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NWChem/QA/runtests.mpi.unix
edoapra 804deccd42
added sync to fix I/O for md runs
2025-12-10 16:51:08 -08:00

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#!/usr/bin/env bash
#
# THIS assumes ./tests/
#
# UNIX workstation parallel and sequential execution of test jobs
# Usage:
# runtest.mpi.unix [procs nproc] testdir1 [testdir2 ...]
#
# Return 0 if all jobs complete successfully and outputs compare OK
# with the correct output
# Return 1 otherwise.
#
# Gets executable from environment variable NWCHEM_EXECUTABLE or
# uses the daily NWChem release build
# Gets mpirun executable from environment variable MPIRUN_PATH or
# assumes it is in your path.
# Gets nwparse.pl from enironement varialle NWPARSE or looks in your
# nwchem tree for $NWCHEM_TOP/QA/nwparse.pl
# A test is specified by the path to the directory containing
# the test inputs and outputs. The input file is assumed to
# begin with the same name as the directory.
#
# E.g., if the test is specified as ./small/o3grad then
# - the input file will be ./small/o3grad/o3grad.nw
# - the verified output will be ./small/o3grad/o3grad.out
# A subdirectory of the current directory named scratchdir is deleted
# and remade for each calculation, and deleted at job end.
export HYDRA_DEBUG=0
# find memory leaks using this glibc feature that
# initialized memory blocks to non-zero values
#if [[ -z "${USE_ASAN}" ]] && [[ "${FC}" != "flang-new-20" ]]; then
if [[ -z "${USE_ASAN}" ]]; then
export MALLOC_PERTURB_=$(($RANDOM % 255 + 1))
fi
source ./qa_funcs.sh
NWCHEM=$(get_nwchem_executable)
NWCHEM_TOP=$(get_nwchem_top)
NWCHEM_TARGET=$(get_nwchem_target)
if [[ ! -z "${BUILD_MPICH}" ]]; then
export MPIRUN_PATH=$NWCHEM_TOP/src/libext/bin/mpiexec
export LD_LIBRARY_PATH=$NWCHEM_TOP/src/libext/lib:$LD_LIBRARY_PATH
fi
cd $NWCHEM_TOP/QA
# A subdirectory of the current directory name testoutputs is made
# if necessary and all outputs are routed there. Existing outputs
# are overwritten. The name of the output file is formed by replacing
# the trailing .nw with .out. In this directory is also put the
# output of nwparse for the verified and the test outputs.
if [ -n "$NONSTD_MPI" ]; then
NONSTD_MPI=1
else
NONSTD_MPI=0
fi
if [[ $# -eq 0 ]] ; then
goto USAGE
fi
NPROC=0
argv_set_nproc=0
get_nproc=0
args_2_use=()
for argument in "$@"
do
#foreach argument ($argv)
if [ $get_nproc -ne 0 ]; then
NPROC=$argument
let argv_set_nproc++
let get_nproc=0
elif [ $argument == "procs" ]; then
let get_nproc=1
else
args_2_use+=($argument)
fi
done
#
# now remove first dummy argument from args_2_use
# args_2_use = ($args_2_use[2-])
CURDIR=$(pwd)
if [[ -x $"NWCHEM" ]]; then
echo failed: cannot execute \"$NWCHEM\"
exit 1
fi
# Figure out where the nwparse.pl script is.
if [ -z "$NWPARSE" ]; then
if [ -f nwparse.pl ]; then
NWPARSE=${CURDIR}/nwparse.pl
elif [[ -n $NWCHEM_TOP ]]; then
NWPARSE=${NWCHEM_TOP}/QA/nwparse.pl
else
echo failed: Cannot find nwparse.pl. Set NWPARSE or NWCHEM_TOP appropriately.
exit 1
fi
fi
#bash script to round ESP
ROUND_ESP=${CURDIR}/round_esp.sh
if [ $NPROC -gt 0 ]; then
# find mpirun
if [[ -n $MPIRUN_PATH ]]; then
MPIRUN="$MPIRUN_PATH"
else
MPIRUN=`which mpirun`
if [ ! -f "$MPIRUN" ]; then
echo " Mpirun is not in your current path. Please do:"
echo " setenv MPIRUN_PATH /home/guido/bagheria/bin/mpirun "
echo " Please make sure you have the right mpirun for your system."
