Merge branch 'develop' of https://github.com/easybuilders/easybuild-e…

…asyblocks into update_r_config_guess

easybuild/easyblocks/f/ferret.py

@@ -31,6 +31,7 @@
 @author: Pieter De Baets (Ghent University)
 @author: Jens Timmerman (Ghent University)
 @author: George Fanourgakis (The Cyprus Institute)
+@author: Samuel Moors (Vrije Universiteit Brussel (VUB))
 """
 
 
@@ -53,7 +54,10 @@ def configure_step(self):
         if LooseVersion(self.version) < LooseVersion("7.3"):
             change_dir('FERRET')
 
-        deps = ['HDF5', 'netCDF', 'Java']
+        if LooseVersion(self.version) >= LooseVersion("7.5"):
+            deps = ['HDF5', 'netCDF-Fortran']
+        else:
+            deps = ['HDF5', 'netCDF', 'Java']
 
         for name in deps:
             if not get_software_root(name):
@@ -75,15 +79,32 @@ def configure_step(self):
             (r"^INSTALL_FER_DIR =.*", "INSTALL_FER_DIR = %s" % self.installdir),
         ]
 
-        for name in deps:
-            regex_subs.append((r"^(%s.*DIR\s*)=.*" % name.upper(), r"\1 = %s" % get_software_root(name)))
+        if LooseVersion(self.version) >= LooseVersion("7.5"):
+            regex_subs.append((r"^(HDF5_LIBDIR\s*)=.*", r"\1 = %s/lib" % get_software_root('HDF5')))
+            regex_subs.append((r"^(NETCDF_LIBDIR\s*)=.*", r"\1 = %s/lib" % get_software_root('netCDF-Fortran')))
+        else:
+            for name in deps:
+                regex_subs.append((r"^(%s.*DIR\s*)=.*" % name.upper(), r"\1 = %s" % get_software_root(name)))
+
 
         if LooseVersion(self.version) >= LooseVersion("7.3"):
             regex_subs.extend([
                 (r"^DIR_PREFIX =.*", "DIR_PREFIX = %s" % self.cfg['start_dir']),
                 (r"^FER_LOCAL_EXTFCNS = $(FER_DIR)", "FER_LOCAL_EXTFCNS = $(INSTALL_FER_DIR)/libs"),
             ])
 
+        if LooseVersion(self.version) >= LooseVersion("7.5"):
+            comp_vars = {
+                'CC': 'CC',
+                'FC': 'FC',
+            }
+
+            for key, value in comp_vars.items():
+                regex_subs.append((r"^(%s\s*)=.*" % key, r"\1= %s " % os.getenv(value)))
+
+            if self.toolchain.comp_family() == toolchain.INTELCOMP:
+                regex_subs.append((r"^(\s*LD\s*)=.*", r"\1 = %s -nofor-main " % os.getenv("FC")))
+
         for fn in fns:
             apply_regex_substitutions(fn, regex_subs)
 
@@ -114,8 +135,8 @@ def configure_step(self):
         fn = 'xgks/CUSTOMIZE.%s' % buildtype
 
         regex_subs = [(r"^(FFLAGS\s*=').*-m64 (.*)", r"\1%s \2" % os.getenv('FFLAGS'))]
-        for x, y in comp_vars.items():
-            regex_subs.append((r"^(%s\s*)=.*" % x, r"\1='%s'" % os.getenv(y)))
+        for key, value in comp_vars.items():
+            regex_subs.append((r"^(%s\s*)=.*" % key, r"\1='%s'" % os.getenv(value)))
 
         x11_root = get_software_root('X11')
         if x11_root:
@@ -148,8 +169,8 @@ def configure_step(self):
             ]
 
         regex_subs = []
-        for x, y in comp_vars.items():
-            regex_subs.append((r"^(\s*%s\s*)=.*" % x, r"\1 = %s" % os.getenv(y)))
+        for key, value in comp_vars.items():
+            regex_subs.append((r"^(\s*%s\s*)=.*" % key, r"\1 = %s" % os.getenv(value)))
 
         if LooseVersion(self.version) >= LooseVersion("7.3"):
             regex_subs.extend([
@@ -179,16 +200,17 @@ def configure_step(self):
             fn = 'gksm2ps/Makefile'
 
             regex_subs = [(r"^(\s*CFLAGS=\")-m64 (.*)", r"\1%s \2" % os.getenv('CFLAGS'))]
-            for x, y in comp_vars.items():
-                regex_subs.append((r"^(\s*%s)=.*" % x, r"\1='%s' \\" % os.getenv(y)))
+            for key, value in comp_vars.items():
+                regex_subs.append((r"^(\s*%s)=.*" % key, r"\1='%s' \\" % os.getenv(value)))
 
             apply_regex_substitutions(fn, regex_subs)
 
     def sanity_check_step(self):
         """Custom sanity check for Ferret."""
 
