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-rw-r--r--var/spack/repos/builtin/packages/bart/Makefile.patch30
-rw-r--r--var/spack/repos/builtin/packages/bart/bart_path.patch107
-rw-r--r--var/spack/repos/builtin/packages/bart/package.py84
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)
generated by cgit v1.2.3-70-g09d2 (git 2.46.0) at 2024-09-09 11:43:31 +0000