ABINIT Discussion Forums

Posted: **Sun Mar 16, 2014 9:20 am**

Dear Sirs,

I`m installing Abinit v 7.6.2 on "Lomonosov" supercomputer, in Russia.
Sorry if my question is silly or is asked second time, but I have searched for the answer and haven`t fount satisfactory solution.

So, my problem is how to run Abinit by queue script on our supercomputer.
In all tutorials Abinit`s launch is implemented only this way:
mpirun -n 1 abinit < t1x.files
(and it works in my case, but it isn`t what I want)

As I understand, it redirects input from stdin to t1x.files

The problem is that I have to make Abinit available for users by running script, the script looks somehow like this:
sbatch -n 1 -p gputest impi abinit < t1x.files

But this way it does`t work, the error is
"Give name for formatted input file:
forrtl: severe (24): end-of-file during read, unit 5, file stdin"

The second idea was to use an option of the script, this one:
-i, --input=in - file for batch script's standard input

but it also didn`t work with the same error.

Also I looked through the topics on your forum, and found this one:
viewtopic.php?f=2&t=53

There is a solution of the same problem - "configure Abinit with the --disable-stdin option"

But this topic is old, and I hope now there is a better one.
Or I have made some mistakes and I hope you will explain them to me.

Sincerely,
Afanasiev Ilya, student of Moscow State University.

Posted: **Sun Mar 16, 2014 9:03 pm**

Hi,

it seems that reading your post :

at first, forgot the GPU
then it would be useful to read the documentation slurm…
Finally, here is a submission file ( run.sh ) as an example ( not tested ! ) :

Code: Select all

#!/bin/bash
#SBATCH --job-name=test
##SBATCH --mail-user=my@email
#SBATCH --mail-type=ALL
#SBATCH --time=30:00
#SBATCH --ntasks=4
#SBATCH --mem-per-cpu=1000
#SBATCH --output=log

module purge
module load gcc/4.7.2
module load intel/clusterstudio/impi/4.1.0p-024
module load netcdf/intel/4.2.1
source /usr/local/intel/ics_2013.0.028/mkl/bin/mklvars.sh intel64

export OMP_NUM_THREADS=1
unset SLURM_CPUS_PER_TASK

cd ~/Working_dir_with_input_files
mpirun abinit < input.file

and use the command :

Code: Select all

sbatch run.sh

good luck...

Posted: **Mon Mar 17, 2014 9:10 am**

Thank you very much, now I understand what I have to do.

ABINIT Discussion Forums

run abinit by script on supercomputer

run abinit by script on supercomputer

Re: run abinit by script on supercomputer [SOLVED]

Re: run abinit by script on supercomputer