ddn-ime-evaluation/batch_job.sh

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#!/bin/bash
#SBATCH -w isc17-c[02,03,04,05,08,09,10,12,14,23]
#SBATCH --dependency=singleton
#SBATCH --output=slurm/slurm-%j.txt
#SBATCH --job-name=DDNIME
##SBATCH -w isc17-c[02-06,08-10,12-14,18]
#These nodes can be used with DDN IME
##SBATCH --distribution=block
SCRIPT="$(readlink -f $0)"
SCRIPTPATH="$(dirname $SCRIPT)"
cd "$SCRIPTPATH"
function die() {
echo "$1" && exit 1
}
export MODULEPATH=/gsfs/betke/software/modules:$MODULEPATH
#module purge
#module load ddn/mvapich/3.1.4
#module load betke/hdf5/1.8.20
#module load betke/netcdf/4.4.1
#module load betke/ior/git
#module load betke/netcdf-bench/git-20171206
#module list
module purge
module load ddn/mvapich/3.1.4
module load betke/hdf5/1.8.20-ddn
module load betke/netcdf/4.4.1-ddn
module load betke/ior/git-ddn
module load betke/netcdf-bench/git-20171206-ddn
module list
type mpiexec 2>&1 || die "mpiexec not found"
type benchtool 2>&1 || die "benchtool not found"
IOR="$(which ior)" # default IOR (path to DDN-IOR is hardcoded in the nested loops)
NCBENCH="$(which benchtool)"
TESTDIR="/ime/isc18/perf"
TIMESTAMP="20171218_162418"
LUSTRE_TESTFILE="/esfs/isc18/perf/file"
FUSE_TESTFILE="/ime/isc18/perf/file"
IME_TESTFILE="ime:///esfs/isc18/perf/file"
OUTPUTDIR="./output"
SLURM_OUTPUT="slurm/slurm-%j.txt"
WORKDIR="/gsfs/betke/git/manny-benchmark/scripts"
cd $WORKDIR
# Benchmarks to run
# NCBENCH - NetCDF bench
# IOR - default IOR and DDN-IOR
PROG_ARR=("$IOR" "$NCBENCH")
# Experiment scaling
# NN_ARR: number of nodes
# PPN_ARR: processes per node
NN_ARR=(10 8 6 4 2 1)
PPN_ARR=(8 6 4 2 1)
# Data geomentry of int (4 bytes) values
# Attention: it was too small in the previous experiments
# TIME, X, Y, Z: size of dimensizion
# size = time * x * y * z * 4 bytes
TIME_ARR=(100)
XGEOM_ARR=($((8 * 2)))
YGEOM_ARR=($((8 * 8)))
ZGEOM_ARR=(2560 256 25 4)
# I/O type (only for NetCDF-Bench, ior runs alway in independent mode)
# ind - independent
# coll - collective
TYPE_ARR=("ind" "coll")
# Interface list
# ime - direct access to IME using DDN-IOR
# mpio - enable MPIO interface in IOR
# posix - enable POSIX interface in IOR
IFACE_ARR=("ime" "mpio" "posix")
# File systems list
# ime - direct access to IMEs using DDN IOR
# fuse - indirect accesss to IMEs over FUSE
# lustre - Lustre files system
FS_ARR=("ime" "lustre" "fuse")
# NetCDF4 chunking
# none - disable chunking
# auto - chunking enabled (see netcdf-bench documentation for details)
CHUNKED_ARR=("none" "-c=auto")
# NetCDF4 unlimited dimensions
# none - disabled unlimited dimensions
# -u - enabled unlimited dimenstions
UNLIMITED_ARR=("none" "-u") # ( "none" "-u" )
# NetCDF4 fill value
# none - disable fill value
# -F - enable fill value
FILL_VALUE_ARR=("none") # "-F" )
