Hello community, here is the log from the commit of package prun-ohpc for openSUSE:Factory checked in at 2019-09-11 10:36:46 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Comparing /work/SRC/openSUSE:Factory/prun-ohpc (Old) and /work/SRC/openSUSE:Factory/.prun-ohpc.new.7948 (New) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "prun-ohpc" Wed Sep 11 10:36:46 2019 rev:4 rq:729851 version:1.2 Changes: -------- --- /work/SRC/openSUSE:Factory/prun-ohpc/prun-ohpc.changes 2017-08-16 16:18:24.173890534 +0200 +++ /work/SRC/openSUSE:Factory/.prun-ohpc.new.7948/prun-ohpc.changes 2019-09-11 10:36:50.707270935 +0200 @@ -1,0 +2,9 @@ +Thu Sep 5 11:06:11 UTC 2019 - Ana Guerrero Lopez <aguerr...@suse.com> + +- Update to version 1.2. +- Refresh patch + * prun-Add-user-config.patch +- License change, from BSD-3-Clause to Apache-2.0. +- Use %license + +------------------------------------------------------------------- ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ prun-ohpc.spec ++++++ --- /var/tmp/diff_new_pack.ljP2dd/_old 2019-09-11 10:36:52.663270367 +0200 +++ /var/tmp/diff_new_pack.ljP2dd/_new 2019-09-11 10:36:52.723270349 +0200 @@ -1,7 +1,7 @@ # # spec file for package prun-ohpc # -# Copyright (c) 2017 SUSE LINUX GmbH, Nuernberg, Germany. +# Copyright (c) 2019 SUSE LINUX GmbH, Nuernberg, Germany. # # All modifications and additions to the file contributed by third parties # remain the property of their copyright owners, unless otherwise agreed @@ -12,22 +12,21 @@ # license that conforms to the Open Source Definition (Version 1.9) # published by the Open Source Initiative. -# Please submit bugfixes or comments via http://bugs.opensuse.org/ +# Please submit bugfixes or comments via https://bugs.opensuse.org/ # Name: prun-ohpc -Version: 1.0 +Version: 1.2 Release: 0 Summary: Convenience utility for parallel job launch -License: BSD-3-Clause +License: Apache-2.0 Group: Productivity/Clustering/Computing BuildArch: noarch -Url: https://github.com/openhpc/ohpc +URL: https://github.com/openhpc/ohpc Source1: prun Source2: LICENSE Patch1: prun-Add-user-config.patch -BuildRoot: %{_tmppath}/%{name}-%{version}-build %description prun provides a unified, script-based wrapper for launching parallel jobs @@ -52,8 +51,7 @@ install -D -m 0644 prunrc %{buildroot}%{_sysconfdir}/skel/.prunrc %files -%defattr(-,root,root,-) -%doc LICENSE +%license LICENSE %{_bindir}/prun %config %{_sysconfdir}/prunrc %config %{_sysconfdir}/skel/.prunrc ++++++ LICENSE ++++++ --- /var/tmp/diff_new_pack.ljP2dd/_old 2019-09-11 10:36:53.043270256 +0200 +++ /var/tmp/diff_new_pack.ljP2dd/_new 2019-09-11 10:36:53.067270249 +0200 @@ -1,24 +1,202 @@ -Copyright (c) 2015, Intel Corporation -Redistribution and use in source and binary forms, with or without -modification, are permitted provided that the following conditions are met: + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ - * Redistributions of source code must retain the above copyright notice, - this list of conditions and the following disclaimer. - * Redistributions in binary form must reproduce the above copyright - notice, this list of conditions and the following disclaimer in the - documentation and/or other materials provided with the distribution. - * Neither the name of Intel Corporation nor the names of its contributors - may be used to endorse or promote products derived from this software - without specific prior written permission. - -THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" -AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -DISCLAIMED. 