Merge branch 'master' of https://github.com/gentoo-science/sci into HTCondor

14 files changed, 319 insertions, 13 deletions

diff --git a/sys-cluster/charm/ChangeLog b/sys-cluster/charm/ChangeLog
new file mode 100644
index 000000000..4d51c0e33
--- /dev/null
+++ b/sys-cluster/charm/ChangeLog
@@ -0,0 +1,13 @@
+# ChangeLog for sys-cluster/charm
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+  02 Jul 2013; Nicolas Bock <nicolasbock@gmail.com>
+  +files/charm-6.5.0-charmc-gentoo.patch, charm-6.5.1.ebuild:
+  Added missing patch.
+
+*charm-6.5.1 (02 Jul 2013)
+
+  02 Jul 2013; Nicolas Bock <nicolasbock@gmail.com> +charm-6.5.1.ebuild,
+  +metadata.xml:
+  Version bump to sys-cluster/charm-6.5.1
diff --git a/sys-cluster/charm/Manifest b/sys-cluster/charm/Manifest
new file mode 100644
index 000000000..0a0377625
--- /dev/null
+++ b/sys-cluster/charm/Manifest
@@ -0,0 +1 @@
+DIST charm-6.5.1.tar.gz 19265741 SHA256 68aa43e2a6e476e116a7e80e385c25c6ac6497807348025505ba8bfa256ed34a SHA512 1a25c76f3699e30d0614e85f39ea0f594896cbc299b0e670c52fcea176171e8834ea7f9ba3ba0c1957598b0f1cbfa6a4ed9279ae0c030fa32faa6acca879b694 WHIRLPOOL 0def514af09c137b951842250fe112c68e573e8eff7d5911a71ccbe55cc38b319f1d9c4587e706777f748b0c1ef69b63c4161bbf663b05984a566ff325fa49c3
diff --git a/sys-cluster/charm/charm-6.5.1.ebuild b/sys-cluster/charm/charm-6.5.1.ebuild
new file mode 100644
index 000000000..74ba894be
--- /dev/null
+++ b/sys-cluster/charm/charm-6.5.1.ebuild
@@ -0,0 +1,181 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sys-cluster/charm/charm-6.5.0.ebuild,v 1.1 2013/06/26 23:58:38 ottxor Exp $
+
+EAPI=5
+
+inherit eutils flag-o-matic fortran-2 multilib toolchain-funcs
+
+DESCRIPTION="Message-passing parallel language and runtime system"
+HOMEPAGE="http://charm.cs.uiuc.edu/"
+SRC_URI="http://charm.cs.uiuc.edu/distrib/${P}.tar.gz"
+
+LICENSE="charm"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="charmdebug charmtracing charmproduction cmkopt doc examples mpi smp static-libs tcp"
+
+RDEPEND="mpi? ( virtual/mpi )"
+DEPEND="
+	${RDEPEND}
+	doc? (
+		>=app-text/poppler-0.12.3-r3[utils]
+		dev-tex/latex2html
+		virtual/tex-base
+	)"
+
+REQUIRED_USE="
+	cmkopt? ( !charmdebug !charmtracing )
+	charmproduction? ( !charmdebug !charmtracing )"
+
+FORTRAN_STANDARD="90"
+
+src_prepare() {
+	# Build shared libraries by default.
+	CHARM_OPTS="--build-shared"
+	if use charmproduction; then
+		CHARM_OPTS+=" --with-production"
+	else
+		if use charmdebug; then
+			CHARM_OPTS+=" --with-charmdebug"
+		fi
+
+		if use charmtracing; then
+			CHARM_OPTS+=" --with-tracing --with-tracing-commthread"
+		fi
+	fi
+
+	# TCP instead of default UDP for socket comunication
+	# protocol
+	CHARM_OPTS+="$(usex tcp ' tcp' '')"
+
+	# enable direct SMP support using shared memory
+	CHARM_OPTS+="$(usex smp ' smp' '')"
+
+	# CMK optimization
+	use cmkopt && append-cppflags -DCMK_OPTIMIZE=1
+
+	sed \
