236 dolfin

easybuild/easyblocks/c/cmakepythonpackage.py

@@ -21,7 +21,7 @@
 from easybuild.easyblocks.p.pythonpackage import PythonPackage
 
 class CMakePythonPackage(CMake, PythonPackage):
-    """Build a Python module with cmake.
+    """Build a Python package and module with cmake.
 
     Some packages use cmake to first build and install c Python modules
     and then put the Python package in lib/pythonX.Y/site-packages
@@ -34,21 +34,22 @@ class CMakePythonPackage(CMake, PythonPackage):
     def __init__(self, *args, **kwargs):
         PythonPackage.__init__(self, *args, **kwargs)
 
-    def configure(self):
+    def configure(self, *args, **kwargs):
         """Main onfiguration is with cmake"""
 
-        PythonPackage.configure(self)
-
-        CMake.configure(self)
+        PythonPackage.configure(self, *args, **kwargs)
 
-    def make(self): 
-        """Build with make"""
-        CMake.make(self)
+        CMake.configure(self, *args, **kwargs)
 
-    def make_install(self): 
-        """Install with make install"""
-        CMake.make_install(self)
+    def make(self, *args, **kwargs):
+        """Build with cmake"""
+        return CMake.make(self, *args, **kwargs)
+
+    def make_install(self):
+        """Install with cmake install"""
+        return CMake.make_install(self)
 
     def make_module_extra(self):
         """Extra Python package module parameters"""
-        PythonPackage.make_module_extra(self)
+        #we return a string here.
+        return PythonPackage.make_module_extra(self)

easybuild/easyblocks/d/dolphin.py → easybuild/easyblocks/d/dolfin.py

@@ -47,7 +47,7 @@ def configure(self):
         self.updatecfg('configopts', ' -DMPI_CXX_COMPILER="$MPICXX"')
 
         # Boost config parameters
-        self.updatecfg('configopts', " -DBoost_DIR=%s" % depsdict['Boost'])
+        #self.updatecfg('configopts', " -DBoost_DIR=%s" % depsdict['Boost'])
         self.updatecfg('configopts', " -DBOOST_INCLUDEDIR=%s/include" % depsdict['Boost'])
         self.updatecfg('configopts', " -DBoost_DEBUG=ON -DBOOST_ROOT=%s" % depsdict['Boost'])
 
@@ -56,8 +56,7 @@ def configure(self):
         self.updatecfg('configopts', "-DARMADILLO_DIR:PATH=%s " % depsdict['Armadillo'])
 
         # specify MPI library
-        # FIXME
-        self.updatecfg('configopts', ' -DMPI_COMPILER="%s"' % self.getenv('MPICC'))
+        self.updatecfg('configopts', ' -DMPI_COMPILER="%s"' % os.getenv('MPICC'))
 
         if not os.getenv('MPI_LIB_SHARED') or not os.getenv('MPI_INC'):
             self.updatecfg('configopts', ' -DMPI_LIBRARY="%s"' % os.getenv('MPI_LIB_SHARED'))
@@ -67,9 +66,9 @@ def configure(self):
 
         # specify Python paths
         python_short_ver = ".".join(os.getenv('SOFTVERSIONPYTHON').split(".")[0:2])
-        self.updatecfg('configopts', " -DPYTHON_INCLUDE_PATH=%s/include/python%s" % (depsdict['Python'], 
+        self.updatecfg('configopts', " -DPYTHON_INCLUDE_PATH=%s/include/python%s" % (depsdict['Python'],
                                                                                      python_short_ver))
-        self.updatecfg('configopts', " -DPYTHON_LIBRARIES=%s/lib/libpython%s.so" % (depsdict['Python'], 
+        self.updatecfg('configopts', " -DPYTHON_LIBRARY=%s/lib/libpython%s.so" % (depsdict['Python'],
                                                                                     python_short_ver))
 
         # SuiteSparse config params
@@ -84,8 +83,9 @@ def configure(self):
         self.updatecfg('configopts', umfpack_params)
 
         # ParMETIS and SCOTCH
+
+        self.updatecfg('configopts', ' -DSCOTCH_DIR="%s" -DSCOTCH_DEBUG:BOOL=ON' % depsdict['SCOTCH'])
         self.updatecfg('configopts', ' -DPARMETIS_DIR="%s"' % depsdict['ParMETIS'])
-        self.updatecfg('configopts', ' -DSCOTCH_DIR="%s"' % depsdict['SCOTCH'])
 
         # BLACS and LAPACK 
         self.updatecfg('configopts', ' -DBLAS_LIBRARIES:PATH="$LIBBLAS"')
@@ -95,14 +95,14 @@ def configure(self):
         openmp = get_openmp_flag(self.log)
         self.updatecfg('configopts', ' -DOpenMP_CXX_FLAGS="%s"' % openmp)
         self.updatecfg('configopts', ' -DOpenMP_C_FLAGS="%s"' % openmp)
-        
+
         CMakePythonPackage.configure(self)
 
     def make_module_extra(self):
         """Set extra environment variables for Dolfin."""
 
