diff options
Diffstat (limited to 'var/spack/repos/builtin/packages/amber/package.py')
| -rw-r--r-- | var/spack/repos/builtin/packages/amber/package.py | 319 |
1 files changed, 159 insertions, 160 deletions
diff --git a/var/spack/repos/builtin/packages/amber/package.py b/var/spack/repos/builtin/packages/amber/package.py index 43912c9bdf..403219facc 100644 --- a/var/spack/repos/builtin/packages/amber/package.py +++ b/var/spack/repos/builtin/packages/amber/package.py @@ -11,151 +11,144 @@ from spack.package import * class Amber(Package, CudaPackage): """Amber is a suite of biomolecular simulation programs together - with Amber tools. + with Amber tools. - A manual download is required for Ambers. Spack will search your current - directory for the download files. Alternatively, add the files to a mirror - so that Spack can find them. For instructions on how to set up a mirror, see - https://spack.readthedocs.io/en/latest/mirrors.html + A manual download is required for Ambers. Spack will search your current + directory for the download files. Alternatively, add the files to a mirror + so that Spack can find them. For instructions on how to set up a mirror, see + https://spack.readthedocs.io/en/latest/mirrors.html - Note: Only certain versions of ambertools are compatible with amber. - Only the latter version of ambertools for each amber version is supported. - """ + Note: Only certain versions of ambertools are compatible with amber. + Only the latter version of ambertools for each amber version is supported. + """ homepage = "https://ambermd.org/" url = "file://{0}/Amber18.tar.bz2".format(os.getcwd()) manual_download = True - maintainers = ['hseara'] + maintainers = ["hseara"] + version("20", sha256="a4c53639441c8cc85adee397933d07856cc4a723c82c6bea585cd76c197ead75") + version("18", sha256="2060897c0b11576082d523fb63a51ba701bc7519ff7be3d299d5ec56e8e6e277") version( - '20', sha256='a4c53639441c8cc85adee397933d07856cc4a723c82c6bea585cd76c197ead75') - version( - '18', sha256='2060897c0b11576082d523fb63a51ba701bc7519ff7be3d299d5ec56e8e6e277') - version( - '16', sha256='3b7ef281fd3c46282a51b6a6deed9ed174a1f6d468002649d84bfc8a2577ae5d', - deprecated=True) + "16", + sha256="3b7ef281fd3c46282a51b6a6deed9ed174a1f6d468002649d84bfc8a2577ae5d", + deprecated=True, + ) resources = { # [version amber, version ambertools , sha256sum] - '20': ('21', 'f55fa930598d5a8e9749e8a22d1f25cab7fcf911d98570e35365dd7f262aaafd'), + "20": ("21", "f55fa930598d5a8e9749e8a22d1f25cab7fcf911d98570e35365dd7f262aaafd"), # '20': ('20', 'b1e1f8f277c54e88abc9f590e788bbb2f7a49bcff5e8d8a6eacfaf332a4890f9'), - '18': ('19', '0c86937904854b64e4831e047851f504ec45b42e593db4ded92c1bee5973e699'), - '16': ('16', '7b876afe566e9dd7eb6a5aa952a955649044360f15c1f5d4d91ba7f41f3105fa'), + "18": ("19", "0c86937904854b64e4831e047851f504ec45b42e593db4ded92c1bee5973e699"), + "16": ("16", "7b876afe566e9dd7eb6a5aa952a955649044360f15c1f5d4d91ba7f41f3105fa"), } for ver, (ambertools_ver, ambertools_checksum) in