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enero, 2014:

How to submit siesta jobs

How to submit siesta jobs

There are three ways:

  • Using the send_siesta command.
  • Using qsub in interactive way.
  • With a scritp for the qsub command.

send_siesta

We have written the send_siesta command to submit Siesta jobs. Execute send_siesta and its usage is shownArina. In the following lines we describe it sintax-

send_siesta JOBNAME NODES PROCS_PER_NODE[property] TIME MEM ["Other queue options"]

JOBNAME: Input file without extension.
NODES: Number of nodes to be used.
PROCS_PER_NODE: Cores per node.
TIME: Walltime in hh:mm:ss format.
MEM: Memoria Gb unitatetan.
["Other queue options"]Other instructions to the queue system inside quotes.

Examples
To submit the job1.fdf input in one itaniumb node and for cores:

send_siesta job1 1 4:itaniumb 04:00:00 1

To submit the job2.fdf input to 2 nodes and for cores in each node, 192 hours and 8gb RAM memory. In adition, the job will start after the job with 1234 identifier finish:

send_siesta job2 2 4 192:00:00 8 ``-W depend=afterany:1234''

To submit the job2.fdf input file in 4 nodes and 8 cores per node, 200 hours, eta 15gb RAM. In addition send an email when the jobs starts and finish:

send_siesta job2 4 8 200:00:00 15 ``-m be -M nire.emaila@ehu.es''

The send_siesta command will use the local /scratch directory or the global file system /gscratch depending on the number of nodes used.

 

Interactive qsub

Exekute

qsub

without arguments and answer the question.

Regular qsub

Build a script for qsub, here there are examples, and to execute Siesta use the following line

/software/bin/siesta/siesta_mpi < input.fdf > log.out

Job monitoring

        If you used

send_siesta

        or interactive

qsub

      to submit a job you can monitor it with the following commands:
remote_vi
 It will open the *.out file with gvim.
remote_xmakemol
xmakemol will be used to open the *.ANI file.
remote_qmde
xmgrace will be used to plot energia vs. time in molecular  dynamics simulations.

Examples to monitor the job with 3465 identifier:

remote_vi 3465
remote_xmakemol 3465
remote_qmde 3465

Siesta

General information

Spanish Initiative for Electronic Simulation with Thousands Atoms. DFT based simulation program for solids and molecules. It can be used for molecular dynamics and relaxations. It uses localized orbitals that allow to make calculations with large number of atoms. The academic license is freely distributed but it is necessary to ask for a license. The 3.0rc1 version is installed in the x87_64 nodes and the 2.0.1 in the Itanium nodes.

How to send siesta

Follow this link.

More information

Siesta home page.

Siesta online manual.