echo " Alternatively set the number of processors to 0."
exit 2
fi
fi
fi
# find the -np option ??
if [ $NPROC -gt 0 ]; then
if [[ -n $MPIRUN_NPOPT ]]; then
NPOPT=$MPIRUN_NPOPT
else
if [ $NONSTD_MPI -eq 1 ]; then
# you are on your own anyway...
echo az
else
NPOPT=-np
$MPIRUN $NPOPT 1 "echo"
status=$?
if [ $status -ne 0 ]; then
echo " Mpirun number of processors option is assumed to be:"
echo " -np "
echo " If this is not the case then please do:"
echo " setenv MPIRUN_NPOPT <nproc_opt> "
echo " where <nproc_opt> is the number of processors option for"
echo " your mpirun."
fi
fi
fi
fi
# Run the tests one at a time
SCRATCHDIR=${CURDIR}/scratchdir
TESTOUTPUTS=${CURDIR}/testoutputs
if [ ! -d $TESTOUTPUTS ]; then
mkdir $TESTOUTPUTS
status=$?
if [ $status -ne 0 ]; then
echo failed: cannot make directory $TESTOUTPUTS
exit 1
fi
fi
let overall_status=0
for TEST_in in "${args_2_use[@]}"
do
cd $CURDIR
TEST=tests/${TEST_in}
TESTDIR=${TEST}
STUB=`basename ${TEST}`
#
# if $TEST is not a directory try use as root of filenames
#
if [ ! -d $TEST ]; then
TESTDIR=`echo $TEST | sed 's+/[^/]*$++'`
fi
#
# if $TESTDIR not directory skip
#
if [ ! -d $TESTDIR ]; then
echo failed: could not find job in $TEST
echo ignoring this failure
continue
fi
echo " "
echo " Running $TESTDIR/$STUB "
echo " "
# Clean the scratch directory and copy the input and verified output
# files to the scratch and test output directories
echo " cleaning scratch"
/bin/rm -rf $SCRATCHDIR
if [ ! -d $SCRATCHDIR ]; then
mkdir $SCRATCHDIR
status=$?
if [ $status -ne 0 ]; then
echo failed: cannot make $SCRATCHDIR
exit 1
fi
fi
echo " copying input and verified output files"
OUTPUTFILE=${STUB}.out
ERRORFILE=${STUB}.err
INPUTFILE=${STUB}.nw
#
# MD input files
#
TESTFILE=${STUB}.tst
RESTARTFILE=${STUB}.rst
RDFINPUTFILE=${STUB}.rdi
MRINPUTFILE=${STUB}.mri
TOPOLOGYFILE=`echo $STUB.top | sed 's/_.*\././'`
PDBFILE=`echo $STUB.pdb | sed 's/_.*\././'`
#
# ESP file
#
ESPFILE=${STUB}.q
#
let md_test_run=0
if [ -f ${TESTDIR}/${TOPOLOGYFILE} ]; then
md_test_run=1
fi
if [ -f $TESTDIR/$PDBFILE ]; then
md_test_run=1
fi
if [ -f $TESTDIR/$TESTFILE ]; then
md_test_run=1
fi
#
let esp_test_run=0
if [ -f $TESTDIR/$ESPFILE ]; then
esp_test_run=1
fi
#
#MV
# qmmm will be signified by the presence of
# empty file named "qmmm"
let qmmm_test_run=0
if [ -f $TESTDIR/qmmm ]; then
qmmm_test_run=1
# if qmmm run md is off
md_test_run=0
fi
#MV
sync
if [ ! -f $TESTDIR/$INPUTFILE ]; then
echo failed: cannot access $TESTDIR/$INPUTFILE
echo directory content
printf "$(ls -lrt $TESTDIR) \n"
overall_status=1
continue
fi
INPUTFILE=${NWCHEM_TOP}/QA/${TESTDIR}/${INPUTFILE}
