Merge develop for v0.8.16 release.v0.8.16

17 files changed, 305 insertions, 125 deletions

diff --git a/lib/spack/docs/site_configuration.rst b/lib/spack/docs/site_configuration.rst
index 44071bbfc6..b03df29573 100644
--- a/lib/spack/docs/site_configuration.rst
+++ b/lib/spack/docs/site_configuration.rst
@@ -8,8 +8,9 @@ Site configuration
 Temporary space
 ----------------------------
 
-.. warning:: Temporary space configuration will be moved to configuration files.
-   The instructions here are old and refer to ``__init__.py``
+.. warning:: Temporary space configuration will eventually be moved to
+   configuration files, but currently these settings are in
+   ``lib/spack/spack/__init__.py``
 
 By default, Spack will try to do all of its building in temporary
 space.  There are two main reasons for this.  First, Spack is designed
diff --git a/lib/spack/env/clang b/lib/spack/env/clang
deleted file mode 120000
index 2652f5f42c..0000000000
--- a/lib/spack/env/clang
+++ /dev/null
@@ -1 +0,0 @@
-cc
\ No newline at end of file
diff --git a/lib/spack/env/clang++ b/lib/spack/env/clang++
deleted file mode 120000
index 2652f5f42c..0000000000
--- a/lib/spack/env/clang++
+++ /dev/null
@@ -1 +0,0 @@
-cc
\ No newline at end of file
diff --git a/lib/spack/env/g++ b/lib/spack/env/g++
deleted file mode 120000
index 2652f5f42c..0000000000
--- a/lib/spack/env/g++
+++ /dev/null
@@ -1 +0,0 @@
-cc
\ No newline at end of file
diff --git a/lib/spack/env/gcc b/lib/spack/env/gcc
deleted file mode 120000
index 2652f5f42c..0000000000
--- a/lib/spack/env/gcc
+++ /dev/null
@@ -1 +0,0 @@
-cc
\ No newline at end of file
diff --git a/lib/spack/llnl/util/filesystem.py b/lib/spack/llnl/util/filesystem.py
index 576aeb16bd..1fdd25f608 100644
--- a/lib/spack/llnl/util/filesystem.py
+++ b/lib/spack/llnl/util/filesystem.py
@@ -22,9 +22,10 @@
 # along with this program; if not, write to the Free Software Foundation,
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-__all__ = ['set_install_permissions', 'install', 'expand_user', 'working_dir',
-           'touch', 'touchp', 'mkdirp', 'force_remove', 'join_path', 'ancestor',
-           'can_access', 'filter_file', 'change_sed_delimiter', 'is_exe']
+__all__ = ['set_install_permissions', 'install', 'install_tree', 'traverse_tree',
+           'expand_user', 'working_dir', 'touch', 'touchp', 'mkdirp',
+           'force_remove', 'join_path', 'ancestor', 'can_access', 'filter_file',
+           'change_sed_delimiter', 'is_exe', 'force_symlink']
 
 import os
 import sys
@@ -140,12 +141,7 @@ def set_install_permissions(path):
         os.chmod(path, 0644)
 
 
-def install(src, dest):
-    """Manually install a file to a particular location."""
-    tty.info("Installing %s to %s" % (src, dest))
-    shutil.copy(src, dest)
-    set_install_permissions(dest)
-
+def copy_mode(src, dest):
     src_mode = os.stat(src).st_mode
     dest_mode = os.stat(dest).st_mode
     if src_mode | stat.S_IXUSR: dest_mode |= stat.S_IXUSR
@@ -154,6 +150,24 @@ def install(src, dest):
     os.chmod(dest, dest_mode)
 
