From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from pigeon.gentoo.org ([69.77.167.62] helo=lists.gentoo.org) by finch.gentoo.org with esmtp (Exim 4.60) (envelope-from ) id 1LSqeD-0000CF-JR for garchives@archives.gentoo.org; Fri, 30 Jan 2009 10:30:53 +0000 Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id D15ECE0403; Fri, 30 Jan 2009 10:30:52 +0000 (UTC) Received: from mail.uj.edu.pl (mail.uj.edu.pl [149.156.89.147]) by pigeon.gentoo.org (Postfix) with ESMTP id 7AB38E0410 for ; Fri, 30 Jan 2009 10:30:52 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-science@lists.gentoo.org Reply-to: gentoo-science@lists.gentoo.org MIME-version: 1.0 Content-type: multipart/mixed; boundary="Boundary_(ID_m0PjRbhtMLXbDCBR8C6mKg)" Received: from [149.156.87.132] by mail.uj.edu.pl (Sun Java(tm) System Messaging Server 6.3-5.02 (built Oct 12 2007; 32bit)) with ESMTPSA id <0KEA00JYN57CPL00@mail.uj.edu.pl> for gentoo-science@lists.gentoo.org; Fri, 30 Jan 2009 11:30:49 +0100 (CET) Message-id: <4982D6D8.9040408@mol.uj.edu.pl> Date: Fri, 30 Jan 2009 11:30:48 +0100 From: Janusz Mordarski Organization: =?ISO-8859-2?Q?Wydzia=B3_Biochemii=2C_Biofizyki_i_B?= =?ISO-8859-2?Q?iotechnologii_=2C_Uniwersytet_Jagiello=F1ski?= User-Agent: Icedove 1.5.0.14eol (X11/20090105) To: gentoo-science@lists.gentoo.org Subject: Re: [gentoo-science] sys-cluster infiniband , mpi related soft. update request References: <497629A5.2060001@mol.uj.edu.pl> <200901220233.58997.alexxy@gentoo.org> <497A088E.20500@mol.uj.edu.pl> <200901252314.20524.alexxy@gentoo.org> In-reply-to: <200901252314.20524.alexxy@gentoo.org> X-Archives-Salt: 695b0d24-ae82-4d6e-9217-88a937e8257c X-Archives-Hash: fe99bbadb3cdeeeedd504913bbfbee33 This is a multi-part message in MIME format. --Boundary_(ID_m0PjRbhtMLXbDCBR8C6mKg) Content-type: text/plain; charset=ISO-8859-2; format=flowed Content-transfer-encoding: 7BIT Hi, is it finally possible to someone put new ebuild for openib-mvapich2, i send my ebuild for this package below, it works well, one think maybe is to add USE flag for SDR or DDR infiniband, and register mvapich2 in virtual-mpi as one of the 'official' mpi's to select? it is easy i think and no effort (just add sys-cluster/openib-mvapich2 as a RDEPEND) also there's something wrong with this new package responsible for programs such as ibdiagnet ibtrace... , paths are wrong, emerge installs these into /usr/bin but when i start those programs, they are looking for others in /usr/local/bin.. need to be fixed openib-mvapich2.ebuild attachment: -- Dept of Computational Biophysics & Bioinformatics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, ul. Gronostajowa 7, 30-387 Krakow, Poland. Tel: (+48-12)-664-6380 --Boundary_(ID_m0PjRbhtMLXbDCBR8C6mKg) Content-type: text/plain; name=openib-mvapich2-1.2.ebuild Content-transfer-encoding: 7BIT Content-disposition: inline; filename=openib-mvapich2-1.2.ebuild # Copyright 1999-2008 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ inherit mpi fortran flag-o-matic eutils multilib toolchain-funcs SLOT="0" LICENSE="BSD" KEYWORDS="~x86 ~amd64" DESCRIPTION="MVAPICH2 MPI-over-infiniband package auto-configured for OpenIB." HOMEPAGE="http://mvapich.cse.ohio-state.edu/" SRC_URI="${HOMEPAGE}/download/mvapich2/mvapich2-${PV/_/-}p1.tgz" S="${WORKDIR}/mvapich2-${PV/_/-}p1" IUSE="debug