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

Conflicts:
	var/spack/repos/builtin/packages/openmpi/package.py

34 files changed, 371 insertions, 46 deletions

diff --git a/var/spack/repos/builtin/packages/adol-c/openmp_exam.patch b/var/spack/repos/builtin/packages/adol-c/openmp_exam.patch
new file mode 100644
index 0000000000..8e21c72d92
--- /dev/null
+++ b/var/spack/repos/builtin/packages/adol-c/openmp_exam.patch
@@ -0,0 +1,13 @@
+diff --git a/ADOL-C/examples/additional_examples/openmp_exam/liborpar.cpp b/ADOL-C/examples/additional_examples/openmp_exam/liborpar.cpp
+index fc6fc28..14103d2 100644
+--- a/ADOL-C/examples/additional_examples/openmp_exam/liborpar.cpp
++++ b/ADOL-C/examples/additional_examples/openmp_exam/liborpar.cpp
+@@ -27,7 +27,7 @@ using namespace std;
+ #include <ctime>
+ #include <cmath>
+ 
+-#include "adolc.h"
++#include <adolc/adolc.h>
+ 
+ #ifdef _OPENMP
+ #include <omp.h>
diff --git a/var/spack/repos/builtin/packages/adol-c/package.py b/var/spack/repos/builtin/packages/adol-c/package.py
new file mode 100644
index 0000000000..70933542ca
--- /dev/null
+++ b/var/spack/repos/builtin/packages/adol-c/package.py
@@ -0,0 +1,80 @@
+from spack import *
+import sys
+
+class AdolC(Package):
+    """A package for the automatic differentiation of first and higher derivatives of vector functions in C and C++ programs by operator overloading."""
+    homepage = "https://projects.coin-or.org/ADOL-C"
+    url      = "http://www.coin-or.org/download/source/ADOL-C/ADOL-C-2.6.1.tgz"
+
+    version('head',  svn='https://projects.coin-or.org/svn/ADOL-C/trunk/')
+    version('2.6.1', '1032b28427d6e399af4610e78c0f087b')
+    
+    variant('doc',      default=True,  description='Install documentation')
+    variant('openmp',   default=False, description='Enable OpenMP support')
+    variant('sparse',   default=False, description='Enable sparse drivers')
+    variant('tests',    default=True,  description='Build all included examples as a test case')
+    
+    patch('openmp_exam.patch')
+
+    def install(self, spec, prefix):
+        make_args = ['--prefix=%s' % prefix]
+
+        # --with-cflags=FLAGS     use CFLAGS=FLAGS (default: -O3 -Wall -ansi)
+        # --with-cxxflags=FLAGS   use CXXFLAGS=FLAGS (default: -O3 -Wall)
+
+        if '+openmp' in spec:
+            if spec.satisfies('%gcc'):
+                make_args.extend([
+                    '--with-openmp-flag=-fopenmp' # FIXME: Is this required? -I <path to omp.h> -L <LLVM OpenMP library path>
+                ])
+            else:
+                raise InstallError("OpenMP flags for compilers other than GCC are not implemented.")
+
+        if '+sparse' in spec:
+            make_args.extend([
+                '--enable-sparse'
+            ])
+
+        # We can simply use the bundled examples to check
+        # whether Adol-C works as expected
+        if '+tests' in spec:
+            make_args.extend([
+                '--enable-docexa', # Documeted examples
+                '--enable-addexa'  # Additional examples
+            ])
+            if '+openmp' in spec:
+                make_args.extend([
+                    '--enable-parexa'  # Parallel examples
+                ])
+
+        configure(*make_args)
+        make()
+        make("install")
+        
+        # Copy the config.h file, as some packages might require it
+        source_directory = self.stage.source_path
+        config_h = join_path(source_directory,'ADOL-C','src','config.h')
+        install(config_h, join_path(prefix.include,'adolc'))
+        
+        # Install documentation to {prefix}/share
+        if '+doc' in spec:
+            install_tree(join_path('ADOL-C','doc'),
+                         join_path(prefix.share,'doc'))
+        
+        # Install examples to {prefix}/share
+        if '+tests' in spec:
+            install_tree(join_path('ADOL-C','examples'),
+                         join_path(prefix.share,'examples'))
+        
+            # Run some examples that don't require user input
+            # TODO: Check that bundled examples produce the correct results
+            with working_dir(join_path(source_directory,'ADOL-C','examples')):
+                Executable('./tapeless_scalar')()
+                Executable('./tapeless_vector')()
+              
+            with working_dir(join_path(source_directory,'ADOL-C','examples','additional_examples')):
+                Executable('./checkpointing/checkpointing')()
+                
+            if '+openmp' in spec:
+                with working_dir(join_path(source_directory,'ADOL-C','examples','additional_examples')):
+                    Executable('./checkpointing/checkpointing')()
diff --git a/var/spack/repos/builtin/packages/autoconf/package.py b/var/spack/repos/builtin/packages/autoconf/package.py
index 6412e810a6..b5e29b8a27 100644
--- a/var/spack/repos/builtin/packages/autoconf/package.py
+++ b/var/spack/repos/builtin/packages/autoconf/package.py
@@ -8,6 +8,8 @@ class Autoconf(Package):
     version('2.69', '82d05e03b93e45f5a39b828dc9c6c29b')
     version('2.62', '6c1f3b3734999035d77da5024aab4fbd')
 
