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authorMartin Mokrejš <mmokrejs@fold.natur.cuni.cz>2017-03-22 23:36:06 +0100
committerMartin Mokrejš <mmokrejs@fold.natur.cuni.cz>2017-03-22 23:36:06 +0100
commit7a59148d303e8937aa9beee0ec888dfed70e37a0 (patch)
treec2f6d862f7dc3db6c52de2f5edf2964bbbde7116 /sys-cluster
parentsci-biology/ncbi-tools++: fix plenty linking issues, still far from completeness (diff)
parentsys-cluster/openmpi: require dev-libs/libevent with threads (diff)
downloadsci-7a59148d303e8937aa9beee0ec888dfed70e37a0.tar.gz
sci-7a59148d303e8937aa9beee0ec888dfed70e37a0.tar.bz2
sci-7a59148d303e8937aa9beee0ec888dfed70e37a0.zip
Merge branch 'master' of git+ssh://git.gentoo.org/proj/sci
Diffstat (limited to 'sys-cluster')
-rw-r--r--sys-cluster/openmpi/Manifest3
-rw-r--r--sys-cluster/openmpi/openmpi-1.10.6.ebuild (renamed from sys-cluster/openmpi/openmpi-1.10.3-r2.ebuild)2
-rw-r--r--sys-cluster/openmpi/openmpi-2.0.2.ebuild2
-rw-r--r--sys-cluster/openmpi/openmpi-2.1.0.ebuild174
4 files changed, 178 insertions, 3 deletions
diff --git a/sys-cluster/openmpi/Manifest b/sys-cluster/openmpi/Manifest
index fd6ca99c7..edffa850d 100644
--- a/sys-cluster/openmpi/Manifest
+++ b/sys-cluster/openmpi/Manifest
@@ -1,3 +1,4 @@
-DIST openmpi-1.10.3.tar.bz2 13368112 SHA256 7484bb664312082fd12edc2445b42362089b53b17fb5fce12efd4fe452cc254d SHA512 1ddad1ffecfd07e68e891a2cfdb9d2f5baa1a91ad5286347f2884820839455c002eb4316ae62d30a4ee2efbcfe460eade7606187ea862ac4aef77ab6a2e2475d WHIRLPOOL bbe9cb0ee0ba34bab71ca10957b694d7e964b78c0efda1fff8da0361f84a8890553aad7e766f062259322dbf478918781853eb743f56ed505ff542f00a1868bd
+DIST openmpi-1.10.6.tar.bz2 13438345 SHA256 65606184a084a0eda6102b01e5a36a8f02d3195d15e91eabbb63e898bd110354 SHA512 61df9d10e1d73ddaab3783bc33390ae1088c995db09cd6e735aa1243dcc61217f136aeae65008a2f3050a958379ef6d48c66dcf8a345c43a6782ee2a3ac4320e WHIRLPOOL 0d90183f5e5be5d14e8df35eb4134041675be2fc06a6c8a93b96fea0ed1495ee58c04c5fee7dbb6739473826c73abcde2448d4867950e0770b5de781a1cbc486
DIST openmpi-1.8.8.tar.bz2 13231433 SHA256 a28382d1e6a36f4073412dc00836ff2524e42b674da9caf6ca7377baad790b94 SHA512 8ca2e3ebb9d9ba0f33faba9bef76fe95293721b73619cbc18176611074a56c277e9ab6cae7fa6c87ace11f16151c1bc495b2a8dbc8ad064d5a8f89f5d431a660 WHIRLPOOL e36186452978ba7a368c83b84b8b089f6995450fa866b7b8300d32eec7e64a816abf5f301dc716bf25b3b45b987489952ffc4b7057f4407677f2a2df5ee67cdd
DIST openmpi-2.0.2.tar.bz2 8311215 SHA256 cae396e643f9f91f0a795f8d8694adf7bacfb16f967c22fb39e9e28d477730d3 SHA512 87dc3c23db4b9cb92dbacc9b384b21ce8c4288fe4edc204fbf4a3bef70d8ac4329269e777ed190fa87933d78b73b9e5550ea3b925b2039599cfef3953567232a WHIRLPOOL 9403135fbf1682597c211b1ca0d1e300bd6f49294e9a70bf21f030c48a54f85d2d7ce8de8693dccaf81e2b46fbfd9a43a817bf598dc1f96e122b3f6ea6ffc3c6
+DIST openmpi-2.1.0.tar.bz2 8300124 SHA256 b169e15f5af81bf3572db764417670f508c0df37ce86ff50deb56bd3acb43957 SHA512 60943c3ec656d49a5c988df33bcd7faeb7afa93f3e60b336fd59403790f697faba0f00ed482b0c8f12ab9dd754d30dfd33771662edddcbb3b1694bc633cd6a56 WHIRLPOOL 6e4e31c5c3309993a8f7b1b44895983aa277f97a6cea82c0045f2d01db5f699b485ee3a69691a8c8af41133391fe6baa878d8adb227c3ee61044cdc1705b243b
diff --git a/sys-cluster/openmpi/openmpi-1.10.3-r2.ebuild b/sys-cluster/openmpi/openmpi-1.10.6.ebuild
index 1a9a5554e..2c13c88e7 100644
--- a/sys-cluster/openmpi/openmpi-1.10.3-r2.ebuild
+++ b/sys-cluster/openmpi/openmpi-1.10.6.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
diff --git a/sys-cluster/openmpi/openmpi-2.0.2.ebuild b/sys-cluster/openmpi/openmpi-2.0.2.ebuild
index a799f29b7..559289ae8 100644
--- a/sys-cluster/openmpi/openmpi-2.0.2.ebuild
+++ b/sys-cluster/openmpi/openmpi-2.0.2.ebuild
@@ -51,7 +51,7 @@ MPI_UNCLASSED_DEP_STR="
"
CDEPEND="
- >=dev-libs/libevent-2.0.22[${MULTILIB_USEDEP}]
+ >=dev-libs/libevent-2.0.22[${MULTILIB_USEDEP},threads]
dev-libs/libltdl:0[${MULTILIB_USEDEP}]
>=sys-apps/hwloc-1.11.2[${MULTILIB_USEDEP},numa?]
