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fsl: new version, updated constraints and patches (#27129)

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- add version 6.0.5
- add patch to allow fsl to use newer gcc versions
- add patch to allow fsl to use newer cuda versions
- remove constraints on gcc and cuda versions
- add filters to prevent using system headers and libraries
- clean up the installed tree
This commit is contained in:
Glenn Johnson 2021-11-02 04:49:22 -05:00 committed by GitHub
parent 1e26e25bc8
commit f972863712
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GPG key ID: 4AEE18F83AFDEB23
4 changed files with 102 additions and 5 deletions
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0
var/spack/repos/builtin/packages/fsl/fslpython_install_v6.patch → var/spack/repos/builtin/packages/fsl/fslpython_install_v604.patch
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42
var/spack/repos/builtin/packages/fsl/fslpython_install_v605.patch Normal file
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@ -0,0 +1,42 @@
diff -ru a/etc/fslconf/fslpython_install.sh b/etc/fslconf/fslpython_install.sh
--- a/etc/fslconf/fslpython_install.sh 2021-07-15 10:05:03.000000000 +0000
+++ b/etc/fslconf/fslpython_install.sh 2021-11-01 01:01:03.088119423 +0000
@@ -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
##############################
@@ -235,7 +235,7 @@
# different on linux. Also is likely to need
# updating whenever the fslpython environment
# specification is changed.
-FSLDIR=$fsl_dir "${miniconda_bin_dir}/conda" env create \
+FSLDIR=$fsl_dir "${miniconda_bin_dir}/python" "${miniconda_bin_dir}/conda" env create \
-f "${script_dir}/fslpython_environment.yml" \
2>> "${miniconda_install_log}" | \
${script_dir}/progress.sh 400 ${quiet} 1>> "${miniconda_install_log}"
Only in b/etc/fslconf: fslpython_install.sh.orig
Only in b/etc/fslconf: fslpython_install.sh.rej

30
var/spack/repos/builtin/packages/fsl/libxmlpp_bool.patch Normal file
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@ -0,0 +1,30 @@
diff -ru a/extras/src/libxmlpp/libxml++/io/istreamparserinputbuffer.cc b/extras/src/libxmlpp/libxml++/io/istreamparserinputbuffer.cc
--- a/extras/src/libxmlpp/libxml++/io/istreamparserinputbuffer.cc 2019-05-20 12:50:12.000000000 +0000
+++ b/extras/src/libxmlpp/libxml++/io/istreamparserinputbuffer.cc 2021-10-31 22:29:47.465118993 +0000
@@ -39,6 +39,6 @@
bool IStreamParserInputBuffer::do_close()
{
- return input_;
+ return static_cast<bool>(input_);
}
}
diff -ru a/extras/src/libxmlpp/libxml++/io/ostreamoutputbuffer.cc b/extras/src/libxmlpp/libxml++/io/ostreamoutputbuffer.cc
--- a/extras/src/libxmlpp/libxml++/io/ostreamoutputbuffer.cc 2019-05-20 12:50:12.000000000 +0000
+++ b/extras/src/libxmlpp/libxml++/io/ostreamoutputbuffer.cc 2021-10-31 22:31:47.656434780 +0000
@@ -29,13 +29,13 @@
// here we rely on the ostream implicit conversion to boolean, to know if the stream can be used and/or if the write succeded.
if(output_)
output_.write(buffer, len);
- return output_;
+ return static_cast<bool>(output_);
}
bool OStreamOutputBuffer::do_close()
{
if(output_)
output_.flush();
- return output_;
+ return static_cast<bool>(output_);
}
}

35
var/spack/repos/builtin/packages/fsl/package.py
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@ -3,6 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import glob
import os
from spack import *
@ -22,6 +23,7 @@ class Fsl(Package, CudaPackage):
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')
@ -33,18 +35,25 @@ class Fsl(Package, CudaPackage):
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('eddy_Makefile.patch', when='@6.0.4')
patch('iconv.patch')
patch('fslpython_install_v5.patch', when='@:5')
patch('fslpython_install_v6.patch', when='@6:')
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
@ -161,10 +170,26 @@ def patch(self):
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('./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'))
install_tree('.', prefix)
@run_after('install')