medium-cluster large-cluster rdma romio threads fortran" RDEPEND=" || ( ( sys-cluster/libibverbs sys-cluster/libibumad sys-cluster/libibmad rdma? ( sys-cluster/librdmacm ) ) sys-cluster/openib-userspace ) $(mpi_imp_deplist)" DEPEND="${RDEPEND}" pkg_setup() { MPI_ESELECT_FILE="eselect.mpi.mvapich2" if [ -z "${MVAPICH_HCA_TYPE}" ]; then elog "${PN} needs to know which HCA it should optimize for. This is" elog "passed to the ebuild with the variable, \${MVAPICH_HCA_TYPE}." elog "Please choose one of: _MLX_PCI_EX_SDR_, _MLX_PCI_EX_DDR_," elog "_MLX_PCI_X, _PATH_HT_, or _IBM_EHCA_." elog "See make.mvapich2.detect in ${S} for more information." die "MVAPICH_HCA_TYPE undefined" fi case ${ARCH} in amd64) if grep Intel /proc/cpuinfo &>/dev/null; then BUILD_ARCH=-D_EM64T_ else BUILD_ARCH=-D_X86_64_ fi ;; x86) BUILD_ARCH=-D_IA32_ ;; ia64) BUILD_ARCH=-D_IA64_ ;; ppc64) BUILD_ARCH=-D_PPC64_ ;; *) die "unsupported architecture: ${ARCH}" ;; esac use fortran && fortran_pkg_setup } src_unpack() { unpack ${A} cd "${S}" einfo "Disabling examples" # Examples are always compiled with the default 'all' target. This # causes problems when we don't build support for everything, including # threads, mpe2, etc. So we're not going to build them. sed -i 's:.*cd examples && ${MAKE} all.*::' Makefile.in } src_compile() { local vcluster="small" use large-cluster && vcluster="large" use medium-cluster && vcluster="medium" local c="--with-device=ch3:sock --with-link=DDR $(use_enable romio) --with-cluster-size=${vcluster} --enable-sharedlibs=gcc" local enable_srq [ "${MVAPICH_HCA_TYPE}" == "_MLX_PCI_X_" ] && enable_srq="-DSRQ" append-flags "${BUILD_ARCH}" append-flags "${enable_srq}" append-flags "-D${MVAPICH_HCA_TYPE}" use debug && c="${c} --enable-g=all --enable-debuginfo" if use threads; then c="${c} --enable-threads=multiple --with-thread-package=pthreads" else c="${c} --with-thread-package=none" fi # enable f90 support for appropriate compilers if use fortran; then case "${FORTRANC}" in gfortran|ifc|ifort|f95) c="${c} --enable-f77 --enable-f90";; g77|f77|f2c) c="${c} --enable-f77 --disable-f90";; esac else c="${c} --disable-f77 --disable-f90" fi sed -i \ -e 's/ ${exec_prefix}/ ${DESTDIR}${exec_prefix}/' \ -e 's/ ${libdir}/ ${DESTDIR}${libdir}/' \ ${S/-beta2/}/Makefile.in sed -i '/bindir/s/ ${bindir}/ ${DESTDIR}${bindir}/' ${S/-beta2/}/src/pm/mpd/Makefile.in cd ${S/-beta2/} ! mpi_classed && c="${c} --sysconfdir=/etc/${PN}" econf $(mpi_econf_args) ${c} # http://www.mcs.anl.gov/research/projects/mpich2/support/index.php?s=faqs#parmake # https://trac.mcs.anl.gov/projects/mpich2/ticket/297 emake -j1 || die "emake failed" #emake || die "emake failed" } src_install() { emake DESTDIR="${D}" install || die "make install failed" mpi_imp_add_eselect } pkg_postinst() { einfo "To allow normal users to use infiniband, it is necessary to" einfo "increase the system limits on locked memory." einfo "You must increase the kernel.shmmax sysctl value, and increase" einfo "the memlock limits in /etc/security/limits.conf. i.e.:" echo einfo "echo 'kernel.shmmax = 512000000' >> /etc/sysctl.conf" einfo "echo 512000000 > /proc/sys/kernel/shmmax" einfo "echo -e '* soft memlock unlimited\n* hard memlock unlimited' > /etc/security/limits.conf" } --Boundary_(ID_m0PjRbhtMLXbDCBR8C6mKg)--