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update Siesta easyblock for v3.2 to 4.1-b3 #1510

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Merged
boegel merged 11 commits into from
Sep 20, 2018
Merged

update Siesta easyblock for v3.2 to 4.1-b3 #1510

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4525c78
Make sure that the mpirun test of siesta doesn't leave cruft in the i…
akesandgren Sep 13, 2018
a8e7747
Newer Siesta versions need to know where the netcdf fortran module fi…
akesandgren Sep 13, 2018
ba034f5
Siesta doesn't have a clean_all.sh before v4.0
akesandgren Sep 13, 2018
5860828
Older Siesta versions lacks execute permission on build_all.sh.
akesandgren Sep 13, 2018
7157f7f
Older Siesta versions don't have Util/Sockets and SimpleTest.
akesandgren Sep 13, 2018
35566d2
Older Siesta versions don't have Util/JobList
akesandgren Sep 13, 2018
03cb9a5
Adjust version range where "clean" needs to be removed from default t…
akesandgren Sep 13, 2018
8477a32
Update version handling of which Utils are available.
akesandgren Sep 13, 2018
36e7c19
Fix too long lines.
akesandgren Sep 13, 2018
2013044
Fix another too long line.
akesandgren Sep 13, 2018
77fe35e
Calculate LooseVersion(self.version) once and use the result when nee…
akesandgren Sep 13, 2018
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151 changes: 100 additions & 51 deletions easybuild/easyblocks/s/siesta.py
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Original file line number Diff line number Diff line change
Expand Up @@ -68,8 +68,10 @@ def configure_step(self):
arch_make = os.path.join(obj_dir, 'arch.make')
bindir = os.path.join(start_dir, 'bin')

loose_ver = LooseVersion(self.version)

par = ''
if LooseVersion(self.version) >= LooseVersion('4.1'):
if loose_ver >= LooseVersion('4.1'):
par = '-j %s' % self.cfg['parallel']

# enable OpenMP support if desired
Expand Down Expand Up @@ -115,7 +117,7 @@ def configure_step(self):
# 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 LooseVersion(self.version) < LooseVersion('4.1-b2'):
if loose_ver < LooseVersion('4.1-b2'):
# MPI?
if self.toolchain.options.get('usempi', None):
self.cfg.update('configopts', '--enable-mpi')
Expand All @@ -135,7 +137,7 @@ def configure_step(self):
# Configure is run in obj_dir, configure script is in ../Src
super(EB_Siesta, self).configure_step(cmd_prefix='../Src/')

if LooseVersion(self.version) > LooseVersion('4.0'):
if loose_ver > LooseVersion('4.0'):
regex_subs_Makefile = [
(r'CFLAGS\)-c', r'CFLAGS) -c'),
]
Expand Down Expand Up @@ -171,9 +173,10 @@ def configure_step(self):
if netcdff_loc:
regex_subs.extend([
(r"^(LIBS\s*=.*)$", r"\1 $(NETCDF_LIBS)"),
(r"^(FPPFLAGS\s*=.*)$", r"\1 -DCDF"),
(r"^(FPPFLAGS\s*=.*)$", r"\1 -DCDF $(NETCDF_INCLUDE)"),
])
regex_newlines.append((r"^(COMP_LIBS\s*=.*)$", r"\1\nNETCDF_LIBS = -lnetcdff"))
netcdf_lib_and_inc = "NETCDF_LIBS = -lnetcdff\nNETCDF_INCLUDE = -I%s/include" % netcdff_loc
regex_newlines.append((r"^(COMP_LIBS\s*=.*)$", r"\1\n%s" % netcdf_lib_and_inc))

apply_regex_substitutions(arch_make, regex_subs)

Expand All @@ -190,11 +193,12 @@ def configure_step(self):
# Make the utils
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)
run_cmd('./clean_all.sh', log_all=True, simple=True, log_output=True)
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 LooseVersion(self.version) >= LooseVersion('4.1'):
if loose_ver >= LooseVersion('4.1'):
regex_subs_TS = [
(r"^default:.*$", r""),
(r"^EXE\s*=.*$", r""),
Expand All @@ -205,52 +209,58 @@ def configure_step(self):
makefile = os.path.join(start_dir, 'Util', 'TS', 'tshs2tshs', 'Makefile')
apply_regex_substitutions(makefile, regex_subs_TS)

