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authorJustin Bronder <jsbronder@gentoo.org>2011-03-28 12:59:58 -0400
committerJustin Bronder <jsbronder@gentoo.org>2011-05-01 21:22:57 -0400
commit15d2c6558b1bb9e8b9eeecaf93da55ab8d3e142f (patch)
tree71754c3ed84d03602b0114e98cf37875f2e0c49c /sys-cluster
parent[sci-chemistry/gromacs] sync with tree (diff)
downloadsci-15d2c6558b1bb9e8b9eeecaf93da55ab8d3e142f.tar.gz
sci-15d2c6558b1bb9e8b9eeecaf93da55ab8d3e142f.tar.bz2
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Fix hardened test failure (#360185) and cleanup.
(Portage version: 2.1.9.44/git/Linux x86_64, RepoMan options: --force, signed Manifest commit with key 4D7043C9)
Diffstat (limited to 'sys-cluster')
-rw-r--r--sys-cluster/openmpi/ChangeLog5
-rw-r--r--sys-cluster/openmpi/Manifest14
-rw-r--r--sys-cluster/openmpi/files/openmpi-1.4.1-r22513.patch72
-rw-r--r--sys-cluster/openmpi/files/openmpi-r24328.patch54
-rw-r--r--sys-cluster/openmpi/openmpi-1.5.3.ebuild3
5 files changed, 69 insertions, 79 deletions
diff --git a/sys-cluster/openmpi/ChangeLog b/sys-cluster/openmpi/ChangeLog
index c8d9a5120..1a5a8ff37 100644
--- a/sys-cluster/openmpi/ChangeLog
+++ b/sys-cluster/openmpi/ChangeLog
@@ -2,6 +2,11 @@
# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 28 Mar 2011; Justin Bronder <jsbronder@gentoo.org>
+ -files/openmpi-1.4.1-r22513.patch, +files/openmpi-r24328.patch,
+ openmpi-1.5.3.ebuild:
+ Fix hardened test failure (#360185) and cleanup.
+
22 Mar 2011; Justin Bronder <jsbronder@gentoo.org> openmpi-1.5.3.ebuild:
Remove libtool if it was installed by USE=vt, bug #359917.
diff --git a/sys-cluster/openmpi/Manifest b/sys-cluster/openmpi/Manifest
index 0272f0df5..db5898e4e 100644
--- a/sys-cluster/openmpi/Manifest
+++ b/sys-cluster/openmpi/Manifest
@@ -2,15 +2,15 @@
Hash: SHA1
AUX eselect.mpi.openmpi 225 RMD160 cf81165864aaad2833f7a8300c20376210a575dd SHA1 8b50b90346b52b831a59ec0abd8e3dbebad2b94e SHA256 df4d363e9fbab74c234b75f426b7f38ef83d16da2b099222c0dde4a2c3ece687
-AUX openmpi-1.4.1-r22513.patch 2460 RMD160 94c6ca7c7d869039e73f1dbd5402ccd0d5949f11 SHA1 a924c63a94546f25a25beb15328ff2ee18c388e8 SHA256 083528f3ccdda8e1654accd5a6d3c79231d7d727cbd1f05293d7850a32503379
+AUX openmpi-r24328.patch 1707 RMD160 4db5f60d692268e1e42ebbc5379cec245b14daa5 SHA1 25a3ac77307b4681e3f917e61ff88daa58dab508 SHA256 3149f47463057e3263a242b2df88b588074f07395d437b585c5ce37f84aadf83
DIST openmpi-1.5.3.tar.bz2 7589097 RMD160 c1d0950c9a5c53c8543838adadf6a7477abe3989 SHA1 669565c708deab82ad4069d82675b2020eb0e0c6 SHA256 70745806cdbe9b945d47d9fa058f99e072328e41e40c0ced6dd75220885c5263