>=sys-libs/zlib-1.2.8-r1[${MULTILIB_USEDEP}]
diff --git a/sys-cluster/openmpi/openmpi-2.1.0.ebuild b/sys-cluster/openmpi/openmpi-2.1.0.ebuild
new file mode 100644
index 000000000..cf808b6ae
--- /dev/null
+++ b/sys-cluster/openmpi/openmpi-2.1.0.ebuild
@@ -0,0 +1,174 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+FORTRAN_NEEDED=fortran
+
+inherit cuda flag-o-matic fortran-2 java-pkg-opt-2 toolchain-funcs versionator multilib-minimal mpi
+
+MY_P=${P/-mpi}
+S=${WORKDIR}/${MY_P}
+
+IUSE_OPENMPI_FABRICS="
+ openmpi_fabrics_ofed
+ openmpi_fabrics_knem
+ openmpi_fabrics_psm"
+
+IUSE_OPENMPI_RM="
+ openmpi_rm_pbs
+ openmpi_rm_slurm"
+
+IUSE_OPENMPI_OFED_FEATURES="
+ openmpi_ofed_features_control-hdr-padding
+ openmpi_ofed_features_connectx-xrc
+ openmpi_ofed_features_udcm
+ openmpi_ofed_features_rdmacm
+ openmpi_ofed_features_dynamic-sl"
+
+DESCRIPTION="A high-performance message passing library (MPI)"
+HOMEPAGE="http://www.open-mpi.org"
+SRC_URI="http://www.open-mpi.org/software/ompi/v$(get_version_component_range 1-2)/downloads/${MY_P}.tar.bz2"
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux"
+IUSE="cma cuda cxx elibc_FreeBSD fortran heterogeneous ipv6 java mpi-threads numa romio threads
+ ${IUSE_OPENMPI_FABRICS} ${IUSE_OPENMPI_RM} ${IUSE_OPENMPI_OFED_FEATURES}"
+
+REQUIRED_USE="openmpi_rm_slurm? ( !openmpi_rm_pbs )
+ openmpi_rm_pbs? ( !openmpi_rm_slurm )
+ openmpi_fabrics_psm? ( openmpi_fabrics_ofed )
+ openmpi_ofed_features_control-hdr-padding? ( openmpi_fabrics_ofed )
+ openmpi_ofed_features_connectx-xrc? ( openmpi_fabrics_ofed )
+ openmpi_ofed_features_udcm? ( openmpi_fabrics_ofed )
+ openmpi_ofed_features_rdmacm? ( openmpi_fabrics_ofed )
+ openmpi_ofed_features_dynamic-sl? ( openmpi_fabrics_ofed )"
+
+MPI_UNCLASSED_DEP_STR="
+ !>=dev-libs/intel-common-16[mpi]
+"
+
+CDEPEND="
+ >=dev-libs/libevent-2.0.22[${MULTILIB_USEDEP},threads]
+ dev-libs/libltdl:0[${MULTILIB_USEDEP}]
+ >=sys-apps/hwloc-1.11.2[${MULTILIB_USEDEP},numa?]