+		-e "/CMK_CF90/s:f90:$(usex mpi "mpif90" "$(tc-getFC)"):g" \
+		-e "/CMK_CXX/s:g++:$(usex mpi "mpic++" "$(tc-getCXX)"):g" \
+		-e "/CMK_CC/s:gcc:$(usex mpi "mpicc" "$(tc-getCC)"):g" \
+		-e '/CMK_F90_MODINC/s:-p:-I:g' \
+		-e "/CMK_LD/s:\"$: ${LDFLAGS} \":g" \
+		-i src/arch/$(usex mpi "mpi" "net")-linux*/*sh || die
+
+	sed \
+		-e "s:-o conv-cpm:${LDFLAGS} &:g" \
+		-e "s:-o charmxi:${LDFLAGS} &:g" \
+		-e "s:-o charmrun-silent:${LDFLAGS} &:g" \
+		-e "s:-o charmrun-notify:${LDFLAGS} &:g" \
+		-e "s:-o charmrun:${LDFLAGS} &:g" \
+		-e "s:-o charmd_faceless:${LDFLAGS} &:g" \
+		-e "s:-o charmd:${LDFLAGS} &:g" \
+		-i \
+		src/scripts/Makefile \
+		src/arch/net/charmrun/Makefile || die
+
+	# Fix QA notice.
+	append-cflags -DALLOCA_H
+
+	einfo "charm opts: ${CHARM_OPTS}"
+}
+
+src_compile() {
+	# Build charmm++ first.
+	./build charm++ $(usex mpi "mpi" "net")-linux$(usex amd64 "-amd64" '') \
+		${CHARM_OPTS} ${MAKEOPTS} ${CFLAGS} || die "Failed to build charm++"
+
+	# make pdf/html docs
+	if use doc; then
+		cd "${S}"/doc
+		make doc || die "failed to create pdf/html docs"
+	fi
+}
+
+src_test() {
+	make -C tests/charm++ test TESTOPTS="++local" || die
+}
+
+src_install() {
+	# Make charmc play well with gentoo before we move it into /usr/bin.
+	epatch "${FILESDIR}/charm-6.5.0-charmc-gentoo.patch"
+
+	sed -e "s|gentoo-include|${P}|" \
+		-e "s|gentoo-libdir|$(get_libdir)|g" \
+		-e "s|VERSION|${P}/VERSION|" \
+		-i ./src/scripts/charmc || die "failed patching charmc script"
+
+	# In the following, some of the files are symlinks to ../tmp which we need
+	# to dereference first (see bug 432834).
+
+	local i
+
+	# Install binaries.
+	for i in bin/*; do
+		if [[ -L ${i} ]]; then
+			i=$(readlink -e "${i}") || die
+		fi
+		dobin "${i}"
+	done
+
+	# Install headers.
+	insinto /usr/include/${P}
+	for i in include/*; do
+		if [[ -L ${i} ]]; then
+			i=$(readlink -e "${i}") || die
+		fi
+		doins "${i}"
+	done
+
+	# Install static libs. Charm has a lot of .o "libs" that it requires at
+	# runtime.
+	if use static-libs; then
+		for i in lib/*.{a,o}; do
+			if [[ -L ${i} ]]; then
+				i=$(readlink -e "${i}") || die
+			fi
+			dolib "${i}"
+		done
+	fi
+
+	# Install shared libs.
+	for i in lib_so/*; do
+		if [[ -L ${i} ]]; then
+			i=$(readlink -e "${i}") || die
+		fi
+		dolib.so "${i}"
+	done
+
+	# Basic docs.
+	dodoc CHANGES README
+
+	# Install examples.
+	if use examples; then
+		find examples/ -name 'Makefile' | xargs sed \
+			-r "s:(../)+bin/charmc:/usr/bin/charmc:" -i || \
+			die "Failed to fix examples"
+		find examples/ -name 'Makefile' | xargs sed \
+			-r "s:./charmrun:./charmrun ++local:" -i || \
+			die "Failed to fix examples"
+		insinto /usr/share/doc/${PF}/examples
+		doins -r examples/charm++/*
+	fi
+
+	# Install pdf/html docs
+	if use doc; then
+		cd "${S}"/doc
+		# Install pdfs.
+		insinto /usr/share/doc/${PF}/pdf
+		doins  doc/pdf/*
+		# Install html.
+		docinto html
