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fsl: updated package, added v6.0.4 (#20201)

Browse Source 
- 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>
This commit is contained in:
Glenn Johnson 2020-12-29 01:27:26 -06:00 committed by GitHub
parent 6c9272677b
commit 747f7decc4
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
8 changed files with 409 additions and 30 deletions
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11
var/spack/repos/builtin/packages/fsl/build_log.patch Normal file
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@ -0,0 +1,11 @@
--- a/build 2020-06-29 10:30:36.000000000 -0500
+++ b/build 2020-11-02 12:34:25.408157699 -0600
@@ -158,7 +158,7 @@
fi #full build
echo "Building projects - see build.log file for progress..."
-./config/common/buildproj $PROJECTS > ./build.log 2>&1
+./config/common/buildproj $PROJECTS
finalStatus=$?
if [ $finalStatus -eq 0 ]; then
echo "Build completed successfully.";

11
var/spack/repos/builtin/packages/fsl/eddy_Makefile.patch Normal file
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@ -0,0 +1,11 @@
--- a/src/eddy/Makefile 2020-07-22 09:11:14.000000000 -0500
+++ b/src/eddy/Makefile 2020-11-10 23:31:09.898903635 -0600
@@ -46,7 +46,7 @@
CUDACXXFLAGS=-DCOMPILE_GPU
CUDAOBJS=CBFKernelDefinitions.o CBFSparseDiagonalMatrix.o CBFSplineField.o LSResampler_cuda.o DiffusionGP_cuda.o PostEddyCF_cuda.o EddyGpuUtils.o EddyInternalGpuUtils.o CudaVolume.o EddyMatrixKernels.o EddyKernels.o GpuPredictorChunk.o StackResampler.o DerivativeCalculator.o
- CUDALDFLAGS= -Xlinker -rpath $(LIB_CUDA) -L$(LIB_CUDA) -lcublas -lcudart
+ CUDALDFLAGS= -Xlinker -rpath -Xlinker $(LIB_CUDA) -L$(LIB_CUDA) -lcublas -lcudart
ifeq ($(fastbuild),1)
GENCODE_FLAGS := -gencode arch=compute_30,code=sm_30
endif

66
var/spack/repos/builtin/packages/fsl/fsl_sub_v5.patch Normal file
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@ -0,0 +1,66 @@
--- a/src/sgeutils/fsl_sub 2017-04-24 05:19:14.000000000 -0500
+++ b/src/sgeutils/fsl_sub 2020-11-15 17:42:28.100657607 -0600
@@ -80,7 +80,7 @@
# "NONE". Note that a user can unset SGE_ROOT if they don't want the
# cluster to be used.
###########################################################################
-METHOD=SGE
+METHOD=NONE
unset module
if [ "x$SGE_ROOT" = "x" ] ; then
METHOD=NONE
@@ -141,7 +141,9 @@
usage ()
{
- cat <<EOF
+ case $METHOD in
+ SGE)
+ cat <<EOF
$command V1.1 - wrapper for job control system such as SGE
@@ -186,7 +188,23 @@
bigmem.q: This queue is like the verylong.q but has no memory limits.
EOF
+ ;;
+ NONE)
+ cat <<EOF
+$command V1.1 - wrapper for job control system such as SGE
+
+Usage: $command [options] <command>
+
+$command gzip *.img *.hdr
+
+ -t <filename> Specify a task file of commands to execute in parallel
+ -l <logdirname> Where to output logfiles
+ -v Verbose mode.
+
+EOF
+ ;;
+ esac
exit 1
}
@@ -195,8 +213,17 @@
usage
fi
-set -- `getopt T:q:a:p:M:j:t:z:N:R:Fvm:l:s: $*`
-result=$?
+case $METHOD in
+ SGE)
+ set -- `getopt T:q:a:p:M:j:t:z:N:R:Fvm:l:s: $*`
+ result=$?
+ ;;
+ NONE)
+ set -- `getopt t:vl: $*`
+ result=$?
+ ;;
+esac
+
if [ $result != 0 ] ; then
echo "What? Your arguments make no sense!"
fi