if [[ ! -z "$USE_SIMINT" ]]; then
rm -f mynewinput.nw
echo 'set int:cando_txs f' >> mynewinput.nw
echo 'set int:cando_nw f' >> mynewinput.nw
cat ${INPUTFILE} >> mynewinput.nw
INPUTFILE=`pwd`/mynewinput.nw
echo INPUTFILE modified for Simint is ${INPUTFILE}
fi
# copy movecs for ducc test
[ -f ${TESTDIR}/*.movecs ] && cp ${TESTDIR}/*movecs ${SCRATCHDIR}
if [ $md_test_run -ne 1 ]; then
if [ ! -f ${TESTDIR}/${OUTPUTFILE} ]; then
echo failed: Could not find verified output file $TESTDIR/$OUTPUTFILE
overall_status=1
continue
fi
fi
# cp $TESTDIR/$INPUTFILE $SCRATCHDIR
[ -f ${TESTDIR}/${STUB}.xyz ] && cp ${TESTDIR}/${STUB}.xyz ${SCRATCHDIR}
[ -f ${TESTDIR}/EMBPOT ] && cp ${TESTDIR}/EMBPOT ${SCRATCHDIR}
[ -f ${TESTOUTPUTS}/${STUB}.ok.out ] && /bin/rm -f ${TESTOUTPUTS}/${STUB}.ok.out
if [ $md_test_run -ne 0 ]; then
[ -f ${TESTDIR}/${OUTPUTFILE} ] && cp $TESTDIR/$OUTPUTFILE $TESTOUTPUTS/$STUB.ok.out
else
cp ${TESTDIR}/${OUTPUTFILE} ${TESTOUTPUTS}/${STUB}.ok.out
fi
#
# copy the MD files
#
if [ $md_test_run -ne 0 ]; then
[ -f ${TESTDIR}/amber.par ] && cp ${TESTDIR}/amber.par ${SCRATCHDIR}
cp ${TESTDIR}/${TESTFILE} ${TESTOUTPUTS}/${STUB}.ok.tst
[ -f ${TESTDIR}/${TOPOLOGYFILE} ] && cp ${TESTDIR}/${TOPOLOGYFILE} ${SCRATCHDIR}
[ -f ${TESTDIR}/${RESTARTFILE} ] && cp ${TESTDIR}/${RESTARTFILE} ${SCRATCHDIR}
[ -f ${TESTDIR}/${RDFINPUTFILE} ] && cp ${TESTDIR}/${RDFINPUTFILE} ${SCRATCHDIR}
[ -f ${TESTDIR}/${PDBFILE} ] && cp ${TESTDIR}/${PDBFILE} ${SCRATCHDIR}
[ -f ${TESTDIR}/${MRINPUTFILE} ] && cp ${TESTDIR}/${MRINPUTFILE} ${SCRATCHDIR}
fi
if [ $qmmm_test_run -ne 0 ]; then
cp ${TESTDIR}/*rst ${SCRATCHDIR}
cp ${TESTDIR}/*top ${SCRATCHDIR}
fi
#
# copy the ESP file
#
if [ $esp_test_run -ne 0 ]; then
cp ${TESTDIR}/$ESPFILE $TESTOUTPUTS/${STUB}.ok.q
fi
#
# copy the Plumed file
#
PLUMEDFILE=${STUB}.plumed.dat
[ -f ${TESTDIR}/${PLUMEDFILE} ] && cp ${TESTDIR}/${PLUMEDFILE} ${SCRATCHDIR}
#
# Run the calculation in the scratch directory
cd ${SCRATCHDIR}
[ -f $TESTOUTPUTS/${STUB}.out ] && /bin/rm -f $TESTOUTPUTS/${STUB}.out
NPROC_out=$NPROC
if [ $NPROC_out == 0 ]; then NPROC_out=1; fi
echo " running nwchem ($NWCHEM) with "$NPROC_out" processors "
x="%Uu %Ss %E %P (%Xt+%Dds+%Kavg+%Mmax)k %Ii+%Oo %Fpf %Wswaps"
time=(1 "$x")
echo " "
#
# MD creates it own ${STUB}.out
#
sync
if [ $md_test_run -ne 0 ]; then
if [ $NPROC -gt 0 ]; then
if [ $NONSTD_MPI -ne 0 ]; then
if [ -z $USE_SLEEPLOOP ]; then
${MPIRUN} ${NWCHEM} ${INPUTFILE} 2> ${ERRORFILE} 1> ${OUTPUTFILE}
else
${NWCHEM_TOP}/QA/sleep_loopqa.sh $MPIRUN $NPOPT $NPROC $NWCHEM $INPUTFILE 2> $ERRORFILE 1> $OUTPUTFILE
fi
runstatus=$?
