Several additions/changes to easyblocks

easybuild/easyblocks/g/gromacs.py

@@ -59,8 +59,8 @@ def configure_step(self):
             # build a release build
             self.cfg.update('configopts', "-DCMAKE_BUILD_TYPE=Release")
 
-            # prefer static libraries, if available
-            self.cfg.update('configopts', "-DGMX_PREFER_STATIC_LIBS=ON")
+#            # prefer static libraries, if available
+#            self.cfg.update('configopts', "-DGMX_PREFER_STATIC_LIBS=ON")
 
             # always specify to use external BLAS/LAPACK
             self.cfg.update('configopts', "-DGMX_EXTERNAL_BLAS=ON -DGMX_EXTERNAL_LAPACK=ON")
@@ -76,7 +76,7 @@ def configure_step(self):
 
             # enable MPI support if desired
             if self.toolchain.options.get('usempi', None):
-                self.cfg.update('configopts', "-DGMX_MPI=ON -DGMX_THREAD_MPI=OFF")
+                self.cfg.update('configopts', "-DGMX_MPI=ON -DGMX_THREAD_MPI=ON")
             else:
                 self.cfg.update('configopts', "-DGMX_MPI=OFF")
 
@@ -147,11 +147,11 @@ def install_step(self):
         # rather than trying to replicate the logic, we just figure out where the library was placed
 
         if LooseVersion(self.version) < LooseVersion('5.0'):
-            # libgmx.a or libgmx_mpi.a
-            libname = 'libgmx*.a'
+            # libgmx.[a|so] or libgmx_mpi.[a|so]
+            libname = 'libgmx*.*'
         else:
-            # libgromacs.a or libgromacs_mpi.a
-            libname = 'libgromacs*.a'
+            # libgromacs.[a|so] or libgromacs_mpi.[a|so]
+            libname = 'libgromacs*.*'
 
         for libdir in ['lib', 'lib64']:
             if os.path.exists(os.path.join(self.installdir, libdir)):
@@ -190,13 +190,34 @@ def sanity_check_step(self):
         if LooseVersion(self.version) >= LooseVersion('5.0'):
             binaries.append('gmx')
 
+        if LooseVersion(self.version) < LooseVersion('5.0'):
+            # libgmx.[a|so] or libgmx_mpi.[a|so]
+            libname = 'libgmx*.*'
+        else:
+            # libgromacs.[a|so] or libgromacs_mpi.[a|so]
+            libname = 'libgromacs*.*'
+
+        for libdir in ['lib', 'lib64']:
+            if os.path.exists(os.path.join(self.installdir, libdir)):
+                for subdir in [libdir, os.path.join(libdir, '*')]:
+                    libpaths = glob.glob(os.path.join(self.installdir, subdir, libname))
+                    if libpaths:
+                        self.lib_subdir = os.path.dirname(libpaths[0])[len(self.installdir)+1:]
+                        self.log.info("Found lib subdirectory that contains %s: %s", libname, self.lib_subdir)
+                        break
+
+        if not self.lib_subdir:
+            raise EasyBuildError("Failed to determine lib subdirectory in %s", self.installdir)
+
         # check for a handful of binaries/libraries that should be there
         if LooseVersion(self.version) < LooseVersion('5.0'):
             libnames = ['gmxana', 'gmx', 'gmxpreprocess', 'md']
         else:
             libnames = ['gromacs']
 
-        libs = ['lib%s%s.a' % (libname, suff) for libname in libnames]
+        libs = ['lib%s%s.so' % (libname, suff) for libname in libnames]
+        print "libdir: %s" % self.lib_subdir
+        print libs
 
         custom_paths = {
             'files': ['bin/%s%s' % (binary, suff) for binary in binaries] +

easybuild/easyblocks/i/icc.py

@@ -74,29 +74,36 @@ def install_step(self):
                 'license_file_name': LICENSE_FILE_NAME_2012,
             }
 
-        super(EB_icc, self).install_step(silent_cfg_names_map=silent_cfg_names_map)
+        if LooseVersion(self.version) >= LooseVersion('2016'):
+            cfg_extras_map = {
+                'COMPONENTS': 'ALL',
+            }
+        super(EB_icc, self).install_step(silent_cfg_names_map=silent_cfg_names_map, silent_cfg_extras=cfg_extras_map)
 
     def sanity_check_step(self):
         """Custom sanity check paths for icc."""
 
