11", "68b5f9a41cfd1a2ac112cc4db0612326")
+    version("1.10", "d1cf3cf3f30586921359f7840171e551")
 
-    # Temporarily install from a git branch
-    url = "https://github.com/Qthreads/qthreads"
-    version("1.10",
-            git="https://github.com/Qthreads/qthreads",
-            branch="release-1.10")
+    patch("restrict.patch", when="@:1.10")
+    patch("trap.patch", when="@:1.10")
 
-    # patch("ldflags.patch")
-    patch("restrict.patch")
-    patch("trap.patch")
-
-    depends_on("autoconf", type="build")
-    depends_on("automake", type="build")
     depends_on("hwloc")
 
     def install(self, spec, prefix):
-        autogen = Executable("./autogen.sh")
-        autogen()
         configure("--prefix=%s" % prefix,
                   "--enable-guard-pages",
                   "--with-topology=hwloc",
diff --git a/var/spack/repos/builtin/packages/r-stringi/package.py b/var/spack/repos/builtin/packages/r-stringi/package.py
index 22774dedec..cc57caf8cd 100644
--- a/var/spack/repos/builtin/packages/r-stringi/package.py
+++ b/var/spack/repos/builtin/packages/r-stringi/package.py
@@ -44,7 +44,7 @@ class RStringi(Package):
 
     extends('R')
 
-    depends_on('icu')
+    depends_on('icu4c')
 
