cp abaqus explicit to zeus examples directory

Author: Chris Bording

zeus_examples/abaqus_exp_mpi/README

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+#!/bin/bash --login
+# This is the README file is an executable script.
+# To run type: ./README
+#
+# Example OBJECTIVE: to demostrate how to run ABAQUS with a simple example
+# on Zeus with the explicit solvers.
+# 
+# E3.inp: This benchmark consists of forming a sheet metal part by the deep drawing process. 
+# The deformable sheet metal blank is meshed with shell elements of type S4R and uses an 
+# isotropic hardening Mises plasticity material model. The tools are meshed using surface 
+# elements of type SFM3D4R which are declared rigid. General contact is defined between the 
+# blank and tools. The analysis sequence consists of two steps. During the first step the 
+# blank is clamped between the binder and die and then during the second step the punch is 
+# displaced to form the part. Since the process is essentially quasi-static the computations 
+# are performed over a sufficiently long time period to render inertial effects negligible. 
+# The performance of this analysis is a direct measure of the performance of the 
+# three-dimensional general contact algorithm.
+
+cp $GE_DIR/src/abaqus/e3.inp .
+
+# To run this code load the necessary modules.
+# and specify the total number of MPI processes.
+
+# SLURM directives
+# 
+# Here we specify to SLURM that we want 2 nodes 
+# "#SBATCH --nodes=2"
+# Then, to specify the queue or "partition" to --partition=workq
+# "#SBATCH --partition=workq"
+# To ensure that we have a correct defined environment use
+# "#SBATCH --export=NONE"
+
+# we need to load the abaqus module as shown below: 
+module load abaqus
+
+# To submit the job to Zeus
+echo "commmand to submit the slurm script is "
+echo "sbatch abaqus_explicit.slurm"
+jobid=`sbatch abaqus_explicit.slurm | cut -d " " -f 4`
+
+echo "The sbatch command returns what the jobid is for this job."
+echo "To check the status of your job, use the slurm command:"
+echo "squeue -u $USER"
+echo " "
+echo "Your job will be run in $MYSCRATCH/run_helloOmpC_gnu/${jobid}."
+echo " "
+echo "Your results will be saved in ${MYGROUP}/helloOmpC_gnu_results_zeus/${jobid}"
+echo "and the scratch directory will then be deleted."
+echo " "
+echo "To check the results change to your jobid directory, type:"
+echo "cd ${MYGROUP}/helloOmpC_gnu_results_zeus/${jobid}"
+echo " " 
+echo "To view the results, use the cat command and type:"
+echo "cat helloOmpC_gnu.log"
+echo " "
+echo " PAWSEY user shortcuts! " 
+echo  '$MYSCRATCH' "is an environment variable it is set to $MYSCRATCH"
+echo  '$MYGROUP' "is an environment variable it is set to $MYGROUP"
+echo " example:  cd \$MYGROUP "
+echo " "  
+echo "more information about Zeus/Zython can be found at:"
+echo " https://support.pawsey.org.au/documentation/pages/viewpage.action?pageId=2162999"
+echo " "
+echo "more information about SLURM and aprun can be found at:"
+echo " https://support.pawsey.org.au/documentation/display/US/Scheduling+and+Running+Jobs"
+echo " "
+echo " "
+

zeus_examples/abaqus_exp_mpi/abaqus_explicit.slurm

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+#!/bin/bash --login
+#SBATCH --job-name=e3_GE-abaqus-mpi
+#SBATCH --partition=workq
+#SBATCH --account=pawsey0001
+#SBATCH --cpus-per-task=16
+#SBATCH --nodes=2
+#SBATCH --time=01:00:00
+##SBATCH --output e3_abaqus-mpi.%j.out
+##SBATCH --error  e3_abaqus-mpi.%j.err
+
+# Default loaded compiler module is gcc module
+# load the necessary modules to compile with GNU
+module load abaqus
+
+# leave in, it lists the environment loaded by the modules
+#module list
+
+#  Note: SLURM_JOBID is a unique number for every job.
+#  These are generic variables
+INPUT=e3
+SRC_DIR=${SLURM_SUBMIT_DIR}
+EXECUTABLE=abaqus
+SCRATCH=$MYSCRATCH/run_abaqus-mpi/$SLURM_JOBID
+RESULTS=$MYGROUP/abaqus-mpi-results_zeus/$SLURM_JOBID
+unset SLURM_GTIDS
+###############################################
+# Creates a unique directory in the SCRATCH directory for this job to run in.
+if [ ! -d $SCRATCH ]; then 
+    mkdir -p $SCRATCH 
+fi 
+echo SCRATCH is $SCRATCH
+
+###############################################
+# Creates a unique directory in your GROUP directory for the results of this job
+if [ ! -d $RESULTS ]; then 
+    mkdir -p $RESULTS 
+fi
+echo the results directory is $RESULTS
+
+################################################
+# declare the name of the output file or log file
+
+OUTPUT=abaqus_${INPUT}_mpi
+
+#############################################
+#   Copy input files to $SCRATCH
+#   then change directory to $SCRATCH
+cp ${INPUT}.inp $SCRATCH
+
+cd $SCRATCH
+
+######################################
+# create the abaqus_v6.env file
+envFile=abaqus_v6.env
+
+# The number of processors/cores per node
+ncpus=`echo $SLURM_CPUS_PER_TASK`
+# | cut -c1-2`
+echo cpu per task $SLURM_CPUS_PER_TASK 
+echo "number of cores per nodes ${ncpus}"
+# total number of cores
+echo "total number of nodes $SLURM_NNODES"
+ncores=`expr $SLURM_NNODES \* $ncpus`
+echo "total number of cores is $ncores"
+# file of the node lists
+node_list=ABAQUS_NODES
+
+srun hostname | sort > $node_list
+echo  'the node list is $node_list'
+mp_host_list="["
+for i in $(cat ${node_list}) ; do
+    mp_host_list="${mp_host_list}['$i', $ncpus],"
+done
+echo host list ${mp_host_list}
+mp_host_list=`echo ${mp_host_list}  | sed -e "s/,$//"`
+mp_host_list="${mp_host_list}]"
+
+export mp_host_list
+#Write the environment variables to abaqus_v6.env
+echo "import os" > ${envFile}
+echo "os.environ['ABA_BATCH_OVERRIDE'] = '1'" >> ${envFile}
+echo "verbose=1" >> $envFile
+echo "mp_host_list=${mp_host_list}" >> ${envFile}
+echo "mp_mpi_implementation=PMPI" >> ${envFile}
+# 
+
+abaqus job=$OUTPUT input=$INPUT cpus=$ncores \
+ standard_parallel=all mp_mode=mpi interactive 
+
+#############################################
+# move entire scratch directory to the unique results directory
+# note this can be a copy or move  
+mv *.dat *.abq *.m* *.odb *.res *.p* *.s* ${RESULTS}
+
+cd $HOME
+
+###########################
+# Clean up $SCRATCH 
+
+rm -r $SCRATCH
+
+echo abaqus-mpi job finished at  `date`