resources.items(): - resource(when='@{0}'.format(ver), - name='AmberTools', - url='file://{0}/AmberTools{1}.tar.bz2'.format( - os.getcwd(), ambertools_ver), - sha256=ambertools_checksum, - destination='', - placement='ambertools_tmpdir', - ) + resource( + when="@{0}".format(ver), + name="AmberTools", + url="file://{0}/AmberTools{1}.tar.bz2".format(os.getcwd(), ambertools_ver), + sha256=ambertools_checksum, + destination="", + placement="ambertools_tmpdir", + ) patches = [ - ('20', '1', '10780cb91a022b49ffdd7b1e2bf4a572fa4edb7745f0fc4e5d93b158d6168e42'), - ('20', '2', '9c973e3f8f33a271d60787e8862901e8f69e94e7d80cda1695f7fad7bc396093'), - ('20', '3', 'acb359dc9b1bcff7e0f1965baa9f3f3dc18eeae99c49f1103c1e2986c0bbeed8'), - ('20', '4', 'fd93c74f5ec80689023648cdd12b2c5fb21a3898c81ebc3fa256ef244932562a'), - ('20', '5', '8e46d5be28c002f560050a71f4851b01ef45a3eb66ac90d7e23553fae1370e68'), - ('20', '6', '8cf9707b3d08ad9242326f02d1861831ad782c9bfb0c46e7b1f0d4640571d5c1'), - ('20', '7', '143b6a09f774aeae8b002afffb00839212020139a11873a3a1a34d4a63fa995d'), - ('20', '8', 'a6fc6d5c8ba0aad3a8afe44d1539cc299ef78ab53721e28244198fd5425d14ad'), - ('20', '9', '5ce6b534bab869b1e9bfefa353d7f578750e54fa72c8c9d74ddf129d993e78cf'), - ('20', '10', '76a683435be7cbb860f5bd26f09a0548c2e77c5a481fc6d64b55a3a443ce481d'), - ('20', '11', 'f40b3612bd3e59efa2fa1ec06ed6fd92446ee0f1d5d99d0f7796f66b18e64060'), - ('20', '12', '194119aed03f80677c4bab78a20fc09b0b3dc17c41a57c5eb3c912b2d73b18ab'), - ('18', '1', '3cefac9a24ece99176d5d2d58fea2722de3e235be5138a128428b9260fe922ad'), - ('18', '2', '3a0707a9a59dcbffa765dcf87b68001450095c51b96ec39d21260ba548a2f66a'), - ('18', '3', '24c2e06f71ae553a408caa3f722254db2cbf1ca4db274542302184e3d6ca7015'), - ('18', '4', '51de613e8fda20cc92979265cf7179288df8c1af4202f02794ad7327fda2657b'), - ('18', '5', 'c70354bfa312603e4819efce11a242ddcc3830895453d9424f0c83f7ae98bc5b'), - ('18', '6', '3450433a8697b27e43172043be68d31515a7c7c00b2b248f84043dd70a2f59a8'), - ('18', '7', '10ba41422b7a3eb5b32bc6453231100544cf620c764ab8332c629a3b9fc749d4'), - ('18', '8', '73968dc0fd99bcbd5eae2223bd54f414879c062ac933948ba6b8b67383dc6a53'), - ('18', '9', 'e7d72fa31560f1e8ea572b8c73259d9fe512f56fbeb1b58ae014c43b9b5b6290'), - ('18', '10', '1bee419a3b0b686a729aa12515b0f96a9a8f43478ca2c01ea1661cc1698c6266'), - ('18', '11', '926557f0c137ea8dbf99a0487b25e131b12dfd39977d3e515f01f49187e6a09c'), - ('18', '12', '7e2645d539d257f7064808308048622818c9083dedfa4ac0a958cd15181231ac'), - ('18', '13', '95d2e33d0d05b8f9b6d8091d1c804271ec3a69e9aef792cc3b1ab8a2165eca3e'), - ('18', '14', 'a1adfb072f60ffcb67adb589df7c5578629441bee4ccb89ab635a6e8d7a35277'), - ('18', '15', '4deb3df329c05729561dcc7310e49059eaddc504c4210ad31fad11dc70f61742'), - ('18', '16', 'cf02f9b949127363bad1aa700ab662a3c7cf9ce0e2e4750e066d2204b9500a99'), - ('18', '17', '480300f949e0dd6402051810a9714adb388cf96e454a55346c76954cdd69413d'), - ('16', '1.txt', 'c7ef2303bb35131a48e2256c5a3c7b391efa73e2acf757d7e39760efb6320ed4'), - ('16', '2', 'a4db183f7c337a67f5d6b5015e3ae0af0d0edaa56894f0e9e3469c99708fed1c'), - ('16', '3', '5b279531c42445c6f58281dd94588460218d2258ec9013c8447f3e2b7b81bf02'), - ('16', '4', '035bddd63bc9d5fd6de26beab31887e5c14c3caa4958d2424d72f3c49832bd42'), - ('16', '5', '02d8a1fcb6baa466de4e3683afa48076394acd805f490fbbe50ab19040675136'), - ('16', '6', '69a3e64d75255d9179c98a2b3a63fe76d5be08c9fc41f27ac197663c97915113'), - ('16', '7', '0d674c907758e90a168345e6b35b7a0de79c2ead390ab372465a354fcab67d17'), - ('16', '8', 