Important: Most software will only consume 1 CPU core - e.g., requesting 8 CPU cores for a PAUP job blocks other people using the unused 7 CPU cores. Most HPC users will have scripts similar to Example 1 below.
|
Directive(s) | Description of purpose |
---|---|
| Sets the working directory for you job to <PATH>. |
| Explicit specification of file that will hold the standard output stream from you job. |
| Export environment variables to the batch job |
For full details on directives that can be used, use "man qsub
" on a HPC login node or look at online documentation for Torque.
Variable | Description |
---|---|
| Job name specified by the user |
| Working directory from which the job was submitted |
| Home directory of user submitting the job |
| Name of user submitting the job |
| Script shell |
| Unique PBS job id |
| Host on which job script is running |
| Name of the job queue |
| File containing line delimited list on nodes allocated to the job |
| Path variable used to locate executables within the job script |
Your requirements | ||
---|---|---|
CPU cores | Total Memory | PBS/Torque options |
1 | 1200 MB | -l nodes=1:ppn=1 -l pmem=1200mb |
1 | 20 GB | -l nodes=1:ppn=1 -l pmem=20gb |
2 | 6 GB | -l nodes=1:ppn=2 -l pmem=3gb |
8 | 4 GB | -l nodes=1:ppn=8 -l pmem=512mb |
24 | 120 GB | -l nodes=1:ppn=24 -l pmem=5gb |
The most important thing to note is that the pmem
parameter is physical memory per core that your job requires.