Calc testjobs linux.sh

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.

#!/bin/bash
# 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 "Only trying single cpu binaries"
  _HIPPO_BINARIES="hippo hippo_p3"
else
  _HIPPO_BINARIES="hippo_mpi hippo hippo_p3_mpi hippo_p3"
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"