ABINIT

Description

From the ABINIT home page: ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis.

ABINIT also includes options to optimize the geometry according to the DFT forces and stresses, or to perform molecular dynamics simulations using these forces, or to generate dynamical matrices, Born effective charges, and dielectric tensors, based on Density-Functional Perturbation Theory, and many more properties. Excited states can be computed within the Many-Body Perturbation Theory (the GW approximation and the Bethe-Salpeter equation), and Time-Dependent Density Functional Theory (for molecules). In addition to the main ABINIT code, different utility programs are provided.

ABINIT Home Page

Version

'7.10.5

Authorized Users

CIRCE account holders

Platforms

CIRCE cluster

Running ABINIT on CIRCE

Modules

ABINIT requires the following module file to run:

' apps/abinit/7.10.5
See Modules for more information.

'NOTE: This module MUST be loaded in order for the application to run. Use:

[user@host ~]$ module load apps/abinit/7.10.5

in order to properly execute ABINIT.

Submitting a Job

The ABINIT user guide is essential to understanding the application and making the most of it. The guide and this page should help you to get started with your simulations.

ABINIT User Guide

Information about the abinit executable can be found using man pages, i.e “man abinit”, after you have loaded the ABINIT module.

'Make sure to run your job from your $WORK directory. You must create a submit script (for testing, call it “abinit-test.sh”) like the following to run ABINIT:

#!/bin/bash
#
#SBATCH --comment=abinit-test
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=5 
#SBATCH --job-name=abinit-test
#SBATCH --output=output.%j.abinit-test
#SBATCH --time=00:10:00

#### Slurm task using 2 Nodes with 5 Processors per Node ABINIT test to run for 10 minutes.

module purge
module load apps/abinit/7.10.5

export PSM_RANKS_PER_CONTEXT=4

mpirun -np $SLURM_NTASKS -ppn $SLURM_NTASKS_PER_NODE abinit < test.files > test.log

Next, you can change to your job’s directory, and run the sbatch command to submit the job:

cd my/job/directory
sbatch ./abinit-test.sh

You can view the status of your job with the “squeue -u <username>” command

Please note that you should alter the number of nodes, and number of processors per node requested to appropriately balance your CPU and node count. For example, for a job requiring a CPU count of 20, the following lines would properly balance your CPU/Node count via SLURM:

-N 2 --ntasks-per-node=10 (2 nodes, 10 cpus per node)
-N 4 --ntasks-per-node=5 (4 nodes, 5 cpus per node)
-N 5 --ntasks-per-node=4 (5 nodes, 4 cpus per node)