Pull patch from upstream to use HDF5 >=1.8.13 with MPI (bug #512502).

Package-Manager: portage-2.2.10/cvs/Linux x86_64
Manifest-Sign-Key: 0x1A5D023975B0583D!

4 files changed, 230 insertions, 16 deletions

diff --git a/sci-libs/netcdf/ChangeLog b/sci-libs/netcdf/ChangeLog
index 97b1e8d15e7e..e2f66142f669 100644
--- a/sci-libs/netcdf/ChangeLog
+++ b/sci-libs/netcdf/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-libs/netcdf
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/netcdf/ChangeLog,v 1.114 2014/06/16 20:06:02 jauhien Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/netcdf/ChangeLog,v 1.115 2014/08/11 07:15:23 dev-zero Exp $
+
+*netcdf-4.3.2-r1 (11 Aug 2014)
+
+  11 Aug 2014; Tiziano Müller <dev-zero@gentoo.org>
+  +files/netcdf-4.3.2-HDF5-1.8.13+-compat.patch, +netcdf-4.3.2-r1.ebuild:
+  Pull patch from upstream to use HDF5 >=1.8.13 with MPI (bug #512502).
 
   16 Jun 2014; Jauhien Piatlicki <jauhien@gentoo.org> netcdf-4.1.3.ebuild,
   netcdf-4.2.1.1.ebuild, netcdf-4.3.0.ebuild, netcdf-4.3.1.1.ebuild,
diff --git a/sci-libs/netcdf/Manifest b/sci-libs/netcdf/Manifest
index 5778c5b2d6f8..a5a22f476825 100644
--- a/sci-libs/netcdf/Manifest
+++ b/sci-libs/netcdf/Manifest
@@ -5,6 +5,7 @@ AUX netcdf-4.1.1-fortran.patch 533 SHA256 0b7ed3bc01dfe23fe8eeace124efb3d49e7933
 AUX netcdf-4.1.1-implicits.patch 2588 SHA256 ffd6d894ea0dc29c56100d9c94fb22e51cb5fe775a41d02aa6367ccf2e091d95 SHA512 12b08ed39cca6a820c67c2ff34006f0b7511c237b596c77b60f35352eb6632c4f3682119a0ef5134176b19d77a86636d78b13e49fceb97130d4dd7d040104327 WHIRLPOOL d387b33ff8216895fce331b99e7d123937f4e6c5c4e37e4185801c74c604b124b5da3ce642ad7178f3780385e9bd3fa911b6fdc42fa7d64bf641ba3bda4957c7
 AUX netcdf-4.1.1-mpi-fix.patch 672 SHA256 8b891b1ce49442158acb77b48fdaeff203a803ec644dd16fa4e85c14b6debc7c SHA512 33846d90899b03bb4f24f9fcea3e46986d6850353c09eca2943ed039396ca03db6caa0df5ef718b2d712e6d136b5e95f255da4efea1cf3ba32bcc4ff43443cee WHIRLPOOL fb979577abac0ede837aa54ec08a5986fe026f590d8d968129be7f8b543a88abfa2bf5edcf94e857e4c9f380af24b106c6ce4be9930250ff7fa464e685b21173
 AUX netcdf-4.1.1-parallel-build.patch 1311 SHA256 e107feb3ae7df1381575e2ce1eac289871bc168ffb56470624a29959af394364 SHA512 934903780535729ce0dd37e74eca35e483ac2d8305cba2ae8efd04d80458ebccec9acfe14a43b7bdc906d716440bf8ee175ad37a78a4801e0c719352401f0b31 WHIRLPOOL 7499c1d8f67e7dbe3b8be51a1af68b5a3f707b90461f1d5a33d73dff853f949c90c2ba0e749d961c95c9d17e5c9abc60e06c05893532d2c4564670f72222d978
+AUX netcdf-4.3.2-HDF5-1.8.13+-compat.patch 5258 SHA256 76cd3f42be4fda5b5c60f6e03a6646e8792d0cd1c52bad61ae8044e694abd60c SHA512 aa54ec936aff884b105217a8c87f5d7722b8b76a4bdd8b8804366c6509abba9962fdcdbfda2361662fec3732be1a1c2b7a2ae8abea1862d2ad7fd3b0f3828f59 WHIRLPOOL 4628a0545ed6347ae8a3459a30c9ad94c9ae283cb66017b628851b31ebb05f94d57c616677943a83f21d2848342f2e6f243846de6bf9ac7a6dcdc6a900e8279a