else
$MPIRUN $NPOPT $NPROC $NWCHEM $INPUTFILE 2> $ERRORFILE 1> $OUTPUTFILE
sync
runstatus=$?
fi
else
$NWCHEM $INPUTFILE 2> $ERRORFILE 1> $OUTPUTFILE
runstatus=$?
fi
[ -f $OUTPUTFILE ] && cp $OUTPUTFILE $TESTOUTPUTS/$OUTPUTFILE
if [ -f $TESTFILE ]; then
cp ${TESTFILE} ${TESTOUTPUTS}/${TESTFILE}
fi
if [ -f $TOPOLOGYFILE ]; then
cp ${TOPOLOGYFILE} ${TESTOUTPUTS}/${TOPOLOGYFILE}
fi
else
#
if [ $NPROC -gt 0 ]; then
#echo "launching"
#echo "mpirun is" $MPIRUN
#echo "-np otp equal to " $NPOPT
#echo "nwchem exex is" $NWCHEM
#if($NONSTD_MPI) then
#echo " command is" $MPIRUN $NWCHEM $INPUTFILE $TESTOUTPUTS/$OUTPUTFILE
#else
#echo " command is" $MPIRUN $NPOPT $NPROC $NWCHEM $INPUTFILE $TESTOUTPUTS/$OUTPUTFIL
#fi
if [ $NONSTD_MPI -eq 1 ]; then
# In case we are using some non-standard MPI environment (e.g. slurm)
# we cannot expect we can construct a sensible command line here.
# Therefore we will depend on some command baked at a point where we
# know what we are doing (i.e. above this script) and simply use that
# verbatim. Set MPIRUN_PATH for this purpose, its value is transfered
# to MPIRUN at some point in this script.
$MPIRUN $NWCHEM $INPUTFILE 2> $TESTOUTPUTS/$ERRORFILE 1> $TESTOUTPUTS/$OUTPUTFILE
runstatus=$?
else
# In the case of standard MPI we construct the appropriate command here.
if [ -z $USE_SLEEPLOOP ]; then
$MPIRUN $NPOPT $NPROC $NWCHEM $INPUTFILE 2> ${TESTOUTPUTS}/${ERRORFILE} 1> ${TESTOUTPUTS}/${OUTPUTFILE}
else
${NWCHEM_TOP}/QA/sleep_loopqa.sh $MPIRUN $NPOPT $NPROC $NWCHEM $INPUTFILE 2> $ERRORFILE 1> $OUTPUTFILE
fi
runstatus=$?
fi
else
$NWCHEM $INPUTFILE 2> $TESTOUTPUTS/$ERRORFILE 1> $TESTOUTPUTS/$OUTPUTFILE
runstatus=$?