+    depends_on("m4")
+
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
 
diff --git a/var/spack/repos/builtin/packages/bbcp/package.py b/var/spack/repos/builtin/packages/bbcp/package.py
new file mode 100644
index 0000000000..e9baa5ccf4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bbcp/package.py
@@ -0,0 +1,17 @@
+from spack import *
+
+class Bbcp(Package):
+    """Securely and quickly copy data from source to target"""
+    homepage = "http://www.slac.stanford.edu/~abh/bbcp/"
+
+    version('git', git='http://www.slac.stanford.edu/~abh/bbcp/bbcp.git', branch="master")
+
+    def install(self, spec, prefix):
+        cd("src")
+        make()
+        # BBCP wants to build the executable in a directory whose name depends on the system type
+        makesname = Executable("../MakeSname")
+        bbcp_executable_path = "../bin/%s/bbcp" % makesname(output=str).rstrip("\n")
+        destination_path = "%s/bin/" % prefix
+        mkdirp(destination_path)
+        install(bbcp_executable_path, destination_path)
diff --git a/var/spack/repos/builtin/packages/cnmem/package.py b/var/spack/repos/builtin/packages/cnmem/package.py
new file mode 100644
index 0000000000..0a83e8fc20
--- /dev/null
+++ b/var/spack/repos/builtin/packages/cnmem/package.py
@@ -0,0 +1,12 @@
+from spack import *
+
+class Cnmem(Package):
+    """CNMem mempool for CUDA devices"""
+    homepage = "https://github.com/NVIDIA/cnmem"
+
+    version('git', git='https://github.com/NVIDIA/cnmem.git', branch="master")
+
+    def install(self, spec, prefix):
+            cmake('.',*std_cmake_args)
+            make()
+            make('install')
diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py
index 674fe3150a..df8330384d 100644
--- a/var/spack/repos/builtin/packages/dealii/package.py
+++ b/var/spack/repos/builtin/packages/dealii/package.py
@@ -12,6 +12,7 @@ class Dealii(Package):
     variant('mpi',      default=True,  description='Compile with MPI')
     variant('arpack',   default=True,  description='Compile with Arpack and PArpack (only with MPI)')
     variant('doc',      default=False, description='Compile with documentation')
+    variant('gsl' ,     default=True,  description='Compile with GSL')
     variant('hdf5',     default=True,  description='Compile with HDF5 (only with MPI)')
     variant('metis',    default=True,  description='Compile with Metis')
     variant('netcdf',   default=True,  description='Compile with Netcdf (only with MPI)')
@@ -39,6 +40,8 @@ class Dealii(Package):
     depends_on ("mpi", when="+mpi")
     depends_on ("arpack-ng+mpi", when='+arpack+mpi')
     depends_on ("doxygen", when='+doc')
+    depends_on ("gsl", when='@8.5.0:+gsl')
+    depends_on ("gsl", when='@dev+gsl')
     depends_on ("hdf5+mpi~cxx", when='+hdf5+mpi') #FIXME NetCDF declares dependency with ~cxx, why?
     depends_on ("metis@5:", when='+metis')
     depends_on ("netcdf+mpi", when="+netcdf+mpi")
@@ -80,7 +83,6 @@ class Dealii(Package):
                 (join_path(spec['lapack'].prefix.lib,'liblapack.%s' % dsuf), # FIXME don't hardcode names
                  join_path(spec['blas'].prefix.lib,'libblas.%s' % dsuf)),    # FIXME don't hardcode names
             '-DMUPARSER_DIR=%s ' % spec['muparser'].prefix,
-            '-DP4EST_DIR=%s' % spec['p4est'].prefix,
             '-DUMFPACK_DIR=%s' % spec['suite-sparse'].prefix,
             '-DTBB_DIR=%s' % spec['tbb'].prefix,
             '-DZLIB_DIR=%s' % spec['zlib'].prefix
@@ -100,7 +102,7 @@ class Dealii(Package):
             ])
 
