updated to latest upstream release with pvfs2 support and shared lib fixes

(Portage version: 2.1.4_rc1)

8 files changed, 245 insertions, 14 deletions

diff --git a/sci-libs/hdf5/ChangeLog b/sci-libs/hdf5/ChangeLog
index 0d6263a9f406..a77bba8390e4 100644
--- a/sci-libs/hdf5/ChangeLog
+++ b/sci-libs/hdf5/ChangeLog
@@ -1,6 +1,15 @@
 # ChangeLog for sci-libs/hdf5
-# Copyright 2002-2006 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/hdf5/ChangeLog,v 1.18 2006/11/01 00:49:30 dberkholz Exp $
+# Copyright 2002-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/hdf5/ChangeLog,v 1.19 2007/12/03 07:21:53 nerdboy Exp $
+
+*hdf5-1.6.6 (03 Dec 2007)
+
+  03 Dec 2007; Steve Arnold <nerdboy@gentoo.org> +files/hdf5-mpich2.patch,
+  +hdf5-1.6.6.ebuild:
+  Updated to latest upstream release, with mpi fixes, however, this version
+  is locked to mpich2-1.0.6 due to pvfs2, however, sparc is dropped until
+  the parallel I/O thing is worked out with other MPI libs.
+  Tests work, including mpi (but needs testing in a real cluster).
 
   01 Nov 2006; Donnie Berkholz <dberkholz@gentoo.org>; ChangeLog:
   Update for my nick change spyderous -> dberkholz.
diff --git a/sci-libs/hdf5/files/digest-hdf5-1.6.6 b/sci-libs/hdf5/files/digest-hdf5-1.6.6
new file mode 100644
index 000000000000..2e9897f5e920
--- /dev/null
+++ b/sci-libs/hdf5/files/digest-hdf5-1.6.6
@@ -0,0 +1,3 @@
+MD5 6c7fcc91f1579555d88bb10c6c9a33a9 hdf5-1.6.6.tar.gz 5299558
+RMD160 e7cf3f8d6aa5f34ef10cabf650ed43d644e54f1b hdf5-1.6.6.tar.gz 5299558
+SHA256 432d02f2d6988999d3d18caa6680af3cef14c8a7537c98e7adbaa8f873fba2a7 hdf5-1.6.6.tar.gz 5299558
diff --git a/sci-libs/hdf5/files/hdf5-mpich2.patch b/sci-libs/hdf5/files/hdf5-mpich2.patch
new file mode 100644
index 000000000000..3ed60bf264b0
--- /dev/null
+++ b/sci-libs/hdf5/files/hdf5-mpich2.patch
@@ -0,0 +1,17 @@
+--- config/mpich.orig	2005-10-26 13:31:41.000000000 -0700
++++ config/mpich	2007-11-04 15:46:53.000000000 -0800
+@@ -31,11 +31,13 @@
+ 	# $CC is an MPICH compiler. Grab the version numbers.
+         ccversion=`echo $ccversion | cut -f3 -d' '`
+ 	case "$ccversion" in
+-	    1.2.[0-5]*)
++	    # modified for mpich2 versioning
++	    1.0.[0-5]*)
+ 		hdf5_mpi_complex_derived_datatype_works='no'
+ 		;;
+ 	    *)
+ 		# assume okay
++		hdf5_mpi_complex_derived_datatype_works='yes'
+ 		;;
+ 	esac
+     fi
diff --git a/sci-libs/hdf5/hdf5-1.6.2.ebuild b/sci-libs/hdf5/hdf5-1.6.2.ebuild
index 62a3ceffbc5f..2f028a20d4e0 100644
--- a/sci-libs/hdf5/hdf5-1.6.2.ebuild
+++ b/sci-libs/hdf5/hdf5-1.6.2.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2006 Gentoo Foundation
+# Copyright 1999-2007 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/hdf5/hdf5-1.6.2.ebuild,v 1.5 2006/05/21 21:44:41 nerdboy Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/hdf5/hdf5-1.6.2.ebuild,v 1.6 2007/12/03 07:21:53 nerdboy Exp $
 
 inherit eutils
 
@@ -57,6 +57,6 @@ src_install() {
 		infodir=${D}/usr/share/info \
 		install || die "make install failed"
 