'd722c0db46af905a5bd13b60e3130c4ddfb0c9da86df0a33253e5f8d53068946'), - ('16', '9', 'b563e744fbc50c1240d23df369750879df2cec69fba933704b97a73a66d9c4f1'), - ('16', '10', '99affc65740080b7a1ab87c5c9119bf5be7cf47b2b2d8fc13407d35bd2ba6238'), - ('16', '11', '86b89dbcae80ef48720fd3c7da88cffbdabfd4021af5a827339b56a33ddae27a'), - ('16', '12', 'c8d61d1efbd44086f88d74ad9e07dfdc3737dc7053c7d2503131ba0918973a03'), - ('16', '13', '5ce28e6e0118a4780ad72fc096e617c874cde7d140e15f87451babb25aaf2d8f'), - ('16', '14', '93703e734e76da30a5e050189a66d5a4d6bec5885752503c4c798e2f44049080'), - ('16', '15', 'a156ec246cd06688043cefde24de0d715fd46b08f5c0235015c2c5c3c6e37488'), + ("20", "1", "10780cb91a022b49ffdd7b1e2bf4a572fa4edb7745f0fc4e5d93b158d6168e42"), + ("20", "2", "9c973e3f8f33a271d60787e8862901e8f69e94e7d80cda1695f7fad7bc396093"), + ("20", "3", "acb359dc9b1bcff7e0f1965baa9f3f3dc18eeae99c49f1103c1e2986c0bbeed8"), + ("20", "4", "fd93c74f5ec80689023648cdd12b2c5fb21a3898c81ebc3fa256ef244932562a"), + ("20", "5", "8e46d5be28c002f560050a71f4851b01ef45a3eb66ac90d7e23553fae1370e68"), + ("20", "6", "8cf9707b3d08ad9242326f02d1861831ad782c9bfb0c46e7b1f0d4640571d5c1"), + ("20", "7", "143b6a09f774aeae8b002afffb00839212020139a11873a3a1a34d4a63fa995d"), + ("20", "8", "a6fc6d5c8ba0aad3a8afe44d1539cc299ef78ab53721e28244198fd5425d14ad"), + ("20", "9", "5ce6b534bab869b1e9bfefa353d7f578750e54fa72c8c9d74ddf129d993e78cf"), + ("20", "10", "76a683435be7cbb860f5bd26f09a0548c2e77c5a481fc6d64b55a3a443ce481d"), + ("20", "11", "f40b3612bd3e59efa2fa1ec06ed6fd92446ee0f1d5d99d0f7796f66b18e64060"), + ("20", "12", "194119aed03f80677c4bab78a20fc09b0b3dc17c41a57c5eb3c912b2d73b18ab"), + ("18", "1", "3cefac9a24ece99176d5d2d58fea2722de3e235be5138a128428b9260fe922ad"), + ("18", "2", "3a0707a9a59dcbffa765dcf87b68001450095c51b96ec39d21260ba548a2f66a"), + ("18", "3", "24c2e06f71ae553a408caa3f722254db2cbf1ca4db274542302184e3d6ca7015"), + ("18", "4", "51de613e8fda20cc92979265cf7179288df8c1af4202f02794ad7327fda2657b"), + ("18", "5", "c70354bfa312603e4819efce11a242ddcc3830895453d9424f0c83f7ae98bc5b"), + ("18", "6", "3450433a8697b27e43172043be68d31515a7c7c00b2b248f84043dd70a2f59a8"), + ("18", "7", "10ba41422b7a3eb5b32bc6453231100544cf620c764ab8332c629a3b9fc749d4"), + ("18", "8", "73968dc0fd99bcbd5eae2223bd54f414879c062ac933948ba6b8b67383dc6a53"), + ("18", "9", "e7d72fa31560f1e8ea572b8c73259d9fe512f56fbeb1b58ae014c43b9b5b6290"), + ("18", "10", "1bee419a3b0b686a729aa12515b0f96a9a8f43478ca2c01ea1661cc1698c6266"), + ("18", "11", "926557f0c137ea8dbf99a0487b25e131b12dfd39977d3e515f01f49187e6a09c"), + ("18", "12", "7e2645d539d257f7064808308048622818c9083dedfa4ac0a958cd15181231ac"), + ("18", "13", "95d2e33d0d05b8f9b6d8091d1c804271ec3a69e9aef792cc3b1ab8a2165eca3e"), + ("18", "14", "a1adfb072f60ffcb67adb589df7c5578629441bee4ccb89ab635a6e8d7a35277"), + ("18", "15", "4deb3df329c05729561dcc7310e49059eaddc504c4210ad31fad11dc70f61742"), + ("18", "16", "cf02f9b949127363bad1aa700ab662a3c7cf9ce0e2e4750e066d2204b9500a99"), + ("18", "17", "480300f949e0dd6402051810a9714adb388cf96e454a55346c76954cdd69413d"), + ("16", "1.txt", "c7ef2303bb35131a48e2256c5a3c7b391efa73e2acf757d7e39760efb6320ed4"), + ("16", "