31 June 2010 by Jae
How to run ur code on space?- u must have user on space (contact me by mail or at p507)
- copy ur code directory from galaxy to space (galaxy - old server, space - new server)
- to copy ur i recommend to use Securre file transfer program (it can copy all file and folder with same time)
- or u can use sftp service
- to compile streamline code on space u need to edit "Makefile" file to specific library on new server
- Compile code to get streamline by command "make". U must pass this step by no error
- Now u have streamline program. to run it on space we not use mpirun (we use it on galaxy) by we use qsub(Service that manage job on sever)
- write script name "xxxxx.qsub" <--- u can choose it name
- in xxxxx.qsub file have detail like this:
- to run this script us command: " qsub -pe orte 2 xxxxx.qsub "
- "2" is number u want to use in this run now we have 2 node2
- "xxxxx.qsub" is ur script
- after u submit job to server u will get job number u can use it for check job status(already run?) by type "qstat" to check what job is running now
- it u want to del job that u already submit use "qdel 1234" to delete job number "1234"
- if streamline get output on screen it would write to file "xxxxx.sh.o1234"
- "xxxxx.qsub" is name of cript file u already write in step: 5
- "1234" is job number of ur run job
PS. No need to specifics what node u want to run for qsub
Our space is "rocks clusters" to submit job u can study from this link, (it 's SGE Manual. Rocks clusters use this service to manage job)
