Added new application for testing: milc-nsf. Retest script not fully completed...

Added new application for testing: milc-nsf. Retest script not fully completed yet, still needing to grab performance results.

milc-nsf/.7.7.11/cle5.2_gnu4.8.2/.owners

+pragnesh

milc-nsf/.7.7.11/cle5.2_gnu4.8.2/build-notes

+
+Source downloaded from : http://www.physics.utah.edu/~detar/milc/milc_qcd-7.7.11.tar.gz

milc-nsf/.7.7.11/cle5.2_gnu4.8.2/rebuild

+#!/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

milc-nsf/.7.7.11/cle5.2_gnu4.8.2/relink

+#!/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

milc-nsf/.7.7.11/cle5.2_gnu4.8.2/remodule

+  ### 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

milc-nsf/.7.7.11/cle5.2_gnu4.8.2/retest

+#!/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

milc-nsf/.check4newver

+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
+
+

milc-nsf/.exceptions

+noweb
+#protected 0022 
+#vendor

milc-nsf/description

+<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>
+

milc-nsf/support

+ncsa/nics

milc-nsf/v1/cle5.2_gnu4.9.3/.owners

+pragnesh

milc-nsf/v1/cle5.2_gnu4.9.3/build-notes

+
+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

milc-nsf/v1/cle5.2_gnu4.9.3/rebuild

+#!/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

milc-nsf/v1/cle5.2_gnu4.9.3/relink

+#!/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

milc-nsf/v1/cle5.2_gnu4.9.3/remodule

+  ### 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

milc-nsf/v1/cle5.2_gnu4.9.3/retest

+#!/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

milc-nsf/versions

+development: 
+current:v1
+deprecated:7.7.8.1