new file: easyblocks/s/siesta.py

easyblocks/s/siesta.py

+##
+# Copyright 2009-2021 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 Siesta, implemented as an easyblock
+
+@author: Miguel Dias Costa (National University of Singapore)
+@author: Ake Sandgren (Umea University)
+"""
+import os
+import stat
+
+import easybuild.tools.toolchain as toolchain
+from distutils.version import LooseVersion
+from easybuild.easyblocks.generic.configuremake import ConfigureMake
+from easybuild.framework.easyconfig import CUSTOM
+from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.config import build_option
+from easybuild.tools.filetools import adjust_permissions, apply_regex_substitutions
+from easybuild.tools.filetools import change_dir, copy_dir, copy_file, mkdir
+from easybuild.tools.modules import get_software_root, get_software_version
+from easybuild.tools.run import run_cmd
+from easybuild.tools.systemtools import get_shared_lib_ext
+
+
+class EB_Siesta(ConfigureMake):
+    """
+    Support for building/installing Siesta.
+    - avoid parallel build for older versions
+    """
+
+    @staticmethod
+    def extra_options(extra_vars=None):
+        """Define extra options for Siesta"""
+        extra = {
+            'with_transiesta': [True, "Build transiesta", CUSTOM],
+            'with_utils': [True, "Build all utils", CUSTOM],
+        }
+        return ConfigureMake.extra_options(extra_vars=extra)
+
+    def configure_step(self):
+        """
+        Custom configure and build procedure for Siesta.
+        - There are two main builds to do, siesta and transiesta
+        - In addition there are multiple support tools to build
+        """
+
+        start_dir = self.cfg['start_dir']
+        obj_dir = os.path.join(start_dir, 'Obj')
+        arch_make = os.path.join(obj_dir, 'arch.make')
+        bindir = os.path.join(start_dir, 'bin')
+
+        loose_ver = LooseVersion(self.version)
+
+        par = ''
+        if loose_ver >= LooseVersion('4.1'):
+            par = '-j %s' % self.cfg['parallel']
+
+        # enable OpenMP support if desired
+        env_var_suff = ''
+        if self.toolchain.options.get('openmp', None):
+            env_var_suff = '_MT'
+
+        scalapack = os.environ['LIBSCALAPACK' + env_var_suff]
+        blacs = os.environ['LIBSCALAPACK' + env_var_suff]
+        lapack = os.environ['LIBLAPACK' + env_var_suff]
+        blas = os.environ['LIBBLAS' + env_var_suff]
+        if get_software_root('imkl') or get_software_root('FFTW'):
+            fftw = os.environ['LIBFFT' + env_var_suff]
+        else:
+            fftw = None
+
+        regex_newlines = []
+        regex_subs = [
+            ('dc_lapack.a', ''),
+            (r'^NETCDF_INTERFACE\s*=.*$', ''),
+            ('libsiestaBLAS.a', ''),
+            ('libsiestaLAPACK.a', ''),
+            # Needed here to allow 4.1-b1 to be built with openmp
+            (r"^(LDFLAGS\s*=).*$", r"\1 %s %s" % (os.environ['FCFLAGS'], os.environ['LDFLAGS'])),
+        ]
+
+        regex_subs_gfortran = [
+            (r"^(FCFLAGS_free_f90\s*=.*)$", r"\1 -ffree-line-length-none"),
+            (r"^(FPPFLAGS_free_F90\s*=.*)$", r"\1 -ffree-line-length-none"),
+        ]
+
+        netcdff_loc = get_software_root('netCDF-Fortran')
+        if netcdff_loc:
+            # Needed for gfortran at least
+            regex_newlines.append((r"^(ARFLAGS_EXTRA\s*=.*)$", r"\1\nNETCDF_INCFLAGS = -I%s/include" % netcdff_loc))
+
+        if fftw:
+            fft_inc, fft_lib = os.environ['FFT_INC_DIR'], os.environ['FFT_LIB_DIR']
+            fppflags = r"\1\nFFTW_INCFLAGS = -I%s\nFFTW_LIBS = -L%s %s" % (fft_inc, fft_lib, fftw)
+            regex_newlines.append((r'(FPPFLAGS\s*:?=.*)$', fppflags))
+
+        # Make a temp installdir during the build of the various parts
+        mkdir(bindir)
+
+        # change to actual build dir
+        change_dir(obj_dir)
+
+        # Populate start_dir with makefiles
+        run_cmd(os.path.join(start_dir, 'Src', 'obj_setup.sh'), log_all=True, simple=True, log_output=True)
+
+        if loose_ver < LooseVersion('4.1-b2'):
+            # MPI?