+ >=sys-libs/zlib-1.2.8-r1[${MULTILIB_USEDEP}]
+ cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.19-r1 )
+ elibc_FreeBSD? ( dev-libs/libexecinfo )
+ openmpi_fabrics_ofed? ( sys-fabric/ofed:* )
+ openmpi_fabrics_knem? ( sys-cluster/knem )
+ openmpi_fabrics_psm? ( sys-fabric/infinipath-psm:* )
+ openmpi_rm_pbs? ( sys-cluster/torque )
+ openmpi_rm_slurm? ( sys-cluster/slurm )
+ openmpi_ofed_features_rdmacm? ( sys-fabric/librdmacm:* )
+ $(mpi_imp_deplist)"
+
+RDEPEND="${CDEPEND}
+ java? ( >=virtual/jre-1.6 )"
+
+DEPEND="${CDEPEND}
+ java? ( >=virtual/jdk-1.6 )"
+
+MULTILIB_WRAPPED_HEADERS=(
+ /usr/include/mpi.h
+ /usr/include/openmpi/ompi/mpi/java/mpiJava.h
+)
+
+pkg_setup() {
+ fortran-2_pkg_setup
+ java-pkg-opt-2_pkg_setup
+ MPI_ESELECT_FILE="eselect.mpi.openmpi"
+
+ elog
+ elog "OpenMPI has an overwhelming count of configuration options."
+ elog "Don't forget the EXTRA_ECONF environment variable can let you"
+ elog "specify configure options if you find them necessary."
+ elog
+}
+
+src_prepare() {
+ default
+
+ # Necessary for scalibility, see
+ # http://www.open-mpi.org/community/lists/users/2008/09/6514.php
+ if use threads; then
+ echo 'oob_tcp_listen_mode = listen_thread' \
+ >> opal/etc/openmpi-mca-params.conf || die
+ fi
+}
+
+multilib_src_configure() {
+ if use java; then
+ # We must always build with the right -source and -target
+ # flags. Passing flags to javac isn't explicitly supported here
+ # but we can cheat by overriding the configure test for javac.
+ export ac_cv_path_JAVAC="$(java-pkg_get-javac) $(java-pkg_javac-args)"
+ fi
+
+ ECONF_SOURCE=${S} econf $(mpi_econf_args) \
+ --sysconfdir="${EPREFIX}/etc/${PN}" \
+ --enable-pretty-print-stacktrace \
+ --enable-orterun-prefix-by-default \
+ --with-hwloc="${EPREFIX}/usr" \
+ --with-libltdl="${EPREFIX}/usr" \
+ --with-libevent="${EPREFIX}/usr" \
+ --enable-mpi-fortran=$(usex fortran all no) \
+ $(use_enable cxx mpi-cxx) \
+ $(use_with cma) \
+ $(use_with cuda cuda "${EPREFIX}"/opt/cuda) \
+ $(use_enable romio io-romio) \
+ $(use_enable heterogeneous) \
+ $(use_enable ipv6) \
+ $(multilib_native_use_enable java) \
+ $(multilib_native_use_enable java mpi-java) \
+ $(multilib_native_use_enable mpi-threads mpi-thread-multiple) \
+ $(multilib_native_use_with openmpi_fabrics_ofed verbs "${EPREFIX}"/usr) \
+ $(multilib_native_use_with openmpi_fabrics_knem knem "${EPREFIX}"/usr) \
+ $(multilib_native_use_with openmpi_fabrics_psm psm "${EPREFIX}"/usr) \
+ $(multilib_native_use_enable openmpi_ofed_features_control-hdr-padding openib-control-hdr-padding) \
+ $(multilib_native_use_enable openmpi_ofed_features_connectx-xrc openib-connectx-xrc) \
+ $(multilib_native_use_enable openmpi_ofed_features_rdmacm openib-rdmacm) \
+ $(multilib_native_use_enable openmpi_ofed_features_udcm openib-udcm) \
+ $(multilib_native_use_enable openmpi_ofed_features_dynamic-sl openib-dynamic-sl) \
+ $(multilib_native_use_with openmpi_rm_pbs tm) \
+ $(multilib_native_use_with openmpi_rm_slurm slurm)
+}
+
+multilib_src_test() {
+ # Doesn't work with the default src_test as the dry run (-n) fails.
+ emake -j1 check
+}
+
+multilib_src_install() {
+ default
+
+ # fortran header cannot be wrapped (bug #540508), workaround part 1
+ if multilib_is_native_abi && use fortran; then
+ mkdir "${T}"/fortran || die
+ mv "${ED}"/$(mpi_root)/usr/include/mpif* "${T}"/fortran || die
+ else
+ # some fortran files get installed unconditionally
+ rm "${ED}"/$(mpi_root)/usr/include/mpif* "${ED}"usr/bin/mpif* || die
+ fi
+}
+
+multilib_src_install_all() {
+ # fortran header cannot be wrapped (bug #540508), workaround part 2
+ if use fortran; then
+ mv "${T}"/fortran/mpif* "${ED}"/$(mpi_root)/usr/include || die
+ fi
+
+ # Remove la files, no static libs are installed and we have pkg-config
+ find "${ED}" -name '*.la' -delete || die
+
+ if use java; then
+ local mpi_jar="${ED}"/$(mpi_root)/usr/$(get_libdir)/mpi.jar
+ java-pkg_dojar "${mpi_jar}"
+ # We don't want to install the jar file twice
+ # so let's clean after ourselves.
+ rm "${mpi_jar}" || die
+ fi
+
+ mpi_dodoc README AUTHORS NEWS VERSION
+ mpi_imp_add_eselect
+}