def install_step(self):
"""Custom installation procedure for BamTools."""
if LooseVersion(self.version) < LooseVersion('2.5.0'):
self.cfg['files_to_copy'] = ['bin', 'lib', 'include', 'docs', 'LICENSE', 'README']
MakeCp.install_step(self)
else:
CMakeMake.install_step(self)
def extra_options(extra_vars=None):
"""
Define list of files or directories to be copied after make
"""
extra_vars = dict(MakeCp.extra_options(extra_vars=extra_vars))
extra_vars['cmds_map'] = [
[('.*', "$CC $CFLAGS %(source)s -o %(target)s")],
"List of regex/template command (with 'source'/'target' fields) tuples",
CUSTOM,
]
return MakeCp.extra_options(extra_vars=extra_vars)
def extra_options(extra_vars=None):
"""
Define list of files or directories to be copied after make
"""
extra_vars = dict(MakeCp.extra_options(extra_vars=extra_vars))
extra_vars['cmds_map'] = [
[('.*', "$CC $CFLAGS %(source)s -o %(target)s")],
"List of regex/template command (with 'source'/'target' fields) tuples",
CUSTOM,
]
return MakeCp.extra_options(extra_vars=extra_vars)
def extra_options():
"""Change default values of options"""
extra = MakeCp.extra_options()
# files_to_copy is not mandatory here
extra['files_to_copy'][2] = CUSTOM
extra['with_configure'][0] = True
return extra
def extra_options():
"""Change default values of options"""
extra = MakeCp.extra_options()
# files_to_copy is not mandatory here
extra['files_to_copy'][2] = CUSTOM
extra['with_configure'][0] = True
return extra
def extra_options():
"""Define extra NAMD-specific easyconfig parameters."""
extra = MakeCp.extra_options()
# files_to_copy is not mandatory here
extra['files_to_copy'][2] = CUSTOM
extra.update({
# see http://charm.cs.illinois.edu/manuals/html/charm++/A.html
'charm_arch': [
None,
"Charm++ target architecture (see the subdirectories in the charm-x.y.z/src/arch subdirectory)",
MANDATORY
],
'charm_opts': [
'--with-numa --with-production',
"Charm++ build options (really those that start with --, the compiler choice and so on are determined based on the toolchain and toolchain optionsi and specific needs for NAMD).",
CUSTOM
],
'namd_basearch': [
'Linux-x86_64',
"NAMD base target architecture (compiler family is appended)",
CUSTOM
],
'namd_cfg_opts': ['', "NAMD configure options", CUSTOM],
'runtest': [True, "Run NAMD test case after building", CUSTOM],
})
return extra
def extra_options(extra_vars=None):
"""Extra easyconfig parameters for BamTools."""
extra_vars = MakeCp.extra_options()
# files_to_copy is not mandatory here, since we overwrite it in install_step
extra_vars['files_to_copy'][2] = CUSTOM
return CMakeMake.extra_options(extra_vars=extra_vars)
def extra_options(extra_vars=None):
"""Extra easyconfig parameters for ORCA."""
extra_vars = MakeCp.extra_options()
extra_vars.update(PackedBinary.extra_options())
# files_to_copy is not mandatory here, since we set it by default in install_step
extra_vars['files_to_copy'][2] = CUSTOM
return extra_vars
def install_step(self):
"""Install by copying specified files and directories."""
if self.cfg.get('separate_build_dir', False):
if self.separate_build_dir:
self.cfg['start_dir'] = self.separate_build_dir
else:
self.cfg['start_dir'] = os.path.join(self.builddir, 'easybuild_obj')
return MakeCp.install_step(self)
def extra_options(extra_vars=None):
"""Extra easyconfig parameters for BamTools."""
