[gentoo-commits] proj/sci:master commit in: sci-biology/fsl/files/, sci-biology/fsl/

[Horea Christian]

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>