commit: 21789df887204e7b98393fb115982ee36a71d8c1
Author: AbstractMethod <paul.polak <AT> med-image <DOT> info>
AuthorDate: Mon Sep 14 23:55:04 2020 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Thu Sep 17 15:14:25 2020 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=21789df8
Changes for fsl CUDA support
Package-Manager: Portage-3.0.6, Repoman-3.0.1
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
.../fsl/files/fsl-6.0.2-cuda_buildsettings.patch | 12 ++
sci-biology/fsl/files/fsl-6.0.2-eddy_cuda.patch | 21 +++
sci-biology/fsl/fsl-6.0.2-r1.ebuild | 202 +++++++++++++++++++++
sci-biology/fsl/metadata.xml | 3 +
4 files changed, 238 insertions(+)
diff --git a/sci-biology/fsl/files/fsl-6.0.2-cuda_buildsettings.patch
b/sci-biology/fsl/files/fsl-6.0.2-cuda_buildsettings.patch
new file mode 100644
index 000000000..a3872acf0
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.2-cuda_buildsettings.patch
@@ -0,0 +1,12 @@
+diff -Naur fsl.orig/config/buildSettings.mk fsl/config/buildSettings.mk
+--- fsl.orig/config/buildSettings.mk 2020-07-23 15:43:42.277064365 -0400
++++ fsl/config/buildSettings.mk 2020-07-23 15:45:17.705069496 -0400
+@@ -141,7 +141,7 @@
+ # CUDA development environment
+ CUDAVER := $(or $(CUDAVER),9.1)
+ #$(info $$CUDAVER is [${CUDAVER}])
+-CUDA_INSTALLATION = /opt/cuda-${CUDAVER}
++CUDA_INSTALLATION = /opt/cuda
+ GENCODE_FLAGS = $(shell ${FSLDIR}/config/common/supportedGencodes.sh
${CUDA_INSTALLATION})
+ LIB_CUDA = ${CUDA_INSTALLATION}/lib64
+ INC_CUDA = ${CUDA_INSTALLATION}/include
diff --git a/sci-biology/fsl/files/fsl-6.0.2-eddy_cuda.patch
b/sci-biology/fsl/files/fsl-6.0.2-eddy_cuda.patch
new file mode 100644
index 000000000..40409ec08
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.2-eddy_cuda.patch
@@ -0,0 +1,21 @@
+diff -Naur fsl.orig/src/eddy/Makefile fsl/src/eddy/Makefile
+--- fsl.orig/src/eddy/Makefile 2020-07-30 14:30:06.414884410 -0400
++++ fsl/src/eddy/Makefile 2020-07-30 14:33:03.400889914 -0400
+@@ -29,6 +29,8 @@
+ TMPCXXFLAGS_2=
+ TMPNAME_1=
+ TMPNAME_2=
++cuda=1
++cpu=1
+
+ ifndef cuda
+ ifndef cpu #Default single cpu, no threading
+@@ -74,7 +75,7 @@
+ ifdef NVCC11
+ NVCC=${NVCC11}
+ endif
+-NVCCFLAGS=-c -DCOMPILE_GPU -O3 -m 64 -std=c++11
++NVCCFLAGS=-c -DCOMPILE_GPU -O3 -m 64 -std=c++11 @@GENTOO_NVCC_FLAGS@@
+ ifeq ($(CLOBBER_CLANG),1)
+ NVCCFLAGS+= -DCLOBBER_CLANG
+ endif
diff --git a/sci-biology/fsl/fsl-6.0.2-r1.ebuild
b/sci-biology/fsl/fsl-6.0.2-r1.ebuild
new file mode 100644
index 000000000..0cadd4e4b
--- /dev/null
+++ b/sci-biology/fsl/fsl-6.0.2-r1.ebuild
@@ -0,0 +1,202 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cuda flag-o-matic toolchain-funcs prefix
+
+DESCRIPTION="Analysis of functional, structural, and diffusion MRI brain
imaging data"