         binprefix = "bin/intel64"
-        libprefix = "lib/intel64/lib"
+        libprefix = "lib/intel64"
         if LooseVersion(self.version) >= LooseVersion("2011"):
             if LooseVersion(self.version) <= LooseVersion("2011.3.174"):
                 binprefix = "bin"
-            elif LooseVersion(self.version) >= LooseVersion("2013_sp1"):
+            elif LooseVersion(self.version) >= LooseVersion("2013_sp1") and LooseVersion(self.version) < LooseVersion("2016"):
+                binprefix = "bin"
+                libprefix = "lib/intel64"
+            elif LooseVersion(self.version) >= LooseVersion("2016"):
                 binprefix = "bin"
-                libprefix = "lib/intel64/lib"
+                libprefix = "lib/intel64_lin"
             else:
-                libprefix = "compiler/lib/intel64/lib"
+                libprefix = "compiler/lib/intel64"
 
         binfiles = ["icc", "icpc"]
         if LooseVersion(self.version) < LooseVersion("2014"):
             binfiles += ["idb"]
 
         custom_paths = {
             'files': ["%s/%s" % (binprefix, x) for x in binfiles] +
-                     ["%s%s" % (libprefix, x) for x in ["iomp5.a", "iomp5.so"]],
+                     ["%s/lib%s" % (libprefix, x) for x in ["iomp5.a", "iomp5.so"]],
             'dirs': [],
         }
 
@@ -105,53 +112,81 @@ def sanity_check_step(self):
     def make_module_req_guess(self):
         """Customize paths to check and add in environment.
         """
+        # New Directory Layout for Intel Parallel Studio XE 2016
+        # https://software.intel.com/en-us/articles/new-directory-layout-for-intel-parallel-studio-xe-2016
+        debuggerpath = 'debugger_%s' % self.version.split('.')[0]
         if self.cfg['m32']:
             # 32-bit toolchain
+            libpaths = ['lib', 'lib/ia32'],
             dirmap = {
                 'PATH': ['bin', 'bin/ia32', 'tbb/bin/ia32'],
-                'LD_LIBRARY_PATH': ['lib', 'lib/ia32'],
-                'LIBRARY_PATH': ['lib', 'lib/ia32'],
+                'LD_LIBRARY_PATH': libpaths,
+                'LIBRARY_PATH': libpaths,
                 'MANPATH': ['man', 'share/man', 'man/en_US'],
                 'IDB_HOME': ['bin/intel64']
             }
         else:
-            # 64-bit toolit
-            dirmap = {
-                'PATH': ['bin', 'bin/intel64', 'tbb/bin/emt64'],
-                'LD_LIBRARY_PATH': ['lib', 'lib/intel64'],
-                'LIBRARY_PATH': ['lib', 'lib/intel64'],
-                'MANPATH': ['man', 'share/man', 'man/en_US'],
-                'IDB_HOME': ['bin/intel64']
-            }
+            if LooseVersion(self.version) < LooseVersion("2016"):
+                # 64-bit toolkit
+                libpaths = ['compiler/lib/intel64', 'lib/intel64', 'debugger/ipt/intel64/lib', 'ipp/lib/intel64', 'tbb/lib/intel64']
+                dirmap = {
+                    'PATH': ['bin/intel64', 'tbb/bin/intel64', 'ipp/bin/intel64', 'debugger/gdb/intel64/bin'],
+                    'LD_LIBRARY_PATH': libpaths, 
+                    'LIBRARY_PATH': libpaths,
+                    'MANPATH': ['man', 'share/man', 'man/en_US', 'debugger/gdb/intel64/share/man'],
+                    'CPATH': ['ipp/include', 'tbb/include'],
+                    'INTEL_PYTHONHOME': ['debugger/python/intel64']
+                }
+            else:
+                # 64-bit toolkit
+                libpaths = ['daal/../compiler/lib/intel64_lin', 'daal/../tbb/lib/intel64_lin/gcc4.4', 'daal/lib/intel64_lin', '%s/libipt/intel64/lib' % debuggerpath,'tbb/lib/intel64/gcc4.4', 'mkl/lib/intel64', 'ipp/lib/intel64', 'ipp/../compiler/lib/intel64', 'compiler/lib/intel64']
+                dirmap = {
+                    'PATH': ['mpi/intel64/bin', 'ipp/bin/intel64', '%s/gdb/intel64/bin' % debuggerpath, 'bin/intel64'],
+                    'LD_LIBRARY_PATH': libpaths,
+                    'LIBRARY_PATH': libpaths,
+                    'MANPATH': ['man/common', 'man/en_US', 'debugger/gdb/intel64/share/man'],
+                    'CPATH': ['daal/include', 'tbb/include', 'mkl/include', 'ipp/include'],
+                    'INTEL_PYTHONHOME': ['%s/python/intel64' % debuggerpath],
+                    'DAALROOT': ['daal'],
+                    'TBBROOT': ['tbb'],
+                    'IPPROOT': ['ipp'],
+                    'CLASSPATH': ['daal/lib/daal.jar'],
+                }
+
 
         # in recent Intel compiler distributions, the actual binaries are
         # in deeper directories, and symlinked in top-level directories
         # however, not all binaries are symlinked (e.g. mcpcom is not)
-        if os.path.isdir("%s/composerxe-%s" % (self.installdir, self.version)):
-            prefix = "composerxe-%s" % self.version
+        # more recent versions of the Intel Compiler (2013.sp1 and newer)
+        if os.path.isdir("%s/composer_xe_%s" % (self.installdir, self.version)):
+            prefix = "composer_xe_%s" % self.version
             oldmap = dirmap
             dirmap = {}
             for k, vs in oldmap.items():
                 dirmap[k] = []
-                if k == "LD_LIBRARY_PATH":
-                    prefix = "composerxe-%s/compiler" % self.version
-                else:
-                    prefix = "composerxe-%s" % self.version
+                prefix = "composer_xe_%s" % self.version
                 for v in vs:
                     v2 = "%s/%s" % (prefix, v)
-                    dirmap[k].append(v2)
+                    if os.path.isdir("%s/%s" % (self.installdir, v2)):
+                        dirmap[k].append(v2)
 
