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-rw-r--r--app-admin/eselect/Manifest1
-rw-r--r--app-admin/eselect/eselect-1.3.2-r100.ebuild (renamed from app-admin/eselect/eselect-1.3.1-r1.ebuild)18
-rw-r--r--app-benchmarks/numbench/ChangeLog5
-rw-r--r--app-benchmarks/numbench/Manifest2
-rw-r--r--app-benchmarks/numbench/numbench-0.2.ebuild4
-rw-r--r--app-benchmarks/numbench/numbench-0.2_beta4-r1.ebuild35
-rw-r--r--app-benchmarks/numbench/numbench-0.2_beta4.ebuild35
-rw-r--r--app-benchmarks/numbench/numbench-9999.ebuild2
-rw-r--r--app-doc/gromacs-manual/ChangeLog9
-rw-r--r--app-doc/gromacs-manual/gromacs-manual-4.6.9999.ebuild49
-rw-r--r--app-doc/gromacs-manual/gromacs-manual-9999.ebuild17
-rw-r--r--dev-java/jlatexmath-fop/ChangeLog6
-rw-r--r--dev-java/jlatexmath-fop/Manifest1
-rw-r--r--dev-java/jlatexmath-fop/jlatexmath-fop-1.0.0.ebuild52
-rw-r--r--dev-java/jlatexmath/ChangeLog6
-rw-r--r--dev-java/jlatexmath/Manifest1
-rw-r--r--dev-java/jlatexmath/jlatexmath-1.0.0.ebuild32
-rw-r--r--dev-java/scirenderer/ChangeLog12
-rw-r--r--dev-java/scirenderer/Manifest2
-rw-r--r--dev-java/scirenderer/scirenderer-1.0.2.ebuild (renamed from dev-java/scirenderer/scirenderer-0.5.6.ebuild)2
-rw-r--r--eclass/cmake-utils.eclass530
-rw-r--r--eclass/intel-sdp.eclass187
-rw-r--r--licenses/chimera13
-rw-r--r--licenses/phenix174
-rw-r--r--profiles/package.mask6
-rw-r--r--sci-chemistry/chemBuild/ChangeLog13
-rw-r--r--sci-chemistry/chemBuild/Manifest1
-rw-r--r--sci-chemistry/chemBuild/chemBuild-1.0.2.ebuild68
-rw-r--r--sci-chemistry/chemBuild/files/chemBuild9
-rw-r--r--sci-chemistry/chemBuild/metadata.xml5
-rw-r--r--sci-chemistry/chimera-bin/ChangeLog16
-rw-r--r--sci-chemistry/chimera-bin/Manifest2
-rw-r--r--sci-chemistry/chimera-bin/chimera-bin-1.6.2.ebuild64
-rw-r--r--sci-chemistry/chimera-bin/metadata.xml5
-rw-r--r--sci-chemistry/gromacs/ChangeLog8
-rw-r--r--sci-chemistry/gromacs/gromacs-4.6.9999.ebuild26
-rw-r--r--sci-chemistry/gromacs/gromacs-9999.ebuild5
-rw-r--r--sci-chemistry/gromacs/metadata.xml1
-rw-r--r--sci-chemistry/phenix-bin/ChangeLog23
-rw-r--r--sci-chemistry/phenix-bin/Manifest2
-rw-r--r--sci-chemistry/phenix-bin/metadata.xml5
-rw-r--r--sci-chemistry/phenix-bin/phenix-bin-1.8.1069.ebuild87
-rw-r--r--sci-chemistry/specView/ChangeLog19
-rw-r--r--sci-chemistry/specView/Manifest1
-rw-r--r--sci-chemistry/specView/files/specView9
-rw-r--r--sci-chemistry/specView/metadata.xml5
-rw-r--r--sci-chemistry/specView/specView-1.0.2.ebuild108
-rw-r--r--sci-libs/acml/ChangeLog6
-rw-r--r--sci-libs/acml/Manifest44
-rw-r--r--sci-libs/acml/acml-5.2.0.ebuild (renamed from sci-libs/acml/acml-5.1.0.ebuild)2
-rw-r--r--sci-libs/mkl/ChangeLog7
-rw-r--r--sci-libs/mkl/Manifest9
-rw-r--r--sci-libs/mkl/mkl-10.3.7.256.ebuild136
-rw-r--r--sci-libs/mkl/mkl-11.0.0.079.ebuild (renamed from sci-libs/mkl/mkl-10.3.4.191.ebuild)9
-rw-r--r--sci-libs/nfft/ChangeLog5
-rw-r--r--sci-libs/nfft/Manifest1
-rw-r--r--sci-libs/nfft/nfft-3.2.1.ebuild36
-rw-r--r--sci-mathematics/petsc/petsc-3.3_p1.ebuild2
-rw-r--r--sci-mathematics/scilab/ChangeLog18
-rw-r--r--sci-mathematics/scilab/Manifest1
-rw-r--r--sci-mathematics/scilab/files/scilab-5.4.0-fix-random-runtime-failure.patch (renamed from sci-mathematics/scilab/files/scilab-5.3.999-fix-random-runtime-failure.patch)0
-rw-r--r--sci-mathematics/scilab/files/scilab-5.4.0-followlinks.patch (renamed from sci-mathematics/scilab/files/scilab-5.3.999-followlinks.patch)0
-rw-r--r--sci-mathematics/scilab/files/scilab-5.4.0-fortran-link.patch (renamed from sci-mathematics/scilab/files/scilab-5.3.999-fortran-link.patch)0
-rw-r--r--sci-mathematics/scilab/files/scilab-5.4.0-gluegen.patch (renamed from sci-mathematics/scilab/files/scilab-5.3.999-gluegen.patch)0
-rw-r--r--sci-mathematics/scilab/files/scilab-5.4.0-java-heap.patch (renamed from sci-mathematics/scilab/files/scilab-5.3.999-java-heap.patch)10
-rw-r--r--sci-mathematics/scilab/scilab-5.4.0.ebuild (renamed from sci-mathematics/scilab/scilab-5.3.999.ebuild)21
-rw-r--r--sci-visualization/paraview/ChangeLog6
-rw-r--r--sci-visualization/paraview/metadata.xml1
-rw-r--r--sci-visualization/paraview/paraview-3.14.1-r4.ebuild (renamed from sci-visualization/paraview/paraview-3.14.1-r3.ebuild)8
-rw-r--r--skel.ChangeLog2
-rw-r--r--skel.ebuild12
-rw-r--r--skel.metadata.xml28
-rw-r--r--sys-cluster/lustre/ChangeLog6
-rw-r--r--sys-cluster/lustre/files/0001-LU-1337-vfs-kernel-3.1-renames-lock-manager-ops.patch190
-rw-r--r--sys-cluster/lustre/files/0002-LU-1337-vfs-kernel-3.1-kills-inode-i_alloc_sem.patch446
-rw-r--r--sys-cluster/lustre/files/0003-LU-1337-vfs-kernel-3.1-changes-open_to_namei_flags.patch95
-rw-r--r--sys-cluster/lustre/files/0004-LU-1337-vfs-provides-ll_get_acl-to-i_op-get_acl.patch150
-rw-r--r--sys-cluster/lustre/files/0005-LU-1337-block-kernel-3.2-make_request_fn-returns-voi.patch108
-rw-r--r--sys-cluster/lustre/files/0006-LU-1337-vfs-kernel-3.2-protects-inode-i_nlink.patch194
-rw-r--r--sys-cluster/lustre/files/0007-LU-1337-vfs-3.3-changes-super_operations-inode_opera.patch217
-rw-r--r--sys-cluster/lustre/files/0008-LU-1337-kernel-remove-unnecessary-includings-of-syst.patch211
-rw-r--r--sys-cluster/lustre/files/0009-LU-1337-vfs-kernel-3.4-touch_atime-switchs-to-1-argu.patch89
-rw-r--r--sys-cluster/lustre/files/0010-LU-1337-vfs-kernel-3.4-converts-d_alloc_root-to-d_ma.patch128
-rw-r--r--sys-cluster/lustre/files/0011-LU-1337-kernel-v3.5-defines-INVALID_UID.patch31
-rw-r--r--sys-cluster/lustre/files/0012-LU-1337-llite-kernel-3.5-renames-end_writeback-to-cl.patch90
-rw-r--r--sys-cluster/lustre/files/0013-LU-1337-kernel-3.5-kernel-encode_fh-passes-in-parent.patch88
-rw-r--r--sys-cluster/lustre/lustre-9999.ebuild73
-rw-r--r--sys-cluster/lustre/metadata.xml11
88 files changed, 3126 insertions, 1048 deletions
diff --git a/app-admin/eselect/Manifest b/app-admin/eselect/Manifest
index e624a0bb4..584ced835 100644
--- a/app-admin/eselect/Manifest
+++ b/app-admin/eselect/Manifest
@@ -1,2 +1 @@
-DIST eselect-1.3.1.tar.xz 163908 SHA256 4fc1c3f1b021dd8d28475ab2115f6a2de843bbbb941a0f70999389d1e0d56444 SHA512 b62e3e9f9c145a92625d136ea14ffa9705fa312971160ee3bb33f285dd67f6e6f415c7b9909b902b872500663a7a79c6fe53f52d179de7b7e120c5de994effd3 WHIRLPOOL a04a20c25617c3a53b0937c7f01f6dc89677beb5e1917a8d078a7f4403d4d77b7342da47766a061bc9158962ada190901db5b99d4b9603c49d9b90d3ad57feb5
DIST eselect-1.3.2.tar.xz 164168 SHA256 8b3906133090229defd6c5017fac0049e14cc0a5185c479cb3e6155a71827a78 SHA512 3225ce8b4313ae15bc7be8f047b29a202976c4a8766005487b78031a0e11e6395da55d74a961b022685126b397f8811babd3ee6580e8ba94e1ddd117964207e5 WHIRLPOOL 94917cad340ab697a35d0b3d4e80e95a6d764829692d54e0ee17fdef84c847aa35da10174352b0d4ffd8f541bbf0280e4b63790a276789a66463d2c8a1a245b0
diff --git a/app-admin/eselect/eselect-1.3.1-r1.ebuild b/app-admin/eselect/eselect-1.3.2-r100.ebuild
index 1bbfdb5a5..f26fecb8c 100644
--- a/app-admin/eselect/eselect-1.3.1-r1.ebuild
+++ b/app-admin/eselect/eselect-1.3.2-r100.ebuild
@@ -4,7 +4,7 @@
EAPI=3
-inherit bash-completion-r1 eutils autotools
+inherit autotools eutils bash-completion-r1
DESCRIPTION="Gentoo's multi-purpose configuration and management tool"
HOMEPAGE="http://www.gentoo.org/proj/en/eselect/"
@@ -12,7 +12,7 @@ SRC_URI="mirror://gentoo/${P}.tar.xz"
LICENSE="GPL-2"
SLOT="0"
-KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ia64 ~m68k ~mips ~ppc ~ppc64 ~s390 ~sh ~sparc ~x86 ~ppc-aix ~sparc-fbsd ~x86-fbsd ~x64-freebsd ~x86-freebsd ~hppa-hpux ~ia64-hpux ~x86-interix ~amd64-linux ~ia64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos ~m68k-mint ~sparc-solaris ~sparc64-solaris ~x64-solaris ~x86-solaris"
+KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ia64 ~m68k ~mips ~ppc ~ppc64 ~s390 ~sh ~sparc ~x86 ~ppc-aix ~amd64-fbsd ~sparc-fbsd ~x86-fbsd ~x64-freebsd ~x86-freebsd ~hppa-hpux ~ia64-hpux ~x86-interix ~amd64-linux ~ia64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos ~m68k-mint ~sparc-solaris ~sparc64-solaris ~x64-solaris ~x86-solaris"
IUSE="doc"
RDEPEND="sys-apps/sed
@@ -34,6 +34,7 @@ RDEPEND="!app-admin/eselect-news
# vim-syntax? ( app-vim/eselect-syntax )"
src_prepare() {
+ epatch "${FILESDIR}/${P}-eroot.patch"
epatch "${FILESDIR}"/${PN}-alternatives.patch
AT_M4DIR="." eautoreconf
}
@@ -57,8 +58,10 @@ src_install() {
# needed by news module
keepdir /var/lib/gentoo/news
- fowners root:portage /var/lib/gentoo/news || die
- fperms g+w /var/lib/gentoo/news || die
+ if ! use prefix; then
+ fowners root:portage /var/lib/gentoo/news || die
+ fperms g+w /var/lib/gentoo/news || die
+ fi
# band aid for prefix
if use prefix; then
@@ -70,7 +73,8 @@ src_install() {
pkg_postinst() {
# fowners in src_install doesn't work for the portage group:
# merging changes the group back to root
- [[ -z ${EROOT} ]] && local EROOT=${ROOT}
- chgrp portage "${EROOT}/var/lib/gentoo/news" \
- && chmod g+w "${EROOT}/var/lib/gentoo/news"
+ if ! use prefix; then
+ chgrp portage "${EROOT}/var/lib/gentoo/news" \
+ && chmod g+w "${EROOT}/var/lib/gentoo/news"
+ fi
}
diff --git a/app-benchmarks/numbench/ChangeLog b/app-benchmarks/numbench/ChangeLog
index 2c3add615..f1101806f 100644
--- a/app-benchmarks/numbench/ChangeLog
+++ b/app-benchmarks/numbench/ChangeLog
@@ -2,6 +2,11 @@
# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 29 Sep 2012; Sébastien Fabbro <bicatali@gentoo.org>
+ -numbench-0.2_beta4-r1.ebuild, -numbench-0.2_beta4.ebuild,
+ numbench-0.2.ebuild, numbench-9999.ebuild:
+ app-benchmarks/numbench: Updated dependency for eselect alternatives
+
*numbench-0.2
8 Aug 2012; Andrea Arteaga <andyspiros@gmail.com> +numbench-0.2.ebuild
diff --git a/app-benchmarks/numbench/Manifest b/app-benchmarks/numbench/Manifest
index 1d965b8cc..57ee294b0 100644
--- a/app-benchmarks/numbench/Manifest
+++ b/app-benchmarks/numbench/Manifest
@@ -1,3 +1 @@
DIST numbench-0.2.tar.gz 78782 SHA256 bca5ef84752da0e449e113b70d57e116decf18a200b9261de47e976454b6d84d SHA512 64f177eb63dfcfebb4c20fb821fe8a730443cfbb860494cc432f8ebad717902629236a38002d27e68f6ac6bc0ea8403ac89a6167898b7ec54f23577ec8c37c83 WHIRLPOOL fa9d3a2e7957a9ac8fb5252c200623f5778ca266e2fab365f586f9a615c6ff9bd43a32099db3909782ce700a80a79c479364e2dfb19a6150cc53550972bf8247
-DIST numbench-0.2_beta4-r1.tbz2 88332 SHA256 086419ecc0f989af7a7a772efc8ab5e16b37d975a5899313e1aea796a199532d SHA512 30604969f70c4600edac0bbd9e0d488348d850052742070ae9a44b8d9f9a15f5b7555d6eaf58d0264330931cd965eeaf4149bdc01e30997862e393b41ff48cb4 WHIRLPOOL 743ab13defff619d0b164cb09b31f90315fc755aacbcf29241debb375376f6382a8a7d7a3d078be1e6ae04b4dcabae7106eb138e6e1eaa1d0d1ede597c714ada
-DIST numbench-0.2_beta4.tbz2 87717 SHA256 cd6192342b34ab11c1de3068a2fdd809c02b70bb3e26af9699640bcb4945191c SHA512 001b76b48c6f73b7512eceffe46d6482cac1bbb84b3af58a0a73bf2235c1fa1b514c3f800cb00c64a15b9ee468f2571b541c808f08cd4072cf95fc14591a889f WHIRLPOOL 2975433e993de2d6ff05b2f8f8663a60e331aa5166c256c13a2297a9f46570c7557416734505262acf02f3522e1cab3f36a89866c4b4f0b11383d7f727aaba30
diff --git a/app-benchmarks/numbench/numbench-0.2.ebuild b/app-benchmarks/numbench/numbench-0.2.ebuild
index 4cb74f6bf..fb279c427 100644
--- a/app-benchmarks/numbench/numbench-0.2.ebuild
+++ b/app-benchmarks/numbench/numbench-0.2.ebuild
@@ -21,8 +21,8 @@ RDEPEND="!app-admin/eselect-blas
!app-admin/eselect-cblas
!app-admin/eselect-lapack
>=dev-python/matplotlib-1.0.0
- =app-admin/eselect-1.3.1-r1"
-
+ >=app-admin/eselect-1.3.2-r100"
+
S="${WORKDIR}/andyspiros-numbench-${CID}"
src_install() {
diff --git a/app-benchmarks/numbench/numbench-0.2_beta4-r1.ebuild b/app-benchmarks/numbench/numbench-0.2_beta4-r1.ebuild
deleted file mode 100644
index 037963ea0..000000000
--- a/app-benchmarks/numbench/numbench-0.2_beta4-r1.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=3
-
-inherit eutils distutils
-
-DESCRIPTION="Automated benchmarks suite"
-HOMEPAGE="http://soc.dev.gentoo.org/~spiros"
-SRC_URI="${HOMEPAGE}/repository/${PF}.tbz2"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-IUSE=""
-
-RDEPEND="!app-admin/eselect-blas
- !app-admin/eselect-cblas
- !app-admin/eselect-lapack
- >=dev-python/matplotlib-1.0.0
- =app-admin/eselect-1.3.1-r1"
-
-src_install() {
- distutils_src_install
-
- chmod +x exec.py
- newbin exec.py numbench
-
- insinto /usr/share/numbench/samples
- doins samples/*.xml
-
- doman doc/numbench.1
-}
diff --git a/app-benchmarks/numbench/numbench-0.2_beta4.ebuild b/app-benchmarks/numbench/numbench-0.2_beta4.ebuild
deleted file mode 100644
index 698342f6e..000000000
--- a/app-benchmarks/numbench/numbench-0.2_beta4.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=3
-
-inherit eutils distutils
-
-DESCRIPTION="Automated benchmarks suite"
-HOMEPAGE="http://soc.dev.gentoo.org/~spiros"
-SRC_URI="${HOMEPAGE}/repository/${P}.tbz2"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-IUSE=""
-
-RDEPEND="!app-admin/eselect-blas
- !app-admin/eselect-cblas
- !app-admin/eselect-lapack
- >=dev-python/matplotlib-1.0.0
- =app-admin/eselect-1.3.1-r1"
-
-src_install() {
- distutils_src_install
-
- chmod +x exec.py
- newbin exec.py numbench
-
- insinto /usr/share/numbench/samples
- doins samples/*.xml
-
- doman doc/numbench.1
-}
diff --git a/app-benchmarks/numbench/numbench-9999.ebuild b/app-benchmarks/numbench/numbench-9999.ebuild
index ac8095f32..98d4d6d5f 100644
--- a/app-benchmarks/numbench/numbench-9999.ebuild
+++ b/app-benchmarks/numbench/numbench-9999.ebuild
@@ -21,7 +21,7 @@ RDEPEND="!app-admin/eselect-blas
!app-admin/eselect-cblas
!app-admin/eselect-lapack
>=dev-python/matplotlib-1.0.0
- =app-admin/eselect-1.3.1-r1"
+ >=app-admin/eselect-1.3.2-r100"
src_install() {
distutils_src_install
diff --git a/app-doc/gromacs-manual/ChangeLog b/app-doc/gromacs-manual/ChangeLog
index b9f148f17..338a2e38c 100644
--- a/app-doc/gromacs-manual/ChangeLog
+++ b/app-doc/gromacs-manual/ChangeLog
@@ -1,7 +1,13 @@
# ChangeLog for app-doc/gromacs-manual
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*gromacs-manual-4.6.9999 (04 Oct 2012)
+
+ 04 Oct 2012; Christoph Junghans <ottxor@gentoo.org>
+ +gromacs-manual-4.6.9999.ebuild, gromacs-manual-9999.ebuild:
+ live ebuild update
+
25 Jun 2011; Justin Lecher <jlec@gentoo.org> gromacs-manual-9999.ebuild:
Merged
@@ -17,4 +23,3 @@
26 Aug 2010; Christoph Junghans <kleiner_otti@gmx.de>
+gromacs-manual-9999.ebuild, +metadata.xml:
initial commit
-
diff --git a/app-doc/gromacs-manual/gromacs-manual-4.6.9999.ebuild b/app-doc/gromacs-manual/gromacs-manual-4.6.9999.ebuild
new file mode 100644
index 000000000..43597e9ab
--- /dev/null
+++ b/app-doc/gromacs-manual/gromacs-manual-4.6.9999.ebuild
@@ -0,0 +1,49 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=4
+
+EGIT_REPO_URI="git://git.gromacs.org/manual"
+if [[ ${PV} = 9999 ]]; then
+ EGIT_BRANCH="master"
+else
+ EGIT_BRANCH="release-4-6"
+fi
+
+inherit cmake-utils git-2
+
+DESCRIPTION="Manual for gromacs"
+HOMEPAGE="http://www.gromacs.org/"
+SRC_URI=""
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+DEPEND="
+ ~sci-chemistry/gromacs-${PV}
+ dev-texlive/texlive-latex
+ sys-apps/coreutils"
+RDEPEND=""
+
+src_prepare() {
+ local progs
+ progs=$(tr '\n' ' ' <${EROOT}usr/share/gromacs/programs.list) || die
+ sed \
+ -e "s/^\(PROGRAMS\).*/\1='${progs}'/" \
+ -e "/^INSTALLED_OPTIONS_PROGRAM_NAME/s!=.*!=${EROOT}usr/bin/g_options!" \
+ -i mkman || die "sed of mkman failed"
+ sed \
+ -e "s!\${GMXSRC}/admin/\(programs.txt\)!${EROOT}usr/share/gromacs/\1!" \
+ -e "s!\${GMXSRC}/share/html!${EROOT}usr/share/doc/gromacs-${PV}/html!" \
+ -e "s!\${GMXBIN}!${EROOT}usr/bin!" \
+ -e '/FATAL_ERROR.*GMX\(SRC\|BIN\)/s/^/#/' \
+ -i CMakeLists.txt || die "sed of CMakeLists.txt failed"
+}
+
+src_install() {
+ insinto /usr/share/doc/gromacs-${PV}
+ newins ${CMAKE_BUILD_DIR}/gromacs.pdf manual-${PV}.pdf
+}
diff --git a/app-doc/gromacs-manual/gromacs-manual-9999.ebuild b/app-doc/gromacs-manual/gromacs-manual-9999.ebuild
index c9f988336..43597e9ab 100644
--- a/app-doc/gromacs-manual/gromacs-manual-9999.ebuild
+++ b/app-doc/gromacs-manual/gromacs-manual-9999.ebuild
@@ -1,11 +1,15 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2012 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
EAPI=4
EGIT_REPO_URI="git://git.gromacs.org/manual"
-EGIT_BRANCH="master"
+if [[ ${PV} = 9999 ]]; then
+ EGIT_BRANCH="master"
+else
+ EGIT_BRANCH="release-4-6"
+fi
inherit cmake-utils git-2
@@ -21,15 +25,16 @@ IUSE=""
DEPEND="
~sci-chemistry/gromacs-${PV}
dev-texlive/texlive-latex
- sys-apps/coreutils
- app-shells/tcsh"
+ sys-apps/coreutils"
RDEPEND=""
src_prepare() {
local progs
progs=$(tr '\n' ' ' <${EROOT}usr/share/gromacs/programs.list) || die
- sed -i "s/^\(PROGRAMS\).*/\1='${progs}'/" mkman || die
- sed -i "s@^\(INSTALLED.*=\).*@\1${EROOT}usr/bin/g_options@" mkoptions || die
+ sed \
+ -e "s/^\(PROGRAMS\).*/\1='${progs}'/" \
+ -e "/^INSTALLED_OPTIONS_PROGRAM_NAME/s!=.*!=${EROOT}usr/bin/g_options!" \
+ -i mkman || die "sed of mkman failed"
sed \
-e "s!\${GMXSRC}/admin/\(programs.txt\)!${EROOT}usr/share/gromacs/\1!" \
-e "s!\${GMXSRC}/share/html!${EROOT}usr/share/doc/gromacs-${PV}/html!" \
diff --git a/dev-java/jlatexmath-fop/ChangeLog b/dev-java/jlatexmath-fop/ChangeLog
index 114d8986f..64edc6043 100644
--- a/dev-java/jlatexmath-fop/ChangeLog
+++ b/dev-java/jlatexmath-fop/ChangeLog
@@ -2,6 +2,12 @@
# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*jlatexmath-fop-1.0.0 (25 Sep 2012)
+
+ 25 Sep 2012; Guillaume Horel <guillaume.horel@gmail.com>
+ +jlatexmath-fop-1.0.0.ebuild:
+ version bump
+
07 Jul 2012; Sébastien Fabbro <bicatali@gentoo.org>
-jlatexmath-fop-0.9.4.ebuild:
dev-java/jlatexmath-fop: remove old
diff --git a/dev-java/jlatexmath-fop/Manifest b/dev-java/jlatexmath-fop/Manifest
index 0541049ef..b3a18c0c6 100644
--- a/dev-java/jlatexmath-fop/Manifest
+++ b/dev-java/jlatexmath-fop/Manifest
@@ -1 +1,2 @@
DIST jlatexmath-src-all-0.9.7.zip 1177126 SHA256 f27772c54e438034ea5cd70fc53b5cef8775578b50b41597bf23e2960c98d4f6 SHA512 1d2f1e66ec55f90e81bf7c4ffe1719589de2527f40fb7872e6e653ca2deb31f5fe6da6f3a90a608e3df02be4b625485403cc1d1d4a2b4738ecf5f2f35604c816 WHIRLPOOL 408f19aca68d494a75b452efdec8d2be1a295e04dafff934715a7af934068edb176b101ef8bd56f07a89a8bf8bb6040a646f83429c8ce706991bb39271c70dd1
+DIST jlatexmath-src-all-1.0.0.zip 1177772 SHA256 0e21fa493d30e878ee533f372ffd4d51cc85084a83c7fc79bf4f89a9d9b7268e SHA512 0d5dcb3d2b02c98be6cf17fa9fe313c4694bc353755b958bdfd3e1da83a99d5447fcb742c7e7bd0cc97a0face0b89dc7f8668abb7f7eb8f7753868986cca1b0f WHIRLPOOL e723c2a86aafcb84e6dec4199ed5df58478e0800a3039f777b89c372c87229c429af936cf0b134fc8f43e8b3f23684606500fa6f81b308132296bdc74d18482a
diff --git a/dev-java/jlatexmath-fop/jlatexmath-fop-1.0.0.ebuild b/dev-java/jlatexmath-fop/jlatexmath-fop-1.0.0.ebuild
new file mode 100644
index 000000000..76f95070f
--- /dev/null
+++ b/dev-java/jlatexmath-fop/jlatexmath-fop-1.0.0.ebuild
@@ -0,0 +1,52 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=4
+
+JAVA_PKG_IUSE="examples source"
+
+inherit java-pkg-2 java-ant-2
+
+MY_PN="${PN/-fop/}"
+MY_P="${P/-fop/}"
+
+DESCRIPTION="jlatexmath plugin for dev-java/fop"
+SRC_URI="http://forge.scilab.org/upload/jlatexmath/files/${MY_PN}-src-all-${PV}.zip"
+HOMEPAGE="http://forge.scilab.org/index.php/p/jlatexmath"
+
+IUSE=""
+CDEPEND="dev-java/jlatexmath
+ dev-java/avalon-framework
+ dev-java/fop"
+REPEND=">=virtual/jdk-1.5
+ ${CDEPEND}"
+RDEPEND=">=virtual/jre-1.5
+ ${CDEPEND}"
+
+LICENSE="GPL-2"
+SLOT="1"
+KEYWORDS="~amd64 ~x86"
+
+EANT_BUILD_TARGET="buildJar"
+
+S="${WORKDIR}/${MY_P}/plugin/fop"
+
+src_prepare() {
+ cd "${WORKDIR}/${MY_P}"
+ sed -i \
+ -e "s:/usr/share/java/fop.jar:$(java-pkg_getjar fop fop.jar):g" \
+ -e "s:/usr/share/java/xmlgraphics-commons.jar:$(java-pkg_getjar xmlgraphics-commons-1.3 xmlgraphics-commons.jar):g" \
+ -e "s:/usr/share/java/batik.jar:$(java-pkg_getjar batik-1.7 batik-all.jar):g" \
+ -e "s:/usr/share/java/avalon-framework.jar:$(java-pkg_getjar avalon-framework-4.2 avalon-framework.jar):g" \
+ -e "s:/usr/share/java/commons-io.jar:$(java-pkg_getjar commons-io-1 commons-io.jar):g" \
+ -e "s:/usr/share/java/commons-logging.jar:$(java-pkg_getjar commons-logging commons-logging.jar):g" \
+ -e "s:/usr/share/java/xml-apis-ext.jar:$(java-pkg_getjar xml-commons-external-1.3 xml-apis-ext.jar):g" \
+ fop.properties || die
+}
+
+src_install() {
+ java-pkg_newjar dist/${P}.jar ${PN}.jar
+ use source && java-pkg_dosrc src/org
+ use examples && java-pkg_doexamples examples
+}
diff --git a/dev-java/jlatexmath/ChangeLog b/dev-java/jlatexmath/ChangeLog
index 27e0eac94..f3a9f0a88 100644
--- a/dev-java/jlatexmath/ChangeLog
+++ b/dev-java/jlatexmath/ChangeLog
@@ -2,6 +2,12 @@
# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*jlatexmath-1.0.0 (25 Sep 2012)
+
+ 25 Sep 2012; Guillaume Horel <guillaume.horel@gmail.com>
+ +jlatexmath-1.0.0.ebuild:
+ version bump
+
07 Jul 2012; Sébastien Fabbro <bicatali@gentoo.org> -jlatexmath-0.8.7.ebuild,
-jlatexmath-0.9.4.ebuild, jlatexmath-0.9.7.ebuild:
dev-java/jlatexmath: do not compile examples, bug #421743
diff --git a/dev-java/jlatexmath/Manifest b/dev-java/jlatexmath/Manifest
index f0ffa3db3..22218fa56 100644
--- a/dev-java/jlatexmath/Manifest
+++ b/dev-java/jlatexmath/Manifest
@@ -1 +1,2 @@
DIST jlatexmath-src-0.9.7.zip 1060786 SHA256 d348ab583359e81390627c8fa2d8d08c1d4ff33fb009c47d8314ea0cfebfe1ea SHA512 dc9a244fd8733a3b3c5dcd1f88a3c8e36ee8a46114d03b02508c3fb728878b03a8040c9dcf468a4ce297c792954b99f25db83e4dc7d4ede101ab09cb2af37eab WHIRLPOOL 8370e07d8013f1ab626c081615f0dcce7766fcfe7219403c88152d366ca6e9bb3c4ebc1afb17cc90ce77f1abd773051e9d8fc3a33232adc3b25310f14ded81e8
+DIST jlatexmath-src-1.0.0.zip 1061432 SHA256 bc8630c8506c333d4bb1e55c0724f0811d18d55664dc4dc1952211fd5560feea SHA512 022f8f05b7dc0906091cb2473aecaad70880a4cf8b18f61929b2714f0dafee1064c26186e576fb94eb3db01d8bfa7bcaa0a4dd185fcedb0913da5ee976615c5d WHIRLPOOL 3242d45c41e575996ff6c4208ebfd5f41eb58df21416384adad4e2b817c06a886d5fec182e41b41282616a4bcc4a698582a20c52409680beed7fa8b1c2f059c7
diff --git a/dev-java/jlatexmath/jlatexmath-1.0.0.ebuild b/dev-java/jlatexmath/jlatexmath-1.0.0.ebuild
new file mode 100644
index 000000000..80245c71b
--- /dev/null
+++ b/dev-java/jlatexmath/jlatexmath-1.0.0.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=4
+
+JAVA_PKG_IUSE="doc source"
+
+inherit java-pkg-2 java-ant-2
+
+DESCRIPTION="A Java API to render LaTeX"
+SRC_URI="http://forge.scilab.org/index.php/p/${PN}/downloads/get/${PN}-src-${PV}.zip"
+HOMEPAGE="http://forge.scilab.org/index.php/p/jlatexmath"
+
+IUSE="doc examples source"
+DEPEND=">=virtual/jdk-1.5
+ app-arch/unzip"
+RDEPEND=">=virtual/jre-1.5"
+
+LICENSE="GPL-2"
+SLOT="1"
+KEYWORDS="~amd64 ~x86"
+
+EANT_BUILD_TARGET="buildJar"
+EANT_DOC_TARGET="doc"
+
+src_install() {
+ java-pkg_newjar dist/${P}.jar ${PN}.jar
+ use doc && java-pkg_dojavadoc doc
+ use source && java-pkg_dosrc src/org
+ use examples && java-pkg_doexamples examples
+}
diff --git a/dev-java/scirenderer/ChangeLog b/dev-java/scirenderer/ChangeLog
index d3a87d1c8..88ab2710c 100644
--- a/dev-java/scirenderer/ChangeLog
+++ b/dev-java/scirenderer/ChangeLog
@@ -2,6 +2,18 @@
# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*scirenderer-1.0.2 (02 Oct 2012)
+
+ 02 Oct 2012; Guillaume Horel <guillaume.horel@gmail.com>
+ -scirenderer-1.0.0.ebuild, +scirenderer-1.0.2.ebuild:
+ version bump
+
+*scirenderer-1.0.0 (25 Sep 2012)
+
+ 25 Sep 2012; Guillaume Horel <guillaume.horel@gmail.com>
+ -scirenderer-0.5.6.ebuild, +scirenderer-1.0.0.ebuild:
+ version bump
+
*scirenderer-0.5.6 (11 Aug 2012)
11 Aug 2012; Guillaume Horel <guillaume.horel@gmail.com>
diff --git a/dev-java/scirenderer/Manifest b/dev-java/scirenderer/Manifest
index 9f0dc8e86..3ebfc76e2 100644
--- a/dev-java/scirenderer/Manifest
+++ b/dev-java/scirenderer/Manifest
@@ -1 +1 @@
-DIST scirenderer-0.5.5.tar.gz 108998 SHA256 174418601858b9cf59bd7732fb614cea3b6b1b441b85db37211d20c0e294fa08 SHA512 941eda1880b13eeac534d8aaf80c45de090b3822b05b5e3dc9d126f3310b3737965a2661ea0d60683057e5d62a21dd5f7099efa2611cdf4ee7c254b44c25ac64 WHIRLPOOL e1f831890147133c3f121c8e717e164e399a2bb0c2cf415166c1a3f0de24b022584961bd6656947369cb72dbe26208f1389a54d0ea62914f113354cc1c8374e0
+DIST scirenderer-1.0.2.tar.gz 111449 SHA256 9fb2e3a152a7b56794286b295291ebec7b8b9fe2f4cf779134c3b216ce0dc17d SHA512 df1fc898fbb09e324eec84cec7559bf6c3a25f5d1df427cb10050e888110cce1e09a66e458b9158bc7da08465a2c214d1c933e55c0e8852b57087119bedd007c WHIRLPOOL a5c51bacbba76ad0a7716550f0a11f88e1301243be5819040c6151ca23d150feb985891df69dc3dba0066923de8fdc8bf4c161df854a18f0e350965eb5038f97
diff --git a/dev-java/scirenderer/scirenderer-0.5.6.ebuild b/dev-java/scirenderer/scirenderer-1.0.2.ebuild
index 3a710e21a..df45d0aaa 100644
--- a/dev-java/scirenderer/scirenderer-0.5.6.ebuild
+++ b/dev-java/scirenderer/scirenderer-1.0.2.ebuild
@@ -19,7 +19,7 @@ DEPEND=">=virtual/jdk-1.5
RDEPEND=">=virtual/jre-1.5"
LICENSE="GPL-2"
-SLOT="0"
+SLOT="1"
KEYWORDS="~amd64 ~x86"
EANT_DOC_TARGET="doc"
diff --git a/eclass/cmake-utils.eclass b/eclass/cmake-utils.eclass
deleted file mode 100644
index 4ab36d10a..000000000
--- a/eclass/cmake-utils.eclass
+++ /dev/null
@@ -1,530 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/eclass/cmake-utils.eclass,v 1.79 2012/05/08 21:27:10 dilfridge Exp $
-
-# @ECLASS: cmake-utils.eclass
-# @MAINTAINER:
-# kde@gentoo.org
-# @AUTHOR:
-# Tomáš Chvátal <scarabeus@gentoo.org>
-# Maciej Mrozowski <reavertm@gentoo.org>
-# (undisclosed contributors)
-# Original author: Zephyrus (zephyrus@mirach.it)
-# @BLURB: common ebuild functions for cmake-based packages
-# @DESCRIPTION:
-# The cmake-utils eclass is base.eclass(5) wrapper that makes creating ebuilds for
-# cmake-based packages much easier.