+HOMEPAGE="http://www.fmrib.ox.ac.uk/fsl";
+SRC_URI="https://fsl.fmrib.ox.ac.uk/fsldownloads/${P}-sources.tar.gz ->
${P}.tar.gz"
+
+LICENSE="FSL BSD-2 newmat"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="cuda"
+
+DEPEND="
+ dev-libs/boost
+ dev-python/fslpy
+ media-gfx/graphviz
+ media-libs/gd
+ media-libs/glu
+ media-libs/libpng:0=
+ sci-libs/ciftilib
+ sci-libs/nlopt
+ sys-libs/zlib
+ dev-lang/tcl:0=
+ dev-lang/tk:0=
+ >=virtual/lapack-3.8
+ >=virtual/blas-3.8
+
+ cuda? (
+ || (
+ ( =dev-util/nvidia-cuda-toolkit-10* =sys-devel/gcc-8* )
+ ( =dev-util/nvidia-cuda-toolkit-11* =sys-devel/gcc-9* )
+ )
+ )
+ "
+RDEPEND="${DEPEND}"
+
+S=${WORKDIR}/${PN}
+UPSTREAM_FSLDIR="/usr/share/fsl"
+
+PATCHES=(
+ "${FILESDIR}/${PN}"-6.0.2-gcc10_include.patch
+ "${FILESDIR}/${PN}"-6.0.2-setup.patch
+ "${FILESDIR}/${PN}"-6.0.2-template.patch
+ "${FILESDIR}/${PN}"-6.0.2-no_xmlpp.patch
+ "${FILESDIR}/${PN}"-5.0.11-niftiio_var_fix.patch
+ "${FILESDIR}/${PN}"-5.0.11-ifstream_use.patch
+ "${FILESDIR}/${PN}"-5.0.11-fslsurface_parallel_make.patch
+ "${FILESDIR}/${PN}"-6.0.2-qstring_compat.patch
+ "${FILESDIR}/${PN}"-5.0.9-headers.patch
+ "${FILESDIR}/${PN}"-6.0.2-fsldir_redux.patch
+)
+
+src_prepare() {
+ default
+
+ sed -i \
+ -e "s:@@GENTOO_RANLIB@@:$(tc-getRANLIB):" \
+ -e "s:@@GENTOO_CC@@:$(tc-getCC):" \
+ -e "s:@@GENTOO_CXX@@:$(tc-getCXX):" \
+ config/buildSettings.mk || die
+
+ eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX src/*) \
+ etc/js/label-div.html
+
+ # Disable mist-clean the hard way for now.
+ rm -rf src/mist-clean
+
+ makefilelist=$(find src/ -name Makefile)
+
+ sed -i \
+ -e "s:-I\${INC_BOOST}::" \
+ -e "s:-I\${INC_ZLIB}::" \
+ -e "s:-I\${INC_GD}::" \
+ -e "s:-I\${INC_PNG}::" \
+ -e "s:-L\${LIB_GD}::" \
+ -e "s:-L\${LIB_PNG}::" \
+ -e "s:-L\${LIB_ZLIB}::" \
+ ${makefilelist} || die
+
+ sed -e "s:\${FSLDIR}/bin/::g" \
+ -e "s:\$FSLDIR/bin/::g" \
+ -i $(grep -rl "\${FSLDIR}/bin" src/*) \
+ -i $(grep -rl "\$FSLDIR/bin" src/*) \
+ $(grep -rl "\${FSLDIR}/bin" etc/matlab/*)\
+ $(grep -rl "\$FSLDIR/bin" etc/matlab/*) || die
+
+ sed -e "s:\$FSLDIR/data:${EPREFIX}/usr/share/fsl/data:g" \
+ -e "s:\${FSLDIR}/data:${EPREFIX}/usr/share/fsl/data:g" \
+ -i $(grep -rl "\$FSLDIR/data" src/*) \
+ $(grep -rl "\${FSLDIR}/data" src/*) || die
+
+ sed -e "s:\$FSLDIR/doc:${EPREFIX}/usr/share/fsl/doc:g" \
+ -e "s:\${FSLDIR}/doc:${EPREFIX}/usr/share/fsl/doc:g" \
+ -i $(grep -rl "\$FSLDIR/doc" src/*) \
+ $(grep -rl "\${FSLDIR}/doc" src/*) || die
+
+ sed -e "s:/usr/share/fsl/doc:${EPREFIX}/usr/share/fsl/doc:g" \
+ -i $(grep -rl "/usr/share/fsl/doc" src/*) || die
+
+ sed -e "s:\$FSLDIR/etc:${EPREFIX}/etc:g" \
+ -e "s:\${FSLDIR}/etc:${EPREFIX}/etc:g" \
+ -i $(grep -rlI "\$FSLDIR/etc" *) \
+ -i $(grep -rlI "\${FSLDIR}/etc" *) || die
+
+ # Use generic blas/lapack rather than openblas
