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ABINIT is an open-source suite of programs for materials science. It implements density functional theory, using a plane wave basis set and pseudopotentials, to compute the electronic density and derived properties of materials ranging from molecules to surfaces to solids. More information and tutorials can be found here.
Below is a walkthrough of a test example for running Abinit
$HOME/.bashrc file to contain these modules to begin working with Abinit. This will load the dependencies required for the Module.
module load gcc/4.5.0 module load openmpi/1.5.4 module load mkl/11.1 module load abinit
Create a directory to run your Abinit jobs in
ABINIT-JOBS, then add the
Psps_for_tests folders to the directory you created. These test require their own pseudopotential files which is why we copy the
razor-l3:jokinsey:~$ mkdir ABINIT-JOBS razor-l3:jokinsey:~$ cd ABINIT-JOBS/ razor-l3:jokinsey:~/ABINIT-JOBS$ cp -r /share/apps/abinit-6.12.3/share/abinit-test/tutorial/Input . razor-l3:jokinsey:~/ABINIT-JOBS$ cp -r /share/apps/abinit-6.12.3/share/abinit-test/Psps_for_tests .
$HOME/ABINIT-JOBS/Input directory modify the
tparal_3.files file to reflect the new relative location of the pseudopotential file used in the job.
Change the line in
So that it reads
In the directory
$HOME/ABINIT-JOBS create a file called
abinit.pbs which will be the PBS script we will use to run our job.
Your PBS script should look like this.
#!/bin/bash #PBS -N abinit #PBS -q tiny12core #PBS -j oe #PBS -o abinit.$PBS_JOBID #PBS -l nodes=1:ppn=12 #PBS -l walltime=1:00:00 #PBS -M email@example.com cd $PBS_O_WORKDIR cp -r $HOME/ABINIT-JOBS/Input /scratch/$PBS_JOBID cp -r $HOME/ABINIT-JOBS/Psps_for_tests /scratch/$PBS_JOBID cd /scratch/$PBS_JOBID/Input NP=$(wc -l < $PBS_NODEFILE) mpirun -np $NP -machinefile $PBS_NODEFILE abinit < tparal_3.files >& tparal_3.log mv *.log *.out *LOG* $PBS_O_WORKDIR/
PBS script first we move into the working directory and copy all of our directories with the necessary files from our home directory to the temporary
/scratch/$PBS_JOBID directory to run our computation. Then once we run the computation we move the output files back to the directory where we submitted the job from.
Then submit the job to the queue. There will be a lot of log files output. I would start looking at
razor-l3:jokinsey:~/ABINIT-JOBS/Input$ qsub abinit.pbs