+            if self.toolchain.options.get('usempi', None):
+                self.cfg.update('configopts', '--enable-mpi')
+
+            # BLAS and LAPACK
+            self.cfg.update('configopts', '--with-blas="%s"' % blas)
+            self.cfg.update('configopts', '--with-lapack="%s"' % lapack)
+
+            # ScaLAPACK (and BLACS)
+            self.cfg.update('configopts', '--with-scalapack="%s"' % scalapack)
+            self.cfg.update('configopts', '--with-blacs="%s"' % blacs)
+
+            # NetCDF-Fortran
+            if netcdff_loc:
+                self.cfg.update('configopts', '--with-netcdf=-lnetcdff')
+
+            # Configure is run in obj_dir, configure script is in ../Src
+            super(EB_Siesta, self).configure_step(cmd_prefix='../Src/')
+
+            if loose_ver > LooseVersion('4.0'):
+                regex_subs_Makefile = [
+                    (r'CFLAGS\)-c', r'CFLAGS) -c'),
+                ]
+                apply_regex_substitutions('Makefile', regex_subs_Makefile)
+
+            if self.toolchain.comp_family() in [toolchain.GCC]:
+                apply_regex_substitutions(arch_make, regex_subs_gfortran)
+
+        else:  # there's no configure on newer versions
+
+            if self.toolchain.comp_family() in [toolchain.INTELCOMP]:
+                copy_file(os.path.join(obj_dir, 'intel.make'), arch_make)
+            elif self.toolchain.comp_family() in [toolchain.GCC]:
+                copy_file(os.path.join(obj_dir, 'gfortran.make'), arch_make)
+            else:
+                raise EasyBuildError("There is currently no support for compiler: %s", self.toolchain.comp_family())
+
+            regex_subs.append((r"^(FPPFLAGS\s*:?=.*)$", r"\1 -DF2003"))
+
+            if self.toolchain.options.get('usempi', None):
+                regex_subs.extend([
+                    (r"^(CC\s*=\s*).*$", r"\1%s" % os.environ['MPICC']),
+                    (r"^(FC\s*=\s*).*$", r"\1%s" % os.environ['MPIF90']),
+                    (r"^(FPPFLAGS\s*:?=.*)$", r"\1 -DMPI"),
+                ])
+                regex_newlines.append((r"^(FPPFLAGS\s*:?=.*)$", r"\1\nMPI_INTERFACE = libmpi_f90.a\nMPI_INCLUDE = ."))
+                complibs = scalapack
+            else:
+                complibs = lapack
+
+            regex_subs.extend([
+                (r"^(LIBS\s*=).*$", r"\1 %s" % complibs),
+                # Needed for a couple of the utils
+                (r"^(FFLAGS\s*=\s*).*$", r"\1 -fPIC %s" % os.environ['FCFLAGS']),
+            ])
+            regex_newlines.append((r"^(COMP_LIBS\s*=.*)$", r"\1\nWXML = libwxml.a"))
+
+            if self.toolchain.comp_family() in [toolchain.GCC]:
+                regex_subs.extend(regex_subs_gfortran)
+
+            if netcdff_loc:
+                regex_subs.extend([
+                    (r"^(LIBS\s*=.*)$", r"\1 $(NETCDF_LIBS)"),
+                    (r"^(FPPFLAGS\s*:?=.*)$", r"\1 -DCDF -DNCDF -DNCDF_4 -DNCDF_PARALLEL $(NETCDF_INCLUDE)"),
+                    (r"^(COMP_LIBS\s*=.*)$", r"\1 libncdf.a libfdict.a"),
+                ])
+                netcdf_lib_and_inc = "NETCDF_LIBS = -lnetcdff\nNETCDF_INCLUDE = -I%s/include" % netcdff_loc
+                netcdf_lib_and_inc += "\nINCFLAGS = $(NETCDF_INCLUDE)"
+                regex_newlines.append((r"^(COMP_LIBS\s*=.*)$", r"\1\n%s" % netcdf_lib_and_inc))
+
+            xmlf90 = get_software_root('xmlf90')
+            if xmlf90:
+                regex_subs.append((r"^(XMLF90_ROOT\s*=).*$", r"\1%s" % xmlf90))
+
+            libpsml = get_software_root('libPSML')
+            if libpsml:
+                regex_subs.append((r"^(PSML_ROOT\s*=).*$.*", r"\1%s" % libpsml))
+
+            libgridxc = get_software_root('libGridXC')
+            if libgridxc:
+                regex_subs.append((r"^(GRIDXC_ROOT\s*=).*$", r"\1%s" % libgridxc))
+
+            libxc = get_software_root('libxc')
+            if libxc:
+                regex_subs.append((r"^#(LIBXC_ROOT\s*=).*$", r"\1 %s" % libxc))