-EBUILD openmpi-1.5.3.ebuild 3015 RMD160 0d6e811491b585c8d83fcbe411b9b6b903223809 SHA1 28da4ecbfdee6ee16a780344bc923575f29f6e61 SHA256 07f46b3b697a461b13b49875fe6e728f20803312b553a29501ee3e39deb2873b
-MISC ChangeLog 3922 RMD160 6cdc5746484524afbfaf5f1543856f786b1c7561 SHA1 1b87dab68f1f71c99fd539600ef406ed92da57f6 SHA256 c5f36ce678dc9461a463da065765b663dc854325f2169a7e1d9e782b3ecf7f5c
+EBUILD openmpi-1.5.3.ebuild 3080 RMD160 4e482cbd034eb65427d2453cc1ae50afdd6ce0d5 SHA1 54cc5216c0094bffab4c1bbe849678e876a1d54d SHA256 67530c2d9172ba89ed5093783440af7c1d08b34429dda230710571043707dae7
+MISC ChangeLog 4117 RMD160 c8dca40ba9e0467cd56994e332dbb26f6b9923c2 SHA1 8b17d306d67417c83ca185447dafd9bcf30d9913 SHA256 ac3bf5229f83c6438730cfea55f2495b84fd95bd8606203fea201061fecda402
MISC metadata.xml 656 RMD160 223aeb0c645345a35fc674e30cc9f17d936db762 SHA1 f0af00a84589ada70477d0fa12afe21c57a16071 SHA256 809b9f410e784da55e240612ca9542e718f25f65819acda4b3429b22114619e6
-----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.16 (GNU/Linux)
+Version: GnuPG v2.0.17 (GNU/Linux)
-iEYEARECAAYFAk2I4CsACgkQ4MrvBE1wQ8n4uACgpHKqz/obm0hmVEXa+fxTRzG4
-Kd0AnjjJxxVv+vbbZGYPOi9pAko/H9Fk
-=tDkk
+iEYEARECAAYFAk2Qvo4ACgkQ4MrvBE1wQ8kTFQCgj30m+GpKF3T58fbdbxthe2Hx
+ANcAn2TlY1STINh+hjm5Px+mBGxljA83
+=dckP
-----END PGP SIGNATURE-----
diff --git a/sys-cluster/openmpi/files/openmpi-1.4.1-r22513.patch b/sys-cluster/openmpi/files/openmpi-1.4.1-r22513.patch
deleted file mode 100644
index 128443be5..000000000
--- a/sys-cluster/openmpi/files/openmpi-1.4.1-r22513.patch
+++ /dev/null
@@ -1,72 +0,0 @@
-From 9657a0fc671dd0987b6954932a08b680c35f480f Mon Sep 17 00:00:00 2001
-From: Justin Bronder <jsbronder@gmail.com>
-Date: Wed, 3 Feb 2010 17:13:13 -0500
-Subject: [PATCH] Backport r22513
-
-Per #2201, move the user arguments up to be the first set of argv
-after the compiler argv tokens.
-
-Not closing #2201 yet; there's still discussion on that ticket about
-whether we want to do more or not.
-
-Refs #2201
-cmr:v1.4.2
-cmr:v1.5
-
-Author: jsquyres
----
- ompi/tools/wrappers/ompi_wrapper_script.in | 4 +++-
- opal/tools/wrappers/opal_wrapper.c | 9 +++++----
- 2 files changed, 8 insertions(+), 5 deletions(-)
-
-diff --git a/ompi/tools/wrappers/ompi_wrapper_script.in b/ompi/tools/wrappers/ompi_wrapper_script.in
-index 24726ad..87fd8a5 100644
---- a/ompi/tools/wrappers/ompi_wrapper_script.in
-+++ b/ompi/tools/wrappers/ompi_wrapper_script.in
-@@ -140,13 +140,15 @@ my @exec_argv = ();
-
- # assemble command
- push(@exec_argv, split(' ', $comp));
-+# Per https://svn.open-mpi.org/trac/ompi/ticket/2201, add all the user
-+# arguments before anything else.