2", "a4db183f7c337a67f5d6b5015e3ae0af0d0edaa56894f0e9e3469c99708fed1c"), + ("16", "3", "5b279531c42445c6f58281dd94588460218d2258ec9013c8447f3e2b7b81bf02"), + ("16", "4", "035bddd63bc9d5fd6de26beab31887e5c14c3caa4958d2424d72f3c49832bd42"), + ("16", "5", "02d8a1fcb6baa466de4e3683afa48076394acd805f490fbbe50ab19040675136"), + ("16", "6", "69a3e64d75255d9179c98a2b3a63fe76d5be08c9fc41f27ac197663c97915113"), + ("16", "7", "0d674c907758e90a168345e6b35b7a0de79c2ead390ab372465a354fcab67d17"), + ("16", "8", "d722c0db46af905a5bd13b60e3130c4ddfb0c9da86df0a33253e5f8d53068946"), + ("16", "9", "b563e744fbc50c1240d23df369750879df2cec69fba933704b97a73a66d9c4f1"), + ("16", "10", "99affc65740080b7a1ab87c5c9119bf5be7cf47b2b2d8fc13407d35bd2ba6238"), + ("16", "11", "86b89dbcae80ef48720fd3c7da88cffbdabfd4021af5a827339b56a33ddae27a"), + ("16", "12", "c8d61d1efbd44086f88d74ad9e07dfdc3737dc7053c7d2503131ba0918973a03"), + ("16", "13", "5ce28e6e0118a4780ad72fc096e617c874cde7d140e15f87451babb25aaf2d8f"), + ("16", "14", "93703e734e76da30a5e050189a66d5a4d6bec5885752503c4c798e2f44049080"), + ("16", "15", "a156ec246cd06688043cefde24de0d715fd46b08f5c0235015c2c5c3c6e37488"), ] for ver, num, checksum in patches: - patch_url_str = 'https://ambermd.org/bugfixes/{0}.0/update.{1}' - patch(patch_url_str.format(ver, num), - sha256=checksum, level=0, when='@{0}'.format(ver)) + patch_url_str = "https://ambermd.org/bugfixes/{0}.0/update.{1}" + patch(patch_url_str.format(ver, num), sha256=checksum, level=0, when="@{0}".format(ver)) # Patch to move the namelist sebomd after the variable declarations # Taken from http://archive.ambermd.org/202105/0098.html - patch('sebomd_fix.patch', when='@20') + patch("sebomd_fix.patch", when="@20") # Patch to add ppc64le in config.guess - patch('ppc64le.patch', when='@18: target=ppc64le:') + patch("ppc64le.patch", when="@18: target=ppc64le:") # Patch to add aarch64 in config.guess - patch('aarch64.patch', when='@18: target=aarch64:') + patch("aarch64.patch", when="@18: target=aarch64:") # Workaround to modify the AmberTools script when using the NVIDIA # compilers - patch('nvhpc.patch', when='@18: %nvhpc') + patch("nvhpc.patch", when="@18: %nvhpc") # Workaround to use NVIDIA compilers to build the bundled Boost - patch('nvhpc-boost.patch', when='@18: %nvhpc') - - variant('mpi', description='Build MPI executables', - default=True) - variant('openmp', description='Use OpenMP pragmas to parallelize', - default=False) - variant('x11', description='Build programs that require X11', - default=False) - variant('update', description='Update the sources prior compilation', - default=False) - - depends_on('zlib') - depends_on('bzip2') - depends_on('flex', type='build') - depends_on('bison', type='build') - depends_on('netcdf-fortran') - depends_on('parallel-netcdf', when='@20:') # when='AmberTools@21:' - depends_on('tcsh', type=('build'), when='@20') # when='AmberTools@21:' + patch("nvhpc-boost.patch", when="@18: %nvhpc") + + variant("mpi", description="Build MPI executables", default=True) + variant("openmp", description="Use OpenMP pragmas to parallelize", default=False) + variant("x11", description="Build programs that require X11", default=False) + variant("update", description="Update