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.
run abinit by script on supercomputer [SOLVED]
Moderators: fgoudreault, mcote
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Please have a look at ~abinit/doc/config/build-config.ac in the source package for detailed and up-to-date information about the configuration of Abinit 8 builds.
For a video explanation on how to build Abinit 7.x for Linux, please go to: http://www.youtube.com/watch?v=DppLQ-KQA68.
IMPORTANT: when an answer solves your problem, please check the little green V-like button on its upper-right corner to accept it.
Please have a look at ~abinit/doc/config/build-config.ac in the source package for detailed and up-to-date information about the configuration of Abinit 8 builds.
For a video explanation on how to build Abinit 7.x for Linux, please go to: http://www.youtube.com/watch?v=DppLQ-KQA68.
IMPORTANT: when an answer solves your problem, please check the little green V-like button on its upper-right corner to accept it.
Re: run abinit by script on supercomputer [SOLVED]
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 ! ) :
and use the command :
good luck...
it seems that reading your post :
- - the batch system is SLURM
- the dev environment is INTEL cluster studio
- and you want to use GPU
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...
------
Jean-Michel Beuken
Computer Scientist
Jean-Michel Beuken
Computer Scientist
Re: run abinit by script on supercomputer
Thank you very much, now I understand what I have to do.