-        elif os.path.isdir("%s/compiler" % (self.installdir)):
-            prefix = "compiler"
+        if os.path.isdir("%s/compilers_and_libraries_%s/linux" % (self.installdir, self.version)):
+            prefix = "compilers_and_libraries_%s/linux" % self.version
             oldmap = dirmap
             dirmap = {}
             for k, vs in oldmap.items():
                 dirmap[k] = []
-                prefix = ''
-                if k == "LD_LIBRARY_PATH":
-                    prefix = "compiler/"
                 for v in vs:
-                    v2 = "%s%s" % (prefix, v)
-                    dirmap[k].append(v2)
+                    v2 = "%s/%s" % (prefix, v)
+                    if os.path.exists("%s/%s" % (self.installdir, v2)):
+                        dirmap[k].append(v2)
 
         return dirmap
+
+    def make_module_extra(self):
+        """Add extra environment variables for icc, for license file and NLS path."""
+        txt = super(EB_icc, self).make_module_extra()
+        txt += self.module_generator.prepend_paths(self.license_env_var, self.cfg['license_file'], allow_abs=True)
+        txt += self.module_generator.prepend_paths('NLSPATH', '$root/idb/intel64/locale/%l_%t/%N')
+        return txt
+

easybuild/easyblocks/l/lapack.py

@@ -143,6 +143,10 @@ def configure_step(self):
             self.log.info('No BLAS library provided, so only building LAPACK library (no testing).')
             self.cfg.update('buildopts', 'lib')
 
+
+        if os.path.exists(os.path.join(self.cfg['start_dir'], 'lapacke')):
+            self.cfg.update('buildopts', 'lapackelib')
+
     # don't create a module if we're only testing
     def build_step(self):
         """

easybuild/easyblocks/q/qt.py

@@ -66,6 +66,7 @@ def configure_step(self):
             "Project MESSAGE:.*",
             "rm -f .*",
             'Creating qmake...',
+            'Running configuration tests...',
         ]
         run_cmd_qa(cmd, qa, no_qa=no_qa, log_all=True, simple=True)
 
@@ -85,3 +86,15 @@ def sanity_check_step(self):
         }
 
         super(EB_Qt, self).sanity_check_step(custom_paths=custom_paths)
+
+    def make_module_extra(self):
+        """Set correct QT* environment variables."""
+
+        txt = super(EB_Qt, self).make_module_extra()
+
+        txt += self.module_generator.set_environment('QTDIR', "$root" )
+        txt += self.module_generator.set_environment('QTLIB', "$root/lib" )
+        txt += self.module_generator.set_environment('QTINC', "$root/include" )
+
+        return txt
+

easybuild/easyblocks/q/qtcreator.py

@@ -0,0 +1,73 @@
+##
+# Copyright 2015 Fokko Masselink
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# 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/>.
+##
+"""
+EasyBuild support for building and installing QtCreator, implemented as an easyblock
+
+@author: Fokko Masselink
+"""
+import os
+import re
+import sys
+import fileinput
+from easybuild.framework.easyblock import EasyBlock
+from easybuild.tools.run import run_cmd
+from easybuild.tools.filetools import mkdir 
+import easybuild.tools.environment as env
+import easybuild.tools.toolchain as toolchain
+
+
+from easybuild.easyblocks.generic.configuremake import ConfigureMake
+class EB_QTCREATOR(ConfigureMake):
+    """Support for building/installing QtCreator."""
+
+    def configure_step(self): 
+        """Adjust configure step"""
+
+        # create separate build directory
+        sep_builddir = 'qt-creator-build'
+        try:
+            os.mkdir(sep_builddir)
+            os.chdir(sep_builddir)
+        except OSError, err:
+            self.log.error("Failed to create separate build dir %s in %s: %s" % (objdir, os.getcwd(), err))
+
+        cmd = "qmake -r ../qtcreator.pro" 
+        run_cmd(cmd, log_all=True, simple=True)
+
+        # update installopts
+        self.cfg.update('installopts', 'INSTALL_ROOT=%s' % ( self.installdir ))
+
+    def sanity_check_step(self):
+        custom_paths = {
+            'files': ["bin/qtcreator", "bin/qbs"],
+            'dirs':  ["lib"],
+        }
+        super(EB_QTCREATOR, self).sanity_check_step(custom_paths=custom_paths)
+
+    def make_module_extra(self):
+        txt = super(EB_QTCREATOR, self).make_module_extra()
+        txt += self.module_generator.prepend_paths("PATH", ['bin'])
+        txt += self.module_generator.prepend_paths("LD_LIBRARY_PATH", ['lib'])
+        return txt