-# It provides all inherited features (DOCS, HTML_DOCS, PATCHES) along with out-of-source
-# builds (default), in-source builds and an implementation of the well-known use_enable
-# and use_with functions for CMake.
-
-# @ECLASS-VARIABLE: WANT_CMAKE
-# @DESCRIPTION:
-# Specify if cmake-utils eclass should depend on cmake optionaly or not.
-# This is usefull when only part of aplication is using cmake build system.
-# Valid values are: always [default], optional (where the value is the useflag
-# used for optionality)
-WANT_CMAKE="${WANT_CMAKE:-always}"
-
-# @ECLASS-VARIABLE: CMAKE_MIN_VERSION
-# @DESCRIPTION:
-# Specify the minimum required CMake version. Default is 2.8.4
-CMAKE_MIN_VERSION="${CMAKE_MIN_VERSION:-2.8.4}"
-
-# @ECLASS-VARIABLE: CMAKE_REMOVE_MODULES_LIST
-# @DESCRIPTION:
-# Space-separated list of CMake modules that will be removed in $S during src_prepare,
-# in order to force packages to use the system version.
-CMAKE_REMOVE_MODULES_LIST="${CMAKE_REMOVE_MODULES_LIST:-FindBLAS FindLAPACK}"
-
-# @ECLASS-VARIABLE: CMAKE_REMOVE_MODULES
-# @DESCRIPTION:
-# Do we want to remove anything? yes or whatever else for no
-CMAKE_REMOVE_MODULES="${CMAKE_REMOVE_MODULES:-yes}"
-
-# @ECLASS-VARIABLE: CMAKE_MAKEFILE_GENERATOR
-# @DESCRIPTION:
-# Specify a makefile generator to be used by cmake. At this point only "make"
-# and "ninja" is supported.
-CMAKE_MAKEFILE_GENERATOR="${CMAKE_MAKEFILE_GENERATOR:-make}"
-
-CMAKEDEPEND=""
-case ${WANT_CMAKE} in
- always)
- ;;
- *)
- IUSE+=" ${WANT_CMAKE}"
- CMAKEDEPEND+="${WANT_CMAKE}? ( "
- ;;
-esac
-inherit toolchain-funcs multilib flag-o-matic base
-
-CMAKE_EXPF="src_compile src_test src_install"
-case ${EAPI:-0} in
- 4|3|2) CMAKE_EXPF+=" src_configure" ;;
- 1|0) ;;
- *) die "Unknown EAPI, Bug eclass maintainers." ;;
-esac
-EXPORT_FUNCTIONS ${CMAKE_EXPF}
-
-: ${DESCRIPTION:="Based on the ${ECLASS} eclass"}
-
-if [[ ${PN} != cmake ]]; then
- CMAKEDEPEND+=" >=dev-util/cmake-${CMAKE_MIN_VERSION}"
-fi
-
-CMAKEDEPEND+=" userland_GNU? ( >=sys-apps/findutils-4.4.0 )"
-
-[[ ${WANT_CMAKE} = always ]] || CMAKEDEPEND+=" )"
-
-DEPEND="${CMAKEDEPEND}"
-unset CMAKEDEPEND
-
-# Internal functions used by cmake-utils_use_*
-_use_me_now() {
- debug-print-function ${FUNCNAME} "$@"
-
- local uper capitalised x
- [[ -z $2 ]] && die "cmake-utils_use-$1 <USE flag> [<flag name>]"
- if [[ ! -z $3 ]]; then
- # user specified the use name so use it
- echo "-D$1$3=$(use $2 && echo ON || echo OFF)"
- else
- # use all various most used combinations
- uper=$(echo ${2} | tr '[:lower:]' '[:upper:]')
- capitalised=$(echo ${2} | sed 's/\<\(.\)\([^ ]*\)/\u\1\L\2/g')
- for x in $2 $uper $capitalised; do
- echo "-D$1$x=$(use $2 && echo ON || echo OFF) "
- done
- fi
-}
-_use_me_now_inverted() {
- debug-print-function ${FUNCNAME} "$@"
-
- local uper capitalised x
- [[ -z $2 ]] && die "cmake-utils_use-$1 <USE flag> [<flag name>]"
- if [[ ! -z $3 ]]; then
- # user specified the use name so use it
- echo "-D$1$3=$(use $2 && echo OFF || echo ON)"
- else
- # use all various most used combinations
- uper=$(echo ${2} | tr '[:lower:]' '[:upper:]')
- capitalised=$(echo ${2} | sed 's/\<\(.\)\([^ ]*\)/\u\1\L\2/g')
- for x in $2 $uper $capitalised; do
- echo "-D$1$x=$(use $2 && echo OFF || echo ON) "
- done
- fi
-}
-
-# @ECLASS-VARIABLE: CMAKE_BUILD_DIR
-# @DESCRIPTION:
-# Build directory where all cmake processed files should be generated.
-# For in-source build it's fixed to ${CMAKE_USE_DIR}.
-# For out-of-source build it can be overriden, by default it uses
-# ${WORKDIR}/${P}_build.
-
-# @ECLASS-VARIABLE: CMAKE_BUILD_TYPE
-# @DESCRIPTION:
-# Set to override default CMAKE_BUILD_TYPE. Only useful for packages
-# known to make use of "if (CMAKE_BUILD_TYPE MATCHES xxx)".
-# If about to be set - needs to be set before invoking cmake-utils_src_configure.
-# You usualy do *NOT* want nor need to set it as it pulls CMake default build-type
-# specific compiler flags overriding make.conf.
-: ${CMAKE_BUILD_TYPE:=Gentoo}
-
-# @ECLASS-VARIABLE: CMAKE_IN_SOURCE_BUILD
-# @DESCRIPTION:
-# Set to enable in-source build.
-
-# @ECLASS-VARIABLE: CMAKE_USE_DIR
-# @DESCRIPTION:
-# Sets the directory where we are working with cmake.
-# For example when application uses autotools and only one
-# plugin needs to be done by cmake.
-# By default it uses ${S}.
-
-# @ECLASS-VARIABLE: CMAKE_VERBOSE
-# @DESCRIPTION:
-# Set to OFF to disable verbose messages during compilation
-: ${CMAKE_VERBOSE:=ON}
-
-# @ECLASS-VARIABLE: PREFIX
-# @DESCRIPTION:
-# Eclass respects PREFIX variable, though it's not recommended way to set
-# install/lib/bin prefixes.
-# Use -DCMAKE_INSTALL_PREFIX=... CMake variable instead.
-: ${PREFIX:=/usr}
-
-# @ECLASS-VARIABLE: CMAKE_BINARY
-# @DESCRIPTION:
-# Eclass can use different cmake binary than the one provided in by system.
-: ${CMAKE_BINARY:=cmake}
-
-# Determine using IN or OUT source build
-_check_build_dir() {
- : ${CMAKE_USE_DIR:=${S}}
- if [[ -n ${CMAKE_IN_SOURCE_BUILD} ]]; then
- # we build in source dir
- CMAKE_BUILD_DIR="${CMAKE_USE_DIR}"
- else
- : ${CMAKE_BUILD_DIR:=${WORKDIR}/${P}_build}
- fi
- mkdir -p "${CMAKE_BUILD_DIR}"
- echo ">>> Working in BUILD_DIR: \"$CMAKE_BUILD_DIR\""
-}
-
-# Determine which generator to use
-_generator_to_use() {
- if [[ ${CMAKE_MAKEFILE_GENERATOR} = "ninja" ]]; then
- has_version dev-util/ninja && echo "Ninja" && return
- fi
- echo "Unix Makefiles"
-}
-
-# @FUNCTION: cmake-utils_use_with
-# @USAGE: <USE flag> [flag name]
-# @DESCRIPTION:
-# Based on use_with. See ebuild(5).
-#
-# `cmake-utils_use_with foo FOO` echoes -DWITH_FOO=ON if foo is enabled
-# and -DWITH_FOO=OFF if it is disabled.
-cmake-utils_use_with() { _use_me_now WITH_ "$@" ; }
-
-# @FUNCTION: cmake-utils_use_enable
-# @USAGE: <USE flag> [flag name]
-# @DESCRIPTION:
-# Based on use_enable. See ebuild(5).
-#
-# `cmake-utils_use_enable foo FOO` echoes -DENABLE_FOO=ON if foo is enabled
-# and -DENABLE_FOO=OFF if it is disabled.
-cmake-utils_use_enable() { _use_me_now ENABLE_ "$@" ; }
-
-# @FUNCTION: cmake-utils_use_disable
-# @USAGE: <USE flag> [flag name]
-# @DESCRIPTION:
-# Based on inversion of use_enable. See ebuild(5).
-#
-# `cmake-utils_use_enable foo FOO` echoes -DDISABLE_FOO=OFF if foo is enabled
-# and -DDISABLE_FOO=ON if it is disabled.
-cmake-utils_use_disable() { _use_me_now_inverted DISABLE_ "$@" ; }
-
-# @FUNCTION: cmake-utils_use_no
-# @USAGE: <USE flag> [flag name]
-# @DESCRIPTION:
-# Based on use_disable. See ebuild(5).
-#
-# `cmake-utils_use_no foo FOO` echoes -DNO_FOO=OFF if foo is enabled
-# and -DNO_FOO=ON if it is disabled.
-cmake-utils_use_no() { _use_me_now_inverted NO_ "$@" ; }
-
-# @FUNCTION: cmake-utils_use_want
-# @USAGE: <USE flag> [flag name]
-# @DESCRIPTION:
-# Based on use_enable. See ebuild(5).
-#
-# `cmake-utils_use_want foo FOO` echoes -DWANT_FOO=ON if foo is enabled
-# and -DWANT_FOO=OFF if it is disabled.
-cmake-utils_use_want() { _use_me_now WANT_ "$@" ; }
-
-# @FUNCTION: cmake-utils_use_build
-# @USAGE: <USE flag> [flag name]
-# @DESCRIPTION:
-# Based on use_enable. See ebuild(5).
-#
-# `cmake-utils_use_build foo FOO` echoes -DBUILD_FOO=ON if foo is enabled
-# and -DBUILD_FOO=OFF if it is disabled.
-cmake-utils_use_build() { _use_me_now BUILD_ "$@" ; }
-
-# @FUNCTION: cmake-utils_use_has
-# @USAGE: <USE flag> [flag name]
-# @DESCRIPTION:
-# Based on use_enable. See ebuild(5).
-#
-# `cmake-utils_use_has foo FOO` echoes -DHAVE_FOO=ON if foo is enabled
-# and -DHAVE_FOO=OFF if it is disabled.
-cmake-utils_use_has() { _use_me_now HAVE_ "$@" ; }
-
-# @FUNCTION: cmake-utils_use_use
-# @USAGE: <USE flag> [flag name]
-# @DESCRIPTION:
-# Based on use_enable. See ebuild(5).
-#
-# `cmake-utils_use_use foo FOO` echoes -DUSE_FOO=ON if foo is enabled
-# and -DUSE_FOO=OFF if it is disabled.
-cmake-utils_use_use() { _use_me_now USE_ "$@" ; }
-
-# @FUNCTION: cmake-utils_use
-# @USAGE: <USE flag> [flag name]
-# @DESCRIPTION:
-# Based on use_enable. See ebuild(5).
-#
-# `cmake-utils_use foo FOO` echoes -DFOO=ON if foo is enabled
-# and -DFOO=OFF if it is disabled.
-cmake-utils_use() { _use_me_now "" "$@" ; }
-
-# Internal function for modifying hardcoded definitions.
-# Removes dangerous definitions that override Gentoo settings.
-_modify-cmakelists() {
- debug-print-function ${FUNCNAME} "$@"
-
- # Only edit the files once
- grep -qs "<<< Gentoo configuration >>>" CMakeLists.txt && return 0
-
- # Comment out all set (<some_should_be_user_defined_variable> value)
- # TODO Add QA checker - inform when variable being checked for below is set in CMakeLists.txt
- find "${CMAKE_USE_DIR}" -name CMakeLists.txt \
- -exec sed -i -e '/^[[:space:]]*[sS][eE][tT][[:space:]]*([[:space:]]*CMAKE_BUILD_TYPE.*)/{s/^/#IGNORE /g}' {} + \
- -exec sed -i -e '/^[[:space:]]*[sS][eE][tT][[:space:]]*([[:space:]]*CMAKE_COLOR_MAKEFILE.*)/{s/^/#IGNORE /g}' {} + \
- -exec sed -i -e '/^[[:space:]]*[sS][eE][tT][[:space:]]*([[:space:]]*CMAKE_INSTALL_PREFIX.*)/{s/^/#IGNORE /g}' {} + \
- -exec sed -i -e '/^[[:space:]]*[sS][eE][tT][[:space:]]*([[:space:]]*CMAKE_VERBOSE_MAKEFILE.*)/{s/^/#IGNORE /g}' {} + \
- || die "${LINENO}: failed to disable hardcoded settings"
-
- # NOTE Append some useful summary here
- cat >> "${CMAKE_USE_DIR}"/CMakeLists.txt <<- _EOF_
-
- MESSAGE(STATUS "<<< Gentoo configuration >>>
- Build type \${CMAKE_BUILD_TYPE}
- Install path \${CMAKE_INSTALL_PREFIX}
- Compiler flags:
- C \${CMAKE_C_FLAGS}
- C++ \${CMAKE_CXX_FLAGS}
- Linker flags:
- Executable \${CMAKE_EXE_LINKER_FLAGS}
- Module \${CMAKE_MODULE_LINKER_FLAGS}
- Shared \${CMAKE_SHARED_LINKER_FLAGS}\n")
- _EOF_
-}
-
-enable_cmake-utils_src_configure() {
- debug-print-function ${FUNCNAME} "$@"
-
- [[ "${CMAKE_REMOVE_MODULES}" == "yes" ]] && {
- local name
- for name in ${CMAKE_REMOVE_MODULES_LIST} ; do
- find "${S}" -name ${name}.cmake -exec rm -v {} +
- done
- }
-
- _check_build_dir
-
- # check if CMakeLists.txt exist and if no then die
- if [[ ! -e ${CMAKE_USE_DIR}/CMakeLists.txt ]] ; then
- eerror "Unable to locate CMakeLists.txt under:"
- eerror "\"${CMAKE_USE_DIR}/CMakeLists.txt\""
- eerror "Consider not inheriting the cmake eclass."
- die "FATAL: Unable to find CMakeLists.txt"
- fi
-
- # Remove dangerous things.
- _modify-cmakelists
-
- # Fix xdg collision with sandbox
- export XDG_CONFIG_HOME="${T}"
-
- # @SEE CMAKE_BUILD_TYPE
- if [[ ${CMAKE_BUILD_TYPE} = Gentoo ]]; then
- # Handle release builds
- if ! has debug ${IUSE//+} || ! use debug; then
- append-cppflags -DNDEBUG
- fi
- fi
-
- # Prepare Gentoo override rules (set valid compiler, append CPPFLAGS)
- local build_rules=${CMAKE_BUILD_DIR}/gentoo_rules.cmake
- cat > "${build_rules}" <<- _EOF_
- SET (CMAKE_C_COMPILER $(type -P $(tc-getCC)) CACHE FILEPATH "C compiler" FORCE)
- SET (CMAKE_C_COMPILE_OBJECT "<CMAKE_C_COMPILER> <DEFINES> ${CPPFLAGS} <FLAGS> -o <OBJECT> -c <SOURCE>" CACHE STRING "C compile command" FORCE)
- SET (CMAKE_CXX_COMPILER $(type -P $(tc-getCXX)) CACHE FILEPATH "C++ compiler" FORCE)
- SET (CMAKE_CXX_COMPILE_OBJECT "<CMAKE_CXX_COMPILER> <DEFINES> ${CPPFLAGS} <FLAGS> -o <OBJECT> -c <SOURCE>" CACHE STRING "C++ compile command" FORCE)
- _EOF_
-
- has "${EAPI:-0}" 0 1 2 && ! use prefix && EPREFIX=
-
- if [[ ${EPREFIX} ]]; then
- cat >> "${build_rules}" <<- _EOF_
- # in Prefix we need rpath and must ensure cmake gets our default linker path
- # right ... except for Darwin hosts
- IF (NOT APPLE)
- SET (CMAKE_SKIP_RPATH OFF CACHE BOOL "" FORCE)
- SET (CMAKE_PLATFORM_REQUIRED_RUNTIME_PATH "${EPREFIX}/usr/${CHOST}/lib/gcc;${EPREFIX}/usr/${CHOST}/lib;${EPREFIX}/usr/$(get_libdir);${EPREFIX}/$(get_libdir)"
- CACHE STRING "" FORCE)
-
- ELSE ()
-
- SET(CMAKE_PREFIX_PATH "${EPREFIX}${PREFIX}" CACHE STRING ""FORCE)
- SET(CMAKE_SKIP_BUILD_RPATH OFF CACHE BOOL "" FORCE)
- SET(CMAKE_SKIP_RPATH OFF CACHE BOOL "" FORCE)
- SET(CMAKE_BUILD_WITH_INSTALL_RPATH TRUE CACHE BOOL "")
- SET(CMAKE_INSTALL_RPATH "${EPREFIX}${PREFIX}/lib;${EPREFIX}/usr/${CHOST}/lib/gcc;${EPREFIX}/usr/${CHOST}/lib;${EPREFIX}/usr/$(get_libdir);${EPREFIX}/$(get_libdir)" CACHE STRING "" FORCE)
- SET(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE CACHE BOOL "" FORCE)
- SET(CMAKE_INSTALL_NAME_DIR "${EPREFIX}${PREFIX}/lib" CACHE STRING "" FORCE)
-
- ENDIF (NOT APPLE)
- _EOF_
- fi
-
- # Common configure parameters (invariants)
- local common_config=${CMAKE_BUILD_DIR}/gentoo_common_config.cmake
- local libdir=$(get_libdir)
- cat > "${common_config}" <<- _EOF_
- SET (LIB_SUFFIX ${libdir/lib} CACHE STRING "library path suffix" FORCE)
- SET (CMAKE_INSTALL_LIBDIR ${PREFIX}/${libdir} CACHE PATH "Output directory for libraries")
- _EOF_
- [[ "${NOCOLOR}" = true || "${NOCOLOR}" = yes ]] && echo 'SET (CMAKE_COLOR_MAKEFILE OFF CACHE BOOL "pretty colors during make" FORCE)' >> "${common_config}"
-
- # Convert mycmakeargs to an array, for backwards compatibility
- # Make the array a local variable since <=portage-2.1.6.x does not
- # support global arrays (see bug #297255).
- if [[ $(declare -p mycmakeargs 2>&-) != "declare -a mycmakeargs="* ]]; then
- local mycmakeargs_local=(${mycmakeargs})
- else
- local mycmakeargs_local=("${mycmakeargs[@]}")
- fi
-
- # Common configure parameters (overridable)
- # NOTE CMAKE_BUILD_TYPE can be only overriden via CMAKE_BUILD_TYPE eclass variable
- # No -DCMAKE_BUILD_TYPE=xxx definitions will be in effect.
- local cmakeargs=(
- --no-warn-unused-cli
- -C "${common_config}"
- -G "$(_generator_to_use)"
- -DCMAKE_INSTALL_PREFIX="${EPREFIX}${PREFIX}"
- "${mycmakeargs_local[@]}"
- -DCMAKE_BUILD_TYPE="${CMAKE_BUILD_TYPE}"
- -DCMAKE_INSTALL_DO_STRIP=OFF
- -DCMAKE_USER_MAKE_RULES_OVERRIDE="${build_rules}"
- "${MYCMAKEARGS}"
- )
-
- pushd "${CMAKE_BUILD_DIR}" > /dev/null
- debug-print "${LINENO} ${ECLASS} ${FUNCNAME}: mycmakeargs is ${mycmakeargs_local[*]}"
- echo "${CMAKE_BINARY}" "${cmakeargs[@]}" "${CMAKE_USE_DIR}"
- "${CMAKE_BINARY}" "${cmakeargs[@]}" "${CMAKE_USE_DIR}" || die "cmake failed"
- popd > /dev/null
-}
-
-enable_cmake-utils_src_compile() {
- debug-print-function ${FUNCNAME} "$@"
-
- has src_configure ${CMAKE_EXPF} || cmake-utils_src_configure
- cmake-utils_src_make "$@"
-}
-
-# @FUNCTION: cmake-utils_src_make
-# @DESCRIPTION:
-# Function for building the package. Automatically detects the build type.
-# All arguments are passed to emake.
-cmake-utils_src_make() {
- debug-print-function ${FUNCNAME} "$@"
-
- _check_build_dir
- pushd "${CMAKE_BUILD_DIR}" > /dev/null
- if [[ $(_generator_to_use) = Ninja ]]; then
- # first check if Makefile exist otherwise die
- [[ -e build.ninja ]] || die "Makefile not found. Error during configure stage."
- if [[ "${CMAKE_VERBOSE}" != "OFF" ]]; then
- #TODO get load average from portage (-l option)
- ninja ${MAKEOPTS} -v "$@"
- else
- ninja "$@"
- fi || die "ninja failed!"
- else
- # first check if Makefile exist otherwise die
- [[ -e Makefile ]] || die "Makefile not found. Error during configure stage."
- if [[ "${CMAKE_VERBOSE}" != "OFF" ]]; then
- emake VERBOSE=1 "$@" || die "Make failed!"
- else
- emake "$@" || die "Make failed!"
- fi
- fi
- popd > /dev/null
-}
-
-enable_cmake-utils_src_install() {
- debug-print-function ${FUNCNAME} "$@"
-
- _check_build_dir
- pushd "${CMAKE_BUILD_DIR}" > /dev/null
- if [[ $(_generator_to_use) = Ninja ]]; then
- DESTDIR=${D} ninja install "$@"
- else
- base_src_install "$@"
- fi
- popd > /dev/null
-
- # Backward compatibility, for non-array variables
- if [[ -n "${DOCS}" ]] && [[ "$(declare -p DOCS 2>/dev/null 2>&1)" != "declare -a"* ]]; then
- dodoc ${DOCS} || die "dodoc failed"
- fi
- if [[ -n "${HTML_DOCS}" ]] && [[ "$(declare -p HTML_DOCS 2>/dev/null 2>&1)" != "declare -a"* ]]; then
- dohtml -r ${HTML_DOCS} || die "dohtml failed"
- fi
-}
-
-enable_cmake-utils_src_test() {
- debug-print-function ${FUNCNAME} "$@"
- local ctestargs
-
- _check_build_dir
- pushd "${CMAKE_BUILD_DIR}" > /dev/null
- [[ -e CTestTestfile.cmake ]] || { echo "No tests found. Skipping."; return 0 ; }
-
- [[ -n ${TEST_VERBOSE} ]] && ctestargs="--extra-verbose --output-on-failure"
-
- if ctest ${ctestargs} "$@" ; then
- einfo "Tests succeeded."
- else
- if [[ -n "${CMAKE_YES_I_WANT_TO_SEE_THE_TEST_LOG}" ]] ; then
- # on request from Diego
- eerror "Tests failed. Test log ${CMAKE_BUILD_DIR}/Testing/Temporary/LastTest.log follows:"
- eerror "--START TEST LOG--------------------------------------------------------------"
- cat "${CMAKE_BUILD_DIR}/Testing/Temporary/LastTest.log"
- eerror "--END TEST LOG----------------------------------------------------------------"
- die "Tests failed."
- else
- die "Tests failed. When you file a bug, please attach the following file: \n\t${CMAKE_BUILD_DIR}/Testing/Temporary/LastTest.log"
- fi
- fi
- popd > /dev/null
-}
-
-# @FUNCTION: cmake-utils_src_configure
-# @DESCRIPTION:
-# General function for configuring with cmake. Default behaviour is to start an
-# out-of-source build.
-cmake-utils_src_configure() {
- _execute_optionaly "src_configure" "$@"
-}
-
-# @FUNCTION: cmake-utils_src_compile
-# @DESCRIPTION:
-# General function for compiling with cmake. Default behaviour is to check for
-# EAPI and respectively to configure as well or just compile.
-# Automatically detects the build type. All arguments are passed to emake.
-cmake-utils_src_compile() {
- _execute_optionaly "src_compile" "$@"
-}
-
-# @FUNCTION: cmake-utils_src_install
-# @DESCRIPTION:
-# Function for installing the package. Automatically detects the build type.
-cmake-utils_src_install() {
- _execute_optionaly "src_install" "$@"
-}
-
-# @FUNCTION: cmake-utils_src_test
-# @DESCRIPTION:
-# Function for testing the package. Automatically detects the build type.
-cmake-utils_src_test() {
- _execute_optionaly "src_test" "$@"
-}
-
-# Optionally executes phases based on WANT_CMAKE variable/USE flag.
-_execute_optionaly() {
- local phase="$1" ; shift
- if [[ ${WANT_CMAKE} = always ]]; then
- enable_cmake-utils_${phase} "$@"
- else
- use ${WANT_CMAKE} && enable_cmake-utils_${phase} "$@"
- fi
-}
diff --git a/eclass/intel-sdp.eclass b/eclass/intel-sdp.eclass
deleted file mode 100644
index 7271b3082..000000000
--- a/eclass/intel-sdp.eclass
+++ /dev/null
@@ -1,187 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-# @ECLASS: intel-sdp.eclass
-# @MAINTAINER: bicatali@gentoo.org
-# @BLURB: simplify Intel Software Development Products package management
-
-# @ECLASS-VARIABLE: INTEL_DPV
-# @DEFAULT_UNSET
-# @DESCRIPTION: the package download version from Intel. It must be defined.
-# To find out its value, see the links to download in
-# https://registrationcenter.intel.com/RegCenter/MyProducts.aspx
-
-# @ECLASS-VARIABLE: INTEL_DID
-# @DEFAULT_UNSET
-# @DESCRIPTION: the package download ID from Intel. It must be defined.
-# To find out its value, see the links to download in
-# https://registrationcenter.intel.com/RegCenter/MyProducts.aspx
-
-# @ECLASS-VARIABLE: INTEL_DPN
-# @DEFAULT_UNSET
-# @DESCRIPTION: the package name to download from Intel. It must be defined.
-# To find out its value, see the links to download in
-# https://registrationcenter.intel.com/RegCenter/MyProducts.aspx
-
-# @ECLASS-VARIABLE: INTEL_SUBDIR
-# @DEFAULT_UNSET
-# @DESCRIPTION: the package sub-directory where it will end-up in /opt/intel
-# To find out its value, you have to do a raw install from the Intel tar ball
-
-# @ECLASS-VARIABLE: INTEL_RPMS_DIRS
-# @DEFAULT_UNSET
-# @DESCRIPTION: a list of subdirectories in the main archive which contains the
-# rpms to extract.
-
-inherit versionator check-reqs multilib
-
-INTEL_PV1=$(get_version_component_range 1)
-INTEL_PV2=$(get_version_component_range 2)
-INTEL_PV3=$(get_version_component_range 3)
-INTEL_PV4=$(get_version_component_range 4)
-INTEL_URI="http://registrationcenter-download.intel.com/irc_nas/${INTEL_DID}/${INTEL_DPN}"
-
-SRC_URI="
- amd64? ( multilib? ( ${INTEL_URI}_${INTEL_DPV}.tgz ) )
- amd64? ( !multilib? ( ${INTEL_URI}_${INTEL_DPV}_intel64.tgz ) )
- x86? ( ${INTEL_URI}_${INTEL_DPV}_ia32.tgz )"
-
-LICENSE="Intel-SDP"
-SLOT="${INTEL_PV1}.${INTEL_PV2}"
-IUSE="multilib"
-KEYWORDS="-* ~amd64 ~x86"
-
-RESTRICT="mirror"
-
-RDEPEND=""
-DEPEND=">=app-arch/rpm2targz-9.0.0.3g"
-INTEL_SDP_YEAR=${INTEL_DPV%_update*}
-INTEL_SDP_YEAR=${INTEL_DPV%_sp*}
-INTEL_SDP_DIR="opt/intel/${INTEL_SUBDIR}-${INTEL_SDP_YEAR:-${INTEL_PV1}}.${INTEL_PV3}.${INTEL_PV4}"
-INTEL_SDP_EDIR="${EROOT%/}/${INTEL_SDP_DIR}"
-
-S="${WORKDIR}"
-
-intel-sdp_pkg_pretend() {
- : ${CHECKREQS_DISK_BUILD:=256M}
- check-reqs_pkg_pretend
-}
-
-intel-sdp_pkg_setup() {
- local arch a p
- if use x86; then
- arch=${INTEL_X86:-i486}
- INTEL_ARCH="ia32"
- elif use amd64; then
- arch=x86_64
- INTEL_ARCH="intel64"
- if has_multilib_profile; then
- arch="x86_64 ${INTEL_X86:-i486}"
- INTEL_ARCH="intel64 ia32"
- fi
- fi
- INTEL_RPMS=""
- for p in ${INTEL_BIN_RPMS}; do
- for a in ${arch}; do
- INTEL_RPMS="${INTEL_RPMS} intel-${p}-${INTEL_PV4}-${INTEL_PV1}.${INTEL_PV2}-${INTEL_PV3}.${a}.rpm"
- done
- done
- for p in ${INTEL_DAT_RPMS}; do
- INTEL_RPMS="${INTEL_RPMS} intel-${p}-${INTEL_PV4}-${INTEL_PV1}.${INTEL_PV2}-${INTEL_PV3}.noarch.rpm"
- done
-
- case "${EAPI:-0}" in
- 0|1|2|3) intel-sdp_pkg_pretend ;;
- esac
-}
-
-intel-sdp_src_unpack() {
- local l r t rpmdir
- for t in ${A}; do
- # TODO: need to find a fast way to find the rpmdir
- # in some cases rpms are in rpms/, in other cases in rpm/
- # tar tvf is too slow for 1.4G tar balls
- for r in ${INTEL_RPMS}; do
- # Find which subdirectory of the archive the rpm is in
- rpm_found="false"
- for subdir in ${INTEL_RPMS_DIRS:-rpm}; do
- [[ "${rpm_found}" == "true" ]] && continue
- rpmdir=${t%%.*}/${subdir}
- l=.${r}_$(date +'%d%m%y_%H%M%S').log
- tar xf "${DISTDIR}"/${t} ${rpmdir}/${r} 2> /dev/null || continue
- einfo "Unpacking ${r}"
- rpm_found="true"
- rpm2tar -O "./${rpmdir}/${r}" | tar xvf - | sed -e \
- "s:^\.:${EROOT#/}:g" > ${l} || die "unpacking ${r} failed"
- mv ${l} opt/intel/ || die "failed moving extract log file"
- done
- done
- done
- mv -v opt/intel/* ${INTEL_SDP_DIR} || die "mv to INTEL_SDP_DIR failed"
-}
-
-intel_link_eclipse_plugins() {
- pushd ${INTEL_SDP_DIR}/eclipse_support > /dev/null
- local c f
- for c in cdt*; do
- local cv=${c#cdt} ev=3.$(( ${cv:0:1} - 1))
- if has_version "dev-util/eclipse-sdk:${ev}"; then
- einfo "Linking eclipse (v${ev}) plugin cdt (v${cv})"
- for f in cdt${cv}/eclipse/features/*; do
- dodir /usr/$(get_libdir)/eclipse-${ev}/features
- dosym "${INTEL_SDP_EDIR}"/eclipse_support/${f} \
- /usr/$(get_libdir)/eclipse-${ev}/features/ || die
- done
- for f in cdt${cv}/eclipse/plugins/*; do
- dodir /usr/$(get_libdir)/eclipse-${ev}/plugins
- dosym "${INTEL_SDP_EDIR}"/eclipse_support/${f} \
- /usr/$(get_libdir)/eclipse-${ev}/plugins/ || die
- done
- fi
- done
- popd > /dev/null
-}
-
-intel-sdp_src_install() {
- [[ -d ${INTEL_SDP_DIR}/eclipse_support ]] && \
- has eclipse ${IUSE} && \
- use eclipse && \
- intel_link_eclipse_plugins
- einfo "Tagging ${PN}"
- find opt -name \*sh -type f -exec sed -i \
- -e "s:<.*DIR>:${INTEL_SDP_EDIR}:g" \
- '{}' \;
- mkdir -p "${ED:-${D}}"/ || die
- mv opt "${ED:-${D}}"/ || die "moving files failed"
-}
-
-intel-sdp_pkg_postinst() {
- # add product registry to intel "database"
- local l r
- INTEL_SDP_DB="${EROOT%/}"/opt/intel/intel-sdp-products.db
- for r in ${INTEL_RPMS}; do
- l="$(ls -1 ${EROOT%/}/opt/intel/.${r}_*.log | head -n 1)"
- echo >> ${INTEL_SDP_DB} \
- "<:${r%-${INTEL_PV4}*}-${INTEL_PV4}:${r}:${INTEL_SDP_EDIR}:${l}:>"
- done
-}
-
-intel-sdp_pkg_postrm() {
- # remove from intel "database"
- if [[ -e ${INTEL_SDP_DB} ]]; then
- local r
- for r in ${INTEL_RPMS}; do
- sed -i \
- -e "/${r}/d" \
- ${INTEL_SDP_DB}
- done
- fi
-}
-
-EXPORT_FUNCTIONS pkg_setup src_unpack src_install pkg_postinst pkg_postrm
-case "${EAPI:-0}" in
- 0|1|2|3) ;;
- 4) EXPORT_FUNCTIONS pkg_pretend ;;
- *) die "EAPI=${EAPI} is not supported" ;;
-esac
diff --git a/licenses/chimera b/licenses/chimera
new file mode 100644
index 000000000..044155369
--- /dev/null
+++ b/licenses/chimera
@@ -0,0 +1,13 @@
+UCSF Chimera Non-Commercial Software License Agreement
+
+This license agreement ("License"), effective today, is made by and between you (hereinafter referred to as the "Licensee") and The Regents of the University of California, a California corporation having its statewide administrative offices at 1111 Franklin Street, Oakland, California 94607-5200, ("Regents") acting through its Office of Technology Management, University of California San Francisco, 185 Berry Street, Suite 4603, San Francisco, California 94107, and concerns certain software known as "UCSF Chimera," a system of software programs for the visualization and interactive manipulation of molecular models, developed by the Computer Graphics Laboratory at the University of California San Francisco for research purposes and includes executable code, source code, and documentation (hereinafter referred to as the "Software").