 
+def install(src, dest):
+    """Manually install a file to a particular location."""
+    tty.info("Installing %s to %s" % (src, dest))
+    shutil.copy(src, dest)
+    set_install_permissions(dest)
+    copy_mode(src, dest)
+
+
+def install_tree(src, dest, **kwargs):
+    """Manually install a file to a particular location."""
+    tty.info("Installing %s to %s" % (src, dest))
+    shutil.copytree(src, dest, **kwargs)
+
+    for s, d in traverse_tree(src, dest, follow_nonexisting=False):
+        set_install_permissions(d)
+        copy_mode(s, d)
+
+
 def is_exe(path):
     """True if path is an executable file."""
     return os.path.isfile(path) and os.access(path, os.X_OK)
@@ -210,6 +224,14 @@ def touchp(path):
     touch(path)
 
 
+def force_symlink(src, dest):
+    try:
+        os.symlink(src, dest)
+    except OSError, e:
+        os.remove(dest)
+        os.symlink(src, dest)
+
+
 def join_path(prefix, *args):
     path = str(prefix)
     for elt in args:
@@ -228,3 +250,84 @@ def ancestor(dir, n=1):
 def can_access(file_name):
     """True if we have read/write access to the file."""
     return os.access(file_name, os.R_OK|os.W_OK)
+
+
+def traverse_tree(source_root, dest_root, rel_path='', **kwargs):
+    """Traverse two filesystem trees simultaneously.
+
+    Walks the LinkTree directory in pre or post order.  Yields each
+    file in the source directory with a matching path from the dest
+    directory, along with whether the file is a directory.
+    e.g., for this tree::
+
+        root/
+          a/
+            file1
+            file2
+          b/
+            file3
+
+    When called on dest, this yields::
+
+        ('root',         'dest')
+        ('root/a',       'dest/a')
+        ('root/a/file1', 'dest/a/file1')
+        ('root/a/file2', 'dest/a/file2')
+        ('root/b',       'dest/b')
+        ('root/b/file3', 'dest/b/file3')
+
+    Optional args:
+
+    order=[pre|post] -- Whether to do pre- or post-order traveral.
+
+    ignore=<predicate> -- Predicate indicating which files to ignore.
+
+    follow_nonexisting -- Whether to descend into directories in
+                          src that do not exit in dest. Default True.
+
+    follow_links -- Whether to descend into symlinks in src.
+
+    """
+    follow_nonexisting = kwargs.get('follow_nonexisting', True)
+    follow_links = kwargs.get('follow_link', False)
+
+    # Yield in pre or post order?
+    order  = kwargs.get('order', 'pre')
+    if order not in ('pre', 'post'):
+        raise ValueError("Order must be 'pre' or 'post'.")
+
+    # List of relative paths to ignore under the src root.
+    ignore = kwargs.get('ignore', lambda filename: False)
+
+    # Don't descend into ignored directories
+    if ignore(rel_path):
+        return
+
+    source_path = os.path.join(source_root, rel_path)
+    dest_path   = os.path.join(dest_root, rel_path)
+
+    # preorder yields directories before children
+    if order == 'pre':
+        yield (source_path, dest_path)
+
+    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)
+
+        # Treat as a directory
+        if os.path.isdir(source_child) and (
+            follow_links or not os.path.islink(source_child)):
+
+            # When follow_nonexisting isn't set, don't descend into dirs
+            # in source that do not exist in dest
+            if follow_nonexisting or os.path.exists(dest_child):
+                tuples = traverse_tree(source_root, dest_root, rel_child, **kwargs)
+                for t in tuples: yield t
+
+        # Treat as a file.
+        elif not ignore(os.path.join(rel_path, f)):
+            yield (source_child, dest_child)
+
+    if order == 'post':
+        yield (source_path, dest_path)
diff --git a/lib/spack/llnl/util/link_tree.py b/lib/spack/llnl/util/link_tree.py
index 4d778eca1e..583f077b79 100644
--- a/lib/spack/llnl/util/link_tree.py
+++ b/lib/spack/llnl/util/link_tree.py
@@ -32,88 +32,6 @@ from llnl.util.filesystem import *
 empty_file_name = '.spack-empty'
 