         # Optional dependencies for which librariy names are the same as CMake variables
-        for library in ('hdf5', 'p4est','petsc', 'slepc','trilinos','metis'):
+        for library in ('gsl','hdf5','p4est','petsc','slepc','trilinos','metis'):
             if library in spec:
                 options.extend([
                     '-D{library}_DIR={value}'.format(library=library.upper(), value=spec[library].prefix),
diff --git a/var/spack/repos/builtin/packages/flex/package.py b/var/spack/repos/builtin/packages/flex/package.py
index b065904912..e4795893e0 100644
--- a/var/spack/repos/builtin/packages/flex/package.py
+++ b/var/spack/repos/builtin/packages/flex/package.py
@@ -6,6 +6,7 @@ class Flex(Package):
     homepage = "http://flex.sourceforge.net/"
     url      = "http://download.sourceforge.net/flex/flex-2.5.39.tar.gz"
 
+    version('2.6.0', '5724bcffed4ebe39e9b55a9be80859ec')
     version('2.5.39', 'e133e9ead8ec0a58d81166b461244fde')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/gcc/package.py b/var/spack/repos/builtin/packages/gcc/package.py
index 6043b62279..8f90757232 100644
--- a/var/spack/repos/builtin/packages/gcc/package.py
+++ b/var/spack/repos/builtin/packages/gcc/package.py
@@ -38,6 +38,7 @@ class Gcc(Package):
     list_url = 'http://open-source-box.org/gcc/'
     list_depth = 2
 
+    version('6.1.0', '8fb6cb98b8459f5863328380fbf06bd1')
     version('5.3.0', 'c9616fd448f980259c31de613e575719')
     version('5.2.0', 'a51bcfeb3da7dd4c623e27207ed43467')
     version('4.9.3', '6f831b4d251872736e8e9cc09746f327')
diff --git a/var/spack/repos/builtin/packages/glm/package.py b/var/spack/repos/builtin/packages/glm/package.py
index d00c301b4c..ecae89f1e8 100644
--- a/var/spack/repos/builtin/packages/glm/package.py
+++ b/var/spack/repos/builtin/packages/glm/package.py
@@ -11,6 +11,8 @@ class Glm(Package):
     url = "https://github.com/g-truc/glm/archive/0.9.7.1.tar.gz"
 
     version('0.9.7.1', '61af6639cdf652d1cdd7117190afced8')
+    
+    depends_on ("cmake")
 
     def install(self, spec, prefix):
         with working_dir('spack-build', create=True):
diff --git a/var/spack/repos/builtin/packages/hwloc/package.py b/var/spack/repos/builtin/packages/hwloc/package.py
index ab7205646e..a461a7482c 100644
--- a/var/spack/repos/builtin/packages/hwloc/package.py
+++ b/var/spack/repos/builtin/packages/hwloc/package.py
@@ -17,6 +17,7 @@ class Hwloc(Package):
     list_url = "http://www.open-mpi.org/software/hwloc/"
     list_depth = 3
 
+    version('1.11.3', 'c1d36a9de6028eac1d18ea4782ef958f')
     version('1.11.2', 'e4ca55c2a5c5656da4a4e37c8fc51b23')
     version('1.11.1', 'feb4e416a1b25963ed565d8b42252fdc')
     version('1.9',    '1f9f9155682fe8946a97c08896109508')
diff --git a/var/spack/repos/builtin/packages/jpeg/package.py b/var/spack/repos/builtin/packages/jpeg/package.py
index 87820467db..2f15e59ad4 100644
--- a/var/spack/repos/builtin/packages/jpeg/package.py
+++ b/var/spack/repos/builtin/packages/jpeg/package.py
@@ -1,14 +1,19 @@
 from spack import *
 
 class Jpeg(Package):
-    """jpeg library"""
+    """libjpeg is a widely used free library with functions for handling the
+    JPEG image data format. It implements a JPEG codec (encoding and decoding)
+    alongside various utilities for handling JPEG data."""
+
     homepage = "http://www.ijg.org"
-    url      = "http://www.ijg.org/files/jpegsrc.v9a.tar.gz"
+    url      = "http://www.ijg.org/files/jpegsrc.v9b.tar.gz"
 
+    version('9b', '6a9996ce116ec5c52b4870dbcd6d3ddb')
     version('9a', '3353992aecaee1805ef4109aadd433e7')
 
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
 
         make()
+        make("test")
         make("install")
diff --git a/var/spack/repos/builtin/packages/libtool/package.py b/var/spack/repos/builtin/packages/libtool/package.py
index 82a54953b2..c804f5ab5d 100644
--- a/var/spack/repos/builtin/packages/libtool/package.py
+++ b/var/spack/repos/builtin/packages/libtool/package.py
@@ -8,6 +8,8 @@ class Libtool(Package):
     version('2.4.6' , 'addf44b646ddb4e3919805aa88fa7c5e')
     version('2.4.2' , 'd2f3b7d4627e69e13514a40e72a24d50')
 
