Merge remote-tracking branch 'upstream/develop' into develop

lib/spack/docs/basic_usage.rst

@@ -794,6 +794,34 @@ Environment modules
 Spack provides some limited integration with environment module
 systems to make it easier to use the packages it provides.
 
+
+Installing Environment Modules
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+In order to use Spack's generated environment modules, you must have
+installed the *Environment Modules* package.  On many Linux
+distributions, this can be installed from the vendor's repository.
+For example: ```yum install environment-modules``
+(Fedora/RHEL/CentOS).  If your Linux distribution does not have
+Environment Modules, you can get it with Spack:
+
+1. Install with::
+
+    spack install environment-modules
+
+2. Activate with::
+
+    MODULES_HOME=`spack location -i environment-modules`
+     MODULES_VERSION=`ls -1 $MODULES_HOME/Modules | head -1`
+     ${MODULES_HOME}/Modules/${MODULES_VERSION}/bin/add.modules
+
+This adds to your ``.bashrc`` (or similar) files, enabling Environment
+Modules when you log in.  It will ask your permission before changing
+any files.
+
+Spack and Environment Modules
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
 You can enable shell support by sourcing some files in the
 ``/share/spack`` directory.
 

lib/spack/spack/build_environment.py

@@ -304,7 +304,7 @@ def setup_package(pkg):
 
     # traverse in postorder so package can use vars from its dependencies
     spec = pkg.spec
-    for dspec in pkg.spec.traverse(order='post'):
+    for dspec in pkg.spec.traverse(order='post', root=False):
         # If a user makes their own package repo, e.g.
         # spack.repos.mystuff.libelf.Libelf, and they inherit from
         # an existing class like spack.repos.original.libelf.Libelf,
@@ -321,6 +321,7 @@ def setup_package(pkg):
         dpkg.setup_dependent_package(pkg.module, spec)
         dpkg.setup_dependent_environment(spack_env, run_env, spec)
 
+    set_module_variables_for_package(pkg, pkg.module)
     pkg.setup_environment(spack_env, run_env)
 
     # Make sure nothing's strange about the Spack environment.

var/spack/repos/builtin/packages/dealii/package.py

@@ -23,8 +23,10 @@ class Dealii(Package):
 
     # required dependencies, light version
     depends_on ("blas")
-    depends_on ("boost",     when='~mpi')
+    # Boost 1.58 is blacklisted, see https://github.com/dealii/dealii/issues/1591
-    depends_on ("boost+mpi", when='+mpi')
+    # require at least 1.59
+    depends_on ("boost@1.59.0:",     when='~mpi')
+    depends_on ("boost@1.59.0:+mpi", when='+mpi')
     depends_on ("bzip2")
     depends_on ("cmake")
     depends_on ("lapack")
@@ -174,6 +176,19 @@ def install(self, spec, prefix):
             make('release')
             make('run',parallel=False)
 
+        # An example which uses Metis + PETSc
+        # FIXME: switch step-18 to MPI
+        with working_dir('examples/step-18'):
+            print('=====================================')
+            print('============= Step-18 ===============')
+            print('=====================================')
+            # list the number of cycles to speed up
+            filter_file(r'(end_time = 10;)',  ('end_time = 3;'), 'step-18.cc')
+            if '^petsc' in spec and '^metis' in spec:
+                cmake('.')
+                make('release')
+                make('run',parallel=False)
+
         # take step-40 which can use both PETSc and Trilinos
         # FIXME: switch step-40 to MPI run
         with working_dir('examples/step-40'):

