commit: 248cdac8246c9b43b970bca62e4ea70808c47cb1 Author: Gergely Nagy <ngg <AT> tresorit <DOT> com> AuthorDate: Mon Jun 26 10:49:26 2017 +0000 Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> CommitDate: Tue Jun 27 09:49:39 2017 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=248cdac8
sci-libs/atlas: version bump to 3.11.39 Patch from upstream is required to build the shared library: https://sourceforge.net/p/math-atlas/bugs/260/ Closes: https://github.com/gentoo/sci/pull/794 sci-libs/atlas/atlas-3.11.39.ebuild | 285 +++++++++++++++++++++ .../atlas/files/atlas-3.11.39-dolastcomp.patch | 13 + 2 files changed, 298 insertions(+) diff --git a/sci-libs/atlas/atlas-3.11.39.ebuild b/sci-libs/atlas/atlas-3.11.39.ebuild new file mode 100644 index 000000000..f4b65140c --- /dev/null +++ b/sci-libs/atlas/atlas-3.11.39.ebuild @@ -0,0 +1,285 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +FORTRAN_NEEDED=fortran + +inherit alternatives-2 eutils fortran-2 linux-info multilib numeric toolchain-funcs versionator + +LAPACKP=lapack-3.7.0.tgz + +DESCRIPTION="Automatically Tuned Linear Algebra Software" +HOMEPAGE="http://math-atlas.sourceforge.net/"; +SRC_URI="mirror://sourceforge/math-atlas/${PN}${PV}.tar.bz2 + fortran? ( lapack? ( http://www.netlib.org/lapack/${LAPACKP} ) )" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="+deprecated doc +fortran generic ifko +lapack static-libs threads" + +REQUIRED_USE=" + deprecated? ( lapack ) + lapack? ( fortran )" + +S="${WORKDIR}/ATLAS" + +PATCHES=( + "${FILESDIR}"/${P}-dolastcomp.patch +) + +pkg_setup() { + local _cpufreq + for _cpufreq in /sys/devices/system/cpu/cpu*/cpufreq/scaling_governor; do + if [ -f ${_cpufreq} ]; then + if ! grep -q performance ${_cpufreq}; then + echo 2> /dev/null performance > ${_cpufreq} || \ + die "${PN} needs all cpu set to performance" + fi + fi + done + [[ -e /sys/devices/system/cpu/intel_pstate ]] \ + && die "Intel P-State driver detected. Please reboot with 'intel_pstate=disable' in your cmdline" + use fortran && fortran-2_pkg_setup + CONFIG_CHECK=" + !~X86_P4_CLOCKMOD + !~X86_INTEL_PSTATE + " + ERROR_KERNEL_X86_P4_CLOCKMOD="P4 Clockmod frequency scaling influences tuning and needs to be disabled at compile time." + ERROR_KERNEL_X86_INTEL_PSTATE="Intel Pstate frequency scaling influences tuning and needs to be disabled at compile time." + linux-info_pkg_setup +} + +src_configure() { + # hack needed to trick the flaky gcc detection + local mycc="$(type -P $(tc-getCC))" + [[ ${mycc} == *gcc* ]] && mycc=gcc + atlas_configure() { + local myconf=( + --prefix="${ED}/usr" + --libdir="${ED}/usr/$(get_libdir)" + --incdir="${ED}/usr/include" + --cc="$(tc-getCC)" + "-D c -DWALL" + "-C acg '${mycc}'" + "-F acg '${CFLAGS}'" + "-Ss pmake '\$(MAKE) ${MAKEOPTS}'" + ) + + # OpenMP shown to decreased performance over POSIX threads + # (at least in 3.9.x, see atlas-dev mailing list) + if use threads; then + if use generic; then # 2 threads is most generic + myconf+=( "-t 2" "-Si omp 0" ) + else + myconf+=( "-t -1" "-Si omp 0" ) + fi + else + myconf+=( "-t 0" "-Si omp 0" ) + fi + + if use amd64 || use ppc64 || use sparc; then + if [ ${ABI} = amd64 ] || [ ${ABI} = ppc64 ] || [ ${ABI} = sparc64 ] ; then + myconf+=( "-b 64" ) + elif [ ${ABI} = x86 ] || [ ${ABI} = ppc ] || [ ${ABI} = sparc32 ] ; then + myconf+=( "-b 32" ) + elif [ ${ABI} = x32 ] ; then + myconf+=( "-b 48" ) + else + myconf+=( "-b 64" ) + fi + elif use ppc || use x86; then + myconf+=( "-b 32" ) + elif use ia64; then + myconf+=( "-b 64" ) + fi + if use fortran; then + myconf+=( + "-C if '$(type -P $(tc-getFC))'" + "-F if '${FFLAGS}'" + ) + if use lapack; then + myconf+=( + "-Si latune 1" + "--with-netlib-lapack-tarfile=${DISTDIR}/${LAPACKP}" + ) + else + myconf+=( "-Si latune 0" ) + fi + else + myconf+=( "-Si latune 0" "--nof77" ) + fi + # generic stuff found by make make xprint_enums in atlas build dir + # basically assuming sse2+sse1 and 2 threads max + use generic && use x86 && myconf+=( "-V 384 -A 13") + use generic && use amd64 && myconf+=( "-V 384 -A 24") + + local confdir="${S}_${1}"; shift + myconf+=( $(usex ifko "--use-ifko" "") ) + myconf+=( $@ ) + mkdir "${confdir}" && cd "${confdir}" || die + # for debugging + echo ${myconf[@]} > myconf.out + "${S}"/configure ${myconf[@]} || die "configure in ${confdir} failed" + + if use deprecated; then + echo "BUILD_DEPRECATED=1" >> src/lapack/reference/make.inc.example || die + fi + } + + atlas_configure shared "-Fa alg -fPIC" ${EXTRA_ECONF} + use static-libs && atlas_configure static ${EXTRA_ECONF} +} + +src_compile() { + atlas_compile() { + pushd "${S}_${1}" > /dev/null || die + # atlas does its own parallel builds + emake -j1 build + cd lib || die + emake libclapack.a + [[ -e libptcblas.a ]] && emake libptclapack.a + popd > /dev/null || die + } + + atlas_compile shared + use static-libs && atlas_compile static +} + +src_test() { + cd "${S}_shared" || die + emake -j1 check time +} + +# transform a static archive into a shared library and install them +# atlas_install_libs <mylib.a> [extra link flags] +atlas_install_libs() { + local libname=$(basename ${1%.*}) + einfo "Installing ${libname}" + local soname=${libname}.so.$(get_major_version) + local _cmd + shift + pushd "${S}_shared"/lib > /dev/null + _cmd="${LINK:-$(tc-getCC)}" + _cmd+=" ${LDFLAGS} -shared -Wl,--no-undefined -Wl,-soname=${soname}" + _cmd+=" -Wl,--whole-archive ${libname}.a -Wl,--no-whole-archive" + _cmd+=" $@ -o ${soname}" + einfo "${_cmd}" + ${_cmd} || die "Creating ${soname} failed" + dolib.so ${soname} + dosym ${soname} /usr/$(get_libdir)/${soname%.*} + popd > /dev/null || die + use static-libs && dolib.a "${S}_static"/lib/${libname}.a +} + +# create and install a pkgconfig file +# atlas_install_pc <libname> <pkg name> [extra link flags] +atlas_install_pc() { + local libname=${1} ; shift + local pcname=${1} ; shift + local extra=() + [[ ${PCREQ} ]] && extra+=( --requires "${PCREQ}" ) + create_pkgconfig \ + --name "${pcname}" \ + --description "${PN} ${pcname}" \ + --libs "-L\${libdir} -l${libname} $@" \ + --libs-private "-L\${libdir} -latlas -lm ${PTLIBS}" \ + --cflags "-I\${includedir}/${PN}" \ + "${extra[@]}" \ + ${pcname} +} + +src_install() { + cd "${S}_shared/lib" || die + # rename to avoid collision with other packages + local l + for l in {,c}{blas,lapack}; do + if [[ -e lib${l}.a ]]; then + mv lib{,atl}${l}.a || die + if use static-libs; then + mv "${S}"_static/lib/lib{,atl}${l}.a || die + fi + fi + done + + [[ -e libptcblas.a ]] && PTLIBS="-lpthread" + + # atlas + atlas_install_libs libatlas.a -lm ${PTLIBS} + + # cblas + atlas_install_libs libatlcblas.a -L. -latlas -lm + atlas_install_pc atlcblas atlas-cblas + alternatives_for cblas atlas 0 \ + /usr/$(get_libdir)/pkgconfig/cblas.pc atlas-cblas.pc \ + /usr/include/cblas.h atlas/cblas.h + + # cblas threaded + if [[ -e libptcblas.a ]]; then + atlas_install_libs libptcblas.a -L. -latlas -lm ${PTLIBS} + atlas_install_pc ptcblas atlas-cblas-threads + alternatives_for cblas atlas-threads 0 \ + /usr/$(get_libdir)/pkgconfig/cblas.pc atlas-cblas-threads.pc \ + /usr/include/cblas.h atlas/cblas.h + fi + + if use lapack; then + PCREQ="cblas" + # clapack + atlas_install_libs libatlclapack.a -L. -latlcblas -latlas -lm + atlas_install_pc atlclapack atlas-clapack + + # clapack threaded + if [[ -e libptclapack.a ]]; then + atlas_install_libs libptclapack.a -L. -lptcblas -latlas -lm ${PTLIBS} + atlas_install_pc ptclapack atlas-clapack-threads + fi + fi + + if use fortran; then + LINK=$(tc-getF77) PCREQ= + + # blas + atlas_install_libs libf77blas.a -L. -latlas -lm + atlas_install_pc f77blas atlas-blas + alternatives_for blas atlas 0 \ + /usr/$(get_libdir)/pkgconfig/blas.pc atlas-blas.pc + + # blas threaded + if [[ -e libptf77blas.a ]]; then + atlas_install_libs libptf77blas.a -L. -latlas -lm ${PTLIBS} + atlas_install_pc ptf77blas atlas-blas-threads + alternatives_for blas atlas-threads 0 \ + /usr/$(get_libdir)/pkgconfig/blas.pc atlas-blas-threads.pc + fi + + if use lapack; then + PCREQ="blas cblas" + # lapack + atlas_install_libs libatllapack.a \ + -L. -latlcblas -lf77blas -latlas -lm + atlas_install_pc atllapack atlas-lapack + alternatives_for lapack atlas 0 \ + /usr/$(get_libdir)/pkgconfig/lapack.pc atlas-lapack.pc + # lapack threaded + if [[ -e libptlapack.a ]]; then + atlas_install_libs libptlapack.a \ + -L. -lptcblas -lptf77blas -latlas -lm ${PTLIBS} + atlas_install_pc ptlapack atlas-lapack-threads + alternatives_for lapack atlas-threads 0 \ + /usr/$(get_libdir)/pkgconfig/lapack.pc atlas-lapack-threads.pc + fi + fi + fi + + cd "${S}" || die + insinto /usr/include/${PN} + doins include/*.h + + cd "${S}/doc" || die + dodoc INDEX.txt AtlasCredits.txt ChangeLog + use doc && dodoc atlas*pdf cblas.pdf cblasqref.pdf + use doc && use fortran && dodoc f77blas*pdf + use doc && use fortran && use lapack && dodoc *lapack*pdf +} diff --git a/sci-libs/atlas/files/atlas-3.11.39-dolastcomp.patch b/sci-libs/atlas/files/atlas-3.11.39-dolastcomp.patch new file mode 100644 index 000000000..3cd554cf4 --- /dev/null +++ b/sci-libs/atlas/files/atlas-3.11.39-dolastcomp.patch @@ -0,0 +1,13 @@ +diff --git a/src/threads/blas/level3/ATL_tammm_G.c b/src/threads/blas/level3/ATL_tammm_G.c +index a43a08b..77c78f4 100644 +--- a/src/threads/blas/level3/ATL_tammm_G.c ++++ b/src/threads/blas/level3/ATL_tammm_G.c +@@ -479,7 +479,7 @@ static void DoCompNoCopy(ATL_tamm_gOOO_t *pd, ATL_UINT rank, TYPE *wC) + #ifndef TCPLX + #undef rC + #endif +-void DoLastComp(ATL_tamm_gOOO_t *pd, ATL_UINT rank, TYPE *wC) ++static void DoLastComp(ATL_tamm_gOOO_t *pd, ATL_UINT rank, TYPE *wC) + { + ipinfo_t *ip=pd->ip; + TYPE *wA=pd->wA, *wB=pd->wB, *C=pd->C;