 
-def traverse_tree(source_root, dest_root, rel_path='', **kwargs):
-    """Traverse two filesystem trees simultaneously.
-
-    Walks the LinkTree directory in pre or post order.  Yields each
-    file in the source directory with a matching path from the dest
-    directory, along with whether the file is a directory.
-    e.g., for this tree::
-
-        root/
-          a/
-            file1
-            file2
-          b/
-            file3
-
-    When called on dest, this yields::
-
-        ('root',         'dest')
-        ('root/a',       'dest/a')
-        ('root/a/file1', 'dest/a/file1')
-        ('root/a/file2', 'dest/a/file2')
-        ('root/b',       'dest/b')
-        ('root/b/file3', 'dest/b/file3')
-
-    Optional args:
-
-    order=[pre|post] -- Whether to do pre- or post-order traveral.
-
-    ignore=<predicate> -- Predicate indicating which files to ignore.
-
-    follow_nonexisting -- Whether to descend into directories in
-                          src that do not exit in dest. Default True.
-
-    follow_links -- Whether to descend into symlinks in src.
-
-    """
-    follow_nonexisting = kwargs.get('follow_nonexisting', True)
-    follow_links = kwargs.get('follow_link', False)
-
-    # Yield in pre or post order?
-    order  = kwargs.get('order', 'pre')
-    if order not in ('pre', 'post'):
-        raise ValueError("Order must be 'pre' or 'post'.")
-
-    # List of relative paths to ignore under the src root.
-    ignore = kwargs.get('ignore', lambda filename: False)
-
-    # Don't descend into ignored directories
-    if ignore(rel_path):
-        return
-
-    source_path = os.path.join(source_root, rel_path)
-    dest_path   = os.path.join(dest_root, rel_path)
-
-    # preorder yields directories before children
-    if order == 'pre':
-        yield (source_path, dest_path)
-
-    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)
-
-        # Treat as a directory
-        if os.path.isdir(source_child) and (
-            follow_links or not os.path.islink(source_child)):
-
-            # When follow_nonexisting isn't set, don't descend into dirs
-            # in source that do not exist in dest
-            if follow_nonexisting or os.path.exists(dest_child):
-                tuples = traverse_tree(source_root, dest_root, rel_child, **kwargs)
-                for t in tuples: yield t
-
-        # Treat as a file.
-        elif not ignore(os.path.join(rel_path, f)):
-            yield (source_child, dest_child)
-
-    if order == 'post':
-        yield (source_path, dest_path)
-
-
-
 class LinkTree(object):
     """Class to create trees of symbolic links from a source directory.
 
diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py
index 59b25d96e7..d11e2e270c 100644
--- a/lib/spack/spack/build_environment.py
+++ b/lib/spack/spack/build_environment.py
@@ -189,18 +189,19 @@ def set_module_variables_for_package(pkg):
     m.std_cmake_args.append('-DCMAKE_INSTALL_RPATH=%s' % ":".join(get_rpaths(pkg)))
 
     # Emulate some shell commands for convenience
-    m.pwd        = os.getcwd
-    m.cd         = os.chdir
-    m.mkdir      = os.mkdir
-    m.makedirs   = os.makedirs
-    m.remove     = os.remove
-    m.removedirs = os.removedirs
-    m.symlink    = os.symlink
-
-    m.mkdirp     = mkdirp
-    m.install    = install
-    m.rmtree     = shutil.rmtree
-    m.move       = shutil.move
+    m.pwd          = os.getcwd
+    m.cd           = os.chdir
+    m.mkdir        = os.mkdir
+    m.makedirs     = os.makedirs
+    m.remove       = os.remove
+    m.removedirs   = os.removedirs
+    m.symlink      = os.symlink
+
+    m.mkdirp       = mkdirp
+    m.install      = install
+    m.install_tree = install_tree
+    m.rmtree       = shutil.rmtree
+    m.move         = shutil.move
 
     # Useful directories within the prefix are encapsulated in
     # a Prefix object.
diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index 75e6142a9d..36f1e8a777 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -62,6 +62,7 @@ from spack.version import *
 from spack.stage import Stage
 from spack.util.web import get_pages
 from spack.util.compression import allowed_archive, extension
+from spack.util.executable import ProcessError
 