     def install(self, spec, prefix):
         R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
diff --git a/var/spack/repos/builtin/packages/root/math_uint.patch b/var/spack/repos/builtin/packages/root/math_uint.patch
new file mode 100644
index 0000000000..ff4a38b91c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/root/math_uint.patch
@@ -0,0 +1,115 @@
+From 5f3faffdd869bce5e254ae70f69290e4651a061d Mon Sep 17 00:00:00 2001
+From: Lorenzo Moneta <Lorenzo.Moneta@cern.ch>
+Date: Mon, 4 Jan 2016 15:38:23 +0100
+Subject: [PATCH] Fix ROOT-7886. Use unsigned int instead of uint
+
+---
+ math/mathcore/inc/Math/Delaunay2D.h |  2 +-
+ math/mathcore/src/Delaunay2D.cxx    | 30 +++++++++++++++---------------
+ 2 files changed, 16 insertions(+), 16 deletions(-)
+
+diff --git a/math/mathcore/inc/Math/Delaunay2D.h b/math/mathcore/inc/Math/Delaunay2D.h
+index 6255e78..472bded 100644
+--- a/math/mathcore/inc/Math/Delaunay2D.h
++++ b/math/mathcore/inc/Math/Delaunay2D.h
+@@ -273,7 +273,7 @@ class Delaunay2D  {
+    double fYCellStep; //! inverse denominator to calculate X cell = fNCells / (fYNmax - fYNmin)
+    std::set<UInt_t> fCells[(fNCells+1)*(fNCells+1)]; //! grid cells with containing triangles
+ 
+-   inline unsigned int Cell(uint x, uint y) const {
++   inline unsigned int Cell(UInt_t x, UInt_t y) const {
+ 	   return x*(fNCells+1) + y;
+    }
+ 
+diff --git a/math/mathcore/src/Delaunay2D.cxx b/math/mathcore/src/Delaunay2D.cxx
+index c4d4680..9a82858 100644
+--- a/math/mathcore/src/Delaunay2D.cxx
++++ b/math/mathcore/src/Delaunay2D.cxx
+@@ -190,7 +190,7 @@ void Delaunay2D::DoFindTriangles() {
+ 
+ 				Triangle tri;
+ 
+-				auto transform = [&] (const uint i) {
++				auto transform = [&] (const unsigned int i) {
+ 					tri.x[i] = face.vertex(i)->point().x();
+ 					tri.y[i] = face.vertex(i)->point().y();
+ 					tri.idx[i] = face.vertex(i)->info();
+@@ -326,7 +326,7 @@ void Delaunay2D::DoFindTriangles() {
+ 	for(int t = 0; t < out.numberoftriangles; ++t){
+ 		Triangle tri;
+ 
+-		auto transform = [&] (const uint v) {
++		auto transform = [&] (const unsigned int v) {
+ 			//each triangle as numberofcorners vertices ( = 3)
+ 			tri.idx[v] = out.trianglelist[t*out.numberofcorners + v];
+ 
+@@ -354,14 +354,14 @@ void Delaunay2D::DoFindTriangles() {
+ 		auto bx = std::minmax({tri.x[0], tri.x[1], tri.x[2]});
+ 		auto by = std::minmax({tri.y[0], tri.y[1], tri.y[2]});
+ 
+-		uint cellXmin = CellX(bx.first);
+-		uint cellXmax = CellX(bx.second);
++		unsigned int cellXmin = CellX(bx.first);
++		unsigned int cellXmax = CellX(bx.second);
+ 
+-		uint cellYmin = CellY(by.first);
+-		uint cellYmax = CellY(by.second);
++		unsigned int cellYmin = CellY(by.first);
++		unsigned int cellYmax = CellY(by.second);
+ 
+-		for(uint i = cellXmin; i <= cellXmax; ++i)
+-			for(uint j = cellYmin; j <= cellYmax; ++j){
++		for(unsigned int i = cellXmin; i <= cellXmax; ++i)
++			for(unsigned int j = cellYmin; j <= cellYmax; ++j){
+ 				//printf("(%u,%u) = %u\n", i, j, Cell(i,j));
+ 				fCells[Cell(i,j)].insert(t);
+ 			}
+@@ -382,7 +382,7 @@ double Delaunay2D::DoInterpolateNormalized(double xx, double yy)
+    ///  FindAllTriangles();
+ 
+     //see comment in header for CGAL fallback section
+-    auto bayCoords = [&] (const uint t) -> std::tuple<double, double, double> {
++    auto bayCoords = [&] (const unsigned int t) -> std::tuple<double, double, double> {
+     	double la = ( (fTriangles[t].y[1] - fTriangles[t].y[2])*(xx - fTriangles[t].x[2])
+     					 + (fTriangles[t].x[2] - fTriangles[t].x[1])*(yy - fTriangles[t].y[2]) ) * fTriangles[t].invDenom;
+     	double lb = ( (fTriangles[t].y[2] - fTriangles[t].y[0])*(xx - fTriangles[t].x[2])
+@@ -401,7 +401,7 @@ double Delaunay2D::DoInterpolateNormalized(double xx, double yy)
+ 	if(cX < 0 || cX > fNCells || cY < 0 || cY > fNCells)
+ 		return fZout; //TODO some more fancy interpolation here
+ 
+-    for(uint t : fCells[Cell(cX, cY)]){
++    for(unsigned int t : fCells[Cell(cX, cY)]){
+     	auto coords = bayCoords(t);
+ 
+     	if(inTriangle(coords)){
+@@ -415,7 +415,7 @@ double Delaunay2D::DoInterpolateNormalized(double xx, double yy)
+ 
+     //debugging
+ 
+-    /*for(uint t = 0; t < fNdt; ++t){
++    /*for(unsigned int t = 0; t < fNdt; ++t){
+     	auto coords = bayCoords(t);
+ 
+     	if(inTriangle(coords)){
+@@ -423,17 +423,17 @@ double Delaunay2D::DoInterpolateNormalized(double xx, double yy)
+     		//brute force found a triangle -> grid not
+     		printf("Found triangle %u for (%f,%f) -> (%u,%u)\n", t, xx,yy, cX, cY);
+     		printf("Triangles in grid cell: ");
+-    		for(uint x : fCells[Cell(cX, cY)])
++    		for(unsigned int x : fCells[Cell(cX, cY)])
+     			printf("%u ", x);
+     		printf("\n");
+ 
+     		printf("Triangle %u is in cells: ", t);
+-    		for(uint i = 0; i <= fNCells; ++i)
+-    			for(uint j = 0; j <= fNCells; ++j)
++    		for(unsigned int i = 0; i <= fNCells; ++i)
++    			for(unsigned int j = 0; j <= fNCells; ++j)
+     				if(fCells[Cell(i,j)].count(t))
+     					printf("(%u,%u) ", i, j);
+     		printf("\n");
+-    		for(uint i = 0; i < 3; ++i)
++    		for(unsigned int i = 0; i < 3; ++i)
+     			printf("\tpoint %u (%u): (%f,%f) -> (%u,%u)\n", i, fTriangles[t].idx[i], fTriangles[t].x[i], fTriangles[t].y[i], CellX(fTriangles[t].x[i]), CellY(fTriangles[t].y[i]));
+ 
+     		//we found the triangle -> interpolate using the barycentric interpolation
diff --git a/var/spack/repos/builtin/packages/root/package.py b/var/spack/repos/builtin/packages/root/package.py
new file mode 100644
index 0000000000..0f66dcebaa
--- /dev/null
+++ b/var/spack/repos/builtin/packages/root/package.py
@@ -0,0 +1,89 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+
+from spack import *
+import sys
+
+
+class Root(Package):
+    """ROOT is a data analysis framework."""
+    homepage = "https://root.cern.ch"
+    url      = "https://root.cern.ch/download/root_v6.07.02.source.tar.gz"
+
+    version('6.06.06', '4308449892210c8d36e36924261fea26')
+    version('6.06.04', '55a2f98dd4cea79c9c4e32407c2d6d17')
+    version('6.06.02', 'e9b8b86838f65b0a78d8d02c66c2ec55')
+
+    if sys.platform == 'darwin':
+        patch('math_uint.patch', when='@6.06.02')
+        patch('root6-60606-mathmore.patch', when='@6.06.06')
+
+    variant('graphviz', default=False, description='Enable graphviz support')
+
+    depends_on("cmake", type='build')
+    depends_on("pcre")
+    depends_on("fftw")
+    depends_on("graphviz", when="+graphviz")
+    depends_on("python")
+    depends_on("gsl")
+    depends_on("libxml2+python")
+    depends_on("jpeg")
+    if sys.platform != 'darwin':
+        depends_on("libpng")
+        depends_on("openssl")
+        depends_on("freetype")
+
+    def install(self, spec, prefix):
+        build_directory = join_path(self.stage.path, 'spack-build')
+        source_directory = self.stage.source_path
+        options = [source_directory]
+        if '+debug' in spec:
+            options.append('-DCMAKE_BUILD_TYPE:STRING=Debug')
+        else:
+            options.append('-DCMAKE_BUILD_TYPE:STRING=Release')
+        options.append('-Dcxx14=on')
+        options.append('-Dcocoa=off')
+        options.append('-Dbonjour=off')
+        options.append('-Dx11=on')
+        options.extend(std_cmake_args)
+        if sys.platform == 'darwin':
+            darwin_options = [
+                '-Dcastor=OFF',
+                '-Drfio=OFF',
+                '-Ddcache=OFF']
+            options.extend(darwin_options)
+        with working_dir(build_directory, create=True):
+            cmake(*options)
+            make()
+            make("install")
+
+    def setup_dependent_environment(self, spack_env, run_env, dspec):
+        spack_env.set('ROOTSYS', self.prefix)
+        spack_env.set('ROOT_VERSION', 'v6')
+        spack_env.prepend_path('PYTHONPATH', self.prefix.lib)
+
+    def url_for_version(self, version):
+        """Handle ROOT's unusual version string."""
+        return "https://root.cern.ch/download/root_v%s.source.tar.gz" % version
diff --git a/var/spack/repos/builtin/packages/root/root6-60606-mathmore.patch b/var/spack/repos/builtin/packages/root/root6-60606-mathmore.patch
new file mode 100644
index 0000000000..d009a5af0d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/root/root6-60606-mathmore.patch
@@ -0,0 +1,29 @@
+diff --git a/math/mathmore/inc/Math/QuantFuncMathMore.h b/math/mathmore/inc/Math/QuantFuncMathMore.h
+index fd6679c..03ccc03 100644
+--- a/math/mathmore/inc/Math/QuantFuncMathMore.h
++++ b/math/mathmore/inc/Math/QuantFuncMathMore.h
+@@ -25,17 +25,6 @@
+   **********************************************************************/
+ 
+ 
+-#if defined(__CINT__) && !defined(__MAKECINT__)
+-// avoid to include header file when using CINT
+-#ifndef _WIN32
+-#include "../lib/libMathMore.so"
+-#else
+-#include "../bin/libMathMore.dll"
+-#endif
+-
+-#else
+-
+-
+ #ifndef ROOT_Math_QuantFuncMathMore
+ #define ROOT_Math_QuantFuncMathMore
+ 
+@@ -190,5 +179,3 @@ namespace MathMore {
+ 
+ 
+ #endif // ROOT_Math_QuantFuncMathMore
+-
+-#endif // if defined (__CINT__) && !defined(__MAKECINT__)
+
diff --git a/var/spack/repos/builtin/packages/samtools/package.py b/var/spack/repos/builtin/packages/samtools/package.py
index 6b0b224785..b82a7e55d6 100644
--- a/var/spack/repos/builtin/packages/samtools/package.py
+++ b/var/spack/repos/builtin/packages/samtools/package.py
@@ -42,7 +42,8 @@ class Samtools(Package):
 
