diff options
| -rw-r--r-- | var/spack/repos/builtin/packages/bart/Makefile.patch | 30 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/bart/bart_path.patch | 107 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/bart/package.py | 84 |
3 files changed, 221 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/bart/Makefile.patch b/var/spack/repos/builtin/packages/bart/Makefile.patch new file mode 100644 index 0000000000..5077d767f1 --- /dev/null +++ b/var/spack/repos/builtin/packages/bart/Makefile.patch @@ -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$(BLAS_BASE)/lib -llapacke -lblas ++BLAS_L := -llapacke -lcblas + endif + endif + endif diff --git a/var/spack/repos/builtin/packages/bart/bart_path.patch b/var/spack/repos/builtin/packages/bart/bart_path.patch new file mode 100644 index 0000000000..c1b6c98da5 --- /dev/null +++ b/var/spack/repos/builtin/packages/bart/bart_path.patch @@ -0,0 +1,107 @@ +diff -ru a/matlab/bart.m b/matlab/bart.m +--- a/matlab/bart.m 2020-04-10 18:50:50.056248692 -0500 ++++ b/matlab/bart.m 2020-04-10 18:52:20.541178180 -0500 +@@ -11,7 +11,7 @@ + return + end + +- bart_path = getenv('TOOLBOX_PATH'); ++ bart_path = [getenv('TOOLBOX_PATH') '/bin']; + isWSL = false; + + if isempty(bart_path) +diff -ru a/python/bart.py b/python/bart.py +--- a/python/bart.py 2020-04-10 18:50:50.056248692 -0500 ++++ b/python/bart.py 2020-04-10 19:18:09.481950358 -0500 +@@ -19,7 +19,7 @@ + return None + + try: +- bart_path = os.environ['TOOLBOX_PATH'] + '/bart ' ++ bart_path = os.environ['TOOLBOX_PATH'] + '/bin ' + except: + bart_path = None + isWSL = False +diff -ru a/scripts/espirit_econ.sh b/scripts/espirit_econ.sh +--- a/scripts/espirit_econ.sh 2020-04-10 18:50:50.055248693 -0500 ++++ b/scripts/espirit_econ.sh 2020-04-10 19:13:06.463193324 -0500 +@@ -56,8 +56,6 @@ + fi + + +-export PATH=$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')); + diff --git a/var/spack/repos/builtin/packages/bart/package.py b/var/spack/repos/builtin/packages/bart/package.py new file mode 100644 index 0000000000..954a4e6930 --- /dev/null +++ b/var/spack/repos/builtin/packages/bart/package.py @@ -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) |