 """Allowed URL schemes for spack packages."""
 _ALLOWED_URL_SCHEMES = ["http", "https", "ftp", "file", "git"]
@@ -805,6 +806,16 @@ class Package(object):
         # package naming scheme it likes.
         spack.install_layout.make_path_for_spec(self.spec)
 
+        def cleanup():
+            if not keep_prefix:
+                # If anything goes wrong, remove the install prefix
+                self.remove_prefix()
+            else:
+                tty.warn("Keeping install prefix in place despite error.",
+                         "Spack will think this package is installed." +
+                         "Manually remove this directory to fix:",
+                         self.prefix)
+
         def real_work():
             try:
                 tty.msg("Building %s." % self.name)
@@ -837,15 +848,20 @@ class Package(object):
                         % (_hms(self._fetch_time), _hms(build_time), _hms(self._total_time)))
                 print_pkg(self.prefix)
 
-            except:
-                if not keep_prefix:
-                    # If anything goes wrong, remove the install prefix
-                    self.remove_prefix()
+            except ProcessError, e:
+                # One of the processes returned an error code.
+                # Suppress detailed stack trace here unless in debug mode
+                if spack.debug:
+                    raise e
                 else:
-                    tty.warn("Keeping install prefix in place despite error.",
-                             "Spack will think this package is installed." +
-                             "Manually remove this directory to fix:",
-                             self.prefix)
+                    tty.error(e)
+
+                # Still need to clean up b/c there was an error.
+                cleanup()
+
+            except:
+                # other exceptions just clean up and raise.
+                cleanup()
                 raise
 
         build_env.fork(self, real_work)
diff --git a/var/spack/packages/SAMRAI/package.py b/var/spack/packages/SAMRAI/package.py
index 3dfb00b391..eef041f0d5 100644
--- a/var/spack/packages/SAMRAI/package.py
+++ b/var/spack/packages/SAMRAI/package.py
@@ -7,10 +7,11 @@ class Samrai(Package):
        structured adaptive mesh refinement (SAMR) technology in large-scale parallel
        application development.
     """
-    homepage = "https://computation-rnd.llnl.gov/SAMRAI/confirm.php"
-    url      = "https://computation-rnd.llnl.gov/SAMRAI/download/SAMRAI-v3.7.3.tar.gz"
+    homepage = "https://computation.llnl.gov/project/SAMRAI/"
+    url      = "https://computation.llnl.gov/project/SAMRAI/download/SAMRAI-v3.9.1.tar.gz"
     list_url = homepage
 
+    version('3.9.1',      '232d04d0c995f5abf20d94350befd0b2')
     version('3.7.3',      '12d574eacadf8c9a70f1bb4cd1a69df6')
     version('3.7.2',      'f6a716f171c9fdbf3cb12f71fa6e2737')
     version('3.6.3-beta', 'ef0510bf2893042daedaca434e5ec6ce')
@@ -24,22 +25,25 @@ class Samrai(Package):
     depends_on("mpi")
     depends_on("zlib")
     depends_on("hdf5")
-    depends_on("boost@1.52.0")
+    depends_on("boost")
 