     def install(self, spec, prefix):
         if self.spec.version >= Version('1.3.1'):
-            configure('--prefix={0}'.format(prefix), '--with-ncurses')
+            configure('--prefix={0}'.format(prefix), '--with-ncurses',
+                      'CURSES_LIB=-lncurses')
             make()
             make('install')
         else:
diff --git a/var/spack/repos/builtin/packages/silo/package.py b/var/spack/repos/builtin/packages/silo/package.py
index 5113c88bdf..691d53a9f1 100644
--- a/var/spack/repos/builtin/packages/silo/package.py
+++ b/var/spack/repos/builtin/packages/silo/package.py
@@ -41,7 +41,8 @@ class Silo(Package):
     variant('silex', default=False,
             description='Builds Silex, a GUI for viewing Silo files')
 
-    depends_on('hdf5')
+    # silo uses the obsolete function H5Pset_fapl_mpiposix:
+    depends_on("hdf5 @:1.8.12")
     depends_on('qt', when='+silex')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/spark/package.py b/var/spack/repos/builtin/packages/spark/package.py
new file mode 100644
index 0000000000..10b0ebed7f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/spark/package.py
@@ -0,0 +1,75 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Alfredo Gimenez, gimenez1@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+
+from spack import *
+
+import shutil
+
+
+class Spark(Package):
+    """Apache Spark is a fast and general engine
+    for large-scale data processing.
+    """
+
+    homepage = "http://spark.apache.org"
+    url      = "http://mirrors.ocf.berkeley.edu/apache/spark/spark-2.0.0/spark-2.0.0-bin-without-hadoop.tgz"
+
+    variant('hadoop', default=False,
+            description='Build with Hadoop')
+
+    depends_on('jdk', type=('build', 'run'))
+    depends_on('hadoop', when='+hadoop', type=('build', 'run'))
+
+    version('2.0.0', '8a5307d973da6949a385aefb6ff747bb')
+    version('1.6.2', '304394fbe2899211217f0cd9e9b2b5d9')
+    version('1.6.1', 'fcf4961649f15af1fea78c882e65b001')
+
+    def install(self, spec, prefix):
+
+        def install_dir(dirname):
+            install_tree(dirname, join_path(prefix, dirname))
+
+        install_dir('bin')
+        install_dir('conf')
+        install_dir('jars')
+        install_dir('python')
+        install_dir('R')
+        install_dir('sbin')
+        install_dir('yarn')
+
+        # required for spark to recognize binary distribution
+        shutil.copy('RELEASE', prefix)
+
+    @when('+hadoop')
+    def setup_environment(self, spack_env, run_env):
+
+        env['JAVA_HOME'] = self.spec['jdk'].prefix
+        # spack_env.set('JAVA_HOME', self.spec['jdk'].prefix)
+
+        hadoop_bin_path = join_path(self.spec['hadoop'].prefix.bin, 'hadoop')
+        hadoop_bin = Executable(hadoop_bin_path)
+        hadoop_classpath = hadoop_bin('classpath', return_output=True)
+
+        run_env.set('SPARK_DIST_CLASSPATH', hadoop_classpath)
diff --git a/var/spack/repos/builtin/packages/stat/package.py b/var/spack/repos/builtin/packages/stat/package.py
index 8c4663c524..eae4971ace 100644
--- a/var/spack/repos/builtin/packages/stat/package.py
+++ b/var/spack/repos/builtin/packages/stat/package.py
@@ -34,8 +34,8 @@ class Stat(Package):
     version('2.2.0', '26bd69dd57a15afdd5d0ebdb0b7fb6fc')
     version('2.1.0', 'ece26beaf057aa9134d62adcdda1ba91')
     version('2.0.0', 'c7494210b0ba26b577171b92838e1a9b')
-    version('3.0.0b', '8851912ba40e31cf7be6dde3be8e702c',
-            url='https://github.com/LLNL/STAT/files/427762/STAT-3.0.0b.tar.gz')
+    version('3.0.0', 'a97cb235c266371c4a26329112de48a2',
+            url='https://github.com/LLNL/STAT/releases/download/v3.0.0/STAT-3.0.0.tar.gz')
 
     # TODO: dysect requires Dyninst patch for version 3.0.0b
     variant('dysect', default=False, description="enable DySectAPI")
diff --git a/var/spack/repos/builtin/packages/subversion/package.py b/var/spack/repos/builtin/packages/subversion/package.py
index 26d143e4aa..02b7d96378 100644
--- a/var/spack/repos/builtin/packages/subversion/package.py
+++ b/var/spack/repos/builtin/packages/subversion/package.py
@@ -46,6 +46,9 @@ class Subversion(Package):
     # depends_on('perl')
     # depends_on('ruby')
 
+    # Installation has race cases.
+    parallel = False
+
     def install(self, spec, prefix):
 
         # configure, build, install:
diff --git a/var/spack/repos/builtin/packages/suite-sparse/package.py b/var/spack/repos/builtin/packages/suite-sparse/package.py
index a71bfd8bd4..d6d8f71313 100644
--- a/var/spack/repos/builtin/packages/suite-sparse/package.py
+++ b/var/spack/repos/builtin/packages/suite-sparse/package.py
@@ -36,6 +36,7 @@ class SuiteSparse(Package):
     version('4.5.1', 'f0ea9aad8d2d1ffec66a5b6bfeff5319')
 
     variant('tbb', default=True, description='Build with Intel TBB')
+    variant('fpic', default=True, description='Build position independent code (required to link with shared libraries)')
 
     depends_on('blas')
     depends_on('lapack')
@@ -63,6 +64,8 @@ class SuiteSparse(Package):
             'CXX=c++',
             'F77=f77',
         ])
+        if '+fpic' in spec:
+            make_args.extend(['CFLAGS=-fPIC', 'FFLAGS=-fPIC'])
 
