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new package: BART (#16016)

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* new package: BART

This PR adds the BART (Berkeley Advanced Reconstruction Toolset)
package.

Despite the presence of CMake files, this package builds with a
Makefile. It looks like the project is moving away from cmake. The patch
for MKL has been committed upstream so should only be necessary for this
version of BART.  The Makefile patch is meant for working with Spack and
would not be useful upstream. The bart scripts are still setup to use
bart with the subcommands being individual binaries. This patches those
to use the single binary with built-in subcommands and assumes that
spack is providing the TOOLBOX environment variable and setting PATH.

* Update var/spack/repos/builtin/packages/bart/package.py

Yes, '==' make more sense for a single string.

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* The python dependencies are run time only.

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
This commit is contained in:
Glenn Johnson 2020-04-12 19:41:37 -05:00 committed by GitHub
parent a1fc761f18
commit 9a0dd631d5
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
3 changed files with 221 additions and 0 deletions
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30
var/spack/repos/builtin/packages/bart/Makefile.patch Normal file
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@ -0,0 +1,30 @@
--- a/Makefile 2020-04-08 17:21:01.982819829 -0500
+++ b/Makefile 2020-04-08 17:21:42.982804931 -0500
@@ -289,7 +289,7 @@
ifeq ($(BUILDTYPE), MacOSX)
CUDA_L := -L$(CUDA_BASE)/lib -lcufft -lcudart -lcublas -m64 -lstdc++
else
-CUDA_L := -L$(CUDA_BASE)/lib64 -lcufft -lcudart -lcublas -lstdc++ -Wl,-rpath $(CUDA_BASE)/lib64
+CUDA_L := -L$(CUDA_BASE)/lib64 -lcufft -lcudart -lcublas -lstdc++
endif
else
CUDA_H :=
@@ -327,14 +327,13 @@
CPPFLAGS += -DUSE_ACML
else
BLAS_H := -I$(BLAS_BASE)/include
-ifeq ($(BUILDTYPE), MacOSX)
-BLAS_L := -L$(BLAS_BASE)/lib -lopenblas
+ifeq ($(OPENBLAS),1)
+BLAS_L := -lopenblas
else
ifeq ($(NOLAPACKE),1)
-BLAS_L := -L$(BLAS_BASE)/lib -llapack -lblas
-CPPFLAGS += -Isrc/lapacke
+BLAS_L := -llapack -lcblas
else
-BLAS_L := -L$(BLAS_BASE)/lib -llapacke -lblas
+BLAS_L := -llapacke -lcblas
endif
endif
endif

107
var/spack/repos/builtin/packages/bart/bart_path.patch Normal file
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@ -0,0 +1,107 @@
diff -ru a/matlab/bart.m b/matlab/bart.m
--- a/matlab/bart.m 2020-04-10 18:50:50.056248692 -0500
+++ b/matlab/bart.m 2020-04-10 18:52:20.541178180 -0500
@@ -11,7 +11,7 @@
return
end
- bart_path = getenv('TOOLBOX_PATH');
+ bart_path = [getenv('TOOLBOX_PATH') '/bin'];
isWSL = false;
if isempty(bart_path)
diff -ru a/python/bart.py b/python/bart.py
--- a/python/bart.py 2020-04-10 18:50:50.056248692 -0500
+++ b/python/bart.py 2020-04-10 19:18:09.481950358 -0500
@@ -19,7 +19,7 @@
return None
try:
- bart_path = os.environ['TOOLBOX_PATH'] + '/bart '
+ bart_path = os.environ['TOOLBOX_PATH'] + '/bin '
except:
bart_path = None
isWSL = False
diff -ru a/scripts/espirit_econ.sh b/scripts/espirit_econ.sh
--- a/scripts/espirit_econ.sh 2020-04-10 18:50:50.055248693 -0500
+++ b/scripts/espirit_econ.sh 2020-04-10 19:13:06.463193324 -0500
@@ -56,8 +56,6 @@
fi
-export PATH=$TOOLBOX_PATH:$PATH
-
input=$(readlink -f "$1")
output=$(readlink -f "$2")
@@ -67,7 +65,7 @@
exit 1
fi
-if [ ! -e $TOOLBOX_PATH/bart ] ; then
+if [ ! -e $TOOLBOX_PATH/bin/bart ] ; then
echo "\$TOOLBOX_PATH is not set correctly!" >&2
exit 1
fi
diff -ru a/scripts/grasp.sh b/scripts/grasp.sh
--- a/scripts/grasp.sh 2020-04-10 18:50:50.055248693 -0500
+++ b/scripts/grasp.sh 2020-04-10 19:13:31.461173327 -0500
@@ -90,8 +90,6 @@
fi
-export PATH=$TOOLBOX_PATH:$PATH
-
input=$(readlink -f "$1")
output=$(readlink -f "$2")
@@ -101,7 +99,7 @@
exit 1
fi
-if [ ! -e $TOOLBOX_PATH/bart ] ; then
+if [ ! -e $TOOLBOX_PATH/bin/bart ] ; then
echo "\$TOOLBOX_PATH is not set correctly!" >&2
exit 1
fi
diff -ru a/scripts/octview.m b/scripts/octview.m
--- a/scripts/octview.m 2020-04-10 18:50:50.055248693 -0500
+++ b/scripts/octview.m 2020-04-10 19:14:33.386123750 -0500
@@ -1,6 +1,6 @@
#! /usr/bin/octave -qf
-addpath(strcat(getenv("TOOLBOX_PATH"), "/matlab"));
+addpath(strcat(getenv("TOOLBOX_PATH"), "/bin", "/matlab"));
arg_list = argv();
diff -ru a/scripts/profile.sh b/scripts/profile.sh
--- a/scripts/profile.sh 2020-04-10 18:50:50.055248693 -0500
+++ b/scripts/profile.sh 2020-04-10 19:15:00.723101850 -0500
@@ -45,7 +45,7 @@
exit 1
fi
-if [ ! -e $TOOLBOX_PATH/bart ] ; then
+if [ ! -e $TOOLBOX_PATH/bin/bart ] ; then
echo "\$TOOLBOX_PATH is not set correctly!" >&2
exit 1
fi
@@ -57,7 +57,7 @@
cd $WORKDIR
-nm --defined-only $TOOLBOX_PATH/bart | cut -c11-16,19- | sort > bart.syms
+nm --defined-only $TOOLBOX_PATH/bin/bart | cut -c11-16,19- | sort > bart.syms
cat $in | grep "^TRACE" \
diff -ru a/startup.m b/startup.m
--- a/startup.m 2020-04-10 18:50:50.048248699 -0500
+++ b/startup.m 2020-04-10 18:51:40.390209486 -0500
@@ -1,4 +1,3 @@
% set Matlab path and TOOLBOX_PATH environment variable
-addpath(fullfile(pwd, 'matlab'));
-setenv('TOOLBOX_PATH', pwd);
+addpath(fullfile(getenv('TOOLBOX_PATH'), 'matlab'));

