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# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import os
import shutil
from spack import *
class Amber(Package, CudaPackage):
"""Amber is a suite of biomolecular simulation programs together
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
http://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.
"""
homepage = "http://ambermd.org/"
url = "file://{0}/Amber18.tar.bz2".format(os.getcwd())
manual_download = True
maintainers = ['hseara']
version(
'20', sha256='a4c53639441c8cc85adee397933d07856cc4a723c82c6bea585cd76c197ead75')
version(
'18', sha256='2060897c0b11576082d523fb63a51ba701bc7519ff7be3d299d5ec56e8e6e277')
version(
'16', sha256='3b7ef281fd3c46282a51b6a6deed9ed174a1f6d468002649d84bfc8a2577ae5d',
deprecated=True)
resources = {
# [version amber, version ambertools , sha256sum]
'20': ('20', 'b1e1f8f277c54e88abc9f590e788bbb2f7a49bcff5e8d8a6eacfaf332a4890f9'),
'18': ('19', '0c86937904854b64e4831e047851f504ec45b42e593db4ded92c1bee5973e699'),
'16': ('16', '7b876afe566e9dd7eb6a5aa952a955649044360f15c1f5d4d91ba7f41f3105fa'),
}
for ver, (ambertools_ver, ambertools_checksum) in resources.items():
resource(when='@{0}'.format(ver),
name='AmberTools',
url='http://ambermd.org/downloads/AmberTools{0}.tar.bz2'.format(
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'),
('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 to add ppc64le in config.guess
patch('ppc64le.patch', when='@18: target=ppc64le')
# Patch to add aarch64 in config.guess
patch('aarch64.patch', when='@18: target=aarch64')
# Workaround to modify the AmberTools script when using the NVIDIA
# compilers
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')
# Potential issues with openmpi 4
# (http://archive.ambermd.org/201908/0105.html)
depends_on('mpi', when='+mpi')
# Cuda dependencies
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')
def setup_build_environment(self, env):
amber_src = self.stage.source_path
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)
# CUDA
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'))
# 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'
else:
raise InstallError('Unknown compiler, exiting!!!')
# Base configuration
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']))
else:
base_args += ['--no-updates']
# Non-x86 architecture
if self.spec.target.family != 'x86_64':
base_args += ['-nosse']
# 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)
|