         txt = CMakePythonPackage.make_module_extra(self)
-    
+
         # Dolfin needs to find Boost and the UFC pkgconfig file
         txt += "setenv\tBOOST_DIR\t%s\n" % get_software_root('Boost')
         txt += "prepend-path\tPKG_CONFIG_PATH\t%s/lib/pkgconfig\n" % get_software_root('UFC')
@@ -111,20 +111,20 @@ def make_module_extra(self):
         envvars = ['I_MPI_CXX', 'I_MPI_CC']
         for envvar in envvars:
             envar_val = os.getenv(envvar)
-            if not envar_val:
+            if not envar_val and self.tk.name in ['ictce', 'iqacml']:
                 self.log.error("%s not defined in environment, needed by DOLFIN" % envvar)
             else:
                 txt += "setenv\t%s\t%s\n" % (envvar, envar_val)
-    
+
         return txt
 
     def sanitycheck(self):
         """Custom sanity check for Dolfin."""
 
         if not self.getcfg('sanityCheckPaths'):
 
-            self.setcfg('sanityCheckPaths', {'files': ['bin/dolfin-%s' % x for x in ['version','convert',
-                                                                                     'order','plot']] 
+            self.setcfg('sanityCheckPaths', {'files': ['bin/dolfin-%s' % x for x in ['version', 'convert',
+                                                                                     'order', 'plot']]
                                                     + ['include/dolfin.h'],
                                              'dirs':['%s/dolfin' % self.pylibdir]
                                             })

easybuild/easyblocks/m/metis.py

@@ -0,0 +1,70 @@
+##
+# Copyright 2009-2012 Stijn Deweirdt, Dries Verdegem, Kenneth Hoste, Pieter De Baets, Jens Timmerman
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of the University of Ghent (http://ugent.be/hpc).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild 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 v2.
+#
+# EasyBuild 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
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+
+import os
+import shutil
+
+from easybuild.framework.application import Application
+from easybuild.tools.filetools import mkdir
+
+class METIS(Application):
+
+
+    def configure(self, *args, **kwargs):
+        """No configuration is done for METIS"""
+        pass
+
+    def make_install(self):
+        """ Manually copy the required files to the right place.
+
+        And create symlins where expected by other applications
+        (in Lib instead of lib)"""
+        libdir = os.path.join(self.installdir, 'lib')
+        mkdir(libdir)
+
+        includedir = os.path.join(self.installdir, 'include')
+        mkdir(includedir)
+
+        try:
+            src = os.path.join(self.getcfg('startfrom'), 'libmetis.a')
+            dst = os.path.join(libdir, 'libmetis.a')
+            shutil.copy2(src, dst)
+        except OSError, err:
+            self.log.error("Copying file libmetis.a to lib dir failed: %s" % err)
+
+        try:
+            for f in ['defs.h', 'macros.h', 'metis.h', 'proto.h', 'rename.h', 'struct.h']:
+                src = os.path.join(self.getcfg('startfrom'), 'Lib', f)
+                dst = os.path.join(includedir, f)
+                shutil.copy2(src, dst)
+                os.chmod(dst, 0755)
+        except OSError, err:
+            self.log.error("Copying file metis.h to include dir failed: %s" % err)
+
+        # Other applications depending on ParMETIS (SuiteSparse for one) look for both ParMETIS libraries
+        # and headerfiles in the Lib directory (capital L). The following symlinks are hence created.
+        try:
+            Libdir = os.path.join(self.installdir, 'Lib')
+            os.symlink(libdir, Libdir)
+            for f in ['defs.h', 'macros.h', 'metis.h', 'proto.h', 'rename.h', 'struct.h']:
+                os.symlink(os.path.join(includedir, file), os.path.join(libdir, f))
+        except OSError, err:
+            self.log.error("Something went wrong during symlink creation: %s" % err)