 DIST netcdf-4.1.1.tar.gz 11201096 SHA256 7933d69d378c57f038375bae4dd78c52442a06e2647fce4b75c13a225e342fb0 SHA512 7817c7ad0f9d1e029099406f2fb3c6d47e151985fc18c36cdfd5ea95ba6b2524d3d2b6e92cc0d6ff574fc96356b564847b5015f5f0fda0dfd0c720331ba8c94e WHIRLPOOL df3b9a0083327571b74b0493e5862c62a8cf8f52a3f037139a05f41aee2d40b89a520d871d18b927c4220d10b2ae9a6f2a040a980fa5e2e6aaa448e5541273a1
 DIST netcdf-4.1.3.tar.gz 11097157 SHA256 315bc385b0750dd85b9a122194382db52f432dea1390de9f7afa11cf91869213 SHA512 e482796b42e3de728dfe7eab542d93548fdc2979a560dd52fd205d2233ff6bc0f0a02af23747c5156d24c32345b9bb32c0286f6d6689e1e20c9c04385cc1eea6 WHIRLPOOL 0ae32c82057d255ee55116e02c1a6467b5fe0ea3c1b7ce768a94a6820aa40ff66fa742926ea45a60f1fb07bf31687029aa2aa3d4dabcad4397540015687d3251
 DIST netcdf-4.2.1.1.tar.gz 4515856 SHA256 11779e5583960a3db13583cd34a4430265dec27318557f4c58b057d6bce070b7 SHA512 a50493c3ccc1b94c200ba3febe87f51b7f392cb402fb60df9a4c4cb7007eb9ebadbbce6c7a46056f107d584280af606c913a88efd44c0966ba6b47fc44696fc5 WHIRLPOOL b7715bce643d6a2559c130c1e6bcdab7d985fd44588acc990b3b11947bb677939fbdf5efcb0003d1072898c3c8b9b6422f4f2bbf6137a58ab819851290b38d01
@@ -16,23 +17,26 @@ EBUILD netcdf-4.1.3.ebuild 2142 SHA256 c91fadaa77f3ac45c3eacb7aea4813b58484c77d9
 EBUILD netcdf-4.2.1.1.ebuild 1221 SHA256 5411f4cabbf0e6771602192bb360a4c2e04bd6bb76360c1956482901bc98dff1 SHA512 8d9173dd162f04725e4ad012d8ee77243a3456bbfa5c2d2e58d5d3f9fccd2212645a63363048889ebe56e8d270217851abb5107a4b28ac9c438454e81a194823 WHIRLPOOL 666709f4c70f031a9e34ff6eb262d40335f5ce42974298a9d29dbec6938bf6c7bc664df71fc29879a660c5da0e53ca8c183031fbfa023402fcd43ddf262929cb
 EBUILD netcdf-4.3.0.ebuild 1286 SHA256 85534c3143260ebe12ca9490d1a4d8bb2c28f16a9b71f2bcbf218f640bc1767d SHA512 345bb4ed6c8de8da07936b88feff6e35d611dcd6b96b39d8f926359f8c20e47beae62e21ded65b440d35a7728172b056d71706e608a5f93bd97906662e17a1da WHIRLPOOL 55aa0c8ff7ddf00ef149f8d1be71f97195347d87bb0669b5016eed6dadcd04afb029e632023d6110d81db9434c89a4e307aeab94cdebbe038f444b5b5c3783a1
 EBUILD netcdf-4.3.1.1.ebuild 1275 SHA256 1076dec72780b9f2267fbe792eb2dc3843332af905a85466840eff0d5a88e2b3 SHA512 ba5bd0c4df2e78032f9ce6d40562e658f49e8a06fa5c98faa823449c60d62cfe9444d7beab90d15eaefeabfb7637d3d523e86bf26197da4388cb6118f165c080 WHIRLPOOL 513e3e8e951aebe02c475999f44003081930b37ddeea159b293daf3427f8d9dc383455bbba9db42b685bf8866fa80356780255cb1cfe448d5535295f425beb28
+EBUILD netcdf-4.3.2-r1.ebuild 1576 SHA256 7784776b616acd6510e33e410d5197eebab4b8013b9402dcbb0c23bc417131f5 SHA512 1c530a072ae97d0911b9b4958c3585864a847b987e07460d467bf445343a4402c7e68f9892b41b8c44e758349ab5ec35420c6870ae6e3b24914939503ed4e044 WHIRLPOOL 602ae5b7886e93ba477a74c32f68543c8eb63284efebd55eae5f6c67846db1236cbf3bad5f65ea6932701a9c0aec17affbe914b648652938dccf6ee63e149252