+ sed -e "s:-lopenblas:-llapack -lblas:g" \
+ -i $(grep -rlI lopenblas *) || die
+
+ # script wanting to have access to flsversion at buildtime
+ sed -e "s:/etc/fslversion:${S}/etc/fslversion:g" \
+ -i ${makefilelist} || die
+
+ if use cuda; then
+ einfo
+
+ gcc_ver=`gcc-fullversion`
+ einfo "GCC version: ${gcc_ver}"
+
+ cuda_gcc=`cuda_gccdir`
+ cuda_NVCC_flags=`cuda_gccdir -f`
+ einfo "CUDA GCC path: ${cuda_gcc}"
+ einfo " ${cuda_NVCC_flags}"
+
+ CUDA_INSTALLATION="/opt/cuda"
+ CUDAVER=`cuda_toolkit_version`
+
+ eapply "${FILESDIR}/${PN}-6.0.2-eddy_cuda.patch"
+ eapply "${FILESDIR}/${PN}-6.0.2-cuda_buildsettings.patch"
+
+ sed -i \
+ -e "s:@@GENTOO_NVCC_FLAGS@@:${cuda_NVCC_flags}:" \
+ src/eddy/Makefile || die
+
+ cuda_sanitize
+ fi
+}
+
+src_compile() {
+ export FSLDIR=${WORKDIR}/${PN}
+ export FSLCONDIR=${WORKDIR}/${PN}/config
+ export FSLMACHTYPE=generic
+
+ export USERLDFLAGS="${LDFLAGS}"
+ export USERCFLAGS="${CFLAGS}"
+ export USERCXXFLAGS="${CXXFLAGS}"
+
+ export CIFTICFLAGS="$($(tc-getPKG_CONFIG) --cflags CiftiLib)"
+ export CIFTILIBS="$($(tc-getPKG_CONFIG) --libs-only-l CiftiLib)"
+
+ if use cuda; then
+ einfo "CUDA_INSTALLATION: ${CUDA_INSTALLATION}"
+ einfo "CUDAVER: ${CUDAVER}"
+ fi
+
+ ./build || die
+}
+
+src_install() {
+ sed -i "s:\${FSLDIR}/tcl:/usr/libexec/fsl:g" \
+ $(grep -lI "\${FSLDIR}/tcl" bin/*) \
+ $(grep -l "\${FSLDIR}/tcl" tcl/*) || die
+ sed -i "s:\$FSLDIR/tcl:/usr/libexec/fsl:g" \
+ $(grep -l "\$FSLDIR/tcl" tcl/*) || die
+
+ dobin bin/*
+
+ insinto /usr/share/${PN}
+ doins -r data
+ dodoc -r doc/. refdoc
+
+ insinto /usr/libexec/fsl
+ doins -r tcl/*
+
+ insinto /etc/fslconf
+ doins etc/fslconf/fsl.sh
+
+ insinto /etc
+ doins etc/fslversion
+ doins -r etc/default_flobs.flobs etc/flirtsch etc/js etc/luts
+
+ #the following is needed for FSL and depending programs to be able
+ #to find its files, since FSL uses an uncommon installation path:
+ #https://github.com/gentoo-science/sci/pull/612#r60289295
+ dosym ../../../etc ${UPSTREAM_FSLDIR}/etc
+ dosym ../doc/${PF} ${UPSTREAM_FSLDIR}/doc
+ dosym ../../bin ${UPSTREAM_FSLDIR}/bin
+
+ doenvd "$(prefixify_ro "${FILESDIR}"/99fsl)"
+ mv "${ED}"/usr/bin/{,fsl_}cluster || die
+}
+
+pkg_postinst() {
+ echo
+ einfo "Please run the following commands if you"
+ einfo "intend to use fsl from an existing shell:"
+ einfo "env-update && source /etc/profile"
+ echo
+}
diff --git a/sci-biology/fsl/metadata.xml b/sci-biology/fsl/metadata.xml
index d3788686e..9d12c769d 100644
--- a/sci-biology/fsl/metadata.xml
+++ b/sci-biology/fsl/metadata.xml
@@ -8,4 +8,7 @@
<longdescription>
FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain
imaging data.
</longdescription>
+ <use>
+ <flag name="cuda">Add support for CUDA</flag>
+ </use>
</pkgmetadata>
