There are three ways:<\/p>\n
send_siesta<\/code> command.<\/li>\n- Using
qsub<\/code> in interactive way.<\/li>\n- With a scritp for the
qsub<\/code> command.<\/li>\n<\/ul>\nsend_siesta<\/h1>\n
We have written the send_siesta<\/code> command to submit Siesta jobs. Execute send_siesta<\/tt> and its usage is shownArina. In the following lines we describe it sintax-<\/tt><\/p>\nsend_siesta JOBNAME NODES PROCS_PER_NODE[property] TIME MEM [\"Other queue options\"]<\/tt><\/pre>\nJOBNAME:<\/tt> Input file without extension.
\nNODES:<\/tt> Number of nodes to be used.
\nPROCS_PER_NODE:<\/tt> Cores per node.
\nTIME:<\/tt> Walltime in hh:mm:ss<\/tt> format.
\nMEM:<\/tt> Memoria Gb unitatetan.
\n[\"Other queue options\"]<\/tt>Other instructions to the queue system inside quotes.<\/p>\n
Examples<\/strong>
\nTo submit the job1.fdf input in one itaniumb node and for cores:<\/p>\nsend_siesta job1 1 4:itaniumb 04:00:00 1<\/pre>\nTo 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:<\/p>\n
send_siesta job2 2 4 192:00:00 8 ``-W depend=afterany:1234''<\/pre>\nTo 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:<\/p>\n
send_siesta job2 4 8 200:00:00 15 ``-m be -M nire.emaila@ehu.es''<\/pre>\nThe send_siesta<\/code> command will use the local \/scratch<\/code> directory or the global file system \/gscratch<\/code> depending on the number of nodes used.<\/p>\n <\/p>\n
Interactive qsub<\/h1>\n
Exekute<\/p>\n
qsub<\/pre>\nwithout arguments and answer the question.<\/p>\n
Regular qsub<\/h1>\n
Build a script for qsub,[intlink id=\u00bb237″ type=\u00bbpost\u00bb] here there are examples[\/intlink], and to execute Siesta use the following line<\/p>\n
\/software\/bin\/siesta\/siesta_mpi < input.fdf > log.out<\/pre>\nJob monitoring<\/h1>\n\n\nIf you used<\/ul>\n<\/ul>\n<\/ul>\nsend_siesta<\/code><\/p>\n\n\nor interactive<\/ul>\n<\/ul>\n<\/ul>\nqsub<\/code><\/p>\n\nto submit a job you can monitor it with the following commands:<\/ul>\n<\/ul>\n\n- remote_vi<\/strong><\/dt>\n
- \u00a0It will open the *.out<\/tt> file with gvim.<\/dd>\n
- remote_xmakemol<\/strong><\/dt>\n
- xmakemol<\/tt> will be used to open the *.ANI<\/tt> file.<\/dd>\n
- remote_qmde<\/strong><\/dt>\n
- xmgrace<\/tt> will be used to plot energia vs. time in molecular\u00a0 dynamics simulations.<\/dd>\n<\/dl>\n
Examples to monitor the job with 3465 identifier:<\/p>\n
remote_vi 3465\r\nremote_xmakemol 3465\r\nremote_qmde 3465<\/pre>\n","protected":false},"excerpt":{"rendered":"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] … Seguir leyendo How to submit siesta jobs<\/span>