fi
#
fi
#
if [ $runstatus -ne 0 ]; then
echo " NWChem execution failed"
let "overall_status+=1"
tail -50 $TESTOUTPUTS/$OUTPUTFILE
cat $TESTOUTPUTS/$ERRORFILE
continue
fi
time=(60 "$x")
cd $TESTOUTPUTS
#
if [ $md_test_run -eq 1 ]; then
echo -n " verifying nwout ...... "
# verify ${STUB}.nwout here for QMD & QM/MM
echo "skipped"
diff1status=0
else
# Now verify the output
echo -n " verifying output ... "
# check if nga_wait is present in the output
grep nga_wait ${STUB}.out > /dev/null
if [ $? -eq 0 ]; then
echo nga_wait warnings in the output file
echo
echo Failed
echo
exit 1
fi
# get rid of HYDRA_DEBUG confusing output
rm -f hydradebugout.txt
grep -v proxy:0:0@ ${STUB}.out > hydradebugout.txt
mv hydradebugout.txt ${STUB}.out
perl $NWPARSE ${STUB}.out >& /dev/null
if [ $? -ne 0 ]; then
echo nwparse.pl failed on test output ${STUB}.out
overall_status=1
continue
fi
perl $NWPARSE ${STUB}.ok.out >& /dev/null
if [ $? -ne 0 ]; then
echo nwparse.pl failed on verified output ${STUB}.ok.out
set overall_status = 1
continue
fi
# delete @GW lines for BSE tests
if [[ `grep -c 'NWChem BSE Module' ${STUB}.out` > 0 ]] ; then
rm -f sort.new
cat ${STUB}.ok.out.nwparse |grep -v @GW > sort.new && mv sort.new ${STUB}.ok.out.nwparse
rm -f sort.new
cat ${STUB}.out.nwparse |grep -v @GW > sort.new && mv sort.new ${STUB}.out.nwparse
fi
#check if output is from EOMCCSD, since EOMCCSD output is non-deterministic
if [[ `grep -c EOMCCSD ${STUB}.out.nwparse` > 0 ]] ; then
rm -f sort.new
sort -n ${STUB}.ok.out.nwparse > sort.new && mv sort.new ${STUB}.ok.out.nwparse
rm -f sort.new
sort -n ${STUB}.out.nwparse > sort.new && mv sort.new ${STUB}.out.nwparse
fi
diff -w ${STUB}.ok.out.nwparse ${STUB}.out.nwparse >& /dev/null
diff1status=$?
cat ${ERRORFILE}
#
fi
#
if [ $diff1status -ne 0 ]; then
echo "failed"
echo "@@@ Comparison of Output Files"
diff -U2 ${STUB}.ok.out.nwparse ${STUB}.out.nwparse | sed 1,2d
# echo "@@@ Paste beginning of Output File"
# head -1000 ${STUB}.out
# echo "@@@ Paste End of Output File"
# tail -1000 ${STUB}.out
let "overall_status+=1"
continue
else
#
# diff MD test files
#
if [ $md_test_run -eq 0 ] && [ $esp_test_run -eq 0 ]; then # Now verify the output
echo "OK"
elif [ $esp_test_run -ne 0 ]; then
cp ${SCRATCHDIR}/$ESPFILE $TESTOUTPUTS/.
# echo "doing ls -l " ${STUB}.ok.q ${STUB}.q
# echo `ls -l ${STUB}.ok.q ${STUB}.q`
rm -f esp_temp.ok.q esp_temp.q
${ROUND_ESP} ${STUB}.ok.q > esp_temp.ok.q
${ROUND_ESP} ${STUB}.q > esp_temp.q
diff -w esp_temp.ok.q esp_temp.q >& /dev/null
# diff -w ${STUB}.ok.q ${STUB}.q >& /dev/null
espstatus=$?
if [[ $espstatus -ne 0 ]]; then
echo "ESP comparison failed"
let "overall_status+=1"
diff -u esp_temp.ok.q esp_temp.q
continue
else
echo "ESP charges match"
fi
rm -f esp_temp.ok.q esp_temp.q
echo
else
echo -n " verifying test ....... "
#
if [ -f ${STUB}.tst ]; then
diff -w ${STUB}.ok.tst ${STUB}.tst >& /dev/null
if [ $? -ne 0 ]; then
echo "failed"
let "overall_status+=1"
continue
else
echo "completed"
fi
else
echo "skipped"
echo -n " verifying topology ... "
ttt=`diff -w ${STUB}.ok.tst ${TOPOLOGYFILE} | wc -l`
if [ $ttt -eq 4 ]; then
echo "completed "
else
echo "failed"
let "overall_status+=1"
continue
fi
fi
fi
fi
done
cd $CURDIR
/bin/rm -rf ${SCRATCHDIR}
echo " "
if [ $overall_status -ne 0 ]; then
echo Failed
else
echo OK
fi
exit $overall_status
USAGE:
echo "runtest.unix [-procs nproc] testdir1 [testdir2 ...]"
echo " -procs nproc sets the number of processors to use"
exit 0
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