diff options
Diffstat (limited to 'var')
| -rw-r--r-- | var/spack/repos/builtin/packages/amber/package.py | 205 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/dealii/package.py | 4 |
2 files changed, 159 insertions, 50 deletions
diff --git a/var/spack/repos/builtin/packages/amber/package.py b/var/spack/repos/builtin/packages/amber/package.py index 93af77bbbc..e33f04c3a1 100644 --- a/var/spack/repos/builtin/packages/amber/package.py +++ b/var/spack/repos/builtin/packages/amber/package.py @@ -5,6 +5,7 @@ from spack import * import os +import shutil class Amber(Package, CudaPackage): @@ -17,63 +18,171 @@ class Amber(Package, CudaPackage): http://spack.readthedocs.io/en/latest/mirrors.html""" homepage = "http://ambermd.org/" - url = "file://{0}/Amber16.tar.bz2".format(os.getcwd()) + url = "file://{0}/Amber18.tar.bz2".format(os.getcwd()) + maintainers = ['hseara'] + version('18', sha256='2060897c0b11576082d523fb63a51ba701bc7519ff7be3d299d5ec56e8e6e277') version('16', sha256='3b7ef281fd3c46282a51b6a6deed9ed174a1f6d468002649d84bfc8a2577ae5d') - variant('mpi', description='Build MPI executables', default=True) + resources = [ + # [version amber, version ambertools , sha256sum] + ('18', '19', '0c86937904854b64e4831e047851f504ec45b42e593db4ded92c1bee5973e699'), + ('16', '16', '7b876afe566e9dd7eb6a5aa952a955649044360f15c1f5d4d91ba7f41f3105fa'), + ] + for ver, ambertools_ver, checksum in resources: + resource(when='@{0}'.format(ver), + name='AmberTools', + url='file://{0}/AmberTools{1}.tar.bz2'.format(os.getcwd(), + ambertools_ver), + sha256=checksum, + destination='', + placement='ambertools_tmpdir', + ) + + patches = [ + ('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)) + + 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) - resource( - name='AmberTools', - sha256='7b876afe566e9dd7eb6a5aa952a955649044360f15c1f5d4d91ba7f41f3105fa', - url='file://{0}/AmberTools16.tar.bz2'.format(os.getcwd()), - destination='.', - ) - - depends_on('mpi', when='+mpi') - depends_on('cuda@7.5.18', when='+cuda') - - depends_on('netcdf-fortran') - depends_on('python+tkinter@2.7:2.8', type=('build', 'run')) - depends_on('py-numpy', type=('build', 'run')) - depends_on('py-scipy', type=('build', 'run')) - depends_on('py-matplotlib@:2.9', type=('build', 'run')) depends_on('zlib') + depends_on('flex', type='build') + depends_on('bison', type='build') + depends_on('netcdf-fortran') + # Potential issues with openmpi 4 + # (http://archive.ambermd.org/201908/0105.html) + depends_on('mpi', when='+mpi') - def setup_run_environment(self, env): - sp_dir = join_path(self.prefix, 'python2.7/site-packages') - - env.set('AMBERHOME', self.prefix) - env.prepend_path('PYTHONPATH', sp_dir) + # Cuda dependencies + depends_on('cuda@:10.1.243', 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 optimizations not available for the clang compiler') + conflicts('+openmp', when='%pgi', + msg='openmp optimizations not available for the pgi compiler') + + def setup_build_environment(self, env): + amber_src = self.stage.source_path + env.set('AMBERHOME', amber_src) + # CUDA + if self.spec.satisfies('+cuda'): + env.set('CUDA_HOME', self.spec['cuda'].prefix) def install(self, spec, prefix): - # install AmberTools where it should be - install_tree('amber16', '.') - - base_args = [ - '-noX11', - '--no-updates', - '--skip-python', - '--with-netcdf', self.spec['netcdf-fortran'].prefix - ] - - configure_env = { - 'AMBERHOME': self.stage.source_path, - 'CUDA_HOME': self.spec['cuda'].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')) + + # 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('%clang'): + compiler = 'clang' + else: + raise InstallError('Unknown compiler, exiting!!!') + + # Base configuration conf = Executable('./configure') - - conf(*(base_args + ['gnu']), extra_env=configure_env) - make('install', extra_env=configure_env) - - if '+mpi' in spec: - conf(*(base_args + ['-mpi', 'gnu']), extra_env=configure_env) - make('install', extra_env=configure_env) - - if '+cuda' in spec: - conf(*(base_args + ['-cuda', 'gnu']), extra_env=configure_env) - make('install', extra_env=configure_env) + 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'])) + else: + base_args += ['--no-updates'] + + # Single core + conf(*(base_args + [compiler])) + make('install') + + # CUDA + 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') + + # 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') # just install everything that was built install_tree('.', prefix) + + def setup_run_environment(self, env): + 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) diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py index 3dc407fa11..f44b25e539 100644 --- a/var/spack/repos/builtin/packages/dealii/package.py +++ b/var/spack/repos/builtin/packages/dealii/package.py @@ -97,7 +97,7 @@ class Dealii(CMakePackage, CudaPackage): patch('boost_1.68.0.patch', level=1, when='@1.68.0'), - ], + ], when='~python') depends_on('boost@1.59.0:1.63,1.65.1,1.67.0:+thread+system+serialization+iostreams+python', patches=[patch('boost_1.65.1_singleton.patch', @@ -106,7 +106,7 @@ class Dealii(CMakePackage, CudaPackage): patch('boost_1.68.0.patch', level=1, when='@1.68.0'), - ], + ], when='+python') # bzip2 is not needed since 9.0 depends_on('bzip2', when='@:8.99') |