MobCal-MPI

Overview

MolCal-MPI is a parallelization of the commonly used MobCal suite to calculate ion mobilities and collision cross sections (v1.2). For full documentation, see the MobCal-MPI user guide.

Restrictions on use

GNU GENERAL PUBLIC LICENSE Version 3 – (free to use, not for profit).

Set up procedure

To access the software you must load one the following modulefile in your jobscript:

module load apps/binapps/mobcal/12Jan2022

module load apps/binapps/mobcal/24Oct2018

Running the application

Please do not run Mobcal-MPI on the login node. Jobs should be submitted to the compute nodes via batch.

Serial batch job submission

To run, MobCal-MPI requires an input file, with the extension “.sub”.
For batch job submission, this is confusing – as this is not a jobscript to submit.

if you wish to run the jobscript examples below, please take the following preparatory steps:

mkdir ~/scratch/mobcal
cd ~/scratch/mobcal
cp /opt/apps/apps/binapps/mobcal/24Oct2018/Test_Files/Mobcal_Inputs/AMIFOSTINE_3.mfj .
echo -e "AMIFOSTINE_3.mfj\nAMIFOSTINE_3.mout" > Amifostine_3.sub

Make sure you have your input files “AMIFOSTINE_3.sub” and “AMIFOSTINE_3.mfj” in the current directory and then create a jobscript in that directory. For a serial job example:

#!/bin/bash --login
#$ -S /bin/bash
#$ -cwd             # Job will run from the current directory

module load apps/binapps/mobcal/24Oct2018
MobCal_MPI.exe Amifostine_3.sub

Submit the jobscript using:

qsub scriptname

where scriptname is the name of your jobscript.

Single-node Parallel batch job submission

Make sure you have your input file in the current directory and then create a jobscript in that directory. For example:

#!/bin/bash --login
#$ -S /bin/bash
#$ -cwd             # Job will run from the current directory
#$ -pe smp.pe 8     # Number of cores (max 32)

module load apps/binapps/mobcal/24Oct2018
mpirun -np $NSLOTS MobCal_MPI.exe Amifostine_3.sub

Submit the jobscript using:

qsub scriptname

Multi-node Parallel batch job submission

If you have access to more than 32 cores, you can run multi-node jobs. These take longer to start but can complete the work faster.
Make sure you have your input file in the current directory and then create a jobscript in that directory. For example:

#!/bin/bash --login
#$ -S /bin/bash
#$ -cwd             # Job will run from the current directory
#$ -pe mpi-24-ib.pe 48 # multiples of 24 cores

module load apps/binapps/mobcal/24Oct2018
mpirun -np $NSLOTS MobCal_MPI.exe Amifostine_3.sub

Submit the jobscript using:

qsub scriptname

The job example creates

AMIFOSTINE_3.mout

with

output_{1-X}.out

output files.