ORCA
Versions Installed
Kay: 5.0.0 / 5.0.2 / 5.0.3
Description
ORCA is an ab initio quantum chemistry program package that contains modern electronic structure methods including density functional theory, many-body perturbation, coupled cluster, multireference methods, and semi-empirical quantum chemistry methods. Its main field of application is larger molecules, transition metal complexes, and their spectroscopic properties. ORCA is developed in the research group of Frank Neese.
License
ORCA, Academic (Computer Center).
Benchmarks
N/A
Job Submission Example
Like other jobs on ICHEC systems, ORCA jobs must be submitted using a Slurm submission script. The following is an example Slurm submission script for allocating 1 node of Kay (40 cores) for 24h , then running ORCA on an example input file. Jobs that use ORCA would typically be submitted to the ProdQ.
The ORCA module is loaded as follows (this is a key part of the sbatch script):
module load orca/5.0.3
Create the submission script (and name it orca_calc.sh) for the SLURM Workload Manager and modify it with your parameters
#!/bin/bash
#SBATCH -p ProdQ
#SBATCH -N 1
#SBATCH -t 24:00:00
#SBATCH --job-name=test
#SBATCH -A yourproject
#SBATCH -o test.stdout
#SBATCH -e test.stderr
module load orca/5.0.3
# Location of the local scratch.
scratchlocation=/scratch/local
# Usage:
#sbatch -J jobname orca_calc.sh -where jobname is the name of your ORCA inputfile (jobname.inp) without the .inp extension
# Set jobname here manually or use as first argument when doing sbatch -J argument job-orca.sh -N argument where "argument" becomes $SLURM_JOBNAME
export job=$SLURM_JOB_NAME
export job=$(basename $job .inp)
echo "SLURM_NODELIST is $SLURM_NODELIST"
#Create scratch
if [ ! -d $scratchlocation/$USER ]
then
mkdir -p $scratchlocation/$USER
fi
tdir=$(mktemp -d $scratchlocation/$USER/orcajob__$SLURM_JOBID-XXXX)
chmod +xr $tdir
if [ ! -d "$tdir" ]; then
echo "Scratch dir does not exist on this node"
echo "Maybe because scratchlocation $scratchlocation does not exist on node??"
echo "Or because permissions did not allow creation of folder?"
echo "Exiting..."
exit
fi
# Copy only the necessary stuff in submit directory to scratch directory.
#Explicit files here instead of general
#Copying submitted inputfile
cp $SLURM_SUBMIT_DIR/$job.inp $tdir/
cp $SLURM_SUBMIT_DIR/*.xyz $tdir/
#Copying possible basis file
cp $SLURM_SUBMIT_DIR/*.basis $tdir/
#Copying xyzfile if referenced in inputfile
xyzfilename=`grep -i xyzfile $SLURM_SUBMIT_DIR/$job.inp | tr ' ' '\n' | tail -2 | grep .xyz`
cp $SLURM_SUBMIT_DIR/$xyzfilename $tdir/
#Copying GBWfile with same name as inputfile and GBW/LOC/MP2NAT if part of %moinp statement
cp $SLURM_SUBMIT_DIR/$job.gbw $tdir/
cp $SLURM_SUBMIT_DIR/*im*.gbw $tdir/
grep -i "%moinp" $SLURM_SUBMIT_DIR/$job.inp
grep -i "%moinp" $SLURM_SUBMIT_DIR/$job.inp | awk '{print $2}'
grep -i "%moinp" $SLURM_SUBMIT_DIR/$job.inp | awk '{print $2}' | tr -d '"'
gbwfilefrommoinp=`grep -i "%moinp" $SLURM_SUBMIT_DIR/$job.inp | awk '{print $2}' | tr -d '"'`
cp $SLURM_SUBMIT_DIR/$gbwfilefrommoinp $tdir/
# Hess file if found in such command
prevhessfile=`grep -i 'InHessName' $SLURM_SUBMIT_DIR/$job.inp | awk '{print $2}' | tr -d '"'`
cp $SLURM_SUBMIT_DIR/$job.*hess $tdir/
cp $SLURM_SUBMIT_DIR/$prevhessfile $tdir/
cp $SLURM_SUBMIT_DIR/*.hess $tdir/
#cp $SLURM_SUBMIT_DIR/*.inp $tdir/
#cp $SLURM_SUBMIT_DIR/*.gbw $tdir/
#cp $SLURM_SUBMIT_DIR/*.xyz $tdir/
#cp $SLURM_SUBMIT_DIR/*.loc $tdir/
#cp $SLURM_SUBMIT_DIR/*.qro $tdir/
#cp $SLURM_SUBMIT_DIR/*.hess $tdir/
echo ${SLURM_NODELIST} > $tdir/$job.nodes
# cd to scratch
cd $tdir
ls
which mpirun
#Start ORCA job. ORCA is started using full pathname (necessary for parallel). Output file is written directly to submit directory
$orcadir/orca $job.inp >> $SLURM_SUBMIT_DIR/$job.out
# ORCA has finished. Now copy important stuff back (xyz files, GBW files etc.). Add files here as required
cp $tdir/*.gbw $SLURM_SUBMIT_DIR
cp $tdir/*.engrad $SLURM_SUBMIT_DIR
cp $tdir/*.xyz $SLURM_SUBMIT_DIR
cp $tdir/*.trj $SLURM_SUBMIT_DIR
cp $tdir/*.loc $SLURM_SUBMIT_DIR
cp $tdir/*.qro $SLURM_SUBMIT_DIR
cp $tdir/*.uno $SLURM_SUBMIT_DIR
cp $tdir/*.unso $SLURM_SUBMIT_DIR
cp $tdir/*.uco $SLURM_SUBMIT_DIR
cp $tdir/*.hess $SLURM_SUBMIT_DIR
cp $tdir/*.cis $SLURM_SUBMIT_DIR
cp $tdir/*.dat $SLURM_SUBMIT_DIR
cp $tdir/*.mp2nat $SLURM_SUBMIT_DIR
cp $tdir/*.nat $SLURM_SUBMIT_DIR
cp $tdir/*.scfp_fod $SLURM_SUBMIT_DIR
cp $tdir/*.scfp $SLURM_SUBMIT_DIR
cp $tdir/*.scfr $SLURM_SUBMIT_DIR
cp $tdir/*.nbo $SLURM_SUBMIT_DIR
cp $tdir/FILE.47 $SLURM_SUBMIT_DIR
cp $tdir/*_property.txt $SLURM_SUBMIT_DIR
cp $tdir/*.allxyz $SLURM_SUBMIT_DIR
cp $tdir/*.log $SLURM_SUBMIT_DIR
cp $tdir/*.interp $SLURM_SUBMIT_DIR
cp $tdir/*spin* $SLURM_SUBMIT_DIR
cp $tdir/*lastscf* $SLURM_SUBMIT_DIR
cp $tdir/*.spectrum $SLURM_SUBMIT_DIR
rm -rf $tdir
Submit the job with the following command
sbatch -J jobname orca_calc.sh
Additional Notes
Further information can be obtained from the ORCA Forum.