#####
SLURMDIR="$(dirname $SLURM_OUTPUT)"
mkdir -p $SLURMDIR
TDIR="$(dirname $IME_TESTFILE)"
srun --nodes=1 --ntasks=1 mkdir -p $TDIR
mkdir -p $OUTPUTDIR
# Run an experiment
function runTest(){
local l_command="$1"
local l_out="$2"
local l_testdir="$3"
local l_stripes="$4"
local l_wml="$(which mpiexec) -ppn 1 -np 1"
local l_timestamp=$(date +"%Y%m%d_%H%M%S")
echo "create $l_out"
touch $l_out
echo "${l_timestamp}" &>> $l_out
echo "FILENAME $l_out" &>> $l_out
rm -rf $l_testdir
mkdir -p $l_testdir
lfs setstripe -c $l_stripes $l_testdir
echo "$l_command" | tee -a $l_out
#eval "$l_command >> $l_out 2>&1"
$l_command >> $l_out 2>&1
lfs getstripe $l_testdir >> $l_out 2>&1
rm -rf $l_testdir
}
# Create function names
function makeOutputName() {
local l_outdir="$1"
local l_tag="$2"
local l_count="${3}"
local l_prog="$4"
local l_nn="$5"
local l_ppn="$6"
local l_t="$7"
local l_x="$8"
local l_y="$9"
local l_z="${10}"
local l_type="${11}"
local l_iface="${12}"
local l_fs="${13}"
local l_c="${14}"
local l_u="${15}"
local l_f="${16}"
[[ "${l_c}" == "none" ]] && l_c="notset" || l_c="auto"
[[ "${l_u}" == "none" ]] && l_u="notset" || l_u="set"
[[ "${l_f}" == "none" ]] && l_f="notset" || l_f="set"
local l_out="${l_outdir}/COUNT:${l_count}#TAG:${l_tag}#PROG:${l_prog}#NN:${l_nn}#PPN:${l_ppn}#TYPE:${l_type}#IFACE:${l_iface}#FS:${l_fs}#CHUNKED:${l_c}#FILLED:${l_f}#UNLIMITED:${l_u}#output:$l_t:${l_x}:${l_y}:${l_z}.txt"
echo ${l_out}
}
# Parameter exploration loops
for COUNT in $(seq 3); do
for PROG in ${PROG_ARR[@]}; do
for NN in ${NN_ARR[@]}; do
for PPN in ${PPN_ARR[@]}; do
for T in ${TIME_ARR[@]}; do
for X in ${XGEOM_ARR[@]}; do
for Y in ${YGEOM_ARR[@]}; do
for Z in ${ZGEOM_ARR[@]}; do
for TYPE in ${TYPE_ARR[@]}; do
for IFACE in ${IFACE_ARR[@]}; do
for FS in ${FS_ARR[@]}; do
for CHUNKED in ${CHUNKED_ARR[@]}; do
for UNLIMITED in ${UNLIMITED_ARR[@]}; do
for FILL_VALUE in ${FILL_VALUE_ARR[@]}; do
BENCHFILE=$(makeOutputName $OUTPUTDIR $TIMESTAMP $COUNT $(basename $PROG) $NN $PPN $T $X $Y $Z $TYPE $IFACE $FS ${CHUNKED} ${UNLIMITED} ${FILL_VALUE})
STRIPES=$(($NN * 2))
if [ ! -e "${BENCHFILE}" ]; then
if [[ $TYPE == "ind" && $UNLIMITED == "-u" ]]; then
echo "skip ${BENCHFILE}, because -t=ind and -u are not supported"
else
HOST_LIST=isc17-c02,isc17-c03,isc17-c04,isc17-c05,isc17-c08,isc17-c09,isc17-c10,isc17-c12,isc17-c14,isc17-c23
#http://www.prace-ri.eu/best-practice-guide-generic-x86-html/
#"$ADAPTIVE " \
#"-genv IM_MONITOR_FILE /dev/shm/native_mon.%p " \
#"-genv IM_CLIENT_NET_BUFFERS 32 " \
# Workload manager configuration
WLM="$(which mpiexec) -ppn ${PPN} -np $(($NN*$PPN)) -hosts $HOST_LIST "
WLM+="-genv IM_CLIENT_NET_BUFFERS 32 "
WLM+="-genv MV2_NUM_HCAS 1 "
WLM+="-genv MV2_CPU_BINDING_LEVEL core "
WLM+="-genv MV2_CPU_BINDING_POLICY scatter "
WLM+="-genv MV2_SHOW_CPU_BINDING 1 "
