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,[intlink id=”237″ type=”post”] here there are examples[/intlink], 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