ABINIT

Introduction

ABINIT is a DFT code based on pseudopotentials and a planewave basis, which calculates the total energy, charge density and electronic structure for molecules and periodic solids. In addition to many other features, it provides the time dependent DFT, or many-body perturbation theory (GW approximation) to compute the excited states.

Running ABINIT at LRZ

Please load the appropriate module environment to access the software:
module load abinit

There are two ways of running abinit at LRZ, submitting a batch job, or running interactively 

Running Interactively

To request an interactive batch session on Linux-Cluster (cm2), issue a command (eg., for cm2 and requesting 28 CPUs):

% salloc --ntasks=16 --partition=ice1_inter

when a new batch session is returned to you, issue the following commands:

% module load abinit
% srun_ps -i input.file abinit  (serial or shared memory)
% srun_ps -n 8 -i input.file abinit out.log (parallel)

Please be aware that on the versions "8.8.2" or newer use the following:

    % mpiexec -n 8 abinit < input.file >& out.log (interactive)

            Inside the job script, please use the mpiexec command to start up your program.

Running ABINIT on Linux Cluster and SuperMUC-NG

A sample batch script:

#!/bin/bash
#SBATCH -o /home/cluster/<group>/<user>/mydir/abinit.%j.out
#SBATCH -D /home/cluster/<group>/<user>/mydir
#SBATCH -J <job_name>
#SBATCH --get-user-env
#SBATCH --clusters=cm2_tiny
#SBATCH --ntasks=28
#SBATCH --mail-type=end
#SBATCH --mail-user=<email_address>@<domain>
#SBATCH --export=NONE
#SBATCH --time=24:00:00

module load slurm_setup
module load abinit
cd mydire

srun -n 28 abinit -i inp.files

#!/bin/bash 
# Job Name and Files (also --job-name) 
#SBATCH -J jobname
#Output and error (also --output, --error): 
#SBATCH -o ./%x.%j.out 
#SBATCH -e ./%x.%j.err 
#Initial working directory (also --chdir): 
#SBATCH -D ./
#Notification and type
#SBATCH --mail-type=END
#SBATCH --mail-user=insert_your_email_here
# Wall clock limit:
#SBATCH --time=24:00:00
#SBATCH --no-requeue
#Setup of execution environment
#SBATCH --export=NONE
#SBATCH --get-user-env
#SBATCH --account=insert your_projectID_here
#SBATCH --partition=insert test, micro, general, large or fat 

module load slurm_setup
module load abinit
cd mydire              

mpiexec -n 48 abinit -i  inp.files >& out.log

Then submit the job script using sbatch command for MPP or ICE Cluster, e.g., assume the job script name is name-job.sh,

% sbatch  name-job.sh

There are many other parameters to the batch system at LRZ. For more details see Batch Queuing and Job Policies

Dokumentation

• After execution of module load namd, the environment variable documentation points to a directory containing the NAMD documentation as it comes with the source code:

  ls -C  $ABINIT_DOC
  

• Other format of the documentation and more information may be found on the ABINIT Homepage

Support

If you have any questions or problems with ABINIT installed on the different LRZ platforms, please don't hesitate to contact LRZ HPC support staff .