Merge pull request #96 from Azure/intersect_cycle

Intersect cyclecloud

apps/intersect/install_case_intersect_2018.2.sh

@@ -1,12 +1,12 @@
 #!/bin/bash
 
-DATA_TAR_SAS_URL=/path/to/casedata.tar
+DATA_TAR_SAS_URL=/path/to/casedata.tar.tgz
 DATA_TAR=BO_192_192_28.tgz
 
-SHARED_DATA=/data
+DATA_INSTALL_DIR=${DATA_INSTALL_DIR:-/data}
 
-pushd $SHARED_DATA
-if [ ! -f ${SHARED_DATA}/${DATA_TAR} ]; then
+pushd $DATA_INSTALL_DIR
+if [ ! -f ${DATA_INSTALL_DIR}/${DATA_TAR} ]; then
 wget -O ${DATA_TAR} "$DATA_TAR_SAS_URL"
 fi
 popd

apps/intersect/install_full_intersect_2018.2.sh

@@ -2,19 +2,19 @@
 DOWNLOAD_DIR=/mnt/resource
 
 # setup IX
-ECLPATH=/apps/ecl
-SHARED_APP=/apps
+APP_INSTALL_DIR=${APP_INSTALL_DIR:-/apps}
+ECLPATH=${APP_INSTALL_DIR}/ecl
 APP_NAME=ecl
 APP_VERSION=2018.2
 PACKAGE=${APP_VERSION}_IX_DVD.iso
 PACKAGE2=${APP_VERSION}_DVD.iso
-MODULE_DIR=${SHARED_APP}/modulefiles
+MODULE_DIR=${APP_INSTALL_DIR}/modulefiles
 MODULE_NAME=intersect_${APP_VERSION}
 
 #NOTE!!! Populate these variables before running the script
 LICENSE_PORT_IP=<PORT@IP for license server>
-IX_ISO_SAS_URL=/path/to/intersect_iso.tar
-ECLIPSE_ISO_SAS_URL=/path/to/eclipse_iso.tar
+IX_ISO_SAS_URL=/path/to/2018.2_IX_DVD.iso
+ECLIPSE_ISO_SAS_URL=/path/to/2018.2_DVD.iso
 
 function create_intersect_modulefile {
 mkdir -p ${MODULE_DIR}
@@ -23,8 +23,8 @@ cat << EOF >> ${MODULE_DIR}/${MODULE_NAME}
 #
 #  intersect module for use with 'environment-modules' package:
 #
-prepend-path            PATH                   ${SHARED_APP}/${APP_NAME}/tools/linux_x86_64/eclpython/bin
-prepend-path            PATH                   ${SHARED_APP}/${APP_NAME}/macros
+prepend-path            PATH                   ${APP_INSTALL_DIR}/${APP_NAME}/tools/linux_x86_64/eclpython/bin
+prepend-path            PATH                   ${APP_INSTALL_DIR}/${APP_NAME}/macros
 setenv                  LM_LICENSE_FILE        ${LICENSE_PORT_IP}
 setenv                  F_UFMTENDIAN           big
 EOF
@@ -40,7 +40,7 @@ sudo mount -t iso9660 -o loop ${DOWNLOAD_DIR}/${PACKAGE2} /mnt/iso2
 csh /mnt/iso2/ECLIPSE/UNIX/install/cdinst.csh <<EOF
 2
 A
-${SHARED_APP}/${APP_NAME}
+${APP_INSTALL_DIR}/${APP_NAME}
 y
 EOF
 
@@ -53,10 +53,11 @@ sudo mount -t iso9660 -o loop ${DOWNLOAD_DIR}/${PACKAGE} /mnt/iso
 
 csh /mnt/iso/UNIX/install/cdinst.csh <<EOF
 A
-${SHARED_APP}/${APP_NAME}
+${APP_INSTALL_DIR}/${APP_NAME}
 y
 EOF
 