+
+            elpa = get_software_root('ELPA')
+            if elpa:
+                elpa_ver = get_software_version('ELPA')
+                regex_subs.extend([
+                    (r"^(FPPFLAGS\s*:?=.*)$", r"\1 -DSIESTA__ELPA"),
+                    (r"^(FPPFLAGS\s*:?=.*)$", r"\1 -I%s/include/elpa-%s/modules" % (elpa, elpa_ver)),
+                    (r"^(LIBS\s*=.*)$", r"\1 -L%s/lib -lelpa" % elpa),
+                ])
+
+            elsi = get_software_root('ELSI')
+            if elsi:
+                if not os.path.isfile(os.path.join(elsi, 'lib', 'libelsi.%s' % get_shared_lib_ext())):
+                    raise EasyBuildError("This easyblock requires ELSI shared libraries instead of static")
+
+                regex_subs.extend([
+                    (r"^(FPPFLAGS\s*:?=.*)$", r"\1 -DSIESTA__ELSI"),
+                    (r"^(FPPFLAGS\s*:?=.*)$", r"\1 -I%s/include" % elsi),
+                    (r"^(LIBS\s*=.*)$", r"\1 $(FFTW_LIBS) -L%s/lib -lelsi" % elsi),
+                ])
+
+            metis = get_software_root('METIS')
+            if metis:
+                regex_subs.extend([
+                    (r"^(FPPFLAGS\s*:?=.*)$", r"\1 -DSIESTA__METIS"),
+                    (r"^(LIBS\s*=.*)$", r"\1 -L%s/lib -lmetis" % metis),
+                ])
+
+        apply_regex_substitutions(arch_make, regex_subs)
+
+        # individually apply substitutions that add lines
+        for regex_nl in regex_newlines:
+            apply_regex_substitutions(arch_make, [regex_nl])
+
+        run_cmd('make %s' % par, log_all=True, simple=True, log_output=True)
+
+        # Put binary in temporary install dir
+        copy_file(os.path.join(obj_dir, 'siesta'), bindir)
+
+        if self.cfg['with_utils']:
+            # Make the utils
+            change_dir(os.path.join(start_dir, 'Util'))
+
+            if loose_ver >= LooseVersion('4'):
+                # clean_all.sh might be missing executable bit...
+                adjust_permissions('./clean_all.sh', stat.S_IXUSR, recursive=False, relative=True)
+                run_cmd('./clean_all.sh', log_all=True, simple=True, log_output=True)
+
+            if loose_ver >= LooseVersion('4.1'):
+                regex_subs_TS = [
+                    (r"^default:.*$", r""),
+                    (r"^EXE\s*=.*$", r""),
+                    (r"^(include\s*..ARCH_MAKE.*)$", r"EXE=tshs2tshs\ndefault: $(EXE)\n\1"),
+                    (r"^(INCFLAGS.*)$", r"\1 -I%s" % obj_dir),
+                ]
+
+                makefile = os.path.join(start_dir, 'Util', 'TS', 'tshs2tshs', 'Makefile')
+                apply_regex_substitutions(makefile, regex_subs_TS)
+
+            if loose_ver >= LooseVersion('4'):
+                # SUFFIX rules in wrong place
+                regex_subs_suffix = [
+                    (r'^(\.SUFFIXES:.*)$', r''),
+                    (r'^(include\s*\$\(ARCH_MAKE\).*)$', r'\1\n.SUFFIXES:\n.SUFFIXES: .c .f .F .o .a .f90 .F90'),
+                ]
+                makefile = os.path.join(start_dir, 'Util', 'Sockets', 'Makefile')
+                apply_regex_substitutions(makefile, regex_subs_suffix)
+                makefile = os.path.join(start_dir, 'Util', 'SiestaSubroutine', 'SimpleTest', 'Src', 'Makefile')
+                apply_regex_substitutions(makefile, regex_subs_suffix)
+
+            regex_subs_UtilLDFLAGS = [
+                (r'(\$\(FC\)\s*-o\s)', r'$(FC) %s %s -o ' % (os.environ['FCFLAGS'], os.environ['LDFLAGS'])),
+            ]
+            makefile = os.path.join(start_dir, 'Util', 'Optimizer', 'Makefile')
+            apply_regex_substitutions(makefile, regex_subs_UtilLDFLAGS)
+            if loose_ver >= LooseVersion('4'):
+                makefile = os.path.join(start_dir, 'Util', 'JobList', 'Src', 'Makefile')
+                apply_regex_substitutions(makefile, regex_subs_UtilLDFLAGS)
+
+            # remove clean at the end of default target
+            # And yes, they are re-introducing this bug.
