diff --git a/milc-nsf/.7.7.11/cle5.2_gnu4.8.2/.owners b/milc-nsf/.7.7.11/cle5.2_gnu4.8.2/.owners new file mode 100644 index 0000000000000000000000000000000000000000..227636eb2ad06e5dbcdb0fcb968e3f92b508150a --- /dev/null +++ b/milc-nsf/.7.7.11/cle5.2_gnu4.8.2/.owners @@ -0,0 +1 @@ +pragnesh diff --git a/milc-nsf/.7.7.11/cle5.2_gnu4.8.2/build-notes b/milc-nsf/.7.7.11/cle5.2_gnu4.8.2/build-notes new file mode 100644 index 0000000000000000000000000000000000000000..927b5283f38bd9c6a02039b44a201361bff8c777 --- /dev/null +++ b/milc-nsf/.7.7.11/cle5.2_gnu4.8.2/build-notes @@ -0,0 +1,2 @@ + +Source downloaded from : http://www.physics.utah.edu/~detar/milc/milc_qcd-7.7.11.tar.gz diff --git a/milc-nsf/.7.7.11/cle5.2_gnu4.8.2/rebuild b/milc-nsf/.7.7.11/cle5.2_gnu4.8.2/rebuild new file mode 100755 index 0000000000000000000000000000000000000000..f589d1caca1caa034a4953c5c9252bf42163d279 --- /dev/null +++ b/milc-nsf/.7.7.11/cle5.2_gnu4.8.2/rebuild @@ -0,0 +1,111 @@ +#!/bin/ksh + +############################## standard interface to /sw tools +# Input: +# Environment variables +# SW_BLDDIR current directory (PWD) minus /autofs/na1_ stuff +# SW_ENVFILE file to be sourced which has alternate prog environment +# only to be used in special circumstances +# SW_WORKDIR unique work dir that local script can use +# Output +# Return code of 0=success or 1=failure +############################## + +if [ -z $SW_BLDDIR ]; then + echo "Error: SW_BLDDIR not set!" + exit 1 +else + cd $SW_BLDDIR +fi + +if [ -z $SW_ENVFILE ]; then + ### Set Environment (do not remove this line only change what is in between) + . ${MODULESHOME}/init/ksh + . ${SW_BLDDIR}/remodule + ### End Environment (do not remove this line only change what is in between) +else + . $SW_ENVFILE +fi + +############################## app specific section +# +set -o verbose +# clear out old installation to prevent potential libtool chmod +# commands from failing when reinstalled by another person +rm -rf bin lib include status test.log $SRCDIR + +#clear out status file since re-making +rm -f status + +tar -zxf /sw/sources/$PACKAGE/$VERSION/$SRCDIR.tar.gz +cd $SRCDIR + +#PAtch test makefile +#perl -pi -e 's/f77$/gfortran/g' $SRCDIR/tests/Makefile + +#make distclean + +./configure --prefix=$SW_BLDDIR \ + --enable-fortran \ + --enable-static \ + --enable-optimization \ + --disable-silex \ + --with-hdf5=${HDF5_DIR}/include,${HDF5_DIR}/lib \ + --without-qt +#./configure --prefix=$SW_BLDDIR \ +# --enable-fortran \ +# --enable-optimization \ +# --disable-silex \ +# --with-szlib=${SZIP_DIR} \ +# --with-hdf5=${HDF5_DIR}/include,${HDF5_DIR}/lib +#--disable-shared +#--disable-fortran-compiler-check +#--host=x86_64-unknown-linux-gnu +if [ $? -ne 0 ] ; then + echo "$PACKAGE configure failed" + exit 1 +fi + +make + if [ $? -ne 0 ] ; then + echo "$PACKAGE make failed" + exit 1 + fi + +make install +if [ $? -ne 0 ] ; then + echo "$PACKAGE install failed" + exit 1 +fi + +#-- Fix mangled include file due to bug in Silo auto-generator +cd $SW_BLDDIR/include +#-- 1. sed: replace newline with @ +sed -i ':a;N;$!ba;s/\n/@/g' silo.inc +#-- 2. sed: replace pattern with empty string ( (1) is necessary because sed +# pattern can't include newline +sed -i "s/@ c//g" silo.inc +#-- 3. tr: replace @ with newline +tr @ '\n' < silo.inc > silo.inc.2 +mv silo.inc.2 silo.inc + +cd $SW_BLDDIR + +#-- Write pkg-config file +mkdir -p $SW_BLDDIR/lib/pkgconfig +cat > $SW_BLDDIR/lib/pkgconfig/${PACKAGE}.pc << EOF +prefix=$SW_BLDDIR +includedir=\${prefix}/include +libdir=\${prefix}/lib + +Name: ${PACKAGE} +Description: ${PACKAGE} Library +URL: https://wci.llnl.gov/codes/silo/ +Version: $VERSION +Cflags: -I\${includedir} +Libs: -L\${libdir} -lsiloh5 -lstdc++ +Requires.private: hdf5 >= 1.8.12 +EOF + +############################### if this far, return 0 +exit 0 diff --git a/milc-nsf/.7.7.11/cle5.2_gnu4.8.2/relink b/milc-nsf/.7.7.11/cle5.2_gnu4.8.2/relink new file mode 100755 index 0000000000000000000000000000000000000000..f72a73f4318a16d45620f960bd91addc3eac2069 --- /dev/null +++ b/milc-nsf/.7.7.11/cle5.2_gnu4.8.2/relink @@ -0,0 +1,64 @@ +#!/bin/ksh + +############################## standard interface to /sw tools +# Input: +# Environment variables +# SW_BLDDIR current directory (PWD) minus /autofs/na1_ stuff +# SW_ENVFILE file to be sourced which has alternate prog environment +# only to be used in special circumstances +# SW_WORKDIR unique work dir that local script can use +# Output +# Return code of 0=success or 1=failure +############################## + +# exit 3 is a signal to the sw infrastructure that this template has not +# been updated; please delete it when ready +exit 3 + +if [ -z $SW_BLDDIR ]; then + echo "Error: SW_BLDDIR not set!" + exit 1 +else + cd $SW_BLDDIR +fi + +if [ -z $SW_ENVFILE ]; then + ### Set Environment (do not remove this line only change what is in between) + . ${MODULESHOME}/init/ksh + . ${SW_BLDDIR}/remodule + ### End Environment (do not remove this line only change what is in between) +else + . $SW_ENVFILE +fi + +############################## app specific section +# + +# clear out old installation to prevent potential libtool chmod +# commands from failing when reinstalled by another person +rm -rf bin lib include doc share man etc libexec info + +#clear out status file since re-making +rm -f status + +cd $SRCDIR + +#probably overkill, need surgical strike on binary executables +make clean + +make all + if [ $? -ne 0 ] ; then + echo "$PACKAGE make failed" + exit 1 + fi + +make install +if [ $? -ne 0 ] ; then + echo "$PACKAGE install failed" + exit 1 +fi + +cd ../ + +############################### if this far, return 0 +exit 0 diff --git a/milc-nsf/.7.7.11/cle5.2_gnu4.8.2/remodule b/milc-nsf/.7.7.11/cle5.2_gnu4.8.2/remodule new file mode 100644 index 0000000000000000000000000000000000000000..60ddd724363453738499d2d00cd4f91ed179743e --- /dev/null +++ b/milc-nsf/.7.7.11/cle5.2_gnu4.8.2/remodule @@ -0,0 +1,35 @@ + ### Set Environment (do not remove this line only change what is in between) + . ${MODULESHOME}/init/ksh + module unload PrgEnv-intel + module unload PrgEnv-cray + module unload PrgEnv-gnu + module load PrgEnv-gnu + module swap gcc gcc/4.9.1 + ### End Environment (do not remove this line only change what is in between) + + PACKAGE=silo + VERSION=4.9.1 + SRCDIR=$PACKAGE-$VERSION + +# load any other module here + +module load cray-hdf5 + +export F77=gfortran +export F90=gfortran +export F9X=gfortran +export FC=gfortran +export F9X=gfortran +export CC=gcc +export CXX=g++ + +#export CRAYPE_LINK_TYPE=static +# +#export F77=ftn +#export F90=ftn +#export F9X=ftn +#export FC=ftn +#export F9X=ftn +#export CC=cc +#export CXX=CC +module load cray-mpich-compat/v7 diff --git a/milc-nsf/.7.7.11/cle5.2_gnu4.8.2/retest b/milc-nsf/.7.7.11/cle5.2_gnu4.8.2/retest new file mode 100755 index 0000000000000000000000000000000000000000..8bb1b5497e728b2145b2893a6c31e1ded6511e10 --- /dev/null +++ b/milc-nsf/.7.7.11/cle5.2_gnu4.8.2/retest @@ -0,0 +1,68 @@ +#!/bin/ksh + +############################## standard interface to /sw tools +# Input: +# Environment variables +# SW_BLDDIR current directory (PWD) minus /autofs/na1_ stuff +# SW_ENVFILE file to be sourced which has alternate prog environment +# only to be used in special circumstances +# SW_WORKDIR work dir that local script can use +# Output: +# Return code of 0=success or 1=failure or 2=job submitted +# +# Notes: +# If this script is called from swtest, then swtest requires +# SW_WORKDIR to be set. Then swtest adds a unique path to what +# user gave swtest (action+timestamp+build) and provides this +# script with a uniquely valued SW_WORKDIR. swtest will +# automatically remove this unique workspace when retest is done. +################################################################## + +# exit 3 is a signal to the sw infrastructure that this template has not +# been updated; please delete it when ready + +if [ -z $SW_BLDDIR ]; then + echo "Error: SW_BLDDIR not set!" + exit 1 +else + cd $SW_BLDDIR +fi + +if [ -z $SW_ENVFILE ]; then + ### Set Environment (do not remove this line only change what is in between) + . ${MODULESHOME}/init/ksh + . ${SW_BLDDIR}/remodule + ### End Environment (do not remove this line only change what is in between) +else + . $SW_ENVFILE +fi + +############################## app specific section +# +set -o verbose +#clear out status file since re-testing +rm -f status + +cd $SRCDIR + +make check +if [ $? -ne 0 ] ; then + echo "$PACKAGE make test failed " + echo unverified > $SW_BLDDIR/status + exit 1 +fi + +a_ok=`grep ": ok" tests/testsuite.log | wc -l` +if [[ $a_ok -ne 111 ]]; then + # error + echo unverified > $SW_BLDDIR/status + exit 1 +else + echo verified > $SW_BLDDIR/status + exit 0 +fi + +cd ../ + +############################### if this far, return 0 +exit 0 diff --git a/milc-nsf/.check4newver b/milc-nsf/.check4newver new file mode 100644 index 0000000000000000000000000000000000000000..cac4dd8f73f864604885c6f41749c2b420d4707a --- /dev/null +++ b/milc-nsf/.check4newver @@ -0,0 +1,4 @@ +2015-11-17: new version installed +2015-11-17: next check of /sw/xe_xk_cle5.2UP02_pe2.3.0/milc-nsf on 2016-2-15 + + diff --git a/milc-nsf/.exceptions b/milc-nsf/.exceptions new file mode 100644 index 0000000000000000000000000000000000000000..ab4585178c665c9b0543084ee1b15de7e21be6ad --- /dev/null +++ b/milc-nsf/.exceptions @@ -0,0 +1,3 @@ +noweb +#protected 0022 +#vendor diff --git a/milc-nsf/description b/milc-nsf/description new file mode 100644 index 0000000000000000000000000000000000000000..99394c0420ddd34a4d85c2ee1a56a8b54d329343 --- /dev/null +++ b/milc-nsf/description @@ -0,0 +1,31 @@ +<h1>The MIMD Lattice Computation (MILC) Collaboration</h1> + +<p> Category: Physics [HEP] + +<h2>Description</h2> + +<p> The benchmark code MILC represents part of a set of codes written by the +MIMD Lattice Computation (MILC) collaboratoration used to study quantum +chromodynamics (QCD), the theory of the strong interactions of subatomic +physics. It performs simulations of four dimensional SU(3) lattice gauge +theory on MIMD parallel machines. "Strong interactions" are responsible for +binding quarks into protons and neutrons and holding them all together in the +atomic nucleus. + +Reference: +https://www.nersc.gov/users/computational-systems/cori/nersc-8-procurement/trinity-nersc-8-rfp/nersc-8-trinity-benchmarks/milc/ + +This code was developed by the MILC collaboration. + +<h2>Use</h2> + +<p> Coming soon + +<pre> +code +code +code +code +code +</pre> + diff --git a/milc-nsf/support b/milc-nsf/support new file mode 100644 index 0000000000000000000000000000000000000000..1cdc3e61e2f3f90fd41ee04dcb8299283625f43b --- /dev/null +++ b/milc-nsf/support @@ -0,0 +1 @@ +ncsa/nics diff --git a/milc-nsf/v1/cle5.2_gnu4.9.3/.owners b/milc-nsf/v1/cle5.2_gnu4.9.3/.owners new file mode 100644 index 0000000000000000000000000000000000000000..227636eb2ad06e5dbcdb0fcb968e3f92b508150a --- /dev/null +++ b/milc-nsf/v1/cle5.2_gnu4.9.3/.owners @@ -0,0 +1 @@ +pragnesh diff --git a/milc-nsf/v1/cle5.2_gnu4.9.3/build-notes b/milc-nsf/v1/cle5.2_gnu4.9.3/build-notes new file mode 100644 index 0000000000000000000000000000000000000000..a19109995aeab2a1c6af19627647e824457b5ca4 --- /dev/null +++ b/milc-nsf/v1/cle5.2_gnu4.9.3/build-notes @@ -0,0 +1,12 @@ + +Source downloaded from : http://www.physics.utah.edu/~detar/milc/milc_qcd-7.7.11.tar.gz + + +tar –zxf milc-nsf.tar.gz +cd milc-nsf/scripts +./build +# should return OK +# edit pbs files to fix some fixed paths (perhaps) +qsub small.pbs +# out file should have +OK diff --git a/milc-nsf/v1/cle5.2_gnu4.9.3/rebuild b/milc-nsf/v1/cle5.2_gnu4.9.3/rebuild new file mode 100755 index 0000000000000000000000000000000000000000..37c9f6a13b7fe661a102949eb1243434a506ed66 --- /dev/null +++ b/milc-nsf/v1/cle5.2_gnu4.9.3/rebuild @@ -0,0 +1,62 @@ +#!/bin/ksh + +############################## standard interface to /sw tools +# Input: +# Environment variables +# SW_BLDDIR current directory (PWD) minus /autofs/na1_ stuff +# SW_ENVFILE file to be sourced which has alternate prog environment +# only to be used in special circumstances +# SW_WORKDIR unique work dir that local script can use +# Output +# Return code of 0=success or 1=failure +############################## + +if [ -z $SW_BLDDIR ]; then + echo "Error: SW_BLDDIR not set!" + exit 1 +else + cd $SW_BLDDIR +fi + +if [ -z $SW_ENVFILE ]; then + ### Set Environment (do not remove this line only change what is in between) + . ${MODULESHOME}/init/ksh + . ${SW_BLDDIR}/remodule + ### End Environment (do not remove this line only change what is in between) +else + . $SW_ENVFILE +fi + +############################## app specific section +# +set -o verbose +# clear out old installation to prevent potential libtool chmod +# commands from failing when reinstalled by another person +rm -rf bin lib include status test.log $SRCDIR + + +#clear out status file since re-making +rm -f status + +tar xf /sw/sources/$PACKAGE/$VERSION/$SRCDIR.tar.gz +cd $SRCDIR/src/milc-nsf/ks_imp_dyn2 + +# Make clean +make -f Make_mpi clean +touch ../libraries/Make_vanilla + +#Make +make -f Make_mpi su3_rmd + +if [[ ! -e su3_rmd ]] ; then + echo "make failed" + exit 1 +fi + +mkdir -p $SW_BLDDIR/bin +cp su3_rmd $SW_BLDDIR/bin + +cd $SW_BLDDIR + +############################### if this far, return 0 +exit 0 diff --git a/milc-nsf/v1/cle5.2_gnu4.9.3/relink b/milc-nsf/v1/cle5.2_gnu4.9.3/relink new file mode 100755 index 0000000000000000000000000000000000000000..f72a73f4318a16d45620f960bd91addc3eac2069 --- /dev/null +++ b/milc-nsf/v1/cle5.2_gnu4.9.3/relink @@ -0,0 +1,64 @@ +#!/bin/ksh + +############################## standard interface to /sw tools +# Input: +# Environment variables +# SW_BLDDIR current directory (PWD) minus /autofs/na1_ stuff +# SW_ENVFILE file to be sourced which has alternate prog environment +# only to be used in special circumstances +# SW_WORKDIR unique work dir that local script can use +# Output +# Return code of 0=success or 1=failure +############################## + +# exit 3 is a signal to the sw infrastructure that this template has not +# been updated; please delete it when ready +exit 3 + +if [ -z $SW_BLDDIR ]; then + echo "Error: SW_BLDDIR not set!" + exit 1 +else + cd $SW_BLDDIR +fi + +if [ -z $SW_ENVFILE ]; then + ### Set Environment (do not remove this line only change what is in between) + . ${MODULESHOME}/init/ksh + . ${SW_BLDDIR}/remodule + ### End Environment (do not remove this line only change what is in between) +else + . $SW_ENVFILE +fi + +############################## app specific section +# + +# clear out old installation to prevent potential libtool chmod +# commands from failing when reinstalled by another person +rm -rf bin lib include doc share man etc libexec info + +#clear out status file since re-making +rm -f status + +cd $SRCDIR + +#probably overkill, need surgical strike on binary executables +make clean + +make all + if [ $? -ne 0 ] ; then + echo "$PACKAGE make failed" + exit 1 + fi + +make install +if [ $? -ne 0 ] ; then + echo "$PACKAGE install failed" + exit 1 +fi + +cd ../ + +############################### if this far, return 0 +exit 0 diff --git a/milc-nsf/v1/cle5.2_gnu4.9.3/remodule b/milc-nsf/v1/cle5.2_gnu4.9.3/remodule new file mode 100644 index 0000000000000000000000000000000000000000..35ff7c1b104d47997b32e6c08f7cf874a21b185e --- /dev/null +++ b/milc-nsf/v1/cle5.2_gnu4.9.3/remodule @@ -0,0 +1,38 @@ + ### Set Environment (do not remove this line only change what is in between) + . ${MODULESHOME}/init/ksh + module unload PrgEnv-intel + module unload PrgEnv-cray + module unload PrgEnv-gnu + module load PrgEnv-gnu + module swap gcc gcc/4.9.3 + ### End Environment (do not remove this line only change what is in between) + + PACKAGE=milc-nsf + VERSION=v1 + #SRCDIR=$PACKAGE-$VERSION + SRCDIR=$PACKAGE + +# load any other module here + +#module load cray-hdf5 + +export F77=gfortran +export F90=gfortran +export F9X=gfortran +export FC=gfortran +export F9X=gfortran +export CC=gcc +export CXX=g++ + +module load craype-hugepages2M + +#export CRAYPE_LINK_TYPE=static +# +#export F77=ftn +#export F90=ftn +#export F9X=ftn +#export FC=ftn +#export F9X=ftn +#export CC=cc +#export CXX=CC +#module load cray-mpich-compat/v7 diff --git a/milc-nsf/v1/cle5.2_gnu4.9.3/retest b/milc-nsf/v1/cle5.2_gnu4.9.3/retest new file mode 100755 index 0000000000000000000000000000000000000000..b85c10597dfcfb417f63e4744069c311e5b818db --- /dev/null +++ b/milc-nsf/v1/cle5.2_gnu4.9.3/retest @@ -0,0 +1,97 @@ +#!