BinAC2/Migrate Moab to Slurm jobs
BinAC 1 Queues -> BinAC 2 Slurm partitions
BinAC 2 uses Slurm scheduler instead of Moab/Torque. Please refer to the BinAC 2 Slurm paritions page for an overview of available Slurm partitions.
Moab/Torque flags -> Slurm flags
Replace Moab/Torque job specification flags in your job scripts by their corresponding Slurm counterparts.
Commonly used Moab job specification flags and their Slurm equivalents
| Option | Moab (msub) | Slurm (sbatch) |
|---|---|---|
| Script directive | #PBS | #SBATCH |
| Job name | -N <name> | --job-name=<name> (-J <name>) |
| Account | -A <account> | --account=<account> (-A <account>) |
| Queue | -q <queue> | --partition=<partition> (-p <partition>) |
| Wall time limit | -l walltime=<hh:mm:ss> | --time=<hh:mm:ss> (-t <hh:mm:ss>) |
| Node count | -l nodes=<count> | --nodes=<count> (-N <count>) |
| Core count | -l procs=<count> | --ntasks=<count> (-n <count>) |
| Process count per node | -l ppn=<count> | --ntasks-per-node=<count> |
| Core count per process | --cpus-per-task=<count> (-c <count>) | |
| Memory limit per node | -l mem=<limit> | --mem=<limit> |
| Memory limit per process | -l pmem=<limit> | --mem-per-cpu=<limit> |
| Job array | -t <array indices> | --array=<indices> (-a <indices>) |
| Node exclusive job | -l naccesspolicy=singlejob | --exclusive |
| Initial working directory | -d <directory> (default: $HOME) | --chdir=<directory> (-D <directory>) (default: submission directory) |
| Standard output file | -o <file path> | --output=<file> (-o <file>) |
| Standard error file | -e <file path> | --error=<file> (-e <file>) |
| Combine stdout/stderr to stdout | -j oe | --output=<combined stdout/stderr file> |
| Mail notification events | -m <event> | --mail-type=<events> (valid types include: NONE, BEGIN, END, FAIL, ALL) |
| Export environment to job | -V | --export=ALL (default) |
| Don't export environment to job | (default) | --export=NONE |
| Export environment variables to job | -v <var[=value][,var2=value2[, ...]]> | --export=<var[=value][,var2=value2[,...]]> |
Moab/Torque environment variables
 |
By default Moab does not export any environment variables to the job's runtime environment. With Slurm most of the login environment variables are exported to your job's runtime environment. This includes environment variables from software modules that were loaded at job submission time (and also $HOSTNAME variable). See sbatch man page for a complete list of flags and environment variables. |
Replace Moab/Torque job specification environment variables in your job scripts by their corresponding Slurm counterparts.
| Information | Moab | Torque | Slurm |
|---|---|---|---|
| Job name | $MOAB_JOBNAME | $PBS_JOBNAME | $SLURM_JOB_NAME |
| Job ID | $MOAB_JOBID | $PBS_JOBID | $SLURM_JOB_ID |
| Submit directory | $MOAB_SUBMITDIR | $PBS_O_WORKDIR | $SLURM_SUBMIT_DIR |
| Number of nodes allocated | $MOAB_NODECOUNT | $PBS_NUM_NODES | $SLURM_JOB_NUM_NODES (and: $SLURM_NNODES) |
| Node list | $MOAB_NODELIST | cat $PBS_NODEFILE | $SLURM_JOB_NODELIST |
| Number of processes | $MOAB_PROCCOUNT | $PBS_TASKNUM | $SLURM_NTASKS |
| Requested tasks per node | --- | $PBS_NUM_PPN | $SLURM_NTASKS_PER_NODE |
| Requested CPUs per task | --- | --- | $SLURM_CPUS_PER_TASK |
| Job array index | $MOAB_JOBARRAYINDEX | $PBS_ARRAY_INDEX | $SLURM_ARRAY_TASK_ID |
| Job array range | $MOAB_JOBARRAYRANGE | - | $SLURM_ARRAY_TASK_COUNT |
| Queue name | $MOAB_CLASS | $PBS_QUEUE | $SLURM_JOB_PARTITION |
| QOS name | $MOAB_QOS | --- | $SLURM_JOB_QOS |
| --- | $PBS_NUM_PPN | $SLURM_TASKS_PER_NODE | |
| Job user | $MOAB_USER | $PBS_O_LOGNAME | $SLURM_JOB_USER |
| Hostname | $MOAB_MACHINE | $PBS_O_HOST | $SLURMD_NODENAME |