-+push(@exec_argv, @appargs);
- if ($want_preproc == 1) {
- push(@exec_argv, split(' ', $preproc_flags));
- }
- if ($want_compile == 1) {
- push(@exec_argv, split(' ', $comp_flags));
- }
--push(@exec_argv, @appargs);
- if ($want_link == 1) {
- push(@exec_argv, split(' ', $linker_flags));
- push(@exec_argv, split(' ', $libs));
-diff --git a/opal/tools/wrappers/opal_wrapper.c b/opal/tools/wrappers/opal_wrapper.c
-index 86ece5b..1b80f53 100644
---- a/opal/tools/wrappers/opal_wrapper.c
-+++ b/opal/tools/wrappers/opal_wrapper.c
-@@ -712,6 +712,11 @@ main(int argc, char *argv[])
- exec_argc = 0;
- }
-
-+ /* Per https://svn.open-mpi.org/trac/ompi/ticket/2201, add all the
-+ user arguments before anything else. */
-+ opal_argv_insert(&exec_argv, exec_argc, user_argv);
-+ exec_argc = opal_argv_count(exec_argv);
-+
- /* preproc flags */
- if (flags & COMP_WANT_PREPROC) {
- opal_argv_insert(&exec_argv, exec_argc, options_data[user_data_idx].preproc_flags);
-@@ -732,10 +737,6 @@ main(int argc, char *argv[])
- exec_argc = opal_argv_count(exec_argv);
- }
-
-- /* add all the user arguments */
-- opal_argv_insert(&exec_argv, exec_argc, user_argv);
-- exec_argc = opal_argv_count(exec_argv);
--
- /* link flags and libs */
- if (flags & COMP_WANT_LINK) {
- opal_argv_insert(&exec_argv, exec_argc, options_data[user_data_idx].link_flags);
---
-1.6.4.4
-
diff --git a/sys-cluster/openmpi/files/openmpi-r24328.patch b/sys-cluster/openmpi/files/openmpi-r24328.patch
new file mode 100644
index 000000000..bbd689d3a
--- /dev/null
+++ b/sys-cluster/openmpi/files/openmpi-r24328.patch
@@ -0,0 +1,54 @@
+From cf054cd92dfac55f3920e805d01c11dcfc2cd4fa Mon Sep 17 00:00:00 2001
+From: jsquyres <jsquyres@cisco.com>
+Date: Mon, 28 Mar 2011 12:44:06 -0400
+Subject: [PATCH] Fix some fairly-important typos (!)
+
+Upstream commit r24328.
+---
+ test/datatype/ddt_lib.c | 2 +-
+ test/datatype/ddt_raw.c | 2 +-
+ test/datatype/opal_ddt_lib.c | 2 +-
+ 3 files changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/test/datatype/ddt_lib.c b/test/datatype/ddt_lib.c
+index 015419d..c349384 100644
+--- a/test/datatype/ddt_lib.c
++++ b/test/datatype/ddt_lib.c
+@@ -209,7 +209,7 @@ int mpich_typeub2( void )
+
+ int mpich_typeub3( void )
+ {
+- int blocklen[2], err = 0, idisp[3];
++ int blocklen[3], err = 0, idisp[3];
+ size_t sz;
+ MPI_Aint disp[3], lb, ub, ex;
+ ompi_datatype_t *types[3], *dt1, *dt2, *dt3, *dt4, *dt5;
+diff --git a/test/datatype/ddt_raw.c b/test/datatype/ddt_raw.c
+index eea9004..7effe65 100644
+--- a/test/datatype/ddt_raw.c
++++ b/test/datatype/ddt_raw.c
+@@ -45,7 +45,7 @@ static int test_upper( unsigned int length )
+ {
+ ompi_datatype_t *pdt;
+ opal_convertor_t * pConv;
+- int rc;
++ int rc = OMPI_SUCCESS;
+ unsigned int i, iov_count, split_chunk, total_length;
+ size_t max_data;
+ struct iovec iov[5];
+diff --git a/test/datatype/opal_ddt_lib.c b/test/datatype/opal_ddt_lib.c
+index e05bb06..dffd86c 100644
+--- a/test/datatype/opal_ddt_lib.c
++++ b/test/datatype/opal_ddt_lib.c
+@@ -759,7 +759,7 @@ int mpich_typeub2( void )
+
+ int mpich_typeub3( void )
+ {
+- int blocklen[2], err = 0, idisp[3];
++ int blocklen[3], err = 0, idisp[3];
+ size_t sz;
+ OPAL_PTRDIFF_TYPE disp[3], lb, ub, ex;
+ opal_datatype_t *types[3], *dt1, *dt2, *dt3, *dt4, *dt5;
+--
+1.7.3.4
+
diff --git a/sys-cluster/openmpi/openmpi-1.5.3.ebuild b/sys-cluster/openmpi/openmpi-1.5.3.ebuild
index 971c5a3e4..16643c4c6 100644
--- a/sys-cluster/openmpi/openmpi-1.5.3.ebuild
+++ b/sys-cluster/openmpi/openmpi-1.5.3.ebuild
@@ -56,6 +56,9 @@ src_prepare() {
echo 'oob_tcp_listen_mode = listen_thread' \
>> opal/etc/openmpi-mca-params.conf
fi
+
+ # Gentoo bug 360185
+ epatch "${FILESDIR}"/openmpi-r24328.patch
}
src_configure() {