extra_vars = MakeCp.extra_options()
extra_vars.update(CMakeMake.extra_options())
# files_to_copy is not mandatory here, since we overwrite it in install_step
extra_vars['files_to_copy'][2] = CUSTOM
# BamTools requires an out of source build
extra_vars['separate_build_dir'][0] = True
return extra_vars
def install_step(self):
"""Install ORCA with MakeCp easyblock"""
if not self.cfg['files_to_copy']:
# Put installation files in standard locations
files_to_copy = [
(['auto*', 'orca*', 'otool*'], 'bin'),
(['*.pdf'], 'share'),
]
# Version 5 extra files
if LooseVersion(self.version) >= LooseVersion('5.0.0'):
compoundmethods = (['ORCACompoundMethods'], 'bin')
files_to_copy.append(compoundmethods)
# Shared builds have additional libraries
libs_to_copy = (['liborca*'], 'lib')
if all([glob.glob(p) for p in libs_to_copy[0]]):
files_to_copy.append(libs_to_copy)
self.cfg['files_to_copy'] = files_to_copy
MakeCp.install_step(self)
def extra_options():
"""Define extra NAMD-specific easyconfig parameters."""
extra = MakeCp.extra_options()
# files_to_copy is not mandatory here
extra['files_to_copy'][2] = CUSTOM
extra.update({
# see http://charm.cs.illinois.edu/manuals/html/charm++/A.html
'charm_arch': [None, "Charm++ target architecture", MANDATORY],
'charm_opts': ['--with-production', "Charm++ build options", CUSTOM],
'namd_basearch': ['Linux-x86_64', "NAMD base target architecture (compiler family is appended", CUSTOM],
'namd_cfg_opts': ['', "NAMD configure options", CUSTOM],
'runtest': [True, "Run NAMD test case after building", CUSTOM],
})
return extra
def extra_options():
"""Define extra NAMD-specific easyconfig parameters."""
extra = MakeCp.extra_options()
# files_to_copy is not mandatory here
extra['files_to_copy'][2] = CUSTOM
extra.update({
# see http://charm.cs.illinois.edu/manuals/html/charm++/A.html
'charm_arch': [None, "Charm++ target architecture", MANDATORY],
'charm_opts': ['--with-production', "Charm++ build options", CUSTOM],
'namd_basearch': ['Linux-x86_64', "NAMD base target architecture (compiler family is appended", CUSTOM],
'namd_cfg_opts': ['', "NAMD configure options", CUSTOM],
'runtest': [True, "Run NAMD test case after building", CUSTOM],
})
return extra
def extra_options():
"""Define extra NAMD-specific easyconfig parameters."""
extra_vars = [
# see http://charm.cs.illinois.edu/manuals/html/charm++/A.html
('charm_arch', [None, "Charm++ target architecture", MANDATORY]),
('charm_opts', ['--with-production', "Charm++ build options", CUSTOM]),
('namd_basearch', ['Linux-x86_64', "NAMD base target architecture (compiler family is appended", CUSTOM]),
('namd_cfg_opts', ['', "NAMD configure options", CUSTOM]),
('runtest', [True, "Run NAMD test case after building", CUSTOM]),
]
extra = dict(MakeCp.extra_options(extra_vars=extra_vars))
# files_to_copy is useless here, and definitely not mandatory, so get rid of it
del extra['files_to_copy']
return extra.items()
def __init__(self, *args, **kwargs):
PythonPackage.__init__(self, *args, **kwargs)
MakeCp.__init__(self, *args, **kwargs)
def extra_options(extra_vars=None):
return MakeCp.extra_options(extra_vars=extra_vars)
def extra_options(extra_vars=None):
"""Change default values of options"""
extra = MakeCp.extra_options()
# files_to_copy is not mandatory here
extra['files_to_copy'][2] = CUSTOM
return extra
def extra_options(extra_vars=None):
extra_vars = MakeCp.extra_options(extra_vars)
return CMakeMake.extra_options(extra_vars=extra_vars)
def extra_options(extra_vars=None):
"""Extra easyconfig parameters specific to ConfigureMake."""