     # don't build tools with gcc
     patch('no-tool-build.patch', when='%gcc')
 
     # TODO: currently hard-coded to use openmpi - be careful!
     def install(self, spec, prefix):
+        mpi = next(m for m in ('openmpi', 'mpich', 'mvapich')
+                   if m in spec)
+
         configure(
             "--prefix=%s" % prefix,
-            "--with-CXX=%s" % spec['openmpi'].prefix.bin + "/mpic++",
-            "--with-CC=%s" % spec['openmpi'].prefix.bin + "/mpicc",
+            "--with-CXX=%s" % spec[mpi].prefix.bin + "/mpic++",
+            "--with-CC=%s" % spec[mpi].prefix.bin + "/mpicc",
             "--with-hdf5=%s" % spec['hdf5'].prefix,
             "--with-boost=%s" % spec['boost'].prefix,
             "--with-zlib=%s" % spec['zlib'].prefix,
-            "--disable-blas",
-            "--disable-lapack",
+            "--without-blas",
+            "--without-lapack",
             "--with-hypre=no",
             "--with-petsc=no",
             "--enable-opt",
diff --git a/var/spack/packages/cram/package.py b/var/spack/packages/cram/package.py
new file mode 100644
index 0000000000..4b8ec56f25
--- /dev/null
+++ b/var/spack/packages/cram/package.py
@@ -0,0 +1,15 @@
+from spack import *
+
+class Cram(Package):
+    """Cram runs many small MPI jobs inside one large MPI job."""
+    homepage = "https://github.com/scalability-llnl/cram"
+    url      = "http://github.com/scalability-llnl/cram/archive/v1.0.1.tar.gz"
+
+    version('1.0.1', 'c73711e945cf5dc603e44395f6647f5e')
+
+    depends_on("mpi")
+
+    def install(self, spec, prefix):
+        cmake(".", *std_cmake_args)
+        make()
+        make("install")
diff --git a/var/spack/packages/metis/package.py b/var/spack/packages/metis/package.py
new file mode 100644
index 0000000000..fa13d52127
--- /dev/null
+++ b/var/spack/packages/metis/package.py
@@ -0,0 +1,32 @@
+from spack import *
+
+class Metis(Package):
+    """METIS is a set of serial programs for partitioning graphs,
+       partitioning finite element meshes, and producing fill reducing
+       orderings for sparse matrices. The algorithms implemented in
+       METIS are based on the multilevel recursive-bisection,
+       multilevel k-way, and multi-constraint partitioning schemes
+       developed in our lab."""
+
+    homepage = "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview"
+    url      = "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/metis-5.1.0.tar.gz"
+
+    version('5.1.0', '5465e67079419a69e0116de24fce58fe')
+
+    # FIXME: Add dependencies if this package requires them.
+    # depends_on("foo")
+
+    def patch(self):
+        filter_file(r'#define IDXTYPEWIDTH 32', '#define IDXTYPEWIDTH 64', 'include/metis.h',
+                    string=True)
+
+
+    def install(self, spec, prefix):
+        with working_dir('spack-build', create=True):
+            cmake('..',
+                  '-DGKLIB_PATH=../GKlib',
+                  '-DBUILD_SHARED_LIBS=TRUE',
+                  *std_cmake_args)
+            make()
+            make("install")
+
diff --git a/var/spack/packages/mpich/package.py b/var/spack/packages/mpich/package.py
index 57378626ab..6aa8f2eca4 100644
--- a/var/spack/packages/mpich/package.py
+++ b/var/spack/packages/mpich/package.py
@@ -38,6 +38,15 @@ class Mpich(Package):
     provides('mpi@:3', when='@3:')
     provides('mpi@:1', when='@1:')
 
+
+    def setup_dependent_environment(self, module, spec, dep_spec):
+        """For dependencies, make mpicc's use spack wrapper."""
+        os.environ['MPICH_CC']  = 'cc'
+        os.environ['MPICH_CXX'] = 'c++'
+        os.environ['MPICH_F77'] = 'f77'
+        os.environ['MPICH_F90'] = 'f90'
+
+
     def install(self, spec, prefix):
         config_args = ["--prefix=" + prefix,
                        "--enable-shared"]
diff --git a/var/spack/packages/muster/package.py b/var/spack/packages/muster/package.py
index 31d03f4b45..722daf3d7f 100644
--- a/var/spack/packages/muster/package.py
+++ b/var/spack/packages/muster/package.py
@@ -10,7 +10,8 @@ class Muster(Package):
     homepage = "https://github.com/scalability-llnl/muster"
     url      = "https://github.com/scalability-llnl/muster/archive/v1.0.tar.gz"
 
