Skip to main content


To provide better Ceres usage report all Ceres users have been assigned Slurm accounts based on their project groups. If you don’t have a project, then your default and only Slurm account is sandbox. If you have more than one project, then your default Slurm account is one of the project names. You can specify a different Slurm account when submitting a job by using “-A ” option on salloc/srun/sbatch command or adding “#SBATCH -A ” to the job script.

To see all your Slurm accounts and your default account at any time, use “sacctmgr -Pns show user format=account,defaultaccount”

You can change your default Slurm account running on the login node.

Interactive Mode

A user can request an interactive session on Ceres using SLURM’s srun or salloc commands. The simplest way to request an interactive job is by entering the command salloc:

$ salloc

which will place you in an interactive shell. This interactive shell has a duration of 2 days and will request a single hyper-threaded core (2 logical cores) with 6000 MB of allocated memory on one of the compute nodes.

To prevent users from requesting interactive nodes and then not using them, there is an inactivity timeout set up. If there is no command running on a node for an hour and a half, the job will be terminated. Otherwise the interactive job is terminated when the user types exit or the allocated time runs out.

For more fine grained control over the interactive environment you can use the srun command. Issue the srun command from a login node. Command syntax is:

$ srun --pty -p queue -t hh:mm:ss -n tasks -N nodes /bin/bash -l
Option Value
-p queue (partition)
-t maximum runtime
-n number of cores
-N number of nodes

The following example commands illustrate an interactive session where the user requests 1 hour in the short queue, using 1 compute node and 20 logical cores (half of the cores available on the original compute node), using the bash shell, followed by a BLAST search of a protein database.

Start the interactive session:

$ srun --pty -p short -t 01:00:00 -n 20 -N 1 /bin/bash -l

Load NCBI-BLAST+ on the compute node:

$ module load blast+

Uncompress the nr.gz FASTA file that contains your sequence database:

$ gzip -d nr.gz

Generate the blast database:

$ makeblastdb -in nr -dbtype prot

Search the nr database in serial mode with a set of queries in the FASTA file blastInputs.fa:

$ blastp -db nr -query blastInputs.fa -out blastout

Return to the login node:

$ exit

Requesting the Proper Number of Nodes and Cores

SLURM allows you to precisely choose the allocation of compute cores across nodes. Below are a number of examples that show different ways to allocate an 8 core job across the Ceres cluster

salloc/srun/sbatch options core distribution across nodes
-n 8 pick any available cores across the cluster (may be on several nodes or not)
-n 8 -N 8 spread 8 cores across 8 distinct nodes (i.e. one core per node)
-n 8 --ntasks-per-node=1 same as -n 8 -N 8
-n 8 -N 4 request 8 cores on 4 nodes (however the spread might be uneven, i.e. one node could end up with 5 cores and one core each for the remaining 3 nodes)
-n 8 --ntasks-per-node=2 request 8 cores on 4 nodes with 2 cores per node
-n 8 -N 1 request 8 cores on a single node
-n 8 --ntasks-per-node=8 same as -n 8 -N 1

Batch Mode

Serial Job

Jobs can be submitted to various partitions or queues using SLURM’s sbatch command. The following is an example of how to run a blastp serial job using a job script named “”. The content of is as follows:

#SBATCH --job-name="blastp"   #name of this job
#SBATCH -p short              #name of the partition (queue) you are submitting to
#SBATCH -N 1                  #number of nodes in this job
#SBATCH -n 40                 #number of cores/tasks in this job, you get all 20 physical cores with 2 threads per core with hyper-threading
#SBATCH -t 01:00:00           #time allocated for this job hours:mins:seconds
#SBATCH --mail-user=emailAddress   #enter your email address to receive emails
#SBATCH --mail-type=BEGIN,END,FAIL #will receive an email when job starts, ends or fails
#SBATCH -o "stdout.%j.%N"     # standard output, %j adds job number to output file name and %N adds the node name
#SBATCH -e "stderr.%j.%N"     #optional, prints our standard error
date                          #optional, prints out timestamp at the start of the job in stdout file
module load blast+            #loading latest NCBI BLAST+ module
blastp -db nr -query blastInputs -out blastout  # protein blast search against nr database
date                          #optional, prints out timestamp when the job ends
#End of file

Launch the job like this:

$ sbatch

Running a Simple OpenMP Job

The following example will demonstrate how to use threads. We will use the following OpenMP C code to print “hello world” on each thread. First copy and paste this code into a file, e.g. “testOpenMP.c”.

