How to use qchem in Mare Nostrum (BSC) [Currently not available!]

Preliminar information

Requirements to acces to qchem

• Have a MareNostrum account (mn1.bsc.es or mn2.bsc.es)

Available qhem compilations

• qchem_group_mpi: Current in development version of qchem parallel MPI [mpi intel mkl version]

Load custom modules

To acces to qchem you should be able to load custom modules located in /home/hpce17/hpce17274/privatemodules privatemodules. To do this you may modify the MODULEPATH environment variable as follows:

export MODULEPATH=/home/hpce17/hpce17274/privatemodules/:$MODULEPATH

Once this is done, you should be able to see the custom modules (qchem_trunk & qchem_group) executing the command:

module avail

To use qchem, just load the corresponding module as usual:

module qchem_group_mpi

Note: $MODULEPATH environment variable definition can be defined in user’s ~/.bashrc configuration file so it becomes defined for all calculation by default.

Run interactive qchem

SLURM queue system allows to run calculation interactivelly for testing purposes using a single node up to 4 cores. To enter to them use the command:

salloc --partition=interactive -n 4

there is a time limit in interactive mode of aprox. 1 hour. For similar purposes debug queue can also be uses with similar time limitations but allowing to use a larger number of cores:

salloc --qos=debug -n 96

Batch job example parallel MPI

All commands described previously can be gathered in a simple script to run in batch. This is a simple example:

#!/bin/bash
#SBATCH --job-name="test qchem"
#SBATCH --workdir=/home/hpce17/hpce17274/test/test1
#SBATCH --output=test_water.log      # standard output dile
#SBATCH --error=test_water.err       # standard error file
#SBATCH --ntasks-per-node=4          # number of cores per node
#SBATCH --nodes=1                    # number of nodes (1 recomended)
#SBATCH --time=01:00:00              # Max time for this job hh:mm:ss

# load module qchem
export MODULEPATH=/home/hpce17/hpce17274/privatemodules/:$MODULEPATH
module load qchem_group_mpi

# set scrach directory
export QCSCRATCH=/home/hpce17/hpce17274/scratch/qchem_scratch/

# launch qchem
qchem -np $SLURM_NTASKS_PER_NODE water_dimer.in water_dime.out