+    depends_on('m4')
+
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
 
diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py
index b317ec6651..5d68f20351 100644
--- a/var/spack/repos/builtin/packages/mpich/package.py
+++ b/var/spack/repos/builtin/packages/mpich/package.py
@@ -55,9 +55,10 @@ class Mpich(Package):
         spack_env.set('MPICH_FC', spack_fc)
 
     def setup_dependent_package(self, module, dep_spec):
-        """For dependencies, make mpicc's use spack wrapper."""
-        # FIXME : is this necessary ? Shouldn't this be part of a contract with MPI providers?
-        module.mpicc = join_path(self.prefix.bin, 'mpicc')
+        self.spec.mpicc  = join_path(self.prefix.bin, 'mpicc')
+        self.spec.mpicxx = join_path(self.prefix.bin, 'mpic++')
+        self.spec.mpifc  = join_path(self.prefix.bin, 'mpif90')
+        self.spec.mpif77 = join_path(self.prefix.bin, 'mpif77')
 
     def install(self, spec, prefix):
         config_args = ["--prefix=" + prefix,
diff --git a/var/spack/repos/builtin/packages/mrnet/package.py b/var/spack/repos/builtin/packages/mrnet/package.py
index a3abb71285..b52233be4a 100644
--- a/var/spack/repos/builtin/packages/mrnet/package.py
+++ b/var/spack/repos/builtin/packages/mrnet/package.py
@@ -6,6 +6,7 @@ class Mrnet(Package):
     url      = "ftp://ftp.cs.wisc.edu/paradyn/mrnet/mrnet_5.0.1.tar.gz"
     list_url = "http://ftp.cs.wisc.edu/paradyn/mrnet"
 
+    version('5.0.1-2', git='https://github.com/dyninst/mrnet.git', commit='20b1eacfc6d680d9f6472146d2dfaa0f900cc2e9')
     version('5.0.1', '17f65738cf1b9f9b95647ff85f69ecdd')
     version('4.1.0', '5a248298b395b329e2371bf25366115c')
     version('4.0.0', 'd00301c078cba57ef68613be32ceea2f')
diff --git a/var/spack/repos/builtin/packages/mvapich2/package.py b/var/spack/repos/builtin/packages/mvapich2/package.py
index 3e60b517db..c68a04d251 100644
--- a/var/spack/repos/builtin/packages/mvapich2/package.py
+++ b/var/spack/repos/builtin/packages/mvapich2/package.py
@@ -147,6 +147,12 @@ class Mvapich2(Package):
         spack_env.set('MPICH_F90', spack_fc)
         spack_env.set('MPICH_FC', spack_fc)
 
+    def setup_dependent_package(self, module, dep_spec):
+        self.spec.mpicc  = join_path(self.prefix.bin, 'mpicc')
+        self.spec.mpicxx = join_path(self.prefix.bin, 'mpicxx')
+        self.spec.mpifc  = join_path(self.prefix.bin, 'mpif90')
+        self.spec.mpif77 = join_path(self.prefix.bin, 'mpif77')
+
     def install(self, spec, prefix):
         # we'll set different configure flags depending on our environment
         configure_args = [
diff --git a/var/spack/repos/builtin/packages/netcdf/package.py b/var/spack/repos/builtin/packages/netcdf/package.py
index b60a2c4e9a..4aad0f6f3c 100644
--- a/var/spack/repos/builtin/packages/netcdf/package.py
+++ b/var/spack/repos/builtin/packages/netcdf/package.py
@@ -12,15 +12,19 @@ class Netcdf(Package):
     version('4.4.0', 'cffda0cbd97fdb3a06e9274f7aef438e')
     version('4.3.3', '5fbd0e108a54bd82cb5702a73f56d2ae')
 
-    variant('mpi', default=True, description='Enables MPI parallelism')
-    variant('hdf4',    default=False, description="Enable HDF4 support")
+    variant('mpi',  default=True,  description='Enables MPI parallelism')
+    variant('hdf4', default=False, description='Enable HDF4 support')
 
-    # Dependencies:
-    depends_on("curl")  # required for DAP support
+    depends_on("m4")
     depends_on("hdf", when='+hdf4')
-    depends_on("hdf5+mpi~cxx", when='+mpi')  # required for NetCDF-4 support
-    depends_on("hdf5~mpi", when='~mpi')  # required for NetCDF-4 support
-    depends_on("zlib")  # required for NetCDF-4 support
+
+    # Required for DAP support
+    depends_on("curl")
+
+    # Required for NetCDF-4 support
+    depends_on("zlib")
+    depends_on("hdf5+mpi", when='+mpi')
+    depends_on("hdf5~mpi", when='~mpi')
 