+
+General. A non-exclusive, nontransferable, perpetual license is granted to the Licensee to install and use the Software for academic, non-profit, or government-sponsored research purposes. Use of the Software under this License is restricted to non-commercial purposes. Commercial use of the Software requires a separately executed written license agreement.
+Permitted Use and Restrictions. Licensee agrees that it will use the Software, and any modifications, improvements, or derivatives to the Software that the Licensee may create (collectively, "Improvements") solely for internal, non-commercial purposes and shall not distribute or transfer the Software or Improvements to any person or third parties without prior written permission from the Regents. The term "non-commercial," as used in this License, means academic or other scholarly research which (a) is not undertaken for profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged in the commercial use, application or exploitation of works similar to the Software.
+Ownership and Assignment of Copyright. The Licensee acknowledges that the Regents hold copyright in the Software and associated documentation, and the Software and associated documentation are the property of the Regents. The Licensee agrees that any Improvements made by Licensee shall be subject to the same terms and conditions as the Software. Licensee agrees not to assert a claim of infringement in Licensee copyrights in Improvements in the event the Regents prepares substantially similar modifications or derivative works. The Licensee agrees to use his/her reasonable best efforts to protect the contents of the Software and to prevent unauthorized disclosure by its agents, officers, employees, and consultants. If the Licensee receives a request to furnish all or any portion of the Software to a third party, Licensee will not fulfill such a request but will refer the third party to http://www.cgl.ucsf.edu/chimera/ so that the third party's use of this Software will be subject to the terms and conditions of this License. Notwithstanding the above, Licensee may disclose any Improvements that do not involve disclosure of the Software.
+Copies. The Licensee may make a reasonable number of copies of the Software for the purposes of backup, maintenance of the Software or the development of derivative works based on the Software. These additional copies shall carry the copyright notice and shall be controlled by this License, and will be destroyed along with the original by the Licensee upon termination of the License.
+Acknowledgement. Licensee agrees that any publication of results obtained with the Software will acknowledge its use by an appropriate citation as specified in the documentation.
+Disclaimer of Warranties and Limitation of Liability. THE LICENSEE AGREES THAT ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. THE REGENTS MAKES NO REPRESENTATION OR WARRANTY THAT THE SOFTWARE WILL NOT INFRINGE ANY PATENT OR OTHER PROPRIETARY RIGHT. IN NO EVENT SHALL THE REGENTS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+Termination. This License is effective until terminated by either party. Your rights under this License will terminate automatically without notice from the Regents if you fail to comply with any term(s) of this License. You may terminate the license by giving written notice of termination to the Regents. Upon termination of this License, you shall immediately discontinue all use of the Software and destroy the original and all copies, full or partial, of the Software, including any modifications or derivative works, and associated documentation.
+Governing Law and General Provisions. This License shall be governed by the laws of the State of California, excluding the application of its conflicts of law rules. This License shall not be governed by the United Nations Convention on Contracts for the International Sale of Goods, the application of which is expressly excluded. If any provisions of this License are held invalid or unenforceable for any reason, the remaining provisions shall remain in full force and effect. This License is binding upon any heirs and assigns of the Licensee. The License granted to Licensee hereunder may not be assigned or transferred to any other person or entity without the express consent of the Regents. This License constitutes the entire agreement between the parties with respect to the use of the Software licensed hereunder and supersedes all other previous or contemporaneous agreements or understandings between the parties, whether verbal or written, concerning the subject matter. Any translation of this License is done for local requirements and in the event of a dispute between the English and any non-English versions, the English version of this License shall govern.
+
diff --git a/licenses/phenix b/licenses/phenix
new file mode 100644
index 000000000..0b6c5c08c
--- /dev/null
+++ b/licenses/phenix
@@ -0,0 +1,174 @@
+NON-COMMERCIAL END USER
+SOURCE CODE & BINARY LICENSE AGREEMENT
+
+Software: PHENIX (LBNL Ref. CR-1770)
+Version: 1 Alpha, Beta and General
+
+Software: LABELIT (LBNL Ref. CR-1960)
+Version: 1.1.4
+
+IMPORTANT - READ CAREFULLY: This License Agreement ("Agreement") is a
+legal agreement between you (in your capacity as an individual and as
+an agent for your company, institution or other entity) and The
+Regents of the University of California, Department of Energy
+contract-operators of the Ernest Orlando Lawrence Berkeley National
+Laboratory ("Berkeley Lab"). Downloading, installing, using, or
+copying of the Software (as defined below) by you or by a third party
+on your behalf indicates your agreement to be bound by the terms and
+conditions of this Agreement. If you do not agree to these terms and
+conditions, do not download, install or use the Software.
+
+1. LICENSE GRANT. Berkeley Lab grants you, and you hereby accept, a
+non-exclusive, royalty-free perpetual license to install, use, modify,
+and prepare derivative works the version noted above of the computer
+software program noted above, in binary and source code format, or any
+derivative work thereof, together with any associated media, printed
+materials, and on-line or electronic documentation (if any) provided
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+NON-COMMERCIAL, RESEARCH AND DEVELOPMENT PURPOSES ONLY, subject to the
+following terms and conditions: (i) you may not distribute, rent,
+lease, loan, or sublicense the Software to any third party, nor may
+you distribute the Software as incorporated into any derivative work
+you may create. This version of the Software constitutes a research
+prototype and may be changed substantially. The license grant set
+forth above is subject to receipt by Berkeley Lab of any required
+U.S. Department of Energy approvals.
+
+2. COPYRIGHT; RETENTION OF RIGHTS. The above license grant is
+conditioned on the following: (i) you must reproduce all copyright
+notices and other proprietary notices on any copies of the Software
+and you must not remove such notices; and (ii) in the event you
+compile the Software, you will include the copyright notice with the
+binary in such a manner as to allow it to be easily viewable. All
+copies of the Software shall be subject to the terms of this
+Agreement. Subject to approval by the U.S. Department of Energy: (a)
+you hereby acknowledge that the Software is protected by United States
+copyright law and international treaty provisions; (b) Berkeley Lab,
+and its licensors (if any), hereby reserve all rights in the Software
+which are not explicitly granted to you herein; (c) without limiting
+the generality of the foregoing, Berkeley Lab and its licensors retain
+all title, copyright, and other proprietary interests in the Software
+and any copies thereof, and you do not acquire any rights, express or
+implied, in the Software, other than those specifically set forth in
+this Agreement. Subject to Berkeley Lab's underlying copyright in the
+Software pursuant to the above, you retain all title, copyright, and
+other proprietary interests in any derivative works of the Software
+that you create and any copies thereof, and Berkeley Lab does not
+acquire any rights, express or implied, in such derivative works.
+
+3. NO MAINTENANCE OR SUPPORT; TREATMENT OF ENHANCEMENTS YOU CHOOSE TO
+PROVIDE TO BERKELEY LAB. Berkeley Lab is under no obligation
+whatsoever to: (i) provide maintenance or support for the Software; or
+(ii) notify you of bug fixes, patches, or upgrades to the features,
+functionality or performance of the Software ("Enhancements") (if
+any), whether developed by Berkeley Lab or third parties. If, in its
+sole discretion, Berkeley Lab makes an Enhancement available to you
+and Berkeley Lab does not separately enter into a written license
+agreement with you relating to such bug fix, patch or upgrade, then it
+shall be deemed incorporated into the Software and subject to this
+Agreement. You are under no obligation whatsoever to provide any
+Enhancements to Berkeley Lab that you may develop over time; however,
+if you choose to provide your Enhancements to Berkeley Lab in source
+code form without contemporaneously requiring Berkeley Lab to enter
+into a separate written license agreement for such Enhancements, then
+you hereby grant Berkeley Lab a non-exclusive, royalty-free perpetual
+license to install, use, modify, prepare derivative works, incorporate
+into the Software or other computer software, distribute, and
+sublicense your Enhancements or derivative works thereof, in binary
+and source code form.
+
+4. U.S. GOVERNMENT RIGHTS. The Software was developed under funding
+from the U.S. Department of Energy and the U.S. Government
+consequently retains certain rights as follows: the U.S. Government
+has been granted for itself and others acting on its behalf a paid-up,
+nonexclusive, irrevocable, worldwide license in the Software to
+reproduce, prepare derivative works, and perform publicly and display
+publicly. Beginning five (5) years after the date permission to
+assert copyright was granted by the U.S. Dept. of Energy, and subject
+to any subsequent five (5) year renewals, the U.S. Government is
+granted for itself and others acting on its behalf a paid-up,
+nonexclusive, irrevocable, worldwide license in the Software to
+reproduce, prepare derivative works, distribute copies to the public,
+perform publicly and display publicly, and to permit others to do so.
+
+5. CONFIDENTIALITY. You agree to take appropriate steps to ensure
+that the source code form of the Software remains confidential and is
+protected against unauthorized disclosure, use, or release, and will
+treat it with at least the same level of care as you would use to
+protect and secure your own confidential information, but in any event
+using no less than a reasonable standard of care.
+
+6. WARRANTY DISCLAIMER. THE SOFTWARE IS SUPPLIED "AS IS" WITHOUT
+WARRANTY OF ANY KIND. BERKELEY LAB, ITS LICENSORS, THE UNITED STATES,
+THE UNITED STATES DEPARTMENT OF ENERGY, AND THEIR EMPLOYEES: (1)
+DISCLAIM ANY WARRANTIES, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED
+TO ANY IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
+PURPOSE, TITLE OR NON-INFRINGEMENT, (2) DO NOT ASSUME ANY LEGAL
+LIABILITY OR RESPONSIBILITY FOR THE ACCURACY, COMPLETENESS, OR
+USEFULNESS OF THE SOFTWARE, (3) DO NOT REPRESENT THAT USE OF THE
+SOFTWARE WOULD NOT INFRINGE PRIVATELY OWNED RIGHTS, (4) DO NOT WARRANT
+THAT THE SOFTWARE WILL FUNCTION UNINTERRUPTED, THAT IT IS ERROR-FREE
+OR THAT ANY ERRORS WILL BE CORRECTED.
+
+7. LIMITATION OF LIABILITY. IN NO EVENT WILL BERKELEY LAB OR ITS
+LICENSORS BE LIABLE FOR ANY INDIRECT, INCIDENTAL, CONSEQUENTIAL,
+SPECIAL OR PUNITIVE DAMAGES OF ANY KIND OR NATURE, INCLUDING BUT NOT
+LIMITED TO LOSS OF PROFITS OR LOSS OF DATA, FOR ANY REASON WHATSOEVER,
+WHETHER SUCH LIABILITY IS ASSERTED ON THE BASIS OF CONTRACT, TORT
+(INCLUDING NEGLIGENCE OR STRICT LIABILITY), OR OTHERWISE, EVEN IF
+BERKELEY LAB HAS BEEN WARNED OF THE POSSIBILITY OF SUCH LOSS OR
+DAMAGES. IN NO EVENT SHALL BERKELEY LAB'S LIABILITY FOR DAMAGES
+ARISING FROM OR IN CONNECTION WITH THIS AGREEMENT EXCEED THE AMOUNT
+PAID BY YOU FOR THE SOFTWARE.
+
+8. INDEMNITY. You shall indemnify, defend, and hold harmless
+Berkeley Lab, the U.S. Government, the Software developers, the
+Software sponsors, and their agents, officers, and employees, against
+any and all claims, suits, losses, damage, costs, fees, and expenses
+arising out of or in connection with this Agreement. You shall pay
+all costs incurred by Berkeley Lab in enforcing this provision,
+including reasonable attorney fees.
+
+9. TERM AND TERMINATION. The license granted to you under this
+Agreement will continue perpetually unless terminated by Berkeley Lab
+in accordance with this Agreement. If you breach any term of this
+Agreement, and fail to cure such breach within thirty (30) days of the
+date of written notice, this Agreement shall immediately
+terminate. Upon such termination, you shall immediately cease using
+the Software, return to Berkeley Lab, or destroy, all copies of the
+Software, and provide Berkeley Lab with written certification of your
+compliance with the foregoing. Termination shall not relieve you from
+your obligations arising prior to such termination. Notwithstanding
+any provision of this Agreement to the contrary, Sections 5 through 12
+shall survive termination of this Agreement.
+
+10. EXPORT CONTROLS. You shall observe all applicable United States
+and foreign laws and regulations (if any) with respect to the export,
+re-export, diversion or transfer of the Software, related technical
+data and direct products thereof, including, without limitation, the
+International Traffic in Arms Regulations (ITAR) and the Export
+Administration Regulations.
+
+11. NO ENDORSEMENT. In accordance with California Education Code
+Section 92000, you shall not use in advertising, publicity or other
+promotional activities any name, trade name, trademark, or other
+designation of the University of California, nor shall you so use
+"Ernest Orlando Lawrence Berkeley National Laboratory" or "United
+States Department of Energy" (including any contraction, abbreviation,
+or simulation of any of the foregoing) without Berkeley Lab's prior
+written consent.
+
+12. GENERAL. This Agreement shall be governed by the laws of the
+State of California, excluding its rules governing conflicts of laws.
+No provision in either party's purchase orders, or in any other
+business forms employed by either party will supersede the terms of
+this Agreement, and no modification or amendment of this Agreement is
+binding, unless in writing signed by a duly authorized representative
+of each party. This Agreement is binding upon and shall inure to the
+benefit of Berkeley Lab, its successors and assigns. This Agreement
+represents the entire understanding of the parties, and supersedes all
+previous communications, written or oral, relating to the subject of
+this Agreement. If you have any questions concerning this license,
+contact Lawrence Berkeley National Laboratory, Technology Transfer
+Department, One Cyclotron Road, MS 90R1070, Berkeley, CA 94720, Attn:
+Software Licensing or via e-mail at TTD@lbl.gov. (rev 010903)
diff --git a/profiles/package.mask b/profiles/package.mask
index 1de782603..b1714bcb0 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -32,6 +32,7 @@
# Guillaume Horel <guillaume.horel@gmail.com> (11 July 2012)
# masked for upcoming scilab-5.4.0
+=sci-mathematics/scilab-5.4.0
=dev-java/jrosetta-1.0.4
=dev-java/flexdock-1.2.0
>=dev-java/jgraphx-1.8
@@ -57,10 +58,6 @@
# live ebuild
=dev-lang/ispc-9999
-# Sebastien Fabbro <bicatali@gentoo.org> (14 May 2012)
-# alpha version for testing
->=sci-mathematics/scilab-5.3.99
-
# Justin Lecher <jlec@gentoo.org> (28 Apr 2012)
# Doesn't install pkg-config files, which many packages rely on
=sci-libs/mmdb-1.24.20111208
@@ -146,6 +143,7 @@ sci-visualization/vtkPOFFReader
=sci-chemistry/gromacs-4.5.9999
=sci-chemistry/gromacs-4.6.9999
=sci-chemistry/gromacs-9999
+=app-doc/gromacs-manual-4.6.9999
=app-doc/gromacs-manual-9999
# Christoph Junghans <ottxor@gentoo.org> (04 Nov 2011)
diff --git a/sci-chemistry/chemBuild/ChangeLog b/sci-chemistry/chemBuild/ChangeLog
new file mode 100644
index 000000000..a592f6b45
--- /dev/null
+++ b/sci-chemistry/chemBuild/ChangeLog
@@ -0,0 +1,13 @@
+# ChangeLog for sci-chemistry/chemBuild
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 21 Sep 2012; Justin Lecher <jlec@gentoo.org> chemBuild-1.0.2.ebuild:
+ Needs webkit support in pyside
+
+*chemBuild-1.0.2 (21 Sep 2012)
+
+ 21 Sep 2012; Justin Lecher <jlec@gentoo.org> +chemBuild-1.0.2.ebuild,
+ +files/chemBuild, +metadata.xml:
+ New addition
+
diff --git a/sci-chemistry/chemBuild/Manifest b/sci-chemistry/chemBuild/Manifest
new file mode 100644
index 000000000..2ba5517a2
--- /dev/null
+++ b/sci-chemistry/chemBuild/Manifest
@@ -0,0 +1 @@
+DIST chemBuild1.0.2_WithApi.tar.gz 15593107 SHA256 f27c5f7c5e557af2cbe1ccdacff6e0896ab041536d127733478d27a963bf2f2c SHA512 85cc5d83c63b230c889bbdeed560ac7043db477d7f1a54e42cc85d6b18733b0279e6de0d3e3f1e3b30eb99f450a236a673eb3202d4e0942a20e857ec285df037 WHIRLPOOL ab8f51284056921cb4eb1cf812cd715036ba38547bb1931e187430b5dd2b01315bfebe12a6ef8de9d57fc6c54acb095dbdef53d60eae86d2f116861ed4f5600c
diff --git a/sci-chemistry/chemBuild/chemBuild-1.0.2.ebuild b/sci-chemistry/chemBuild/chemBuild-1.0.2.ebuild
new file mode 100644
index 000000000..dece95eb2
--- /dev/null
+++ b/sci-chemistry/chemBuild/chemBuild-1.0.2.ebuild
@@ -0,0 +1,68 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=4
+
+PYTHON_DEPEND="2"
+
+inherit python toolchain-funcs
+
+DESCRIPTION="Graphical tool to construct chemical compound definitions for NMR"
+HOMEPAGE="http://www.ccpn.ac.uk/software/chembuild"
+SRC_URI="http://www2.ccpn.ac.uk/download/ccpnmr/${PN}${PV}_WithApi.tar.gz"
+
+SLOT="0"
+LICENSE="|| ( CCPN LGPL-2.1 )"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND="dev-python/pyside[webkit]"
+DEPEND=""
+
+S="${WORKDIR}"/ccpnmr/ccpnmr3.0/
+
+#TODO:
+#install in sane place
+#unbundle data model
+#unbundle inchi
+#parallel build
+
+pkg_setup() {
+ python_set_active_version 2
+ python_pkg_setup
+}
+
+src_install() {
+ local in_path=$(python_get_sitedir)/${PN}
+ local _file
+
+ find . -name "*.pyc" -type f -delete
+ dodir /usr/bin
+ sed \
+ -e "s|gentoo_sitedir|${EPREFIX}$(python_get_sitedir)|g" \
+ -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \
+ -e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \
+ -e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \
+ -e "s|gentoopython|$(PYTHON -a)|g" \
+ -e "s|gentoousr|${EPREFIX}/usr|g" \
+ -e "s|//|/|g" \
+ "${FILESDIR}"/${PN} > "${ED}"/usr/bin/${PN} || die
+ fperms 755 /usr/bin/${PN}
+
+ insinto ${in_path}
+
+ rm -rf cNg license || die
+
+ ebegin "Installing main files"
+ doins -r *
+ eend
+}
+
+pkg_postinst() {
+ python_mod_optimize ${PN}
+}
+
+pkg_postrm() {
+ python_mod_cleanup ${PN}
+}
diff --git a/sci-chemistry/chemBuild/files/chemBuild b/sci-chemistry/chemBuild/files/chemBuild
new file mode 100644
index 000000000..c6d3d31ac
--- /dev/null
+++ b/sci-chemistry/chemBuild/files/chemBuild
@@ -0,0 +1,9 @@
+#!/bin/bash
+
+export CCPNMR_TOP_DIR=gentoo_sitedir
+export PYTHONPATH=.:${CCPNMR_TOP_DIR}/chemBuild/python
+export LD_LIBRARY_PATH=gentoolibdir
+export TCL_LIBRARY=gentootcl
+export TK_LIBRARY=gentootk
+export PSIPRED_DIR=gentoousr
+gentoopython -O ${CCPNMR_TOP_DIR}/chemBuild/python/ccpnmr/chemBuild/ChemBuild.py $@
diff --git a/sci-chemistry/chemBuild/metadata.xml b/sci-chemistry/chemBuild/metadata.xml
new file mode 100644
index 000000000..d369d068f
--- /dev/null
+++ b/sci-chemistry/chemBuild/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci</herd>
+</pkgmetadata>
diff --git a/sci-chemistry/chimera-bin/ChangeLog b/sci-chemistry/chimera-bin/ChangeLog
new file mode 100644
index 000000000..3b78d92d6
--- /dev/null
+++ b/sci-chemistry/chimera-bin/ChangeLog
@@ -0,0 +1,16 @@
+# ChangeLog for sci-chemistry/chimera-bin
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 21 Sep 2012; Justin Lecher <jlec@gentoo.org> chimera-bin-1.6.2.ebuild:
+ Don't strip
+
+ 21 Sep 2012; Justin Lecher <jlec@gentoo.org> chimera-bin-1.6.2.ebuild:
+ Set rpath on prefix
+
+*chimera-bin-1.6.2 (20 Sep 2012)
+
+ 20 Sep 2012; Justin Lecher <jlec@gentoo.org> +chimera-bin-1.6.2.ebuild,
+ +metadata.xml:
+ New addition
+
diff --git a/sci-chemistry/chimera-bin/Manifest b/sci-chemistry/chimera-bin/Manifest
new file mode 100644
index 000000000..7d8ba0309
--- /dev/null
+++ b/sci-chemistry/chimera-bin/Manifest
@@ -0,0 +1,2 @@
+DIST chimera-1.6.2-linux.bin 83913372 SHA256 06285c0beb3dd61af98fcc5f7d3e0d71e90dd2c26070d9db8ee0c71dae378487 SHA512 3de715261eaafe3c4435221e919196e38ebc5a5815a2df6b035c45797be3a164a55d535b0cb774e588b9ffaee00c70bbb907d558be910fc13c5a8ccdf1fee5e3 WHIRLPOOL 47aa46b0d67a73a19a13619cccbbe7f4c41aba83f3616647d5390d14639a4335dcab7f209129a18f75400240114f1b40cf525e30c9269f6af88ebb9f5025c6f0
+DIST chimera-1.6.2-linux_x86_64.bin 89089984 SHA256 b5ade75e5759e53d29153b4dc3a88fd2fab501e4aa1599efd0f46a1b46e7bd2c SHA512 9cdb99167e39084c483ba192d921c45fbe54b453f71fa24d39eac307f24f799dcd3cc6b0374904f4e9c4836161d81864c5204dda07383a422732b5f81936b59b WHIRLPOOL 0cb90af5b073443aa6b432842fef4371941e684b9fcde6adf0e80a4abcc9654e1e80cd817acb0b9741dc43b9ac33b67b648c0f29d9b938fdb86de0550bd07140
diff --git a/sci-chemistry/chimera-bin/chimera-bin-1.6.2.ebuild b/sci-chemistry/chimera-bin/chimera-bin-1.6.2.ebuild
new file mode 100644
index 000000000..50ba959df
--- /dev/null
+++ b/sci-chemistry/chimera-bin/chimera-bin-1.6.2.ebuild
@@ -0,0 +1,64 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=4
+
+inherit eutils
+
+DESCRIPTION="An extensible Molecular Modelling System"
+HOMEPAGE="http://www.cgl.ucsf.edu/chimera"
+SRC_URI="
+ amd64? ( chimera-1.6.2-linux_x86_64.bin )
+ x86? ( chimera-1.6.2-linux.bin )"
+
+SLOT="0"
+LICENSE="chimera"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+DEPEND="prefix? ( dev-util/patchelf )"
+
+S="${WORKDIR}"
+
+RESTRICT="fetch strip"
+
+QA_PREBUILT="opt/.*"
+
+pkg_nofetch() {
+ elog "Please visit"
+ elog "http://www.cgl.ucsf.edu/chimera/download.html"
+ elog "and download ${A} into ${DISTDIR}"
+}
+
+src_unpack() {
+ cp "${DISTDIR}"/${A} ${A}.zip
+ unzip ${A}.zip || die
+}
+
+src_install() {
+ chmod +x ./chimera.bin
+ dodir /opt/
+ ./chimera.bin -d foo || die
+ doicon foo/chimeraIcon.png
+ mv foo "${ED}/opt/${PN}" || die
+
+ cat >> "${T}"/chimera <<- EOF
+ #!${EPREFX}/bin/bash
+
+ export PATH="${EPREFIX}/opt/${PN}/bin:\${PATH}"
+ "${EPREFIX}/opt/${PN}/bin/chimera" \$@
+ EOF
+
+ exeinto /opt/bin/
+ doexe "${T}"/chimera
+
+ make_desktop_entry "${EPREFIX}/opt/bin/chimera" Chimera chimeraIcon
+
+ if use prefix; then
+ local i
+ for i in "${ED}"/opt/${PN}/bin/{tiffcp,povray,al2co} "${ED}"/opt/${PN}/lib/*.so; do
+ patchelf --set-rpath "${EPREFIX}/usr/lib:${EPREFIX}/opt/${PN}/lib" "${i}" || die
+ done
+ fi
+}
diff --git a/sci-chemistry/chimera-bin/metadata.xml b/sci-chemistry/chimera-bin/metadata.xml
new file mode 100644
index 000000000..d369d068f
--- /dev/null
+++ b/sci-chemistry/chimera-bin/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci</herd>
+</pkgmetadata>
diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index e597ab8bd..197705fa3 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,14 @@
# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 04 Oct 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
+ gromacs-9999.ebuild:
+ live ebuild update
+
+ 03 Oct 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
+ metadata.xml:
+ hybrid stuff got merged
+
09 Aug 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
use ninja if available
diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index f54af37be..d95a7cfb9 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -5,7 +5,6 @@
EAPI="4"
TEST_PV="4.0.4"
-MANUAL_PV="4.5.4"
#to find external blas/lapack
CMAKE_MIN_VERSION="2.8.5-r2"
@@ -14,8 +13,7 @@ CMAKE_MAKEFILE_GENERATOR="ninja"
inherit bash-completion-r1 cmake-utils eutils fortran-2 multilib toolchain-funcs
-SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
- doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> gromacs-manual-${MANUAL_PV}.pdf )"
+SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )"
if [[ $PV = *9999* ]]; then
EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
@@ -23,8 +21,8 @@ if [[ $PV = *9999* ]]; then
git://github.com/gromacs/gromacs.git
http://repo.or.cz/r/gromacs.git"
EGIT_BRANCH="release-4-6"
- use hybrid && EGIT_BRANCH="nbnxn_hybrid_acc"
inherit git-2
+ PDEPEND="doc? ( ~app-doc/gromacs-manual-${PV} )"
else
SRC_URI="${SRC_URI} ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz"
fi
@@ -37,7 +35,7 @@ HOMEPAGE="http://www.gromacs.org/"
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos"
-IUSE="X blas cuda doc -double-precision +fftw gsl hybrid lapack
+IUSE="X blas cuda doc -double-precision +fftw gsl lapack
mpi openmp +single-precision test +threads xml zsh-completion ${ACCE_IUSE}"
CDEPEND="
@@ -56,12 +54,11 @@ CDEPEND="
xml? ( dev-libs/libxml2:2 )"
DEPEND="${CDEPEND}