         # use Spack's metis in CHOLMOD/Partition module,
         # otherwise internal Metis will be compiled
@@ -80,8 +83,8 @@ class SuiteSparse(Package):
 
         # Make sure Spack's Blas/Lapack is used. Otherwise System's
         # Blas/Lapack might be picked up.
-        blas = to_link_flags(spec['blas'].blas_shared_lib)
-        lapack = to_link_flags(spec['lapack'].lapack_shared_lib)
+        blas = spec['blas'].blas_libs.ld_flags
+        lapack = spec['lapack'].lapack_libs.ld_flags
         if '@4.5.1' in spec:
             # adding -lstdc++ is clearly an ugly way to do this, but it follows
             # with the TCOV path of SparseSuite 4.5.1's Suitesparse_config.mk
diff --git a/var/spack/repos/builtin/packages/sundials/package.py b/var/spack/repos/builtin/packages/sundials/package.py
index 7582954ab1..6ee247b7ea 100644
--- a/var/spack/repos/builtin/packages/sundials/package.py
+++ b/var/spack/repos/builtin/packages/sundials/package.py
@@ -31,7 +31,7 @@ class Sundials(Package):
     Solvers)"""
 
     homepage = "http://computation.llnl.gov/casc/sundials/"
-    url      = "http://computation.llnl.gov/projects/sundials-suite-nonlinear-differential-algebraic-equation-solvers/download/sundials-2.6.2.tar.gz"
+    url = "http://computation.llnl.gov/projects/sundials-suite-nonlinear-differential-algebraic-equation-solvers/download/sundials-2.6.2.tar.gz"
 
     version('2.6.2', '3deeb0ede9f514184c6bd83ecab77d95')
 
@@ -79,9 +79,9 @@ class Sundials(Package):
         if '+lapack' in spec:
             cmake_args.extend([
                 '-DLAPACK_ENABLE=ON',
-                '-DLAPACK_LIBRARIES={0};{1}'.format(
-                    spec['lapack'].lapack_shared_lib,
-                    spec['blas'].blas_shared_lib
+                '-DLAPACK_LIBRARIES={0}'.format(
+                    (spec['lapack'].lapack_libs +
+                     spec['blas'].blas_libs).joined(';')
                 )
             ])
         else:
@@ -113,7 +113,7 @@ class Sundials(Package):
             elif '+pthread' in spec:
                 cmake_args.append('-DSUPERLUMT_THREAD_TYPE=Pthread')
             else:
-                msg  = 'You must choose either +openmp or +pthread when '
+                msg = 'You must choose either +openmp or +pthread when '
                 msg += 'building with SuperLU_MT'
                 raise RuntimeError(msg)
         else:
diff --git a/var/spack/repos/builtin/packages/superlu-dist/package.py b/var/spack/repos/builtin/packages/superlu-dist/package.py
index 85b7f689d0..a29b74bf08 100644
--- a/var/spack/repos/builtin/packages/superlu-dist/package.py
+++ b/var/spack/repos/builtin/packages/superlu-dist/package.py
@@ -46,15 +46,14 @@ class SuperluDist(Package):
     depends_on('metis@5:')
 
     def install(self, spec, prefix):
+        lapack_blas = spec['lapack'].lapack_libs + spec['blas'].blas_libs
         makefile_inc = []
         makefile_inc.extend([
             'PLAT         = _mac_x',
             'DSuperLUroot = %s' % self.stage.source_path,
             'DSUPERLULIB  = $(DSuperLUroot)/lib/libsuperlu_dist.a',
             'BLASDEF      = -DUSE_VENDOR_BLAS',
-            'BLASLIB      = %s %s' %
-                (to_link_flags(spec['lapack'].lapack_shared_lib),
-                 to_link_flags(spec['blas'].blas_shared_lib)),
+            'BLASLIB      = %s' % lapack_blas.ld_flags,
             'METISLIB     = -L%s -lmetis' % spec['metis'].prefix.lib,
             'PARMETISLIB  = -L%s -lparmetis' % spec['parmetis'].prefix.lib,
             'FLIBS        =',
diff --git a/var/spack/repos/builtin/packages/superlu-mt/package.py b/var/spack/repos/builtin/packages/superlu-mt/package.py
index e849273e08..ea94c2d4c5 100644
--- a/var/spack/repos/builtin/packages/superlu-mt/package.py
+++ b/var/spack/repos/builtin/packages/superlu-mt/package.py
@@ -86,7 +86,7 @@ class SuperluMt(Package):
         if '+blas' in spec:
             config.extend([
                 'BLASDEF    = -DUSE_VENDOR_BLAS',
-                'BLASLIB    = -L{0} -lblas'.format(spec['blas'].prefix.lib)
+                'BLASLIB    = {0}'.format(spec['blas'].blas_libs.ld_flags)
             ])
         else:
             config.append('BLASLIB    = ../lib/libblas$(PLAT).a')
diff --git a/var/spack/repos/builtin/packages/superlu/package.py b/var/spack/repos/builtin/packages/superlu/package.py
index c634c1d1ba..d9cff650b6 100644
--- a/var/spack/repos/builtin/packages/superlu/package.py
+++ b/var/spack/repos/builtin/packages/superlu/package.py
@@ -42,7 +42,7 @@ class Superlu(Package):
             '-DCMAKE_POSITION_INDEPENDENT_CODE=ON',
             # BLAS support
             '-Denable_blaslib=OFF',
-            '-DBLAS_blas_LIBRARY={0}'.format(spec['blas'].blas_shared_lib)
+            '-DBLAS_blas_LIBRARY={0}'.format(spec['blas'].blas_libs.joined())
         ]
 
         cmake_args.extend(std_cmake_args)
diff --git a/var/spack/repos/builtin/packages/tmux/package.py b/var/spack/repos/builtin/packages/tmux/package.py
index 573ee38a79..89c9751486 100644
--- a/var/spack/repos/builtin/packages/tmux/package.py
+++ b/var/spack/repos/builtin/packages/tmux/package.py
@@ -35,9 +35,10 @@ class Tmux(Package):
     homepage = "http://tmux.github.io"
     url = "https://github.com/tmux/tmux/releases/download/2.2/tmux-2.2.tar.gz"
 
