Merge branch 'it4i-salomon'

easyblocks/a/amber.py

+##
+# Copyright 2009-2018 Ghent University
+# Copyright 2015-2018 Stanford 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://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).
+#
+# 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 Amber, implemented as an easyblock
+
+Original author: Benjamin Roberts (The University of Auckland)
+Modified by Stephane Thiell (Stanford University) for Amber14
+Enhanced/cleaned up by Kenneth Hoste (HPC-UGent)
+"""
+import os
+
+import easybuild.tools.environment as env
+import easybuild.tools.toolchain as toolchain
+from easybuild.easyblocks.generic.configuremake import ConfigureMake
+from easybuild.easyblocks.generic.pythonpackage import det_pylibdir
+from easybuild.framework.easyconfig import CUSTOM, MANDATORY, BUILD
+from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.modules import get_software_root, get_software_version
+from easybuild.tools.run import run_cmd
+
+
+class EB_Amber(ConfigureMake):
+    """Easyblock for building and installing Amber"""
+
+    @staticmethod
+    def extra_options(extra_vars=None):
+        """Extra easyconfig parameters specific to ConfigureMake."""
+        extra_vars = dict(ConfigureMake.extra_options(extra_vars))
+        extra_vars.update({
+            # 'Amber': [True, "Build Amber in addition to AmberTools", CUSTOM],
+            'patchlevels': ["latest", "(AmberTools, Amber) updates to be applied", CUSTOM],
+            # The following is necessary because some patches to the Amber update
+            # script update the update script itself, in which case it will quit
+            # and insist on being run again. We don't know how many times will
+            # be needed, but the number of times is patchlevel specific.
+            'patchruns': [1, "Number of times to run Amber's update script before building", CUSTOM],
+            # enable testing by default
+            'runtest': [True, "Run tests after each build", CUSTOM],
+        })
+        return ConfigureMake.extra_options(extra_vars)
+
+    def __init__(self, *args, **kwargs):
+        """Easyblock constructor: initialise class variables."""
+        super(EB_Amber, self).__init__(*args, **kwargs)
+        self.build_in_installdir = True
+        self.pylibdir = None
+
+        self.with_cuda = False
+        self.with_mpi = False
+
+        env.setvar('AMBERHOME', self.installdir)
+
+    def extract_step(self):
+        """Extract sources; strip off parent directory during unpack"""
+        self.cfg.update('unpack_options', "--strip-components=1")
+        super(EB_Amber, self).extract_step()
+
+    def patch_step(self, *args, **kwargs):
+        """Patch Amber using 'update_amber' tool, prior to applying listed patch files (if any)."""
+
+        if self.cfg['patchlevels'] == "latest":
+            cmd = "./update_amber --update"
+            # Run as many times as specified. It is the responsibility
+            # of the easyconfig author to get this right, especially if
+            # he or she selects "latest". (Note: "latest" is not
+            # recommended for this reason and others.)
+            for _ in range(self.cfg['patchruns']):
+                run_cmd(cmd, log_all=True)
+        else:
+            for (tree, patch_level) in zip(['AmberTools', 'Amber'], self.cfg['patchlevels']):
+                if patch_level == 0:
+                    continue
+                cmd = "./update_amber --update-to %s/%s" % (tree, patch_level)
+                # Run as many times as specified. It is the responsibility
+                # of the easyconfig author to get this right.
+                for _ in range(self.cfg['patchruns']):
+                    run_cmd(cmd, log_all=True)
+
+        super(EB_Amber, self).patch_step(*args, **kwargs)
+
+    def configure_step(self):
+        """Configuring Amber is done in install step."""
+        pass
+
+    def build_step(self):
+        """Building Amber is done in install step."""
+        pass
+
+    def test_step(self):
+        """Testing Amber build is done in install step."""
+        pass
+
+    def install_step(self):
+        """Custom build, test & install procedure for Amber."""
+
+        # unset $LIBS since it breaks the build
+        env.unset_env_vars(['LIBS'])
+
+        # define environment variables for MPI, BLAS/LAPACK & dependencies
+        mklroot = get_software_root('imkl')
+        openblasroot = get_software_root('OpenBLAS')
+        if mklroot:
+            env.setvar('MKL_HOME', mklroot)
+        elif openblasroot:
+	    lapack = os.getenv('LIBLAPACK')
+	    if lapack is None:
+		raise EasyBuildError("LIBLAPACK (from OpenBLAS) not found in environement.")
