spack/var/spack/repos/builtin/packages/fsl/package.py
2022-01-14 22:50:21 -08:00

230 lines
10 KiB
Python

# Copyright 2013-2022 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 glob
import os
from spack import *
from spack.util.environment import EnvironmentModifications
class Fsl(Package, CudaPackage):
"""FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI
brain imaging data."""
# NOTE: A manual download is required for FSL. Spack will search your
# current directory for the download file. Alternatively, add this file to
# a mirror so that Spack can find it. For instructions on how to set up a
# mirror, see https://spack.readthedocs.io/en/latest/mirrors.html
homepage = "https://fsl.fmrib.ox.ac.uk"
url = "file://{0}/fsl-5.0.10-sources.tar.gz".format(os.getcwd())
manual_download = True
version('6.0.5', sha256='df12b0b1161a26470ddf04e4c5d5d81580a04493890226207667ed8fd2b4b83f')
version('6.0.4', sha256='58b88f38e080b05d70724d57342f58e1baf56e2bd3b98506a72b4446cad5033e')
version('5.0.10', sha256='ca183e489320de0e502a7ba63230a7f55098917a519e8c738b005d526e700842')
depends_on('python', type=('build', 'run'))
depends_on('expat')
depends_on('libx11')
depends_on('glu')
depends_on('libiconv')
depends_on('openblas', when='@6:')
depends_on('vtk@:8')
conflicts('cuda_arch=none', when='+cuda',
msg='must select a CUDA architecture')
conflicts('platform=darwin',
msg='currently only packaged for linux')
patch('build_log.patch')
patch('eddy_Makefile.patch', when='@6.0.4')
patch('iconv.patch')
patch('fslpython_install_v5.patch', when='@:5')
patch('fslpython_install_v604.patch', when='@6.0.4')
patch('fslpython_install_v605.patch', when='@6.0.5')
# Allow fsl to use newer versions of cuda
patch('https://aur.archlinux.org/cgit/aur.git/plain/005-fix_cuda_thrust_include.patch?h=fsl',
sha256='9471addfc2f880350eedadcb99cb8b350abf42be1c0652ccddf49e34e5e48734',
level=2)
# allow newer compilers
patch('libxmlpp_bool.patch')
# These patches disable FSL's attempts to try to submit a subset of FSL
# computations to an SGE queue system. That auto-submit mechanism only
# works for SGE and requires someone to edit the fsl_sub script to
# accommodate their system. These patches disable the auto submission
# scheme and allow the fsl_sub script to behave the same on all systems,
# and without further modification, whether the computation is submitted to
# a "local" system, like a workstation, or as a batch job to a cluster
# queueing system, regardless of queue system type.
patch('fsl_sub_v5.patch', when='@:5')
patch('fsl_sub_v6.patch', when='@6:')
def patch(self):
# Uncomment lines in source file to allow building from source
with working_dir(join_path(self.stage.source_path, 'etc', 'fslconf')):
sourced = FileFilter('fsl.sh')
sourced.filter('#FSLCONFDIR', 'FSLCONFDIR')
if self.spec.satisfies('@6:'):
sourced.filter('#FSLMACHTYPE', 'FSLMACHTYPE')
else:
sourced.filter(r'#(FSLMACHTYPE).*', r'\1=linux_64-gcc4.8')
if self.spec.satisfies('@:5'):
with working_dir(join_path(self.stage.source_path, 'config',
'common')):
buildproj = FileFilter('buildproj')
buildproj.filter(r'(^FSLMACHTYPE).*', r'\1=linux_64-gcc4.8')
# Capture the settings file
if self.spec.satisfies('@6:'):
settings_file = join_path(self.stage.source_path, 'config',
'buildSettings.mk')
vtk_file = settings_file
else:
settings_file = join_path(self.stage.source_path, 'config',
'linux_64-gcc4.8', 'systemvars.mk')
externals_file = join_path(self.stage.source_path, 'config',
'linux_64-gcc4.8', 'externallibs.mk')
vtk_file = externals_file
build_settings = FileFilter(settings_file)
vtk_settings = FileFilter(vtk_file)
build_settings.filter(r'^CUDAVER', '#CUDAVER')
build_settings.filter(r'(^CC)\s*=.*', r'\1 = {0}'.format(spack_cc))
build_settings.filter(r'(^CXX)\s*=.*', r'\1 = {0}'.format(spack_cxx))
