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Added Miguel as author.
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Fixed lots of comments from Kenneth.
Removed all tabs.
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@akesandgren
akesandgren committed Apr 6, 2017
1 parent 2c31444 commit 5f8a309
Showing 1 changed file with 43 additions and 65 deletions.
108 changes: 43 additions & 65 deletions easybuild/easyblocks/s/siesta.py
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@@ -1,5 +1,5 @@
##
# Copyright 2009-2016 Ghent University
# Copyright 2009-2017 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
Expand All @@ -25,36 +25,28 @@
"""
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 re
import shutil
import stat
import tempfile

import easybuild.tools.config as config
import easybuild.tools.environment as env
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.filetools import adjust_permissions, apply_regex_substitutions, copy_file, mkdir, write_file
from easybuild.tools.modules import get_software_libdir, get_software_root, get_software_version
from easybuild.tools.filetools import adjust_permissions, apply_regex_substitutions, change_dir, copy_file, copytree, mkdir
from easybuild.tools.modules import get_software_root
from easybuild.tools.run import run_cmd


class EB_Siesta(ConfigureMake):
"""
Support for building/installing Siesta.
- avoid parallel build, doesn't work
- avoid parallel build for older versions
"""

def __init__(self, *args, **kwargs):
"""Initialisation of custom class variables for Siesta."""
super(EB_Siesta, self).__init__(*args, **kwargs)

@staticmethod
def extra_options(extra_vars=None):
"""Define extra options for Siesta"""
Expand Down Expand Up @@ -83,21 +75,17 @@ def configure_step(self):
par = '-j %s' % self.cfg['parallel']

# enable OpenMP support if desired
env_var_suff = ''
openmp = self.toolchain.options.get('openmp', None)
if openmp:
scalapack = os.environ['LIBSCALAPACK_MT']
blacs = os.environ['LIBSCALAPACK_MT']
lapack = os.environ['LIBLAPACK_MT']
blas = os.environ['LIBBLAS_MT']
if get_software_root('imkl') or get_software_root('FFTW'):
fftw = os.environ['LIBFFT_MT']
else:
scalapack = os.environ['LIBSCALAPACK']
blacs = os.environ['LIBSCALAPACK']
lapack = os.environ['LIBLAPACK']
blas = os.environ['LIBBLAS']
if get_software_root('imkl') or get_software_root('FFTW'):
fftw = os.environ['LIBFFT']
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]

regex_subs = [
('dc_lapack.a', ''),
Expand All @@ -108,28 +96,23 @@ def configure_step(self):
(r"^(LDFLAGS\s*=).*$", r"\1 %s %s" % (os.environ['FCFLAGS'], os.environ['LDFLAGS'])),
]

if netcdff_loc:
# Needed for gfortran at least
regex_subs.extend([
(r"^(ARFLAGS_EXTRA\s*=.*)$", r"\1\nNETCDF_INCFLAGS = -I%s/include" % netcdff_loc),
])
if netcdff_loc:
# Needed for gfortran at least
regex_subs.extend([
(r"^(ARFLAGS_EXTRA\s*=.*)$", r"\1\nNETCDF_INCFLAGS = -I%s/include" % netcdff_loc),
])

if fftw is not None:
if fftw:
fftw_inc, fftw_lib = os.environ['FFTW_INC_DIR'], os.environ['FFTW_LIB_DIR']
regex_subs.extend([
(r'(FPPFLAGS\s*=.*)$', r'\1\nFFTW_INCFLAGS = -I%s\nFFTW_LIBS = -L%s %s' % (os.environ['FFTW_INC_DIR'], os.environ['FFTW_LIB_DIR'], fftw)),
(r'(FPPFLAGS\s*=.*)$', r'\1\nFFTW_INCFLAGS = -I%s\nFFTW_LIBS = -L%s %s' % (fftw_inc, fftw_lib, fftw)),
])

# Make a temp installdir during the build of the various parts
try:
mkdir(bindir)
except OSError, err:
raise EasyBuildError("Failed to create temp installdir %s: %s", bindir, err)
mkdir(bindir)

