747f7decc4
- added several patches - added some missing dependencies - remove unneeded dependencies - add CUDA support - disable queue support, which was limited, and broken anyway - move package text that was specific to the package to a comment, so it does not show up the environment module - set conflicts for cuda and compilers Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
204 lines
8.9 KiB
Python
204 lines
8.9 KiB
Python
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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from spack import *
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from spack.util.environment import EnvironmentModifications
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import os
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class Fsl(Package, CudaPackage):
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"""FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI
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brain imaging data."""
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# NOTE: A manual download is required for FSL. Spack will search your
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# current directory for the download file. Alternatively, add this file to
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# a mirror so that Spack can find it. For instructions on how to set up a
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# mirror, see http://spack.readthedocs.io/en/latest/mirrors.html
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homepage = "https://fsl.fmrib.ox.ac.uk"
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url = "file://{0}/fsl-5.0.10-sources.tar.gz".format(os.getcwd())
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manual_download = True
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version('6.0.4', sha256='58b88f38e080b05d70724d57342f58e1baf56e2bd3b98506a72b4446cad5033e')
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version('5.0.10', sha256='ca183e489320de0e502a7ba63230a7f55098917a519e8c738b005d526e700842')
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depends_on('python', type=('build', 'run'))
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depends_on('expat')
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depends_on('libx11')
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depends_on('glu')
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depends_on('libiconv')
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depends_on('openblas', when='@6:')
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depends_on('vtk@:8')
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conflicts('%gcc@:4.7,5.5:')
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conflicts('^cuda@9.2:')
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conflicts('cuda_arch=none', when='+cuda',
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msg='must select a CUDA architecture')
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conflicts('platform=darwin',
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msg='currently only packaged for linux')
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patch('build_log.patch')
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patch('eddy_Makefile.patch', when='@6:')
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patch('iconv.patch')
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patch('fslpython_install_v5.patch', when='@:5')
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patch('fslpython_install_v6.patch', when='@6:')
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# These patches disable FSL's attempts to try to submit a subset of FSL
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# computations to an SGE queue system. That auto-submit mechanism only
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# works for SGE and requires someone to edit the fsl_sub script to
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# accommodate their system. These patches disable the auto submission
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# scheme and allow the fsl_sub script to behave the same on all systems,
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# and without further modification, whether the computation is submitted to
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# a "local" system, like a workstation, or as a batch job to a cluster
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# queueing system, regardless of queue system type.
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patch('fsl_sub_v5.patch', when='@:5')
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patch('fsl_sub_v6.patch', when='@6:')
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def patch(self):
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# Uncomment lines in source file to allow building from source
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with working_dir(join_path(self.stage.source_path, 'etc', 'fslconf')):
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sourced = FileFilter('fsl.sh')
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sourced.filter('#FSLCONFDIR', 'FSLCONFDIR')
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if self.spec.satisfies('@6:'):
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sourced.filter('#FSLMACHTYPE', 'FSLMACHTYPE')
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else:
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sourced.filter(r'#(FSLMACHTYPE).*', r'\1=linux_64-gcc4.8')
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if self.spec.satisfies('@:5'):
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with working_dir(join_path(self.stage.source_path, 'config',
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'common')):
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buildproj = FileFilter('buildproj')
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buildproj.filter(r'(^FSLMACHTYPE).*', r'\1=linux_64-gcc4.8')
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# Capture the settings file
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if self.spec.satisfies('@6:'):
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settings_file = join_path(self.stage.source_path, 'config',
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'buildSettings.mk')
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vtk_file = settings_file
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else:
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settings_file = join_path(self.stage.source_path, 'config',
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'linux_64-gcc4.8', 'systemvars.mk')
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externals_file = join_path(self.stage.source_path, 'config',
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'linux_64-gcc4.8', 'externallibs.mk')
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vtk_file = externals_file
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build_settings = FileFilter(settings_file)
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vtk_settings = FileFilter(vtk_file)
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build_settings.filter(r'^CUDAVER', '#CUDAVER')
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build_settings.filter(r'(^CC)\s*=.*', r'\1 = {0}'.format(spack_cc))
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build_settings.filter(r'(^CXX)\s*=.*', r'\1 = {0}'.format(spack_cxx))
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build_settings.filter(r'(^CXX11)\s*=.*', r'\1 = {0}'.format(spack_cxx))
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vtk_suffix = self.spec['vtk'].version.up_to(2)
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vtk_lib_dir = self.spec['vtk'].prefix.lib64