86
var/spack/repos/builtin/packages/fsl/fsl_sub_v6.patch Normal file
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@ -0,0 +1,86 @@
--- a/src/sgeutils/fsl_sub 2020-07-25 09:36:17.000000000 -0500
+++ b/src/sgeutils/fsl_sub 2020-11-15 17:04:41.484972803 -0600
@@ -81,7 +81,7 @@
# "NONE". Note that a user can unset SGE_ROOT if they don't want the
# cluster to be used.
###########################################################################
-METHOD=SGE
+METHOD=NONE
unset module
if [[ "x$SGE_ROOT" = "x" ]] ; then
METHOD=NONE
@@ -145,7 +145,10 @@
usage ()
{
- cat <<EOF
+ case "$METHOD" in
+ SGE)
+
+ cat <<EOF
$command V1.1 - wrapper for job control system such as SGE
@@ -190,7 +193,24 @@
bigmem.q: This queue is like the verylong.q but has no memory limits.
EOF
+ ;;
+ NONE)
+
+ cat <<EOF
+$command V1.1 - wrapper for job control system such as SGE
+
+Usage: $command [options] <command>
+
+$command gzip *.img *.hdr
+
+ -t <filename> Specify a task file of commands to execute in parallel
+ -l <logdirname> Where to output logfiles
+ -v Verbose mode.
+
+EOF
+ ;;
+ esac
exit 1
}
@@ -199,14 +219,29 @@
usage
fi
-#if the newer whitespace-safe getopt format is available, use it
-if [[ $(getopt -T >/dev/null 2>&1; echo $?) == 4 ]]; then
- eval set -- $(getopt -s bash T:q:a:p:M:j:t:z:N:R:Fvm:l:s: "$@")
- result=$?
-else
- set -- $(getopt T:q:a:p:M:j:t:z:N:R:Fvm:l:s: "$@")
- result=$?
-fi
+case "$METHOD" in
+ SGE)
+ #if the newer whitespace-safe getopt format is available, use it
+ if [[ $(getopt -T >/dev/null 2>&1; echo $?) == 4 ]]; then
+ eval set -- $(getopt -s bash T:q:a:p:M:j:t:z:N:R:Fvm:l:s: "$@")
+ result=$?
+ else
+ set -- $(getopt T:q:a:p:M:j:t:z:N:R:Fvm:l:s: "$@")
+ result=$?
+ fi
+ ;;
+ NONE)
+ #if the newer whitespace-safe getopt format is available, use it
+ if [[ $(getopt -T >/dev/null 2>&1; echo $?) == 4 ]]; then
+ eval set -- $(getopt -s bash t:vl: "$@")
+ result=$?
+ else
+ set -- $(getopt t:vl: "$@")
+ result=$?
+ fi
+ ;;
+esac
+
if [[ "$result" != 0 ]] ; then
echo "What? Your arguments make no sense!"
fi

18
var/spack/repos/builtin/packages/fsl/fslpython_install_v5.patch Normal file
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@ -0,0 +1,18 @@
--- a/etc/fslconf/fslpython_install.sh 2017-04-07 10:29:52.000000000 -0500
+++ b/etc/fslconf/fslpython_install.sh 2020-11-12 13:34:06.665816528 -0600
@@ -129,7 +129,7 @@
exit 2
fi
-curl_opts='--fail' # Returns 22 on error
+curl_opts='--fail -L' # Returns 22 on error
if [ ${quiet} -eq 1 ]; then
curl_opts="${curl_opts} -s"
fi
@@ -184,4 +184,4 @@
# binary into $FSLDIR/bin/
ln -sf "${fslpython_env_dir}/bin/python" "${fsl_dir}/bin/fslpython"
rm "${miniconda_install_log}"
-drop_sudo rmdir "${miniconda_tmp}"
\ No newline at end of file
+drop_sudo rmdir "${miniconda_tmp}"