virtual/pkgconfig"
-RDEPEND="${CDEPEND}
- app-shells/tcsh"
+RDEPEND="${CDEPEND}"
RESTRICT="test"
-REQUIRED_USE="cuda? ( !double-precision hybrid )"
+REQUIRED_USE="cuda? ( !double-precision )"
pkg_pretend() {
[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
@@ -121,9 +118,6 @@ src_configure() {
use avx128fma && acce="AVX_128_FMA"
use avx256 && acce="AVX_256"
- #workaround for now
- use sse2 && use hybrid && CFLAGS+=" -msse2"
-
#to create man pages, build tree binaries are executed (bug #398437)
[[ ${CHOST} = *-darwin* ]] && \
extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
@@ -209,8 +203,11 @@ src_install() {
cd "${S}"
dodoc AUTHORS INSTALL* README*
if use doc; then
- newdoc "${DISTDIR}/gromacs-manual-${MANUAL_PV}.pdf" "manual-${MANUAL_PV}.pdf"
dohtml -r "${ED}usr/share/gromacs/html/"
+ insinto /usr/share/gromacs
+ doins "admin/programs.txt"
+ ls -1 "${ED}"/usr/bin | sed -e '/_d$/d' > "${T}"/programs.list
+ doins "${T}"/programs.list
fi
rm -rf "${ED}usr/share/gromacs/html/"
}
@@ -225,9 +222,4 @@ pkg_postinst() {
einfo "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc"
einfo
elog "Gromacs can use sci-chemistry/vmd to read additional file formats"
- if use hybrid; then
- elog "Cuda and hybrid acceleration is still experimental,"
- elog "use 'cutoff-scheme = Verlet' in your mdp file and"
- elog "report bugs: http://redmine.gromacs.org/issues"
- fi
}
diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index d74f3cd01..1e7bf0c9b 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -42,9 +42,8 @@ CDEPEND="
xml? ( dev-libs/libxml2:2 )"
DEPEND="${CDEPEND}
virtual/pkgconfig"
-RDEPEND="${CDEPEND}
- app-shells/tcsh"
-PDEPEND="doc? ( app-doc/gromacs-manual )"
+RDEPEND="${CDEPEND}"
+PDEPEND="doc? ( ~app-doc/gromacs-manual-${PV} )"
RESTRICT="test"
diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml
index dd3f082b0..acbcd53ae 100644
--- a/sci-chemistry/gromacs/metadata.xml
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -9,7 +9,6 @@
<use>
<flag name="cuda">Enable cuda non-bonded kernels</flag>
<flag name="double-precision">More precise calculations at the expense of speed</flag>
- <flag name="hybrid">Enable hybrid acceleration kernels</flag>
<flag name="single-precision">Single precision version of gromacs (default)</flag>
<!-- acceleration optimization flags -->
<flag name="fkernels">Enable building of Fortran Kernels for platforms that dont have assembly loops</flag>
diff --git a/sci-chemistry/phenix-bin/ChangeLog b/sci-chemistry/phenix-bin/ChangeLog
new file mode 100644
index 000000000..22c887a87
--- /dev/null
+++ b/sci-chemistry/phenix-bin/ChangeLog
@@ -0,0 +1,23 @@
+# ChangeLog for sci-chemistry/phenix-bin
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 21 Sep 2012; Justin Lecher <jlec@gentoo.org> phenix-bin-1.8.1069.ebuild:
+ Add missing dep
+
+ 21 Sep 2012; Justin Lecher <jlec@gentoo.org> phenix-bin-1.8.1069.ebuild:
+ Don't double prefix
+
+ 21 Sep 2012; Justin Lecher <jlec@gentoo.org> phenix-bin-1.8.1069.ebuild:
+ Not everyone installs on my box
+
+ 20 Sep 2012; Justin Lecher <jlec@gentoo.org> +phenix-bin-1.8.1069.ebuild,
+ +metadata.xml:
+ New Addition
+
+*phenix-bin-1.8.1069 (20 Sep 2012)
+
+ 20 Sep 2012; Justin Lecher <jlec@gentoo.org> +phenix-bin-1.8.1069.ebuild,
+ +metadata.xml:
+ New Addition
+
diff --git a/sci-chemistry/phenix-bin/Manifest b/sci-chemistry/phenix-bin/Manifest
new file mode 100644
index 000000000..444122b38
--- /dev/null
+++ b/sci-chemistry/phenix-bin/Manifest
@@ -0,0 +1,2 @@
+DIST phenix-installer-1.8-1069-intel-linux-2.6-fc3.tar 624865280 SHA256 71effa3e58be1acc94687ae89c9350b7088883af1c71e533bdae1c426d1770db SHA512 352a964b8c5235ae9a8a7a051fb182bae45c4ef136d140014d8d415d9039bc55cb5625f98b8ac7ed3c6b1f49202cc46277d6757313659b655ebc681a6bfdcf0c WHIRLPOOL c00d79fd11af4caf958aad6e28b74547cdb81016ccc1c72998361c078a3e6fa5782eb562e104b2fdf11bff986e4596a04aca523f88dbcee1707ed3ac9a6c4388
+DIST phenix-installer-1.8-1069-intel-linux-2.6-x86_64-fc15.tar 632821760 SHA256 8b237a437043364bf39e3316931d895d3dd317823f9a98a01404eb424b5224cd SHA512 6160d5d85d1374c0b9c65cdd57c36c51b88cdb53af4341b567820d824727300403025da22de5619c8a6e742446dfe094f99e7727c5209338c33d6676876b91f2 WHIRLPOOL 70d2d3abd07f67094490d3307af31478c2236010473b1ed7f8ac1263c5f2da249640be0f99346bc6c5e8eb74acc9cce46a13cf76b530691125527e67ac302ac4
diff --git a/sci-chemistry/phenix-bin/metadata.xml b/sci-chemistry/phenix-bin/metadata.xml
new file mode 100644
index 000000000..d369d068f
--- /dev/null
+++ b/sci-chemistry/phenix-bin/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci</herd>
+</pkgmetadata>
diff --git a/sci-chemistry/phenix-bin/phenix-bin-1.8.1069.ebuild b/sci-chemistry/phenix-bin/phenix-bin-1.8.1069.ebuild
new file mode 100644
index 000000000..fa7088c6f
--- /dev/null
+++ b/sci-chemistry/phenix-bin/phenix-bin-1.8.1069.ebuild
@@ -0,0 +1,87 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=4
+
+PYTHON_DEPEND="2"
+
+inherit python versionator
+
+MY_PV="$(replace_version_separator 2 -)"
+MY_P="phenix-installer-${MY_PV}"
+
+DESCRIPTION="Python-based Hierarchical ENvironment for Integrated Xtallography"
+HOMEPAGE="http://phenix-online.org/"
+SRC_URI="
+ amd64? ( phenix-installer-${MY_PV}-intel-linux-2.6-x86_64-fc15.tar )
+ x86? ( phenix-installer-${MY_PV}-intel-linux-2.6-fc3.tar )
+"
+
+SLOT="0"
+LICENSE="phenix"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND="
+ media-libs/jpeg:62"
+DEPEND=""
+
+RESTRICT="fetch"
+
+QA_PREBUILT="opt/phenix-${MY_PV}/.*"
+
+S="${WORKDIR}"/${MY_P}
+
+pkg_nofetch() {
+ elog "Please visit"
+ elog "http://www.phenix-online.org/phenix_request/index.cgi"
+ elog "and request a download password. With that done,"
+ elog "visit http://www.phenix-online.org/download/phenix/release"
+ elog "and downlaod ${A} to ${DISTDIR}"
+}
+
+pkg_setup() {
+ python_set_active_version 2
+ python_pkg_setup
+}
+
+src_prepare() {
+ ./install --prefix="${S}/foo"
+
+}
+
+src_install() {
+# find -name "*.py[co]" -delete
+# find -name SConstruct -delete
+ sed \
+ -e "s:${S}/foo:${EPREFIX}/opt:g" \
+ -i \
+ build-binary/intel-linux-2.6-*/*/log/*.log \
+ build-final/intel-linux-2.6-*/*/log/*.log \
+ foo/phenix-${MY_PV}/build/intel-linux-2.6-*/*_env \
+ foo/phenix-${MY_PV}/build/intel-linux-*/*sh \
+ foo/phenix-${MY_PV}/build/intel-linux-*/bin/* \
+ foo/phenix-${MY_PV}/build/intel-linux-2.6-*/base/etc/{gtk*,pango}/* \
+ foo/phenix-${MY_PV}/phenix_env* \
+ || die
+# grep ${S} * -R
+ dodir /opt
+ mv "${S}/foo/phenix-${MY_PV}" "${ED}/opt/"
+
+ cat >> phenix <<- EOF
+ #!${EPREFIX}/bin/bash
+
+ source "${EPREFIX}/opt/phenix-${MY_PV}/phenix_env.sh"
+ exec phenix
+ EOF
+ dobin phenix
+}
+
+pkg_postinst() {
+ python_mod_optimize "/opt/phenix-${MY_PV}"
+}
+
+pkg_postrm() {
+ python_mod_cleanup "/opt/phenix-${MY_PV}"
+}
diff --git a/sci-chemistry/specView/ChangeLog b/sci-chemistry/specView/ChangeLog
new file mode 100644
index 000000000..ed8647ed7
--- /dev/null
+++ b/sci-chemistry/specView/ChangeLog
@@ -0,0 +1,19 @@
+# ChangeLog for sci-chemistry/specView
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 21 Sep 2012; Justin Lecher <jlec@gentoo.org> specView-1.0.2.ebuild:
+ Needs webkit support in pyside
+
+ 21 Sep 2012; Justin Lecher <jlec@gentoo.org> specView-1.0.2.ebuild:
+ Prefix offset for header dirs
+
+ 21 Sep 2012; Justin Lecher <jlec@gentoo.org> specView-1.0.2.ebuild:
+ Copile py code
+
+*specView-1.0.2 (21 Sep 2012)
+
+ 21 Sep 2012; Justin Lecher <jlec@gentoo.org> +specView-1.0.2.ebuild,
+ +files/specView, +metadata.xml:
+ New addition
+
diff --git a/sci-chemistry/specView/Manifest b/sci-chemistry/specView/Manifest
new file mode 100644
index 000000000..9ad3c9159
--- /dev/null
+++ b/sci-chemistry/specView/Manifest
@@ -0,0 +1 @@
+DIST specView1.0.2.tar.gz 15811413 SHA256 3a8d8b9e0f15e6481d8d6ea9a1f51d06a3cd2a4295acc3dfaf9e4ee0e3b1509f SHA512 f3194148f90d9dbe706c33fefda9cb6db71e0812f83bbf94bb170170bd9d4fcd4eae6295ccc78c6544b093dfbf09512555405dfab5b0516152dce2cb25b18965 WHIRLPOOL d35dd8753565f29b36c55014b8b34f0a5c60fad9f4353d4a094b6a7d2010a9936e9e3e42d27c4d5e6076a861fe7eb424acf86c7847e0218e8877ffb4a9865411
diff --git a/sci-chemistry/specView/files/specView b/sci-chemistry/specView/files/specView
new file mode 100644
index 000000000..bca546ca7
--- /dev/null
+++ b/sci-chemistry/specView/files/specView
@@ -0,0 +1,9 @@
+#!/bin/bash
+
+export CCPNMR_TOP_DIR=gentoo_sitedir
+export PYTHONPATH=.:${CCPNMR_TOP_DIR}/specView/python
+export LD_LIBRARY_PATH=gentoolibdir
+export TCL_LIBRARY=gentootcl
+export TK_LIBRARY=gentootk
+export PSIPRED_DIR=gentoousr
+gentoopython -O ${CCPNMR_TOP_DIR}/specView/python/ccpnmr/specView/SpecView.py $@
diff --git a/sci-chemistry/specView/metadata.xml b/sci-chemistry/specView/metadata.xml
new file mode 100644
index 000000000..d369d068f
--- /dev/null
+++ b/sci-chemistry/specView/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci</herd>
+</pkgmetadata>
diff --git a/sci-chemistry/specView/specView-1.0.2.ebuild b/sci-chemistry/specView/specView-1.0.2.ebuild
new file mode 100644
index 000000000..f435c6067
--- /dev/null
+++ b/sci-chemistry/specView/specView-1.0.2.ebuild
@@ -0,0 +1,108 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=4
+
+PYTHON_DEPEND="2"
+
+inherit python toolchain-funcs
+
+DESCRIPTION="Fast way to visualise NMR spectrum and peak data"
+HOMEPAGE="http://www.ccpn.ac.uk/software/specview"
+SRC_URI="http://www2.ccpn.ac.uk/download/ccpnmr/${PN}${PV}.tar.gz"
+
+SLOT="0"
+LICENSE="|| ( CCPN LGPL-2.1 )"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND="
+ dev-python/pyopengl
+ dev-python/pyside[webkit]"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}"/ccpnmr/ccpnmr3.0/
+
+#TODO:
+#install in sane place
+#unbundle data model
+#unbundle inchi
+#parallel build
+
+pkg_setup() {
+ python_set_active_version 2
+ python_pkg_setup
+}
+
+src_prepare() {
+ sed \
+ -e "s|/usr|${EPREFIX}/usr|g" \
+ -e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \
+ -e '/^MALLOC_FLAG/s:^:#:g' \
+ -e "/^OPT_FLAG/s:=.*$:= ${CFLAGS}:g" \
+ -e "/^LINK_FLAGS/s:$: ${LDFLAGS}:g" \
+ -e "/^PYTHON_DIR/s:=.*:= ${EPREFIX}/usr:g" \
+ -e "/^PYTHON_LIB/s:=.*:= $(python_get_library -l):g" \
+ -e "/^PYTHON_INCLUDE_FLAGS/s:=.*:= -I${EPREFIX}$(python_get_includedir) -I${EPREFIX}$(python_get_sitedir)/numpy/core/include/numpy:g" \
+ -e "/^PYTHON_LIB_FLAGS/s:=.*:= -L${EPREFIX}/usr/$(get_libdir):g" \
+ -e "/^SHARED_FLAGS/s:=.*:= -shared:g" \
+ -e "/^GL_DIR/s:=.*:= ${EPREFIX}/usr/$(get_libdir):g" \
+ -e "/^GL_INCLUDE_FLAGS/s:=.*:= -I${EPREFIX}/usr/include:g" \
+ -e "/^GL_LIB_FLAGS/s:=.*:= -L${EPREFIX}/usr/$(get_libdir):g" \
+ cNg/environment_default.txt > cNg/environment.txt || die
+ echo "SHARED_LINK_PARM = ${LDFLAGS}" >> cNg/environment.txt || die
+
+ rm -rf license || die
+
+ sed \
+ -e 's:ln -s:cp -f:g' \
+ -i $(find python -name linkSharedObjs) || die
+}
+
+src_compile() {
+ emake -C cNg all
+ emake -j1 -C cNg links
+}
+
+src_install() {
+ local in_path=$(python_get_sitedir)/${PN}
+ local _file
+
+ find . -name "*.pyc" -type f -delete
+ dodir /usr/bin
+ sed \
+ -e "s|gentoo_sitedir|${EPREFIX}$(python_get_sitedir)|g" \
+ -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \
+ -e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \
+ -e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \
+ -e "s|gentoopython|$(PYTHON -a)|g" \
+ -e "s|gentoousr|${EPREFIX}/usr|g" \
+ -e "s|//|/|g" \
+ "${FILESDIR}"/${PN} > "${ED}"/usr/bin/${PN} || die
+ fperms 755 /usr/bin/${PN}
+
+ insinto ${in_path}
+
+ dodir ${in_path}/cNg
+ rm -rf cNg || die
+
+ ebegin "Installing main files"
+ doins -r *
+ eend
+
+ ebegin "Adjusting permissions"
+
+ for _file in $(find "${ED}" -type f -name "*so"); do
+ chmod 755 ${_file}
+ done
+ eend
+}
+
+pkg_postinst() {
+ python_mod_optimize ${PN}
+}
+
+pkg_postrm() {
+ python_mod_cleanup ${PN}
+}
diff --git a/sci-libs/acml/ChangeLog b/sci-libs/acml/ChangeLog
index c2e09179d..d59bce9f9 100644
--- a/sci-libs/acml/ChangeLog
+++ b/sci-libs/acml/ChangeLog
@@ -2,6 +2,12 @@
# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
# $Header: /var/cvsroot/gentoo-x86/sci-libs/acml/ChangeLog,v 1.40 2009/07/07 23:27:59 flameeyes Exp $
+*acml-5.2.0 (29 Sep 2012)
+
+ 29 Sep 2012; Sébastien Fabbro <bicatali@gentoo.org> +acml-5.2.0.ebuild,
+ -acml-5.1.0.ebuild:
+ sci-libs/acml: Version bump
+
*acml-5.1.0 (24 Jan 2012)
24 Jan 2012; Sébastien Fabbro <bicatali@gentoo.org> +acml-5.1.0.ebuild:
diff --git a/sci-libs/acml/Manifest b/sci-libs/acml/Manifest
index 432a9ead0..19856e1ea 100644
--- a/sci-libs/acml/Manifest
+++ b/sci-libs/acml/Manifest
@@ -1,22 +1,22 @@
-DIST acml-4-4-0-gfortran-32bit.tgz 20457025 RMD160 f3b0b67cea3d6343de4012c9339b606c513968e9 SHA1 b794e9da0d9ad3bf56b00b3a195956eb13862c78 SHA256 86f74cc28ecc988aee4244989549534e72e6703a5846d5c021723ff78d7e6690
-DIST acml-4-4-0-gfortran-64bit-int64.tgz 26792011 RMD160 a6533be7beada7c384e3b51d6d0bcd9d24f34d83 SHA1 88fa5e5e172f66a4736ab7f1ffda109a774c66a0 SHA256 bb2e478f47afac6acfbf68975f7562599168801bcc313b82208ec423c49fc1cf
-DIST acml-4-4-0-gfortran-64bit.tgz 27564183 RMD160 69a5addd8cfb47b59e404ff760c06c5754505954 SHA1 79d11e8a0883b991595b4ea65eac8f98b0b0c88d SHA256 a68547018c471e1a91b3e04663418e852455c42af4bd8248ca4f79bbfdd3d9ea
-DIST acml-4-4-0-ifort-32bit.tgz 26513669 RMD160 2216d42b4b18a751c0deb5d5970321064532c0df SHA1 c2ad1bfc1de5311228b62eca3cd71fb99b91a98e SHA256 2c274d580f749cf4ca7b5b0c250341a648d6305f8677a9306ddbbadfedbbcad1
-DIST acml-4-4-0-ifort-64bit-int64.tgz 36063135 RMD160 65466a110ef502235484c3cb7f830ea052b436eb SHA1 670abe749778ffee814cfe3fa0c8d11fd93787c5 SHA256 5a09bc347c92d726608b611674930167cce76d2d8238a339bef0f318b8bc0a21
-DIST acml-4-4-0-ifort-64bit.tgz 36707660 RMD160 96f426956a2233b96cdb3d7346bf979dd35154e3 SHA1 79a80ca51edfb248dd1fc742f47c78a08cbe44d9 SHA256 28657e7d54f95f411dd7fb3b1c75a86bd73c6bc8930a470541b8b7af53d0c840
-DIST acml-4-4-0-nag-32bit.tgz 13662569 RMD160 add84bccbba5e9a5abd8188b19834246dd3888dc SHA1 4a5fcc7f667d4351cb0362643ee45f16fd7a2e45 SHA256 9d30a129cda47f95c04fc964218a02b3b14e952ab9b7569fdb3809d130b39ef2
-DIST acml-4-4-0-nag-64bit-int64.tgz 18978245 RMD160 ee1d5b2d7784b339f1a6650a5cfb7650e8650fe5 SHA1 3b51b933f0e5a75c860a74b5b92854644b212b35 SHA256 3871e4e5fea35e8b7d55d9a96f31b764bed00e654e8ca82497061853e4485f3a
-DIST acml-4-4-0-nag-64bit.tgz 19062935 RMD160 3998794f8628b964c1f9fd80b91eb41cb9824bde SHA1 192d5199136b72377d92cbe0722e86245c8b2c5d SHA256 aa53a29ae88123dd82f16ba0f27588a667545e22e6a0e41ac01d1bfbb7128150
-DIST acml-4-4-0-open64-64bit-int64.tgz 42270987 RMD160 6b5accc19c7ae69b97f287cfe2ae3c0ef13192d5 SHA1 501434a2ded74c4103c445d4e0fc7b2c514f7f38 SHA256 2acd89b6cda5f4a5395906afb5dbbacb3f4074818f9d482ff3e42bd2ed5d0097
-DIST acml-4-4-0-open64-64bit.tgz 42812747 RMD160 aa29a615cf2b3294294162ccb89e9ade78735aa9 SHA1 64cc4d97a323427a959147476b828cca7199ca53 SHA256 42bee6d56deedd2817ac95c8cf99f84a0adaef5ebbb36059e600b58ec36d5188
-DIST acml-4-4-0-pgi-32bit.tgz 24562671 RMD160 78677d7f178e725ebe086d9690c8ee72026929ba SHA1 cc0ceff8e8f5cb4a15175e2256c8708a8a7d2fb6 SHA256 f956b3fdd3e825c4b993a16179a8df2f772eda851aa4dd7f4a16fffb20c10580
-DIST acml-4-4-0-pgi-64bit-int64.tgz 78664596 RMD160 2a0e9af1eef74009dce2a256d4da8382baf39133 SHA1 6648385c614d367bd18e29eb60be3f99df07ae1e SHA256 f1290edb9c5a91b667139ae4e8eec2486e7ccd3f2aa19f7f65667eef0d85eca0
-DIST acml-4-4-0-pgi-64bit.tgz 77842523 RMD160 e4c6770837f9eb511999872d280715e6827b5f65 SHA1 2087b20359d72b2e7886b12356d4da0d2d563503 SHA256 9c07dc0b90e9e491a0ddcf7849690338f21011aa4aa197ff3408f32a0b3fd6cf
-DIST acml-5-1-0-gfortran-64bit-int64.tgz 68399628 SHA256 6d01ac165e97a67d34e769b9c7ca1f0e74b5ba28357168815f8bbae38275a2e7 SHA512 146367a25dc28c228845dc13d95e889cd4a804988c26de39156f553356978c93124fdf8d553d8b0afa7526847a7faa68887be49481518c2b853e438c35e2ea29 WHIRLPOOL 6f1f20da53871d782f71d3166100f71e9cf7aaf79917fee8fc8a980e4d52d99d2f263d83e0eb29845bcdc313b2f3e9617d07edc88701a99be77c02564a97abb0
-DIST acml-5-1-0-gfortran-64bit.tgz 70565763 SHA256 9a123fcd959310a57fd16387e90571733f0ca2711ec807e361edd839ac98e90c SHA512 1397483f41402ad9238b59a3018a404f7904bfe3ea017fd5f22fdba629bf18c127fc4564028f67d23eff597018f03050c2ec3e83686bf3576f70a24a812ac277 WHIRLPOOL 121807289ea4a7321c171e6d328011942effad5e5d0a40b5d72a2d987adae01ec24aa1bc7a734ff71bfcfb330f3e49a78b1705ad00e8ae91516cc51b8e890b7b
-DIST acml-5-1-0-ifort-64bit-int64.tgz 100970937 SHA256 c3068fc39f6b073ec415d621fe1e3df964a503c7adc98a0048bd9c392a5da83e SHA512 676186913cb2fdc448509f3f6d6b2a2a3da7d113a4dca303c57a00515efd470d687fb7d768f86a986c79e720510cf2c7c02a70b537dec657666274ae8049aee5 WHIRLPOOL cad29a07981fc9a5c5f3dd679f581c912b1c41aa7ff6b7a59aa296bd12114f424ff98a5ce68ed54f2cef0bc438d43a8f306c5323d2651427c689b2db8cf383f6
-DIST acml-5-1-0-ifort-64bit.tgz 102257810 SHA256 8c39dabaad828b24f7ab9a27d1a93bd57725288f67fc9aee6fcc5b7b5820cf1b SHA512 cecb73f88e99d1abf24b4bedf19f5fd32bbac86fd938133f95f6843819dab28d762a7c056eebb29b1654c0d8739791fd6b3b25fd9241409472e1cea293de6ee4 WHIRLPOOL bb71d1223dd8b6e2d36524dd895f690ecb5cfb23d3773d185370bf7e0236dd39b8b74d08073e0968380cdec205a86565e845504d748eb12864f89955f2b9d9f9
-DIST acml-5-1-0-open64-64bit-int64.tgz 83129851 SHA256 27492c9d44c10bbdf6ab0776a1cfd6288875c72eb119bde5ab7a5167f42125c1 SHA512 de69e2b63f46d23e3978aa135427f0aac9fa45adc05ec9da22a58471df572fd954445496ce15c5d3d42312228156539fd68f63ad565fba04fa98ef3b67626236 WHIRLPOOL 78a123bed2c8afe46930de6948663be47d63f380bf33bafca463ed925bacb974ac7b9097d294d7a5f8ca2c13d6c3364de4fc6a015640547961c82dfc4134c252
-DIST acml-5-1-0-open64-64bit.tgz 84231481 SHA256 f7ff59ad173c1420aae73f4483c85b8d3898dbeb1f0a38052f4850517a2fe12f SHA512 2797d14cd7301c6da994896ee12732ad772bf5b1f4dc30a3d20286ebf9b2d912a55f69d136c588e1aeb052c0d6cc586698b6aa7b70f33df9e53c8dca76f8c643 WHIRLPOOL ec0e82cc63eb7ad80fc1eddb393363b3fa45a6cad0621001711529f5030ef3e40f6a19bf160a78bfc85dfcf7b5ea8bf8c301426a9aa21e0780af0ffe0051c7cd
-DIST acml-5-1-0-pgi-64bit-int64.tgz 137961398 SHA256 9e04a9c3e2e03b2490e94086589d22c8d3cb33c0fd6702df0b02c6baceff1abe SHA512 93b17f7284a4f724bdfa9caecb3e26787725a36283de9a06c4445f0414c6108133f14293033161d1bc9a0a51d92ac59b37160f76f4742a7f732f05369e899deb WHIRLPOOL 249959aa106f5a9dfcc5c5c6ea1035c36b7f99c476e9d71018215b54aa4804e3ede6d65ce60c88bb8794fb8c83113102de995b7b1bb1aa0f1c1dea715cff141f
-DIST acml-5-1-0-pgi-64bit.tgz 139099324 SHA256 2dbb2b81a24d699c3e6116c730851e85b0b777e12eb08ca30e8f30849d2c24f9 SHA512 7fcd9e7390cb6be6914afcae8cfa250416d7df816831cd4d8bce5ec042d1c773036f1907559e6c784d2318cd5818c477eea7372f441058b0c63e6b0296bd3b83 WHIRLPOOL 21f625517447af5717a923450ffa5ead460a6d64d1735fca9837361cbdf858b8d1b12dd8ee8074e3eaefc432b46209d242115f96bade78ab2b5d6d0a7781695c
+DIST acml-4-4-0-gfortran-32bit.tgz 20457025 SHA256 86f74cc28ecc988aee4244989549534e72e6703a5846d5c021723ff78d7e6690
+DIST acml-4-4-0-gfortran-64bit-int64.tgz 26792011 SHA256 bb2e478f47afac6acfbf68975f7562599168801bcc313b82208ec423c49fc1cf
+DIST acml-4-4-0-gfortran-64bit.tgz 27564183 SHA256 a68547018c471e1a91b3e04663418e852455c42af4bd8248ca4f79bbfdd3d9ea
+DIST acml-4-4-0-ifort-32bit.tgz 26513669 SHA256 2c274d580f749cf4ca7b5b0c250341a648d6305f8677a9306ddbbadfedbbcad1
+DIST acml-4-4-0-ifort-64bit-int64.tgz 36063135 SHA256 5a09bc347c92d726608b611674930167cce76d2d8238a339bef0f318b8bc0a21
+DIST acml-4-4-0-ifort-64bit.tgz 36707660 SHA256 28657e7d54f95f411dd7fb3b1c75a86bd73c6bc8930a470541b8b7af53d0c840
+DIST acml-4-4-0-nag-32bit.tgz 13662569 SHA256 9d30a129cda47f95c04fc964218a02b3b14e952ab9b7569fdb3809d130b39ef2
+DIST acml-4-4-0-nag-64bit-int64.tgz 18978245 SHA256 3871e4e5fea35e8b7d55d9a96f31b764bed00e654e8ca82497061853e4485f3a
+DIST acml-4-4-0-nag-64bit.tgz 19062935 SHA256 aa53a29ae88123dd82f16ba0f27588a667545e22e6a0e41ac01d1bfbb7128150
+DIST acml-4-4-0-open64-64bit-int64.tgz 42270987 SHA256 2acd89b6cda5f4a5395906afb5dbbacb3f4074818f9d482ff3e42bd2ed5d0097
+DIST acml-4-4-0-open64-64bit.tgz 42812747 SHA256 42bee6d56deedd2817ac95c8cf99f84a0adaef5ebbb36059e600b58ec36d5188
+DIST acml-4-4-0-pgi-32bit.tgz 24562671 SHA256 f956b3fdd3e825c4b993a16179a8df2f772eda851aa4dd7f4a16fffb20c10580
+DIST acml-4-4-0-pgi-64bit-int64.tgz 78664596 SHA256 f1290edb9c5a91b667139ae4e8eec2486e7ccd3f2aa19f7f65667eef0d85eca0
+DIST acml-4-4-0-pgi-64bit.tgz 77842523 SHA256 9c07dc0b90e9e491a0ddcf7849690338f21011aa4aa197ff3408f32a0b3fd6cf
+DIST acml-5-2-0-gfortran-64bit-int64.tgz 69344338 SHA256 bbf16c30acdb82f462081e3500aec9e272e701bb2022fe32acb29f58ea78ff50 SHA512 085fa7dd7b9a8dc034fec645c1ad9d0f2439d7c72bf6e07a3ba9af494e0bbe4d2b42487ae60d983baa18360dcaee621cb8bb1d4385672a9fb11fdf3ae1c861fd WHIRLPOOL 1b0e0ec79654eda1e20a22f12f9a27eafd3f004fcf799a0fc945f015d5de4c9efe01e43cd84c681d1fe1d18c7b4384347bf2efbeff7a26d29d591a0cd6048d09
+DIST acml-5-2-0-gfortran-64bit.tgz 71676355 SHA256 acdb46cd9c9041656bbe36df7640586273d5993ff2dc3ca07676bfb7c56ac866 SHA512 78c45596abddfd3283054dd3620ed2bdd182aa9407d9cdf05e4523594b1df6ad250381d459ddd8d29999bc9d294eb58544f5df914b89c0b57e4e59282a070eae WHIRLPOOL 1cfe7cfef7101e4bfbd96f34ffa5bad3566fa311fb0900b582a9b6a391ba0ce8e9677347d569756940515424c2b197847a47bcb086b52d59ada2f2d2acb416b2
+DIST acml-5-2-0-ifort-64bit-int64.tgz 106635190 SHA256 97627ee0481b086fc66321130f27e1e9f9c779a475530a7c20be9bf55ee6c476 SHA512 200935dac85fcf8967bbcfcfd3d6e30cda014d5db3a39ca4880f9e7eece1db8685d88e7faa45d418aa59932fb492fbbf23139fcbc4753ab95402b1d559bc4ed5 WHIRLPOOL 1a2ba79db08236873d9044ea419dc87e4f5878da8ba052fa8088a50e4cc5c1f9493dfb1f4ca5672aed296d15602e0cac6f76152c84105b03a6b910a64bf73ce4
+DIST acml-5-2-0-ifort-64bit.tgz 107998032 SHA256 1b401801ecd80d64bce3f66d12260637fd414ef1715bdade0e0d3e9cf58a11c4 SHA512 52ed8167f8402fb9821232e7e8e12b0d2347d22bb20ae2c2afea0de193e9c3df1c0637133dec84252c7bc44ceb4434c81151f7bdd3fceeb3101835f309184bab WHIRLPOOL 8a70dea5298176b92ee6015aea3ba9c8c61c49a9a2895c5cd7e858031dfab030a1942bdb98dff99ce320afdd121116fcf9b3d8126516c032a38efb6d10f28b97
+DIST acml-5-2-0-open64-64bit-int64.tgz 84931905 SHA256 0c299f9868452cdb2b123d682af441c1c90318fd51d86a29aa7899def3065c70 SHA512 a035f1d7309811a6128b71d74a98b382f34c36958ea2a20a77bc6c37a260d05be26534b648dd57839abb5a43636700b5738ffd8f5ade6fd3fdb4d7d906d85a5e WHIRLPOOL 905ce859b92fc909fa760c9007b8af65433f29562f35f7303f46ea99a3c6e21439dd501122eb77783e80dcab0934b133d288a1aa954e9318546c8d8d8bc37c2f
+DIST acml-5-2-0-open64-64bit.tgz 86055158 SHA256 0e4c0e39079126cffe4455adf3481d6e47aecd1d5b1d3752fce2a59e15372e7c SHA512 aad1eaae9c455579bd5bafe08638f6a59858a6b05119e51ffbb7f81626a67f78b7826c209fc54e5870fcb59f2a56d8ef305af768fd9e2c62380c595898b44955 WHIRLPOOL f217cb5a88cd6a24eddaa5d7e07c732780d37a9a03078eaa72ecdcda29ee9e8457282fb2af399b7a82936d7281fc7f28d96a66b494c579650c5e7d2b3dd0e5a8
+DIST acml-5-2-0-pgi-64bit-int64.tgz 145633201 SHA256 b893e48abc5b1c72bf6329385de2473bbeebf13269e80f246c072199320805a0 SHA512 8feb351665df5e16f2716f6adb9f65dd7d91051cab36a5262ced73aa3e8ae5716aa32d1692189f0b0c26c184f751614d76f522e57b105b8d7d1c5e82774ac155 WHIRLPOOL ed3e9b2ce4dcddf6a9962ae04f50ce9f52a1b7a07023a718c78c421c78711f10396cb73e01e2851377b688b0561a101843fba25d443a7cd81fd0134614ceb753
+DIST acml-5-2-0-pgi-64bit.tgz 146752015 SHA256 1cc856df359014e151d0dcc2be95e20be8c0793b63f2f96bfae088de2b53fdf6 SHA512 3f10a92ece35e96e43278148076cbd83070b9aa35669787bf2035e78dfe62f7384dbeec57bf82897b0b813bdb8c3d855c6a57ca29537cb331c676890423eb8a5 WHIRLPOOL ebe8223195ea123be512b6d553757638571b2a71edec3a2ddcad3a259422dfa70be78e6d156c8ac79ec81e904c14de130b7b66a584a15c60afc6283e7564de41
diff --git a/sci-libs/acml/acml-5.1.0.ebuild b/sci-libs/acml/acml-5.2.0.ebuild
index a4919fd20..df74d72e0 100644
--- a/sci-libs/acml/acml-5.1.0.ebuild
+++ b/sci-libs/acml/acml-5.2.0.ebuild
@@ -4,7 +4,7 @@
EAPI=4
-inherit eutils toolchain-funcs versionator alternatives-2
+inherit eutils multilib toolchain-funcs versionator alternatives-2
ACML_INST_DIR=opt/${PN}${PV}
QA_PREBUILT="${ACML_INST_DIR}/*/lib/*"
diff --git a/sci-libs/mkl/ChangeLog b/sci-libs/mkl/ChangeLog
index 487c89790..f298a3f8d 100644
--- a/sci-libs/mkl/ChangeLog
+++ b/sci-libs/mkl/ChangeLog
@@ -2,6 +2,12 @@
# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*mkl-11.0.0.079 (29 Sep 2012)
+
+ 29 Sep 2012; Sébastien Fabbro <bicatali@gentoo.org> +mkl-11.0.0.079.ebuild,
+ -mkl-10.3.4.191.ebuild, -mkl-10.3.7.256.ebuild:
+ sci-libs/mkl: Version bump
+
*mkl-10.3.7.256 (16 Feb 2012)
16 Feb 2012; Sébastien Fabbro <bicatali@gentoo.org> +mkl-10.3.7.256.ebuild:
@@ -24,4 +30,3 @@
03 Dec 2010; Sébastien Fabbro <bicatali@gentoo.org> mkl-10.3.0.084.ebuild:
Version bump. refactored ebuilds
-
diff --git a/sci-libs/mkl/Manifest b/sci-libs/mkl/Manifest
index 0045be04f..d22f77a92 100644
--- a/sci-libs/mkl/Manifest
+++ b/sci-libs/mkl/Manifest
@@ -1,6 +1,3 @@
-DIST parallel_studio_xe_2011_sp1_update1.tgz 1608904361 SHA256 b2d66360aba8b26736ec6ed819a0b4f79fa989eab99bf343217c95554a116ef9 SHA512 6df28624891b94ff0ecabae1c59fb1c360703194ba14ddef382cfd7f789123da055882040642d656b9f9c9ca2c448ff17ef517b1983cecc85b24a1ede8332c00 WHIRLPOOL 4b21fc9224c93323b50fad80a20cd4620e978cd119bf4d5a97c67e2473900f0a74818fa3e8da97ed337b5716d41f1df83f9a17ecaf9ad75acb7def20db7835dd
-DIST parallel_studio_xe_2011_sp1_update1_ia32.tgz 881192408 SHA256 58b2241b38fce637d90223816959a1e3ad8d4285be8475a5255d50051ca99625 SHA512 07d8ae1a3477e3b1d31f7f4a5f4e27e59917a2a23e8e5af79c5c09c36c3e4d7d08f3a93a7d834ef001ee3b32acf1dfed4220bb3880a66a1355a8a576aead471d WHIRLPOOL 2fe5399fe4caae04acaa0cc332e73cfdc880208cbde31a360e0965ad91214eafee1b7c3b011a47de1ae54dd4cc12432d92a226f5e51c6bff3d8d60504942c710
