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 (MPP or ICE), issue a command (eg., for ICE and requesting 16 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 "6.0.3" 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 SuperMUC and Linux-Cluster

A sample batch script:

MPP Cluster (SLURM)

SuperMUC (LoadLeveler)

#!/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=mpp1
# or use ice1_batch for SGI ICE
#SBATCH --ntasks=32
#SBATCH --mail-type=end
#SBATCH --mail-user=<email_address>@<domain>
#SBATCH --export=NONE
#SBATCH --time=24:00:00

source /etc/profile.d/modules.sh
 cd mydire    
 module load abinit
srun_ps -n 32  -i inp.files abinit
#!/bin/bash
#@ wall_clock_limit = 24:00:00
#@ job_type = parallel
#@ class = general
#@ node = 1
#@ tasks_per_node = 40
#@ initialdir = $(home)/mydir
#@ output = job$(jobid).out
#@ error = job$(jobid).err
#@ queue

. /etc/profile
cd  mydire                   
module load abinit
mpiexec -n 40 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

For LoadLeveler with

% llsubmit  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 .