MOLCAS@UU
Overview
MOLCAS@UU is a serial-only pre-compiled version of MOLCAS, provided by Uppsala University (UU).
Version 8.0 SP1 is installed on the CSF.
The GV graphics viewer application is also available (see below for how to run this correctly on the CSF).
Restrictions on use
MOLCAS@UU used to require registration with the software provider , however, development of the software has been discontinued. We are only granting access to people from the Nick Chilton Group. In Jan 2019 we will be making openmolcas available.
Set up procedure
To access the software you must first load the modulefiles
module load apps/binapps/molcasuu/8.0sp1 # Can only run serial jobs
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.
Running the application
Please do not run MOLCAS@UU on the login node. Jobs should be submitted to the compute nodes via batch. NOTE we now recommend loading modules within your batch scripts.
Serial batch job submission
Create a batch submission script, for example:
#!/bin/bash --login #$ -cwd # Job will run from the current directory module load apps/binapps/molcasuu/8.0sp1 molcas mymol.input ### Use molcas -clean mymol.input to have the temporary scratch directory ### deleted at the end of the job (see below)
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
MOLCAS Scratch (temp) files
It is possible to modify how MOLCAS uses your scratch directory for temporary files. Please read the following section so that you are aware of what MOLCAS is doing with your scratch directory (you may create a lot of temporary junk files you do not need to keep).
The modulefiles above set the following environment variable:
MOLCAS_WORKDIR=/scratch/username
where username is your CSF username. This instructs MOLCAS to create a directory in your scratch area named after your input file. For example if your input file is called test000.input then MOLCAS will create a directory named
/scratch/username/test000
in which to store temporary files used during the computation. This directory will not 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!
To instruct MOLCAS to delete this directory at the end of the job add the flag -clean to the molcas command in your jobscript. For example:
# Automatically delete the temporary scratch directory at the end of the job (RECOMMENDED) molcas -clean test000.input
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 input with a different number of CPU cores to do some timing tests) you should instruct MOLCAS to add a random number to the directory name by adding the following to your jobscript:
# Molcas will add a random number to the temporary directory name export MOLCAS_PROJECT=NAMEPID
Removing the -clean flag from the molcas command in your jobscript will prevent MOLCAS from deleting it.
Using a Job Array
If running MOLCAS in a job array you may need to create a directory per task otherwise the temporary directories and files created by MOLCAS will overwrite each other when a job array task runs. Remember that MOLCAS will use the name of your input file when creating its temporary directory. If each task in the job array uses the same MOLCAS 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 MOLCAS:
export MOLCAS_WORKDIR=/scratch/$USER/molcas_${JOB_ID}_${SGE_TASK_ID}
mkdir -p $MOLCAS_WORKDIR
Each task in the job array will have its own directory. Within there will be a directory named after the input file (see above).
GV – Graphics Viewer
MOLCAS developers have developed a graphical interface that can be used both to create input for the MOLCAS program and to analyze the results in a graphical manner by visualizing molecular orbitals, density plots, and other output properties.
The GV program should be run interactively on the CSF. This means you request an interactive session from the batch system. If resources are free it will run the GV program on a backend node. You should not run GV on the login node for all but the simplest of geometries.
To run the GV program interactively first load the MOLCAS modulefile then run the following command on the login node:
qrsh -l short -V -cwd molcas gv filename.xyz
Other input files can then be loaded from the GV user interface.
Further info
Updates
None.