How to compute/Quick start
|How to compute|
|PBS Pro Quick Start [PDF]||
}} This Step by Step tutorial shows how to run a job on MetaCentrum machines, see the How to compute topic for more information or follow steps bellow to run an example job. You can also see video tutorial, which covers this topic (works with PuTTY and Windows).
1. Log on a frontend
Write the line below into your terminal and fill in your META password:
ssh 'META username'@'frontend' Password: <Enter META password>
Please type your MetaCentrum username, which you set during registration. You can choose any front end of MetaCentrum, e.g.
2. Prepare a startup script
Create myJob.sh text file (in your favourite text editor) with the following lines:
#!/bin/bash # sets home directory DATADIR="/storage/brno2/home/$LOGNAME/" # loads the Gaussian's module, version 03 module add g03 # setup SCRATCH cleaning in case of an error trap 'clean_scratch' TERM EXIT # enters user's scratch directory cd $SCRATCHDIR || exit 1 # prepares job's input data wget http://www.cerit-sc.cz/en/docs/quickstart/gaussian_test.com # starts the Gaussian application g03 <gaussian_test.com >results.out # moves the produced (output) data to user's home directory or leave it in SCRATCH if error occured cp results.out $DATADIR || export CLEAN_SCRATCH=false
3. Specify job's parameters & submit the job
Type the following line into your terminal with the script's name at the end:
qsub -l select=1:ncpus=2:mem=4gb:scratch_local=10gb -l walltime=1:00:00 myJob.sh
You should see an output with 12345.arien-pro.ics.muni.cz. JobID is 12345 in this case.
4. Track job's status
|Tracking job status||
You can use jobID and qstat command to track the job. Type line below into your terminal:
qstat 'jobID'.arien-pro.ics.muni.cz # writes info about running and queued jobs qstat -x 'jobID'.arien-pro.ics.muni.cz # writes infor about finished jobs
You should see an output similar to these lines:
Req'd Req'd Elap Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time --------------- --------------- -------- ---------- ------ --- --- ------ ----- - ----- 12345.arien-pr 'your username' q_2h myJob.sh 6866 1 8 2gb 01:00 F 00:00 # F=Finished, R=running, Q=Queued
5. Examine job's standard output and standard error output
When the job is completed you can examine it's outputs in your terminal:
cat ~/results.out # job's output data cat ~/myjob.sh.o12345 # job's standard output, empty for now (forwarded to results.out) cat ~/myjob.sh.e12345 # job's standard error output