84
var/spack/repos/builtin/packages/bart/package.py Normal file
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@ -0,0 +1,84 @@
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class Bart(MakefilePackage, CudaPackage):
"""BART: Toolbox for Computational Magnetic Resonance Imaging"""
homepage = "https://mrirecon.github.io/bart/"
url = "https://github.com/mrirecon/bart/archive/v0.5.00.tar.gz"
version('0.5.00', sha256='30eedcda0f0ef3808157542e0d67df5be49ee41e4f41487af5c850632788f643')
# patch to fix build with MKL
patch('https://github.com/mrirecon/bart/commit/b62ca4972d5ac41a44217a5c27123c15daae74db.patch',
sha256='8fd1be181da928448da750b32d45ee6dce7ba6af0424617c4f8d653cf3f05445',
when='@0.5.00')
# patch to fix Makefile for openblas and cuda
patch('Makefile.patch')
# patch to set path to bart
patch('bart_path.patch')
depends_on('libpng')
depends_on('fftw')
depends_on('blas')
depends_on('lapack')
depends_on('py-numpy', type='run')
depends_on('py-matplotlib', type='run')
extends('python')
conflicts('^atlas', msg='BART does not currently support atlas')
def edit(self, spec, prefix):
env['PREFIX'] = prefix
env['FFTW_BASE'] = spec['fftw'].prefix
if spec['blas'].name == 'openblas':
env['OPENBLAS'] = '1'
if spec['blas'].name in ['intel-mkl', 'intel-parallel-studio']:
env['MKL'] = '1'
env['MKL_BASE'] = env['MKLROOT']
else:
env['BLAS_BASE'] = spec['blas'].prefix
if '^netlib-lapack+lapacke' not in spec:
env['NOLAPACKE'] = '1'
if '+cuda' in spec:
cuda_arch = self.spec.variants['cuda_arch'].value
env['CUDA'] = '1'
env['CUDA_BASE'] = spec['cuda'].prefix
env['GPUARCH_FLAGS'] = ' '.join(self.cuda_flags(cuda_arch))
def install(self, spec, prefix):
python_dir = join_path(prefix,
spec['python'].package.site_packages_dir)
make('install')
install_tree('scripts', prefix.scripts)
install_tree('matlab', prefix.matlab)
install('startup.m', prefix)
install('python/bart.py', python_dir)
install('python/cfl.py', python_dir)
install('python/wslsupport.py', python_dir)
if '^python@3:' in spec:
install('python/bartview3.py', join_path(prefix.bin, 'bartview'))
filter_file(r'#!/usr/bin/python3', '#!/usr/bin/env python',
prefix.bin.bartview)
else:
install('python/bartview.py', join_path(prefix.bin, 'bartview'))
filter_file(r'#!/usr/bin/python', '#!/usr/bin/env python',
prefix.bin.bartview)
def setup_run_environment(self, env):
env.set('TOOLBOX_PATH', self.prefix)