     def install(self, spec, prefix):
         # Environment variables
@@ -48,7 +52,7 @@ class Netcdf(Package):
         # /usr/lib/x86_64-linux-gnu/libcurl.so: undefined reference to `SSL_CTX_use_certificate_chain_file@OPENSSL_1.0.0'
         LIBS.append("-lcurl")
         CPPFLAGS.append("-I%s" % spec['curl'].prefix.include)
-        LDFLAGS.append ("-L%s" % spec['curl'].prefix.lib)
+        LDFLAGS.append( "-L%s" % spec['curl'].prefix.lib)
 
         if '+mpi' in spec:
             config_args.append('--enable-parallel4')
diff --git a/var/spack/repos/builtin/packages/openblas/make.patch b/var/spack/repos/builtin/packages/openblas/make.patch
new file mode 100644
index 0000000000..851214211a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/openblas/make.patch
@@ -0,0 +1,35 @@
+diff --git a/Makefile.system b/Makefile.system
+index b89f60e..2dbdad0 100644
+--- a/Makefile.system
++++ b/Makefile.system
+@@ -139,6 +139,10 @@ NO_PARALLEL_MAKE=0
+ endif
+ GETARCH_FLAGS  += -DNO_PARALLEL_MAKE=$(NO_PARALLEL_MAKE)
+ 
++ifdef MAKE_NO_J
++GETARCH_FLAGS += -DMAKE_NO_J=$(MAKE_NO_J)
++endif
++
+ ifdef MAKE_NB_JOBS
+ GETARCH_FLAGS += -DMAKE_NB_JOBS=$(MAKE_NB_JOBS)
+ endif
+diff --git a/getarch.c b/getarch.c
+index f9c49e6..dffad70 100644
+--- a/getarch.c
++++ b/getarch.c
+@@ -1012,6 +1012,7 @@ int main(int argc, char *argv[]){
+ #endif
+ #endif
+ 
++#ifndef MAKE_NO_J
+ #ifdef MAKE_NB_JOBS
+     printf("MAKE += -j %d\n", MAKE_NB_JOBS);
+ #elif NO_PARALLEL_MAKE==1
+@@ -1021,6 +1022,7 @@ int main(int argc, char *argv[]){
+     printf("MAKE += -j %d\n", get_num_cores());
+ #endif
+ #endif
++#endif
+ 
+     break;
+ 
diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py
index f5d656f659..99649da9ca 100644
--- a/var/spack/repos/builtin/packages/openblas/package.py
+++ b/var/spack/repos/builtin/packages/openblas/package.py
@@ -20,13 +20,15 @@ class Openblas(Package):
     provides('blas')
     provides('lapack')
 
+    patch('make.patch')
 
     def install(self, spec, prefix):
         # Openblas is picky about compilers. Configure fails with
         # FC=/abs/path/to/f77, whereas FC=f77 works fine.
         # To circumvent this, provide basename only:
         make_defs = ['CC=%s' % os.path.basename(spack_cc),
-                     'FC=%s' % os.path.basename(spack_f77)]
+                     'FC=%s' % os.path.basename(spack_f77),
+                     'MAKE_NO_J=1']
 
         make_targets = ['libs', 'netlib']
 
diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py
index 52de026a15..45cf71954b 100644
--- a/var/spack/repos/builtin/packages/openmpi/package.py
+++ b/var/spack/repos/builtin/packages/openmpi/package.py
@@ -44,6 +44,8 @@ class Openmpi(Package):
     provides('mpi@:2.2', when='@1.6.5')
     provides('mpi@:3.0', when='@1.7.5:')
 
+    depends_on('hwloc')
+
 
     def url_for_version(self, version):
         return "http://www.open-mpi.org/software/ompi/v%s/downloads/openmpi-%s.tar.bz2" % (version.up_to(2), version)
@@ -55,6 +57,12 @@ class Openmpi(Package):
         spack_env.set('OMPI_FC', spack_fc)
         spack_env.set('OMPI_F77', spack_f77)
 
+    def setup_dependent_package(self, module, dep_spec):
+        self.spec.mpicc  = join_path(self.prefix.bin, 'mpicc')
+        self.spec.mpicxx = join_path(self.prefix.bin, 'mpic++')
+        self.spec.mpifc  = join_path(self.prefix.bin, 'mpif90')
+        self.spec.mpif77 = join_path(self.prefix.bin, 'mpif77')
+
     @property
     def verbs(self):
         # Up through version 1.6, this option was previously named --with-openib
@@ -66,6 +74,7 @@ class Openmpi(Package):
 
     def install(self, spec, prefix):
         config_args = ["--prefix=%s" % prefix,
+                       "--with-hwloc=%s" % spec['hwloc'].prefix,
                        "--enable-shared",
                        "--enable-static"]
         # Variant based arguments
diff --git a/var/spack/repos/builtin/packages/openssl/package.py b/var/spack/repos/builtin/packages/openssl/package.py
index 9e3109bfed..d0c95731a2 100644
--- a/var/spack/repos/builtin/packages/openssl/package.py
+++ b/var/spack/repos/builtin/packages/openssl/package.py
@@ -15,10 +15,12 @@ class Openssl(Package):
 