+        major_minor_version = '.'.join(self.version.split('.')[:2])
         custom_paths = {
-            'files': ["bin/ferret_v%s" % self.version],
+            'files': ["bin/ferret_v%s" % major_minor_version],
             'dirs': [],
         }
 

easybuild/easyblocks/generic/pythonpackage.py

@@ -219,6 +219,8 @@ def extra_options(extra_vars=None):
             'use_easy_install': [False, "Install using '%s' (deprecated)" % EASY_INSTALL_INSTALL_CMD, CUSTOM],
             'use_pip': [None, "Install using '%s'" % PIP_INSTALL_CMD, CUSTOM],
             'use_pip_editable': [False, "Install using 'pip install --editable'", CUSTOM],
+            # see https://packaging.python.org/tutorials/installing-packages/#installing-setuptools-extras
+            'use_pip_extras': [None, "String with comma-separated list of 'extras' to install via pip", CUSTOM],
             'use_pip_for_deps': [False, "Install dependencies using '%s'" % PIP_INSTALL_CMD, CUSTOM],
             'use_setup_py_develop': [False, "Install using '%s' (deprecated)" % SETUP_PY_DEVELOP_CMD, CUSTOM],
             'zipped_egg': [False, "Install as a zipped eggs (requires use_easy_install)", CUSTOM],
@@ -392,7 +394,8 @@ def compose_install_command(self, prefix, extrapath=None, installopts=None):
         if self.install_cmd.startswith(EASY_INSTALL_INSTALL_CMD):
             run_cmd("%s setup.py easy_install --version" % self.python_cmd, verbose=False, trace=False)
 
-        if self.install_cmd.startswith(PIP_INSTALL_CMD):
+        using_pip = self.install_cmd.startswith(PIP_INSTALL_CMD)
+        if using_pip:
 
             pip_version = det_pip_version()
             if pip_version:
@@ -428,6 +431,11 @@ def compose_install_command(self, prefix, extrapath=None, installopts=None):
             else:
                 loc = self.src[0]['path']
 
+        if using_pip:
+            extras = self.cfg.get('use_pip_extras')
+            if extras:
+                loc += '[%s]' % extras
+
         if installopts is None:
             installopts = self.cfg['installopts']
 

easybuild/easyblocks/i/impi.py

@@ -167,7 +167,7 @@ def post_install_step(self):
             regex_subs = [(r"^setenv I_MPI_ROOT.*", r"setenv I_MPI_ROOT %s" % self.installdir)]
             for script in [os.path.join(script_path, 'mpivars.csh') for script_path in script_paths]:
                 apply_regex_substitutions(os.path.join(self.installdir, script), regex_subs)
-            regex_subs = [(r"^I_MPI_ROOT=.*", r"I_MPI_ROOT=%s; export I_MPI_ROOT" % self.installdir)]
+            regex_subs = [(r"^(\s*)I_MPI_ROOT=[^;\n]*", r"\1I_MPI_ROOT=%s" % self.installdir)]
             for script in [os.path.join(script_path, 'mpivars.sh') for script_path in script_paths]:
                 apply_regex_substitutions(os.path.join(self.installdir, script), regex_subs)
 
@@ -230,7 +230,7 @@ def make_module_req_guess(self):
         else:
             guesses = {}
             if LooseVersion(self.version) >= LooseVersion('2019'):
-                # Keep release_mt and release in front, to give priority to the possible symlinks in intel64/lib.
+                # Keep release_mt and release in front, to give them priority over the possible symlinks in intel64/lib.
                 # IntelMPI 2019 changed the default library to be the non-mt version.
                 lib_dirs = ['intel64/%s' % x for x in ['lib/release_mt', 'lib/release', 'lib']]
                 include_dirs = ['intel64/include']

easybuild/easyblocks/l/lammps.py

@@ -282,7 +282,7 @@ def make_module_extra(self):
 def get_cuda_gpu_arch(cuda_cc):
     """Return CUDA gpu ARCH in LAMMPS required format. Example: 'sm_32' """
     # Get largest cuda supported
-    return 'sm_%s' % str(cuda_cc.sorted(reverse=True)[0]).replace(".", "")
+    return 'sm_%s' % str(sorted(cuda_cc, reverse=True)[0]).replace(".", "")
 
 
 def get_kokkos_arch(cuda_cc, kokkos_arch):
@@ -317,7 +317,7 @@ def get_kokkos_arch(cuda_cc, kokkos_arch):
     if cuda:
         # CUDA below
         gpu_arch = None
-        for cc in cuda_cc.sorted(reverse=True):
+        for cc in sorted(cuda_cc, reverse=True):
             gpu_arch = KOKKOS_GPU_ARCH_TABLE.get(str(cc))
             if gpu_arch:
                 break