# change to actual build dir
try:
os.chdir(obj_dir)
except OSError, err:
raise EasyBuildError("Failed to change to build dir: %s", err)
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)
Expand Down Expand Up @@ -163,8 +146,10 @@ def configure_step(self):

if self.toolchain.comp_family() in [toolchain.INTELCOMP]:
copy_file(os.path.join(obj_dir, 'intel.make'), arch_make)
else:
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())

if self.toolchain.options.get('usempi', None):
regex_subs.extend([
Expand Down Expand Up @@ -196,15 +181,11 @@ def configure_step(self):
run_cmd('make %s' % par, log_all=True, simple=True, log_output=True)

# Put binary in temporary install dir
shutil.copy(os.path.join(self.cfg['start_dir'], 'Obj', 'siesta'),
bindir)
copy_file(os.path.join(self.cfg['start_dir'], 'Obj', 'siesta'), bindir)

if self.cfg['with_utils']:
# Make the utils
try:
os.chdir(os.path.join(start_dir, 'Util'))
except OSError, err:
raise EasyBuildError("Failed to change to Util dir: %s", err)
change_dir(os.path.join(start_dir, 'Util'))

# clean_all.sh might be missing executable bit...
adjust_permissions('./clean_all.sh', stat.S_IXUSR, recursive=False, relative=True)
Expand All @@ -225,14 +206,18 @@ def configure_step(self):
(r'^(\.SUFFIXES:.*)$', r''),
(r'^(include\s*\$\(ARCH_MAKE\).*)$', r'\1\n.SUFFIXES:\n.SUFFIXES: .c .f .F .o .a .f90 .F90'),
]
apply_regex_substitutions(os.path.join(self.cfg['start_dir'], 'Util', 'Sockets', 'Makefile'), regex_subs_suffix)
apply_regex_substitutions(os.path.join(self.cfg['start_dir'], 'Util', 'SiestaSubroutine', 'SimpleTest', 'Src', 'Makefile'), regex_subs_suffix)
makefile = os.path.join(self.cfg['start_dir'], 'Util', 'Sockets', 'Makefile')
apply_regex_substitutions(makefile, regex_subs_suffix)
makefile = os.path.join(self.cfg['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'])),
]
apply_regex_substitutions(os.path.join(self.cfg['start_dir'], 'Util', 'Optimizer', 'Makefile'), regex_subs_UtilLDFLAGS)
apply_regex_substitutions(os.path.join(self.cfg['start_dir'], 'Util', 'JobList', 'Src', 'Makefile'), regex_subs_UtilLDFLAGS)
makefile = os.path.join(self.cfg['start_dir'], 'Util', 'Optimizer', 'Makefile')
apply_regex_substitutions(makefile, regex_subs_UtilLDFLAGS)
makefile = os.path.join(self.cfg['start_dir'], 'Util', 'JobList', 'Src', 'Makefile')
apply_regex_substitutions(makefile, regex_subs_UtilLDFLAGS)

run_cmd('./build_all.sh', log_all=True, simple=True, log_output=True)

Expand Down Expand Up @@ -293,19 +278,16 @@ def configure_step(self):
])

for f in expected_utils:
shutil.copy(os.path.join(self.cfg['start_dir'], 'Util', f), bindir)
copy_file(os.path.join(self.cfg['start_dir'], 'Util', f), bindir)

if self.cfg['with_transiesta']:
# Build transiesta
try:
os.chdir(obj_dir)
except OSError, err:
raise EasyBuildError("Failed to change back to Obj dir: %s", err)
change_dir(obj_dir)

run_cmd('make clean', log_all=True, simple=True, log_output=True)
run_cmd('make %s transiesta' % par, log_all=True, simple=True, log_output=True)

shutil.copy(os.path.join(self.cfg['start_dir'], 'Obj', 'transiesta'),
copy_file(os.path.join(self.cfg['start_dir'], 'Obj', 'transiesta'),
bindir)

def build_step(self):
Expand All @@ -315,13 +297,9 @@ def build_step(self):
def install_step(self):
"""Custom install procedure for Siesta."""

try:
# binary
bindir = os.path.join(self.installdir, 'bin')
shutil.copytree(os.path.join(self.cfg['start_dir'], 'bin'), bindir)

except OSError, err:
raise EasyBuildError("Failed to install Siesta: %s", err)
# binary
bindir = os.path.join(self.installdir, 'bin')
copytree(os.path.join(self.cfg['start_dir'], 'bin'), bindir)

def sanity_check_step(self):
"""Custom sanity check for Siesta."""
Expand Down

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