-DIST parallel_studio_xe_2011_sp1_update1_intel64.tgz 1039713499 SHA256 0a95872af59df087d1c9d024a88929ba70279b4d68a1ac18f157eec2decced2d SHA512 3f7d51b66fd45688819d24d955c035d8edb88f3e7d380db4a631415359973b1e1f65299858285679cd7c68b8d8a2bc2b4d992837375bc818bd5e82ec0f4f691e WHIRLPOOL cd9619a38d77a12ac312d338921c135e8dda7a7599f96010df3df81b83094c2c20fb96ad30656c424cb59feb1c1d00231ba108fc05f76ab82cec89130b20890a
-DIST parallel_studio_xe_2011_update2.tgz 1551817814 RMD160 7f1c770a1ad5fe626718a5c352d2db6d628b22aa SHA1 b216e25ec4f1254e7e07defa5ab0ec835965a018 SHA256 3e77fb39fc05e0c4eafa594617674858ae9c59a5cfddb0f95651bbf7d4baa907
-DIST parallel_studio_xe_2011_update2_ia32.tgz 810216099 RMD160 33293a7f524722b1e2f4fc839aea3984dff490c5 SHA1 73368f9f14ff530dc953aeeca1ec5de90607774d SHA256 e2d040774cc4888a294dbd2081882b7f90fef7280ad1c4dcb04026871d6e638d
-DIST parallel_studio_xe_2011_update2_intel64.tgz 966899604 RMD160 e14ebd58b2e626431c3b796d925ff460752fc689 SHA1 55cfdb64f7c84222ff599f4e9def3cb66e45c962 SHA256 f6d9acacb350cccb3e29c2309ced7b9564d86d53d59409b4a79d7a79b396f2f1
+DIST parallel_studio_xe_2013.tgz 2097190124 SHA256 22ac8d6dd1bf9fd646c1d1322c0a9051b89b6dba975112d492cccd8359f8dc0a SHA512 d49c519c0b2f82e6fc0db6820d5f84999d2a973d8caa0e103c0ad355644f52d209147a2b3a884effad9bbae117bd9ebbad4869f5440009355ffacb65cae274fa WHIRLPOOL bb5f05ceeae39f794dcd6c4fafafb2e5ebf8e5332083f7eaf357dddb9b2a1e94f52f82f850a8b0aefe1920f2fd21be67bfa8aafa9590707e25e84e9f2be07bd5
+DIST parallel_studio_xe_2013_ia32.tgz 1161979592 SHA256 3f0ff2ece4cfc5ec3d7c2fddefeda2b55b1295a0d62440c172a14d8e60b7b551 SHA512 9818d0e8ee1f36527f5899480381c252528274248974001f136e7aecc196ab4a049aeabed5835c18f0b08153d3a36a7fc8d850aec455bb9b5f71d95d17dc161e WHIRLPOOL 2772bb70b968f765af1c47ecb11a9e0b0220890ed37d0a81cb911f9ec43dda8cbdd85f3b0cacf1b1794ca239684f3381e54bada668b0b4a40244da684c3b04a5
+DIST parallel_studio_xe_2013_intel64.tgz 1448188683 SHA256 6d3f5a635e86bc6d71d970458d746df8f4f239e8892347d76b4eda18946048f3 SHA512 679abcb2089fc9570bad0fe8b7dd6aeb0e13831f2f79e485ce150e593e7c0d2c8c25c03520124261291f0fa418a9b873e86a81b6962ad8bbae60bc2acbc594b6 WHIRLPOOL 85ee892aac2691375edf4624842a6931b3eaab34be64b97282c025810cb2db4ea05426263af5249525724d3437da6337189e6a4af6a1efc8f7713a854b8e4ce1
diff --git a/sci-libs/mkl/mkl-10.3.7.256.ebuild b/sci-libs/mkl/mkl-10.3.7.256.ebuild
deleted file mode 100644
index 2e5cb6252..000000000
--- a/sci-libs/mkl/mkl-10.3.7.256.ebuild
+++ /dev/null
@@ -1,136 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=4
-INTEL_DPN=parallel_studio_xe
-INTEL_DID=2405
-INTEL_DPV=2011_sp1_update1
-INTEL_SUBDIR=composerxe
-
-inherit intel-sdp multilib alternatives-2
-
-DESCRIPTION="Intel Math Kernel Library: linear algebra, fft, math functions"
-HOMEPAGE="http://software.intel.com/en-us/articles/intel-mkl/"
-
-IUSE=""
-
-DEPEND=""
-RDEPEND=">=dev-libs/intel-common-12"
-
-QA_PREBUILT="
- ${INTEL_SDP_DIR}/mkl/lib/*/*
- ${INTEL_SDP_DIR}/mkl/examples/lapack/lib/*
- ${INTEL_SDP_DIR}/mkl/tests/cblas/source/*
- ${INTEL_SDP_DIR}/mkl/benchmarks/linpack/*
- ${INTEL_SDP_DIR}/mkl/benchmarks/mp_linpack/*/*/*"
-
-CHECKREQS_DISK_BUILD=1536M
-
-INTEL_BIN_RPMS="mkl-sp1 mkl-sp1-devel"
-INTEL_DAT_RPMS="mkl-sp1-common"
-
-src_prepare() {
- chmod u+w -R opt
-}
-
-mkl_add_prof() {
- local pcname=${1} libs cflags x
- shift
- [[ ${pcname} = *int64* ]] && cflags=-DMKL_ILP64
- cat <<-EOF > ${pcname}.pc
- prefix=${INTEL_SDP_EDIR}/mkl
- libdir=\${prefix}/lib/${IARCH}
- includedir=\${prefix}/include
- Name: ${pcname}
- Description: ${DESCRIPTION}
- Version: ${PV}
- URL: ${HOMEPAGE}
- Libs: -L\${libdir} ${libs}
- Cflags: -I\${includedir} ${cflags}
- EOF
- insinto /usr/$(get_libdir)/pkgconfig
- doins ${pcname}.pc
- for x in $*; do
- alternatives_for ${x} ${pcname/-${x}} 0 \
- /usr/$(get_libdir)/pkgconfig/${x}.pc ${pcname}.pc
- done
-}
-
-# mkl_prof [_ilp64 or _lp64]
-# help: http://software.intel.com/en-us/articles/intel-mkl-link-line-advisor/
-mkl_prof() {
- local bits=""
- if [[ ${IARCH} == intel64 ]]; then
- bits=_lp64
- [[ ${1} == int64 ]] && bits=_ilp64
- fi
- local gf="-Wl,--start-group -lmkl_gf${bits}"
- local intel="-Wl,--start-group -lmkl_intel${bits}"
- local core="-lmkl_core -Wl,--end-group"
- local prof=mkl${IARCH:((${#IARCH} - 2)):2}
- [[ ${1} == int64 ]] && prof=${prof}-int64
- local libs
-
- libs="${gf} -lmkl_sequential ${core} -lpthread" \
- mkl_add_prof ${prof}-gfortran blas lapack
- libs="${intel} -lmkl_sequential ${core} -lpthread" \
- mkl_add_prof ${prof}-intel blas lapack cblas lapacke
- libs="${gf} -lmkl_gnu_thread ${core} -fopenmp -lpthread" \
- mkl_add_prof ${prof}-gfortran-openmp blas lapack
- libs="${intel} -lmkl_gnu_thread ${core} -fopenmp -lpthread" \
- mkl_add_prof ${prof}-gcc-openmp cblas lapacke
- libs="${intel} -lmkl_intel_thread ${core} -openmp -lpthread" \
- mkl_add_prof ${prof}-intel-openmp blas lapack cblas lapacke
- libs="-lmkl_rt -lpthread" \
- mkl_add_prof ${prof}-dynamic blas lapack cblas lapacke
- libs="-lmkl_rt -liomp5 -lpthread" \
- mkl_add_prof ${prof}-dynamic-openmp blas lapack cblas lapacke
-
- # blacs and scalapack
- local scal="-lmkl_scalapack${bits:-_core}"
- local blacs="-lmkl_blacs_intelmpi${bits}"
- core="-lmkl_core ${blacs} -Wl,--end-group"
-
- libs="${gf} -lmkl_sequential ${core} -lpthread" \
- mkl_add_prof ${prof}-gfortran-blacs blacs
- libs="${scal} ${gf} -lmkl_sequential ${core} -lpthread" \
- mkl_add_prof ${prof}-gfortran-scalapack scalapack
- libs="${intel} -lmkl_sequential ${core} -lpthread" \
- mkl_add_prof ${prof}-intel-blacs blacs
- libs="${scal} ${intel} -lmkl_sequential ${core} -lpthread" \
- mkl_add_prof ${prof}-intel-scalapack scalapack
- libs="${gf} -lmkl_gnu_thread ${core} -fopenmp -lpthread" \
- mkl_add_prof ${prof}-gfortran-openmp-blacs blacs
- libs="${scal} ${gf} -lmkl_gnu_thread ${core} -fopenmp -lpthread" \
- mkl_add_prof ${prof}-gfortran-openmp-scalapack scalapack
- libs="${intel} -lmkl_gnu_thread ${core} -fopenmp -lpthread" \
- mkl_add_prof ${prof}-gcc-openmp-blacs blacs
- libs="${scal} ${intel} -lmkl_gnu_thread ${core} -fopenmp -lpthread" \
- mkl_add_prof ${prof}-gcc-openmp-scalapack scalapack
- libs="${intel} -lmkl_intel_thread ${core} -liomp5 -lpthread" \
- mkl_add_prof ${prof}-intel-openmp-blacs blacs
- libs="${scal} ${intel} -lmkl_intel_thread ${core} -liomp5 -lpthread" \
- mkl_add_prof ${prof}-intel-openmp-scalapack scalapack
- libs="-lmkl_rt ${blacs} -lpthread" \
- mkl_add_prof ${prof}-dynamic-blacs blacs
- libs="${scal} -lmkl_rt ${blacs} -lpthread" \
- mkl_add_prof ${prof}-dynamic-scalapack scalapack
- libs="-lmkl_rt ${blacs} -liomp5 -lpthread" \
- mkl_add_prof ${prof}-dynamic-openmp-blacs blacs
- libs="${scal} -lmkl_rt ${blacs} -liomp5 -lpthread" \
- mkl_add_prof ${prof}-dynamic-openmp-scalapack scalapack
-}
-
-src_install() {
- intel-sdp_src_install
- echo -n > 35mkl "LDPATH="
- for IARCH in ${INTEL_ARCH}; do
- mkl_prof
- sed -i -e '/mkl/s/$/:/' 35mkl
- echo -n >> 35mkl "${INTEL_SDP_EDIR}/mkl/lib/${IARCH}"
- [[ ${IARCH} == intel64 ]] && mkl_prof int64
- done
- echo >> 35mkl
- doenvd 35mkl
-}
diff --git a/sci-libs/mkl/mkl-10.3.4.191.ebuild b/sci-libs/mkl/mkl-11.0.0.079.ebuild
index a2634cf5e..54aa19301 100644
--- a/sci-libs/mkl/mkl-10.3.4.191.ebuild
+++ b/sci-libs/mkl/mkl-11.0.0.079.ebuild
@@ -1,11 +1,12 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2012 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
EAPI=4
+
INTEL_DPN=parallel_studio_xe
-INTEL_DID=2158
-INTEL_DPV=2011_update2
+INTEL_DID=2749
+INTEL_DPV=2013
INTEL_SUBDIR=composerxe
inherit intel-sdp multilib alternatives-2
@@ -25,7 +26,7 @@ QA_PREBUILT="
${INTEL_SDP_DIR}/mkl/benchmarks/linpack/*
${INTEL_SDP_DIR}/mkl/benchmarks/mp_linpack/*/*/*"
-CHECKREQS_DISK_BUILD=1536
+CHECKREQS_DISK_BUILD=1536M
INTEL_BIN_RPMS="mkl mkl-devel"
INTEL_DAT_RPMS="mkl-common"
diff --git a/sci-libs/nfft/ChangeLog b/sci-libs/nfft/ChangeLog
index a0d25f7f1..93e715219 100644
--- a/sci-libs/nfft/ChangeLog
+++ b/sci-libs/nfft/ChangeLog
@@ -2,6 +2,11 @@
# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*nfft-3.2.1 (30 Sep 2012)
+
+ 30 Sep 2012; Christoph Junghans <ottxor@gentoo.org> +nfft-3.2.1.ebuild:
+ version bump
+
*nfft-3.2.0 (07 Jul 2012)
07 Jul 2012; Christoph Junghans <ottxor@gentoo.org> +nfft-3.2.0.ebuild,
diff --git a/sci-libs/nfft/Manifest b/sci-libs/nfft/Manifest
index ad1e81701..635ac7e0b 100644
--- a/sci-libs/nfft/Manifest
+++ b/sci-libs/nfft/Manifest
@@ -1 +1,2 @@
DIST nfft-3.2.0.tar.gz 2053826 SHA256 8f35288affefd853c0c14c98445405c0acfe14360a9d19f7411865fc6f026126 SHA512 d26e4470cd3ef3b3a2cb4f0d11f32446690628010c87fec0093aa1f7392a94e122da44f89f30f97de482e8e777e8f5b694f4b0b6f47e028412277800d13d3334 WHIRLPOOL f3625d972e711e9522cb5f21da8409b03a781a482a6b6e29d0a94bd9923e5cc55efb035bc099483d31ed65365ec21e984641a30016a386f5e799a2eab157845d
+DIST nfft-3.2.1.tar.gz 2501629 SHA256 9ee1c48b7846dea92098a700d3753ecbc095259979ef1e415bebd09abe159ed4 SHA512 227cef1fe6a707c44451498fd446a450a5f34871ae0819a9ed87136dcb3e10288934233b15117bd143c5614a50df6b0d5be1934b4e176942f32ada9eaf01c119 WHIRLPOOL 18cd38e29882ca0660348b501f9f595ddf41babe4b175139b2cd5ed8bf546dc32408005bf768331e2576ad43ae5e1000326e3bfbabeddf62b756ccae9e33632b
diff --git a/sci-libs/nfft/nfft-3.2.1.ebuild b/sci-libs/nfft/nfft-3.2.1.ebuild
new file mode 100644
index 000000000..41c380162
--- /dev/null
+++ b/sci-libs/nfft/nfft-3.2.1.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI="4"
+
+inherit autotools-utils eutils toolchain-funcs
+
+DESCRIPTION="library for nonequispaced discrete Fourier transform"
+HOMEPAGE="http://www-user.tu-chemnitz.de/~potts/nfft"
+SRC_URI="http://www-user.tu-chemnitz.de/~potts/nfft/download/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~x86 ~amd64"
+IUSE="openmp static-libs"
+
+RDEPEND="sci-libs/fftw:3.0"
+DEPEND="${RDEPEND}"
+
+pkg_pretend() {
+ use openmp && ! tc-has-openmp && \
+ die "Please switch to an openmp compatible compiler"
+}
+
+src_prepare() {
+ sed -i '25s/"\?$/"/' examples/nfsft/nfsft_benchomp.c || die
+}
+
+src_configure() {
+ local myeconfargs=(
+ --enable-all
+ $(use_enable openmp)
+ )
+ autotools-utils_src_configure
+}
diff --git a/sci-mathematics/petsc/petsc-3.3_p1.ebuild b/sci-mathematics/petsc/petsc-3.3_p1.ebuild
index 36e2d7aaf..0490a56ef 100644
--- a/sci-mathematics/petsc/petsc-3.3_p1.ebuild
+++ b/sci-mathematics/petsc/petsc-3.3_p1.ebuild
@@ -74,7 +74,7 @@ src_configure() {
if use ${1}; then
myuse="--with-${p}=1"
if [[ $# -ge 4 ]]; then
- myuse="${myuse} --with-${p}-include=${3}"
+ myuse="${myuse} --with-${p}-include=${EPREFIX}${3}"
shift 3
myuse="${myuse} --with-${p}-lib=$@"
else
diff --git a/sci-mathematics/scilab/ChangeLog b/sci-mathematics/scilab/ChangeLog
index 5de66d43f..241fe4e9b 100644
--- a/sci-mathematics/scilab/ChangeLog
+++ b/sci-mathematics/scilab/ChangeLog
@@ -2,6 +2,24 @@
# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*scilab-5.4.0 (02 Oct 2012)
+
+ 02 Oct 2012; Guillaume Horel <guillaume.horel@gmail.com>
+ -scilab-5.3.999.ebuild,
+ -files/scilab-5.3.999-fix-random-runtime-failure.patch,
+ -files/scilab-5.3.999-followlinks.patch,
+ -files/scilab-5.3.999-fortran-link.patch,
+ -files/scilab-5.3.999-gluegen.patch, -files/scilab-5.3.999-java-heap.patch,
+ +scilab-5.4.0.ebuild, +files/scilab-5.4.0-fix-random-runtime-failure.patch,
+ +files/scilab-5.4.0-followlinks.patch,
+ +files/scilab-5.4.0-fortran-link.patch, +files/scilab-5.4.0-gluegen.patch,
+ +files/scilab-5.4.0-java-heap.patch:
+ version bump and delete live ebuild
+
+ 25 Sep 2012; Guillaume Horel <guillaume.horel@gmail.com>
+ scilab-5.3.999.ebuild:
+ update dependencies
+
11 Aug 2012; Guillaume Horel <guillaume.horel@gmail.com>
scilab-5.3.999.ebuild:
drop dependency on hdf-java
diff --git a/sci-mathematics/scilab/Manifest b/sci-mathematics/scilab/Manifest
index ee6bad85e..55b73e608 100644
--- a/sci-mathematics/scilab/Manifest
+++ b/sci-mathematics/scilab/Manifest
@@ -1 +1,2 @@
DIST scilab-5.3.3-src.tar.gz 47253497 SHA256 e6edd7d241f2a09bd2dadaaafff5c152509db240220933b87305875302401335 SHA512 334ff05239efa2c9c378a86521a979aa5578f5a79324dc4f16805a995c673d5bd9656567de127939bf30409e2ba6f5904b75508046adfcfa4a5d6390f53d8ffa WHIRLPOOL 635666dbc52280fd797f01402c42429acd3e55c1bcdd9a2af584e349838e1bb935cef97f0f9f061d7b1c44f6078a0d84fb44f2c4cb17fcf9d3ba59e79c45493e
+DIST scilab-5.4.0-src.tar.gz 47991386 SHA256 d123fb0f091554b6e0621d59fca53ea0fd68c58a339cc40f0b1b4d08531fbb1f SHA512 93af4929535beac61924bf2fe0cab139356d58a8499a29cb499294445406b5273592668f5eda0f7e2d3a1bf45d184bd8eb9615be2deb7afdebd3972e77284536 WHIRLPOOL 0e17ed494c45887a48e179ce1c17925eddb860e6ba1a13243c51c51236029b1c45569afc642a39cd7d7a532fefe85d4a5fef9f86a49bd2e586bae4a58fa93081
diff --git a/sci-mathematics/scilab/files/scilab-5.3.999-fix-random-runtime-failure.patch b/sci-mathematics/scilab/files/scilab-5.4.0-fix-random-runtime-failure.patch
index 92ac45339..92ac45339 100644
--- a/sci-mathematics/scilab/files/scilab-5.3.999-fix-random-runtime-failure.patch
+++ b/sci-mathematics/scilab/files/scilab-5.4.0-fix-random-runtime-failure.patch
diff --git a/sci-mathematics/scilab/files/scilab-5.3.999-followlinks.patch b/sci-mathematics/scilab/files/scilab-5.4.0-followlinks.patch
index 118df3b1a..118df3b1a 100644
--- a/sci-mathematics/scilab/files/scilab-5.3.999-followlinks.patch
+++ b/sci-mathematics/scilab/files/scilab-5.4.0-followlinks.patch
diff --git a/sci-mathematics/scilab/files/scilab-5.3.999-fortran-link.patch b/sci-mathematics/scilab/files/scilab-5.4.0-fortran-link.patch
index 53277783c..53277783c 100644
--- a/sci-mathematics/scilab/files/scilab-5.3.999-fortran-link.patch
+++ b/sci-mathematics/scilab/files/scilab-5.4.0-fortran-link.patch
diff --git a/sci-mathematics/scilab/files/scilab-5.3.999-gluegen.patch b/sci-mathematics/scilab/files/scilab-5.4.0-gluegen.patch
index 64717a75a..64717a75a 100644
--- a/sci-mathematics/scilab/files/scilab-5.3.999-gluegen.patch
+++ b/sci-mathematics/scilab/files/scilab-5.4.0-gluegen.patch
diff --git a/sci-mathematics/scilab/files/scilab-5.3.999-java-heap.patch b/sci-mathematics/scilab/files/scilab-5.4.0-java-heap.patch
index 3523dae95..66aadc0a7 100644
--- a/sci-mathematics/scilab/files/scilab-5.3.999-java-heap.patch
+++ b/sci-mathematics/scilab/files/scilab-5.4.0-java-heap.patch
@@ -1,12 +1,12 @@
diff -urN scilab-orig/etc/jvm_options.xml scilab/etc/jvm_options.xml
---- scilab-orig/etc/jvm_options.xml 2012-08-06 20:47:17.116007011 -0400
-+++ scilab/etc/jvm_options.xml 2012-08-06 20:59:02.889052072 -0400
+--- scilab-orig/etc/jvm_options.xml 2012-09-26 23:04:51.301102957 -0400
++++ scilab/etc/jvm_options.xml 2012-09-26 23:07:24.822118228 -0400
@@ -22,7 +22,7 @@
<!-- ENABLE Just In Time java compiler -->
<option value="-Djava.compiler=JIT"/>
<!-- Set Java Heap space to 256mb -->
- <option value="-Xmx256m"/>
+ <option value="-Xmx512m"/>
- <option value="-Dawt.useSystemAAFontSettings=on" os="linux"/>
- <option value="-Dapple.laf.useScreenMenuBar=true" os="macosx"/>
-
+
+ <!-- Set Java space for direct buffer allocation -->
+ <!--
diff --git a/sci-mathematics/scilab/scilab-5.3.999.ebuild b/sci-mathematics/scilab/scilab-5.4.0.ebuild
index b25dbabc7..56ccebfba 100644
--- a/sci-mathematics/scilab/scilab-5.3.999.ebuild
+++ b/sci-mathematics/scilab/scilab-5.4.0.ebuild
@@ -8,7 +8,7 @@ JAVA_PKG_OPT_USE="gui"
VIRTUALX_REQUIRED="manual"
inherit eutils autotools bash-completion-r1 check-reqs fdo-mime flag-o-matic \
- fortran-2 git-2 java-pkg-opt-2 toolchain-funcs virtualx
+ fortran-2 java-pkg-opt-2 toolchain-funcs virtualx
# Comments:
# - we don't rely on the configure script to find the right version of java
@@ -23,11 +23,10 @@ inherit eutils autotools bash-completion-r1 check-reqs fdo-mime flag-o-matic \
DESCRIPTION="Scientific software package for numerical computations"
LICENSE="CeCILL-2"
HOMEPAGE="http://www.scilab.org/"
-#SRC_URI="http://guillaume.horel.free.fr/${P}.tar.gz"
-EGIT_REPO_URI="git://git.scilab.org/scilab"
+SRC_URI="http://www.scilab.org/download/${PV}/${P}-src.tar.gz"
SLOT="0"
-IUSE="bash-completion debug doc fftw +gui +matio nls openmp
+IUSE="bash-completion debug +doc fftw +gui +matio nls openmp
static-libs test tk +umfpack xcos"
REQUIRED_USE="xcos? ( gui ) doc? ( gui )"
@@ -60,10 +59,10 @@ CDEPEND="dev-libs/libpcre
dev-java/javahelp:0
dev-java/jeuclid-core:0
dev-java/jgoodies-looks:2.0
- >=dev-java/jlatexmath-0.9.4:0
+ >=dev-java/jlatexmath-1.0.0:1
dev-java/jogl:2
>=dev-java/jrosetta-1.0.4:0
- dev-java/scirenderer:0
+ dev-java/scirenderer:1
dev-java/skinlf:0
dev-java/xmlgraphics-commons:1.3
virtual/opengl
@@ -83,15 +82,13 @@ DEPEND="${CDEPEND}
gui? (
>=virtual/jdk-1.5
doc? ( app-text/docbook-xsl-stylesheets
- >=dev-java/jlatexmath-fop-0.9.4
- dev-java/xml-commons-external )
+ >=dev-java/jlatexmath-fop-1.0.0:1
+ dev-java/xml-commons-external:1.4 )
xcos? ( dev-lang/ocaml ) )
test? (
- dev-java/junit
+ dev-java/junit:4
gui? ( ${VIRTUALX_DEPEND} ) )"
-EGIT_SOURCEDIR="${WORKDIR}/${PN}"
-S="${WORKDIR}/${PN}/${PN}"
DOCS=( "ACKNOWLEDGEMENTS" "README_Unix" "Readme_Visual.txt" )
pkg_pretend() {
@@ -129,7 +126,7 @@ src_prepare() {
append-ldflags $(no-as-needed)
# increases java heap to 512M when building docs (sync with cheqreqs above)
- use doc && epatch "${FILESDIR}"/${P}-java-heap.patch
+ use doc && epatch "${FILESDIR}/${P}-java-heap.patch"
# make sure library path are preloaded in binaries
sed -i \
diff --git a/sci-visualization/paraview/ChangeLog b/sci-visualization/paraview/ChangeLog
index 703030192..f5ecfaf0a 100644
--- a/sci-visualization/paraview/ChangeLog
+++ b/sci-visualization/paraview/ChangeLog
@@ -2,6 +2,12 @@
# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*paraview-3.14.1-r4 (20 Sep 2012)
+
+ 20 Sep 2012; François Bissey <francois.bissey@canterbury.ac.nz>
+ -paraview-3.14.1-r3.ebuild, +paraview-3.14.1-r4.ebuild, metadata.xml:
+ change postscript useflag to gl2ps as in opencascade
+
*paraview-3.14.1-r3 (16 Sep 2012)
16 Sep 2012; François Bissey <francois.bissey@canterbury.ac.nz>
diff --git a/sci-visualization/paraview/metadata.xml b/sci-visualization/paraview/metadata.xml
index c12360820..5a805e383 100644
--- a/sci-visualization/paraview/metadata.xml
+++ b/sci-visualization/paraview/metadata.xml
@@ -16,6 +16,7 @@
<flag name='mysql'>Build support for MySQL data item in the XDMF format</flag>
<flag name='nvcontrol'>Add NVCONTROL support for OpenGL options</flag>
<flag name='webkit'>Built support for qt-webkit in vtk</flag>
+ <flag name='gl2ps'>Enables gl2ps PostScript printing library</flag>
<flag name='coprocessing'>Enable the coprocessing infrastructure which is mainly useful in the context of clusters</flag>
</use>
</pkgmetadata>
diff --git a/sci-visualization/paraview/paraview-3.14.1-r3.ebuild b/sci-visualization/paraview/paraview-3.14.1-r4.ebuild
index 5eb288da8..0f65b02d2 100644
--- a/sci-visualization/paraview/paraview-3.14.1-r3.ebuild
+++ b/sci-visualization/paraview/paraview-3.14.1-r4.ebuild
@@ -20,7 +20,7 @@ RESTRICT="mirror"
LICENSE="paraview GPL-2"
KEYWORDS="~x86 ~amd64"
SLOT="0"
-IUSE="boost cg -coprocessing doc examples +gui mpi mysql postscript nvcontrol +plugins +python webkit ffmpeg theora"
+IUSE="boost cg -coprocessing doc examples +gui mpi mysql gl2ps nvcontrol +plugins +python webkit ffmpeg theora"
RDEPEND="
~sci-libs/netcdf-4.1.3[cxx,hdf5]
@@ -45,7 +45,7 @@ RDEPEND="
)
ffmpeg? ( virtual/ffmpeg )
theora? ( media-libs/libtheora )
- postscript? ( x11-libs/gl2ps )
+ gl2ps? ( x11-libs/gl2ps )
dev-libs/libxml2:2
dev-db/sqlite:3
media-libs/libpng
@@ -161,8 +161,8 @@ src_configure() {
$(cmake-utils_use nvcontrol VTK_USE_NVCONTROL)
$(cmake-utils_use mysql XDMF_USE_MYSQL)
$(cmake-utils_use mysql VTK_USE_MYSQL)
- $(cmake-utils_use postscript VTK_USE_GL2PS)
- $(cmake-utils_use postscript VTK_USE_SYSTEM_GL2PS)
+ $(cmake-utils_use gl2ps VTK_USE_GL2PS)
+ $(cmake-utils_use gl2ps VTK_USE_SYSTEM_GL2PS)
$(cmake-utils_use coprocessing PARAVIEW_ENABLE_COPROCESSING)
$(cmake-utils_use ffmpeg VTK_USE_FFMPEG_ENCODER)
$(cmake-utils_use theora VTK_USE_THEORA_ENCODER)
diff --git a/skel.ChangeLog b/skel.ChangeLog
index 6eff27d09..e41b5576e 100644
--- a/skel.ChangeLog
+++ b/skel.ChangeLog
@@ -1,5 +1,5 @@
# ChangeLog for <CATEGORY>/<PACKAGE_NAME>
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
*<PACKAGE_NAME>-<PACKAGE_VERSION>-<PACKAGE_RELEASE> (DD MMM YYYY)
diff --git a/skel.ebuild b/skel.ebuild
index 7c3273ced..59562205d 100644
--- a/skel.ebuild
+++ b/skel.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2012 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
@@ -13,7 +13,7 @@
# The EAPI variable tells the ebuild format in use.
# Defaults to 0 if not specified.
-# It is suggested that you the latest EAPI approved by the Council.
+# It is suggested that you use the latest EAPI approved by the Council.
# The PMS contains specifications for all EAPIs. Eclasses will test for this
# variable if they need to use EAPI > 0 features.
EAPI=4
@@ -30,17 +30,17 @@ inherit eutils
# epatch "${FILESDIR}"/patch-name-here
#
# eclasses tend to list descriptions of how to use their functions properly.
-# take a look at /usr/portage/eclasses/ for more examples.
+# take a look at /usr/portage/eclass/ for more examples.
# Short one-line description of this package.
DESCRIPTION="This is a sample skeleton ebuild file"
# Homepage, not used by Portage directly but handy for developer reference
-HOMEPAGE="http://foo.bar.com/"
+HOMEPAGE="http://foo.example.org/"
# Point to any required sources; these will be automatically downloaded by
# Portage.
-SRC_URI="ftp://foo.bar.com/${P}.tar.gz"
+SRC_URI="ftp://foo.example.org/${P}.tar.gz"
# License of the package. This must match the name of file(s) in
@@ -107,7 +107,7 @@ RDEPEND="${DEPEND}"
# unpacked) inside ${WORKDIR}. The default value for S is ${WORKDIR}/${P}
# If you don't need to change it, leave the S= line out of the ebuild
# to keep it tidy.
-#S="${WORKDIR}/${P}"
+#S=${WORKDIR}/${P}
# The following src_configure function is implemented as default by portage, so
diff --git a/skel.metadata.xml b/skel.metadata.xml
index d31449d1d..4dcddcb75 100644
--- a/skel.metadata.xml
+++ b/skel.metadata.xml
@@ -1,34 +1,34 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<!--
+<!--
+$Header: /var/cvsroot/gentoo-x86/skel.metadata.xml,v 1.21 2012/02/07 00:03:15 idl0r Exp $
+
This is the example metadata file.
-The root element of this file is <pkgmetadata>. Within this element a
-number of subelements are allowed: herd, maintainer, and
+The root element of this file is <pkgmetadata>. Within this element a
+number of subelements are allowed: herd, maintainer, and
longdescription. herd is a required subelement.
For a full description look at:
http://www.gentoo.org/proj/en/devrel/handbook/handbook.xml?part=2&chap=4
-Before committing, please remove the comments from this file. They are
+Before committing, please remove the comments from this file. They are
not relevant for general metadata.xml files.
-->
<pkgmetadata>
-<herd>sci</herd>
+ <herd>sci</herd>
<maintainer>
- <email>@gentoo.org</email>
+ <email>@gentoo.org</email>
<!-- <description>Description of the maintainership</description> -->
</maintainer>
-<longdescription>
- Long description of the package
-</longdescription>
+<!-- <longdescription>Long description of the package</longdescription> -->
<!--
<use>
- <flag name='flag'>Description of how USE='flag' affects this package</flag>
- <flag name='userland_GNU'>Description of how USERLAND='GNU' affects this
- package</flag>
- <flag name='aspell'>Uses <pkg>app-text/aspell</pkg> for spell checking.
- Requires an installed dictionary from <cat>app-dicts</cat></flag>
+ <flag name="flag">Description of how USE='flag' affects this package</flag>
+ <flag name="userland_GNU">Description of how USERLAND='GNU' affects this
+ package</flag>
+ <flag name="aspell">Uses <pkg>app-text/aspell</pkg> for spell checking.
+ Requires an installed dictionary from <cat>app-dicts</cat></flag>
</use>
-->
</pkgmetadata>
diff --git a/sys-cluster/lustre/ChangeLog b/sys-cluster/lustre/ChangeLog
new file mode 100644
index 000000000..129d39a56
--- /dev/null
+++ b/sys-cluster/lustre/ChangeLog
@@ -0,0 +1,6 @@
+# ChangeLog for sys-cluster/lustre
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 20 Sep 2012; Alexey Shvetsov <alexxy@gentoo.org> lustre-9999.ebuild:
+ [sys-cluster/lustre] call apply_user_patches
diff --git a/sys-cluster/lustre/files/0001-LU-1337-vfs-kernel-3.1-renames-lock-manager-ops.patch b/sys-cluster/lustre/files/0001-LU-1337-vfs-kernel-3.1-renames-lock-manager-ops.patch
new file mode 100644
index 000000000..44cc8cec3
--- /dev/null
+++ b/sys-cluster/lustre/files/0001-LU-1337-vfs-kernel-3.1-renames-lock-manager-ops.patch
@@ -0,0 +1,190 @@
+From 0635f4d7cde2da46e05ba6be6d6dd26e72814ff8 Mon Sep 17 00:00:00 2001
+From: Liu Xuezhao <xuezhao.liu@emc.com>
+Date: Thu, 9 Aug 2012 10:37:39 +0800
+Subject: [PATCH 01/13] LU-1337 vfs: kernel 3.1 renames lock-manager ops
+
+Kernel 3.1 renames lock-manager ops(lock_manager_operations) from
+fl_xxx to lm_xxx (commit 8fb47a4fbf858a164e973b8ea8ef5e83e61f2e50).
+
+Add LC_LM_XXX_LOCK_MANAGER_OPS/HAVE_LM_XXX_LOCK_MANAGER_OPS to check.
+
+Re-arrange several macro definitions in lustre-core.m4 as kernel
+version sequence.