extra_vars = MakeCp.extra_options(extra_vars=extra_vars)
extra_vars.update({
'with_png': [
False, "Support export of PNG files (only valid with MPI)",
CUSTOM
],
'with_jpeg': [
False, "Support export of JPEG files (only valid with MPI)",
CUSTOM
],
'use_asphere': [
False, "Include the optional, standard \"asphere\" package",
CUSTOM
],
'use_body':
[False, "Include the optional, standard \"body\" package", CUSTOM],
'use_class2': [
False, "Include the optional, standard \"class2\" package",
CUSTOM
],
'use_colloid': [
False, "Include the optional, standard \"colloid\" package",
CUSTOM
],
'use_compress': [
False, "Include the optional, standard \"compress\" package",
CUSTOM
],
'use_coreshell': [
False, "Include the optional, standard \"coreshell\" package",
CUSTOM
],
'use_dipole': [
False, "Include the optional, standard \"dipole\" package",
CUSTOM
],
'use_fld':
[False, "Include the optional, standard \"fld\" package", CUSTOM],
'use_gpu':
[False, "Include the optional, standard \"gpu\" package", CUSTOM],
'use_granular': [
False, "Include the optional, standard \"granular\" package",
CUSTOM
],
'use_kim':
[False, "Include the optional, standard \"kim\" package", CUSTOM],
'use_kokkos': [
False, "Include the optional, standard \"kokkos\" package",
CUSTOM
],
'use_kspace': [
False, "Include the optional, standard \"kspace\" package",
CUSTOM
],
'use_manybody': [
False, "Include the optional, standard \"manybody\" package",
CUSTOM
],
'use_mc':
[False, "Include the optional, standard \"mc\" package", CUSTOM],
'use_meam':
[False, "Include the optional, standard \"meam\" package", CUSTOM],
'use_misc':
[False, "Include the optional, standard \"misc\" package", CUSTOM],
'use_molecule': [
False, "Include the optional, standard \"molecule\" package",
CUSTOM
],
'use_mpiio': [
False, "Include the optional, standard \"mpiio\" package",
CUSTOM
],
'use_opt':
[False, "Include the optional, standard \"opt\" package", CUSTOM],
'use_peri':
[False, "Include the optional, standard \"peri\" package", CUSTOM],
'use_poems': [
False, "Include the optional, standard \"poems\" package",
CUSTOM
],
'use_python': [
False, "Include the optional, standard \"python\" package",
CUSTOM
],
'use_qeq':
[False, "Include the optional, standard \"qeq\" package", CUSTOM],
'use_reax':
[False, "Include the optional, standard \"reax\" package", CUSTOM],
'use_replica': [
False, "Include the optional, standard \"replica\" package",
CUSTOM
],
'use_rigid': [
False, "Include the optional, standard \"rigid\" package",
CUSTOM
],
'use_shock': [
False, "Include the optional, standard \"shock\" package",
CUSTOM
],
'use_snap':
[False, "Include the optional, standard \"snap\" package", CUSTOM],
'use_srd': [
False, "Include the optional, standard \"srd\" package", CUSTOM
],
'use_voronoi': [
False, "Include the optional, standard \"voronoi\" package",
CUSTOM
],
'use_xtc': [
False, "Include the optional, standard \"xtc\" package", CUSTOM
],
'use_atc': [
False,
"Include the optional, user-contributed \"user-atc\" package",
CUSTOM
],
'use_awpmd': [
False,
"Include the optional, user-contributed \"user-awpmd\" package",
CUSTOM
],
'use_cg_cmm': [
False,
"Include the optional, user-contributed \"user-cg-cmm\" package",
CUSTOM
],
'use_colvars': [
False,
"Include the optional, user-contributed \"user-colvars\" package",
CUSTOM
],
'use_cuda': [
False,
"Include the optional, user-contributed \"user-cuda\" package",
CUSTOM
],
'use_diffraction': [
False,
"Include the optional, user-contributed \"user-diffraction\" package",
CUSTOM
],
'use_drude': [
False,
"Include the optional, user-contributed \"user-drude\" package",
