diff options
Diffstat (limited to 'var/spack/repos/builtin/packages/plumed/package.py')
| -rw-r--r-- | var/spack/repos/builtin/packages/plumed/package.py | 323 |
1 files changed, 162 insertions, 161 deletions
diff --git a/var/spack/repos/builtin/packages/plumed/package.py b/var/spack/repos/builtin/packages/plumed/package.py index d1466e42ff..a7a1d28fb3 100644 --- a/var/spack/repos/builtin/packages/plumed/package.py +++ b/var/spack/repos/builtin/packages/plumed/package.py @@ -22,49 +22,50 @@ class Plumed(AutotoolsPackage): The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. """ - homepage = 'https://www.plumed.org/' - url = 'https://github.com/plumed/plumed2/archive/v2.7.4.tar.gz' - git = 'https://github.com/plumed/plumed2.git' - maintainers = ['marcodelapierre'] - - version('master', branch='master') - - version('2.8.0', sha256='8357eca6f280125037ad4e7c427f96f2af2f60ddfedce1a2e36e1e1cc3bff32b') - - version('2.7.4', sha256='6f5dc16a753c71ed719f17f9cbb61642ab8e716fb7f77e22960dfa145c3b8211') - version('2.7.3', sha256='aa1f6200c2ed351e40ce4391a9590f171532474b30f384feddfab10e36d7e08e') - version('2.7.2', sha256='c9a31e68d6440828cf186ca43c9e11a5e5c7ad1c96b2b66ed5a5a141fc954373') - version('2.7.1', sha256='cb8b5735d8dd61980fa6441f3dde3f33544240ae4177da0f529fb5abb355cd4a') - version('2.7.0', sha256='14450ea566c25ac9bf71fd77bb9c0c95e9038462b5739c73a515be82e2011cd6') - - version('2.6.6', sha256='43a7bb410280141c020363671c685a759d4497b3db3eb3c04899264b51a26859') - version('2.6.5', sha256='3b72587ba6fe72def46bcc7d917974123279879de7f8335acf542bba57865eed') - version('2.6.4', sha256='53e49c0db6cc769d238834bea884e856f4e7bb8f71c9929e5584bd977113f03b') - version('2.6.3', sha256='d05b9e4a4c1329fc932d5bdd04f20419be230f98159bdc012a91716461ab4a2f') - version('2.6.2', sha256='bbc2ef0cb08d404513b8b737c72333b6656389e15effd6a0f9ace2a5758c9a4a') - version('2.6.1', sha256='c1b3c397b2d971140aa240dde50e48a04ce78e3dedb02b6dca80fa53f8026e4e') - version('2.6.0', sha256='3d57ae460607a49547ef38a52c4ac93493a3966857c352280a9c05f5dcdb1820') - - version('2.5.7', sha256='aa10d2879c3edeaef9d5a530fe8b05f67ecfbec2e9423e0f95701d0bc54826c7') - version('2.5.6', sha256='1bc29b0274196fb553cdf7ba8ecb7a93a91d60a920d99863edbcd536d618ce8c') - version('2.5.5', sha256='70faa9ff1938e286dc388cb793b39840953e5646855b684f48df1bc864b737e8') - version('2.5.4', sha256='a1647e598191f261e75d06351e607475d395af481315052a4c28563ac9989a7f') - version('2.5.3', sha256='543288be667dc4201fc461ecd2dd4878ddfbeac682d0c021c99ea8e501c7c9dc') - version('2.5.2', sha256='85d10cc46e2e37c7719cf51c0931278f56c2c8f8a9d86188b2bf97c2535a2ab4') - version('2.5.1', sha256='de309980dcfd6f6e0e70e138856f4bd9eb4d8a513906a5e6389f18a5af7f2eba') - version('2.5.0', sha256='53e08187ec9f8af2326fa84407e34644a7c51d2af93034309fb70675eee5e4f7') - version('2.4.6', sha256='c22ad19f5cd36ce9fe4ba0b53158fc2a3d985c48fc04606e3f3b3e835b994cb3') - - version('2.4.4', sha256='1e5c24109314481fad404da97d61c7339b219e27e120c9c80bacc79c9f6a51a8') - version('2.4.2', sha256='528ce57f1f5330480bcd403140166a4580efd2acaea39c85dfeca5e2cd649321') - version('2.4.1', sha256='f00410ebdd739c2ddf55fcd714ff4bd88a1029e02d2fc9cea0b5fca34e0fc4eb') - - version('2.3.5', sha256='a6a66ca4582c1aecc6138c96be015e13cd06a718e8446b2f13e610fe34602e4f') - version('2.3.3', sha256='ac058ff529f207d5b4169fb5a87bdb3c77307dfef1ac543ad8b6c74c5de7fc91') - version('2.3.0', sha256='b1c8a54a313a0569e27e36420770074f35406453f73de70e55c424652abeddf1') - - version('2.2.4', sha256='d7a1dba34a7fe03f23e8d39ab6e15b230c4851373fdceb3602e2de26ea53ce37') - version('2.2.3', sha256='2db19c5f6a2918833941d0bf47b5431d0865529d786df797ccc966d763ed7b0c') + + homepage = "https://www.plumed.org/" + url = "https://github.com/plumed/plumed2/archive/v2.7.4.tar.gz" + git = "https://github.com/plumed/plumed2.git" + maintainers = ["marcodelapierre"] + + version("master", branch="master") + + version("2.8.0", sha256="8357eca6f280125037ad4e7c427f96f2af2f60ddfedce1a2e36e1e1cc3bff32b") + + version("2.7.4", sha256="6f5dc16a753c71ed719f17f9cbb61642ab8e716fb7f77e22960dfa145c3b8211") + version("2.7.3", sha256="aa1f6200c2ed351e40ce4391a9590f171532474b30f384feddfab10e36d7e08e") + version("2.7.2", sha256="c9a31e68d6440828cf186ca43c9e11a5e5c7ad1c96b2b66ed5a5a141fc954373") + version("2.7.1", sha256="cb8b5735d8dd61980fa6441f3dde3f33544240ae4177da0f529fb5abb355cd4a") + version("2.7.0", sha256="14450ea566c25ac9bf71fd77bb9c0c95e9038462b5739c73a515be82e2011cd6") + + version("2.6.6", sha256="43a7bb410280141c020363671c685a759d4497b3db3eb3c04899264b51a26859") + version("2.6.5", sha256="3b72587ba6fe72def46bcc7d917974123279879de7f8335acf542bba57865eed") + version("2.6.4", sha256="53e49c0db6cc769d238834bea884e856f4e7bb8f71c9929e5584bd977113f03b") + version("2.6.3", sha256="d05b9e4a4c1329fc932d5bdd04f20419be230f98159bdc012a91716461ab4a2f") + version("2.6.2", sha256="bbc2ef0cb08d404513b8b737c72333b6656389e15effd6a0f9ace2a5758c9a4a") + version("2.6.1", sha256="c1b3c397b2d971140aa240dde50e48a04ce78e3dedb02b6dca80fa53f8026e4e") + version("2.6.0", sha256="3d57ae460607a49547ef38a52c4ac93493a3966857c352280a9c05f5dcdb1820") + + version("2.5.7", sha256="aa10d2879c3edeaef9d5a530fe8b05f67ecfbec2e9423e0f95701d0bc54826c7") + version("2.5.6", sha256="1bc29b0274196fb553cdf7ba8ecb7a93a91d60a920d99863edbcd536d618ce8c") + version("2.5.5", sha256="70faa9ff1938e286dc388cb793b39840953e5646855b684f48df1bc864b737e8") + version("2.5.4", sha256="a1647e598191f261e75d06351e607475d395af481315052a4c28563ac9989a7f") + version("2.5.3", sha256="543288be667dc4201fc461ecd2dd4878ddfbeac682d0c021c99ea8e501c7c9dc") + version("2.5.2", sha256="85d10cc46e2e37c7719cf51c0931278f56c2c8f8a9d86188b2bf97c2535a2ab4") + version("2.5.1", sha256="de309980dcfd6f6e0e70e138856f4bd9eb4d8a513906a5e6389f18a5af7f2eba") + version("2.5.0", sha256="53e08187ec9f8af2326fa84407e34644a7c51d2af93034309fb70675eee5e4f7") + version("2.4.6", sha256="c22ad19f5cd36ce9fe4ba0b53158fc2a3d985c48fc04606e3f3b3e835b994cb3") + + version("2.4.4", sha256="1e5c24109314481fad404da97d61c7339b219e27e120c9c80bacc79c9f6a51a8") + version("2.4.2", sha256="528ce57f1f5330480bcd403140166a4580efd2acaea39c85dfeca5e2cd649321") + version("2.4.1", sha256="f00410ebdd739c2ddf55fcd714ff4bd88a1029e02d2fc9cea0b5fca34e0fc4eb") + + version("2.3.5", sha256="a6a66ca4582c1aecc6138c96be015e13cd06a718e8446b2f13e610fe34602e4f") + version("2.3.3", sha256="ac058ff529f207d5b4169fb5a87bdb3c77307dfef1ac543ad8b6c74c5de7fc91") + version("2.3.0", sha256="b1c8a54a313a0569e27e36420770074f35406453f73de70e55c424652abeddf1") + + version("2.2.4", sha256="d7a1dba34a7fe03f23e8d39ab6e15b230c4851373fdceb3602e2de26ea53ce37") + version("2.2.3", sha256="2db19c5f6a2918833941d0bf47b5431d0865529d786df797ccc966d763ed7b0c") # Variants. PLUMED by default builds a number of optional modules. # The ones listed here are not built by default for various reasons, @@ -84,72 +85,80 @@ class Plumed(AutotoolsPackage): # https://www.plumed.org/doc-v2.8/user-doc/html/mymodules.html # These are implemented using multi-valued variants (`disjoint_sets`), # and the `conditional` option to handle version conflicts. - single_optional_modules = (conditional('adjmat', when='@2.3:'), - 'analysis', - conditional('annfunc', when='@2.6:'), - 'bias', 'cltools', 'colvar', 'crystallization', - conditional('dimred', when='@2.5:'), - conditional('drr', when='@2.4:'), - conditional('eds', when='@2.4:'), - conditional('fisst', when='@2.7:'), - 'function', - conditional('funnel', when='@2.7:'), - 'generic', - conditional('imd', when='@:2.2.99'), - conditional('isdb', when='@2.4:'), - conditional('logmfd', when='@2.5:'), - 'manyrestraints', 'mapping', - conditional('maze', when='@2.6:'), - 'molfile', - 'multicolvar', - conditional('opes', when='@2.7:'), - conditional('pamm', - when='@2.5: optional_modules=adjmat'), - conditional('piv', when='@2.5:'), - conditional('reference', when='@:2.2.99'), - conditional('s2cm', when='@2.8:'), - conditional('sasa', when='@2.8:'), - 'secondarystructure', 'setup', 'vatom', - conditional('ves', when='@2.4:'), - conditional('vesselbase', when='@:2.2.99'), - conditional('xdrfile', when='@2.8:')) + single_optional_modules = ( + conditional("adjmat", when="@2.3:"), + "analysis", + conditional("annfunc", when="@2.6:"), + "bias", + "cltools", + "colvar", + "crystallization", + conditional("dimred", when="@2.5:"), + conditional("drr", when="@2.4:"), + conditional("eds", when="@2.4:"), + conditional("fisst", when="@2.7:"), + "function", + conditional("funnel", when="@2.7:"), + "generic", + conditional("imd", when="@:2.2.99"), + conditional("isdb", when="@2.4:"), + conditional("logmfd", when="@2.5:"), + "manyrestraints", + "mapping", + conditional("maze", when="@2.6:"), + "molfile", + "multicolvar", + conditional("opes", when="@2.7:"), + conditional("pamm", when="@2.5: optional_modules=adjmat"), + conditional("piv", when="@2.5:"), + conditional("reference", when="@:2.2.99"), + conditional("s2cm", when="@2.8:"), + conditional("sasa", when="@2.8:"), + "secondarystructure", + "setup", + "vatom", + conditional("ves", when="@2.4:"), + conditional("vesselbase", when="@:2.2.99"), + conditional("xdrfile", when="@2.8:"), + ) variant( - 'optional_modules', - values=disjoint_sets( - ('all',), - ('reset',), - single_optional_modules - ).prohibit_empty_set().with_default('all'), - description='Activates optional modules: all, reset, or custom list (advanced)' + "optional_modules", + values=disjoint_sets(("all",), ("reset",), single_optional_modules) + .prohibit_empty_set() + .with_default("all"), + description="Activates optional modules: all, reset, or custom list (advanced)", ) - variant('shared', default=True, description='Builds shared libraries') - variant('mpi', default=True, description='Activates MPI support') - variant('gsl', default=True, description='Activates GSL support') - variant('arrayfire', default='none', - values=('none', 'cpu', 'cuda', 'opencl'), - description='Activates FireArray support') + variant("shared", default=True, description="Builds shared libraries") + variant("mpi", default=True, description="Activates MPI support") + variant("gsl", default=True, description="Activates GSL support") + variant( + "arrayfire", + default="none", + values=("none", "cpu", "cuda", "opencl"), + description="Activates FireArray support", + ) # Dependencies. LAPACK and BLAS are recommended but not essential. - depends_on('zlib') - depends_on('blas') - depends_on('lapack') + depends_on("zlib") + depends_on("blas") + depends_on("lapack") # For libmatheval support through the 'function' module # which is enabled by default (or when