#WLM="srun --nodes=$NN --ntasks-per-node=$PPN --ntasks=$(($NN*$PPN))"
#WLM="mpiexec --allow-run-as-root -npernode $(($NN*$PPN)) -N $PPN" # for DDN IME system
#WLM="/opt/ddn/mvapich/bin/mpiexec.hydra -ppn $PPN -np $(($PPN*$NN)) -hosts `nodeset -S "," -e manny[600-607]`"
case "$PROG" in
$IOR)
echo "RUN $IOR"
#set -x
B=$(($X*$Y*$Z*4))
S=$T
if [[ "none" == "${CHUNKED}" ]]; then
if [[ "none" == "${UNLIMITED}" ]]; then
if [[ "none" == "${FILL_VALUE}" ]]; then
$PARAMS="-e -g -z"
PARAMS="-e -g"
if [[ "lustre" == "${FS}" ]]; then
if [[ "posix" == "${IFACE}" ]]; then
if [[ "ind" == "${TYPE}" ]]; then
runTest "$WLM $IOR -s $S -t $B -b $B -o $LUSTRE_TESTFILE $PARAMS -f ./tests/POSIX-individual" "${BENCHFILE}" "$(dirname $LUSTRE_TESTFILE)" "$STRIPES"
fi
elif [[ "mpio" == "${IFACE}" ]]; then
if [[ "ind" == "${TYPE}" ]]; then
runTest "$WLM $IOR -s $S -t $B -b $B -o $LUSTRE_TESTFILE $PARAMS -f ./tests/MPI-shared" "${BENCHFILE}" "$(dirname $LUSTRE_TESTFILE)" "$STRIPES"
fi
fi
elif [[ "fuse" == "${FS}" ]]; then
if [[ "posix" == "${IFACE}" ]]; then
if [[ "ind" == "${TYPE}" ]]; then
runTest "$WLM $IOR -s $S -t $B -b $B -o $FUSE_TESTFILE $PARAMS -f ./tests/POSIX-individual" "${BENCHFILE}" "$(dirname $FUSE_TESTFILE)" "$STRIPES"
fi
elif [[ "mpio" == "${IFACE}" ]]; then
if [[ "ind" == "${TYPE}" ]]; then
runTest "$WLM $IOR -s $S -t $B -b $B -o $FUSE_TESTFILE $PARAMS -f ./tests/MPI-shared" "${BENCHFILE}" "$(dirname $FUSE_TESTFILE)" "$STRIPES"
fi
fi
elif [[ "ime" == "${FS}" ]]; then
if [[ "ime" == "${IFACE}" ]]; then
if [[ "ind" == "${TYPE}" ]]; then
runTest "$WLM /opt/ddn/ior/bin/IOR-mvapich -s $S -t $B -b $B -o $IME_TESTFILE $PARAMS -a "IM"" "${BENCHFILE}" "$TESTDIR" "$STRIPES"
fi
fi
fi
fi
fi
fi
#runTest "$WLM $IOR -a IM -s $S -t $B -b $B -o ime://$TESTFILE -e -f ./tests/MPI-shared" "shared" "${BENCHFILE}" "$TESTDIR" "$STRIPES"
#set +x
;;
$NCBENCH)
echo "RUN $NCBENCH"
#set -x
PARAMS=""
if [[ "none" != "${CHUNKED}" ]]; then
PARAMS+="${CHUNKED} "
fi
if [[ "none" != "${UNLIMITED}" ]]; then
PARAMS+="${UNLIMITED} "
fi
if [[ "none" != "${FILL_VALUE}" ]]; then
PARAMS+="${FILL_VALUE} "
fi
if [[ "lustre" == "${FS}" ]]; then
if [[ "mpio" == "${IFACE}" ]]; then
runTest "$WLM $NCBENCH -f=$LUSTRE_TESTFILE -n=$NN -p=$PPN -d=$T:$(($X*$NN)):$(($Y*$PPN)):$Z -w -r -t=$TYPE $PARAMS" "${BENCHFILE}" "$(dirname ${LUSTRE_TESTFILE})" "$STRIPES" "$DEBUG"
fi
elif [[ "fuse" == "${FS}" ]]; then
if [[ "mpio" == "${IFACE}" ]]; then
runTest "$WLM $NCBENCH -f=$FUSE_TESTFILE -n=$NN -p=$PPN -d=$T:$(($X*$NN)):$(($Y*$PPN)):$Z -w -r -t=$TYPE $PARAMS" "${BENCHFILE}" "$(dirname ${FUSE_TESTFILE})" "$STRIPES" "$DEBUG"
fi
fi
#set +x
;;
*)
echo "$PROG not supported"
exit 1
esac
fi
else
echo "skip $(readlink -f $BENCHFILE), already exists"
fi
#exit
done
done
done
done
done
done
done
done
done
done
done
done
done
done
exit 0