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hoffman_common_ccpr.md

Commonly Used Hoffman2 Commands

CCPR

Common Linux: File Directory Navigation Tools

https://www.ccn.ucla.edu/wiki/index.php/Hoffman2:Linux_Tutorial

Interactive Session Common Hard/Soft-ware Resources

  • NOTE: Multiple commands can fit into a single line by separating commands with a semi colon

Request Hardware

  • interactive session, 16g ram 1 hour, any available node
qrsh -l i,h_data=16g,h_rt=1:00:00;
  • interactive session, ... , using special highpriority CCPR node '1234' (1234 is a fake example)
qrsh -l i,h_data=16g,h_rt=1:00:00,highp -q *@n1234

Request Software

Using Rstudio

module av R
module load R/3.2.1; module load Rstudio; rstudio

Using Stata (se/mp)

module av stata
module load stata/16; xstata-se
module load stata/15; xstata-mp

Batch Session Common Hard/Soft-ware Resources

Helper foo.q menu to create basic .cmd file

For batch jobs, you can use the R.q or stata.q menu helpers to initially generate a template .cmd file.

stata.q
R.q

Specifically Edit the Resources in a .cmd file

Use any text editor to further modify the generated .cmd file. Specifically, parallel cores, modify ram/runtime. Look for the line in the .cmd file that looks similar to the below

-l h_data=512M,h_rt=48:00:00,highp -pe shared 8

Using specific node 1234

-l h_data=248G,h_rt=00:5:00 -q *@n1234

Find and remove all core dump files

find $HOME -name core.'[0-9]*' -print | xargs rm
  • NOTE: this removes ALL core files

When a batch job errors out, a huge core dump file is automatically created.
If you are unaware that this core file exists, you might run into hard disk space issues.
Hard disk space issues might prevent GUI apps from loading, say Rstudio.

See the group's jobs

mygroupjobs

See the group's users

qconf -su ccpr

See the details of resource group's jobs

qstat -u $(qconf -su ccpr)

See the jobs on a specific node

qstat -q *@n1234
  • NOTE: if the node in question is 'n1234'

See the resource group's jobs on a specific node

qstat -u $(qconf -su ccpr) -q *@n1234
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