TEMPLATE on HPC
Description
References:
- Paper
Documentation
- Module Name: TEMPLATE (see the modules page for more information)
- Multithreaded/singlethreaded/MPI...
- environment variables set
- TEMPLATE_HOME
- Example files in ???
- Reference data in /fdb/TEMPLATE/
Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.
Allocate an interactive session and run the program. Sample session:
[user@biowulf]$ sinteractive salloc.exe: Pending job allocation 46116226 salloc.exe: job 46116226 queued and waiting for resources salloc.exe: job 46116226 has been allocated resources salloc.exe: Granted job allocation 46116226 salloc.exe: Waiting for resource configuration salloc.exe: Nodes cn3144 are ready for job [user@cn3144 ~]$ [user@cn3144 ~]$ exit salloc.exe: Relinquishing job allocation 46116226 [user@biowulf ~]$
Batch job
Most jobs should be run as batch jobs.
Create a batch input file (e.g. batch.sh). For example:
#!/bin/bash set -e module load TEMPLATE TEMPLATE < TEMPLATE.in > TEMPLATE.out
Submit this job using the Slurm sbatch command.
sbatch [--cpus-per-task=#] [--mem=#] batch.sh
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.
Create a swarmfile (e.g. job.swarm). For example:
TEMPLATE < TEMPLATE.in > TEMPLATE.out TEMPLATE < TEMPLATE.in > TEMPLATE.out TEMPLATE < TEMPLATE.in > TEMPLATE.out TEMPLATE < TEMPLATE.in > TEMPLATE.out
Submit this job using the swarm command.
swarm -f job.swarm [-g #] [-t #] --module TEMPLATEwhere
| -g # | Number of Gigabytes of memory required for each process (1 line in the swarm command file) |
| -t # | Number of threads/CPUs required for each process (1 line in the swarm command file). |
| --module | Loads the module for each subjob in the swarm |