-    version('1.9a', 'b07601711f96f1d260b390513b509a2d')
-    version('2.1', '74a2855695bccb51b6e301383ad4818c')
+    version('2.3', 'fcfd1611d705d8b31df3c26ebc93bd3e')
     version('2.2', 'bd95ee7205e489c62c616bb7af040099')
+    version('2.1', '74a2855695bccb51b6e301383ad4818c')
+    version('1.9a', 'b07601711f96f1d260b390513b509a2d')
 
     depends_on('libevent')
     depends_on('ncurses')
diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 3a88f67340..203e1502d6 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -45,6 +45,7 @@ class Trilinos(Package):
     homepage = "https://trilinos.org/"
     base_url = "https://github.com/trilinos/Trilinos/archive"
 
+    version('12.8.1', '01c0026f1e2050842857db941060ecd5')
     version('12.6.4', 'c2ea7b5aa0d10bcabdb9b9a6e3bac3ea')
     version('12.6.3', '8de5cc00981a0ca0defea6199b2fe4c1')
     version('12.6.2', 'dc7f9924872778798149ecadd81605a5')
@@ -132,6 +133,8 @@ class Trilinos(Package):
 
         mpi_bin = spec['mpi'].prefix.bin
         # Note: -DXYZ_LIBRARY_NAMES= needs semicolon separated list of names
+        blas = spec['blas'].blas_libs
+        lapack = spec['lapack'].lapack_libs
         options.extend([
             '-DTrilinos_ENABLE_ALL_PACKAGES:BOOL=ON',
             '-DTrilinos_ENABLE_ALL_OPTIONAL_PACKAGES:BOOL=ON',
@@ -145,12 +148,10 @@ class Trilinos(Package):
             '-DTPL_ENABLE_MPI:BOOL=ON',
             '-DMPI_BASE_DIR:PATH=%s' % spec['mpi'].prefix,
             '-DTPL_ENABLE_BLAS=ON',
-            '-DBLAS_LIBRARY_NAMES=%s' % to_lib_name(
-                spec['blas'].blas_shared_lib),
+            '-DBLAS_LIBRARY_NAMES=%s' % ';'.join(blas.names),
             '-DBLAS_LIBRARY_DIRS=%s' % spec['blas'].prefix.lib,
             '-DTPL_ENABLE_LAPACK=ON',
-            '-DLAPACK_LIBRARY_NAMES=%s' % to_lib_name(
-                spec['lapack'].lapack_shared_lib),
+            '-DLAPACK_LIBRARY_NAMES=%s' % ';'.join(lapack.names),
             '-DLAPACK_LIBRARY_DIRS=%s' % spec['lapack'].prefix.lib,
             '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON',
             '-DTrilinos_ENABLE_CXX11:BOOL=ON',
@@ -177,6 +178,15 @@ class Trilinos(Package):
         else:
             options.extend(['-DTPL_ENABLE_Boost:BOOL=OFF'])
 
+        if '+hdf5' in spec:
+            options.extend([
+                '-DTPL_ENABLE_HDF5:BOOL=ON',
+                '-DHDF5_INCLUDE_DIRS:PATH=%s' % spec['hdf5'].prefix.include,
+                '-DHDF5_LIBRARY_DIRS:PATH=%s' % spec['hdf5'].prefix.lib
+            ])
+        else:
+            options.extend(['-DTPL_ENABLE_HDF5:BOOL=OFF'])
+
         # Fortran lib
         libgfortran = os.path.dirname(os.popen(
             '%s --print-file-name libgfortran.a' %
diff --git a/var/spack/repos/builtin/packages/turbomole/package.py b/var/spack/repos/builtin/packages/turbomole/package.py
index 6ccce23f97..b2d7e90057 100644
--- a/var/spack/repos/builtin/packages/turbomole/package.py
+++ b/var/spack/repos/builtin/packages/turbomole/package.py
@@ -29,14 +29,14 @@ import subprocess
 
 class Turbomole(Package):
     """TURBOMOLE: Program Package for ab initio Electronic Structure
-       Calculations. NB: Requires a license to download."""
-
-    # NOTE: Turbomole requires purchase of a license to download. Go to the
-    # NOTE: Turbomole home page, http://www.turbomole-gmbh.com, for details.
-    # NOTE: Spack will search the current directory for this file. It is
-    # NOTE: probably best to add this file to a Spack mirror so that it can be
-    # NOTE: found from anywhere.  For information on setting up a Spack mirror
-    # NOTE: see http://software.llnl.gov/spack/mirrors.html
+    Calculations.
+
+    Note: Turbomole requires purchase of a license to download. Go to the
+    Turbomole home page, http://www.turbomole-gmbh.com, for details.
+    Spack will search the current directory for this file. It is
+    probably best to add this file to a Spack mirror so that it can be
+    found from anywhere.  For information on setting up a Spack mirror
+    see http://spack.readthedocs.io/en/latest/mirrors.html"""
 
     homepage = "http://www.turbomole-gmbh.com/"
 
diff --git a/var/spack/repos/builtin/packages/uberftp/package.py b/var/spack/repos/builtin/packages/uberftp/package.py
new file mode 100644
index 0000000000..b1b7dada6f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/uberftp/package.py
@@ -0,0 +1,44 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Uberftp(Package):
+    """UberFTP is an interactive (text-based) client for GridFTP"""
+
+    homepage = "http://toolkit.globus.org/grid_software/data/uberftp.php"
+    url      = "https://github.com/JasonAlt/UberFTP/archive/Version_2_8.tar.gz"
+
+    version('2_8', 'bc7a159955a9c4b9f5f42f3d2b8fc830')
+    version('2_7', 'faaea2d6e1958c1105cfc9147824e03c')
+    version('2_6', '784210976f259f9d19c0798c19778d34')
+
+    depends_on('globus_toolkit')
+
+    def install(self, spec, prefix):
+        configure('--prefix={0}'.format(prefix))
+
+        make()
+        make('install')
diff --git a/var/spack/repos/builtin/packages/vim/package.py b/var/spack/repos/builtin/packages/vim/package.py
index 5f2e5e19d9..26aeb4aad9 100644
--- a/var/spack/repos/builtin/packages/vim/package.py
+++ b/var/spack/repos/builtin/packages/vim/package.py
@@ -38,6 +38,7 @@ class Vim(Package):
     url      = "ftp://ftp.vim.org/pub/vim/unix/vim-7.4.tar.bz2"
     list_url = "http://ftp.vim.org/pub/vim/unix/"
 