 EBUILD netcdf-4.3.2.ebuild 1532 SHA256 a752520ad57231e047bb2239e0ebfa5e0453ae678a69a7905aaa9c46581f5494 SHA512 af35a133095706b893905d903c9c92a6189d9594144f13788204cb8db7e964c626c44447ebaeabb9f0b8ad0c6e37edecb74f657e05d3d8fa1c6f356a9ee86c1f WHIRLPOOL 6de8627acbb70c92bbca9cc78060424d167178410bbe070f042a0535d8b33af91268644ed20bedfa46b3c7d722cb64717b6a9148091a090054b9dca06e69be21
-MISC ChangeLog 20365 SHA256 ab46ee60ecc4f73fd861461491186540b06b9e88e5ccdfecb02bb5dc9ee929c6 SHA512 a570f455070576579641e18a3723e3e56eb74d9351f4cf815a2d934894a84869fcb361bb326c23a7f544df89fa88ca30695a54f41960c2e0a58ee153bea72613 WHIRLPOOL ad62f289af825143e1a0d65f1852395cd564a59ba49c9979e0f8ce53c85d6738537a27a116d68955103cb1aed4430281b8838d6d576727c8a3e7bee39a99fbd7
+MISC ChangeLog 20598 SHA256 f4f56c37ea3fe6da137539fe4b8fccdb4075c4bd837afb2961ad7165babbdd22 SHA512 6e242520827c1e9b5283e5e8f48a586d109bee0c9112f7ed942a2d80ae95f61e2195a7612a0635448970ebf3ac139d8ab0dd2dfec92ddff90215b9e38e472ffe WHIRLPOOL e63e76c1be9f4ef3d62f51bb866fe3b645d7e1f2f3ce8daa81282cd3d3254347e19893f46a1cf6cce2c83af52d5a6d9f9d4b7262cd3a754f53d85fb25bb46d9c
 MISC metadata.xml 862 SHA256 9c27407b048f86a8cf1fd94d7bf30f68bfb742a6e793e1211c5900cab4e703cf SHA512 e16b6cf453424843cc4407540773f86ae1233843c3066dc230b6e58c1829ac0a5ddb4f8ed329f179a1ebfc63326c525811da276f01c533667da827f9194be43b WHIRLPOOL 8d3a040e1968b34eb850e1564a0e16353305fdf6728e38336a9cdbe230ecf9da101b44f77f7173d62108b8d86a983cb7675f7b5adaf9086967ceb104659eccb6
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diff --git a/sci-libs/netcdf/files/netcdf-4.3.2-HDF5-1.8.13+-compat.patch b/sci-libs/netcdf/files/netcdf-4.3.2-HDF5-1.8.13+-compat.patch
new file mode 100644
index 000000000000..783a5b06e991
--- /dev/null
+++ b/sci-libs/netcdf/files/netcdf-4.3.2-HDF5-1.8.13+-compat.patch
@@ -0,0 +1,145 @@
+From 435d8a03ed28bb5ad63aff12cbc6ab91531b6bc8 Mon Sep 17 00:00:00 2001
+From: Quincey Koziol <quincey@koziol.cc>
+Date: Wed, 7 May 2014 08:45:15 -0500
+Subject: [PATCH] Account for the HDF5 library not having the MPI-POSIX VFD
+ configured in.
+
+---
+ RELEASE_NOTES.md         |  2 ++
+ libsrc4/nc4file.c        | 40 ++++++++++++++++++++++++++++++++++++++++
+ nc_test4/tst_nc4perf.c   |  5 +++++
+ nc_test4/tst_parallel3.c |  5 +++++
+ 4 files changed, 52 insertions(+)
+
+diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md
+index 27f228c..1a69d17 100644
+--- a/RELEASE_NOTES.md
++++ b/RELEASE_NOTES.md
+@@ -9,6 +9,8 @@ This file contains a high-level description of this package's evolution. Release
+ 
+ ### 4.3.3-rc1 Released TBD
+ 
++* When the NC_MPIPOSIX flag is given for parallel I/O access and the HDF5 library does not have the MPI-POSIX VFD configured in, the NC_MPIPOSIX flag is transparently aliased to the NC_MPIIO flag within the netCDF-4 library.
