First time you run a Molcas job?

This page contains info aimed at first time users of Molcas on Stallo. Please look carefully through the provided examples. Also note that the job-script example is rather richly commented to provide additional and relevant info.

If you want to run this testjob, copy the input example and the job script example shown below into your test job folder (which I assume you have created in advance).

Molcas comes with one input file and one geometry file. For simplicity, we have tarred them together and you may download them here: Ethane-input

Molcas runscrip example:

#!/bin/bash -l
################### VASP Job Batch Script Example ###################
# Section for defining queue-system variables:
#-------------------------------------
# This script asks for a given set of cores nodes and cores. Stallo has got 16 or 20 cores/node,
# asking for something that adds up to both is our general recommodation (80, 160 etc), you would
# then need to use --ntasks instead of -N and --ntasks-per-node. (replace both).
# Runtime for this job is 59 minutes; syntax is hh:mm:ss. 
# Memory is set to the maximum advised for a full node, 1500MB/core - giving a total 
# of 30000MB/node and leaving some for the system to use. Memory  
# can be specified pr core, virtual or total pr job (be carefull).   
#-------------------------------------
# SLURM-section 
#SBATCH --job-name=molcas_runex
#SBATCH -N 1
#SBATCH --ntasks-per-node=20
##SBATCH --ntasks=20
#SBATCH --time=00:59:00
#SBATCH --mem-per-cpu=1500MB
#SBATCH --output=molcas_runex.log
#SBATCH --mail-type=ALL
#SBATCH --exclusive
######################################
# Section for defining job variables and settings:
#-------------------------------------
# Area for defining variables:

proj=ehtane # Name of project/folder
input=C2H6 # Name of job input

#-------------------------------

# We load all the default program system settings with module load:

module purge

module load Molcas/molcas82-intel-2015a

# Check other available versions with "module avail Molcas"

#-------------------------------

# Now we create working directory and temporary scratch for the job(s):
# Necessary variables are defined in the notur and the software modules.

export MOLCAS_WORKDIR=/global/work/$USER/$SLURM_JOBID
mkdir -p $MOLCAS_WORKDIR

# Preparing and moving inputfiles to tmp:

submitdir=$SLURM_SUBMIT_DIR
tempdir=$MOLCAS_WORKDIR

cd $submitdir
cp ${input}.* $tempdir
cd $tempdir

######################################
# Section for running the program and cleaning up:
#-------------------------------------

# Running the program:
time molcas  Project=${proj} -f ${input}*.input 

# Cleaning up and moving files back to home/submitdir:
# Make sure to move all essential files 
# specific for the given job/software.

cp * $submitdir

# To zip some of the output might be a good idea!
#gzip $resultszip
#mv $resultzip.gz $SUBMITDIR/

# Investigate potentially other files to keep:

echo `pwd`
echo `ls -ltr`

# ALLWAYS clean up after yourself. Please do uncomment the following line
#cd $submitdir
#rm  $tempdir/*
#rmdir $tempdir


echo "Job finished at"
date
################### Job Ended ###################
exit 0

NB: Note that some of Molcas´s various modules are not mpi scalable. Consult the vendor-provided manual for scaling issues. Our example is based on a single-node all cores job.

You can also download the runscript file here: Molcas run script

The runscript example and the input are also on Stallo:

Type:

module load Molcas/molcas82-intel-2015a
cd <whereevertestfolderyouhave> # For instance testmolcas
cp -R $RUNEX/* .

When you have all the necessary files in the correct folders, submit the job by typing:

sbatch job_molcas.sh

To verify that nothing has gone wrong, check the status file. If it concludes “happy landing” you are on the safe side, most probably. Good luck.