#include <omp.h>
#include <stdio.h>
int main(int argc, char* argv[]){
 int id;
 #pragma omp parallel private(id)
  printf("%d: hello world \n",id);
 return 0;

Now load the gcc module and compile the code :

$ module load gcc
$ gcc testOpenMP.c -fopenmp -o testOpenMP

Now create a batch job script ( to test number of threads you requested:

#SBATCH --job-name=OpenMP
#SBATCH -p short
#SBATCH -n 20
#SBATCH --threads-per-core=1
#SBATCH -t 00:30:00
#SBATCH -o "stdout.%j.%N"
#SET the number of openmp threads
# End of file

Launch the job using the batch script like this:

$ sbatch

The stdout* file from the above job script should contain 20 lines with “hello world” from each thread.

Parallel MPI Job

The following is the example to run Hybrid RAxML which uses both MPI and PTHREADS. It will start 2 MPI processes (one per node) and each process will run 40 threads (one thread per logical core).

Create a SLURM script like this (for example,, but use your own alignment file rather than “align.fasta”):

#SBATCH --job-name=raxmlMPI
#SBATCH -p short
#SBATCH --ntasks-per-node=40
#SBATCH -t 01:00:00
#SBATCH -o "stdout.%j.%N"
# We requested 2 nodes, 40 logical cores per node for a total of 80 logical cores for this job
module load raxml            #loading latest raxml module, which will also load an MPI module
mpirun -np 2 raxmlHPC-MPI-AVX -T 40 -n raxmlMPI -f a -x 12345 -p 12345 -m GTRGAMMA -# 100 -s align.fasta
# End of file

And execute it with sbatch:

$ sbatch

Recurring Jobs - Scrontab

scrontab is slurm-managed crontab. It is used to submit recurring jobs via slurm scheduler.

scrontab uses syntax that is similar to crontab


Issue scrontab -e to edit scrontab.

Lines starting with #SCRON indicate a recurring batch job. It is equivalent to #SBATCH in normal batch jobs and users can use the sbatch options.

scrontab uses the same syntax for date and time specifiers as cron. Each line has five fields that have the following meanings:

field allowed values
minute 0-59
hour 0-23
day of month 1-31
month 1-12 (or name)
day of week 0-7 (0 and 7 are Sunday, or use name)

The entries follow the same syntax as cron. Websites like provide useful information on when your job will be executed.


Submit job

$ scrontab FILE.job

Check scrontab status

$ scrontab -l

Clear scrontab

$ scrontab -r

Check job queue

$ squeue

Cancel job

$ scancel ID

Example jobs

A python script that runs every 30 minutes and requests 1 node with 4 cores and a timelimit of 1 hour.

#SCRON -t 1:00:00
#SCRON -n 4
30 * * * * python $HOME/

Runs every hour with a timelimit of 1 minute.

#SCRON -p high
#SCRON -A sub1
#SCRON -t 1:00
@hourly $DIR/date.printer.job

Note that the default working directory is $HOME and can be modified with either setting DIR variable or with #SCRON --chdir

Useful SLURM Commands

Command Description Example
squeue Gives information about jobs squeue or squeue -u jane.webb
scancel Stop and remove jobs scancel <job id> or scancel -u jane.webb
sinfo Gives information about queues (partitions) or nodes sinfo or sinfo -N -l
scontrol Provides more detailed information about jobs, partitions or nodes scontrol show job <job id> or scontrol show partition <partition name> or scontrol show nodes
seff Provides resource usage report for a finished job seff <job id>