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author | Justin Bronder <jbronder@gentoo.org> | 2013-07-01 22:14:17 -0400 |
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committer | Justin Bronder <jbronder@gentoo.org> | 2013-07-01 22:14:17 -0400 |
commit | 346d974b25441804e803c0cbb4c57935a3a203c3 (patch) | |
tree | db06d4ce4bc1555dd81e4b27e5d13d94f7ca49f0 /sys-cluster/openmpi | |
parent | workaround OpenMPI build issue #462602 (diff) | |
download | sci-346d974b25441804e803c0cbb4c57935a3a203c3.tar.gz sci-346d974b25441804e803c0cbb4c57935a3a203c3.tar.bz2 sci-346d974b25441804e803c0cbb4c57935a3a203c3.zip |
Do not override malloc when in a sandbox environment. Resolves #462602.
Package-Manager: portage-2.1.12.2
Diffstat (limited to 'sys-cluster/openmpi')
-rw-r--r-- | sys-cluster/openmpi/ChangeLog | 8 | ||||
-rw-r--r-- | sys-cluster/openmpi/files/hooks-disable-malloc-override-inside-of-Gentoo-sandb.patch | 42 | ||||
-rw-r--r-- | sys-cluster/openmpi/openmpi-1.6.4-r1.ebuild | 162 |
3 files changed, 211 insertions, 1 deletions
diff --git a/sys-cluster/openmpi/ChangeLog b/sys-cluster/openmpi/ChangeLog index 695797172..f457326d8 100644 --- a/sys-cluster/openmpi/ChangeLog +++ b/sys-cluster/openmpi/ChangeLog @@ -2,6 +2,13 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*openmpi-1.6.4-r1 (02 Jul 2013) + + 02 Jul 2013; Justin Bronder <jsbronder@gentoo.org> + +files/hooks-disable-malloc-override-inside-of-Gentoo-sandb.patch, + +openmpi-1.6.4-r1.ebuild: + Do not override malloc when in a sandbox environment. Resolves #462602. + *openmpi-1.6.4 (09 Apr 2013) 09 Apr 2013; Justin Bronder <jsbronder@gentoo.org> -openmpi-1.6.3.ebuild, @@ -137,4 +144,3 @@ 20 Jan 2009; Alexey Shvetsov <alexxy@gentoo.org> +openmpi-1.3.ebuild: Version bump - diff --git a/sys-cluster/openmpi/files/hooks-disable-malloc-override-inside-of-Gentoo-sandb.patch b/sys-cluster/openmpi/files/hooks-disable-malloc-override-inside-of-Gentoo-sandb.patch new file mode 100644 index 000000000..5683c81b4 --- /dev/null +++ b/sys-cluster/openmpi/files/hooks-disable-malloc-override-inside-of-Gentoo-sandb.patch @@ -0,0 +1,42 @@ +From 094de74dc5e518a931c495692143ea3282553674 Mon Sep 17 00:00:00 2001 +From: Justin Bronder <jsbronder@gmail.com> +Date: Mon, 1 Jul 2013 20:37:17 -0400 +Subject: [PATCH] hooks: disable malloc override inside of Gentoo sandbox + +As described in the comments in the source, Gentoo's own version of +fakeroot, sandbox, also runs into hangs when malloc is overridden. +Sandbox environments can easily be detected by looking for SANDBOX_PID +in the environment. When detected, employ the same fix used for +fakeroot. + +See https://bugs.gentoo.org/show_bug.cgi?id=462602 +--- + opal/mca/memory/linux/hooks.c | 11 +++++++++-- + 1 file changed, 9 insertions(+), 2 deletions(-) + +diff --git a/opal/mca/memory/linux/hooks.c b/opal/mca/memory/linux/hooks.c +index 6a1646f..ce91e76 100644 +--- a/opal/mca/memory/linux/hooks.c ++++ b/opal/mca/memory/linux/hooks.c +@@ -747,9 +747,16 @@ static void opal_memory_linux_malloc_init_hook(void) + "fakeroot" build environment that allocates memory during + stat() (see http://bugs.debian.org/531522). It may not be + necessary any more since we're using access(), not stat(). But +- we'll leave the check, anyway. */ ++ we'll leave the check, anyway. ++ ++ This is also an issue when using Gentoo's version of 'fakeroot', ++ sandbox v2.5. Sandbox environments can also be detected fairly ++ easily by looking for SANDBOX_PID. ++ */ ++ + if (getenv("FAKEROOTKEY") != NULL || +- getenv("FAKED_MODE") != NULL) { ++ getenv("FAKED_MODE") != NULL || ++ getenv("SANDBOX_PID") != NULL ) { + return; + } + +-- +1.8.1.5 + diff --git a/sys-cluster/openmpi/openmpi-1.6.4-r1.ebuild b/sys-cluster/openmpi/openmpi-1.6.4-r1.ebuild new file mode 100644 index 000000000..1016b4209 --- /dev/null +++ b/sys-cluster/openmpi/openmpi-1.6.4-r1.ebuild @@ -0,0 +1,162 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sys-cluster/openmpi/openmpi-1.2.4.ebuild,v 1.2 2007/12/13 22:39:53 jsbronder Exp $ + +EAPI=5 + +FORTRAN_NEEDED=fortran + +inherit eutils flag-o-matic fortran-2 multilib mpi toolchain-funcs versionator + +MY_P=${P/-mpi} +S=${WORKDIR}/${MY_P} + +IUSE_OPENMPI_FABRICS=" + openmpi_fabrics_dapl + openmpi_fabrics_ofed + openmpi_fabrics_knem + openmpi_fabrics_open-mx + openmpi_fabrics_psm + openmpi_fabrics_sctp" + +IUSE_OPENMPI_RM=" + openmpi_rm_pbs + openmpi_rm_slurm" + +IUSE_OPENMPI_OFED_FEATURES=" + openmpi_ofed_features_control-hdr-padding + openmpi_ofed_features_connectx-xrc + openmpi_ofed_features_rdmacm + openmpi_ofed_features_dynamic-sl + openmpi_ofed_features_failover" + +DESCRIPTION="A high-performance message passing library (MPI)" +HOMEPAGE="http://www.open-mpi.org" +SRC_URI="http://www.open-mpi.org/software/ompi/v$(get_version_component_range 1-2)/downloads/${MY_P}.tar.bz2" +LICENSE="BSD" +SLOT="0" +KEYWORDS="~alpha ~amd64 ~ia64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-fbsd ~x86-fbsd ~amd64-linux" +IUSE="+cxx elibc_FreeBSD fortran heterogeneous ipv6 mpi-threads romio threads vt + ${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_rdmacm? ( openmpi_fabrics_ofed ) + openmpi_ofed_features_dynamic-sl? ( openmpi_fabrics_ofed ) + openmpi_ofed_features_failover? ( openmpi_fabrics_ofed )" + +MPI_UNCLASSED_DEP_STR=" + vt? ( + !dev-libs/libotf + !app-text/lcdf-typetools + )" + +RDEPEND=" + >=sys-apps/hwloc-1.3 + elibc_FreeBSD? ( dev-libs/libexecinfo ) + openmpi_fabrics_dapl? ( sys-infiniband/dapl ) + openmpi_fabrics_ofed? ( sys-infiniband/ofed ) + openmpi_fabrics_knem? ( sys-cluster/knem ) + openmpi_fabrics_open-mx? ( sys-cluster/open-mx ) + openmpi_fabrics_psm? ( sys-infiniband/infinipath-psm ) + openmpi_fabrics_sctp? ( net-misc/lksctp-tools ) + openmpi_rm_pbs? ( sys-cluster/torque ) + openmpi_rm_slurm? ( sys-cluster/slurm ) + openmpi_ofed_features_rdmacm? ( sys-infiniband/librdmacm ) + $(mpi_imp_deplist)" +DEPEND="${RDEPEND}" + +pkg_setup() { + fortran-2_pkg_setup + MPI_ESELECT_FILE="eselect.mpi.openmpi" + + if use mpi-threads; then + echo + ewarn "WARNING: use of MPI_THREAD_MULTIPLE is still disabled by" + ewarn "default and officially unsupported by upstream." + ewarn "You may stop now and set USE=-mpi-threads" + echo + fi + + echo + 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." + echo +} + +src_prepare() { + # 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 + fi + + # 462602 + epatch "${FILESDIR}"/hooks-disable-malloc-override-inside-of-Gentoo-sandb.patch +} + +src_configure() { + local myconf=( + --sysconfdir="${EPREFIX}/etc/${PN}" + --enable-pretty-print-stacktrace + --enable-orterun-prefix-by-default + --with-hwloc="${EPREFIX}/usr" + ) + + if use mpi-threads; then + myconf+=(--enable-mpi-threads + --enable-opal-multi-threads) + fi + + if use fortran; then + if [[ $(tc-getFC) =~ g77 ]]; then + myconf+=(--disable-mpi-f90) + elif [[ $(tc-getFC) =~ if ]]; then + # Enabled here as gfortran compile times are huge with this enabled. + myconf+=(--with-mpi-f90-size=medium) + fi + else + myconf+=(--disable-mpi-f90 --disable-mpi-f77) + fi + + ! use vt && myconf+=(--enable-contrib-no-build=vt) + + econf $(mpi_econf_args) "${myconf[@]}" \ + $(use_enable cxx mpi-cxx) \ + $(use_enable romio io-romio) \ + $(use_enable heterogeneous) \ + $(use_enable ipv6) \ + $(use_with openmpi_fabrics_dapl udapl "${EPREFIX}"/usr) \ + $(use_with openmpi_fabrics_ofed openib "${EPREFIX}"/usr) \ + $(use_with openmpi_fabrics_knem knem "${EPREFIX}"/usr) \ + $(use_with openmpi_fabrics_open-mx mx "${EPREFIX}"/usr) \ + $(use_with openmpi_fabrics_psm psm "${EPREFIX}"/usr) \ + $(use_enable openmpi_ofed_features_control-hdr-padding openib-control-hdr-padding) \ + $(use_enable openmpi_ofed_features_connectx-xrc openib-connectx-xrc) \ + $(use_enable openmpi_ofed_features_rdmacm openib-rdmacm) \ + $(use_enable openmpi_ofed_features_dynamic-sl openib-dynamic-sl) \ + $(use_enable openmpi_ofed_features_failover btl-openib-failover) \ + $(use_with openmpi_fabrics_sctp sctp) \ + $(use_with openmpi_rm_pbs tm) \ + $(use_with openmpi_rm_slurm slurm) +} + +src_install () { + emake DESTDIR="${D}" install || die "make install failed" + # From USE=vt see #359917 + rm "${ED}"/$(mpi_root)/usr/share/libtool &> /dev/null + mpi_dodoc README AUTHORS NEWS VERSION || die + mpi_imp_add_eselect +} + +src_test() { + # Doesn't work with the default src_test as the dry run (-n) fails. + + # Do not override malloc during build. Works around #462602 + emake -j1 check || die "emake check failed" +} |