/bin/ksh + +############################## standard interface to /sw tools +# Input: +# Environment variables +# SW_BLDDIR current directory (PWD) minus /autofs/na1_ stuff +# SW_ENVFILE file to be sourced which has alternate prog environment +# only to be used in special circumstances +# SW_WORKDIR work dir that local script can use +# Output: +# Return code of 0=success or 1=failure or 2=job submitted +# +# Notes: +# If this script is called from swtest, then swtest requires +# SW_WORKDIR to be set. Then swtest adds a unique path to what +# user gave swtest (action+timestamp+build) and provides this +# script with a uniquely valued SW_WORKDIR. swtest will +# automatically remove this unique workspace when retest is done. +################################################################## + +# exit 3 is a signal to the sw infrastructure that this template has not +# been updated; please delete it when ready + +if [ -z $SW_BLDDIR ]; then + echo "Error: SW_BLDDIR not set!" + exit 1 +else + cd $SW_BLDDIR +fi + +if [ -z $SW_ENVFILE ]; then + ### Set Environment (do not remove this line only change what is in between) + . ${MODULESHOME}/init/ksh + . ${SW_BLDDIR}/remodule + ### End Environment (do not remove this line only change what is in between) +else + . $SW_ENVFILE +fi + +############################## app specific section +# +set -o verbose +#clear out status file since re-testing +rm -f status + +cp $SRCDIR/input/* $SW_WORKDIR +cd $SW_WORKDIR + +cat > ${PACKAGE}.pbs << EOF +#!/bin/bash +#PBS -N ${PACKAGE} +#PBS -j oe +##PBS -l nodes=64:ppn=32,walltime=01:00:00 +#PBS -l nodes=8:ppn=32,walltime=01:00:00 + +set -o verbose +cd \$PBS_O_WORKDIR + +module swap PrgEnv-cray PrgEnv-gnu +module add craype-hugepages2M + +MILC_BIN=${SW_BLDDIR}/bin/su3_rmd +#aprun -n 2048 \$MILC_BIN < large.in > ${PACKAGE}.out +aprun -n 256 \$MILC_BIN < large.in > ${PACKAGE}.out + +#-- Check result +${SW_BLDDIR}/${SRCDIR}/scripts/checkout ${PACKAGE}.out + +JOBID=\`echo \$PBS_JOBID | cut -d "." -f1 \` +chmod 775 ${SW_BLDDIR}/status +rm ${SW_BLDDIR}/.running +cat \${JOBID}.OU >> ${SW_BLDDIR}/test.log +cat ${PACKAGE}.out >> ${SW_BLDDIR}/test.log +chmod 664 ${SW_BLDDIR}/test.log +EOF + + +#submit job and touch .running file - marker to infrastructure that +qsub ${PACKAGE}.pbs &> ${SW_BLDDIR}/.running + +# qsub returns 0 on successful job launch, so if failure return 1 +if [ $? -ne 0 ]; then + echo "Error submitting job" + rm -f .running + exit 1 +else + echo "Job submitted" + cat ${SW_BLDDIR}/.running + exit 2 +fi + +cd ../ + +cd ../../ + +############################### if this far, return 0 +exit 0 diff --git a/milc-nsf/versions b/milc-nsf/versions new file mode 100644 index 0000000000000000000000000000000000000000..fc8b4ddfe3f89f75040142d2843c1465c8b03371 --- /dev/null +++ b/milc-nsf/versions @@ -0,0 +1,3 @@ +development: +current:v1 +deprecated:7.7.8.1