# SUFFIX rules in wrong place
regex_subs_suffix = [
(r'^(\.SUFFIXES:.*)$', r''),
(r'^(include\s*\$\(ARCH_MAKE\).*)$', r'\1\n.SUFFIXES:\n.SUFFIXES: .c .f .F .o .a .f90 .F90'),
]
makefile = os.path.join(start_dir, 'Util', 'Sockets', 'Makefile')
apply_regex_substitutions(makefile, regex_subs_suffix)
makefile = os.path.join(start_dir, 'Util', 'SiestaSubroutine', 'SimpleTest', 'Src', 'Makefile')
apply_regex_substitutions(makefile, regex_subs_suffix)
if loose_ver >= LooseVersion('4'):
# SUFFIX rules in wrong place
regex_subs_suffix = [
(r'^(\.SUFFIXES:.*)$', 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)
makefile = os.path.join(start_dir, 'Util', 'JobList', 'Src', '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
if self.version == '4.0.1' or self.version == '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")])

# 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 = [
'Bands/eigfat2plot',
'CMLComp/ccViz',
'Contrib/APostnikov/eig2bxsf', 'Contrib/APostnikov/rho2xsf',
'Contrib/APostnikov/vib2xsf', 'Contrib/APostnikov/fmpdos',
'Contrib/APostnikov/xv2xsf', 'Contrib/APostnikov/md2axsf',
'COOP/mprop', 'COOP/fat',
'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/dm2cdf', 'DensityMatrix/cdf2dm',
'DensityMatrix/cdf2dm', 'DensityMatrix/dm2cdf',
'Eig2DOS/Eig2DOS',
'Gen-basis/ioncat', 'Gen-basis/gen-basis',
'Grid/cdf2grid', 'Grid/cdf_laplacian', 'Grid/cdf2xsf',
'Grid/grid2cube',
'Grid/grid_rotate', 'Grid/g2c_ng', 'Grid/grid2cdf', 'Grid/grid2val',
'Gen-basis/gen-basis', 'Gen-basis/ioncat',
'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/getResults', 'JobList/Src/countJobs',
'JobList/Src/runJobs', 'JobList/Src/horizontal',
'JobList/Src/countJobs', 'JobList/Src/getResults',
'JobList/Src/horizontal', 'JobList/Src/runJobs',
'Macroave/Src/macroave',
'ON/lwf2cdf',
'Optimizer/simplex', 'Optimizer/swarm',
Expand All @@ -259,33 +269,69 @@ def configure_step(self):
'SiestaSubroutine/FmixMD/Src/driver',
'SiestaSubroutine/FmixMD/Src/para',
'SiestaSubroutine/FmixMD/Src/simple',
'STM/simple-stm/plstm', 'STM/ol-stm/Src/stm',
'VCA/mixps', 'VCA/fractional',
'Vibra/Src/vibra', 'Vibra/Src/fcbuild',
'WFS/info_wfsx', 'WFS/wfsx2wfs',
'WFS/readwfx', 'WFS/wfsnc2wfsx', 'WFS/readwf', 'WFS/wfs2wfsx',
'STM/ol-stm/Src/stm', 'STM/simple-stm/plstm',
'VCA/fractional', 'VCA/mixps',
'Vibra/Src/fcbuild', 'Vibra/Src/vibra',
'WFS/info_wfsx',
'WFS/readwf', 'WFS/readwfx', 'WFS/wfs2wfsx',
'WFS/wfsnc2wfsx', 'WFS/wfsx2wfs',
]

if LooseVersion(self.version) <= LooseVersion('4.0'):
if loose_ver >= LooseVersion('3.2'):
expected_utils.extend([
'Bands/new.gnubands',
'TBTrans/tbtrans',
'Bands/eigfat2plot',
])

if LooseVersion(self.version) >= LooseVersion('4.0'):
if loose_ver >= LooseVersion('4.0'):
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',
'Sockets/f2fmaster', 'Sockets/f2fslave',
])

if LooseVersion(self.version) >= LooseVersion('4.1'):
if self.toolchain.options.get('usempi', None):
expected_utils.extend([
'SiestaSubroutine/SimpleTest/Src/simple_mpi_parallel',
'SiestaSubroutine/SimpleTest/Src/simple_mpi_serial',
])

if loose_ver < LooseVersion('4.1'):
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/ts2ts/ts2ts', 'TS/tshs2tshs/tshs2tshs', 'TS/TBtrans/tbtrans',
'TS/TBtrans/tbtrans', 'TS/tselecs.sh',
'TS/ts2ts/ts2ts', 'TS/tshs2tshs/tshs2tshs',
])

for util in expected_utils:
Expand Down Expand Up @@ -327,6 +373,9 @@ def sanity_check_step(self):
custom_commands = []
if self.toolchain.options.get('usempi', None):
# make sure Siesta was indeed built with support for running in parallel
custom_commands.append("echo 'SystemName test' | mpirun -np 2 siesta 2>/dev/null | grep 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)