Calc testjobs linux.sh
From Biowerkzeug Wiki
This script allows running Hippo benchmarks without having to think too much about finding the correct binary and supplemental files. In addition it gives the total wall time required to run each test case; this can be used for crude benchmarks.
- The testing of the mpi binaries is not tested and probably does not work. However, they are only needed for replica exchange simulations and there are no test cases for those anyway.
- Not all tests support multi-threaded runs (with OpenMP); these tests ignore the NSLOTS argument.
#!/bin/bash # $Id: calc_testjobs_linux.sh 2535 2008-12-07 16:07:19Z www-data $ # Running Hippo tests (Linux) # Copyright (c) 2008 Biowerkzeug # Oliver Beckstein <orbeckst@gmail.com> #set -x prog=$(basename $0) CURDIR=${PWD} # defaults (: can be set in environment) : ${HIPPO_DIR:="${CURDIR}/.."} HIPPO_TESTS="hexane_NVT_dp_MD octane_NPT_sp_MC pentadecane_NPT_sp_MD tip3p_NPT_sp_MD trpzip2_GBSA_MC vpu_GBIM_MC walp_octane_NPT_sp_MD" RUN_TESTS=${HIPPO_TESTS} USE_MPI=0 usage="usage $prog [opts] [tests] Run Hippo tests. By default it runs all of them: ${HIPPO_TESTS} OPTIONS: -h help -n number of threads (not possible for all tests) -D directory where we look for Hippo executables [${HIPPO_DIR}] -M use mpi (replica exchange) binaries [${USE_MPI}] Environment variables: HIPPO_DIR overrides -D [${HIPPO_DIR}] " function die () { local msg="$1" err=${2:-1} echo 1>&2 "ERROR: failed in $PWD: ${msg}" cd ${CURDIR} exit $err } NSLOTS=1 # opt processing while getopts hn:D:M: opt; do case $opt in h) echo "$usage"; exit 0;; n) NSLOTS=${OPTARG};; D) HIPPO_DIR=${OPTARG};; M) USE_MPI=${OPTARG};; *) die "Unknown option" 1;; esac done #echo "OPTIND=$OPTIND OPTARG=$OPTARG argv=$*" shift $((OPTIND - 1)) if [ -n "$*" ]; then RUN_TESTS="$*" fi echo "Running the following tests using ${NSLOTS} threads: ${RUN_TESTS}" # find working executable # we'll use the first one that only complain about missing input file # if [ ${USE_MPI} = 0 ]; then echo "Trying standard binaries (with OpenMP)" _HIPPO_BINARIES="hippo hippo_p3" else echo "Testing mpi binaries. Note: these are ONLY needed for replica exchange simulations" _HIPPO_BINARIES="hippo_mpi hippo_p3_mpi" fi HIPPO="not_found" rm -f hippo_input.txt # clean any input files for h in ${_HIPPO_BINARIES}; do exe="${HIPPO_DIR}/${h}" if ${exe} 2>&1 | egrep "^Hippo.*Copyright.*Biowerkzeug" >/dev/null; then HIPPO=${exe} break fi done if [ "${HIPPO}" = "not_found" ]; then ARCH=$(uname -m); OS=$(uname -s); die "No usable hippo executable found; see if there is one at http://www.biowerkzeug.com for your architecture ${ARCH} and operating system ${OS}. " fi echo "Using executable ${HIPPO}" TOPOLOGY=${HIPPO_DIR}/hippo_protein_database.dat FF=${HIPPO_DIR}/oplsaa_forcefield.dat echo "Setting up test directory" rm -rf test mkdir test cd test topdir="${CURDIR}/test" function setup_hippo () { local numthreads=${1:-1} local input=hippo_input.txt cp ${HIPPO} ./hippo || return $? cp ${TOPOLOGY} . || return $? cp ${FF} . || return $? test -e $input || die "Missing run input file $input in $PWD" if [ $NSLOTS -gt 1 ]; then # adjusting for OpenMP run sed -i.orig -e "s/[[:space:]]*openMP numthreads.*/openMP numthreads ${numthreads}/" $input fi return 0 } function run_test () { local testdir="$1" numthreads="${2:-1}" echo "---------------------------------------------------------" cd ${testdir} || die "Cannot 'cd ${testdir}'" setup_hippo ${numthreads} || die "setup_hippo() failed" echo "Set up all files for NSLOTS=${numthreads}" echo "Running hippo test case ${testdir}..." t_start=$(date +%s) ./hippo t_stop=$(date +%s) delta_t=$(( t_stop-t_start )) echo "Completed hippo test case ${testdir} in ${delta_t} seconds, running ${numthreads} threads" echo "BENCHMARK: ${testdir} ${numthreads} ${delta_t}" cd ${topdir} } cp -r ../jobs/* . for t in ${RUN_TESTS}; do run_test $t ${NSLOTS} done echo "Finished running hippo test suite"