39
var/spack/repos/builtin/packages/fsl/fslpython_install_v6.patch Normal file
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@ -0,0 +1,39 @@
--- a/etc/fslconf/fslpython_install.sh 2020-07-25 09:20:04.000000000 -0500
+++ b/etc/fslconf/fslpython_install.sh 2020-11-09 20:12:59.458736979 -0600
@@ -204,19 +204,19 @@
# - https://github.com/conda/conda/issues/8804
# Try to make downloads more resilient
-"${miniconda_bin_dir}/conda" config --file "${miniconda_root_dir}"/.condarc --set remote_read_timeout_secs 240
-"${miniconda_bin_dir}/conda" config --file "${miniconda_root_dir}"/.condarc --set remote_connect_timeout_secs 20
-"${miniconda_bin_dir}/conda" config --file "${miniconda_root_dir}"/.condarc --set remote_max_retries 10
-"${miniconda_bin_dir}/conda" config --file "${miniconda_root_dir}"/.condarc --set remote_backoff_factor 5
-"${miniconda_bin_dir}/conda" config --file "${miniconda_root_dir}"/.condarc --set safety_checks warn
+"${miniconda_bin_dir}/python" "${miniconda_bin_dir}/conda" config --file "${miniconda_root_dir}"/.condarc --set remote_read_timeout_secs 240
+"${miniconda_bin_dir}/python" "${miniconda_bin_dir}/conda" config --file "${miniconda_root_dir}"/.condarc --set remote_connect_timeout_secs 20
+"${miniconda_bin_dir}/python" "${miniconda_bin_dir}/conda" config --file "${miniconda_root_dir}"/.condarc --set remote_max_retries 10
+"${miniconda_bin_dir}/python" "${miniconda_bin_dir}/conda" config --file "${miniconda_root_dir}"/.condarc --set remote_backoff_factor 5
+"${miniconda_bin_dir}/python" "${miniconda_bin_dir}/conda" config --file "${miniconda_root_dir}"/.condarc --set safety_checks warn
# Channel priority:
# - conda-forge (highest priority)
# - defaults (gets automatically added on the first call)
# - fsl (lowest priority)
-"${miniconda_bin_dir}/conda" config --file "${miniconda_root_dir}"/.condarc --set channel_priority strict
-"${miniconda_bin_dir}/conda" config --file "${miniconda_root_dir}"/.condarc --add channels conda-forge
-"${miniconda_bin_dir}/conda" config --file "${miniconda_root_dir}"/.condarc --append channels https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/channel
+"${miniconda_bin_dir}/python" "${miniconda_bin_dir}/conda" config --file "${miniconda_root_dir}"/.condarc --set channel_priority strict
+"${miniconda_bin_dir}/python" "${miniconda_bin_dir}/conda" config --file "${miniconda_root_dir}"/.condarc --add channels conda-forge
+"${miniconda_bin_dir}/python" "${miniconda_bin_dir}/conda" config --file "${miniconda_root_dir}"/.condarc --append channels https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/channel
##############################
@@ -229,7 +229,7 @@
if [ ${quiet} -ne 1 ]; then
echo "Stage 2"
fi
-FSLDIR=$fsl_dir "${miniconda_bin_dir}/conda" env create -v \
+FSLDIR=$fsl_dir "${miniconda_bin_dir}/python" "${miniconda_bin_dir}/conda-env" create -v \
-f "${script_dir}/fslpython_environment.yml" \
2>> "${miniconda_install_log}" | \
${script_dir}/progress.sh 133 ${quiet} 1>> "${miniconda_install_log}"

28
var/spack/repos/builtin/packages/fsl/iconv.patch Normal file
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@ -0,0 +1,28 @@
diff -ru a/src/flameo/Makefile b/src/flameo/Makefile
--- a/src/flameo/Makefile 2018-10-02 08:46:58.000000000 -0500
+++ b/src/flameo/Makefile 2020-11-07 20:19:56.732547025 -0600
@@ -6,9 +6,7 @@
USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_ZLIB}
UNAME := $(shell uname)
-ifeq (${UNAME},Darwin)
- LIBS = -liconv
-endif
+LIBS = -liconv
LIBS += -lutils -lnewimage -lmiscmaths -lm -lnewmat -lNewNifti -lcifti -lxml++-2.6 -lxml2 -lboost_filesystem -lboost_system -lznz -lprob -lz
diff -ru a/src/melodic/Makefile b/src/melodic/Makefile
--- a/src/melodic/Makefile 2020-03-30 08:51:19.000000000 -0500
+++ b/src/melodic/Makefile 2020-11-07 20:21:45.625518576 -0600
@@ -11,9 +11,7 @@
USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_GD} -L${LIB_GDC} -L${LIB_PNG} -L${LIB_ZLIB}
UNAME := $(shell uname)
-ifeq (${UNAME},Darwin)
- LIBS = -liconv
-endif
+LIBS = -liconv
LIBS += -lutils -lnewimage -lmiscplot -lmiscpic -lmiscmaths -lNewNifti -lcifti -lxml++-2.6 -lxml2 -lboost_filesystem -lboost_system -lznz -lnewmat -lprob -lm -lgdc -lgd -lpng -lz

180
var/spack/repos/builtin/packages/fsl/package.py
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@ -8,42 +8,157 @@
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')
depends_on('libiconv')
depends_on('openblas', when='@6:')
depends_on('vtk@:8')
conflicts('%gcc@6:', when='@5.0.10')
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 @@ def install(self, spec, prefix):
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 @@ def setup_build_environment(self, env):
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')
fslsetup = join_path(self.prefix, 'etc', 'fslconf', 'fsl.sh')
env.prepend_path('PATH', self.prefix)
if os.path.isfile(fslsetup):
env.extend(EnvironmentModifications.from_sourcing_file(fslsetup))