diff --git a/docs.it4i/software/chemistry/orca.md b/docs.it4i/software/chemistry/orca.md index ca0242b8f716465646cf20dc744308229c843c6e..682bda210390e485e1868024b7af6205ed4f5c3c 100644 --- a/docs.it4i/software/chemistry/orca.md +++ b/docs.it4i/software/chemistry/orca.md @@ -180,13 +180,76 @@ You can see, that the program was running with 64 parallel MPI-processes. In ver * SOC * Numerical Gradients and Frequencies +## Running ORCA version 5.0.0 in parallel + +On Barbora cluster, version 5.0.0 is available. However, to run it in parallel you need to specify execution nodes via `inputfilename.nodes` file. Additionally, all calculations **must** be run on SCRATCH. + +Example submission script would look like this: + +``` +#!/bin/bash +#PBS -S /bin/bash +#PBS -A OPEN-00-00 +#PBS -N jobname +#PBS -q qprod +#PBS -l select=2 +#PBS -l walltime=00:05:00 + +ml purge +ml ORCA/5.0.0-OpenMPI-4.1.1 + +echo $PBS_O_WORKDIR +cd $PBS_O_WORKDIR + +# create /scratch dir +b=$(basename $PBS_O_WORKDIR) +SCRDIR=/scratch/project/OPEN-00-00/$USER/${b}_${PBS_JOBID}/ +echo $SCRDIR +mkdir -p $SCRDIR +cd $SCRDIR || exit + +### specify nodes used for the parallel run +cat $(echo $PBS_NODEFILE) > ${PBS_JOBNAME}.nodes +### + +# get number of cores used for our job +ncpus=$(qstat -f $PBS_JOBID | grep resources_used.ncpus | awk '{print $3}') + + +### create ORCA input file +cat > ${PBS_JOBNAME}.inp <<EOF +! HF def2-TZVP +%pal + nprocs $ncpus +end +* xyz 0 1 +C 0.0 0.0 + 0.0 +O 0.0 0.0 + 1.13 +* +EOF +### + +# copy input files to /scratch +cp -r $PBS_O_WORKDIR/* . + +# run calculations +/apps/all/ORCA/5.0.0-OpenMPI-4.1.1/orca ${PBS_JOBNAME}.inp > $PBS_O_WORKDIR/${PBS_JOBNAME}.out + +# copy output files to home, delete the rest +cp * $PBS_O_WORKDIR/ && cd $PBS_O_WORKDIR +rm -rf $SCRDIR +exit +``` + ## Register as a User You are encouraged to register as a user of ORCA [here][a] in order to take advantage of updates, announcements, and the users forum. ## Documentation -A comprehensive [manual][b] is available online. +A comprehensive [manual][b] is available online for registered users. -[a]: https://orcaforum.kofo.mpg.de/ -[b]: https://kofo.mpg.de/media/2/D19114521/4329011608/orca_manual-opt.pdf +[a]: https://orcaforum.kofo.mpg.de/app.php/portal +[b]: https://orcaforum.kofo.mpg.de/app.php/dlext/?cat=1