+            is_ver40_to_401 = loose_ver >= LooseVersion('4.0') and loose_ver < LooseVersion('4.0.2')
+            if (is_ver40_to_401 or loose_ver == LooseVersion('4.1-b3')):
+                makefile = os.path.join(start_dir, 'Util', 'SiestaSubroutine', 'SimpleTest', 'Src', 'Makefile')
+                apply_regex_substitutions(makefile, [(r"simple_mpi_parallel clean", r"simple_mpi_parallel")])
+                makefile = os.path.join(start_dir, 'Util', 'SiestaSubroutine', 'ProtoNEB', 'Src', 'Makefile')
+                apply_regex_substitutions(makefile, [(r"protoNEB clean", r"protoNEB")])
+
+            # build_all.sh might be missing executable bit...
+            adjust_permissions('./build_all.sh', stat.S_IXUSR, recursive=False, relative=True)
+            run_cmd('./build_all.sh', log_all=True, simple=True, log_output=True)
+
+            # Now move all the built utils to the temp installdir
+            expected_utils = [
+                'CMLComp/ccViz',
+                'Contrib/APostnikov/eig2bxsf', 'Contrib/APostnikov/fmpdos',
+                'Contrib/APostnikov/md2axsf', 'Contrib/APostnikov/rho2xsf',
+                'Contrib/APostnikov/vib2xsf', 'Contrib/APostnikov/xv2xsf',
+                'COOP/fat', 'COOP/mprop',
+                'Denchar/Src/denchar',
+                'DensityMatrix/cdf2dm', 'DensityMatrix/dm2cdf',
+                'Eig2DOS/Eig2DOS',
+                'Gen-basis/ionplot.sh',
+                'Grid/cdf2grid', 'Grid/cdf2xsf', 'Grid/cdf_laplacian',
+                'Grid/g2c_ng', 'Grid/grid2cdf', 'Grid/grid2cube',
+                'Grid/grid2val', 'Grid/grid_rotate',
+                'Helpers/get_chem_labels',
+                'HSX/hs2hsx', 'HSX/hsx2hs',
+                'JobList/Src/countJobs', 'JobList/Src/getResults',
+                'JobList/Src/horizontal', 'JobList/Src/runJobs',
+                'Macroave/Src/macroave',
+                'ON/lwf2cdf',
+                'Optimizer/simplex', 'Optimizer/swarm',
+                'pdosxml/pdosxml',
+                'Projections/orbmol_proj',
+                'SiestaSubroutine/FmixMD/Src/driver',
+                'SiestaSubroutine/FmixMD/Src/para',
+                'SiestaSubroutine/FmixMD/Src/simple',
+                'STM/ol-stm/Src/stm', 'STM/simple-stm/plstm',
+                'Vibra/Src/fcbuild', 'Vibra/Src/vibra',
+                'WFS/readwf', 'WFS/readwfx', 'WFS/wfs2wfsx',
+                'WFS/wfsnc2wfsx', 'WFS/wfsx2wfs',
+            ]
+
+            # skip broken utils in 4.1-MaX-1.0 release, hopefully will be fixed later
+            if self.version != '4.1-MaX-1.0':
+                expected_utils.extend([
+                    'VCA/fractional', 'VCA/mixps',
+                ])
+
+            if loose_ver >= LooseVersion('3.2'):
+                expected_utils.extend([
+                    'Bands/eigfat2plot',
+                ])
+
+            if loose_ver >= LooseVersion('4.0'):
+                if self.version != '4.1-MaX-1.0':
+                    expected_utils.extend([
+                        'SiestaSubroutine/ProtoNEB/Src/protoNEB',
+                        'SiestaSubroutine/SimpleTest/Src/simple_pipes_parallel',
+                        'SiestaSubroutine/SimpleTest/Src/simple_pipes_serial',
+                        'SiestaSubroutine/SimpleTest/Src/simple_sockets_parallel',
+                        'SiestaSubroutine/SimpleTest/Src/simple_sockets_serial',
+                    ])
+                expected_utils.extend([
+                    'Sockets/f2fmaster', 'Sockets/f2fslave',
+                ])
+                if self.toolchain.options.get('usempi', None):
+                    if self.version != '4.1-MaX-1.0':
+                        expected_utils.extend([
+                            'SiestaSubroutine/SimpleTest/Src/simple_mpi_parallel',
+                            'SiestaSubroutine/SimpleTest/Src/simple_mpi_serial',
+                        ])
+
+            if loose_ver < LooseVersion('4.1'):
+                expected_utils.append('WFS/info_wfsx')
+                if loose_ver >= LooseVersion('4.0'):
+                    expected_utils.extend([
+                        'COOP/dm_creator',
+                        'TBTrans_rep/tbtrans',
+                    ])
+                else:
+                    expected_utils.extend([
+                        'TBTrans/tbtrans',
+                    ])
+
+            if loose_ver < LooseVersion('4.0.2'):
+                expected_utils.extend([
+                    'Bands/new.gnubands',
+                ])
+            else:
+                expected_utils.extend([
+                    'Bands/gnubands',
+                ])
+                # Need to revisit this when 4.1 is officialy released.
