{"id":2002,"date":"2019-01-21T11:53:24","date_gmt":"2019-01-21T11:53:24","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf3\/?page_id=2002"},"modified":"2025-07-09T08:40:57","modified_gmt":"2025-07-09T07:40:57","slug":"openmolcas","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/applications\/openmolcas\/","title":{"rendered":"OpenMolcas"},"content":{"rendered":"

Overview<\/h2>\n

OpenMolcas<\/a> is an open source version of MOLCAS.<\/p>\n

Version v18.09,v19.11,v21.02, v22.06, and v25.02 are installed on the CSF.<\/p>\n

Restrictions on use<\/h2>\n

OpenMolcas is open source software released under the Lesser General Public License (LGPL).\u00a0 It is free to use by all members of the University.<\/p>\n

Set up procedure<\/h2>\n

To access the software you must first load one of the modulefiles<\/p>\n

module load apps\/gcc\/openmolcas\/18.09\r\nmodule load apps\/gcc\/openmolcas\/19.11\r\nmodule load apps\/gcc\/openmolcas\/21.02\r\nmodule load apps\/gcc\/openmolcas\/22.06\r\nmodule load apps\/gcc\/openmolcas\/25.02\r\n<\/pre>\n
Of these, only v25.02 works correctly.  Attempts to load other modulefiles will result in an error.<\/p>\n
We now recommend that for batch jobs you load the modulefile in the jobscript rather than loading it on the command line prior to submission. See below for examples.<\/p>\n
Running the application<\/h2>\n
Please do not run OpenMolcas on the login node. Jobs should be submitted to the compute nodes via batch. NOTE we now recommend loading modules within your batch scripts.<\/p>\n
Serial batch job submission<\/h3>\n
Create a batch submission script, for example:<\/p>\n
#!\/bin\/bash --login\r\n#SBATCH -p serial          # (or --partiion=) Run on nodes dedicated to 1-core jobs\r\n#SBATCH -t 2-0             # Wallclock time limit (2-0 is 2 days, max permitted is 7-0)\r\n\r\nmodule purge\r\nmodule load apps\/gcc\/openmolcas\/25.02\r\npymolcas mymol.input\r\n  # \r\n  # Use: pymolcas -clean mymol.input\r\n  # to have the temporary scratch<\/em> directory \r\n  # deleted at the end of the job (see below)\r\n<\/pre>\n
Submit the jobscript using:
\nsbatch scriptname<\/em><\/code>
\nwhere scriptname<\/em> is the name of your jobscript.<\/p>\n
Parallel batch job submission<\/h3>\n
Parallel jobs on a single node using OpenMP are currently possible. Multi-node calculations using MPI are not currently supported.<\/p>\n
Create a batch submission script, for example:<\/p>\n
\r\n#!\/bin\/bash --login\r\n#SBATCH -p multicore       # (or --partiion=) Run on the 168-core AMD Genoa nodes\r\n#SBATCH -c 8               # (or --cpus-per-task=) Number of OpenMP cores\r\n#SBATCH -t 2-0             # Wallclock time limit (2-0 is 2 days, max permitted is 7-0)\r\n\r\nmodule purge\r\nmodule load apps\/gcc\/openmolcas\/25.02\r\nexport OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK\r\npymolcas mymol.input \r\n  # \r\n  # Use: pymolcas -clean mymol.input\r\n  # to have the temporary scratch<\/em> directory \r\n  # deleted at the end of the job (see below)\r\n<\/pre>\n
Submit the jobscript using:
\nsbatch scriptname<\/em><\/code>
\nwhere scriptname<\/em> is the name of your jobscript.<\/p>\n
OpenMolcas Scratch (temp) files<\/h3>\n
It is possible to modify how OpenMolcas uses your scratch directory for temporary files. Please read the following section so that you are aware of what OpenMolcas is doing with your scratch directory (you may create a lot of temporary junk files you do not need to keep).<\/p>\n
The modulefiles above set the following environment variable:<\/p>\n
MOLCAS_WORKDIR=\/scratch\/username<\/em>\r\n<\/pre>\n
where username<\/em><\/code> is your CSF username. This instructs OpenMolcas to create a directory in your scratch<\/em> area named after your input file. For example if your input file is called test000.input<\/code> then OpenMolcas will create a directory named<\/p>\n
\/scratch\/username<\/em>\/test000\r\n<\/pre>\n
in which to store temporary files used during the computation. This directory will not<\/strong> be deleted at the end of the job. Hence you may end up with a lot of these temporary directories if you run many jobs!<\/p>\n
To instruct OpenMolcas to delete this directory at the end of the job add the flag -clean<\/code> to the pymolcas<\/code> command in your jobscript. For example:<\/p>\n
# Automatically delete the temporary scratch directory at the end of the job (RECOMMENDED)\r\npymolcas -clean test000.input\r\n<\/pre>\n
If you wish to keep temporary directories and use a different temporary directory name each time you run (and rerun) the same input file (e.g., if you run the test000.input<\/code> input with a different number of CPU cores to do some timing tests) you should instruct OpenMolcas to add a random number to the directory name by adding the following to your jobscript:<\/p>\n
# OpenMolcas will add a random number to the temporary directory name\r\nexport MOLCAS_PROJECT=NAMEPID\r\n<\/pre>\n
Removing the -clean<\/code> flag from the pymolcas<\/code> command in your jobscript will prevent OpenMolcas from deleting it.<\/p>\n
Using a Job Array<\/h3>\n
If running OpenMolcas in a job array<\/a> you may need to create a directory per task otherwise the temporary directories and files created by OpenMolcas will overwrite each other when a job array task runs. Remember that OpenMolcas will use the name of your input file when creating its temporary directory. If each task in the job array uses the same OpenMolcas input filename then this will cause a problem when several job array tasks run at the same time. To fix this, please add the following to your jobscript before the lines that runs OpenMolcas:<\/p>\n
\r\nexport MOLCAS_WORKDIR=\/scratch\/$USER\/molcas_${SLURM_ARRAY_JOB_ID}_${SLURM_ARRAY_TASK_ID}\r\nmkdir -p $MOLCAS_WORKDIR\r\n<\/pre>\n
Each task in the job array will have its own directory. Within there will be a directory named after the input file (see above).<\/p>\n
Further info<\/h2>\n