easybuild/easyblocks/p/parmetis.py

@@ -0,0 +1,134 @@
+##
+# Copyright 2009-2012 Stijn Deweirdt, Dries Verdegem, Kenneth Hoste, Pieter De Baets, Jens Timmerman
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of the University of Ghent (http://ugent.be/hpc).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild 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 v2.
+#
+# EasyBuild 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
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+"""
+ParMETIS easyblock
+"""
+
+import os
+import shutil
+
+from distutils.version import LooseVersion
+from easybuild.easyblocks.m.metis import METIS
+from easybuild.tools.filetools import run_cmd, mkdir
+
+class ParMETIS(METIS):
+    """
+    Easyblock for the ParMETIS package
+    Parmetis 
+    """
+
+    def configure(self):
+        """
+        For versions of ParMETIS < 4 configure METIS separately
+        New versions of ParMETIS include METIS
+
+        Run 'cmake' in the build dir to get rid of a 'user friendly' 
+        help message that is displayed without this step.
+        """
+        if self.version() < LooseVersion("4"):
+            return METIS.configure(self)
+        #tested with 4.0.2, now actually requires cmake to be run first
+        #for bot parmetis and metis
+        for buildir in [ 'build' ] :
+            cmd = 'cd %s && cmake .. %s -DCMAKE_INSTALL_PREFIX="%s" && cd %s' % \
+                (buildir, self.getcfg('configopts'), self.installdir, self.getcfg('startfrom'))
+            run_cmd(cmd, log_all=True, simple=True)
+
+
+
+    def make(self, verbose=False):
+        """
+        make ParMETIS and Metis
+
+        Calling make
+        for version > 4 cmake is run in the build dir.
+        """
+        paracmd = ''
+        if self.getcfg('parallel'):
+            paracmd = "-j %s" % self.getcfg('parallel')
+
+        cmd = "%s make %s %s" % (self.getcfg('premakeopts'), paracmd, self.getcfg('makeopts'))
+        if self.version() >= LooseVersion("4"):
+            #this is done in the build dir.
+            cmd = "cd build && %s && cd %s " % (cmd, self.getcfg('startfrom'))
+        run_cmd(cmd, log_all=True, simple=True, log_output=verbose)
+
+    def make_install(self):
+        """
+        Manually copy files over to the right places
+        (libmetis.a, libparmetis.a, metis.h, parmetis.h)
+        Also create symlinks where expected by other packages (Lib directory)
+        """
+        includedir = os.path.join(self.installdir, 'include')
+        libdir = os.path.join(self.installdir, 'lib')
+
+        if self.version() >= LooseVersion("4"):
+            #includedir etc changed in v4, use a normal makeinstall
+            cmd = "cd build && make install %s && cd %s" % (self.getcfg('installopts'),
+                                                            self.getcfg('startfrom'))
+            run_cmd(cmd, log_all=True, simple=True)
+
+            try:
+                src = os.path.join(self.getcfg('startfrom'), 'build/libmetis/libmetis.a')
+                dst = os.path.join(libdir, 'libmetis.a')
+                shutil.copy2(src, dst)
+            except OSError, err:
+                self.log.error("Copying files to installation dir failed: %s" % err)
+            try:
+                src = os.path.join(self.getcfg('startfrom'), 'build/metis/include/metis.h')
+                dst = os.path.join(includedir, 'metis.h')
+                shutil.copy2(src, dst)
+            except OSError, err:
+                self.log.error("Copying files to installation dir failed: %s" % err)
+
+        else:
+
+            mkdir(libdir)
+            mkdir(includedir)
+
+            try:
+                for fil in ['libmetis.a', 'libparmetis.a']:
+                    src = os.path.join(self.getcfg('startfrom'), fil)
+                    dst = os.path.join(libdir, fil)
+                    shutil.copy2(src, dst)
+            except OSError, err:
+                self.log.error("Copying files to installation dir failed: %s" % err)
+
+            try:
+                src = os.path.join(self.getcfg('startfrom'), 'parmetis.h')
+                dst = os.path.join(includedir, 'parmetis.h')
+                shutil.copy2(src, dst)
+                # Some applications (SuiteSparse) can only use METIS (not ParMETIS), but header files are the same
+                dst = os.path.join(includedir, 'metis.h')
+                shutil.copy2(src, dst)
+            except OSError, err:
+                self.log.error("Copying files to installation dir failed: %s" % err)
+
+        # Other applications depending on ParMETIS (SuiteSparse for one) look for both ParMETIS libraries
+        # and headerfiles in the Lib directory (capital L). The following symlink are hence created.
+        try:
+            llibdir = os.path.join(self.installdir, 'Lib')
+            os.symlink(libdir, llibdir)
+            os.symlink(os.path.join(includedir, 'metis.h'), os.path.join(libdir, 'metis.h'))
+            os.symlink(os.path.join(includedir, 'parmetis.h'),
+                       os.path.join(libdir, 'parmetis.h'))
+        except OSError, err:
+            self.log.error("Something went wrong during symlink creation: %s" % err)

easybuild/easyblocks/p/pythonpackage.py

@@ -47,14 +47,14 @@ def make(self):
 
         cmd = "python setup.py build"
 
-        run_cmd(cmd, logall=True, simple=True)
+        run_cmd(cmd, log_all=True, simple=True)
 
     def make_install(self):
         """Install Python package to a custom path using setup.py"""
 
         cmd = "python setup.py install --prefix=%s %s" % (self.installdir, self.getcfg('installopts'))
 
-        run_cmd(cmd, logall=True, simple=True)
+        run_cmd(cmd, log_all=True, simple=True)
 
     def make_module_extra(self):
         """Add install path to PYTHONPATH"""
@@ -75,4 +75,4 @@ def make_module_extra(self):
 
         txt += "prepend-path\tPYTHONPATH\t%s\n" % installdir
 
-        return txt
+        return txt