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We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright [yyyy] [name of copyright owner] + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. ++++++ prun ++++++ --- /var/tmp/diff_new_pack.ljP2dd/_old 2019-09-11 10:36:53.335270171 +0200 +++ /var/tmp/diff_new_pack.ljP2dd/_new 2019-09-11 10:36:53.355270165 +0200 @@ -1,47 +1,32 @@ #!/bin/bash -#------------------------------------------------------------------------------- -# Copyright (c) 2015, Intel Corporation -# -# Redistribution and use in source and binary forms, with or without -# modification, are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, -# this list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright -# notice, this list of conditions and the following disclaimer in the -# documentation and/or other materials provided with the distribution. -# * Neither the name of Intel Corporation nor the names of its contributors -# may be used to endorse or promote products derived from this software -# without specific prior written permission. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS 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. -#------------------------------------------------------------------------------- +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. CONFIG=/etc/sysconfig/prun MODE=native LOGLEVEL=2 # 0=error,1=warn,2=info,3=debug -RM=slurm function usage () { echo " " - echo "This utility can be use to launch parallel (MPI) applications within " - echo "a supported resource manager." + echo "This OpenHPC utility is used to launch parallel (MPI) applications" + echo "within a supported resource manager." echo " " echo "Usage: $DELIM <options> executable [arguments]" echo " " echo "where available options are as follows:" echo " " echo " -h generate help message and exit" + echo " -v enable verbose output" echo " " exit 1 } @@ -88,25 +73,69 @@ fi } +function set_variable () { + + local var=$1 + local set=$2 + + _debug "Setting env variable: $var=$2" + export $var="$2" +} + function launch_impi () { if [ $MODE == "native" ];then LAUNCHER="mpiexec.hydra" verify_launcher_avail $LAUNCHER - cmd="$LAUNCHER -bootstrap slurm $@" - _info "Launch cmd = $cmd" + if [ ${RM} == "slurm" ];then + cmd="$LAUNCHER -bootstrap slurm $@" + elif [ ${RM} == "pbspro" ];then + cmd="$LAUNCHER -rmk pbs $@" + fi + + _info "Launch cmd = $cmd (family=$LMOD_FAMILY_MPI)" $cmd fi } +function launch_mpich () { + + if [[ ${RM} == "slurm" ]];then + if [[ ${OHPC_MPI_LAUNCHERS} =~ "pmix" ]];then + verify_launcher_avail srun + cmd="srun --mpi=pmix $@" + else + verify_launcher_avail mpiexec.hydra + cmd="mpiexec.hydra -bootstrap slurm $@" + fi + elif [[ ${RM} == "pbspro" ]];then + verify_launcher_avail mpiexec.hydra + cmd="mpiexec.hydra -rmk pbs $@" + else + _error "Unknown resource manager -> ${RM}" + fi + + _info "Launch cmd = $cmd (family=$LMOD_FAMILY_MPI)" + $cmd + + return $? +} + function launch_mvapich2 () { if [ $MODE == "native" ];then LAUNCHER="mpiexec.hydra" verify_launcher_avail $LAUNCHER + + if [ ${RM} == "slurm" ];then + cmd="$LAUNCHER -bootstrap slurm $@" + elif [ ${RM} == "pbspro" ];then + cmd="$LAUNCHER -rmk pbs $@" + else + _error "Unknown resource manager -> ${RM}" + fi - cmd="$LAUNCHER -bootstrap slurm $@" - _info "Launch cmd = $cmd" + _info "Launch cmd = $cmd (family=$LMOD_FAMILY_MPI)" $cmd local _status=$? @@ -115,32 +144,72 @@ fi } +function setupenv_openmpi () { + # disable plugin loader warnings if not not available + set_variable OMPI_MCA_mca_base_component_show_load_errors 0 + set_variable PMIX_MCA_mca_base_component_show_load_errors 0 + + # no tm module avail when using slurm + if [[ ${RM} == "slurm" ]];then + set_variable OMPI_MCA_ras ^tm + set_variable OMPI_MCA_ess ^tm + set_variable OMPI_MCA_plm ^tm + fi + + # use romio for openmpi3 + if [[ $LMOD_FAMILY_MPI == "openmpi3" ]];then + set_variable OMPI_MCA_io romio314 + fi +} + function launch_openmpi () { - if [ $MODE == "native" ];then - LAUNCHER="mpirun" - verify_launcher_avail $LAUNCHER - cmd="mpirun $@" - _info "Launch cmd = $cmd" - $cmd + setupenv_openmpi + + if [[ ${RM} == "slurm" ]];then + if [[ ${OHPC_MPI_LAUNCHERS} =~ "pmix" ]];then + verify_launcher_avail srun + cmd="srun --mpi=pmix $@" + else + verify_launcher_avail mpirun + cmd="mpirun $@" + fi + elif [[ ${RM} == "pbspro" ]];then + verify_launcher_avail mpiexec + cmd="mpiexec -x LD_LIBRARY_PATH --prefix ${MPI_DIR} --hostfile ${PBS_NODEFILE} $@" + else + _error "Unknown resource manager -> ${RM}" fi + + _info "Launch cmd = $cmd (family=$LMOD_FAMILY_MPI)" + $cmd + + return $? } + + + + DELIM=prun # Parse command-line args -while getopts ":h" opt; do +while getopts "hv" opt; do case $opt in h) usage ;; + v) + LOGLEVEL=3 + ;; \?) echo "Invalid option: -$OPTARG" >&2 exit 1 ;; esac done +shift $((OPTIND-1)) if [ $# -lt 1 ];then usage @@ -153,6 +222,14 @@ shift ARGS=$@ +# Resource manager detection. If not specified from the config file, determine +# from locally installed packages. Like Highlander, we assume there can be only one. + +if [ -z "$RM" ];then + [[ -s /etc/pbs.conf ]] && RM=pbspro + [[ -s /etc/slurm/slurm.conf ]] && RM=slurm +fi + if ! [ -x "$(command -v $EXEC)" ];then if [ ! -x $EXEC ];then _error "Unable to access executable -> $EXEC" @@ -167,13 +244,18 @@ masterHost=`hostname -s` _info "Master compute host = $masterHost" +_info "Resource manager = $RM" if [ $LMOD_FAMILY_MPI == "impi" ];then launch_impi $EXEC $ARGS +elif [ $LMOD_FAMILY_MPI == "mpich" ];then + launch_mpich $EXEC $ARGS elif [ $LMOD_FAMILY_MPI == "mvapich2" ];then launch_mvapich2 $EXEC $ARGS elif [ $LMOD_FAMILY_MPI == "openmpi" ];then launch_openmpi $EXEC $ARGS +elif [ $LMOD_FAMILY_MPI == "openmpi3" ];then + launch_openmpi $EXEC $ARGS else _error "Unsupported or unknown MPI family -> $LMOD_FAMILY_MPI" fi ++++++ prun-Add-user-config.patch ++++++ --- /var/tmp/diff_new_pack.ljP2dd/_old 2019-09-11 10:36:53.411270149 +0200 +++ /var/tmp/diff_new_pack.ljP2dd/_new 2019-09-11 10:36:53.411270149 +0200 @@ -3,19 +3,19 @@ Common config file: /etc/prunrc User config file: $HOME/.prunrc ---- prun 2016-10-17 09:59:23.092593217 +0200 -+++ prun.suse 2016-10-19 17:23:30.473084829 +0200 -@@ -26,7 +26,8 @@ - # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - #------------------------------------------------------------------------------- +--- prun ++++ prun.suse +@@ -11,7 +11,8 @@ + # See the License for the specific language governing permissions and + # limitations under the License. -CONFIG=/etc/sysconfig/prun +CONFIG=/etc/prunrc +LOCALCONFIG=$HOME/.prunrc MODE=native LOGLEVEL=2 # 0=error,1=warn,2=info,3=debug - RM=slurm -@@ -48,7 +49,9 @@ + +@@ -33,7 +34,9 @@ function parse_config_file () {
