Adding mdtest sbatch script

        57, 46, 52, 38, 26, 32, 41, 50, 36, 17, 19, 29, 10, 13, 21, 56,

        45, 25, 31, 35, 16, 9, 12, 44, 24, 15, 8, 23, 7, 6, 5, 63 };

    assert(n > 0);

    assert(n > 0); // TODO This needs to be removed and a check for CHUNKSIZE has to be put somewhere

    n |= n >> 1;

    n |= n >> 2;

#!/bin/bash

# Slurm stuff

#SBATCH -J adafs_mdtest

#SBATCH -p nodeshort

#SBATCH -t 300

#SBATCH -A zdvresearch

#SBATCH --gres=ramdisk:20G

usage_short() {

        echo "

usage: adafs_mdtest.sh [-h] [-n <MD_PROC_N>] [-i <MD_ITER>] [-I <NUM_ITEMS>] [-u]

                    benchmark_dir

        "

}

help_msg() {

        usage_short

    echo "

This slurm batch script is for mdtesting adafs

positional arguments:

        benchmark_dir           path where the dependency downloads are put

optional arguments:

        -h, --help              shows this help message and exits

        -n <MD_PROC_N>

                                number of processes used in mdtest

                                defaults to '1'

        -i <MD_ITER>

                                number of iterations done in mdtest

                                defaults to '1'

        -I <NUM_ITEMS>          number of files per process in mdtest

                                defaults to '500000'

        -u, --unique            use if files should be placed in a unique directory per-process in mdtest

        "

}

MD_PROC_N=16

MD_ITER=1

MD_ITEMS="500000"

MD_UNIQUE=""

POSITIONAL=()

while [[ $# -gt 0 ]]

do

key="$1"

case ${key} in

    -n)

    MD_PROC_N="$2"

    shift # past argument

    shift # past value

    ;;

    -i)

    MD_ITER="$2"

    shift # past argument

    shift # past value

    ;;

    -I)

    MD_ITEMS="$2"

    shift # past argument

    shift # past value

    ;;

    -u|--unique)

    MD_UNIQUE="-u"

    shift # past argument

    ;;

    -h|--help)

    help_msg

    exit

    #shift # past argument

    ;;

    *)    # unknown option

    POSITIONAL+=("$1") # save it in an array for later

    shift # past argument

    ;;

esac

done

set -- "${POSITIONAL[@]}" # restore positional parameters

# positional arguments

if [[ -z ${1+x} ]]; then

    echo "Positional arguments missing."

    usage_short

    exit

fi

VEF_HOME="/home/vef"

HOSTFILE="${VEF_HOME}/jobdir/hostfile_${SLURM_JOB_ID}"

MD_DIR=$1

ROOTDIR="/localscratch/${SLURM_JOB_ID}/ramdisk"

# Load modules and set environment variables

PATH=$PATH:/home/vef/adafs/install/bin:/home/vef/.local/bin

C_INCLUDE_PATH=$C_INCLUDE_PATH:/home/vef/adafs/install/include

CPATH=$C_PATH:/home/vef/adafs/install/include

CPLUS_INCLUDE_PATH=$CPLUS_INCLUDE_PATH:/home/vef/adafs/install/include

LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/vef/adafs/install/lib

LIBRARY_PATH=$LIBRARY_PATH:/home/vef/adafs/install/lib

export PATH

export CPATH

export C_INCLUDE_PATH

export CPLUS_INCLUDE_PATH

export LD_LIBRARY_PATH

export LIBRARY_PATH

export LDFLAGS='-L/home/vef/adafs/install/lib/'

export CPPFLAGS='-I/home/vef/adafs/install/include/'

module load devel/CMake/3.8.0

module load mpi/OpenMPI/2.0.2-GCC-6.3.0

module load devel/Boost/1.63.0-foss-2017a

export CC=$(which gcc)

export CXX=$(which g++)

# printing stuff

echo "files per process: ${MD_ITEMS}"

# create a proper hostfile to run

srun -n ${SLURM_NNODES} hostname -s | sort -u > ${HOSTFILE} && sed -e 's/$/ max_slots=32/' -i ${HOSTFILE}

echo "Generated hostfile no of nodes:"

cat ${HOSTFILE} | wc -l

NONODES=$(cat ${HOSTFILE} | wc -l)

let MD_PROC_N=${NONODES}*16

echo "

############################################################################

############################### DAEMON START ############################### ############################################################################

"

# start adafs daemon on the nodes

python2 ${VEF_HOME}/ifs/scripts/startup_adafs.py -c -J ${SLURM_JOB_ID} --numactl "--cpunodebind=0,1 --membind=0,1" ${VEF_HOME}/ifs/build/bin/adafs_daemon ${ROOTDIR} ${MD_DIR} ${HOSTFILE}

#echo "logfiles:"

#cat /tmp/adafs_daemon.log

# pssh to get logfiles. hostfile is created by startup script

${VEF_HOME}/.local/bin/pssh -O StrictHostKeyChecking=no -i -h /tmp/hostfile_pssh_${SLURM_JOB_ID} "tail /tmp/adafs_daemon.log"

echo "

############################################################################

############################ RUNNING BENCHMARK #############################

############################################################################

"

# Run benchmark

echo "Executing: mpiexec -np ${MD_PROC_N} --map-by node --hostfile ${HOSTFILE} -x LD_PRELOAD=/gpfs/fs2/project/zdvresearch/vef/fs/ifs/build/lib/libadafs_preload_client.so ${VEF_HOME}/benchmarks/mogon1/mdtest-1.9.3-modified/mdtest -z 0 -b 1 -i ${MD_ITER} -d ${MD_DIR} -F -I ${MD_ITEMS} -C -r -T -v 1 ${MD_UNIQUE}"

mpiexec -np ${MD_PROC_N} --map-by node --hostfile ${HOSTFILE} -x LD_PRELOAD=/gpfs/fs2/project/zdvresearch/vef/fs/ifs/build/lib/libadafs_preload_client.so ${VEF_HOME}/benchmarks/mogon1/mdtest-1.9.3-modified/mdtest -z 0 -b 1 -i ${MD_ITER} -d ${MD_DIR} -F -I ${MD_ITEMS} -C -r -T -v 1 ${MD_UNIQUE}

echo "

############################################################################

############################### DAEMON STOP ############################### ############################################################################

"

# shut down adafs daemon on the nodes

python2 ${VEF_HOME}/ifs/scripts/shutdown_adafs.py -J ${SLURM_JOB_ID} ${VEF_HOME}/ifs/build/bin/adafs_daemon ${HOSTFILE}

# cleanup

rm ${HOSTFILE}