     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('1.0.2h', '9392e65072ce4b614c1392eefc1f23d0')
 
     depends_on("zlib")
     parallel = False
diff --git a/var/spack/repos/builtin/packages/p4est/package.py b/var/spack/repos/builtin/packages/p4est/package.py
index 017c4e3fbf..adf75babb9 100644
--- a/var/spack/repos/builtin/packages/p4est/package.py
+++ b/var/spack/repos/builtin/packages/p4est/package.py
@@ -7,6 +7,8 @@ class P4est(Package):
 
     version('1.1', '37ba7f4410958cfb38a2140339dbf64f')
 
+    variant('tests', default=True, description='Run small tests')
+
     # build dependencies
     depends_on('automake')
     depends_on('autoconf')
@@ -24,14 +26,20 @@ class P4est(Package):
                    '--without-blas',
                    'CPPFLAGS=-DSC_LOG_PRIORITY=SC_LP_ESSENTIAL',
                    'CFLAGS=-O2',
-                   'CC=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpicc'), # TODO: use ENV variables or MPI class wrappers
-                   'CXX=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpic++'),
-                   'FC=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif90'),
-                   'F77=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif77'),
+                   'CC=%s'  % self.spec['mpi'].mpicc,
+                   'CXX=%s' % self.spec['mpi'].mpicxx,
+                   'FC=%s'  % self.spec['mpi'].mpifc,
+                   'F77=%s' % self.spec['mpi'].mpif77
                   ]
 
         configure('--prefix=%s' % prefix, *options)
 
         make()
-        make("check")
+        # Make tests optional as sometimes mpiexec can't be run with an error:
+        # mpiexec has detected an attempt to run as root.
+        # Running at root is *strongly* discouraged as any mistake (e.g., in
+        # defining TMPDIR) or bug can result in catastrophic damage to the OS
+        # file system, leaving your system in an unusable state.
+        if '+tests' in self.spec:
+          make("check")
         make("install")
diff --git a/var/spack/repos/builtin/packages/paradiseo/package.py b/var/spack/repos/builtin/packages/paradiseo/package.py
index c254234b32..34766099da 100644
--- a/var/spack/repos/builtin/packages/paradiseo/package.py
+++ b/var/spack/repos/builtin/packages/paradiseo/package.py
@@ -20,15 +20,20 @@ class Paradiseo(Package):
     #variant('tests',    default=False, description='Compile with build tests')
     #variant('doc',      default=False, description='Compile with documentation')
     variant('debug',    default=False, description='Builds a debug version of the libraries')
+    variant('openmp',   default=False, description='Enable OpenMP support')
+    variant('gnuplot',  default=False, description='Enable GnuPlot support')
     
     # Required dependencies
     depends_on ("cmake")
-    depends_on ("eigen")
 
     # Optional dependencies
     depends_on ("mpi", when="+mpi")
     depends_on ("doxygen", when='+doc')
-    
+    depends_on ("gnuplot", when='+gnuplot')
+    depends_on ("eigen", when='+edo')
+    depends_on ("boost~mpi", when='+edo~mpi')
+    depends_on ("boost+mpi", when='+edo+mpi')
+
     # Patches
     patch('enable_eoserial.patch')
     patch('fix_osx_detection.patch')
@@ -45,7 +50,9 @@ class Paradiseo(Package):
             '-DMPI:BOOL=%s' % ('TRUE' if '+mpi' in spec else 'FALSE'),
             '-DSMP:BOOL=%s' % ('TRUE' if '+smp' in spec else 'FALSE'), # Note: This requires a C++11 compatible compiler
             '-DEDO:BOOL=%s' % ('TRUE' if '+edo' in spec else 'FALSE'),
-            '-DENABLE_CMAKE_TESTING:BOOL=%s' % ('TRUE' if '+tests' in spec else 'FALSE')
+            '-DENABLE_CMAKE_TESTING:BOOL=%s' % ('TRUE' if '+tests' in spec else 'FALSE'),
+            '-DENABLE_OPENMP:BOOL=%s' % ('TRUE' if '+openmp' in spec else 'FALSE'),
+            '-DENABLE_GNUPLOT:BOOL=%s' % ('TRUE' if '+gnuplot' in spec else 'FALSE')
         ])
  
         with working_dir('spack-build', create=True):
diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py
index 93688fb777..1e1d6302f3 100644
--- a/var/spack/repos/builtin/packages/qt/package.py
+++ b/var/spack/repos/builtin/packages/qt/package.py
@@ -101,7 +101,7 @@ class Qt(Package):
 
     @property
     def common_config_args(self):
-        return [
+        config_args = [
             '-prefix', self.prefix,
             '-v',
             '-opensource',
@@ -115,7 +115,16 @@ class Qt(Package):
             '-no-openvg',
             '-no-pch',
             # NIS is deprecated in more recent glibc
-            '-no-nis']
+            '-no-nis'
+        ]
+
+        if '+gtk' in self.spec:
+            config_args.append('-gtkstyle')
+        else:
+            config_args.append('-no-gtkstyle')
+
+        return config_args
+
     # Don't disable all the database drivers, but should
     # really get them into spack at some point.
 