optional_modules=all) - depends_on('libmatheval', when='@:2.4') - depends_on('arrayfire', when='arrayfire=cpu') - depends_on('arrayfire+cuda', when='arrayfire=cuda') - depends_on('arrayfire+opencl', when='arrayfire=opencl') + depends_on("libmatheval", when="@:2.4") + depends_on("arrayfire", when="arrayfire=cpu") + depends_on("arrayfire+cuda", when="arrayfire=cuda") + depends_on("arrayfire+opencl", when="arrayfire=opencl") - depends_on('mpi', when='+mpi') - depends_on('gsl', when='+gsl') + depends_on("mpi", when="+mpi") + depends_on("gsl", when="+gsl") - depends_on('autoconf', type='build') - depends_on('automake', type='build') - depends_on('libtool', type='build') - depends_on('m4', type='build') - depends_on('py-cython', type='build', when='@2.5:') + depends_on("autoconf", type="build") + depends_on("automake", type="build") + depends_on("libtool", type="build") + depends_on("m4", type="build") + depends_on("py-cython", type="build", when="@2.5:") force_autoreconf = True @@ -158,59 +167,58 @@ class Plumed(AutotoolsPackage): def apply_patch(self, other): # The name of MD engines differ slightly from the ones used in Spack - format_strings = collections.defaultdict( - lambda: '{0.name}-{0.version}' - ) - format_strings['espresso'] = 'q{0.name}-{0.version}' - format_strings['amber'] = '{0.name}{0.version}' + format_strings = collections.defaultdict(lambda: "{0.name}-{0.version}") + format_strings["espresso"] = "q{0.name}-{0.version}" + format_strings["amber"] = "{0.name}{0.version}" get_md = lambda x: format_strings[x.name].format(x) # Get available patches - plumed_patch = Executable( - os.path.join(self.spec.prefix.bin, 'plumed-patch') - ) + plumed_patch = Executable(os.path.join(self.spec.prefix.bin, "plumed-patch")) - out = plumed_patch('-q', '-l', output=str) - available = out.split(':')[-1].split() + out = plumed_patch("-q", "-l", output=str) + available = out.split(":")[-1].split() # Check that `other` is among the patchable applications if get_md(other) not in available: - msg = '{0.name}@{0.version} is not among the MD engine' - msg += ' that can be patched by {1.name}@{1.version}.\n' - msg += 'Supported engines are:\n' + msg = "{0.name}@{0.version} is not among the MD engine" + msg += " that can be patched by {1.name}@{1.version}.\n" + msg += "Supported engines are:\n" for x in available: - msg += x + '\n' + msg += x + "\n" raise RuntimeError(msg.format(other, self.spec)) # Call plumed-patch to patch executables target = format_strings[other.name].format(other) - plumed_patch('-p', '-e', target) + plumed_patch("-p", "-e", target) def setup_dependent_package(self, module, dependent_spec): # Make plumed visible from dependent packages - module.plumed = dependent_spec['plumed'].command + module.plumed = dependent_spec["plumed"].command @property def plumed_inc(self): - return os.path.join( - self.prefix.lib, 'plumed', 'src', 'lib', 'Plumed.inc' - ) + return os.path.join(self.prefix.lib, "plumed", "src", "lib", "Plumed.inc") - @run_before('autoreconf') + @run_before("autoreconf") def filter_gslcblas(self): # This part is needed to avoid linking with gsl cblas # interface which will mask the cblas interface # provided by optimized libraries due to linking order - filter_file('-lgslcblas', '', 'configure.ac') + filter_file("-lgslcblas", "", "configure.ac") def patch(self): # Ensure Spack's wrappers are used to compile the Python interface - env = 'CXX={0} LDSHARED="{0} -pthread -shared" ' \ - 'LDCXXSHARED="{0} -pthread -shared"'.format(spack_cxx) - filter_file('plumed_program_name=plumed', - '{0} plumed_program_name=plumed'.format(env), - 'src/lib/Makefile', 'python/Makefile') + env = ( + 'CXX={0} LDSHARED="{0} -pthread -shared" ' + 'LDCXXSHARED="{0} -pthread -shared"'.format(spack_cxx) + ) + filter_file( + "plumed_program_name=plumed", + "{0} plumed_program_name=plumed".format(env), + "src/lib/Makefile", + "python/Makefile", + ) def configure_args(self): spec = self.spec @@ -227,62 +235,55 @@ class Plumed(AutotoolsPackage): # The configure.ac script may detect the wrong linker for # LD_RO which causes issues at link time. Here we work around # the issue saying we have no LD_RO executable. - configure_opts = ['--disable-ld-r'] + configure_opts = ["--disable-ld-r"] # If using MPI then ensure the correct compiler wrapper is used. - if '+mpi' in spec: - configure_opts.extend([ - '--enable-mpi', - 'CXX={0}'.format(spec['mpi'].mpicxx) - ]) + if "+mpi" in spec: + configure_opts.extend(["--enable-mpi", "CXX={0}".format(spec["mpi"].mpicxx)]) # If the MPI dependency is provided by the intel-mpi package then # the following additional argument is required to allow it to # build. - if 'intel-mpi' in spec: - configure_opts.extend([ - 'STATIC_LIBS=-mt_mpi' - ]) + if "intel-mpi" in spec: + configure_opts.extend(["STATIC_LIBS=-mt_mpi"]) extra_libs = [] # Set flags to help find gsl - if '+gsl' in spec: - gsl_libs = spec['gsl'].libs - blas_libs = spec['blas'].libs - extra_libs.append( - (gsl_libs + blas_libs).ld_flags - ) + if "+gsl" in spec: + gsl_libs = spec["gsl"].libs + blas_libs = spec["blas"].libs + extra_libs.append((gsl_libs + blas_libs).ld_flags) # Set flags to help with ArrayFire - if 'arrayfire=none' not in spec: - libaf = 'arrayfire:{0}'.format(spec.variants['arrayfire'].value) + if "arrayfire=none" not in spec: + libaf = "arrayfire:{0}".format(spec.variants["arrayfire"].value) extra_libs.append(spec[libaf].libs.search_flags) if extra_libs: - configure_opts.append('LDFLAGS={0}'.format( - ' '.join(extra_libs) - )) + configure_opts.append("LDFLAGS={0}".format(" ".join(extra_libs))) # Additional arguments - configure_opts.extend([ - '--enable-shared={0}'.format('yes' if '+shared' in spec else 'no'), - '--enable-gsl={0}'.format('yes' if '+gsl' in spec else 'no'), - '--enable-af_cpu={0}'.format('yes' if 'arrayfire=cpu' in spec else 'no'), - '--enable-af_cuda={0}'.format('yes' if 'arrayfire=cuda' in spec else 'no'), - '--enable-af_ocl={0}'.format('yes' if 'arrayfire=ocl' in spec else 'no') - ]) + configure_opts.extend( + [ + "--enable-shared={0}".format("yes" if "+shared" in spec else "no"), + "--enable-gsl={0}".format("yes" if "+gsl" in spec else "no"), + "--enable-af_cpu={0}".format("yes" if "arrayfire=cpu" in spec else "no"), + "--enable-af_cuda={0}".format("yes" if "arrayfire=cuda" in spec else "no"), + "--enable-af_ocl={0}".format("yes" if "arrayfire=ocl" in spec else "no"), + ] + ) # Construct list of optional modules - optional_modules = self.spec.variants['optional_modules'].value + optional_modules = self.spec.variants["optional_modules"].value # Predefined set of modules - if 'all' in optional_modules: - selected_modules = 'all' - elif 'reset' in optional_modules: - selected_modules = 'reset' + if "all" in optional_modules: + selected_modules = "all" + elif "reset" in optional_modules: + selected_modules = "reset" # Custom set of modules else: - selected_modules = 'none' + selected_modules = "none" for mod in optional_modules: - selected_modules += ':+{0}'.format(mod) - configure_opts.append('--enable-modules={0}'.format(selected_modules)) + selected_modules += ":+{0}".format(mod) + configure_opts.append("--enable-modules={0}".format(selected_modules)) return configure_opts |