+
+Signed-off-by: Liu Xuezhao <xuezhao.liu@emc.com>
+Change-Id: Ic86ec9db2f8262ef7ab9f5f2fb51ca79591120a4
+---
+ lustre/autoconf/lustre-core.m4 | 85 +++++++++++++++++++++-------------
+ lustre/include/linux/lustre_compat25.h | 4 ++
+ lustre/llite/file.c | 18 +++----
+ 3 files changed, 67 insertions(+), 40 deletions(-)
+
+diff --git a/lustre/autoconf/lustre-core.m4 b/lustre/autoconf/lustre-core.m4
+index 64c14e5..403add5 100644
+--- a/lustre/autoconf/lustre-core.m4
++++ b/lustre/autoconf/lustre-core.m4
+@@ -1729,6 +1729,18 @@ EXTRA_KCFLAGS="$tmp_flags"
+ ])
+
+ #
++# 2.6.38 export simple_setattr
++#
++AC_DEFUN([LC_EXPORT_SIMPLE_SETATTR],
++[LB_CHECK_SYMBOL_EXPORT([simple_setattr],
++[fs/libfs.c],[
++AC_DEFINE(HAVE_SIMPLE_SETATTR, 1,
++ [simple_setattr is exported by the kernel])
++],[
++])
++])
++
++#
+ # 2.6.39 remove unplug_fn from request_queue.
+ #
+ AC_DEFUN([LC_REQUEST_QUEUE_UNPLUG_FN],
+@@ -1798,14 +1810,42 @@ LB_LINUX_TRY_COMPILE([
+ ])
+
+ #
+-# 2.6.38 export simple_setattr
++# 3.1.1 has ext4_blocks_for_truncate
+ #
+-AC_DEFUN([LC_EXPORT_SIMPLE_SETATTR],
+-[LB_CHECK_SYMBOL_EXPORT([simple_setattr],
+-[fs/libfs.c],[
+-AC_DEFINE(HAVE_SIMPLE_SETATTR, 1,
+- [simple_setattr is exported by the kernel])
++AC_DEFUN([LC_BLOCKS_FOR_TRUNCATE],
++[AC_MSG_CHECKING([if kernel has ext4_blocks_for_truncate])
++LB_LINUX_TRY_COMPILE([
++ #include <linux/fs.h>
++ #include "$LINUX/fs/ext4/ext4_jbd2.h"
++ #include "$LINUX/fs/ext4/truncate.h"
+ ],[
++ ext4_blocks_for_truncate(NULL);
++],[
++ AC_MSG_RESULT([yes])
++ AC_DEFINE(HAVE_BLOCKS_FOR_TRUNCATE, 1,
++ [kernel has ext4_blocks_for_truncate])
++],[
++ AC_MSG_RESULT([no])
++])
++])
++
++#
++# 3.1 renames lock-manager ops(lock_manager_operations) from fl_xxx to lm_xxx
++# see kernel commit 8fb47a4fbf858a164e973b8ea8ef5e83e61f2e50
++#
++AC_DEFUN([LC_LM_XXX_LOCK_MANAGER_OPS],
++[AC_MSG_CHECKING([if lock-manager ops renamed to lm_xxx])
++LB_LINUX_TRY_COMPILE([
++ #include <linux/fs.h>
++],[
++ struct lock_manager_operations lm_ops;
++ lm_ops.lm_compare_owner = NULL;
++],[
++ AC_DEFINE(HAVE_LM_XXX_LOCK_MANAGER_OPS, 1,
++ [lock-manager ops renamed to lm_xxx])
++ AC_MSG_RESULT([yes])
++],[
++ AC_MSG_RESULT([no])
+ ])
+ ])
+
+@@ -1848,26 +1888,6 @@ LB_LINUX_TRY_COMPILE([
+ ])
+
+ #
+-# 3.1.1 has ext4_blocks_for_truncate
+-#
+-AC_DEFUN([LC_BLOCKS_FOR_TRUNCATE],
+-[AC_MSG_CHECKING([if kernel has ext4_blocks_for_truncate])
+-LB_LINUX_TRY_COMPILE([
+- #include <linux/fs.h>
+- #include "$LINUX/fs/ext4/ext4_jbd2.h"
+- #include "$LINUX/fs/ext4/truncate.h"
+-],[
+- ext4_blocks_for_truncate(NULL);
+-],[
+- AC_MSG_RESULT([yes])
+- AC_DEFINE(HAVE_BLOCKS_FOR_TRUNCATE, 1,
+- [kernel has ext4_blocks_for_truncate])
+-],[
+- AC_MSG_RESULT([no])
+-])
+-])
+-
+-#
+ # LC_PROG_LINUX
+ #
+ # Lustre linux kernel checks
+@@ -2008,15 +2028,18 @@ AC_DEFUN([LC_PROG_LINUX],
+
+ # 2.6.39
+ LC_REQUEST_QUEUE_UNPLUG_FN
+- LC_HAVE_FSTYPE_MOUNT
+-
+- # 3.3
+- LC_HAVE_MIGRATE_HEADER
+- LC_MIGRATEPAGE_4ARGS
++ LC_HAVE_FSTYPE_MOUNT
+
+ # 3.1.1
+ LC_BLOCKS_FOR_TRUNCATE
+
++ # 3.1
++ LC_LM_XXX_LOCK_MANAGER_OPS
++
++ # 3.3
++ LC_HAVE_MIGRATE_HEADER
++ LC_MIGRATEPAGE_4ARGS
++
+ #
+ if test x$enable_server = xyes ; then
+ AC_DEFINE(HAVE_SERVER_SUPPORT, 1, [support server])
+diff --git a/lustre/include/linux/lustre_compat25.h b/lustre/include/linux/lustre_compat25.h
+index 172da72..41b4516 100644
+--- a/lustre/include/linux/lustre_compat25.h
++++ b/lustre/include/linux/lustre_compat25.h
+@@ -808,5 +808,9 @@ static inline bool selinux_is_enabled(void)
+ }
+ #endif
+
++#ifndef HAVE_LM_XXX_LOCK_MANAGER_OPS
++# define lm_compare_owner fl_compare_owner
++#endif
++
+ #endif /* __KERNEL__ */
+ #endif /* _COMPAT25_H */
+diff --git a/lustre/llite/file.c b/lustre/llite/file.c
+index 96379d6..1525b07 100644
+--- a/lustre/llite/file.c
++++ b/lustre/llite/file.c
+@@ -2150,15 +2150,15 @@ int ll_file_flock(struct file *file, int cmd, struct file_lock *file_lock)
+ }
+ flock.l_flock.pid = file_lock->fl_pid;
+
+- /* Somewhat ugly workaround for svc lockd.
+- * lockd installs custom fl_lmops->fl_compare_owner that checks
+- * for the fl_owner to be the same (which it always is on local node
+- * I guess between lockd processes) and then compares pid.
+- * As such we assign pid to the owner field to make it all work,
+- * conflict with normal locks is unlikely since pid space and
+- * pointer space for current->files are not intersecting */
+- if (file_lock->fl_lmops && file_lock->fl_lmops->fl_compare_owner)
+- flock.l_flock.owner = (unsigned long)file_lock->fl_pid;
++ /* Somewhat ugly workaround for svc lockd.
++ * lockd installs custom fl_lmops->lm_compare_owner that checks
++ * for the fl_owner to be the same (which it always is on local node
++ * I guess between lockd processes) and then compares pid.
++ * As such we assign pid to the owner field to make it all work,
++ * conflict with normal locks is unlikely since pid space and
++ * pointer space for current->files are not intersecting */
++ if (file_lock->fl_lmops && file_lock->fl_lmops->lm_compare_owner)
++ flock.l_flock.owner = (unsigned long)file_lock->fl_pid;
+
+ switch (file_lock->fl_type) {
+ case F_RDLCK:
+--
+1.7.12
+
diff --git a/sys-cluster/lustre/files/0002-LU-1337-vfs-kernel-3.1-kills-inode-i_alloc_sem.patch b/sys-cluster/lustre/files/0002-LU-1337-vfs-kernel-3.1-kills-inode-i_alloc_sem.patch
new file mode 100644
index 000000000..04ccefe11
--- /dev/null
+++ b/sys-cluster/lustre/files/0002-LU-1337-vfs-kernel-3.1-kills-inode-i_alloc_sem.patch
@@ -0,0 +1,446 @@
+From 13a22da522d306d69511e439406d2f986a596adb Mon Sep 17 00:00:00 2001
+From: Liu Xuezhao <xuezhao.liu@emc.com>
+Date: Sun, 22 Jul 2012 01:07:18 +0800
+Subject: [PATCH 02/13] LU-1337 vfs: kernel 3.1 kills inode->i_alloc_sem
+
+Kernel 3.1 kills inode->i_alloc_sem, use i_dio_count and
+inode_dio_wait/inode_dio_done instead.
+(kernel commit bd5fe6c5eb9c548d7f07fe8f89a150bb6705e8e3).
+
+Add HAVE_INODE_DIO_WAIT to differentiate it.
+Add INODE_DIO_LOCK_WRITE/INODE_DIO_RELEASE_WRITE,
+ INODE_DIO_LOCK_READ/INODE_DIO_RELEASE_READ macros.
+
+Signed-off-by: Liu Xuezhao <xuezhao.liu@emc.com>
+Change-Id: Ife36e07a85c76153985a4a86ee1973262c4c0e27
+---
+ lustre/autoconf/lustre-core.m4 | 22 ++++++++++++
+ lustre/include/linux/lustre_compat25.h | 18 ++++++----
+ lustre/llite/llite_lib.c | 4 +--
+ lustre/llite/vvp_io.c | 27 ++++++--------
+ lustre/llite/vvp_page.c | 1 -
+ lustre/obdfilter/filter.c | 65 +++++++++++++++++-----------------
+ lustre/obdfilter/filter_io.c | 28 ++++++++-------
+ lustre/obdfilter/filter_io_26.c | 10 +++---
+ lustre/osc/osc_cache.c | 6 ++--
+ lustre/osd-ldiskfs/osd_io.c | 1 -
+ 10 files changed, 102 insertions(+), 80 deletions(-)
+
+diff --git a/lustre/autoconf/lustre-core.m4 b/lustre/autoconf/lustre-core.m4
+index 403add5..0aef14f 100644
+--- a/lustre/autoconf/lustre-core.m4
++++ b/lustre/autoconf/lustre-core.m4
+@@ -1850,6 +1850,27 @@ LB_LINUX_TRY_COMPILE([
+ ])
+
+ #
++# 3.1 kills inode->i_alloc_sem, use i_dio_count and inode_dio_wait/
++# inode_dio_done instead.
++# see kernel commit bd5fe6c5eb9c548d7f07fe8f89a150bb6705e8e3
++#
++AC_DEFUN([LC_INODE_DIO_WAIT],
++[AC_MSG_CHECKING([if inode->i_alloc_sem is killed and use inode_dio_wait/done.])
++LB_LINUX_TRY_COMPILE([
++ #include <linux/fs.h>
++],[
++ inode_dio_wait((struct inode *)0);
++ inode_dio_done((struct inode *)0);
++],[
++ AC_DEFINE(HAVE_INODE_DIO_WAIT, 1,
++ [inode->i_alloc_sem is killed and use inode_dio_wait/done])
++ AC_MSG_RESULT([yes])
++],[
++ AC_MSG_RESULT([no])
++])
++])
++
++#
+ # 3.3 introduces migrate_mode.h and migratepage has 4 args
+ #
+ AC_DEFUN([LC_HAVE_MIGRATE_HEADER],
+@@ -2035,6 +2056,7 @@ AC_DEFUN([LC_PROG_LINUX],
+
+ # 3.1
+ LC_LM_XXX_LOCK_MANAGER_OPS
++ LC_INODE_DIO_WAIT
+
+ # 3.3
+ LC_HAVE_MIGRATE_HEADER
+diff --git a/lustre/include/linux/lustre_compat25.h b/lustre/include/linux/lustre_compat25.h
+index 41b4516..bb45125 100644
+--- a/lustre/include/linux/lustre_compat25.h
++++ b/lustre/include/linux/lustre_compat25.h
+@@ -269,13 +269,17 @@ static inline int mapping_has_pages(struct address_space *mapping)
+ (type *)( (char *)__mptr - offsetof(type,member) );})
+ #endif
+
+-#define UP_WRITE_I_ALLOC_SEM(i) up_write(&(i)->i_alloc_sem)
+-#define DOWN_WRITE_I_ALLOC_SEM(i) down_write(&(i)->i_alloc_sem)
+-#define LASSERT_I_ALLOC_SEM_WRITE_LOCKED(i) LASSERT(down_read_trylock(&(i)->i_alloc_sem) == 0)
+-
+-#define UP_READ_I_ALLOC_SEM(i) up_read(&(i)->i_alloc_sem)
+-#define DOWN_READ_I_ALLOC_SEM(i) down_read(&(i)->i_alloc_sem)
+-#define LASSERT_I_ALLOC_SEM_READ_LOCKED(i) LASSERT(down_write_trylock(&(i)->i_alloc_sem) == 0)
++#ifdef HAVE_INODE_DIO_WAIT
++# define INODE_DIO_LOCK_WRITE(i) inode_dio_wait(i)
++# define INODE_DIO_RELEASE_WRITE(i) do {} while (0)
++# define INODE_DIO_LOCK_READ(i) atomic_inc(&(i)->i_dio_count)
++# define INODE_DIO_RELEASE_READ(i) inode_dio_done(i)
++#else
++# define INODE_DIO_LOCK_WRITE(i) down_write(&(i)->i_alloc_sem)
++# define INODE_DIO_RELEASE_WRITE(i) up_write(&(i)->i_alloc_sem)
++# define INODE_DIO_LOCK_READ(i) down_read(&(i)->i_alloc_sem)
++# define INODE_DIO_RELEASE_READ(i) up_read(&(i)->i_alloc_sem)
++#endif
+
+ #include <linux/mpage.h> /* for generic_writepages */
+
+diff --git a/lustre/llite/llite_lib.c b/lustre/llite/llite_lib.c
+index 9980c2c..7f3ac28 100644
+--- a/lustre/llite/llite_lib.c
++++ b/lustre/llite/llite_lib.c
+@@ -1439,12 +1439,12 @@ int ll_setattr_raw(struct dentry *dentry, struct iattr *attr)
+
+ if (!S_ISDIR(inode->i_mode)) {
+ if (ia_valid & ATTR_SIZE)
+- UP_WRITE_I_ALLOC_SEM(inode);
++ INODE_DIO_RELEASE_WRITE(inode);
+ mutex_unlock(&inode->i_mutex);
+ cfs_down_write(&lli->lli_trunc_sem);
+ mutex_lock(&inode->i_mutex);
+ if (ia_valid & ATTR_SIZE)
+- DOWN_WRITE_I_ALLOC_SEM(inode);
++ INODE_DIO_LOCK_WRITE(inode);
+ }
+
+ /* We need a steady stripe configuration for setattr to avoid
+diff --git a/lustre/llite/vvp_io.c b/lustre/llite/vvp_io.c
+index 50a19c9..0b4cfb5 100644
+--- a/lustre/llite/vvp_io.c
++++ b/lustre/llite/vvp_io.c
+@@ -295,7 +295,7 @@ static int vvp_io_setattr_iter_init(const struct lu_env *env,
+ */
+ mutex_unlock(&inode->i_mutex);
+ if (cl_io_is_trunc(ios->cis_io))
+- UP_WRITE_I_ALLOC_SEM(inode);
++ INODE_DIO_RELEASE_WRITE(inode);
+ cio->u.setattr.cui_locks_released = 1;
+ return 0;
+ }
+@@ -348,7 +348,7 @@ static int vvp_io_setattr_trunc(const struct lu_env *env,
+ const struct cl_io_slice *ios,
+ struct inode *inode, loff_t size)
+ {
+- DOWN_WRITE_I_ALLOC_SEM(inode);
++ INODE_DIO_LOCK_WRITE(inode);
+ return 0;
+ }
+
+@@ -420,7 +420,7 @@ static void vvp_io_setattr_fini(const struct lu_env *env,
+ if (cio->u.setattr.cui_locks_released) {
+ mutex_lock(&inode->i_mutex);
+ if (cl_io_is_trunc(io))
+- DOWN_WRITE_I_ALLOC_SEM(inode);
++ INODE_DIO_LOCK_WRITE(inode);
+ cio->u.setattr.cui_locks_released = 0;
+ }
+ vvp_io_fini(env, ios);
+@@ -689,28 +689,26 @@ static int vvp_io_fault_start(const struct lu_env *env,
+
+ /* must return locked page */
+ if (fio->ft_mkwrite) {
+- /* we grab alloc_sem to exclude truncate case.
+- * Otherwise, we could add dirty pages into osc cache
+- * while truncate is on-going. */
+- DOWN_READ_I_ALLOC_SEM(inode);
+-
+- LASSERT(cfio->ft_vmpage != NULL);
+- lock_page(cfio->ft_vmpage);
++ LASSERT(cfio->ft_vmpage != NULL);
++ lock_page(cfio->ft_vmpage);
+ } else {
+ result = vvp_io_kernel_fault(cfio);
+ if (result != 0)
+ return result;
+ }
+
+- vmpage = cfio->ft_vmpage;
+- LASSERT(PageLocked(vmpage));
++ vmpage = cfio->ft_vmpage;
++ LASSERT(PageLocked(vmpage));
+
+ if (OBD_FAIL_CHECK(OBD_FAIL_LLITE_FAULT_TRUNC_RACE))
+ ll_invalidate_page(vmpage);
+
++
++ size = i_size_read(inode);
+ /* Though we have already held a cl_lock upon this page, but
+ * it still can be truncated locally. */
+- if (unlikely(vmpage->mapping == NULL)) {
++ if (unlikely((vmpage->mapping != inode->i_mapping) ||
++ (page_offset(vmpage) > size))) {
+ CDEBUG(D_PAGE, "llite: fault and truncate race happened!\n");
+
+ /* return +1 to stop cl_io_loop() and ll_fault() will catch
+@@ -758,7 +756,6 @@ static int vvp_io_fault_start(const struct lu_env *env,
+ }
+ }
+
+- size = i_size_read(inode);
+ last = cl_index(obj, size - 1);
+ LASSERT(fio->ft_index <= last);
+ if (fio->ft_index == last)
+@@ -777,8 +774,6 @@ out:
+ /* return unlocked vmpage to avoid deadlocking */
+ if (vmpage != NULL)
+ unlock_page(vmpage);
+- if (fio->ft_mkwrite)
+- UP_READ_I_ALLOC_SEM(inode);
+ #ifdef HAVE_VM_OP_FAULT
+ cfio->fault.ft_flags &= ~VM_FAULT_LOCKED;
+ #endif
+diff --git a/lustre/llite/vvp_page.c b/lustre/llite/vvp_page.c
+index b428744..66842a0 100644
+--- a/lustre/llite/vvp_page.c
++++ b/lustre/llite/vvp_page.c
+@@ -420,7 +420,6 @@ static void vvp_transient_page_verify(const struct cl_page *page)
+ struct inode *inode = ccc_object_inode(page->cp_obj);
+
+ LASSERT(!mutex_trylock(&inode->i_mutex));
+- /* LASSERT_SEM_LOCKED(&inode->i_alloc_sem); */
+ }
+
+ static int vvp_transient_page_own(const struct lu_env *env,
+diff --git a/lustre/obdfilter/filter.c b/lustre/obdfilter/filter.c
+index 23a992e..a93501d 100644
+--- a/lustre/obdfilter/filter.c
++++ b/lustre/obdfilter/filter.c
+@@ -3343,13 +3343,13 @@ int filter_setattr_internal(struct obd_export *exp, struct dentry *dentry,
+ }
+ if (ia_valid & (ATTR_SIZE | ATTR_UID | ATTR_GID)) {
+ unsigned long now = jiffies;
+- /* Filter truncates and writes are serialized by
+- * i_alloc_sem, see the comment in
+- * filter_preprw_write.*/
+- if (ia_valid & ATTR_SIZE)
+- down_write(&inode->i_alloc_sem);
++ /* Filter truncates and writes are serialized.
++ * See the comment in filter_preprw_write.*/
+ mutex_lock(&inode->i_mutex);
+- fsfilt_check_slow(exp->exp_obd, now, "i_alloc_sem and i_mutex");
++ if (ia_valid & ATTR_SIZE)
++ INODE_DIO_LOCK_WRITE(inode);
++ fsfilt_check_slow(exp->exp_obd, now,
++ "i_mutex and INODE_DIO_LOCK_WRITE");
+ old_size = i_size_read(inode);
+ }
+
+@@ -3473,7 +3473,7 @@ out_unlock:
+ if (ia_valid & (ATTR_SIZE | ATTR_UID | ATTR_GID))
+ mutex_unlock(&inode->i_mutex);
+ if (ia_valid & ATTR_SIZE)
+- up_write(&inode->i_alloc_sem);
++ INODE_DIO_RELEASE_WRITE(inode);
+ if (fcc)
+ OBD_FREE(fcc, sizeof(*fcc));
+
+@@ -3554,14 +3554,14 @@ int filter_setattr(const struct lu_env *env, struct obd_export *exp,
+ */
+ if (oa->o_valid &
+ (OBD_MD_FLMTIME | OBD_MD_FLATIME | OBD_MD_FLCTIME)) {
+- unsigned long now = jiffies;
+- down_write(&dentry->d_inode->i_alloc_sem);
+- fsfilt_check_slow(exp->exp_obd, now, "i_alloc_sem");
+- fmd = filter_fmd_get(exp, oa->o_id, oa->o_seq);
+- if (fmd && fmd->fmd_mactime_xid < oti->oti_xid)
+- fmd->fmd_mactime_xid = oti->oti_xid;
+- filter_fmd_put(exp, fmd);
+- up_write(&dentry->d_inode->i_alloc_sem);
++ unsigned long now = jiffies;
++ INODE_DIO_LOCK_WRITE(dentry->d_inode);
++ fsfilt_check_slow(exp->exp_obd, now, "INODE_DIO_LOCK_WRITE");
++ fmd = filter_fmd_get(exp, oa->o_id, oa->o_seq);
++ if (fmd && fmd->fmd_mactime_xid < oti->oti_xid)
++ fmd->fmd_mactime_xid = oti->oti_xid;
++ filter_fmd_put(exp, fmd);
++ INODE_DIO_RELEASE_WRITE(dentry->d_inode);
+ }
+
+ /* setting objects attributes (including owner/group) */
+@@ -4292,28 +4292,29 @@ int filter_destroy(const struct lu_env *env, struct obd_export *exp,
+ *fcc = oa->o_lcookie;
+ }
+
+- /* we're gonna truncate it first in order to avoid possible deadlock:
+- * P1 P2
+- * open trasaction open transaction
+- * down(i_zombie) down(i_zombie)
+- * restart transaction
+- * (see BUG 4180) -bzzz
+- *
+- * take i_alloc_sem too to prevent other threads from writing to the
+- * file while we are truncating it. This can cause lock ordering issue
+- * between page lock, i_mutex & starting new journal handle.
+- * (see bug 20321) -johann
+- */
++ /* we're gonna truncate it first in order to avoid possible deadlock:
++ * P1 P2
++ * open trasaction open transaction
++ * down(i_zombie) down(i_zombie)
++ * restart transaction
++ * (see BUG 4180) -bzzz
++ *
++ * INODE_DIO_LOCK_WRITE too to prevent other threads from writing to the
++ * file while we are truncating it. This can cause lock ordering issue
++ * between page lock, i_mutex & starting new journal handle.
++ * (see bug 20321) -johann
++ */
+ now = jiffies;
+- down_write(&dchild->d_inode->i_alloc_sem);
++ INODE_DIO_LOCK_WRITE(dchild->d_inode);
+ mutex_lock(&dchild->d_inode->i_mutex);
+- fsfilt_check_slow(exp->exp_obd, now, "i_alloc_sem and i_mutex");
++ fsfilt_check_slow(exp->exp_obd, now,
++ "INODE_DIO_LOCK_WRITE and i_mutex");
+
+ /* VBR: version recovery check */
+ rc = filter_version_get_check(exp, oti, dchild->d_inode);
+ if (rc) {
+ mutex_unlock(&dchild->d_inode->i_mutex);
+- up_write(&dchild->d_inode->i_alloc_sem);
++ INODE_DIO_RELEASE_WRITE(dchild->d_inode);
+ GOTO(cleanup, rc);
+ }
+
+@@ -4321,7 +4322,7 @@ int filter_destroy(const struct lu_env *env, struct obd_export *exp,
+ NULL, 1);
+ if (IS_ERR(handle)) {
+ mutex_unlock(&dchild->d_inode->i_mutex);
+- up_write(&dchild->d_inode->i_alloc_sem);
++ INODE_DIO_RELEASE_WRITE(dchild->d_inode);
+ GOTO(cleanup, rc = PTR_ERR(handle));
+ }
+
+@@ -4333,7 +4334,7 @@ int filter_destroy(const struct lu_env *env, struct obd_export *exp,
+ rc = fsfilt_setattr(obd, dchild, handle, &iattr, 1);
+ rc2 = fsfilt_commit(obd, dchild->d_inode, handle, 0);
+ mutex_unlock(&dchild->d_inode->i_mutex);
+- up_write(&dchild->d_inode->i_alloc_sem);
++ INODE_DIO_RELEASE_WRITE(dchild->d_inode);
+ if (rc)
+ GOTO(cleanup, rc);
+ if (rc2)
+diff --git a/lustre/obdfilter/filter_io.c b/lustre/obdfilter/filter_io.c
+index a946d90..3c4dcad 100644
+--- a/lustre/obdfilter/filter_io.c
++++ b/lustre/obdfilter/filter_io.c
+@@ -634,7 +634,8 @@ static int filter_grant_check(struct obd_export *exp, struct obdo *oa,
+ * on mulitple inodes. That isn't all, because there still exists the
+ * possibility of a truncate starting a new transaction while holding the ext3
+ * rwsem = write while some writes (which have started their transactions here)
+- * blocking on the ext3 rwsem = read => lock inversion.
++ * blocking on the ext3 rwsem = read => lock inversion. (kernel 3.1 kills the
++ * rwsem and replaces it by i_dio_count and inode_dio_wait/done.)
+ *
+ * The handling gets very ugly when dealing with locked pages. It may be easier
+ * to just get rid of the locked page code (which has problems of its own) and
+@@ -730,14 +731,15 @@ static int filter_preprw_write(int cmd, struct obd_export *exp, struct obdo *oa,
+
+ fsfilt_check_slow(obd, now, "preprw_write setup");
+
+- /* Filter truncate first locks i_mutex then partially truncated
+- * page, filter write code first locks pages then take
+- * i_mutex. To avoid a deadlock in case of concurrent
+- * punch/write requests from one client, filter writes and
+- * filter truncates are serialized by i_alloc_sem, allowing
+- * multiple writes or single truncate. */
+- down_read(&dentry->d_inode->i_alloc_sem);
+- fsfilt_check_slow(obd, now, "i_alloc_sem");
++ /* Filter truncate first locks i_mutex then partially truncated
++ * page, filter write code first locks pages then take
++ * i_mutex. To avoid a deadlock in case of concurrent
++ * punch/write requests from one client, filter writes and
++ * filter truncates are serialized by INODE_DIO_LOCK_READ, allowing
++ * multiple writes or single truncate. */
++
++ INODE_DIO_LOCK_READ(dentry->d_inode);
++ fsfilt_check_slow(obd, now, "INODE_DIO_LOCK_READ");
+
+ /* Don't update inode timestamps if this write is older than a
+ * setattr which modifies the timestamps. b=10150 */
+@@ -895,11 +897,11 @@ cleanup:
+ }
+ }
+ }
+- case 3:
+- if (rc)
+- up_read(&dentry->d_inode->i_alloc_sem);
++ case 3:
++ if (rc)
++ INODE_DIO_RELEASE_READ(dentry->d_inode);
+
+- filter_iobuf_put(&obd->u.filter, iobuf, oti);
++ filter_iobuf_put(&obd->u.filter, iobuf, oti);
+ case 2:
+ pop_ctxt(&saved, &obd->obd_lvfs_ctxt, NULL);
+ if (rc)
+diff --git a/lustre/obdfilter/filter_io_26.c b/lustre/obdfilter/filter_io_26.c
+index 853e4f5..6d2b89f 100644
+--- a/lustre/obdfilter/filter_io_26.c
++++ b/lustre/obdfilter/filter_io_26.c
+@@ -635,10 +635,10 @@ int filter_commitrw_write(struct obd_export *exp, struct obdo *oa,
+ LASSERT(PageLocked(lnb->page));
+ LASSERT(!PageWriteback(lnb->page));
+
+- /* since write & truncate are serialized by the i_alloc_sem,
+- * even partial truncate should not leave dirty pages in
+- * the page cache */
+- LASSERT(!PageDirty(lnb->page));
++ /* since write & truncate are serialized by the inode_dio_wait,
++ * even partial truncate should not leave dirty pages in
++ * the page cache */
++ LASSERT(!PageDirty(lnb->page));
+
+ SetPageUptodate(lnb->page);
+
+@@ -867,7 +867,7 @@ cleanup:
+ if (fo->fo_writethrough_cache == 0 ||
+ i_size_read(inode) > fo->fo_readcache_max_filesize)
+ filter_release_cache(obd, obj, nb, inode);
+- up_read(&inode->i_alloc_sem);
++ INODE_DIO_RELEASE_READ(inode);
+ }
+
+ RETURN(rc);
+diff --git a/lustre/osc/osc_cache.c b/lustre/osc/osc_cache.c
+index 23dc755..b42e41c 100644
+--- a/lustre/osc/osc_cache.c
++++ b/lustre/osc/osc_cache.c
+@@ -2695,9 +2695,9 @@ void osc_cache_truncate_end(const struct lu_env *env, struct osc_io *oio,
+ * The caller must have called osc_cache_writeback_range() to issue IO
+ * otherwise it will take a long time for this function to finish.
+ *
+- * Caller must hold inode_mutex and i_alloc_sem, or cancel exclusive
+- * dlm lock so that nobody else can dirty this range of file while we're
+- * waiting for extents to be written.
++ * Caller must hold inode_mutex , or cancel exclusive dlm lock so that
++ * nobody else can dirty this range of file while we're waiting for
++ * extents to be written.
+ */
+ int osc_cache_wait_range(const struct lu_env *env, struct osc_object *obj,
+ pgoff_t start, pgoff_t end)
+diff --git a/lustre/osd-ldiskfs/osd_io.c b/lustre/osd-ldiskfs/osd_io.c
+index af3d6af..d266805 100644
+--- a/lustre/osd-ldiskfs/osd_io.c
++++ b/lustre/osd-ldiskfs/osd_io.c
+@@ -433,7 +433,6 @@ struct page *osd_get_page(struct dt_object *dt, loff_t offset, int rw)
+ /*
+ * there are following "locks":
+ * journal_start
+- * i_alloc_sem
+ * i_mutex
+ * page lock
+
+--
+1.7.12
+
diff --git a/sys-cluster/lustre/files/0003-LU-1337-vfs-kernel-3.1-changes-open_to_namei_flags.patch b/sys-cluster/lustre/files/0003-LU-1337-vfs-kernel-3.1-changes-open_to_namei_flags.patch
new file mode 100644
index 000000000..19e29ffb2
--- /dev/null
+++ b/sys-cluster/lustre/files/0003-LU-1337-vfs-kernel-3.1-changes-open_to_namei_flags.patch
@@ -0,0 +1,95 @@
+From 1bece6cbb7d810ef085d00ac4c664bbb37c8bc7b Mon Sep 17 00:00:00 2001
+From: Liu Xuezhao <xuezhao.liu@emc.com>
+Date: Thu, 26 Jul 2012 15:38:30 +0800
+Subject: [PATCH 03/13] LU-1337 vfs: kernel 3.1 changes open_to_namei_flags
+
+Kernel 3.1 changes the translation from open_flag to namei_flag,
+(kernel commit 8a5e929dd2e05ab4d3d89f58c5e8fca596af8f3a).
+
+So after 3.1, kernel's nameidata.intent.open.flags is different
+with lustre's lookup_intent.it_flags, as lustre's it_flags'
+lower bits equal to FMODE_xxx while kernel doesn't transliterate
+lower bits of nameidata.intent.open.flags to FMODE_xxx.
+
+This patch keeps lustre it_flags' semantics and add
+ll_namei_to_lookup_intent_flag for translation.
+
+Signed-off-by: Liu Xuezhao <xuezhao.liu@emc.com>
+Change-Id: I408685040688bae574d04cf288abb6ca967607df
+---
+ lustre/include/linux/lustre_compat25.h | 15 +++++++++++++++
+ lustre/llite/namei.c | 32 ++++++++++++++++----------------
+ 2 files changed, 31 insertions(+), 16 deletions(-)
+
+diff --git a/lustre/include/linux/lustre_compat25.h b/lustre/include/linux/lustre_compat25.h
+index bb45125..914069a 100644
+--- a/lustre/include/linux/lustre_compat25.h
++++ b/lustre/include/linux/lustre_compat25.h
+@@ -816,5 +816,20 @@ static inline bool selinux_is_enabled(void)
+ # define lm_compare_owner fl_compare_owner
+ #endif
+
++/*
++ * After 3.1, kernel's nameidata.intent.open.flags is different
++ * with lustre's lookup_intent.it_flags, as lustre's it_flags'
++ * lower bits equal to FMODE_xxx while kernel doesn't transliterate
++ * lower bits of nameidata.intent.open.flags to FMODE_xxx.
