ORCA

ORCA

Introduction

The program ORCA is a modern electronic structure program package that is able to carry out geometry optimizations and to predict a large number of spectroscopic parameters at different levels of theory. Besides the use of Hartee Fock theory, density functional theory (DFT) and semiempirical methods, high level ab initio quantum chemical methods, based on the configuration interaction and coupled cluster methods, are included into ORCA to an increasing degree.

For more details please refer the offical home of ORCA where you can also find a thorough documentation on using the program. Note that ORCA is free of charge for non-commercial use and by using ORCA on the cluster you are accepting the ORCA license. In particular, any scientific work using ORCA should at least cite

F. Neese: The ORCA program system (WIREs Comput Mol Sci 2012, 2: 73-78)

as well as other related works as apropriate.

Below, a short introduction to using ORCA on the cluster is given.

Using ORCA on the Cluster

The first thing that you need to do is to load the ORCA module using the command

module load orca

This will load the latest version of ORCA installed (currently, 3.0.3). More specifically, it adds the path of the ORCA executables to your environment.

Serial Runs

Next, you will need to prepare a job script which could look as follows in case of a serial run (no line starting with %pal):

#!/bin/bash

### the following lines are used by SGE to determine your job requirements
### you may want to modify the requested resources, e.g. h_vmem or h_rt,
### if you need more memory or run time (respectively)
#$ -S /bin/bash
#$ -cwd
#$ -l h_rt=1:00:0
#$ -l h_vmem=1500M
#$ -l h_fsize=100G
#$ -N ORCA
#$ -j n

### maybe useful to receive emails when a job begins (b) and has finished (e)
### (to activate change email address and remove extra # in the next 2 lines)
##$ -m be
##$ -M your.name@uni-oldenburg.de

### here the actual job script begins
### you may want to modify this part according to your needs
### the script expect input files in the directory from where you submitted
### the job and any output will appear in that directory as well, however
### some files may not show up until the job has finished
echo Job started on `date`   # put a time stamp in log file

# load module orca
module load orca

# settings (here you need to make your own modifications)
MODEL=TiF3     # MODEL is the basename for all files

# settings (may have to adjusted but not always)
ORCAEXE=`which orca`     # no need to be touched
INPUTEXT="inp xyz gbw"   # files with these extension will be copied
OUTPUTEXT="gbw prop"     # files with these extensions will saved to SGE_O_WORKDIR

# preparing $TMPDIR for run by copying file
for ext in $INPUTEXT
do
   if [ -e $MODEL.$ext ]
   then
      echo "Copying $MODEL.$ext to TMPDIR"
      cp $MODEL.$ext $TMPDIR/${MODEL}_${JOB_ID}.$ext
   fi
done

# change to $TMPDIR for running ORCA
cd $TMPDIR

# run ORCA
$ORCAEXE ${MODEL}_${JOB_ID}.inp > $SGE_O_WORKDIR/${MODEL}_${JOB_ID}.out

# saving files from $TMPDIR
for ext in $OUTPUTEXT
do
   if [ -e ${MODEL}_${JOB_ID}.$ext ]
   then
      echo "Copying $MODEL.$ext to $SGE_O_WORKDIR"
      cp ${MODEL}_${JOB_ID}.$ext $SGE_O_WORKDIR
   fi
done



echo Job finished on `date`   # put a time stamp in log file

exit

You can download this job script orca_ser.sge and modify it to your needs (e.g. to change the requested resources). The job script requires additional input files for ORCA, in this case TiF3.inp and TiF3.xyz and all three files have to be placed in the same directory. Note: all downloads have to be unzipped first.

Once the job script and your input files are ready, a job can be submitted as usual with the command:

qsub orca_ser.sge

The job script works roughly in the following way

1. the ORCA module is loaded and the name of the model is set (must be identical to the name of the .inp file)
2. all input files (identified by the model name and given extensions) are copied to $TMPDIR, more files can be included by adding their extensions to the variable INPUTEXT
3. the directory is changed to $TMPDIR and the run is started, a log file for the run (extension .out) is written to the directory from where the job was submitted
4. all other files are created in $TMPDIR, which is automatically deleted after the job; if additional files need to be saved, they need to be copied (not yet implemented in the job script)

Parallel Run

The job script orca_par.sge for parallel runs is quite similar to the one for serial runs. The example also requires an input file (silole_rad_zora_epr_pbe0.inp), which contains a line starting with %pal which indicates to ORCA that computations can be done in parallel. The additional lines in the job script are explained here:

1. A parallel environment (PE) and the number of compute cores have to be requested

### setting up parallel environment
#$ -pe smp 8        # use PE smp to make sure all cores are on the same host
##$ -pe openmpi 4   # use PE openmpi if you need more than 12 cores

ORCA uses OpenMPI to parallelize parts of the code, so in principle the PE openmpi should be used (PE openmpi not tested yet). However, on HERO this means that the job is likely to be distributed among multiple nodes resulting in a larger communication overhead due to the ethernet communication. As an alternative you can use the PE smp with up to 12 cores which ensures that ORCA only runs on one node in parallel (for more effective communication). In addition, you may need to request much more memory (h_vmem) per core with PE openmpi (not verified yet).

2. set the number of cores in the ORCA input file

# modify inputfile to match the number of available slots
SETNPROCS=`echo "%pal nprocs $NSLOTS"`
sed -i "/^%pal/c$SETNPROCS" $MODEL.inp

This ensures the number of cores/nprocs are matched with the requested number of cores in the previous step. This overwrites any setting in your input file, i.e. only the setting in the job script is relevant. The input file in your working directory is not changed, however. It is also important that you input file contains the line starting with %pal (do not use the other format to set nprocs in ORCA).

3. for PE openmpi the list of nodes to be used is given as a file which is (copied and) renamed as expected by ORCA.

# copy file machines to the name ORCA expects
if [ -e machines ]
then
   cp machines $MODEL.nodes
fi

Typically, you only need to modify the number of cores you want to use (1.), in addition to the modification explained above for serial runs (e.g. model name).

Troubleshooting

In case of problems the following hints may help you to identify the cause:

1. check the log files from the SGE (<job-name>.x<job-id> where x is e, o, pe, and/or po) as well as the ORCA log file (<model>.out) for error messages.
2. check the exit status of the job by using

qacct -j <job-id>

The last command should show a number of lines, including the exit code, which could look like this:

failed       100 : assumedly after job
exit_status  137                 

this indicates that a resource (memory, run time, file size) was over-used.

If you need help to identify the problem you can contact Scientific Computing, please include the job-id in your request.