var/spack/repos/builtin/packages/environment-modules/package.py

@@ -0,0 +1,38 @@
+from spack import *
+
+
+class EnvironmentModules(Package):
+    """The Environment Modules package provides for the dynamic
+    modification of a user's environment via modulefiles."""
+
+    homepage = "https://sourceforge.net/p/modules/wiki/Home/"
+    url      = "http://prdownloads.sourceforge.net/modules/modules-3.2.10.tar.gz"
+
+    version('3.2.10', '8b097fdcb90c514d7540bb55a3cb90fb')
+
+    # Dependencies:
+    depends_on('tcl')
+
+    def install(self, spec, prefix):
+        tcl_spec = spec['tcl']
+
+        # See: https://sourceforge.net/p/modules/bugs/62/
+        CPPFLAGS = ['-DUSE_INTERP_ERRORLINE']
+        config_args = [
+            "--without-tclx",
+            "--with-tclx-ver=0.0",
+            "--prefix=%s" % prefix,
+            "--with-tcl=%s" % join_path(tcl_spec.prefix, 'lib'),    # It looks for tclConfig.sh
+            "--with-tcl-ver=%d.%d" % (tcl_spec.version.version[0], tcl_spec.version.version[1]),
+            '--disable-debug',
+            '--disable-dependency-tracking',
+            '--disable-silent-rules',
+            '--disable-versioning', 
+            '--datarootdir=%s' % prefix.share,
+            'CPPFLAGS=%s' % ' '.join(CPPFLAGS)
+        ]
+
+
+        configure(*config_args)
+        make()
+        make('install')

var/spack/repos/builtin/packages/ipopt/package.py

@@ -0,0 +1,51 @@
+from spack import *
+
+class Ipopt(Package):
+    """Ipopt (Interior Point OPTimizer, pronounced eye-pea-Opt) is a
+       software package for large-scale nonlinear optimization."""
+    homepage = "https://projects.coin-or.org/Ipopt"
+    url      = "http://www.coin-or.org/download/source/Ipopt/Ipopt-3.12.4.tgz"
+
+    version('3.12.4', '12a8ecaff8dd90025ddea6c65b49cb03')
+    version('3.12.3', 'c560cbfa9cbf62acf8b485823c255a1b')
+    version('3.12.2', 'ec1e855257d7de09e122c446506fb00d')
+    version('3.12.1', 'ceaf895ce80c77778f2cab68ba9f17f3')
+    version('3.12.0', 'f7dfc3aa106a6711a85214de7595e827')
+
+    depends_on("blas")
+    depends_on("lapack")
+    depends_on("pkg-config")
+    depends_on("mumps+double~mpi") 
+    
+    def install(self, spec, prefix):
+        # Dependency directories
+        blas_dir = spec['blas'].prefix
+        lapack_dir = spec['lapack'].prefix
+        mumps_dir = spec['mumps'].prefix
+
+        # Add directory with fake MPI headers in sequential MUMPS
+        # install to header search path
+        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"
+        
+        configure_args = [
+            "--prefix=%s" % prefix,
+            "--with-mumps-incdir=%s" % mumps_dir.include,
+            "--with-mumps-lib=%s" % mumps_libcmd,
+            "--enable-shared",
+            "--with-blas-incdir=%s" % blas_dir.include,
+            "--with-blas-lib=%s" % blas_lib,
+            "--with-lapack-incdir=%s" % lapack_dir.include,
+            "--with-lapack-lib=%s" % lapack_lib
+            ]
+        
+        configure(*configure_args)
+
+        # IPOPT does not build correctly in parallel on OS X
+        make(parallel=False)
+        make("test", parallel=False)
+        make("install", parallel=False)

var/spack/repos/builtin/packages/metis/package.py

@@ -79,10 +79,28 @@ def install(self, spec, prefix):
         if '+double' 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
+        # Adopted from 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:
+            for f in ["4elt", "copter2", "mdual"]:
+                graph = join_path(source_directory,'graphs','%s.graph' % f)
+                Executable(join_path(prefix.bin,'graphchk'))(graph)
+                Executable(join_path(prefix.bin,'gpmetis'))(graph,'2')
+                Executable(join_path(prefix.bin,'ndmetis'))(graph)
+
+            graph = join_path(source_directory,'graphs','test.mgraph')
+            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')