++ * */
++#include <linux/version.h>
++static inline int ll_namei_to_lookup_intent_flag(int flag)
++{
++#if LINUX_VERSION_CODE >= KERNEL_VERSION(3, 1, 0)
++ flag = (flag & ~O_ACCMODE) | OPEN_FMODE(flag);
++#endif
++ return flag;
++}
++
+ #endif /* __KERNEL__ */
+ #endif /* _COMPAT25_H */
+diff --git a/lustre/llite/namei.c b/lustre/llite/namei.c
+index 7521e3d..4cb3bf4 100644
+--- a/lustre/llite/namei.c
++++ b/lustre/llite/namei.c
+@@ -552,23 +552,23 @@ static struct dentry *ll_lookup_it(struct inode *parent, struct dentry *dentry,
+ struct lookup_intent *ll_convert_intent(struct open_intent *oit,
+ int lookup_flags)
+ {
+- struct lookup_intent *it;
+-
+- OBD_ALLOC(it, sizeof(*it));
+- if (!it)
+- return ERR_PTR(-ENOMEM);
+-
+- if (lookup_flags & LOOKUP_OPEN) {
+- it->it_op = IT_OPEN;
+- if (lookup_flags & LOOKUP_CREATE)
+- it->it_op |= IT_CREAT;
+- it->it_create_mode = (oit->create_mode & S_IALLUGO) | S_IFREG;
+- it->it_flags = oit->flags;
+- } else {
+- it->it_op = IT_GETATTR;
+- }
++ struct lookup_intent *it;
++
++ OBD_ALLOC(it, sizeof(*it));
++ if (!it)
++ return ERR_PTR(-ENOMEM);
++
++ if (lookup_flags & LOOKUP_OPEN) {
++ it->it_op = IT_OPEN;
++ if (lookup_flags & LOOKUP_CREATE)
++ it->it_op |= IT_CREAT;
++ it->it_create_mode = (oit->create_mode & S_IALLUGO) | S_IFREG;
++ it->it_flags = ll_namei_to_lookup_intent_flag(oit->flags);
++ } else {
++ it->it_op = IT_GETATTR;
++ }
+
+- return it;
++ return it;
+ }
+
+ static struct dentry *ll_lookup_nd(struct inode *parent, struct dentry *dentry,
+--
+1.7.12
+
diff --git a/sys-cluster/lustre/files/0004-LU-1337-vfs-provides-ll_get_acl-to-i_op-get_acl.patch b/sys-cluster/lustre/files/0004-LU-1337-vfs-provides-ll_get_acl-to-i_op-get_acl.patch
new file mode 100644
index 000000000..deaf4ad54
--- /dev/null
+++ b/sys-cluster/lustre/files/0004-LU-1337-vfs-provides-ll_get_acl-to-i_op-get_acl.patch
@@ -0,0 +1,150 @@
+From 734984d6c88784cde03d17e115dd6478a67daa58 Mon Sep 17 00:00:00 2001
+From: Liu Xuezhao <xuezhao.liu@emc.com>
+Date: Mon, 27 Aug 2012 17:19:22 +0800
+Subject: [PATCH 04/13] LU-1337 vfs: provides ll_get_acl to ->i_op->get_acl
+
+Since kernel 3.1 generic_permission() has lost the check_acl
+argument, ACL checking has been taken to VFS and filesystems
+need to provide a non-NULL ->i_op->get_acl to read an ACL
+from disk.
+
+This patch is a complementarity to http://review.whamcloud.com/3397
+(d018b087c962b8c66e8dc479fc66e964a2e5fd94), to fix failure of test_25
+of sanityn.sh.
+
+Signed-off-by: Liu Xuezhao <xuezhao.liu@emc.com>
+Change-Id: Ica96adac03c1792e2e8b668b959457a4ffec9a43
+---
+ lustre/autoconf/lustre-core.m4 | 3 +++
+ lustre/llite/file.c | 28 +++++++++++++++++++++-------
+ lustre/llite/llite_internal.h | 3 +++
+ lustre/llite/namei.c | 6 ++++++
+ 4 files changed, 33 insertions(+), 7 deletions(-)
+
+diff --git a/lustre/autoconf/lustre-core.m4 b/lustre/autoconf/lustre-core.m4
+index 0aef14f..a2d8efc 100644
+--- a/lustre/autoconf/lustre-core.m4
++++ b/lustre/autoconf/lustre-core.m4
+@@ -1783,6 +1783,9 @@ LB_LINUX_TRY_COMPILE([
+ #
+ # 3.1 generic_permission taken 2 parameters.
+ # see kernel commit 2830ba7f34ebb27c4e5b8b6ef408cd6d74860890
++# When generic_permission taken 2 parameters, it also means
++# inode_operations has get_acl member function,
++# see kernel commit 4e34e719e457f2e031297175410fc0bd4016a085
+ #
+ AC_DEFUN([LC_GENERIC_PERMISSION],
+ [AC_MSG_CHECKING([if generic_permission take 2 or 4 arguments])
+diff --git a/lustre/llite/file.c b/lustre/llite/file.c
+index 1525b07..bf9ba2f 100644
+--- a/lustre/llite/file.c
++++ b/lustre/llite/file.c
+@@ -2536,16 +2536,29 @@ int ll_fiemap(struct inode *inode, struct fiemap_extent_info *fieinfo,
+ }
+ #endif
+
++struct posix_acl * ll_get_acl(struct inode *inode, int type)
++{
++ struct ll_inode_info *lli = ll_i2info(inode);
++ struct posix_acl *acl = NULL;
++ ENTRY;
++
++ cfs_spin_lock(&lli->lli_lock);
++ /* VFS' acl_permission_check->check_acl will release the refcount */
++ acl = posix_acl_dup(lli->lli_posix_acl);
++ cfs_spin_unlock(&lli->lli_lock);
++
++ RETURN(acl);
++}
++
+ #ifndef HAVE_GENERIC_PERMISSION_2ARGS
+ static int
+ # ifdef HAVE_GENERIC_PERMISSION_4ARGS
+-lustre_check_acl(struct inode *inode, int mask, unsigned int flags)
++ll_check_acl(struct inode *inode, int mask, unsigned int flags)
+ # else
+-lustre_check_acl(struct inode *inode, int mask)
++ll_check_acl(struct inode *inode, int mask)
+ # endif
+ {
+ # ifdef CONFIG_FS_POSIX_ACL
+- struct ll_inode_info *lli = ll_i2info(inode);
+ struct posix_acl *acl;
+ int rc;
+ ENTRY;
+@@ -2554,9 +2567,7 @@ lustre_check_acl(struct inode *inode, int mask)
+ if (flags & IPERM_FLAG_RCU)
+ return -ECHILD;
+ # endif
+- cfs_spin_lock(&lli->lli_lock);
+- acl = posix_acl_dup(lli->lli_posix_acl);
+- cfs_spin_unlock(&lli->lli_lock);
++ acl = ll_get_acl(inode, ACL_TYPE_ACCESS);
+
+ if (!acl)
+ RETURN(-EAGAIN);
+@@ -2608,7 +2619,7 @@ int ll_inode_permission(struct inode *inode, int mask, struct nameidata *nd)
+ return lustre_check_remote_perm(inode, mask);
+
+ ll_stats_ops_tally(ll_i2sbi(inode), LPROC_LL_INODE_PERM, 1);
+- rc = ll_generic_permission(inode, mask, flags, lustre_check_acl);
++ rc = ll_generic_permission(inode, mask, flags, ll_check_acl);
+
+ RETURN(rc);
+ }
+@@ -2703,6 +2714,9 @@ struct inode_operations ll_file_inode_operations = {
+ #ifdef HAVE_LINUX_FIEMAP_H
+ .fiemap = ll_fiemap,
+ #endif
++#ifdef HAVE_GENERIC_PERMISSION_2ARGS
++ .get_acl = ll_get_acl,
++#endif
+ };
+
+ /* dynamic ioctl number support routins */
+diff --git a/lustre/llite/llite_internal.h b/lustre/llite/llite_internal.h
+index 0c9f6d6..a1c02e5 100644
+--- a/lustre/llite/llite_internal.h
++++ b/lustre/llite/llite_internal.h
+@@ -748,6 +748,8 @@ int ll_getattr_it(struct vfsmount *mnt, struct dentry *de,
+ struct lookup_intent *it, struct kstat *stat);
+ int ll_getattr(struct vfsmount *mnt, struct dentry *de, struct kstat *stat);
+ struct ll_file_data *ll_file_data_get(void);
++struct posix_acl * ll_get_acl(struct inode *inode, int type);
++
+ #ifdef HAVE_GENERIC_PERMISSION_4ARGS
+ int ll_inode_permission(struct inode *inode, int mask, unsigned int flags);
+ #else
+@@ -757,6 +759,7 @@ int ll_inode_permission(struct inode *inode, int mask, struct nameidata *nd);
+ int ll_inode_permission(struct inode *inode, int mask);
+ # endif
+ #endif
++
+ int ll_lov_setstripe_ea_info(struct inode *inode, struct file *file,
+ int flags, struct lov_user_md *lum,
+ int lum_size);
+diff --git a/lustre/llite/namei.c b/lustre/llite/namei.c
+index 4cb3bf4..036674f 100644
+--- a/lustre/llite/namei.c
++++ b/lustre/llite/namei.c
+@@ -1193,6 +1193,9 @@ struct inode_operations ll_dir_inode_operations = {
+ .getxattr = ll_getxattr,
+ .listxattr = ll_listxattr,
+ .removexattr = ll_removexattr,
++#ifdef HAVE_GENERIC_PERMISSION_2ARGS
++ .get_acl = ll_get_acl,
++#endif
+ };
+
+ struct inode_operations ll_special_inode_operations = {
+@@ -1203,4 +1206,7 @@ struct inode_operations ll_special_inode_operations = {
+ .getxattr = ll_getxattr,
+ .listxattr = ll_listxattr,
+ .removexattr = ll_removexattr,
++#ifdef HAVE_GENERIC_PERMISSION_2ARGS
++ .get_acl = ll_get_acl,
++#endif
+ };
+--
+1.7.12
+
diff --git a/sys-cluster/lustre/files/0005-LU-1337-block-kernel-3.2-make_request_fn-returns-voi.patch b/sys-cluster/lustre/files/0005-LU-1337-block-kernel-3.2-make_request_fn-returns-voi.patch
new file mode 100644
index 000000000..3630fc24f
--- /dev/null
+++ b/sys-cluster/lustre/files/0005-LU-1337-block-kernel-3.2-make_request_fn-returns-voi.patch
@@ -0,0 +1,108 @@
+From b489d154ef9a88421939b20b146361122a4704d6 Mon Sep 17 00:00:00 2001
+From: Liu Xuezhao <xuezhao.liu@emc.com>
+Date: Thu, 9 Aug 2012 10:18:32 +0800
+Subject: [PATCH 05/13] LU-1337 block: kernel 3.2 make_request_fn returns void
+
+3.2 request_queue.make_request_fn defined as function returns void.
+(kernel commit 5a7bbad27a410350e64a2d7f5ec18fc73836c14f)
+Add LC_HAVE_VOID_MAKE_REQUEST_FN/HAVE_VOID_MAKE_REQUEST_FN for check.
+
+Signed-off-by: Liu Xuezhao <xuezhao.liu@emc.com>
+Change-Id: I49a27873c1754addc9fef7c5f50cbf84592adf05
+---
+ lustre/autoconf/lustre-core.m4 | 24 ++++++++++++++++++++++++
+ lustre/include/linux/lustre_compat25.h | 8 ++++++++
+ lustre/llite/lloop.c | 9 +++++----
+ 3 files changed, 37 insertions(+), 4 deletions(-)
+
+diff --git a/lustre/autoconf/lustre-core.m4 b/lustre/autoconf/lustre-core.m4
+index a2d8efc..420d81e 100644
+--- a/lustre/autoconf/lustre-core.m4
++++ b/lustre/autoconf/lustre-core.m4
+@@ -1874,6 +1874,27 @@ LB_LINUX_TRY_COMPILE([
+ ])
+
+ #
++# 3.2 request_queue.make_request_fn defined as function returns with void
++# see kernel commit 5a7bbad27a410350e64a2d7f5ec18fc73836c14f
++#
++AC_DEFUN([LC_HAVE_VOID_MAKE_REQUEST_FN],
++[AC_MSG_CHECKING([if request_queue.make_request_fn returns void but not int])
++LB_LINUX_TRY_COMPILE([
++ #include <linux/blkdev.h>
++],[
++ int ret;
++ make_request_fn *mrf;
++ ret = mrf(NULL, NULL);
++],[
++ AC_MSG_RESULT([no])
++],[
++ AC_DEFINE(HAVE_VOID_MAKE_REQUEST_FN, 1,
++ [request_queue.make_request_fn returns void but not int])
++ AC_MSG_RESULT([yes])
++])
++])
++
++#
+ # 3.3 introduces migrate_mode.h and migratepage has 4 args
+ #
+ AC_DEFUN([LC_HAVE_MIGRATE_HEADER],
+@@ -2061,6 +2082,9 @@ AC_DEFUN([LC_PROG_LINUX],
+ LC_LM_XXX_LOCK_MANAGER_OPS
+ LC_INODE_DIO_WAIT
+
++ # 3.2
++ LC_HAVE_VOID_MAKE_REQUEST_FN
++
+ # 3.3
+ LC_HAVE_MIGRATE_HEADER
+ LC_MIGRATEPAGE_4ARGS
+diff --git a/lustre/include/linux/lustre_compat25.h b/lustre/include/linux/lustre_compat25.h
+index 914069a..2d0dd0e 100644
+--- a/lustre/include/linux/lustre_compat25.h
++++ b/lustre/include/linux/lustre_compat25.h
+@@ -831,5 +831,13 @@ static inline int ll_namei_to_lookup_intent_flag(int flag)
+ return flag;
+ }
+
++#ifdef HAVE_VOID_MAKE_REQUEST_FN
++# define ll_mrf_ret void
++# define LL_MRF_RETURN(rc) EXIT
++#else
++# define ll_mrf_ret int
++# define LL_MRF_RETURN(rc) RETURN(rc)
++#endif
++
+ #endif /* __KERNEL__ */
+ #endif /* _COMPAT25_H */
+diff --git a/lustre/llite/lloop.c b/lustre/llite/lloop.c
+index 5f4dec3..59814e6 100644
+--- a/lustre/llite/lloop.c
++++ b/lustre/llite/lloop.c
+@@ -338,7 +338,8 @@ static unsigned int loop_get_bio(struct lloop_device *lo, struct bio **req)
+ return count;
+ }
+
+-static int loop_make_request(struct request_queue *q, struct bio *old_bio)
++static ll_mrf_ret
++loop_make_request(struct request_queue *q, struct bio *old_bio)
+ {
+ struct lloop_device *lo = q->queuedata;
+ int rw = bio_rw(old_bio);
+@@ -366,10 +367,10 @@ static int loop_make_request(struct request_queue *q, struct bio *old_bio)
+ goto err;
+ }
+ loop_add_bio(lo, old_bio);
+- return 0;
++ LL_MRF_RETURN(0);
+ err:
+- cfs_bio_io_error(old_bio, old_bio->bi_size);
+- return 0;
++ cfs_bio_io_error(old_bio, old_bio->bi_size);
++ LL_MRF_RETURN(0);
+ }
+
+ #ifdef HAVE_REQUEST_QUEUE_UNPLUG_FN
+--
+1.7.12
+
diff --git a/sys-cluster/lustre/files/0006-LU-1337-vfs-kernel-3.2-protects-inode-i_nlink.patch b/sys-cluster/lustre/files/0006-LU-1337-vfs-kernel-3.2-protects-inode-i_nlink.patch
new file mode 100644
index 000000000..4866ce2dd
--- /dev/null
+++ b/sys-cluster/lustre/files/0006-LU-1337-vfs-kernel-3.2-protects-inode-i_nlink.patch
@@ -0,0 +1,194 @@
+From 7fefbc7487f55b0edaa7a85f0e5b9fea68d5ff15 Mon Sep 17 00:00:00 2001
+From: Liu Xuezhao <xuezhao.liu@emc.com>
+Date: Thu, 9 Aug 2012 10:31:10 +0800
+Subject: [PATCH 06/13] LU-1337 vfs: kernel 3.2 protects inode->i_nlink
+
+Kernel 3.2 protects inode->i_nlink from direct modification.
+Filesystems may only read i_nlink directly. They shall use the
+(set|clear|inc|drop)_nlink for modification.
+See kernel commit a78ef704a8dd430225955f0709b22d4a6ba21deb.
+
+This patch adds LC_HAVE_PROTECT_I_NLINK checking and implements
+set_nlink for old kernel, clear/inc/drop_nlink exists after 2.6.18
+so need not to be re-implemented.
+
+Signed-off-by: Liu Xuezhao <xuezhao.liu@emc.com>
+Change-Id: Ie958cb308291ecc48d409a1282fed7ea3549a561
+---
+ lustre/autoconf/lustre-core.m4 | 22 ++++++++++++++++++++++
+ lustre/include/linux/lustre_compat25.h | 8 ++++++++
+ lustre/llite/dcache.c | 4 ++--
+ lustre/llite/file.c | 2 +-
+ lustre/llite/llite_lib.c | 4 ++--
+ lustre/osd-ldiskfs/osd_handler.c | 12 ++++++------
+ 6 files changed, 41 insertions(+), 11 deletions(-)
+
+diff --git a/lustre/autoconf/lustre-core.m4 b/lustre/autoconf/lustre-core.m4
+index 420d81e..84f1678 100644
+--- a/lustre/autoconf/lustre-core.m4
++++ b/lustre/autoconf/lustre-core.m4
+@@ -1895,6 +1895,27 @@ LB_LINUX_TRY_COMPILE([
+ ])
+
+ #
++# 3.2 protects inode->i_nlink from direct modification
++# see kernel commit a78ef704a8dd430225955f0709b22d4a6ba21deb
++# at the same time, add set_nlink()
++#
++AC_DEFUN([LC_HAVE_PROTECT_I_NLINK],
++[AC_MSG_CHECKING([if inode->i_nlink is protected from direct modification])
++LB_LINUX_TRY_COMPILE([
++ #include <linux/fs.h>
++],[
++ struct inode i;
++ i.i_nlink = 0;
++],[
++ AC_MSG_RESULT([no])
++],[
++ AC_DEFINE(HAVE_PROTECT_I_NLINK, 1,
++ [inode->i_nlink is protected from direct modification])
++ AC_MSG_RESULT([yes])
++])
++])
++
++#
+ # 3.3 introduces migrate_mode.h and migratepage has 4 args
+ #
+ AC_DEFUN([LC_HAVE_MIGRATE_HEADER],
+@@ -2084,6 +2105,7 @@ AC_DEFUN([LC_PROG_LINUX],
+
+ # 3.2
+ LC_HAVE_VOID_MAKE_REQUEST_FN
++ LC_HAVE_PROTECT_I_NLINK
+
+ # 3.3
+ LC_HAVE_MIGRATE_HEADER
+diff --git a/lustre/include/linux/lustre_compat25.h b/lustre/include/linux/lustre_compat25.h
+index 2d0dd0e..7ead133 100644
+--- a/lustre/include/linux/lustre_compat25.h
++++ b/lustre/include/linux/lustre_compat25.h
+@@ -839,5 +839,13 @@ static inline int ll_namei_to_lookup_intent_flag(int flag)
+ # define LL_MRF_RETURN(rc) RETURN(rc)
+ #endif
+
++#include <linux/fs.h>
++#ifndef HAVE_PROTECT_I_NLINK
++static inline void set_nlink(struct inode *inode, unsigned int nlink)
++{
++ inode->i_nlink = nlink;
++}
++#endif
++
+ #endif /* __KERNEL__ */
+ #endif /* _COMPAT25_H */
+diff --git a/lustre/llite/dcache.c b/lustre/llite/dcache.c
+index 14fb634..b507408 100644
+--- a/lustre/llite/dcache.c
++++ b/lustre/llite/dcache.c
+@@ -187,7 +187,7 @@ static int ll_ddelete(HAVE_D_DELETE_CONST struct dentry *de)
+ /* if not ldlm lock for this inode, set i_nlink to 0 so that
+ * this inode can be recycled later b=20433 */
+ if (de->d_inode && !find_cbdata(de->d_inode))
+- de->d_inode->i_nlink = 0;
++ clear_nlink(de->d_inode);
+ #endif
+
+ if (d_lustre_invalid((struct dentry *)de))
+@@ -687,7 +687,7 @@ void ll_d_iput(struct dentry *de, struct inode *inode)
+ {
+ LASSERT(inode);
+ if (!find_cbdata(inode))
+- inode->i_nlink = 0;
++ clear_nlink(inode);
+ iput(inode);
+ }
+
+diff --git a/lustre/llite/file.c b/lustre/llite/file.c
+index bf9ba2f..8840295 100644
+--- a/lustre/llite/file.c
++++ b/lustre/llite/file.c
+@@ -2315,7 +2315,7 @@ ldlm_mode_t ll_take_md_lock(struct inode *inode, __u64 bits,
+ static int ll_inode_revalidate_fini(struct inode *inode, int rc) {
+ if (rc == -ENOENT) { /* Already unlinked. Just update nlink
+ * and return success */
+- inode->i_nlink = 0;
++ clear_nlink(inode);
+ /* This path cannot be hit for regular files unless in
+ * case of obscure races, so no need to to validate
+ * size. */
+diff --git a/lustre/llite/llite_lib.c b/lustre/llite/llite_lib.c
+index 7f3ac28..07efcfc 100644
+--- a/lustre/llite/llite_lib.c
++++ b/lustre/llite/llite_lib.c
+@@ -1218,7 +1218,7 @@ int ll_md_setattr(struct dentry *dentry, struct md_op_data *op_data,
+ if (rc) {
+ ptlrpc_req_finished(request);
+ if (rc == -ENOENT) {
+- inode->i_nlink = 0;
++ clear_nlink(inode);
+ /* Unlinked special device node? Or just a race?
+ * Pretend we done everything. */
+ if (!S_ISREG(inode->i_mode) &&
+@@ -1724,7 +1724,7 @@ void ll_update_inode(struct inode *inode, struct lustre_md *md)
+ if (body->valid & OBD_MD_FLFLAGS)
+ inode->i_flags = ll_ext_to_inode_flags(body->flags);
+ if (body->valid & OBD_MD_FLNLINK)
+- inode->i_nlink = body->nlink;
++ set_nlink(inode, body->nlink);
+ if (body->valid & OBD_MD_FLRDEV)
+ inode->i_rdev = old_decode_dev(body->rdev);
+
+diff --git a/lustre/osd-ldiskfs/osd_handler.c b/lustre/osd-ldiskfs/osd_handler.c
+index 1c37bd9..ec9dfb6 100644
+--- a/lustre/osd-ldiskfs/osd_handler.c
++++ b/lustre/osd-ldiskfs/osd_handler.c
+@@ -1518,7 +1518,7 @@ static int osd_inode_setattr(const struct lu_env *env,
+ if (bits & LA_GID)
+ inode->i_gid = attr->la_gid;
+ if (bits & LA_NLINK)
+- inode->i_nlink = attr->la_nlink;
++ set_nlink(inode, attr->la_nlink);
+ if (bits & LA_RDEV)
+ inode->i_rdev = attr->la_rdev;
+
+@@ -2076,7 +2076,7 @@ static int osd_object_destroy(const struct lu_env *env,
+ LASSERT(osd_inode_unlinked(inode) ||
+ inode->i_nlink == 1);
+ cfs_spin_lock(&obj->oo_guard);
+- inode->i_nlink = 0;
++ clear_nlink(inode);
+ cfs_spin_unlock(&obj->oo_guard);
+ inode->i_sb->s_op->dirty_inode(inode);
+ } else {
+@@ -2283,11 +2283,11 @@ static int osd_object_ref_add(const struct lu_env *env,
+ * do not actually care whether this flag is set or not.
+ */
+ cfs_spin_lock(&obj->oo_guard);
+- inode->i_nlink++;
++ inc_nlink(inode);
+ if (S_ISDIR(inode->i_mode) && inode->i_nlink > 1) {
+ if (inode->i_nlink >= LDISKFS_LINK_MAX ||
+ inode->i_nlink == 2)
+- inode->i_nlink = 1;
++ set_nlink(inode, 1);
+ }
+ LASSERT(inode->i_nlink <= LDISKFS_LINK_MAX);
+ cfs_spin_unlock(&obj->oo_guard);
+@@ -2333,12 +2333,12 @@ static int osd_object_ref_del(const struct lu_env *env, struct dt_object *dt,
+
+ cfs_spin_lock(&obj->oo_guard);
+ LASSERT(inode->i_nlink > 0);
+- inode->i_nlink--;
++ drop_nlink(inode);
+ /* If this is/was a many-subdir directory (nlink > LDISKFS_LINK_MAX)
+ * then the nlink count is 1. Don't let it be set to 0 or the directory
+ * inode will be deleted incorrectly. */
+ if (S_ISDIR(inode->i_mode) && inode->i_nlink == 0)
+- inode->i_nlink++;
++ inc_nlink(inode);
+ cfs_spin_unlock(&obj->oo_guard);
+ inode->i_sb->s_op->dirty_inode(inode);
+ LINVRNT(osd_invariant(obj));
+--
+1.7.12
+
diff --git a/sys-cluster/lustre/files/0007-LU-1337-vfs-3.3-changes-super_operations-inode_opera.patch b/sys-cluster/lustre/files/0007-LU-1337-vfs-3.3-changes-super_operations-inode_opera.patch
new file mode 100644
index 000000000..43cc7842d
--- /dev/null
+++ b/sys-cluster/lustre/files/0007-LU-1337-vfs-3.3-changes-super_operations-inode_opera.patch
@@ -0,0 +1,217 @@
+From 87c734aec5ec3a73c8eeab425f501568b05874ba Mon Sep 17 00:00:00 2001
+From: Liu Xuezhao <xuezhao.liu@emc.com>
+Date: Thu, 19 Jul 2012 17:43:16 +0800
+Subject: [PATCH 07/13] LU-1337 vfs: 3.3 changes
+ super_operations/inode_operations
+
+1. Kernel 3.3 switchs super_operations to use dentry as parameter
+ (kernel commit 34c80b1d93e6e20ca9dea0baf583a5b5510d92d4).
+ Add LC_SUPEROPS_USE_DENTRY/HAVE_SUPEROPS_USE_DENTRY to check it.
+2. Kernel 3.3 switchs inode_operations to use umode_t as parameter
+ (kernel commit 1a67aafb5f72a436ca044293309fa7e6351d6a35).
+ Add LC_INODEOPS_USE_UMODE_T/HAVE_INODEOPS_USE_UMODE_T to check it.
+
+Signed-off-by: Liu Xuezhao <xuezhao.liu@emc.com>
+Change-Id: I7564506cf4365c8da113a81058f68b9ef8b092a4
+---
+ lustre/autoconf/lustre-core.m4 | 57 ++++++++++++++++++++++++++++++++++
+ lustre/include/linux/lustre_compat25.h | 6 ++++
+ lustre/llite/llite_internal.h | 4 +++
+ lustre/llite/llite_lib.c | 13 ++++++--
+ lustre/llite/namei.c | 13 +++++---
+ 5 files changed, 87 insertions(+), 6 deletions(-)
+
+diff --git a/lustre/autoconf/lustre-core.m4 b/lustre/autoconf/lustre-core.m4
+index 84f1678..15f58ab 100644
+--- a/lustre/autoconf/lustre-core.m4
++++ b/lustre/autoconf/lustre-core.m4
+@@ -1954,6 +1954,61 @@ LB_LINUX_TRY_COMPILE([
+ ])
+
+ #
++# 3.3 switchs super_operations to use dentry as parameter (but not vfsmount)
++# see kernel commit 34c80b1d93e6e20ca9dea0baf583a5b5510d92d4
++#
++AC_DEFUN([LC_SUPEROPS_USE_DENTRY],
++[AC_MSG_CHECKING([if super_operations use dentry as parameter])
++tmp_flags="$EXTRA_KCFLAGS"
++EXTRA_KCFLAGS="-Werror"
++LB_LINUX_TRY_COMPILE([
++ #include <linux/fs.h>
++ int show_options(struct seq_file *seq, struct dentry *root){
++ return 0;
++ }
++],[
++ struct super_operations ops;
++ ops.show_options = show_options;
++],[
++ AC_DEFINE(HAVE_SUPEROPS_USE_DENTRY, 1,
++ [super_operations use dentry as parameter])
++ AC_MSG_RESULT([yes])
++],[
++ AC_MSG_RESULT([no])
++])
++EXTRA_KCFLAGS="$tmp_flags"
++])
++
++#
++# 3.3 switchs inode_operations to use umode_t as parameter (but not int)
++# see kernel commit 1a67aafb5f72a436ca044293309fa7e6351d6a35
++#
++AC_DEFUN([LC_INODEOPS_USE_UMODE_T],
++[AC_MSG_CHECKING([if inode_operations use umode_t as parameter])
++tmp_flags="$EXTRA_KCFLAGS"
++EXTRA_KCFLAGS="-Werror"
++LB_LINUX_TRY_COMPILE([
++ #include <linux/fs.h>
++ #include <linux/types.h>
++ int my_mknod(struct inode *dir, struct dentry *dchild,
++ umode_t mode, dev_t dev)
++ {
++ return 0;
++ }
++],[
++ struct inode_operations ops;
++ ops.mknod = my_mknod;
++],[
++ AC_DEFINE(HAVE_INODEOPS_USE_UMODE_T, 1,
++ [inode_operations use umode_t as parameter])
++ AC_MSG_RESULT([yes])
++],[
++ AC_MSG_RESULT([no])
++])
++EXTRA_KCFLAGS="$tmp_flags"
++])
++
++#
+ # LC_PROG_LINUX
+ #
+ # Lustre linux kernel checks
+@@ -2110,6 +2165,8 @@ AC_DEFUN([LC_PROG_LINUX],
+ # 3.3
+ LC_HAVE_MIGRATE_HEADER
+ LC_MIGRATEPAGE_4ARGS
++ LC_SUPEROPS_USE_DENTRY
++ LC_INODEOPS_USE_UMODE_T
+
+ #
+ if test x$enable_server = xyes ; then
+diff --git a/lustre/include/linux/lustre_compat25.h b/lustre/include/linux/lustre_compat25.h
+index 7ead133..070ad83 100644
+--- a/lustre/include/linux/lustre_compat25.h
++++ b/lustre/include/linux/lustre_compat25.h
+@@ -847,5 +847,11 @@ static inline void set_nlink(struct inode *inode, unsigned int nlink)
+ }
+ #endif
+
++#ifdef HAVE_INODEOPS_USE_UMODE_T
++# define ll_umode_t umode_t
++#else
++# define ll_umode_t int
++#endif
++
+ #endif /* __KERNEL__ */
+ #endif /* _COMPAT25_H */
+diff --git a/lustre/llite/llite_internal.h b/lustre/llite/llite_internal.h
+index a1c02e5..a942134 100644
+--- a/lustre/llite/llite_internal.h
++++ b/lustre/llite/llite_internal.h
+@@ -830,7 +830,11 @@ void ll_umount_begin(struct vfsmount *vfsmnt, int flags);
+ void ll_umount_begin(struct super_block *sb);
+ #endif
+ int ll_remount_fs(struct super_block *sb, int *flags, char *data);
++#ifdef HAVE_SUPEROPS_USE_DENTRY
++int ll_show_options(struct seq_file *seq, struct dentry *dentry);
++#else
+ int ll_show_options(struct seq_file *seq, struct vfsmount *vfs);
++#endif
+ int ll_prep_inode(struct inode **inode, struct ptlrpc_request *req,
+ struct super_block *);
+ void lustre_dump_dentry(struct dentry *, int recur);
+diff --git a/lustre/llite/llite_lib.c b/lustre/llite/llite_lib.c
+index 07efcfc..18246ac 100644
+--- a/lustre/llite/llite_lib.c
++++ b/lustre/llite/llite_lib.c
+@@ -2294,12 +2294,21 @@ void ll_finish_md_op_data(struct md_op_data *op_data)
+ OBD_FREE_PTR(op_data);
+ }
+
++#ifdef HAVE_SUPEROPS_USE_DENTRY
++int ll_show_options(struct seq_file *seq, struct dentry *dentry)
++#else
+ int ll_show_options(struct seq_file *seq, struct vfsmount *vfs)
++#endif
+ {
+ struct ll_sb_info *sbi;
+
+- LASSERT((seq != NULL) && (vfs != NULL));
+- sbi = ll_s2sbi(vfs->mnt_sb);
++#ifdef HAVE_SUPEROPS_USE_DENTRY
++ LASSERT((seq != NULL) && (dentry != NULL));
++ sbi = ll_s2sbi(dentry->d_sb);
++#else
++ LASSERT((seq != NULL) && (vfs != NULL));
++ sbi = ll_s2sbi(vfs->mnt_sb);
++#endif
+
+ if (sbi->ll_flags & LL_SBI_NOLCK)
+ seq_puts(seq, ",nolock");
+diff --git a/lustre/llite/namei.c b/lustre/llite/namei.c
+index 036674f..a439e2f 100644
+--- a/lustre/llite/namei.c
++++ b/lustre/llite/namei.c
+@@ -815,7 +815,7 @@ static int ll_mknod_generic(struct inode *dir, struct qstr *name, int mode,
+ }
+
+ static int ll_create_nd(struct inode *dir, struct dentry *dentry,
+- int mode, struct nameidata *nd)
++ ll_umode_t mode, struct nameidata *nd)
+ {
+ struct lookup_intent *it = ll_d2d(dentry)->lld_it;
+ int rc;
+@@ -1128,8 +1128,8 @@ static int ll_rename_generic(struct inode *src, struct dentry *src_dparent,
+ RETURN(err);
+ }
+
+-static int ll_mknod(struct inode *dir, struct dentry *dchild, int mode,
+- ll_dev_t rdev)
++static int ll_mknod(struct inode *dir, struct dentry *dchild,
++ ll_umode_t mode, ll_dev_t rdev)
+ {
+ return ll_mknod_generic(dir, &dchild->d_name, mode,
+ old_encode_dev(rdev), dchild);
+@@ -1139,25 +1139,30 @@ static int ll_unlink(struct inode * dir, struct dentry *dentry)
+ {
+ return ll_unlink_generic(dir, NULL, dentry, &dentry->d_name);
+ }
+-static int ll_mkdir(struct inode *dir, struct dentry *dentry, int mode)
++
++static int ll_mkdir(struct inode *dir, struct dentry *dentry, ll_umode_t mode)
+ {
+ return ll_mkdir_generic(dir, &dentry->d_name, mode, dentry);
+ }
++
+ static int ll_rmdir(struct inode *dir, struct dentry *dentry)
+ {
+ return ll_rmdir_generic(dir, NULL, dentry, &dentry->d_name);
+ }
++
+ static int ll_symlink(struct inode *dir, struct dentry *dentry,
+ const char *oldname)
+ {
+ return ll_symlink_generic(dir, &dentry->d_name, oldname, dentry);
+ }
++
+ static int ll_link(struct dentry *old_dentry, struct inode *dir,
+ struct dentry *new_dentry)
+ {
+ return ll_link_generic(old_dentry->d_inode, dir, &new_dentry->d_name,
+ new_dentry);
+ }
++
+ static int ll_rename(struct inode *old_dir, struct dentry *old_dentry,
+ struct inode *new_dir, struct dentry *new_dentry)
+ {
+--
+1.7.12
+
diff --git a/sys-cluster/lustre/files/0008-LU-1337-kernel-remove-unnecessary-includings-of-syst.patch b/sys-cluster/lustre/files/0008-LU-1337-kernel-remove-unnecessary-includings-of-syst.patch
new file mode 100644
index 000000000..5b22c94a9
--- /dev/null
+++ b/sys-cluster/lustre/files/0008-LU-1337-kernel-remove-unnecessary-includings-of-syst.patch
@@ -0,0 +1,211 @@
+From 3d5f9b7679cfc5bb0a1c21c232478c17cfeb77e2 Mon Sep 17 00:00:00 2001
+From: Liu Xuezhao <xuezhao.liu@emc.com>
+Date: Mon, 16 Jul 2012 11:08:56 +0800
+Subject: [PATCH 08/13] LU-1337 kernel: remove unnecessary includings of
+ system.h
+
+<asm/system.h> is removed in kernel 3.4, and it is indeed not needed.