+		dohtml -r doc/html/*
+	fi
+}
+
+pkg_postinst() {
+	einfo "Please test your charm installation by copying the"
+	einfo "content of /usr/share/doc/${PF}/examples to a"
+	einfo "temporary location and run 'make test'."
+}
diff --git a/sys-cluster/charm/files/charm-6.5.0-charmc-gentoo.patch b/sys-cluster/charm/files/charm-6.5.0-charmc-gentoo.patch
new file mode 100644
index 000000000..34923e3f7
--- /dev/null
+++ b/sys-cluster/charm/files/charm-6.5.0-charmc-gentoo.patch
@@ -0,0 +1,25 @@
+--- src/scripts/charmc.old	2013-05-30 10:18:02.261819771 -0600
++++ src/scripts/charmc	2013-05-30 10:19:50.839661634 -0600
+@@ -361,19 +361,9 @@
+ 	PROG_EXT=".exe"
+ fi
+ 
+-CHARMLIB="$CHARMBIN/../lib"
+-CHARMINC="$CHARMBIN/../include"
+-CHARMLIBSO=
+-if test -d "$CHARMBIN/../lib_so" 
+-then
+-  CHARMLIBSO=`cd $CHARMBIN/../lib_so 2>/dev/null && pwd`
+-  #getting absolute path is harder than thought because of symbolic links and ..
+-  #ksh needs cd -P to resolve werid symbolic links, however -P is not portable
+-  #csh is ok too if it exists 
+-  test -z "$CHARMLIBSO" && CHARMLIBSO=`cd -P $CHARMBIN/../lib_so 2>/dev/null && pwd`
+-  test -z "$CHARMLIBSO" && CHARMLIBSO=`csh -c "cd $CHARMBIN/../lib_so >& /dev/null && pwd"`
+-  test -z "$CHARMLIBSO" && echo "$CHARMBIN/../lib_so: not found" && exit 1
+-fi
++CHARMLIB="/usr/gentoo-libdir"
++CHARMINC="/usr/include/gentoo-include"
++CHARMLIBSO="/usr/gentoo-libdir"
+ 
+ ##############################################################################
+ #
diff --git a/sys-cluster/charm/metadata.xml b/sys-cluster/charm/metadata.xml
new file mode 100644
index 000000000..ea5896e21
--- /dev/null
+++ b/sys-cluster/charm/metadata.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<herd>sci</herd>
+	<maintainer>
+		<email>nicolasbock@gmail.com</email>
+	</maintainer>
+	<use>
+		<flag name="charmdebug">Enable the charm debugger</flag>
+		<flag name="charmproduction">Optimize performance of Charm++ runtime</flag>
+		<flag name="charmtracing">Enable tracing support in Charm++</flag>
+		<flag name="cmkopt">Enable CMK optimisation</flag>
+		<flag name="tcp">Use TCP (instead of UPD) for socket communication</flag>
+	</use>
+</pkgmetadata>
diff --git a/sys-cluster/empi/ChangeLog b/sys-cluster/empi/ChangeLog
index b69a7dfb4..067558d85 100644
--- a/sys-cluster/empi/ChangeLog
+++ b/sys-cluster/empi/ChangeLog
@@ -2,6 +2,20 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  02 Jul 2013; Justin Lecher <jlec@gentoo.org> empi-0.9.ebuild,
+  -files/ChangeLog-0.8, -files/eselect.mpi-0.8, +files/ChangeLog-0.9,
+  +files/eselect.mpi-0.9:
+  Fix version Bump
+
+  02 Jul 2013; Justin Lecher <jlec@gentoo.org> empi-0.9.ebuild, metadata.xml:
+  Bump EAPI, fix DESCRIPTION
+
+*empi-0.9 (02 Jul 2013)
+
+  02 Jul 2013; Justin Bronder <jsbronder@gentoo.org> -empi-0.8.ebuild,
+  +empi-0.9.ebuild, -files/empi-0.8, +files/empi-0.9:
+  bump
+
 *empi-0.8 (22 Feb 2013)
 