CUSTOM
],
'use_eff': [
False,
"Include the optional, user-contributed \"user-eff\" package",
CUSTOM
],
'use_fep': [
False,
"Include the optional, user-contributed \"user-fep\" package",
CUSTOM
],
'use_h5md': [
False,
"Include the optional, user-contributed \"user-h5md\" package",
CUSTOM
],
'use_intel': [
False,
"Include the optional, user-contributed \"user-intel\" package",
CUSTOM
],
'use_lb': [
False,
"Include the optional, user-contributed \"user-lb\" package",
CUSTOM
],
'use_mgpt': [
False,
"Include the optional, user-contributed \"user-mgpt\" package",
CUSTOM
],
'use_misc': [
False,
"Include the optional, user-contributed \"user-misc\" package",
CUSTOM
],
'use_molfile': [
False,
"Include the optional, user-contributed \"user-molfile\" package",
CUSTOM
],
'use_omp': [
False,
"Include the optional, user-contributed \"user-omp\" package",
CUSTOM
],
'use_phonon': [
False,
"Include the optional, user-contributed \"user-phonon\" package",
CUSTOM
],
'use_qmmm': [
False,
"Include the optional, user-contributed \"user-qmmm\" package",
CUSTOM
],
'use_qtb': [
False,
"Include the optional, user-contributed \"user-qtb\" package",
CUSTOM
],
'use_quip': [
False,
"Include the optional, user-contributed \"user-quip\" package",
CUSTOM
],
'use_reaxc': [
False,
"Include the optional, user-contributed \"user-reaxc\" package",
CUSTOM
],
'use_smd': [
False,
"Include the optional, user-contributed \"user-smd\" package",
CUSTOM
],
'use_smtbq': [
False,
"Include the optional, user-contributed \"user-smtbq\" package",
CUSTOM
],
'use_sph': [
False,
"Include the optional, user-contributed \"user-sph\" package",
CUSTOM
],
'use_tally': [
False,
"Include the optional, user-contributed \"user-tally\" package",
CUSTOM
],
'gpu_base_makefile': [
'Makefile.linux',
"Makefile to use when generating GPU build instructions",
CUSTOM
],
'gpu_arch_string': [
'sm_20',
"Architecture code to use when generating GPU build instructions",
CUSTOM
],
'gpu_prec_string': [
'mixed',
"Precision to use when generating GPU build instructions",
CUSTOM
],
'cuda_prec_val': [
1,
"Numeric code designating the precision to which to build the CUDA library",
CUSTOM
],
'cuda_arch_val': [
20, "Numeric code designating the CUDA architecture to use",
CUSTOM
],
'cuda_use_prec_timers': [
False,
"Use high-precision timers when building the CUDA library",
CUSTOM
],
'cuda_use_debug': [
False, "Enable debug mode in the CUDA library", CUSTOM
],
'cuda_use_cufft': [False, "Enable CUDA FFT library", CUSTOM],
})
return extra_vars
def install_step(self):
MakeCp.install_step(self)
def configure_step(self, cmd_prefix=''):
MakeCp.configure_step(self, cmd_prefix=cmd_prefix)
def extra_options(extra_vars=None):
"""Extra easyconfig parameters for BamTools."""
extra = MakeCp.extra_options()
# files_to_copy is not mandatory here, since we overwrite it in install_step
extra['files_to_copy'][2] = CUSTOM
return extra
def install_step(self):
files_to_copy = self.cfg.get('files_to_copy', [])
self.log.info("Starting install_step with files_to_copy: %s" %
files_to_copy)
PythonPackage.install_step(self)
return MakeCp.install_step(self)
def extra_options(extra_vars=None):
"""Change default values of options"""
extra = MakeCp.extra_options()
# files_to_copy is not mandatory here
extra['files_to_copy'][2] = CUSTOM
return extra
def sanity_check_step(self, *args, **kwargs):
return MakeCp.sanity_check_step(self, *args, **kwargs)
def extra_options(extra_vars=None):
if extra_vars is None:
extra_vars = {}
extra = MakeCp.extra_options(extra_vars=extra_vars)
return GitCloneConfigureMake.extra_options(extra_vars=extra)