var/spack/repos/builtin/packages/modules/package.py

@@ -1,25 +0,0 @@
-from spack import *
-
-class Modules(Package):
-    """ The Environment Modules package provides for the dynamic modification of a user's environment via modulefiles. """
-
-    homepage = "http://modules.sf.net"
-    url      = "http://downloads.sourceforge.net/project/modules/Modules/modules-3.2.10/modules-3.2.10.tar.gz"
-
-    version('3.2.10', '8b097fdcb90c514d7540bb55a3cb90fb')
-
-    depends_on("tcl")
-
-    def install(self, spec, prefix):
-
-	options = ['--prefix=%s' % prefix, 
-                   '--disable-debug',
-                   '--disable-dependency-tracking',
-                   '--disable-silent-rules',
-                   '--disable-versioning', 
-                   '--datarootdir=%s' % prefix.share,
-                   'CPPFLAGS=-DUSE_INTERP_ERRORLINE']
-
-        configure(*options)
-        make()
-        make("install")

var/spack/repos/builtin/packages/mumps/package.py

@@ -1,5 +1,5 @@
 from spack import *
-import os, sys
+import os, sys, glob
 
 class Mumps(Package):
     """MUMPS: a MUltifrontal Massively Parallel sparse direct Solver"""
@@ -164,10 +164,13 @@ def install(self, spec, prefix):
 
         install_tree('lib', prefix.lib)
         install_tree('include', prefix.include)
+
         if '~mpi' in spec:            
             lib_dsuffix = '.dylib' if sys.platform == 'darwin' else '.so'
             lib_suffix = lib_dsuffix if '+shared' in spec else '.a'
             install('libseq/libmpiseq%s' % lib_suffix, prefix.lib)
+            for f in glob.glob(join_path('libseq','*.h')):
+                install(f, prefix.include)
 
         # FIXME: extend the tests to mpirun -np 2 (or alike) when build with MPI
         # FIXME: use something like numdiff to compare blessed output with the current

var/spack/repos/builtin/packages/suite-sparse/package.py

@@ -10,10 +10,18 @@ class SuiteSparse(Package):
 
     version('4.5.1', 'f0ea9aad8d2d1ffec66a5b6bfeff5319')
 
+    # FIXME: (see below)
+    # variant('tbb', default=True, description='Build with Intel TBB')
+
     depends_on('blas')
     depends_on('lapack')
 
     depends_on('metis@5.1.0', when='@4.5.1')
+    # FIXME:
+    # in @4.5.1. TBB support in SPQR seems to be broken as TBB-related linkng flags
+    # does not seem to be used, which leads to linking errors on Linux.
+    # Try re-enabling in future versions.
+    # depends_on('tbb', when='+tbb')
 
     def install(self, spec, prefix):
         # The build system of SuiteSparse is quite old-fashioned
@@ -21,16 +29,35 @@ def install(self, spec, prefix):
         # with a lot of convoluted logic in it.
         # Any kind of customization will need to go through filtering of that file
 
-        # FIXME : this actually uses the current workaround
+        make_args = ['INSTALL=%s' % prefix]
-        # FIXME : (blas / lapack always provide libblas and liblapack as aliases)
-        make('install', 'INSTALL=%s' % prefix,
 
         # inject Spack compiler wrappers
+        make_args.extend([
              'AUTOCC=no',
              'CC=cc',
              'CXX=c++',
              'F77=f77',
+        ])
+
+        # use Spack's metis in CHOLMOD/Partition module,
+        # otherwise internal Metis will be compiled
+        make_args.extend([
+             'MY_METIS_LIB=-L%s -lmetis' % spec['metis'].prefix.lib,
+             'MY_METIS_INC=%s' % spec['metis'].prefix.include,
+        ])
+
+        # Intel TBB in SuiteSparseQR
+        if '+tbb' in spec:
+            make_args.extend([
+                'SPQR_CONFIG=-DHAVE_TBB',
+                'TBB=-L%s -ltbb' % spec['tbb'].prefix.lib,
+            ])
 
         # BLAS arguments require path to libraries
+        # FIXME : (blas / lapack always provide libblas and liblapack as aliases)
+        make_args.extend([
             'BLAS=-lblas',
-             'LAPACK=-llapack')
+            'LAPACK=-llapack'
+        ])
+
+        make('install', *make_args)