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.

Version

  • 7.10.5

Authorized Users

  • CIRCE account holders
  • RRA account holders
  • SC account holders

Platforms

  • CIRCE cluster
  • RRA cluster
  • SC cluster

Modules

ABINIT requires the following module file to run:

  • apps/abinit/7.10.5

Running ABINIT on CIRCE

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. Please refer to the Documentation section for a link to the guide.

  • Note on CIRCE: Make sure to run your jobs from your $WORK directory!
  • Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.

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. Please refer to the Documentation section for a link to the guide.

  • Note on CIRCE: Make sure to run your jobs from your $WORK directory!
  • Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.

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: 

[user@login0 ~]$ cd my/jobdir
[user@login0 jobdir]$ 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)

Documentation

Home Page, User Guides, and Manuals

Benchmarks, Known Tests, Examples, Tutorials, and Other Resources

More Job Information

See the following for more detailed job submission information:

Reporting Bugs

Report bugs with ABINIT to the IT Help Desk: rc-help@usf.edu

Retrieved from "https://wiki.rc.usf.edu/index.php?title=ABINIT&oldid=951"