Scripts: Added mogon2 mdtest slurm script

usage_short() {

        echo "

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

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

                    benchmark_dir

        "

}

#!/bin/bash

# Slurm stuff

#SBATCH -J adafs_ior

#SBATCH -p nodeshort

#SBATCH -t 300

#SBATCH -A zdvresearch

##SBATCH --gres=ramdisk:16G

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=""

START_TIME="$(date -u +%s)"

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_m2/install/bin:/home/vef/.local/bin

C_INCLUDE_PATH=$C_INCLUDE_PATH:/home/vef/adafs_m2/install/include

CPATH=$CPATH:/home/vef/adafs_m2/install/include

CPLUS_INCLUDE_PATH=$CPLUS_INCLUDE_PATH:/home/vef/adafs_m2/install/include

LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/vef/adafs_m2/install/lib

LIBRARY_PATH=$LIBRARY_PATH:/home/vef/adafs_m2/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_m2/install/lib/'

export CPPFLAGS='-I/home/vef/adafs_m2/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=64/' -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_m2/scripts/startup_adafs.py -c -J ${SLURM_JOB_ID} --numactl "--cpunodebind=0 --membind=0" ${VEF_HOME}/ifs_m2/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

BENCHCMD="mpiexec -np ${MD_PROC_N} --map-by node --hostfile ${HOSTFILE} -x LD_PRELOAD=/lustre/project/zdvresearch/vef/fs/ifs/build/lib/libadafs_preload_client.so --cpunodebind=1 --membind=1 /lustre/miifs01/project/zdvresearch/vef/benchmarks/ior/build/src/mdtest -z 0 -b 1 -i ${MD_ITER} -d ${MD_DIR} -F -I ${MD_ITEMS} -C -r -T -v 1 ${MD_UNIQUE}"

eval ${BENCHCMD}

echo "

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

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

"

END_TIME="$(date -u +%s)"

ELAPSED="$((${END_TIME}-${START_TIME}))"

MINUTES=$((${ELAPSED} / 60))

echo "##Elapsed time: ${MINUTES} minutes or ${ELAPSED} seconds elapsed for test set."

# 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}