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-rw-r--r--var/spack/repos/builtin/packages/fsl/package.py270
1 files changed, 125 insertions, 145 deletions
diff --git a/var/spack/repos/builtin/packages/fsl/package.py b/var/spack/repos/builtin/packages/fsl/package.py
index e5df50f058..9dea6e9386 100644
--- a/var/spack/repos/builtin/packages/fsl/package.py
+++ b/var/spack/repos/builtin/packages/fsl/package.py
@@ -12,7 +12,7 @@ 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."""
+ 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
@@ -20,40 +20,40 @@ class Fsl(Package, CudaPackage):
# 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())
+ 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')
+ 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)
+ 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')
+ 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
@@ -63,167 +63,147 @@ class Fsl(Package, CudaPackage):
# 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:')
+ 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')
+ 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')
+ if self.spec.satisfies("@6:"):
+ sourced.filter("#FSLMACHTYPE", "FSLMACHTYPE")
else:
- sourced.filter(r'#(FSLMACHTYPE).*', r'\1=linux_64-gcc4.8')
+ 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')
+ 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')
+ 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')
+ 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')
+ 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')
+ 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'))
+ 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 = 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'))
+ 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)
+ install_tree(".", prefix)
- @run_after('install')
+ @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']
+ 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)
+ 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)
+ 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')
+ 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')
+ 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))
generated by cgit v1.2.3-60-g2f50 (git 2.42.0) at 2024-07-16 23:49:48 +0000