+    version('8.0',     '808d2ebdab521e18bc5e0eaede0db867')
     version('7.4',     '607e135c559be642f210094ad023dc65')
     version('7.3',     '5b9510a17074e2b37d8bb38ae09edbf2')
     version('7.2',     'f0901284b338e448bfd79ccca0041254')
@@ -66,6 +67,8 @@ class Vim(Package):
     variant('gui', default=False, description="build with gui (gvim)")
     # virtual dependency?
 
+    depends_on('ncurses', when="@8.0:")
+
     def install(self, spec, prefix):
         feature_set = None
         for fs in self.feature_sets:
diff --git a/var/spack/repos/builtin/packages/visit/package.py b/var/spack/repos/builtin/packages/visit/package.py
index d88caeb00a..5d2ab24cc5 100644
--- a/var/spack/repos/builtin/packages/visit/package.py
+++ b/var/spack/repos/builtin/packages/visit/package.py
@@ -31,13 +31,15 @@ class Visit(Package):
     homepage = "https://wci.llnl.gov/simulation/computer-codes/visit/"
     url = "http://portal.nersc.gov/project/visit/releases/2.10.1/visit2.10.1.tar.gz"
 
-    version('2.10.1', '3cbca162fdb0249f17c4456605c4211e')
+    version('2.10.3', 'a1082a6f6dab3e2dcb58993603456c2b')
     version('2.10.2', '253de0837a9d69fb689befc98ea4d068')
+    version('2.10.1', '3cbca162fdb0249f17c4456605c4211e')
 
     depends_on("vtk@6.1.0~opengl2")
     depends_on("qt@4.8.6")
     depends_on("python")
     depends_on("silo+shared")
+    depends_on("hdf5~mpi")
 
     def install(self, spec, prefix):
         with working_dir('spack-build', create=True):
@@ -46,6 +48,7 @@ class Visit(Package):
             feature_args.extend([
                 "-DVTK_MAJOR_VERSION=6",
                 "-DVTK_MINOR_VERSION=1",
+                "-DVISIT_USE_GLEW=OFF",
                 "-DVISIT_LOC_QMAKE_EXE:FILEPATH=%s/qmake-qt4" % spec[
                     'qt'].prefix.bin,
                 "-DPYTHON_EXECUTABLE:FILEPATH=%s/python" % spec[
diff --git a/var/spack/repos/builtin/packages/vtk/gcc.patch b/var/spack/repos/builtin/packages/vtk/gcc.patch
new file mode 100644
index 0000000000..37ba5ac45a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/vtk/gcc.patch
@@ -0,0 +1,21 @@
+--- old/CMake/vtkCompilerExtras.cmake
++++ new/CMake/vtkCompilerExtras.cmake
+@@ -26,6 +26,8 @@
+   execute_process(COMMAND ${CMAKE_C_COMPILER} --version
+     OUTPUT_VARIABLE _gcc_version_info
+     ERROR_VARIABLE _gcc_version_info)
++
++  string (REPLACE ";" "" _gcc_version_info "${_gcc_version_info}")
+ 
+   string (REGEX MATCH "[345]\\.[0-9]\\.[0-9]"
+     _gcc_version "${_gcc_version_info}")
+--- old/CMake/GenerateExportHeader.cmake
++++ new/CMake/GenerateExportHeader.cmake
+@@ -166,6 +166,7 @@
+     execute_process(COMMAND ${CMAKE_C_COMPILER} --version
+       OUTPUT_VARIABLE _gcc_version_info
+       ERROR_VARIABLE _gcc_version_info)
++    string (REPLACE ";" "" _gcc_version_info "${_gcc_version_info}")
+     string(REGEX MATCH "[345]\\.[0-9]\\.[0-9]"
+       _gcc_version "${_gcc_version_info}")
+     # gcc on mac just reports: "gcc (GCC) 3.3 20030304 ..." without the
diff --git a/var/spack/repos/builtin/packages/vtk/package.py b/var/spack/repos/builtin/packages/vtk/package.py
index 087c0e93eb..f7015904b0 100644
--- a/var/spack/repos/builtin/packages/vtk/package.py
+++ b/var/spack/repos/builtin/packages/vtk/package.py
@@ -40,6 +40,8 @@ class Vtk(Package):
 
     version('6.1.0', '25e4dfb3bad778722dcaec80cd5dab7d')
 
+    patch("gcc.patch")
+
     depends_on('cmake', type='build')
     depends_on("qt")
 