++
+ ## 4.3.2 Released 2014-04-23
+ 
+ * As part of an ongoing project, the Doxygen-generated netcdf documentation has been reorganized.  The goal is to make the documentation easier to parse, and to eliminate redundant material.  This project is ongoing.
+diff --git a/libsrc4/nc4file.c b/libsrc4/nc4file.c
+index ec3bb0c..5c957be 100644
+--- a/libsrc4/nc4file.c
++++ b/libsrc4/nc4file.c
+@@ -308,12 +308,21 @@ nc4_create_file(const char *path, int cmode, MPI_Comm comm, MPI_Info info,
+ 	 if (H5Pset_fapl_mpio(fapl_id, comm, info) < 0)
+ 	    BAIL(NC_EPARINIT);
+       }
++#ifdef USE_PARALLEL_POSIX
+       else /* MPI/POSIX */
+       {
+ 	 LOG((4, "creating parallel file with MPI/posix"));
+ 	 if (H5Pset_fapl_mpiposix(fapl_id, comm, 0) < 0)
+ 	    BAIL(NC_EPARINIT);
+       }
++#else /* USE_PARALLEL_POSIX */
++      /* Should not happen! Code in NC4_create/NC4_open should alias the
++       *        NC_MPIPOSIX flag to NC_MPIIO, if the MPI-POSIX VFD is not
++       *        available in HDF5. -QAK
++       */
++      else /* MPI/POSIX */
++         BAIL(NC_EPARINIT);
++#endif /* USE_PARALLEL_POSIX */
+ 
+       /* Keep copies of the MPI Comm & Info objects */
+       if (MPI_SUCCESS != MPI_Comm_dup(comm, &nc4_info->comm))
+@@ -465,6 +474,17 @@ NC4_create(const char* path, int cmode, size_t initialsz, int basepe,
+       )
+       return NC_EINVAL;
+ 
++#ifndef USE_PARALLEL_POSIX
++/* If the HDF5 library has been compiled without the MPI-POSIX VFD, alias
++ *      the NC_MPIPOSIX flag to NC_MPIIO. -QAK
++ */
++   if(cmode & NC_MPIPOSIX)
++   {
++      cmode &= ~NC_MPIPOSIX;
++      cmode |= NC_MPIIO;
++   }
++#endif /* USE_PARALLEL_POSIX */
++
+    cmode |= NC_NETCDF4;
+ 
+    /* Apply default create format. */
+@@ -2168,12 +2188,21 @@ nc4_open_file(const char *path, int mode, MPI_Comm comm,
+ 	 if (H5Pset_fapl_mpio(fapl_id, comm, info) < 0)
+ 	    BAIL(NC_EPARINIT);
+       }
++#ifdef USE_PARALLEL_POSIX
+       else /* MPI/POSIX */
+       {
+ 	 LOG((4, "opening parallel file with MPI/posix"));
+ 	 if (H5Pset_fapl_mpiposix(fapl_id, comm, 0) < 0)
+ 	    BAIL(NC_EPARINIT);
+       }
++#else /* USE_PARALLEL_POSIX */
++      /* Should not happen! Code in NC4_create/NC4_open should alias the
++       *        NC_MPIPOSIX flag to NC_MPIIO, if the MPI-POSIX VFD is not
++       *        available in HDF5. -QAK
++       */
++      else /* MPI/POSIX */
++         BAIL(NC_EPARINIT);
++#endif /* USE_PARALLEL_POSIX */
+ 
+       /* Keep copies of the MPI Comm & Info objects */
+       if (MPI_SUCCESS != MPI_Comm_dup(comm, &nc4_info->comm))
+@@ -2640,6 +2669,17 @@ NC4_open(const char *path, int mode, int basepe, size_t *chunksizehintp,
+        (mode & NC_MPIIO && mode & NC_MPIPOSIX))
+       return NC_EINVAL;
+ 
++#ifndef USE_PARALLEL_POSIX
++/* If the HDF5 library has been compiled without the MPI-POSIX VFD, alias
++ *      the NC_MPIPOSIX flag to NC_MPIIO. -QAK
++ */
++   if(mode & NC_MPIPOSIX)
++   {
++      mode &= ~NC_MPIPOSIX;
++      mode |= NC_MPIIO;
++   }
++#endif /* USE_PARALLEL_POSIX */
++
+ 
+    /* Depending on the type of file, open it. */
+ 
