[gentoo-commits] proj/sci:master commit in: sys-cluster/openmpi/files/, sys-cluster/openmpi/

[Justin Bronder]

commit:     346d974b25441804e803c0cbb4c57935a3a203c3
Author:     Justin Bronder <jbronder <AT> gentoo <DOT> org>
AuthorDate: Tue Jul  2 02:14:17 2013 +0000
Commit:     Justin Bronder <jsbronder <AT> gentoo <DOT> org>
CommitDate: Tue Jul  2 02:14:17 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=346d974b

Do not override malloc when in a sandbox environment.  Resolves #462602.

Package-Manager: portage-2.1.12.2

---
 sys-cluster/openmpi/ChangeLog                      |   8 +-
 ...le-malloc-override-inside-of-Gentoo-sandb.patch |  42 ++++++
 sys-cluster/openmpi/openmpi-1.6.4-r1.ebuild        | 162 +++++++++++++++++++++
 3 files changed, 211 insertions(+), 1 deletion(-)

diff --git a/sys-cluster/openmpi/ChangeLog b/sys-cluster/openmpi/ChangeLog
index 6957971..f457326 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@g.o>
+  +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@g.o> -openmpi-1.6.3.ebuild,
@@ -137,4 +144,3 @@
 
   20 Jan 2009; Alexey Shvetsov <alexxy@g.o> +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 0000000..5683c81
--- /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@×××××.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 0000000..1016b42
--- /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"
+}