diff --git a/var/spack/repos/builtin/packages/wannier90/make.sys b/var/spack/repos/builtin/packages/wannier90/make.sys
new file mode 100644
index 0000000000..f96fa23fb2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/wannier90/make.sys
@@ -0,0 +1,7 @@
+F90 = @F90
+COMMS=mpi
+MPIF90=@MPIF90
+FCOPTS=-O2 -fpic
+LDOPTS=-O2 -fpic
+
+LIBS = @LIBS
diff --git a/var/spack/repos/builtin/packages/wannier90/package.py b/var/spack/repos/builtin/packages/wannier90/package.py
new file mode 100644
index 0000000000..119d2cf769
--- /dev/null
+++ b/var/spack/repos/builtin/packages/wannier90/package.py
@@ -0,0 +1,116 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+import inspect
+import os.path
+import shutil
+
+from spack import *
+
+
+class Wannier90(Package):
+    """Wannier90 calculates maximally-localised Wannier functions (MLWFs).
+
+    Wannier90 is released under the GNU General Public License.
+    """
+    homepage = 'http://wannier.org'
+    url = 'http://wannier.org/code/wannier90-2.0.1.tar.gz'
+
+    version('2.0.1', '4edd742506eaba93317249d33261fb22')
+
+    depends_on('mpi')
+    depends_on('lapack')
+    depends_on('blas')
+
+    parallel = False
+
+    def install(self, spec, prefix):
+
+        lapack = self.spec['lapack'].lapack_libs
+        blas = self.spec['blas'].blas_libs
+        substitutions = {
+            '@F90': spack_fc,
+            '@MPIF90': self.spec['mpi'].mpifc,
+            '@LIBS': (lapack + blas).joined()
+        }
+        #######
+        # TODO : this part is replicated in PEXSI
+        # TODO : and may be a common pattern for Editable Makefiles
+        # TODO : see #1186
+        template = join_path(
+            os.path.dirname(inspect.getmodule(self).__file__),
+            'make.sys'
+        )
+        makefile = join_path(
+            self.stage.source_path,
+            'make.sys'
+        )
+
+        shutil.copy(template, makefile)
+        for key, value in substitutions.items():
+            filter_file(key, value, makefile)
+        ######
+
+        make('wannier')
+        mkdirp(self.prefix.bin)
+        install(
+            join_path(self.stage.source_path, 'wannier90.x'),
+            join_path(self.prefix.bin, 'wannier90.x')
+        )
+
+        make('post')
+        install(
+            join_path(self.stage.source_path, 'postw90.x'),
+            join_path(self.prefix.bin, 'postw90.x')
+        )
+
+        make('lib')
+        mkdirp(self.prefix.lib)
+        install(
+            join_path(self.stage.source_path, 'libwannier.a'),
+            join_path(self.prefix.lib, 'libwannier.a')
+        )
+
+        make('w90chk2chk')
+        install(
+            join_path(self.stage.source_path, 'w90chk2chk.x'),
+            join_path(self.prefix.bin, 'w90chk2chk.x')
+        )
+
+        make('w90vdw')
+        install(
+            join_path(self.stage.source_path, 'utility', 'w90vdw', 'w90vdw.x'),
+            join_path(self.prefix.bin, 'w90vdw.x')
+        )
+
+        make('w90pov')
+        install(
+            join_path(self.stage.source_path, 'utility', 'w90pov', 'w90pov'),
+            join_path(self.prefix.bin, 'w90pov')
+        )
+
+        install_tree(
+            join_path(self.stage.source_path, 'pseudo'),
+            join_path(self.prefix.bin, 'pseudo')
+        )
diff --git a/var/spack/repos/builtin/packages/xorg-util-macros/package.py b/var/spack/repos/builtin/packages/xorg-util-macros/package.py
index cd50d46826..3cfc4c2408 100644
--- a/var/spack/repos/builtin/packages/xorg-util-macros/package.py
+++ b/var/spack/repos/builtin/packages/xorg-util-macros/package.py
@@ -28,7 +28,7 @@ from spack import *
 class XorgUtilMacros(Package):
     """The m4 macros used by all of the Xorg packages."""
 
-    homepage = "http://www.example.com"
+    homepage = "https://cgit.freedesktop.org/xorg/util/macros/"
     url = "http://ftp.x.org/pub/individual/util/util-macros-1.19.0.tar.bz2"
 
     version('1.19.0', '1cf984125e75f8204938d998a8b6c1e1')
diff --git a/var/spack/repos/builtin/packages/icu/package.py b/var/spack/repos/builtin/packages/xrootd/package.py
index b8d366b905..db076dbc56 100644
--- a/var/spack/repos/builtin/packages/icu/package.py
+++ b/var/spack/repos/builtin/packages/xrootd/package.py
@@ -22,27 +22,31 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
+
 from spack import *
 
 
-class Icu(Package):
-    """The International Components for Unicode (ICU) package is a
-       mature, widely used set of C/C++ libraries providing Unicode and
-       Globalization support for software applications. ICU is widely
-       portable and gives applications the same results on all
-       platforms."""
-    # FIXME: add a proper url for your package's homepage here.
-    homepage = "http://www.example.com"
-    url      = "http://download.icu-project.org/files/icu4c/54.1/icu4c-54_1-src.tgz"
+class Xrootd(Package):
+    """The XROOTD project aims at giving high performance, scalable fault
+       tolerant access to data repositories of many kinds."""
+    homepage = "http://xrootd.org"
+    url      = "http://xrootd.org/download/v4.3.0/xrootd-4.3.0.tar.gz"
 
-    version('54.1', 'e844caed8f2ca24c088505b0d6271bc0')
+    version('4.3.0', '39c2fab9f632f35e12ff607ccaf9e16c')
 
-    def url_for_version(self, version):
-        return "http://download.icu-project.org/files/icu4c/%s/icu4c-%s-src.tgz" % (
-            version, str(version).replace('.', '_'))
+    depends_on('cmake', type='build')
 
     def install(self, spec, prefix):
-        with working_dir("source"):
-            configure("--prefix=%s" % prefix)
+        options = []
+        options.extend(std_cmake_args)
+
+        build_directory = join_path(self.stage.path, 'spack-build')
+        source_directory = self.stage.source_path
+
+        if '+debug' in spec:
+            options.append('-DCMAKE_BUILD_TYPE:STRING=Debug')
+
+        with working_dir(build_directory, create=True):
+            cmake(source_directory, *options)
             make()
             make("install")
diff --git a/var/spack/repos/builtin/packages/zoltan/package.py b/var/spack/repos/builtin/packages/zoltan/package.py
index 0094395968..8d4dd321b0 100644
--- a/var/spack/repos/builtin/packages/zoltan/package.py
+++ b/var/spack/repos/builtin/packages/zoltan/package.py
@@ -22,10 +22,11 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
+
+from spack import *
 import re
 import os
 import glob
-from spack import *
 
 
 class Zoltan(Package):
@@ -47,23 +48,28 @@ class Zoltan(Package):
     version('3.6', '9cce794f7241ecd8dbea36c3d7a880f9')
     version('3.3', '5eb8f00bda634b25ceefa0122bd18d65')
 
-    variant('debug', default=False,
-            description='Builds a debug version of the library')
-    variant('shared', default=True,
-            description='Builds a shared version of the library')
+    variant('debug', default=False, description='Builds a debug version of the library.')
+    variant('shared', default=True, description='Builds a shared version of the library.')
 