+	    else:
+		env.setvar('GOTO', lapack)
+
+        mpiroot = get_software_root(self.toolchain.MPI_MODULE_NAME[0])
+        if mpiroot and self.toolchain.options.get('usempi', None):
+            env.setvar('MPI_HOME', mpiroot)
+            self.with_mpi = True
+            if self.toolchain.mpi_family() == toolchain.INTELMPI:
+                self.mpi_option = '-intelmpi'
+            else:
+                self.mpi_option = '-mpi'
+
+        common_configopts = [self.cfg['configopts'], '--no-updates', '-noX11']
+        if self.name == 'Amber':
+            common_configopts.append('-static')
+
+        netcdfroot = get_software_root('netCDF')
+        if netcdfroot:
+            common_configopts.extend(["--with-netcdf", netcdfroot])
+
+        pythonroot = get_software_root('Python')
+        if pythonroot:
+            common_configopts.extend(["--with-python", os.path.join(pythonroot, 'bin', 'python')])
+
+            self.pylibdir = det_pylibdir()
+            pythonpath = os.environ.get('PYTHONPATH', '')
+            env.setvar('PYTHONPATH', os.pathsep.join([os.path.join(self.installdir, self.pylibdir), pythonpath]))
+
+        comp_fam = self.toolchain.comp_family()
+        if comp_fam == toolchain.INTELCOMP:
+            comp_str = 'intel'
+
+        elif comp_fam == toolchain.GCC:
+            comp_str = 'gnu'
+
+        else:
+            raise EasyBuildError("Don't know how to compile with compiler family '%s' -- check EasyBlock?", comp_fam)
+
+        # The NAB compiles need openmp flag
+        if self.toolchain.options.get('openmp', None):
+            env.setvar('CUSTOMBUILDFLAGS', self.toolchain.get_flag('openmp'))
+
+        # compose list of build targets
+        build_targets = [('', 'test')]
+
+        if self.with_mpi:
+            build_targets.append((self.mpi_option, 'test.parallel'))
+            # hardcode to 4 MPI processes, minimal required to run all tests
+            env.setvar('DO_PARALLEL', 'mpirun -np 4')
+
+        cudaroot = get_software_root('CUDA')
+        if cudaroot:
+            env.setvar('CUDA_HOME', cudaroot)
+            self.with_cuda = True
+            build_targets.append(('-cuda', 'test.cuda'))
+            if self.with_mpi:
+                build_targets.append(("-cuda %s" % self.mpi_option, 'test.cuda_parallel'))
+
+        ld_lib_path = os.environ.get('LD_LIBRARY_PATH', '')
+        env.setvar('LD_LIBRARY_PATH', os.pathsep.join([os.path.join(self.installdir, 'lib'), ld_lib_path]))
+
+        for flag, testrule in build_targets:
+            # configure
+            cmd = "%s ./configure %s" % (self.cfg['preconfigopts'], ' '.join(common_configopts + [flag, comp_str]))
+            (out, _) = run_cmd(cmd, log_all=True, simple=False)
+
+            # build in situ using 'make install'
+            # note: not 'build'
+            super(EB_Amber, self).install_step()
+
+            # test
+            if self.cfg['runtest']:
+                run_cmd("make %s" % testrule, log_all=True, simple=False)
+
+            # clean, overruling the normal 'build'
+            run_cmd("make clean")
+
+    def sanity_check_step(self):
+        """Custom sanity check for Amber."""
+        binaries = ['sander', 'tleap']
+        if self.name == 'Amber':
+            binaries.append('pmemd')
+            if self.with_cuda:
+                binaries.append('pmemd.cuda')
+                if self.with_mpi:
+                    binaries.append('pmemd.cuda.MPI')
+
+        if self.with_mpi:
+            binaries.extend(['sander.MPI'])
+            if self.name == 'Amber':
+                binaries.append('pmemd.MPI')
+
+        custom_paths = {
+            'files': [os.path.join(self.installdir, 'bin', binary) for binary in binaries],
+            'dirs': [],
+        }
+        super(EB_Amber, self).sanity_check_step(custom_paths=custom_paths)
+
+    def make_module_extra(self):
+        """Add module entries specific to Amber/AmberTools"""
+        txt = super(EB_Amber, self).make_module_extra()
+
+        txt += self.module_generator.set_environment('AMBERHOME', self.installdir)
+        if self.pylibdir:
+            txt += self.module_generator.prepend_paths('PYTHONPATH', self.pylibdir)
+
+        return txt