+diff --git a/nc_test4/tst_nc4perf.c b/nc_test4/tst_nc4perf.c
+index 47af70e..3528b82 100644
+--- a/nc_test4/tst_nc4perf.c
++++ b/nc_test4/tst_nc4perf.c
+@@ -244,6 +244,11 @@ int test_pio_4d(size_t cache_size, int facc_type, int access_flag, MPI_Comm comm
+    return 0;
+ }
+ 
++/* Note: When the MPI-POSIX VFD is not compiled in to HDF5, the NC_MPIPOSIX
++ *      flag will be aliased to the NC_MPIIO flag within the library, and
++ *      therefore this test will exercise the aliasing, with the MPI-IO VFD,
++ *      under that configuration. -QAK
++ */
+ #define NUM_MODES 2
+ #define NUM_FACC 2
+ #define NUM_CHUNK_COMBOS_2D 3
+diff --git a/nc_test4/tst_parallel3.c b/nc_test4/tst_parallel3.c
+index 27f9c98..9fa534f 100644
+--- a/nc_test4/tst_parallel3.c
++++ b/nc_test4/tst_parallel3.c
+@@ -129,6 +129,11 @@ int main(int argc, char **argv)
+    if (mpi_rank == 0)
+       SUMMARIZE_ERR;
+ 
++/* Note: When the MPI-POSIX VFD is not compiled in to HDF5, the NC_MPIPOSIX
++ *      flag will be aliased to the NC_MPIIO flag within the library, and
++ *      therefore this test will exercise the aliasing, with the MPI-IO VFD,
++ *      under that configuration. -QAK
++ */
+    if (mpi_rank == 0)
+       printf("*** Testing parallel IO for raw-data with MPIPOSIX-IO (driver)...");
+    facc_type = NC_NETCDF4|NC_MPIPOSIX;
+-- 
+2.0.3
+
diff --git a/sci-libs/netcdf/netcdf-4.3.2-r1.ebuild b/sci-libs/netcdf/netcdf-4.3.2-r1.ebuild
new file mode 100644
index 000000000000..3155d923c1f6
--- /dev/null
+++ b/sci-libs/netcdf/netcdf-4.3.2-r1.ebuild
@@ -0,0 +1,59 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/netcdf/netcdf-4.3.2-r1.ebuild,v 1.1 2014/08/11 07:15:23 dev-zero Exp $
+
+EAPI=5
+
+inherit autotools-utils
+
+DESCRIPTION="Scientific library and interface for array oriented data access"
+HOMEPAGE="http://www.unidata.ucar.edu/software/netcdf/"
+SRC_URI="ftp://ftp.unidata.ucar.edu/pub/netcdf/${P}.tar.gz"
+
+LICENSE="UCAR-Unidata"
+SLOT="0/7"
+KEYWORDS="~amd64 ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="+dap examples hdf +hdf5 mpi static-libs szip test tools"
+
+RDEPEND="
+	dap? ( net-misc/curl:0= )
+	hdf? ( sci-libs/hdf:0= sci-libs/hdf5:0= )
+	hdf5? ( sci-libs/hdf5:0=[mpi=,szip=,zlib] )"
+DEPEND="${RDEPEND}"
+# doc generation is missing many doxygen files in tar ball
+#	doc? ( app-doc/doxygen[dot] )"
+
+REQUIRED_USE="test? ( tools ) szip? ( hdf5 ) mpi? ( hdf5 )"
+
+PATCHES=( "${FILESDIR}/${P}-HDF5-1.8.13+-compat.patch" )
+
+src_configure() {
+	#	--docdir="${EPREFIX}"/usr/share/doc/${PF}
+	#	$(use_enable doc doxygen)
+	local myeconfargs=(
+		--disable-examples
+		--disable-dap-remote-tests
+		$(use_enable dap)
+		$(use_enable hdf hdf4)
+		$(use_enable hdf5 netcdf-4)
+		$(use_enable tools utilities)
+	)
+	if use mpi; then
+		export CC=mpicc
+		myeconfargs+=( --enable-parallel )
+		use test && myeconfargs+=( --enable-parallel-tests )
+	fi
+	autotools-utils_src_configure
+}
+
+src_test() {
+	autotools-utils_src_test -j1
+}
+
+src_install() {
+	autotools-utils_src_install
+	if use examples; then
+		insinto /usr/share/doc/${PF}
+		doins -r examples
+	fi
+}