build_settings.filter(r'(^CXX11)\s*=.*', r'\1 = {0}'.format(spack_cxx))
vtk_suffix = self.spec['vtk'].version.up_to(2)
vtk_lib_dir = self.spec['vtk'].prefix.lib64
vtk_include_dir = join_path(self.spec['vtk'].prefix.include,
'vtk-{0}'.format(vtk_suffix))
vtk_settings.filter(r'(^VTKDIR_INC)\s*=.*',
r'\1 = {0}'.format(vtk_include_dir))
vtk_settings.filter(r'(^VTKDIR_LIB)\s*=.*',
r'\1 = {0}'.format(vtk_lib_dir))
vtk_settings.filter(r'(^VTKSUFFIX)\s*=.*',
r'\1 = -{0}'.format(vtk_suffix))
if '+cuda' in self.spec:
cuda_arch = self.spec.variants['cuda_arch'].value
cuda_gencode = ' '.join(self.cuda_flags(cuda_arch))
cuda_installation = self.spec['cuda'].prefix
build_settings.filter(r'(^CUDA_INSTALLATION)\s*=.*',
r'\1 = {0}'.format(cuda_installation))
build_settings.filter(r'(^LIB_CUDA)\s*=.*',
r'\1 = {0}'.format(
join_path(
cuda_installation,
'lib64')))
build_settings.filter(r'(^INC_CUDA)\s*=.*',
r'\1 = {0}'.format(
join_path(
cuda_installation,
'include')))
build_settings.filter(r'(^NVCC11)\s*=.*',
r'\1 = {0}'.format(
join_path(
cuda_installation, 'bin',
'nvcc')))
build_settings.filter(r'(^NVCC)\s*=.*',
r'\1 = {0}'.format(
join_path(
cuda_installation, 'bin',
'nvcc')))
build_settings.filter(r'(^GENCODE_FLAGS)\s*=.*',
r'\1 = {0}'.format(cuda_gencode))
if self.spec.satisfies('@6:'):
build_settings.filter(r'(^EDDYBUILDPARAMETERS)\s*=.*',
r'\1 = "cuda=1" "cpu=1"')
build_settings.filter(r'(^fdt_MASTERBUILD)\s*=.*',
r'\1 = COMPILE_GPU=1')
build_settings.filter(r'(^ptx2_MASTERBUILD)\s*=.*',
r'\1 = COMPILE_GPU=1')
else:
with open(settings_file, 'a') as f:
f.write('COMPILE_GPU=1\n')
else:
build_settings.filter(r'^CUDA_INSTALLATION', '#CUDA_INSTALLATION')
build_settings.filter(r'^GENCODE_FLAGS', '#GENCODE_FLAGS')
build_settings.filter(r'^LIB_CUDA', '#LIB_CUDA')
build_settings.filter(r'^INC_CUDA', '#INC_CUDA')
build_settings.filter(r'^NVCC', '#NVCC')
if self.spec.satisfies('@6:'):
build_settings.filter(r'(^EDDYBUILDPARAMETERS)\s*=.*',
r'\1 = "cpu=1"')
build_settings.filter(r'(^fdt_MASTERBUILD)\s*=.*',
r'\1 = COMPILE_GPU=0')
build_settings.filter(r'(^ptx2_MASTERBUILD)\s*=.*',
r'\1 = COMPILE_GPU=0')
filter_file(r'(configure_opts=".*)"',
r'\1 --x-includes={0} --x-libraries={1}"'.format(
self.spec['libx11'].prefix.include,
self.spec['libx11'].prefix.lib),
join_path('extras', 'src', 'tk', 'unix', 'fslconfigure'))
filter_file(r' -L/lib64',
r'',
join_path('src', 'fabber_core', 'Makefile'))
def install(self, spec, prefix):
build = Executable(join_path(self.stage.source_path, 'build'))
build()
rm = which('rm')
for file in glob.glob('build*'):
rm('-f', file)
rm('-r', '-f', 'src')
rm('-r', '-f', join_path('extras', 'src'))
rm('-r', '-f', join_path('extras', 'include'))
install_tree('.', prefix)
@run_after('install')
def postinstall(self):
# The PYTHON related environment variables need to be unset here so
# the post install script does not get confused.
vars_to_unset = ['PYTHONPATH', 'PYTHONHOME']
with spack.util.environment.preserve_environment(*vars_to_unset):
for v in vars_to_unset:
del os.environ[v]
script = Executable(join_path(prefix, 'etc', 'fslconf',
'post_install.sh'))
script('-f', prefix)
def setup_build_environment(self, env):
if not self.stage.source_path:
self.stage.fetch()
self.stage.expand_archive()
env.set('FSLDIR', self.stage.source_path)
# Below is for sourcing purposes during building
fslsetup = join_path(self.stage.source_path, 'etc', 'fslconf',
'fsl.sh')
if os.path.isfile(fslsetup):
env.extend(EnvironmentModifications.from_sourcing_file(fslsetup))
def setup_run_environment(self, env):
# Set the environment variables after copying tree
env.set('FSLDIR', self.prefix)
fslsetup = join_path(self.prefix, 'etc', 'fslconf', 'fsl.sh')
if os.path.isfile(fslsetup):
env.extend(EnvironmentModifications.from_sourcing_file(fslsetup))