-    version('1.0', '2eec6979a4a36d3a65a792d12969be16')
+    version('1.0.1', 'd709787db7e080447afb6571ac17723c')
+    version('1.0',   '2eec6979a4a36d3a65a792d12969be16')
 
     depends_on("boost")
     depends_on("mpi")
diff --git a/var/spack/packages/otf/package.py b/var/spack/packages/otf/package.py
new file mode 100644
index 0000000000..52893dd265
--- /dev/null
+++ b/var/spack/packages/otf/package.py
@@ -0,0 +1,21 @@
+from spack import *
+
+class Otf(Package):
+    """To improve scalability for very large and massively parallel
+       traces the Open Trace Format (OTF) is developed at ZIH as a
+       successor format to the Vampir Trace Format (VTF3)."""
+
+    homepage = "http://tu-dresden.de/die_tu_dresden/zentrale_einrichtungen/zih/forschung/projekte/otf/index_html/document_view?set_language=en"
+    url      = "http://wwwpub.zih.tu-dresden.de/%7Emlieber/dcount/dcount.php?package=otf&get=OTF-1.12.5salmon.tar.gz"
+
+    version('1.12.5salmon', 'bf260198633277031330e3356dcb4eec')
+
+    depends_on('zlib')
+
+    def install(self, spec, prefix):
+        configure('--prefix=%s' % prefix,
+                  '--without-vtf3',
+                  '--with-zlib',
+                  '--with-zlibsymbols')
+        make()
+        make("install")
diff --git a/var/spack/packages/ravel/package.py b/var/spack/packages/ravel/package.py
new file mode 100644
index 0000000000..01fa941cfe
--- /dev/null
+++ b/var/spack/packages/ravel/package.py
@@ -0,0 +1,23 @@
+from spack import *
+
+class Ravel(Package):
+    """Ravel is a parallel communication trace visualization tool that
+       orders events according to logical time."""
+
+    homepage = "https://github.com/scalability-llnl/ravel"
+    url = 'https://github.com/scalability-llnl/ravel/archive/v1.0.0.tar.gz'
+
+    version('1.0.0', 'b25fece58331c2adfcce76c5036485c2')
+
+    # TODO: make this a build dependency
+    depends_on('cmake@2.8.9:')
+
+    depends_on('muster@1.0.1:')
+    depends_on('otf')
+    depends_on('otf2')
+    depends_on('qt@5:')
+
+    def install(self, spec, prefix):
+        cmake('-Wno-dev', *std_cmake_args)
+        make()
+        make("install")
diff --git a/var/spack/packages/scotch/package.py b/var/spack/packages/scotch/package.py
new file mode 100644
index 0000000000..79289ff2ad
--- /dev/null
+++ b/var/spack/packages/scotch/package.py
@@ -0,0 +1,40 @@
+from spack import *
+import glob
+import os
+
+class Scotch(Package):
+    """Scotch is a software package for graph and mesh/hypergraph
+       partitioning, graph clustering, and sparse matrix ordering."""
+    homepage = "http://www.labri.fr/perso/pelegrin/scotch/"
+    url      = "http://gforge.inria.fr/frs/download.php/file/34099/scotch_6.0.3.tar.gz"
+    list_url = "http://gforge.inria.fr/frs/?group_id=248"
+
+    version('6.0.3', '10b0cc0f184de2de99859eafaca83cfc')
+
+    depends_on('mpi')
+
+
+    def patch(self):
+        with working_dir('src/Make.inc'):
+            makefiles = glob.glob('Makefile.inc.x86-64_pc_linux2*')
+            filter_file(r'^CCS\s*=.*$', 'CCS = cc', *makefiles)
+            filter_file(r'^CCD\s*=.*$', 'CCD = cc', *makefiles)
+
+
+    def install(self, spec, prefix):
+        # Currently support gcc and icc on x86_64 (maybe others with
+        # vanilla makefile)
+        makefile = 'Make.inc/Makefile.inc.x86-64_pc_linux2'
+        if spec.satisfies('%icc'):
+            makefile += '.icc'
+
+        with working_dir('src'):
+            force_symlink(makefile, 'Makefile.inc')
+            for app in ('scotch', 'ptscotch'):
+                make(app)
+
+        install_tree('bin', prefix.bin)
+        install_tree('lib', prefix.lib)
+        install_tree('include', prefix.include)
+        install_tree('man/man1', prefix.share_man1)
+