-	dodoc README.txt COPYING MANIFEST
+	dodoc README.txt MANIFEST
 	dohtml doc/html/*
 }
diff --git a/sci-libs/hdf5/hdf5-1.6.4.ebuild b/sci-libs/hdf5/hdf5-1.6.4.ebuild
index bebffd1bf7a8..3e53edefeb58 100644
--- a/sci-libs/hdf5/hdf5-1.6.4.ebuild
+++ b/sci-libs/hdf5/hdf5-1.6.4.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2006 Gentoo Foundation
+# Copyright 1999-2007 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/hdf5/hdf5-1.6.4.ebuild,v 1.8 2007/06/26 02:43:01 mr_bones_ Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/hdf5/hdf5-1.6.4.ebuild,v 1.9 2007/12/03 07:21:53 nerdboy Exp $
 
 inherit eutils
 
@@ -64,6 +64,6 @@ src_install() {
 		infodir=${D}/usr/share/info \
 		install || die "make install failed"
 
-	dodoc README.txt COPYING MANIFEST
+	dodoc README.txt MANIFEST
 	dohtml doc/html/*
 }
diff --git a/sci-libs/hdf5/hdf5-1.6.5-r1.ebuild b/sci-libs/hdf5/hdf5-1.6.5-r1.ebuild
index b27d51522c10..40d8049abec8 100644
--- a/sci-libs/hdf5/hdf5-1.6.5-r1.ebuild
+++ b/sci-libs/hdf5/hdf5-1.6.5-r1.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2006 Gentoo Foundation
+# Copyright 1999-2007 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/hdf5/hdf5-1.6.5-r1.ebuild,v 1.3 2006/07/13 05:05:56 nerdboy Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/hdf5/hdf5-1.6.5-r1.ebuild,v 1.4 2007/12/03 07:21:53 nerdboy Exp $
 
 inherit fortran eutils toolchain-funcs
 
@@ -161,7 +161,7 @@ src_install() {
 	fi
 
 	dobin ${S}/bin/iostats || die "dobin failed"
-	dodoc README.txt COPYING MANIFEST
+	dodoc README.txt MANIFEST
 	dohtml doc/html/*
 
 	if use mpi ; then
diff --git a/sci-libs/hdf5/hdf5-1.6.5.ebuild b/sci-libs/hdf5/hdf5-1.6.5.ebuild
index 1ce8ad82661f..4424e82e775e 100644
--- a/sci-libs/hdf5/hdf5-1.6.5.ebuild
+++ b/sci-libs/hdf5/hdf5-1.6.5.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2006 Gentoo Foundation
+# Copyright 1999-2007 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/hdf5/hdf5-1.6.5.ebuild,v 1.3 2006/06/24 16:13:48 nerdboy Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/hdf5/hdf5-1.6.5.ebuild,v 1.4 2007/12/03 07:21:53 nerdboy Exp $
 
 inherit eutils
 
@@ -77,7 +77,7 @@ src_install() {
 
 	dobin ${S}/bin/iostats || die "dobin failed"
 
-	dodoc README.txt COPYING MANIFEST
+	dodoc README.txt MANIFEST
 	dohtml doc/html/*
 
