Abinit

Abinit

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Contents

            1. Description

            2. Requirement

            3. How to run job Abinit using HPC

            4. Contact Us

Description:

ABINIT is a quantum chemistry software based on the DFT (Density Functional Theory) method.
Documentation is available on the ABINIT Website.
Version 7.10.5 of ABINIT

Requirement

Step 1: Please register to UTM HPC Account
Step 2: HPC admin (hpc@utm.my) will sent HPC account to your email.

How to run job Abinit using HPC

Submit a Abinit job in Parallel

In the example below the input files tbasepar_1.files will be run after submit a job using PBS script, pbs-script. For example, create a submission script file called pbs-script that contains the lines below. This example requests one node and two processor cores.

#!/bin/sh

#PBS -N abinit_test
#PBS -l nodes=1:ppn=2

INP_FILE=tbasepar_1.files

module load abinit/7.10.5

cd $PBS_O_WORKDIR

export PATH=$MPI_OPENMPI_PATH/bin:$PATH
export LD_LIBRARY_PATH=$MPI_OPENMPI_PATH/lib:$LD_LIBRARY_PATH

cd $HOME/abinit/tutorial/Input

mpirun abinit < $INP_FILE > filename.out

Pseudo-potentials and Abinit files

Complete sets of pseudopotentials for the whole periodic table are available on the ABINIT Website. Our pseudopotentials example below (line 6) copy from the ~abinit-7.10.5/tests/Psps_for_tests. In the examples of launching scripts, abinit files is necessary. It contains the list of input files, the prefixes for the output files, as well as the list of pseudopotentials for calculation.

Example abinit files, tbasepar.files

tbasepar_1.in
tbasepar_1.out
tbasepar_1i
tbasepar_1o
/home/syedanwar/abinit/tutorial/Input/tbasepar_1
../../Psps_for_tests/HGH/82pb.4.hgh

Transfering Files & Submitting Job

Then, upload the submission script, launching scripts above and your input file to the HPC using WinSCP tool. To submit a job, please using a Putty tool and run the command below. How to access the HPC server, please go to our New User Guide page.
 
Submit the Abinit submission job to the queue:

Users can submit the job using two options as below. The pbs-script name below is the name of your submission script.

qsub -q bigmem pbs-script
OR
qsub -q hpc pbs-script
Please note that queue for hpc above have 8 core’s for each cluster/node so if you are using this cluster please make sure in the script, you state “ppn=8″ to make sure your job can run.

Contact Us

Any problem about HPC, please email to hpc@utm.my or our facebook (Abinit)