+                # This is based on b1-b3 releases
+                if loose_ver < LooseVersion('4.1'):
+                    expected_utils.extend([
+                        'Contour/grid1d', 'Contour/grid2d',
+                        'Optical/optical', 'Optical/optical_input',
+                        'sies2arc/sies2arc',
+                    ])
+
+            if loose_ver >= LooseVersion('4.1'):
+                expected_utils.extend([
+                    'DensityMatrix/dmbs2dm', 'DensityMatrix/dmUnblock',
+                    'Grimme/fdf2grimme',
+                    'SpPivot/pvtsp',
+                    'TS/TBtrans/tbtrans', 'TS/tselecs.sh',
+                    'TS/ts2ts/ts2ts',
+                ])
+                if self.version != '4.1-MaX-1.0':
+                    expected_utils.extend([
+                        'TS/tshs2tshs/tshs2tshs',
+                    ])
+
+            for util in expected_utils:
+                copy_file(os.path.join(start_dir, 'Util', util), bindir)
+
+        if self.cfg['with_transiesta']:
+            # Build transiesta
+            change_dir(obj_dir)
+
+            ts_clean_target = 'clean'
+            if loose_ver >= LooseVersion('4.1-b4'):
+                ts_clean_target += '-transiesta'
+
+            run_cmd('make %s' % ts_clean_target, log_all=True, simple=True, log_output=True)
+            run_cmd('make %s transiesta' % par, log_all=True, simple=True, log_output=True)
+
+            copy_file(os.path.join(obj_dir, 'transiesta'), bindir)
+
+    def build_step(self):
+        """No build step for Siesta."""
+        pass
+
+    def test_step(self):
+        """Custom test step for Siesta."""
+        change_dir(os.path.join(self.cfg['start_dir'], 'Obj', 'Tests'))
+        super(EB_Siesta, self).test_step()
+
+    def install_step(self):
+        """Custom install procedure for Siesta: copy binaries."""
+        bindir = os.path.join(self.installdir, 'bin')
+        copy_dir(os.path.join(self.cfg['start_dir'], 'bin'), bindir)
+
+    def sanity_check_step(self):
+        """Custom sanity check for Siesta."""
+
+        bins = ['bin/siesta']
+
+        if self.cfg['with_transiesta']:
+            bins.append('bin/transiesta')
+
+        if self.cfg['with_utils']:
+            bins.append('bin/denchar')
+
+        custom_paths = {
+            'files': bins,
+            'dirs': [],
+        }
+        custom_commands = []
+        if self.toolchain.options.get('usempi', None) and build_option('mpi_tests'):
+            # make sure Siesta was indeed built with support for running in parallel
+            # The "cd to builddir" is required to not contaminate the install dir with cruft from running siesta
+            mpi_test_cmd = "cd %s && " % self.builddir
+            mpi_test_cmd = mpi_test_cmd + "echo 'SystemName test' | mpirun -np 2 siesta 2>/dev/null | grep PARALLEL"
+            custom_commands.append(mpi_test_cmd)
+
+        super(EB_Siesta, self).sanity_check_step(custom_paths=custom_paths, custom_commands=custom_commands)