Merge develop for v0.8.16 release.v0.8.16

8 files changed, 153 insertions, 8 deletions

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)
+