 	if use mpi ; then
diff --git a/sci-libs/hdf5/hdf5-1.6.6.ebuild b/sci-libs/hdf5/hdf5-1.6.6.ebuild
new file mode 100644
index 000000000000..38f8b482e04a
--- /dev/null
+++ b/sci-libs/hdf5/hdf5-1.6.6.ebuild
@@ -0,0 +1,202 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/hdf5/hdf5-1.6.6.ebuild,v 1.1 2007/12/03 07:21:53 nerdboy Exp $
+
+inherit eutils flag-o-matic fortran toolchain-funcs
+
+DESCRIPTION="General purpose library and file format for storing scientific data"
+HOMEPAGE="http://hdf.ncsa.uiuc.edu/HDF5/"
+SRC_URI="ftp://ftp.hdfgroup.org/HDF5/current/src/${P}.tar.gz"
+
+LICENSE="NCSA-HDF"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~ppc64 ~x86"
+# need to update szip to get alpha, ia64, etc back in here,
+IUSE="cxx debug fortran mpi ssl szip threads zlib "
+
+DEPEND="mpi? ( >=sys-cluster/mpich2-1.0.6
+		net-fs/nfs-utils )
+	ssl? ( dev-libs/openssl )
+	szip? ( sci-libs/szip )
+	zlib? ( sys-libs/zlib )
+	threads? ( virtual/libc )
+	sys-devel/gcc
+	sys-apps/coreutils
+	sys-apps/which
+	sys-process/time"
+
+RDEPEND="${DEPEND}
+	dev-lang/perl"
+
+pkg_setup() {
+	# The above gcc dep is a hack to insure at least one Fortran 90
+	# compiler is installed if the user enables fortran support.  Feel
+	# free to improve it...
+	if use fortran ; then
+	    if [ $(gcc-major-version) -ge 4 ] \
+		&& built_with_use sys-devel/gcc fortran ; then
+	    	    FORTRAN="gfortran"
+		    fortran_pkg_setup
+		    export F9X="gfortran"
+		    einfo "Configuring for GNU gfortran..."
+	    elif
+		test -d /opt/intel/fortran90 ; then
+		    FORTRAN="ifc"
+		    fortran_pkg_setup
+		    export F9X="ifc"
+		    einfo "Configuring for Intel fortran..."
+	    else
+		einfo "No F90 compiler found; please install either gcc 4 with"
+		einfo "fortran support or some other Fortran 90 compiler such"
+		einfo "as ifc or pgf90 (or disable fortran support)."
+		die "No usable Fortran 90 compiler found."
+	    fi
+	fi
+	if use mpi && ! built_with_use sys-cluster/mpich2 pvfs2 ; then
+	    ewarn "Your MPI library needs parallel IO support for HDF5. You"
+	    ewarn "must re-emerge mpich2 with USE=pvfs2."
+	    die "requires parallel IO support"
+	fi
+}
+
+src_unpack() {
+	unpack "${A}"
+	cd "${S}"
+
+	if use mpi; then
+	    # this is required for mpich2, and should be safe otherwise
+	    epatch "${FILESDIR}/${PN}-mpich2.patch" || die "mpich2 patch failed"
+	fi
+
+	sed -i -e "s/tail +/tail -n +/" "${S}"/bin/release \
+		"${S}"/tools/h5dump/testh5dump.sh.in
+
+}
+
+src_compile() {
+	local myconf="--with-pic --enable-shared"
+
+	if use cxx && ! use mpi ; then
+	    myconf="${myconf} --enable-cxx"
+	elif use cxx && use mpi ; then
+	    ewarn "C++ support is not compatible with the mpi interface."
+	    die "Please disable either cxx or mpi."
+	else
+	    myconf="${myconf} --disable-cxx"
+	fi
+
+	if use fortran && use mpi ; then
+	    ewarn "Requires Fortran 90 support in your mpi library..."
+	    myconf="${myconf} --enable-fortran --enable-parallel"
+	fi
+
+	use threads && myconf="${myconf} --with-pthread --enable-threadsafe"
+
+	if use debug; then
+	    myconf="${myconf} --enable-debug=all"
+	else
+	    myconf="${myconf} --enable-production"
+	fi
+
+	# NOTE: the hdf5 configure script has its own interpretation of