easybuild/easyblocks/l/libdrm.py

@@ -0,0 +1,53 @@
+##
+# Copyright 2013-2020 Ghent University
+#
+# 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://www.vscentrum.be),
+# Flemish Research Foundation (FWO) (http://www.fwo.be/en)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# https://github.com/easybuilders/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 libdrm, implemented as an easyblock
+
+@author: Andrew Edmondson (University of Birmingham)
+"""
+
+from easybuild.easyblocks.generic.configuremake import ConfigureMake
+from easybuild.tools.systemtools import X86_64, get_cpu_architecture, get_shared_lib_ext
+
+
+class EB_libdrm(ConfigureMake):
+    """
+    Support for building libdrm on different architectures
+    """
+
+    def sanity_check_step(self):
+        """Custom sanity check for libdrm"""
+        shlib_ext = get_shared_lib_ext()
+        custom_paths = {
+            'files': ['include/xf86drm.h', 'include/xf86drmMode.h',
+                      'lib/libdrm_radeon.%s' % shlib_ext, 'lib/libdrm.%s' % shlib_ext, 'lib/libkms.%s' % shlib_ext],
+            'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'],
+        }
+
+        arch = get_cpu_architecture()
+        if arch == X86_64:
+            custom_paths['files'].append('lib/libdrm_intel.%s' % shlib_ext)
+
+        super(EB_libdrm, self).sanity_check_step(custom_paths=custom_paths)

easybuild/easyblocks/o/openfoam.py

@@ -347,7 +347,13 @@ def sanity_check_step(self):
         shlib_ext = get_shared_lib_ext()
 
         # OpenFOAM >= 3.0.0 can use 64 bit integers
-        if 'extend' not in self.name.lower() and self.looseversion >= LooseVersion('3.0'):
+        # same goes for OpenFOAM-Extend >= 4.1
+        if 'extend' in self.name.lower():
+            set_int_size = self.looseversion >= LooseVersion('4.1')
+        else:
+            set_int_size = self.looseversion >= LooseVersion('3.0')
+
+        if set_int_size:
             if self.toolchain.options['i8']:
                 int_size = 'Int64'
             else:

easybuild/easyblocks/p/petsc.py

@@ -36,11 +36,13 @@
 from easybuild.easyblocks.generic.configuremake import ConfigureMake
 from easybuild.framework.easyconfig import BUILD, CUSTOM
 from easybuild.tools.build_log import EasyBuildError
-from easybuild.tools.filetools import symlink
+from easybuild.tools.filetools import symlink, apply_regex_substitutions
 from easybuild.tools.modules import get_software_root
 from easybuild.tools.run import run_cmd
 from easybuild.tools.systemtools import get_shared_lib_ext
 
+NO_MPI_CXX_EXT_FLAGS = '-DOMPI_SKIP_MPICXX -DMPICH_SKIP_MPICXX'
+
 
 class EB_PETSc(ConfigureMake):
     """Support for building and installing PETSc"""
@@ -112,13 +114,16 @@ def configure_step(self):
             self.cfg.update('configopts', '--with-fc="%s"' % os.getenv('F90'))
 
             # compiler flags
+            # Don't build with MPI c++ bindings as this leads to a hard dependency
+            # on libmpi and libmpi_cxx even for C code and non-MPI code
+            cxxflags = os.getenv('CXXFLAGS') + ' ' + NO_MPI_CXX_EXT_FLAGS
             if LooseVersion(self.version) >= LooseVersion("3.5"):
                 self.cfg.update('configopts', '--CFLAGS="%s"' % os.getenv('CFLAGS'))
-                self.cfg.update('configopts', '--CXXFLAGS="%s"' % os.getenv('CXXFLAGS'))
+                self.cfg.update('configopts', '--CXXFLAGS="%s"' % cxxflags)
                 self.cfg.update('configopts', '--FFLAGS="%s"' % os.getenv('F90FLAGS'))
             else:
                 self.cfg.update('configopts', '--with-cflags="%s"' % os.getenv('CFLAGS'))
-                self.cfg.update('configopts', '--with-cxxflags="%s"' % os.getenv('CXXFLAGS'))
+                self.cfg.update('configopts', '--with-cxxflags="%s"' % cxxflags)
                 self.cfg.update('configopts', '--with-fcflags="%s"' % os.getenv('F90FLAGS'))
 
             if not self.toolchain.comp_family() == toolchain.GCC:  #@UndefinedVariable
@@ -280,6 +285,15 @@ def install_step(self):
         if LooseVersion(self.version) >= LooseVersion("3"):
             if not self.cfg['sourceinstall']:
                 super(EB_PETSc, self).install_step()
+                petsc_root = self.installdir
+            else:
+                petsc_root = os.path.join(self.installdir, self.petsc_subdir)
+            # Remove MPI-CXX flags added during configure to prevent them from being passed to consumers of PETsc
+            petsc_variables_path = os.path.join(petsc_root, 'lib', 'petsc', 'conf', 'petscvariables')
+            if os.path.isfile(petsc_variables_path):
+                fix = (r'^(CXX_FLAGS|CXX_LINKER_FLAGS|CONFIGURE_OPTIONS)( = .*)%s(.*)$' % NO_MPI_CXX_EXT_FLAGS,
+                       r'\1\2\3')
+                apply_regex_substitutions(petsc_variables_path, [fix])
 
         else:  # old versions (< 3.x)