the sources prior compilation", default=False) + + depends_on("zlib") + depends_on("bzip2") + depends_on("flex", type="build") + depends_on("bison", type="build") + depends_on("netcdf-fortran") + depends_on("parallel-netcdf", when="@20:") # when='AmberTools@21:' + depends_on("tcsh", type=("build"), when="@20") # when='AmberTools@21:' # Potential issues with openmpi 4 # (http://archive.ambermd.org/201908/0105.html) - depends_on('mpi', when='+mpi') + depends_on("mpi", when="+mpi") # Cuda dependencies # /AmberTools/src/configure2:1329 - depends_on('cuda@:11.1', when='@20:+cuda') # when='AmberTools@21:' - depends_on('cuda@:10.2.89', when='@18+cuda') - depends_on('cuda@7.5.18', when='@:16+cuda') + depends_on("cuda@:11.1", when="@20:+cuda") # when='AmberTools@21:' + depends_on("cuda@:10.2.89", when="@18+cuda") + depends_on("cuda@7.5.18", when="@:16+cuda") # conflicts - conflicts('+x11', when='platform=cray', - msg='x11 amber applications not available for cray') - conflicts('+openmp', when='%clang', - msg='OpenMP not available for the clang compiler') - conflicts('+openmp', when='%apple-clang', - msg='OpenMP not available for the Apple clang compiler') - conflicts('+openmp', when='%pgi', - msg='OpenMP not available for the pgi compiler') + conflicts("+x11", when="platform=cray", msg="x11 amber applications not available for cray") + conflicts("+openmp", when="%clang", msg="OpenMP not available for the clang compiler") + conflicts( + "+openmp", when="%apple-clang", msg="OpenMP not available for the Apple clang compiler" + ) + conflicts("+openmp", when="%pgi", msg="OpenMP not available for the pgi compiler") def url_for_version(self, version): url = "file://{0}/Amber{1}.tar.bz2".format(os.getcwd(), version) @@ -163,96 +156,102 @@ class Amber(Package, CudaPackage): def setup_build_environment(self, env): amber_src = self.stage.source_path - env.set('AMBERHOME', amber_src) + env.set("AMBERHOME", amber_src) # The bundled Boost does not detect the bzip2 package, but # will silently fall back to a system install (if available). # Force it to use the bzip2 package. - env.prepend_path('CPATH', self.spec['bzip2'].prefix.include) + env.prepend_path("CPATH", self.spec["bzip2"].prefix.include) # CUDA - if self.spec.satisfies('+cuda'): - env.set('CUDA_HOME', self.spec['cuda'].prefix) + if self.spec.satisfies("+cuda"): + env.set("CUDA_HOME", self.spec["cuda"].prefix) def install(self, spec, prefix): # The resource command does not allow us to expand the package in the # root stage folder as required, as it already contains files. Here we # install AmberTools where it should be, which results in 3 copies of # the ambertools (~9 GB). This has to be improved in the future. - install_tree('ambertools_tmpdir', '.') - shutil.rmtree(join_path(self.stage.source_path, 'ambertools_tmpdir')) + install_tree("ambertools_tmpdir", ".") + shutil.rmtree(join_path(self.stage.source_path, "ambertools_tmpdir")) # Select compiler style - if self.spec.satisfies('%cce'): - compiler = 'cray' - elif self.spec.satisfies('%gcc'): - compiler = 'gnu' - elif self.spec.satisfies('%intel'): - compiler = 'intel' - elif self.spec.satisfies('%pgi'): - compiler = 'pgi' - elif self.spec.satisfies('%nvhpc'): - compiler = 'pgi' - elif self.spec.satisfies('%clang'): - compiler = 'clang' + if self.spec.satisfies("%cce"): + compiler = "cray" + elif self.spec.satisfies("%gcc"): + compiler = "gnu" + elif self.spec.satisfies("%intel"): + compiler = "intel" + elif self.spec.satisfies("%pgi"): + compiler = "pgi" + elif self.spec.satisfies("%nvhpc"): + compiler = "pgi" + elif self.spec.satisfies("%clang"): + compiler = "clang" else: - raise InstallError('Unknown compiler, exiting!!!') + raise InstallError("Unknown compiler, exiting!!!") # Alternative way to make csh/tcsh detection work with modules - filter_file(r'-x /bin/csh', 'command -v csh &> /dev/null/', - 'AmberTools/src/configure2', string=True) + filter_file( + r"-x /bin/csh", + "command -v csh &> /dev/null/", + "AmberTools/src/configure2", + string=True, + ) # Base configuration - conf = Executable('./configure') - base_args = ['--skip-python', - '--with-netcdf', self.spec['netcdf-fortran'].prefix, - ] - if self.spec.satisfies('~x11'): - base_args += ['-noX11'] + conf = Executable("./configure") + base_args = [ + "--skip-python", + "--with-netcdf", + self.spec["netcdf-fortran"].prefix, + ] + if self.spec.satisfies("~x11"): + base_args += ["-noX11"] # Update the sources: Apply all upstream patches - if self.spec.satisfies('+update'): - update = Executable('./update_amber') - update(*(['--update'])) + if self.spec.satisfies("+update"): + update = Executable("./update_amber") + update(*(["--update"])) else: - base_args += ['--no-updates'] + base_args += ["--no-updates"] # Non-x86 architecture - if self.spec.target.family != 'x86_64': - base_args += ['-nosse'] + if self.spec.target.family != "x86_64": + base_args += ["-nosse"] # Single core conf(*(base_args + [compiler])) - make('install') + make("install") # CUDA - if self.spec.satisfies('+cuda'): - conf(*(base_args + ['-cuda', compiler])) - make('install') + if self.spec.satisfies("+cuda"): + conf(*(base_args + ["-cuda", compiler])) + make("install") # MPI - if self.spec.satisfies('+mpi'): - conf(*(base_args + ['-mpi', compiler])) - make('install') + if self.spec.satisfies("+mpi"): + conf(*(base_args + ["-mpi", compiler])) + make("install") # Openmp - if self.spec.satisfies('+openmp'): - make('clean') - conf(*(base_args + ['-openmp', compiler])) - make('openmp') + if self.spec.satisfies("+openmp"): + make("clean") + conf(*(base_args + ["-openmp", compiler])) + make("openmp") # CUDA + MPI - if self.spec.satisfies('+cuda') and self.spec.satisfies('+mpi'): - make('clean') - conf(*(base_args + ['-cuda', '-mpi', compiler])) - make('install') + if self.spec.satisfies("+cuda") and self.spec.satisfies("+mpi"): + make("clean") + conf(*(base_args + ["-cuda", "-mpi", compiler])) + make("install") # just install everything that was built - install_tree('.', prefix) + install_tree(".", prefix) def setup_run_environment(self, env): - env.set('AMBER_PREFIX', self.prefix) - env.set('AMBERHOME', self.prefix) + env.set("AMBER_PREFIX", self.prefix) + env.set("AMBERHOME", self.prefix) # CUDA - if self.spec.satisfies('+cuda'): - env.prepend_path('LD_LIBRARY_PATH', self.spec['cuda'].prefix.lib) + if self.spec.satisfies("+cuda"): + env.prepend_path("LD_LIBRARY_PATH", self.spec["cuda"].prefix.lib) |