+	# the ARCH environment variable which conflicts with that of
+	# ebuild/emerge. As a work around, we save the ARCH variable as
+	# EBUILD_ARCH and restore it when we are done.
+	EBUILD_ARCH="${ARCH}"
+	unset ARCH
+
+	if use mpi ; then
+	    export NPROCS=1
+	    export CC="mpicc"
+	    export F9X="mpif90"
+	    export LIBS="$(sh pvfs2-config --libs) -lmpich"
+	    if built_with_use sys-cluster/mpich2 mpe ; then
+		myconf="${myconf} --with-mpe=/usr/include,/usr/$(get_libdir)"
+	    fi
+	    append-ldflags "${LIBS}"
+	fi
+
+	./configure --prefix=/usr "${myconf}" \
+		$(use_enable zlib) \
+		$(use_with ssl) \
+		--enable-linux-lfs  \
+		--sysconfdir=/etc \
+		--infodir=/usr/share/info \
+		--libdir=/usr/$(get_libdir) \
+		--mandir=/usr/share/man || die "configure failed"
+
+	# restore the ARCH environment variable
+	ARCH="${EBUILD_ARCH}"
+
+	# emake has occasional segfaults
+	make || die "make failed"
+}
+
+src_test() {
+	# make test is not reliable, and the mpi tests have a weird failure
+	export HDF5_Make_Ignore=yes
+	if use mpi ; then
+	    export HDF5_PARAPREFIX="${S}/testpar"
+	    export CC="/usr/bin/mpicc"
+	    install -g portage -o portage -m 0600 "${FILESDIR}"/mpd.conf "${HOME}"/.mpd.conf
+	    /usr/bin/mpd --daemon
+	fi
+	make check || die "make test failed"
+	use mpi && /usr/bin/mpdallexit
+	export HDF5_Make_Ignore=no
+}
+
+src_install() {
+	make \
+		prefix="${D}"usr \
+		mandir="${D}"usr/share/man \
+		docdir="${D}"usr/share/doc/"${PF}" \
+		libdir="${D}"usr/$(get_libdir) \
+		infodir="${D}usr"/share/info \
+		install || die "make install failed"
+
+	dolib.a "${S}"/tools/lib/.libs/libh5tools.a \
+	    "${S}"/test/.libs/libh5test.a || die "dolib.a failed"
+	insinto /usr/$(get_libdir)
+	doins "${S}"/tools/lib/libh5tools.la \
+	    "${S}"/test/libh5test.la || die "doins failed"
+	dolib.so" ${S}"/test/.libs/lib*so* || die "dolib.so failed"
+
+	exeinto /usr/bin
+	newexe "${S}"/bin/iostats iostats.pl || die "newexe failed"
+
+	dodoc README.txt MANIFEST
+	dohtml doc/html/*
+
+	if use mpi ; then
+	    mv "${D}"usr/bin/h5pcc "${D}"usr/bin/h5cc
+	fi
+	if use fortran ; then
+	    mv "${D}"usr/bin/h5pfc "${D}"usr/bin/h5fc
+	fi
+	# change the SHLIB default for C
+	dosed "s/SHLIB:-no/SHLIB:-yes/g" "${D}"usr/bin/h5cc || die "dosed failed"
+}
+
+pkg_postinst() {
+	elog
+	elog "There are currently 2 non-fatal test errors in the mpi tests,"
+	elog "however, all C++, Fortran, and other tests pass successfully."
+	elog "The only expected failure is currently in the PHDF5 section"
+	elog "under MPI functionality tests. The second section using the"
+	elog "MPIPOSIX driver should work, along with all other tests."
+	elog
+	elog "Suggested USE flags for fortran and mpi support using gfortran:"
+	elog "USE=\"fortran mpi -cxx\""
+	elog
+	ewarn "Note 1: currently testing pvfs2 support (with mpi).  Please"
+	ewarn "report any problems in the usual way."
+	elog
+	ewarn "Note 2: you'll need rawio support enabled in your kernel or"
+	ewarn "certain asynchronous IO operations will fail.  Either enable"
+	ewarn "the RAW driver (under Character Devices) or patch your kernel"
+	ewarn "with the new PAIO drivers and use libposix-aio.  See both:"
+	ewarn "http://sourceforge.net/projects/paiol  and"
+	ewarn "http://www.bullopensource.org/posix  for more info."
+	elog
+}