@@ -128,8 +137,7 @@ class Qt(Package):
                   '-thread',
                   '-shared',
                   '-release',
-                  '-fast'
-                  )
+                  '-fast')
 
     @when('@4')
     def configure(self):
diff --git a/var/spack/repos/builtin/packages/qthreads/ldflags.patch b/var/spack/repos/builtin/packages/qthreads/ldflags.patch
new file mode 100644
index 0000000000..0c15eab386
--- /dev/null
+++ b/var/spack/repos/builtin/packages/qthreads/ldflags.patch
@@ -0,0 +1,11 @@
+--- 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 dacdb71524..5da9340927 100644
--- a/var/spack/repos/builtin/packages/qthreads/package.py
+++ b/var/spack/repos/builtin/packages/qthreads/package.py
@@ -16,7 +16,12 @@ class Qthreads(Package):
 
     version('1.10', '5af8c8bbe88c2a6d45361643780d1671')
 
+    patch("ldflags.patch")
+    patch("restrict.patch")
+    patch("trap.patch")
+
     def install(self, spec, prefix):
-        configure("--prefix=%s" % prefix)
+        configure("--prefix=%s" % prefix,
+                  "--enable-guard-pages")
         make()
         make("install")
diff --git a/var/spack/repos/builtin/packages/qthreads/restrict.patch b/var/spack/repos/builtin/packages/qthreads/restrict.patch
new file mode 100644
index 0000000000..4c95714f6b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/qthreads/restrict.patch
@@ -0,0 +1,12 @@
+--- a/include/qthread/common.h.in
++++ b/include/qthread/common.h.in
+@@ -84,7 +84,9 @@
+ /* Define to the equivalent of the C99 'restrict' keyword, or to
+    nothing if this is not supported.  Do not define if restrict is
+    supported directly.  */
++#ifndef restrict
+ #undef restrict
++#endif
+ /* Work around a bug in Sun C++: it does not support _Restrict or
+    __restrict__, even though the corresponding Sun C compiler ends up with
+    "#define restrict _Restrict" or "#define restrict __restrict__" in the
diff --git a/var/spack/repos/builtin/packages/qthreads/trap.patch b/var/spack/repos/builtin/packages/qthreads/trap.patch
new file mode 100644
index 0000000000..7aa94d82d5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/qthreads/trap.patch
@@ -0,0 +1,11 @@
+--- a/include/qthread/qthread.hpp
++++ b/include/qthread/qthread.hpp
+@@ -236,7 +236,7 @@
+             return qthread_incr64((uint64_t *)operand, incr);
+ 
+         default:
+-            *(int *)(0) = 0;
++            __builtin_trap();
+     }
+     return T(0);                       // never hit - keep compiler happy
+ }
diff --git a/var/spack/repos/builtin/packages/raja/package.py b/var/spack/repos/builtin/packages/raja/package.py
new file mode 100644
index 0000000000..f807ab71af
--- /dev/null
+++ b/var/spack/repos/builtin/packages/raja/package.py
@@ -0,0 +1,12 @@
+from spack import *
+
+class Raja(Package):
+    """RAJA Parallel Framework."""
+    homepage = "http://software.llnl.gov/RAJA/"
+
+    version('git', git='https://github.com/LLNL/RAJA.git', branch="master")
+
+    def install(self, spec, prefix):
+            cmake('.',*std_cmake_args)
+            make()
+            make('install')
diff --git a/var/spack/repos/builtin/packages/scons/package.py b/var/spack/repos/builtin/packages/scons/package.py
new file mode 100644
index 0000000000..594aeced88
--- /dev/null
+++ b/var/spack/repos/builtin/packages/scons/package.py
@@ -0,0 +1,13 @@
+from spack import *
+
+class Scons(Package):
+    """SCons is a software construction tool"""
+    homepage = "http://scons.org"
+    url      = "http://downloads.sourceforge.net/project/scons/scons/2.5.0/scons-2.5.0.tar.gz"
+
+    version('2.5.0', '9e00fa0df8f5ca5c5f5975b40e0ed354')
+
+    extends('python')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/repos/builtin/packages/serf/package.py b/var/spack/repos/builtin/packages/serf/package.py
new file mode 100644
index 0000000000..a5c9057b99
--- /dev/null
+++ b/var/spack/repos/builtin/packages/serf/package.py
@@ -0,0 +1,51 @@
+##############################################################################
+# 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://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 Serf(Package):
+    """Apache Serf - a high performance C-based HTTP client library built upon the Apache Portable Runtime (APR) library"""
+    homepage  = 'https://serf.apache.org/'
+    url       = 'https://archive.apache.org/dist/serf/serf-1.3.8.tar.bz2'
+
+    version('1.3.8',     '1d45425ca324336ce2f4ae7d7b4cfbc5567c5446')
+
+    depends_on('apr')
+    depends_on('apr-util')
+    depends_on('scons')
+    depends_on('expat')
+    depends_on('openssl')
+
+    def install(self, spec, prefix):
+        scons = which("scons")
+
+        options = ['PREFIX=%s' % prefix]
+        options.append('APR=%s' % spec['apr'].prefix)
+        options.append('APU=%s' % spec['apr-util'].prefix)
+        options.append('OPENSSL=%s' % spec['openssl'].prefix)
+        options.append('LINKFLAGS=-L%s/lib' % spec['expat'].prefix)
+        options.append('CPPFLAGS=-I%s/include' % spec['expat'].prefix)
+
+        scons(*options)
+        scons('install')
diff --git a/var/spack/repos/builtin/packages/subversion/package.py b/var/spack/repos/builtin/packages/subversion/package.py
index 5db1c3eb92..04cde94aad 100644
--- a/var/spack/repos/builtin/packages/subversion/package.py
+++ b/var/spack/repos/builtin/packages/subversion/package.py
@@ -37,6 +37,7 @@ class Subversion(Package):
     depends_on('apr-util')
     depends_on('zlib')
     depends_on('sqlite')
+    depends_on('serf')
 