+
+Signed-off-by: Liu Xuezhao <xuezhao.liu@emc.com>
+Change-Id: Ic4d0a086656c5dfb05669aae40680b41e8ea00c7
+---
+ libcfs/include/libcfs/linux/kp30.h | 1 -
+ libcfs/libcfs/linux/linux-debug.c | 1 -
+ libcfs/libcfs/linux/linux-proc.c | 1 -
+ lnet/klnds/mxlnd/mxlnd.h | 1 -
+ lnet/klnds/o2iblnd/o2iblnd.h | 1 -
+ lnet/klnds/ptllnd/ptllnd.h | 1 -
+ lnet/klnds/qswlnd/qswlnd.h | 1 -
+ lnet/klnds/ralnd/ralnd.h | 1 -
+ lnet/klnds/socklnd/socklnd_lib-linux.h | 1 -
+ lustre/llite/llite_mmap.c | 1 -
+ lustre/llite/rw.c | 1 -
+ lustre/llite/rw26.c | 1 -
+ lustre/mdt/mdt_identity.c | 1 -
+ lustre/mdt/mdt_idmap.c | 1 -
+ lustre/obdclass/linux/linux-module.c | 1 -
+ 15 files changed, 15 deletions(-)
+
+diff --git a/libcfs/include/libcfs/linux/kp30.h b/libcfs/include/libcfs/linux/kp30.h
+index 2e1ead7..b8c0aff 100644
+--- a/libcfs/include/libcfs/linux/kp30.h
++++ b/libcfs/include/libcfs/linux/kp30.h
+@@ -45,7 +45,6 @@
+ #include <linux/init.h>
+ #include <linux/errno.h>
+ #include <linux/unistd.h>
+-#include <asm/system.h>
+ #include <linux/kmod.h>
+ #include <linux/notifier.h>
+ #include <linux/fs.h>
+diff --git a/libcfs/libcfs/linux/linux-debug.c b/libcfs/libcfs/linux/linux-debug.c
+index 9fc64e6..5ff5771 100644
+--- a/libcfs/libcfs/linux/linux-debug.c
++++ b/libcfs/libcfs/linux/linux-debug.c
+@@ -51,7 +51,6 @@
+ #endif
+ #include <linux/unistd.h>
+ #include <linux/interrupt.h>
+-#include <asm/system.h>
+ #include <asm/uaccess.h>
+ #include <linux/completion.h>
+
+diff --git a/libcfs/libcfs/linux/linux-proc.c b/libcfs/libcfs/linux/linux-proc.c
+index 5294e08..e9c5018 100644
+--- a/libcfs/libcfs/linux/linux-proc.c
++++ b/libcfs/libcfs/linux/linux-proc.c
+@@ -50,7 +50,6 @@
+ #include <net/sock.h>
+ #include <linux/uio.h>
+
+-#include <asm/system.h>
+ #include <asm/uaccess.h>
+
+ #include <linux/fs.h>
+diff --git a/lnet/klnds/mxlnd/mxlnd.h b/lnet/klnds/mxlnd/mxlnd.h
+index 69b2978..fdb0942 100644
+--- a/lnet/klnds/mxlnd/mxlnd.h
++++ b/lnet/klnds/mxlnd/mxlnd.h
+@@ -49,7 +49,6 @@
+ #include <linux/uio.h>
+ #include <linux/fs.h>
+
+-#include <asm/system.h>
+ #include <asm/uaccess.h>
+ #include <asm/io.h>
+
+diff --git a/lnet/klnds/o2iblnd/o2iblnd.h b/lnet/klnds/o2iblnd/o2iblnd.h
+index ce80d76..f3add0b 100644
+--- a/lnet/klnds/o2iblnd/o2iblnd.h
++++ b/lnet/klnds/o2iblnd/o2iblnd.h
+@@ -47,7 +47,6 @@
+ #include <linux/unistd.h>
+ #include <linux/uio.h>
+
+-#include <asm/system.h>
+ #include <asm/uaccess.h>
+ #include <asm/io.h>
+
+diff --git a/lnet/klnds/ptllnd/ptllnd.h b/lnet/klnds/ptllnd/ptllnd.h
+index c51d82d..7862952 100644
+--- a/lnet/klnds/ptllnd/ptllnd.h
++++ b/lnet/klnds/ptllnd/ptllnd.h
+@@ -45,7 +45,6 @@
+ #include <linux/unistd.h>
+ #include <linux/uio.h>
+
+-#include <asm/system.h>
+ #include <asm/uaccess.h>
+ #include <asm/io.h>
+
+diff --git a/lnet/klnds/qswlnd/qswlnd.h b/lnet/klnds/qswlnd/qswlnd.h
+index 33e44b0..14a2845 100644
+--- a/lnet/klnds/qswlnd/qswlnd.h
++++ b/lnet/klnds/qswlnd/qswlnd.h
+@@ -55,7 +55,6 @@
+ #include <net/sock.h>
+ #include <linux/uio.h>
+
+-#include <asm/system.h>
+ #include <asm/uaccess.h>
+
+ #include <linux/fs.h>
+diff --git a/lnet/klnds/ralnd/ralnd.h b/lnet/klnds/ralnd/ralnd.h
+index fbea48d..606e8cd 100644
+--- a/lnet/klnds/ralnd/ralnd.h
++++ b/lnet/klnds/ralnd/ralnd.h
+@@ -45,7 +45,6 @@
+ #include <linux/unistd.h>
+ #include <linux/uio.h>
+
+-#include <asm/system.h>
+ #include <asm/uaccess.h>
+ #include <asm/io.h>
+
+diff --git a/lnet/klnds/socklnd/socklnd_lib-linux.h b/lnet/klnds/socklnd/socklnd_lib-linux.h
+index 2a943c0..41ba9c3 100644
+--- a/lnet/klnds/socklnd/socklnd_lib-linux.h
++++ b/lnet/klnds/socklnd/socklnd_lib-linux.h
+@@ -50,7 +50,6 @@
+ #include <linux/uio.h>
+ #include <linux/if.h>
+
+-#include <asm/system.h>
+ #include <asm/uaccess.h>
+ #include <asm/irq.h>
+
+diff --git a/lustre/llite/llite_mmap.c b/lustre/llite/llite_mmap.c
+index 2549bad..5310b14 100644
+--- a/lustre/llite/llite_mmap.c
++++ b/lustre/llite/llite_mmap.c
+@@ -41,7 +41,6 @@
+ #include <linux/errno.h>
+ #include <linux/unistd.h>
+ #include <linux/version.h>
+-#include <asm/system.h>
+ #include <asm/uaccess.h>
+
+ #include <linux/fs.h>
+diff --git a/lustre/llite/rw.c b/lustre/llite/rw.c
+index 310cf45..76e259d 100644
+--- a/lustre/llite/rw.c
++++ b/lustre/llite/rw.c
+@@ -45,7 +45,6 @@
+ #include <linux/errno.h>
+ #include <linux/unistd.h>
+ #include <linux/version.h>
+-#include <asm/system.h>
+ #include <asm/uaccess.h>
+
+ #include <linux/fs.h>
+diff --git a/lustre/llite/rw26.c b/lustre/llite/rw26.c
+index 917ba3f..83cbe55 100644
+--- a/lustre/llite/rw26.c
++++ b/lustre/llite/rw26.c
+@@ -45,7 +45,6 @@
+ #include <linux/errno.h>
+ #include <linux/unistd.h>
+ #include <linux/version.h>
+-#include <asm/system.h>
+ #include <asm/uaccess.h>
+
+ #ifdef HAVE_MIGRATE_H
+diff --git a/lustre/mdt/mdt_identity.c b/lustre/mdt/mdt_identity.c
+index 23c7ce4..0e2a3e2 100644
+--- a/lustre/mdt/mdt_identity.c
++++ b/lustre/mdt/mdt_identity.c
+@@ -50,7 +50,6 @@
+ #include <linux/errno.h>
+ #include <linux/version.h>
+ #include <linux/unistd.h>
+-#include <asm/system.h>
+ #include <asm/uaccess.h>
+ #include <linux/fs.h>
+ #include <linux/stat.h>
+diff --git a/lustre/mdt/mdt_idmap.c b/lustre/mdt/mdt_idmap.c
+index 2b50225..68f4391 100644
+--- a/lustre/mdt/mdt_idmap.c
++++ b/lustre/mdt/mdt_idmap.c
+@@ -48,7 +48,6 @@
+ #include <linux/errno.h>
+ #include <linux/version.h>
+ #include <linux/unistd.h>
+-#include <asm/system.h>
+ #include <asm/uaccess.h>
+ #include <linux/fs.h>
+ #include <linux/stat.h>
+diff --git a/lustre/obdclass/linux/linux-module.c b/lustre/obdclass/linux/linux-module.c
+index af3fd9a..cae8397 100644
+--- a/lustre/obdclass/linux/linux-module.c
++++ b/lustre/obdclass/linux/linux-module.c
+@@ -62,7 +62,6 @@
+ #include <linux/highmem.h>
+ #include <asm/io.h>
+ #include <asm/ioctls.h>
+-#include <asm/system.h>
+ #include <asm/poll.h>
+ #include <asm/uaccess.h>
+ #include <linux/miscdevice.h>
+--
+1.7.12
+
diff --git a/sys-cluster/lustre/files/0009-LU-1337-vfs-kernel-3.4-touch_atime-switchs-to-1-argu.patch b/sys-cluster/lustre/files/0009-LU-1337-vfs-kernel-3.4-touch_atime-switchs-to-1-argu.patch
new file mode 100644
index 000000000..9e4311797
--- /dev/null
+++ b/sys-cluster/lustre/files/0009-LU-1337-vfs-kernel-3.4-touch_atime-switchs-to-1-argu.patch
@@ -0,0 +1,89 @@
+From 9e6789a41f3b1afd1a8a2575a4abbc49f0b10727 Mon Sep 17 00:00:00 2001
+From: Liu Xuezhao <xuezhao.liu@emc.com>
+Date: Thu, 9 Aug 2012 10:34:49 +0800
+Subject: [PATCH 09/13] LU-1337 vfs: kernel 3.4 touch_atime switchs to 1
+ argument
+
+touch_atime switchs to use 1 argument of struct path since
+kernel 3.4 (commit 68ac1234fb949b66941d94dce4157742799fc581).
+
+Add LC_TOUCH_ATIME_1ARG/HAVE_TOUCH_ATIME_1ARG to check it.
+
+Signed-off-by: Liu Xuezhao <xuezhao.liu@emc.com>
+Change-Id: I1a0478459538376761b96e1dc65328eeeef60d0f
+---
+ lustre/autoconf/lustre-core.m4 | 22 ++++++++++++++++++++++
+ lustre/llite/dir.c | 9 +++++++++
+ 2 files changed, 31 insertions(+)
+
+diff --git a/lustre/autoconf/lustre-core.m4 b/lustre/autoconf/lustre-core.m4
+index 15f58ab..3b3115c 100644
+--- a/lustre/autoconf/lustre-core.m4
++++ b/lustre/autoconf/lustre-core.m4
+@@ -2009,6 +2009,25 @@ EXTRA_KCFLAGS="$tmp_flags"
+ ])
+
+ #
++# 3.4 switchs touch_atime to struct path
++# see kernel commit 68ac1234fb949b66941d94dce4157742799fc581
++#
++AC_DEFUN([LC_TOUCH_ATIME_1ARG],
++[AC_MSG_CHECKING([if touch_atime use one argument])
++LB_LINUX_TRY_COMPILE([
++ #include <linux/fs.h>
++],[
++ touch_atime((struct path *)NULL);
++],[
++ AC_DEFINE(HAVE_TOUCH_ATIME_1ARG, 1,
++ [touch_atime use one argument])
++ AC_MSG_RESULT([yes])
++],[
++ AC_MSG_RESULT([no])
++])
++])
++
++#
+ # LC_PROG_LINUX
+ #
+ # Lustre linux kernel checks
+@@ -2168,6 +2187,9 @@ AC_DEFUN([LC_PROG_LINUX],
+ LC_SUPEROPS_USE_DENTRY
+ LC_INODEOPS_USE_UMODE_T
+
++ # 3.4
++ LC_TOUCH_ATIME_1ARG
++
+ #
+ if test x$enable_server = xyes ; then
+ AC_DEFINE(HAVE_SERVER_SUPPORT, 1, [support server])
+diff --git a/lustre/llite/dir.c b/lustre/llite/dir.c
+index f985625..f418631 100644
+--- a/lustre/llite/dir.c
++++ b/lustre/llite/dir.c
+@@ -500,6 +500,9 @@ int ll_readdir(struct file *filp, void *cookie, filldir_t filldir)
+ int hash64 = sbi->ll_flags & LL_SBI_64BIT_HASH;
+ struct page *page;
+ struct ll_dir_chain chain;
++#ifdef HAVE_TOUCH_ATIME_1ARG
++ struct path path;
++#endif
+ int done;
+ int rc;
+ ENTRY;
+@@ -627,7 +630,13 @@ int ll_readdir(struct file *filp, void *cookie, filldir_t filldir)
+ filp->f_pos = pos;
+ }
+ filp->f_version = inode->i_version;
++#ifdef HAVE_TOUCH_ATIME_1ARG
++ path.mnt = filp->f_vfsmnt;
++ path.dentry = filp->f_dentry;
++ touch_atime(&path);
++#else
+ touch_atime(filp->f_vfsmnt, filp->f_dentry);
++#endif
+
+ ll_dir_chain_fini(&chain);
+
+--
+1.7.12
+
diff --git a/sys-cluster/lustre/files/0010-LU-1337-vfs-kernel-3.4-converts-d_alloc_root-to-d_ma.patch b/sys-cluster/lustre/files/0010-LU-1337-vfs-kernel-3.4-converts-d_alloc_root-to-d_ma.patch
new file mode 100644
index 000000000..6f727170e
--- /dev/null
+++ b/sys-cluster/lustre/files/0010-LU-1337-vfs-kernel-3.4-converts-d_alloc_root-to-d_ma.patch
@@ -0,0 +1,128 @@
+From 9d5b2096640f5a9ed1d9307748cc79a35def59fb Mon Sep 17 00:00:00 2001
+From: Liu Xuezhao <xuezhao.liu@emc.com>
+Date: Mon, 16 Jul 2012 17:05:04 +0800
+Subject: [PATCH 10/13] LU-1337 vfs: kernel 3.4 converts d_alloc_root to
+ d_make_root
+
+kernel 3.4 converts d_alloc_root to d_make_root.
+(kernel commit 32991ab305ace7017c62f8eecbe5eb36dc32e13b)
+
+Add LC_HAVE_D_MAKE_ROOT/HAVE_D_MAKE_ROOT to ckeck it.
+
+Signed-off-by: Liu Xuezhao <xuezhao.liu@emc.com>
+Change-Id: I7ff1f0eff25495b655e650997016377ca0a200aa
+---
+ lustre/autoconf/lustre-core.m4 | 20 ++++++++++++++++++++
+ lustre/include/linux/lustre_compat25.h | 14 ++++++++++++++
+ lustre/llite/llite_lib.c | 7 ++++++-
+ lustre/obdclass/obd_mount.c | 13 ++++++-------
+ 4 files changed, 46 insertions(+), 8 deletions(-)
+
+diff --git a/lustre/autoconf/lustre-core.m4 b/lustre/autoconf/lustre-core.m4
+index 3b3115c..bc92b4f 100644
+--- a/lustre/autoconf/lustre-core.m4
++++ b/lustre/autoconf/lustre-core.m4
+@@ -2028,6 +2028,25 @@ LB_LINUX_TRY_COMPILE([
+ ])
+
+ #
++# 3.4 converts d_alloc_root to d_make_root
++# see kernel commit 32991ab305ace7017c62f8eecbe5eb36dc32e13b
++#
++AC_DEFUN([LC_HAVE_D_MAKE_ROOT],
++[AC_MSG_CHECKING([if have d_make_root])
++LB_LINUX_TRY_COMPILE([
++ #include <linux/fs.h>
++],[
++ d_make_root((struct inode *)NULL);
++],[
++ AC_DEFINE(HAVE_D_MAKE_ROOT, 1,
++ [have d_make_root])
++ AC_MSG_RESULT([yes])
++],[
++ AC_MSG_RESULT([no])
++])
++])
++
++#
+ # LC_PROG_LINUX
+ #
+ # Lustre linux kernel checks
+@@ -2189,6 +2208,7 @@ AC_DEFUN([LC_PROG_LINUX],
+
+ # 3.4
+ LC_TOUCH_ATIME_1ARG
++ LC_HAVE_D_MAKE_ROOT
+
+ #
+ if test x$enable_server = xyes ; then
+diff --git a/lustre/include/linux/lustre_compat25.h b/lustre/include/linux/lustre_compat25.h
+index 070ad83..b1d3056 100644
+--- a/lustre/include/linux/lustre_compat25.h
++++ b/lustre/include/linux/lustre_compat25.h
+@@ -853,5 +853,19 @@ static inline void set_nlink(struct inode *inode, unsigned int nlink)
+ # define ll_umode_t int
+ #endif
+
++#include <linux/dcache.h>
++#ifndef HAVE_D_MAKE_ROOT
++static inline struct dentry *d_make_root(struct inode *root_inode)
++{
++ struct dentry *res;
++
++ res = d_alloc_root(root_inode);
++ if (res == NULL)
++ iput(root_inode);
++
++ return res;
++}
++#endif
++
+ #endif /* __KERNEL__ */
+ #endif /* _COMPAT25_H */
+diff --git a/lustre/llite/llite_lib.c b/lustre/llite/llite_lib.c
+index 18246ac..f125461 100644
+--- a/lustre/llite/llite_lib.c
++++ b/lustre/llite/llite_lib.c
+@@ -539,7 +539,12 @@ static int client_common_fill_super(struct super_block *sb, char *md, char *dt,
+ NULL);
+ cl_sb_init(sb);
+
+- sb->s_root = d_alloc_root(root);
++ sb->s_root = d_make_root(root);
++ if (sb->s_root == NULL) {
++ CERROR("Can't make root dentry\n");
++ GOTO(out_lock_cn_cb, err = -ENOMEM);
++ }
++
+ #ifdef HAVE_DCACHE_LOCK
+ sb->s_root->d_op = &ll_d_root_ops;
+ #else
+diff --git a/lustre/obdclass/obd_mount.c b/lustre/obdclass/obd_mount.c
+index b2ec636..c2481bf 100644
+--- a/lustre/obdclass/obd_mount.c
++++ b/lustre/obdclass/obd_mount.c
+@@ -1609,14 +1609,13 @@ static int server_fill_super_common(struct super_block *sb)
+ /* apparently we need to be a directory for the mount to finish */
+ root->i_mode = S_IFDIR;
+
+- sb->s_root = d_alloc_root(root);
+- if (!sb->s_root) {
+- CERROR("Can't make root dentry\n");
+- iput(root);
+- RETURN(-EIO);
+- }
++ sb->s_root = d_make_root(root);
++ if (!sb->s_root) {
++ CERROR("Can't make root dentry\n");
++ RETURN(-EIO);
++ }
+
+- RETURN(0);
++ RETURN(0);
+ }
+
+ static int osd_start(struct lustre_sb_info *lsi, unsigned long mflags)
+--
+1.7.12
+
diff --git a/sys-cluster/lustre/files/0011-LU-1337-kernel-v3.5-defines-INVALID_UID.patch b/sys-cluster/lustre/files/0011-LU-1337-kernel-v3.5-defines-INVALID_UID.patch
new file mode 100644
index 000000000..7f20e90b1
--- /dev/null
+++ b/sys-cluster/lustre/files/0011-LU-1337-kernel-v3.5-defines-INVALID_UID.patch
@@ -0,0 +1,31 @@
+From 2c89f077618a5017fb61b57a8d358a5fb9542a5f Mon Sep 17 00:00:00 2001
+From: Peng Tao <tao.peng@emc.com>
+Date: Wed, 22 Aug 2012 16:55:22 +0800
+Subject: [PATCH 11/13] LU-1337 kernel: v3.5 defines INVALID_UID
+
+With kernel commit 7a4e7408, Lustre doesn't need to redefine
+INVALID_UID.
+
+Signed-off-by: Peng Tao <tao.peng@emc.com>
+Change-Id: I96b854cc51db735d8c985528c879fbeb5b049ab9
+---
+ lustre/include/lustre_cfg.h | 2 ++
+ 1 file changed, 2 insertions(+)
+
+diff --git a/lustre/include/lustre_cfg.h b/lustre/include/lustre_cfg.h
+index 7262be3..9d0fd52 100644
+--- a/lustre/include/lustre_cfg.h
++++ b/lustre/include/lustre_cfg.h
+@@ -286,7 +286,9 @@ static inline int lustre_cfg_sanity_check(void *buf, int len)
+
+ #include <lustre/lustre_user.h>
+
++#ifndef INVALID_UID
+ #define INVALID_UID (-1)
++#endif
+
+ /** @} cfg */
+
+--
+1.7.12
+
diff --git a/sys-cluster/lustre/files/0012-LU-1337-llite-kernel-3.5-renames-end_writeback-to-cl.patch b/sys-cluster/lustre/files/0012-LU-1337-llite-kernel-3.5-renames-end_writeback-to-cl.patch
new file mode 100644
index 000000000..3289fded2
--- /dev/null
+++ b/sys-cluster/lustre/files/0012-LU-1337-llite-kernel-3.5-renames-end_writeback-to-cl.patch
@@ -0,0 +1,90 @@
+From 9e05a2ac1524f4d7d3aa3f5cc6f278ee3e460b17 Mon Sep 17 00:00:00 2001
+From: Peng Tao <tao.peng@emc.com>
+Date: Wed, 22 Aug 2012 17:57:04 +0800
+Subject: [PATCH 12/13] LU-1337 llite: kernel 3.5 renames end_writeback to
+ clear_inode
+
+kernel commit dbd5768f8 renames end_writeback to clear_inode,
+which used to exist for ~2.6.36 kernels.
+
+Signed-off-by: Peng Tao <tao.peng@emc.com>
+Change-Id: I2435e820092085c0fb55539818f4bad9e48ff386
+---
+ lustre/autoconf/lustre-core.m4 | 22 ++++++++++++++++++++++
+ lustre/include/linux/lustre_compat25.h | 3 +++
+ lustre/llite/llite_lib.c | 4 +---
+ 3 files changed, 26 insertions(+), 3 deletions(-)
+
+diff --git a/lustre/autoconf/lustre-core.m4 b/lustre/autoconf/lustre-core.m4
+index bc92b4f..3f47dab 100644
+--- a/lustre/autoconf/lustre-core.m4
++++ b/lustre/autoconf/lustre-core.m4
+@@ -2047,6 +2047,25 @@ LB_LINUX_TRY_COMPILE([
+ ])
+
+ #
++# 3.5 renames end_writeback() back to clear_inode()...
++# see kernel commit dbd5768f87ff6fb0a4fe09c4d7b6c4a24de99430
++#
++AC_DEFUN([LC_HAVE_CLEAR_INODE],
++[AC_MSG_CHECKING([if have clear_inode])
++LB_LINUX_TRY_COMPILE([
++ #include <linux/fs.h>
++],[
++ clear_inode((struct inode *)NULL);
++],[
++ AC_DEFINE(HAVE_CLEAR_INODE, 1,
++ [have clear_inode])
++ AC_MSG_RESULT([yes])
++],[
++ AC_MSG_RESULT([no])
++])
++])
++
++#
+ # LC_PROG_LINUX
+ #
+ # Lustre linux kernel checks
+@@ -2210,6 +2229,9 @@ AC_DEFUN([LC_PROG_LINUX],
+ LC_TOUCH_ATIME_1ARG
+ LC_HAVE_D_MAKE_ROOT
+
++ # 3.5
++ LC_HAVE_CLEAR_INODE
++
+ #
+ if test x$enable_server = xyes ; then
+ AC_DEFINE(HAVE_SERVER_SUPPORT, 1, [support server])
+diff --git a/lustre/include/linux/lustre_compat25.h b/lustre/include/linux/lustre_compat25.h
+index b1d3056..b2bba25 100644
+--- a/lustre/include/linux/lustre_compat25.h
++++ b/lustre/include/linux/lustre_compat25.h
+@@ -866,6 +866,9 @@ static inline struct dentry *d_make_root(struct inode *root_inode)
+ return res;
+ }
+ #endif
++#ifndef HAVE_CLEAR_INODE
++#define clear_inode(i) end_writeback(i)
++#endif
+
+ #endif /* __KERNEL__ */
+ #endif /* _COMPAT25_H */
+diff --git a/lustre/llite/llite_lib.c b/lustre/llite/llite_lib.c
+index f125461..ccbaad0 100644
+--- a/lustre/llite/llite_lib.c
++++ b/lustre/llite/llite_lib.c
+@@ -1881,10 +1881,8 @@ void ll_delete_inode(struct inode *inode)
+
+ #ifdef HAVE_SBOPS_EVICT_INODE
+ ll_clear_inode(inode);
+- end_writeback(inode);
+-#else
+- clear_inode(inode);
+ #endif
++ clear_inode(inode);
+
+ EXIT;
+ }
+--
+1.7.12
+
diff --git a/sys-cluster/lustre/files/0013-LU-1337-kernel-3.5-kernel-encode_fh-passes-in-parent.patch b/sys-cluster/lustre/files/0013-LU-1337-kernel-3.5-kernel-encode_fh-passes-in-parent.patch
new file mode 100644
index 000000000..28f02823c
--- /dev/null
+++ b/sys-cluster/lustre/files/0013-LU-1337-kernel-3.5-kernel-encode_fh-passes-in-parent.patch
@@ -0,0 +1,88 @@
+From c3b73bfe1e157ec42be9015d231da66808483554 Mon Sep 17 00:00:00 2001
+From: Peng Tao <tao.peng@emc.com>
+Date: Thu, 23 Aug 2012 13:55:46 +0800
+Subject: [PATCH 13/13] LU-1337 kernel: 3.5 kernel encode_fh passes in parent
+ inode
+
+Changed by upsteam commit b0b0382b.
+
+Signed-off-by: Peng Tao <tao.peng@emc.com>
+Change-Id: I6d7223b934bfe4151371744ad72bdab6b170c700
+---
+ lustre/autoconf/lustre-core.m4 | 30 ++++++++++++++++++++++++++++++
+ lustre/llite/llite_nfs.c | 6 ++++++
+ 2 files changed, 36 insertions(+)
+
+diff --git a/lustre/autoconf/lustre-core.m4 b/lustre/autoconf/lustre-core.m4
+index 3f47dab..dbf7233 100644
+--- a/lustre/autoconf/lustre-core.m4
++++ b/lustre/autoconf/lustre-core.m4
+@@ -2066,6 +2066,35 @@ LB_LINUX_TRY_COMPILE([
+ ])
+
+ #
++# 3.5 encode_fh has parent inode passed in directly
++# see kernel commit b0b0382b
++#
++AC_DEFUN([LC_HAVE_ENCODE_FH_PARENT],
++[AC_MSG_CHECKING([if encode_fh have parent inode as parameter])
++tmp_flags="$EXTRA_KCFLAGS"
++EXTRA_KCFLAGS="-Werror"
++LB_LINUX_TRY_COMPILE([
++ #include <linux/exportfs.h>
++ #include <linux/fs.h>
++ #include <linux/types.h>
++ int ll_encode_fh(struct inode *i, __u32 *a, int *b, struct inode*p)
++ {
++ return 0;
++ }
++],[
++ struct export_operations exp_op;
++ exp_op.encode_fh = ll_encode_fh;
++],[
++ AC_DEFINE(HAVE_ENCODE_FH_PARENT, 1,
++ [have parent inode as parameter])
++ AC_MSG_RESULT([yes])
++],[
++ AC_MSG_RESULT([no])
++])
++EXTRA_KCFLAGS="$tmp_flags"
++])
++
++#
+ # LC_PROG_LINUX
+ #
+ # Lustre linux kernel checks
+@@ -2231,6 +2260,7 @@ AC_DEFUN([LC_PROG_LINUX],
+
+ # 3.5
+ LC_HAVE_CLEAR_INODE
++ LC_HAVE_ENCODE_FH_PARENT
+
+ #
+ if test x$enable_server = xyes ; then
+diff --git a/lustre/llite/llite_nfs.c b/lustre/llite/llite_nfs.c
+index 809a564..ba4f9f1 100644
+--- a/lustre/llite/llite_nfs.c
++++ b/lustre/llite/llite_nfs.c
+@@ -173,11 +173,17 @@ ll_iget_for_nfs(struct super_block *sb, struct lu_fid *fid, struct lu_fid *paren
+ * 2 -- contains child file handle and parent file handle;
+ * 255 -- error.
+ */
++#ifndef HAVE_ENCODE_FH_PARENT
+ static int ll_encode_fh(struct dentry *de, __u32 *fh, int *plen,
+ int connectable)
+ {
+ struct inode *inode = de->d_inode;
+ struct inode *parent = de->d_parent->d_inode;
++#else
++static int ll_encode_fh(struct inode *inode, __u32 *fh, int *plen,
++ struct inode *parent)
++{
++#endif
+ struct lustre_nfs_fid *nfs_fid = (void *)fh;
+ ENTRY;
+
+--
+1.7.12
+
diff --git a/sys-cluster/lustre/lustre-9999.ebuild b/sys-cluster/lustre/lustre-9999.ebuild
new file mode 100644
index 000000000..80ef89cf2
--- /dev/null
+++ b/sys-cluster/lustre/lustre-9999.ebuild
@@ -0,0 +1,73 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5_pre1
+
+WANT_AUTOCONF="2.5"
+WANT_AUTOMAKE="1.9"
+
+inherit git-2 autotools linux-mod linux-info toolchain-funcs
+
+DESCRIPTION="Lustre is a parallel distributed file system"
+HOMEPAGE="http://wiki.whamcloud.com/"
+EGIT_REPO_URI="git://git.whamcloud.com/fs/lustre-release.git"
+SRC_URI=""
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS=""
+IUSE="utils"
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+BUILD_PARAMS="-C ${KV_DIR} SUBDIRS=${S}"
+
+PATCHES=(
+"${FILESDIR}/0001-LU-1337-vfs-kernel-3.1-renames-lock-manager-ops.patch"
+"${FILESDIR}/0002-LU-1337-vfs-kernel-3.1-kills-inode-i_alloc_sem.patch"
+"${FILESDIR}/0003-LU-1337-vfs-kernel-3.1-changes-open_to_namei_flags.patch"
+"${FILESDIR}/0004-LU-1337-vfs-provides-ll_get_acl-to-i_op-get_acl.patch"
+"${FILESDIR}/0005-LU-1337-block-kernel-3.2-make_request_fn-returns-voi.patch"
+"${FILESDIR}/0006-LU-1337-vfs-kernel-3.2-protects-inode-i_nlink.patch"
+"${FILESDIR}/0007-LU-1337-vfs-3.3-changes-super_operations-inode_opera.patch"
+"${FILESDIR}/0008-LU-1337-kernel-remove-unnecessary-includings-of-syst.patch"
+"${FILESDIR}/0009-LU-1337-vfs-kernel-3.4-touch_atime-switchs-to-1-argu.patch"
+"${FILESDIR}/0010-LU-1337-vfs-kernel-3.4-converts-d_alloc_root-to-d_ma.patch"
+"${FILESDIR}/0011-LU-1337-kernel-v3.5-defines-INVALID_UID.patch"
+"${FILESDIR}/0012-LU-1337-llite-kernel-3.5-renames-end_writeback-to-cl.patch"
+"${FILESDIR}/0013-LU-1337-kernel-3.5-kernel-encode_fh-passes-in-parent.patch"
+)
+
+pkg_setup() {
+ linux-mod_pkg_setup
+ linux-info_pkg_setup
+ ARCH="$(tc-arch-kernel)"
+ ABI="${KERNEL_ABI}"
+}
+
+src_prepare() {
+ epatch ${PATCHES[@]}
+ apply_user_patches
+ sh ./autogen.sh
+}
+
+src_configure() {
+ econf \
+ --enable-client \
+ --disable-server \
+ --without-ldiskfs \
+ --disable-ldiskfs-build \
+ --with-linux="${KERNEL_DIR}" \
+ --with-linux-release=${KV_FULL} \
+ $(use_enable utils)
+}
+
+src_compile() {
+ default
+}
+
+src_install() {
+ default
+}
diff --git a/sys-cluster/lustre/metadata.xml b/sys-cluster/lustre/metadata.xml
new file mode 100644
index 000000000..29db6a2a1
--- /dev/null
+++ b/sys-cluster/lustre/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>cluster</herd>
+<longdescription>
+Lustre is a parallel distributed file system, generally used for large scale cluster computing
+</longdescription>
+<use>
+ <flag name='utils'>Enable lustre utils</flag>
+</use>
+</pkgmetadata>