summaryrefslogtreecommitdiff
path: root/var/spack/repos/builtin/packages/fsl/package.py
diff options
context:
space:
mode:
Diffstat (limited to 'var/spack/repos/builtin/packages/fsl/package.py')
-rw-r--r--var/spack/repos/builtin/packages/fsl/package.py184
1 files changed, 152 insertions, 32 deletions
diff --git a/var/spack/repos/builtin/packages/fsl/package.py b/var/spack/repos/builtin/packages/fsl/package.py
index 35f4978698..5511096e53 100644
--- a/var/spack/repos/builtin/packages/fsl/package.py
+++ b/var/spack/repos/builtin/packages/fsl/package.py
@@ -8,42 +8,157 @@ from spack.util.environment import EnvironmentModifications
import os
-class Fsl(Package):
+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 a mirror so that Spack can find it.
- For instructions on how to set up a mirror, see
- http://spack.readthedocs.io/en/latest/mirrors.html"""
+ # 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 http://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('5.0.10', '64823172a08aad679833240ba64c8e30')
+ 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('zlib')
- depends_on('libpng')
- depends_on('boost')
- depends_on('sqlite')
-
- conflicts('%gcc@6:', when='@5.0.10')
+ depends_on('libiconv')
+ depends_on('openblas', when='@6:')
+ depends_on('vtk@:8')
+
+ conflicts('%gcc@:4.7,5.5:')
+ conflicts('^cuda@9.2:')
+ 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:')
+ patch('iconv.patch')
+ patch('fslpython_install_v5.patch', when='@:5')
+ patch('fslpython_install_v6.patch', when='@6:')
+
+ # 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')
- sourced.filter('#FSLMACHTYPE', 'FSLMACHTYPE')
- # Fix error in build script
- buildscript = FileFilter('build')
- buildscript.filter('mist-clean', 'mist')
+
+ 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')
def install(self, spec, prefix):
build = Executable('./build')
@@ -51,6 +166,20 @@ class Fsl(Package):
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()
@@ -66,18 +195,9 @@ class Fsl(Package):
env.extend(EnvironmentModifications.from_sourcing_file(fslsetup))
def setup_run_environment(self, env):
- # Here, run-time environment variables are being set manually.
- # Normally these would be added to the modulefile at build-time
- # by sourcing fsl.sh, but incorrect paths were being set, pointing to
- # the staging directory rather than the install directory.
+ # Set the environment variables after copying tree
env.set('FSLDIR', self.prefix)
- env.set('FSLOUTPUTTYPE', 'NIFTI_GZ')
- env.set('FSLMULTIFILEQUIT', 'TRUE')
- env.set('FSLTCLSH', self.prefix.bin.fsltclsh)
- env.set('FSLWISH', self.prefix.bin.fslwish)
- env.set('FSLLOCKDIR', '')
- env.set('FSLMACHINELIST', '')
- env.set('FSLREMOTECALL', '')
- env.set('FSLGECUDAQ', 'cuda.q')
-
- env.prepend_path('PATH', 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 v1.2.3-70-g09d2 (git 2.46.0) at 2024-09-13 08:29:35 +0000