 create_intersect_modulefile
 
-sudo sed -i 's/\/opt\/intel\/compilers_and_libraries_2018.1.163\/linux\/mpi/\/apps\/ecl\/tools\/linux_x86_64\/intel\/mpi\/2018.1.163/g' ${ECLPATH}/tools/linux_x86_64/intel/mpi/2018.1.163/intel64/bin/mpivars.sh
+SED_STR="s/\/opt\/intel\/compilers_and_libraries_2018.1.163\/linux\/mpi/\\"${APP_INSTALL_DIR}"\/ecl\/tools\/linux_x86_64\/intel\/mpi\/2018.1.163/g"
+sudo sed -i $SED_STR ${ECLPATH}/tools/linux_x86_64/intel/mpi/2018.1.163/intel64/bin/mpivars.sh

apps/intersect/readme.md

@@ -60,3 +60,44 @@ To see if the job is running do
 ````
 qstat -aw
 ````
+
+## Install and run intersect Benchmarks using [Azure CycleCloud](https://docs.microsoft.com/en-us/azure/cyclecloud/) Cluster
+
+## Prerequisites
+
+These steps require a Azure CycleCloud cluster with PBS.  The `cyclecloud_simple_pbs` template in the examples directory a suitable choice.
+
+Follow the steps in the examples/cyclecloud_simple_pbs/readme.md to setup cycle, import the template and start cluster.
+
+Log in to the headnode of the cluster (from cycleserver):
+
+```
+    $ cyclecloud connect master -c <cyclecloud cluster name>
+```
+
+## Installing Intersect
+
+You will need to copy the apps/intersect folder to the cyclecloud master.
+
+Run the following to install ntersect on the cluster (in /scratch):
+
+export APP_INSTALL_DIR=/scratch
+```
+apps/intersect/install_full_intersect_2018.2.sh
+```
+
+## Install the data sets for intersect
+
+export DATA_INSTALL_DIR=/scratch
+```
+apps/intersect/install_case_intersect_2018.2.sh
+```
+
+## Running Intersect
+
+Copy apps/intersect to the cyclecloud master node.
+
+To run on two HB nodes with 8 total cores (4 cores on each node) run ( Intersect installation and case model are in /scratch)
+```
+qsub -l select=2:ncpus=60:mpiprocs=4 -v case=BO_192_192_28,APP_INSTALL_DIR=/scratch,DATA_INSTALL_DIR=/scratch apps/intersect/run_intersect_2018.2.sh
+```

apps/intersect/run_intersect_2018.2.sh

@@ -4,19 +4,21 @@ set -o pipefail
 
 APP_NAME=intersect
 APP_VERSION=2018.2
-SHARED_APP=/apps
-SHARED_DATA=/data
-ECLPATH=$SHARED_APP/ecl
+case=${case:-BO_192_192_28}
+APP_INSTALL_DIR=${APP_INSTALL_DIR:-/apps}
+DATA_INSTALL_DIR=${DATA_INSTALL_DIR:-/scratch}
+ECLPATH=$APP_INSTALL_DIR/ecl
 #NOTE!! this path will depend on the dataset tar structure. the tar we used had case files under data e.g. data/BO_192_192_28 
-CASEPATH=data/${case}
-source /etc/profile # so we can load modules
-module use $SHARED_APP/modulefiles
+CASEPATH=${PBS_O_WORKDIR}/${case}
+export MODULEPATH=${APP_INSTALL_DIR}/modulefiles:$MODULEPATH
+module use $APP_INSTALL_DIR/modulefiles
 module load intersect_${APP_VERSION}
 source ${ECLPATH}/tools/linux_x86_64/intel/mpi/2018.1.163/intel64/bin/mpivars.sh
 
 cores=`cat $PBS_NODEFILE | wc -l`
 
-cp $SHARED_DATA/${case}.tgz .
+cd $PBS_O_WORKDIR
+cp $DATA_INSTALL_DIR/${case}.tgz .
 tar xvf ${case}.tgz
 #
 start_time=$SECONDS
@@ -31,8 +33,6 @@ eclrun_time=$(($end_time - $start_time))
 
 case_output=$CASEPATH/${case}.LOG
 
-cp -r $CASEPATH $SHARED_DATA
-
 # extract telemetry
 if [ -f "${case_output}" ]; then
     # SECTION Simulation complete. E 215s = 0h03m35s | C [198s,206s] | M [879.1M,1.2G,29.1G]