From 79e8f729e17450ef6033bdeafb8190c4f0ba3e0a Mon Sep 17 00:00:00 2001 From: Justin Bronder Date: Tue, 2 Jul 2013 02:04:53 +0000 Subject: Do not override malloc when in a sandbox environment. Resolves #462602. Package-Manager: portage-2.1.12.2/cvs/Linux x86_64 Manifest-Sign-Key: 0x4D7043C9 --- sys-cluster/openmpi/ChangeLog | 9 +- sys-cluster/openmpi/Manifest | 13 +- ...le-malloc-override-inside-of-Gentoo-sandb.patch | 42 ++++++ sys-cluster/openmpi/openmpi-1.6.4-r1.ebuild | 160 ++++++++++++++++++++ sys-cluster/openmpi/openmpi-1.6.4.ebuild | 162 --------------------- 5 files changed, 217 insertions(+), 169 deletions(-) create mode 100644 sys-cluster/openmpi/files/hooks-disable-malloc-override-inside-of-Gentoo-sandb.patch create mode 100644 sys-cluster/openmpi/openmpi-1.6.4-r1.ebuild delete mode 100644 sys-cluster/openmpi/openmpi-1.6.4.ebuild (limited to 'sys-cluster') diff --git a/sys-cluster/openmpi/ChangeLog b/sys-cluster/openmpi/ChangeLog index 9f65aeec11d3..444501817fd6 100644 --- a/sys-cluster/openmpi/ChangeLog +++ b/sys-cluster/openmpi/ChangeLog @@ -1,6 +1,13 @@ # ChangeLog for sys-cluster/openmpi # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sys-cluster/openmpi/ChangeLog,v 1.118 2013/04/05 18:11:44 jsbronder Exp $ +# $Header: /var/cvsroot/gentoo-x86/sys-cluster/openmpi/ChangeLog,v 1.119 2013/07/02 02:04:18 jsbronder Exp $ + +*openmpi-1.6.4-r1 (02 Jul 2013) + + 02 Jul 2013; Justin Bronder -openmpi-1.6.4.ebuild, + +openmpi-1.6.4-r1.ebuild, + +files/hooks-disable-malloc-override-inside-of-Gentoo-sandb.patch: + Do not override malloc when in a sandbox environment. Resolves #462602. 05 Apr 2013; Justin Bronder openmpi-1.6.4.ebuild: Export FAKEROOTKEY in src_test to workaround hang in sandbox. See #462602. diff --git a/sys-cluster/openmpi/Manifest b/sys-cluster/openmpi/Manifest index 7262aa4a1d15..18159f8350ac 100644 --- a/sys-cluster/openmpi/Manifest +++ b/sys-cluster/openmpi/Manifest @@ -1,6 +1,7 @@ -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 +AUX hooks-disable-malloc-override-inside-of-Gentoo-sandb.patch 1604 SHA256 5f15d8d54e6dee3485114c86bcbdf395f54da3eff22fb5fe8e99462ec87c326e SHA512 6ddd2cc8ba5df2176abd6b714938e5f906bb455b66418d6f79f4fc4af1f29a5b6d11b820338787efc2f984d03b28bc992710b4e441c7562e00289bdacca30e39 WHIRLPOOL 00c40323b7cec6035271948c111e0be3fcbcf4552f99c51f22c9b8dc4a39e70ad14f9aa855e4485116bab94d3fb20d8988073d12e8ae771c696cedaa47f8f7a1 AUX openmpi-1.4.1-r22513.patch 2460 SHA256 083528f3ccdda8e1654accd5a6d3c79231d7d727cbd1f05293d7850a32503379 SHA512 96d986e7b10b340027872f92b24f62efee7be626a887d410163df956595afa932e002175265ead66d2c31a8bbf86246341671b388d13ef4bda7c16f2ebf23f37 WHIRLPOOL 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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 000000000000..aa6503360b18 --- /dev/null +++ b/sys-cluster/openmpi/openmpi-1.6.4-r1.ebuild @@ -0,0 +1,160 @@ +# 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-1.6.4-r1.ebuild,v 1.1 2013/07/02 02:04:18 jsbronder Exp $ + +EAPI=5 + +FORTRAN_NEEDED=fortran + +inherit eutils fortran-2 multilib flag-o-matic 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} ${IUSE_OPENMPI_OFED_FEATURES}" + +REQUIRED_USE="openmpi_rm_slurm? ( !openmpi_rm_pbs ) + openmpi_rm_pbs? ( !openmpi_rm_slurm ) + openmpi_fabrics_psm? ( openmpi_fabrics_ofed ) + openmpi_ofed_features_control-hdr-padding? ( openmpi_fabrics_ofed ) + openmpi_ofed_features_connectx-xrc? ( openmpi_fabrics_ofed ) + openmpi_ofed_features_rdmacm? ( openmpi_fabrics_ofed ) + openmpi_ofed_features_dynamic-sl? ( openmpi_fabrics_ofed ) + openmpi_ofed_features_failover? ( openmpi_fabrics_ofed )" + +RDEPEND=" + !sys-cluster/mpich2 + !sys-cluster/mpiexec + >=sys-apps/hwloc-1.3 + elibc_FreeBSD? ( dev-libs/libexecinfo ) + openmpi_fabrics_dapl? ( sys-infiniband/dapl ) + openmpi_fabrics_ofed? ( sys-infiniband/ofed ) + openmpi_fabrics_knem? ( sys-cluster/knem ) + openmpi_fabrics_open-mx? ( sys-cluster/open-mx ) + openmpi_fabrics_psm? ( sys-infiniband/infinipath-psm ) + openmpi_fabrics_sctp? ( net-misc/lksctp-tools ) + openmpi_rm_pbs? ( sys-cluster/torque ) + openmpi_rm_slurm? ( sys-cluster/slurm ) + openmpi_ofed_features_rdmacm? ( sys-infiniband/librdmacm ) + vt? ( + !dev-libs/libotf + !app-text/lcdf-typetools + ) + " +DEPEND="${RDEPEND}" +# TODO: Newer releases of Vampir use otf2 which would resolve the above blockers. + +pkg_setup() { + fortran-2_pkg_setup + 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 + 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-thread-multiple + --enable-opal-multi-threads + ) + fi + + if use fortran; then + if [[ $(tc-getFC) =~ g77 ]]; then + myconf+=(--disable-mpi-f90) + elif [[ $(tc-getFC) =~ if ]]; then + # Enabled here as gfortran compile times are huge with this enabled. + myconf+=(--with-mpi-f90-size=medium) + fi + else + myconf+=(--disable-mpi-f90 --disable-mpi-f77) + fi + + ! use vt && myconf+=(--enable-contrib-no-build=vt) + + econf "${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}"/usr/share/libtool &> /dev/null + dodoc README AUTHORS NEWS VERSION || die +} + +src_test() { + # Doesn't work with the default src_test as the dry run (-n) fails. + emake -j1 check || die "emake check failed" +} diff --git a/sys-cluster/openmpi/openmpi-1.6.4.ebuild b/sys-cluster/openmpi/openmpi-1.6.4.ebuild deleted file mode 100644 index 52e6815eb895..000000000000 --- a/sys-cluster/openmpi/openmpi-1.6.4.ebuild +++ /dev/null @@ -1,162 +0,0 @@ -# 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-1.6.4.ebuild,v 1.2 2013/04/05 18:11:44 jsbronder Exp $ - -EAPI=5 - -FORTRAN_NEEDED=fortran - -inherit eutils fortran-2 multilib flag-o-matic 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} ${IUSE_OPENMPI_OFED_FEATURES}" - -REQUIRED_USE="openmpi_rm_slurm? ( !openmpi_rm_pbs ) - openmpi_rm_pbs? ( !openmpi_rm_slurm ) - openmpi_fabrics_psm? ( openmpi_fabrics_ofed ) - openmpi_ofed_features_control-hdr-padding? ( openmpi_fabrics_ofed ) - openmpi_ofed_features_connectx-xrc? ( openmpi_fabrics_ofed ) - openmpi_ofed_features_rdmacm? ( openmpi_fabrics_ofed ) - openmpi_ofed_features_dynamic-sl? ( openmpi_fabrics_ofed ) - openmpi_ofed_features_failover? ( openmpi_fabrics_ofed )" - -RDEPEND=" - !sys-cluster/mpich2 - !sys-cluster/mpiexec - >=sys-apps/hwloc-1.3 - elibc_FreeBSD? ( dev-libs/libexecinfo ) - openmpi_fabrics_dapl? ( sys-infiniband/dapl ) - openmpi_fabrics_ofed? ( sys-infiniband/ofed ) - openmpi_fabrics_knem? ( sys-cluster/knem ) - openmpi_fabrics_open-mx? ( sys-cluster/open-mx ) - openmpi_fabrics_psm? ( sys-infiniband/infinipath-psm ) - openmpi_fabrics_sctp? ( net-misc/lksctp-tools ) - openmpi_rm_pbs? ( sys-cluster/torque ) - openmpi_rm_slurm? ( sys-cluster/slurm ) - openmpi_ofed_features_rdmacm? ( sys-infiniband/librdmacm ) - vt? ( - !dev-libs/libotf - !app-text/lcdf-typetools - ) - " -DEPEND="${RDEPEND}" -# TODO: Newer releases of Vampir use otf2 which would resolve the above blockers. - -pkg_setup() { - fortran-2_pkg_setup - 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 -} - -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-thread-multiple - --enable-opal-multi-threads - ) - fi - - if use fortran; then - if [[ $(tc-getFC) =~ g77 ]]; then - myconf+=(--disable-mpi-f90) - elif [[ $(tc-getFC) =~ if ]]; then - # Enabled here as gfortran compile times are huge with this enabled. - myconf+=(--with-mpi-f90-size=medium) - fi - else - myconf+=(--disable-mpi-f90 --disable-mpi-f77) - fi - - ! use vt && myconf+=(--enable-contrib-no-build=vt) - - econf "${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}"/usr/share/libtool &> /dev/null - dodoc README AUTHORS NEWS VERSION || die -} - -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 - export FAKEROOTKEY=1 - emake -j1 check || die "emake check failed" -} -- cgit v1.2.3-65-gdbad