     # Optional: We need swig if we want the Perl, Python or Ruby
     # bindings.
@@ -54,6 +55,7 @@ class Subversion(Package):
         options.append('--with-apr-util=%s' % spec['apr-util'].prefix)
         options.append('--with-zlib=%s' % spec['zlib'].prefix)
         options.append('--with-sqlite=%s' % spec['sqlite'].prefix)
+        options.append('--with-serf=%s' % spec['serf'].prefix)
         #options.append('--with-swig=%s' % spec['swig'].prefix)
 
         configure(*options)
diff --git a/var/spack/repos/builtin/packages/superlu-dist/package.py b/var/spack/repos/builtin/packages/superlu-dist/package.py
index 5cf5e129b4..3420d9b90a 100644
--- a/var/spack/repos/builtin/packages/superlu-dist/package.py
+++ b/var/spack/repos/builtin/packages/superlu-dist/package.py
@@ -6,7 +6,9 @@ class SuperluDist(Package):
     homepage = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
     url      = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/superlu_dist_4.1.tar.gz"
 
-    version('4.3', 'ee66c84e37b4f7cc557771ccc3dc43ae')
+    version('5.0.0', '2b53baf1b0ddbd9fcf724992577f0670')
+    # default to version 4.3 since petsc and trilinos are not tested with 5.0.
+    version('4.3', 'ee66c84e37b4f7cc557771ccc3dc43ae', preferred=True)
     version('4.2', 'ae9fafae161f775fbac6eba11e530a65')
     version('4.1', '4edee38cc29f687bd0c8eb361096a455')
     version('4.0', 'c0b98b611df227ae050bc1635c6940e0')
diff --git a/var/spack/repos/builtin/packages/the_silver_searcher/package.py b/var/spack/repos/builtin/packages/the_silver_searcher/package.py
index e4020b6766..30f06354bf 100644
--- a/var/spack/repos/builtin/packages/the_silver_searcher/package.py
+++ b/var/spack/repos/builtin/packages/the_silver_searcher/package.py
@@ -9,6 +9,7 @@ class TheSilverSearcher(Package):
 
     depends_on('pcre')
     depends_on('xz')
+    depends_on('pkg-config')
 
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
diff --git a/var/spack/repos/builtin/packages/xerces-c/package.py b/var/spack/repos/builtin/packages/xerces-c/package.py
index e36fb936e0..bd02ddcd4b 100644
--- a/var/spack/repos/builtin/packages/xerces-c/package.py
+++ b/var/spack/repos/builtin/packages/xerces-c/package.py
@@ -1,19 +1,3 @@
-# FIXME:
-# This is a template package file for Spack.  We've conveniently
-# put "FIXME" labels next to all the things you'll want to change.
-#
-# Once you've edited all the FIXME's, delete this whole message,
-# save this file, and test out your package like this:
-#
-#     spack install xerces-c
-#
-# You can always get back here to change things with:
-#
-#     spack edit xerces-c
-#
-# See the spack documentation for more information on building
-# packages.
-#
 from spack import *
 
 class XercesC(Package):