   22 Feb 2013; Justin Bronder <jsbronder@gentoo.org> -files/ChangeLog-0.7,
diff --git a/sys-cluster/empi/empi-0.8.ebuild b/sys-cluster/empi/empi-0.9.ebuild
index bb3daffe0..a78565a9e 100644
--- a/sys-cluster/empi/empi-0.8.ebuild
+++ b/sys-cluster/empi/empi-0.9.ebuild
@@ -2,9 +2,11 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
+EAPI=5
+
 inherit eutils
 
-DESCRIPTION="empi"
+DESCRIPTION="Handling Multiple MPI Implementations"
 HOMEPAGE="http://dev.gentoo.org/~jsbronder/empi.xml"
 SRC_URI=""
 
@@ -15,13 +17,15 @@ IUSE=""
 DEPEND="app-admin/eselect"
 RDEPEND="${DEPEND}"
 
+S="${WORKDIR}"
+
 src_install() {
-	newbin "${FILESDIR}"/${P} ${PN} || die
-	dodoc "${FILESDIR}"/README.txt || die
-	dodoc "${FILESDIR}"/ChangeLog-${PV} || die
+	newbin "${FILESDIR}"/${P} ${PN}
+	dodoc "${FILESDIR}"/README.txt
+	dodoc "${FILESDIR}"/ChangeLog-${PV}
 
 	insinto /usr/share/eselect/modules
-	newins "${FILESDIR}"/eselect.mpi-${PV} mpi.eselect || die
+	newins "${FILESDIR}"/eselect.mpi-${PV} mpi.eselect
 	exeinto /etc/profile.d
 	doexe "${FILESDIR}"/mpi.sh
 	doexe "${FILESDIR}"/mpi.csh
diff --git a/sys-cluster/empi/files/ChangeLog-0.8 b/sys-cluster/empi/files/ChangeLog-0.9
index 15652b092..15652b092 100644
--- a/sys-cluster/empi/files/ChangeLog-0.8
+++ b/sys-cluster/empi/files/ChangeLog-0.9
diff --git a/sys-cluster/empi/files/empi-0.8 b/sys-cluster/empi/files/empi-0.9
index a1e6009b6..8a9523c58 100755
--- a/sys-cluster/empi/files/empi-0.8
+++ b/sys-cluster/empi/files/empi-0.9
@@ -1,5 +1,5 @@
 #!/bin/bash
-VERSION=0.8
+VERSION=0.9
 
 source /etc/init.d/functions.sh
 
@@ -356,7 +356,7 @@ add_packages(){
         fi
 
         # I don't know about this, but do you have a better idea?
-        deps="$(emerge --color=n --onlydeps -p --quiet ${TARGETS[i]})"
+        deps="$(emerge --color=n --onlydeps -p --quiet ${TARGETS[i]} | grep '^\[')"
         if [[ $? -ne 0 ]]; then
             emerge --onlydeps -p ${TARGETS[i]}
             die "Unable to calculate deps for ${TARGETS[i]}"
diff --git a/sys-cluster/empi/files/eselect.mpi-0.8 b/sys-cluster/empi/files/eselect.mpi-0.9
index e1f0902a9..e1f0902a9 100644
--- a/sys-cluster/empi/files/eselect.mpi-0.8
+++ b/sys-cluster/empi/files/eselect.mpi-0.9
diff --git a/sys-cluster/empi/metadata.xml b/sys-cluster/empi/metadata.xml
index 3d994f9db..16a601fe0 100644
--- a/sys-cluster/empi/metadata.xml
+++ b/sys-cluster/empi/metadata.xml
@@ -1,8 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<herd>cluster</herd>
-	<maintainer>
-		<email>jsbronder@gentoo.org</email>
-	</maintainer>
+  <herd>cluster</herd>
+  <maintainer>
+    <email>jsbronder@gentoo.org</email>
+  </maintainer>
 </pkgmetadata>
diff --git a/sys-cluster/openmpi/ChangeLog b/sys-cluster/openmpi/ChangeLog
index 695797172..9b844ff43 100644
--- a/sys-cluster/openmpi/ChangeLog
+++ b/sys-cluster/openmpi/ChangeLog
@@ -2,6 +2,16 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  02 Jul 2013; Justin Bronder <jsbronder@gentoo.org> -openmpi-1.6.4.ebuild:
+  Remove old
+
+*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 +147,3 @@
 
   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.ebuild b/sys-cluster/openmpi/openmpi-1.6.4-r1.ebuild
index 3625aa196..1016b4209 100644
--- a/sys-cluster/openmpi/openmpi-1.6.4.ebuild
+++ b/sys-cluster/openmpi/openmpi-1.6.4-r1.ebuild
@@ -95,6 +95,9 @@ src_prepare() {
 		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() {
@@ -155,6 +158,5 @@ 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"
 }