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vtk_include_dir = join_path(self.spec['vtk'].prefix.include,
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'vtk-{0}'.format(vtk_suffix))
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vtk_settings.filter(r'(^VTKDIR_INC)\s*=.*',
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r'\1 = {0}'.format(vtk_include_dir))
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vtk_settings.filter(r'(^VTKDIR_LIB)\s*=.*',
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r'\1 = {0}'.format(vtk_lib_dir))
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vtk_settings.filter(r'(^VTKSUFFIX)\s*=.*',
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r'\1 = -{0}'.format(vtk_suffix))
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if '+cuda' in self.spec:
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cuda_arch = self.spec.variants['cuda_arch'].value
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cuda_gencode = ' '.join(self.cuda_flags(cuda_arch))
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cuda_installation = self.spec['cuda'].prefix
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build_settings.filter(r'(^CUDA_INSTALLATION)\s*=.*',
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r'\1 = {0}'.format(cuda_installation))
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build_settings.filter(r'(^LIB_CUDA)\s*=.*',
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r'\1 = {0}'.format(
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join_path(
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cuda_installation,
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'lib64')))
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build_settings.filter(r'(^INC_CUDA)\s*=.*',
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r'\1 = {0}'.format(
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join_path(
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cuda_installation,
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'include')))
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build_settings.filter(r'(^NVCC11)\s*=.*',
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r'\1 = {0}'.format(
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join_path(
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cuda_installation, 'bin',
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'nvcc')))
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build_settings.filter(r'(^NVCC)\s*=.*',
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r'\1 = {0}'.format(
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join_path(
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cuda_installation, 'bin',
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'nvcc')))
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build_settings.filter(r'(^GENCODE_FLAGS)\s*=.*',
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r'\1 = {0}'.format(cuda_gencode))
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if self.spec.satisfies('@6:'):
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build_settings.filter(r'(^EDDYBUILDPARAMETERS)\s*=.*',
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r'\1 = "cuda=1" "cpu=1"')
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build_settings.filter(r'(^fdt_MASTERBUILD)\s*=.*',
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r'\1 = COMPILE_GPU=1')
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build_settings.filter(r'(^ptx2_MASTERBUILD)\s*=.*',
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r'\1 = COMPILE_GPU=1')
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else:
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with open(settings_file, 'a') as f:
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f.write('COMPILE_GPU=1\n')
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else:
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build_settings.filter(r'^CUDA_INSTALLATION', '#CUDA_INSTALLATION')
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build_settings.filter(r'^GENCODE_FLAGS', '#GENCODE_FLAGS')
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build_settings.filter(r'^LIB_CUDA', '#LIB_CUDA')
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build_settings.filter(r'^INC_CUDA', '#INC_CUDA')
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build_settings.filter(r'^NVCC', '#NVCC')
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if self.spec.satisfies('@6:'):
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build_settings.filter(r'(^EDDYBUILDPARAMETERS)\s*=.*',
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r'\1 = "cpu=1"')
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build_settings.filter(r'(^fdt_MASTERBUILD)\s*=.*',
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r'\1 = COMPILE_GPU=0')
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build_settings.filter(r'(^ptx2_MASTERBUILD)\s*=.*',
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r'\1 = COMPILE_GPU=0')
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def install(self, spec, prefix):
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build = Executable('./build')
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build()
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install_tree('.', prefix)
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@run_after('install')
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def postinstall(self):
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# The PYTHON related environment variables need to be unset here so
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# the post install script does not get confused.
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vars_to_unset = ['PYTHONPATH', 'PYTHONHOME']
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with spack.util.environment.preserve_environment(*vars_to_unset):
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for v in vars_to_unset:
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del os.environ[v]
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script = Executable(join_path(prefix, 'etc', 'fslconf',
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'post_install.sh'))
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script('-f', prefix)
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def setup_build_environment(self, env):
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if not self.stage.source_path:
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self.stage.fetch()
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self.stage.expand_archive()
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env.set('FSLDIR', self.stage.source_path)
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# Below is for sourcing purposes during building
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fslsetup = join_path(self.stage.source_path, 'etc', 'fslconf',
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'fsl.sh')
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if os.path.isfile(fslsetup):
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env.extend(EnvironmentModifications.from_sourcing_file(fslsetup))
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def setup_run_environment(self, env):
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# Set the environment variables after copying tree
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env.set('FSLDIR', self.prefix)
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fslsetup = join_path(self.prefix, 'etc', 'fslconf', 'fsl.sh')
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if os.path.isfile(fslsetup):
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env.extend(EnvironmentModifications.from_sourcing_file(fslsetup))
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