-    variant('fortran', default=True, description='Enable Fortran support')
-    variant('mpi', default=False, description='Enable MPI support')
+    variant('fortran', default=True, description='Enable Fortran support.')
+    variant('mpi', default=True, description='Enable MPI support.')
 
     depends_on('mpi', when='+mpi')
 
+    def url_for_version(self, version):
+        return '%s/zoltan_distrib_v%s.tar.gz' % (Zoltan.base_url, version)
+
     def install(self, spec, prefix):
-        config_args = [
-            '--enable-f90interface'
-            if '+fortan' in spec else '--disable-f90interface',
+        # FIXME: The older Zoltan versions fail to compile the F90 MPI wrappers
+        # because of some complicated generic type problem.
+        if spec.satisfies('@:3.6+fortran+mpi'):
+            raise RuntimeError(('Cannot build Zoltan v{0} with +fortran and '
+                                '+mpi; please disable one of these features '
+                                'or upgrade versions.').format(self.version))
 
-            '--enable-mpi'
-            if '+mpi' in spec else '--disable-mpi',
+        config_args = [
+            self.get_config_flag('f90interface', 'fortran'),
+            self.get_config_flag('mpi', 'mpi'),
         ]
         config_cflags = [
             '-O0' if '+debug' in spec else '-O3',
@@ -71,49 +77,70 @@ class Zoltan(Package):
         ]
 
         if '+shared' in spec:
-            config_args.append('--with-ar=$(CXX) -shared $(LDFLAGS) -o')
             config_args.append('RANLIB=echo')
+            config_args.append('--with-ar=$(CXX) -shared $(LDFLAGS) -o')
             config_cflags.append('-fPIC')
+            if spec.satisfies('%gcc'):
+                config_args.append('--with-libs={0}'.format('-lgfortran'))
 
         if '+mpi' in spec:
-            config_args.append('CC=%s/mpicc' % spec['mpi'].prefix.bin)
-            config_args.append('CXX=%s/mpicxx' % spec['mpi'].prefix.bin)
-            config_args.append('--with-mpi=%s' % spec['mpi'].prefix)
-            config_args.append('--with-mpi-compilers=%s' %
-                               spec['mpi'].prefix.bin)
+            config_args.append('CC={0}'.format(spec['mpi'].mpicc))
+            config_args.append('CXX={0}'.format(spec['mpi'].mpicxx))
+            config_args.append('FC={0}'.format(spec['mpi'].mpifc))
+
+            mpi_libs = ' -l'.join(self.get_mpi_libs())
+            config_args.append('--with-mpi={0}'.format(spec['mpi'].prefix))
+            config_args.append('--with-mpi-libs=-l{0}'.format(mpi_libs))
 
         # NOTE: Early versions of Zoltan come packaged with a few embedded
         # library packages (e.g. ParMETIS, Scotch), which messes with Spack's
         # ability to descend directly into the package's source directory.
+        source_directory = self.stage.source_path
         if spec.satisfies('@:3.6'):
-            cd('Zoltan_v%s' % self.version)
-
-        mkdirp('build')
-        cd('build')
-
-        config_zoltan = Executable('../configure')
-        config_zoltan(
-            '--prefix=%s' % pwd(),
-            '--with-cflags=%s' % ' '.join(config_cflags),
-            '--with-cxxflags=%s' % ' '.join(config_cflags),
-            *config_args)
-
-        make()
-        make('install')
+            zoltan_directory = 'Zoltan_v{0}'.format(self.version)
+            source_directory = join_path(source_directory, zoltan_directory)
+
+        build_directory = join_path(source_directory, 'build')
+        with working_dir(build_directory, create=True):
+            config = Executable(join_path(source_directory, 'configure'))
+            config(
+                '--prefix={0}'.format(prefix),
+                '--with-cflags={0}'.format(' '.join(config_cflags)),
+                '--with-cxxflags={0}'.format(' '.join(config_cflags)),
+                '--with-fcflags={0}'.format(' '.join(config_cflags)),
+                *config_args
+            )
+
+            # NOTE: Earlier versions of Zoltan cannot be built in parallel
+            # because they contain nested Makefile dependency bugs.
+            make(parallel=not spec.satisfies('@:3.6+fortran'))
+            make('install')
 
         # NOTE: Unfortunately, Zoltan doesn't provide any configuration
         # options for the extension of the output library files, so this
         # script must change these extensions as a post-processing step.
         if '+shared' in spec:
-            for libpath in glob.glob('lib/*.a'):
-                libdir, libname = (os.path.dirname(libpath),
-                                   os.path.basename(libpath))
-                move(libpath, os.path.join(
-                    libdir, re.sub(r'\.a$', '.so', libname)))
-
-        mkdirp(prefix)
-        move('include', prefix)
-        move('lib', prefix)
-
-    def url_for_version(self, version):
-        return '%s/zoltan_distrib_v%s.tar.gz' % (Zoltan.base_url, version)
+            for lib_path in glob.glob(join_path(prefix, 'lib', '*.a')):
+                lib_static_name = os.path.basename(lib_path)
+                lib_shared_name = re.sub(r'\.a$', '.{0}'.format(dso_suffix),
+                                         lib_static_name)
+                move(lib_path, join_path(prefix, 'lib', lib_shared_name))
+
+    def get_config_flag(self, flag_name, flag_variant):
+        flag_pre = 'en' if '+{0}'.format(flag_variant) in self.spec else 'dis'
+        return '--{0}able-{1}'.format(flag_pre, flag_name)
+
+    # NOTE: Zoltan assumes that it's linking against an MPI library that can
+    # be found with '-lmpi,' which isn't the case for many MPI packages.  This
+    # function finds the names of the actual libraries for Zoltan's MPI dep.
+    def get_mpi_libs(self):
+        mpi_libs = set()
+
+        for lib_path in glob.glob(join_path(self.spec['mpi'].prefix.lib, '*')):
+            mpi_lib_match = re.match(
+                r'^(lib)((\w*)mpi(\w*))\.((a)|({0}))$'.format(dso_suffix),
+                os.path.basename(lib_path))
+            if mpi_lib_match:
+                mpi_libs.add(mpi_lib_match.group(2))
+
+        return list(mpi_libs)