1. Tutorial to run a file in HPC (example for Gromacs)

Steps:

1. Prepare a system and ensure it is working in your local computer.

2. Transfer the files to the HPC System.

   1. Command: scp -r localid@localip:/home/location userid@paramshakti.iitkgp.ac.in:/location

OR using WINSCP

3. Access the folder you want.

4. Create a script file.

e.g.

#!/bin/bash

#SBATCH -J job_name                # name of the job

#SBATCH -p shared            # name of the partition: available options "large, medium or shared"

#SBATCH -n 4                      # no of processes or tasks

#SBATCH --cpus-per-task=4          # no of threads per process or task

#SBATCH -t 70:00:00                # walltime in HH:MM:SS, Max value 72:00:00

#list of modules you want to use, for example

module load apps/gromacs/2020/cpu

#name of the executable

exe="gmx_mpi"

export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK

#run the application

mpirun -bootstrap slurm -n $SLURM_NTASKS $exe mdrun -v -deffnm eql

5. Save the file as eql.sh

6. Run the command 

sbatch eql.sh