- General SLURM documentation found here
- SLURM tutorials
- SLURM tools youtube video
- SLURM tutorial @ Harvard
Submitting and cancelling SLURM jobs
Submit a job script called my_script.sh requesting
- 5GB RAM per cpu
- 20 CPUs on a single node
- use the scheduler queue $MYQUEUE
- use the job name $MYJOB_NAME
- provide a time ceiling of 3 HRs
- write STDOUT to file $MYLOG.log
Submit an interactive job
- 2GB RAM per cpu
- 4 CPUs on a single node
- use the scheduler queue $MYQUEUE
- provide a time ceiling of 1 HR
- execute task zero in pseudo terminal mode. The option “pty” is important because it allows an interactive terminal mode. Without “pty” every command issued would be run 4 times (-c 4)
Jobs can be submitted by passing all SLURM parameters through bash script
Run the RAxML analysis as
Find information about partitions and jobs
List job information
- The sacct command displays job accounting data stored in the job accounting log file or Slurm database in a variety of forms for your analysis. The sacct command displays information on jobs, job steps, status, and exitcodes by default. For the non-root user, the sacct command limits the display of job accounting data to jobs that were launched with their own user identifier (UID) by default. Data for other users can be displayed with the –allusers, –user, or –uid options.