Slurm is the utility used for batch processing support, so all jobs must be run through it. This section provides information for getting started with job execution at the cluster.
All jobs requesting more cores than what a full node can offer, will automatically use all requested nodes in exclusive mode. For example, if you ask for n+1 cores and nodes have n cores, you will receive two complete nodes (2 x n cores), and the consumed runtime of these 2n cores will be reflected in your budget.
Several queues are present in the machines, and users may access different queues. Queues have unlike limits regarding the number of cores and duration for the jobs.
Anytime you can check all queues you have access to and their limits by using:
Besides, special queues are available upon request for longer/bigger executions and will require proof of scalability and application performance. To apply for access to these special queues, please get in touch with us.
A job is the execution unit for Surm. A job is defined by a text file containing a set of directives describing the job's requirements, and the commands to execute.
The method for submitting jobs is to use the SLURM sbatch directives directly.
For more information:
Bear in mind there are execution limitations on the number of nodes and cores that can be used simultaneously by a group to ensure the proper scheduling of jobs.
These are the primary directives to submit jobs with sbatch:
Submit a job script to the queue system (see Job directives):
Show all the submitted jobs:
Remove a job from the queue system, canceling the execution of the processes (if they were still running):
To set up X11 forwarding on a srun allocation (so that you will be able to execute a graphical command):
You will get a graphical window as long as you don't close the current terminal.
Also, X11 forwarding can be set through interactive sessions:
salloc -J interactive --x11
Allocation of an interactive session has to be done through Slurm:
salloc [ OPTIONS ]
Some of the parameters you can use with salloc are the following (see also Job directives):
Interactive session for 10 minutes, 1 task, 4 CPUs (cores) per task:
salloc -t 00:10:00 -n 1 -c 4 -J myjob
A job must contain a series of directives to inform the batch system about the characteristics of the job. These directives appear as comments in the job script and have to conform to either the sbatch syntaxes.
sbatch syxtax is of the form:
Additionally, the job script may contain a set of commands to execute. If not, an external script may be provided with the 'executable' directive.
Here you may find the most common directives for both syntaxes:
Request the queue for the job:
- Slurm will use the user's default queue if it is not specified.
- The queue 'debug' is only intended for small test.
Set the limit of wall clock time:
This is a mandatory field and you must set it to a value greater than real execution time for your application and smaller than the time limits granted to the user. Notice that your job will be killed after the time has passed.
Set the working directory of your job (i.e. where the job will run):
#SBATCH -D pathnamecaution
If not specified, it is the current working directory at the time the job was submitted.
Set the name of the file to collect the standard output (stdout) of the job:
Set the name of the file to collect the standard error output (stderr) of the job:
Request an exclusive use of a compute node without sharing the resources with other users:
This only applies to jobs requesting less than one full node. All jobs with more cores than the number of cores of a full node will automatically use all requested nodes in exclusive mode.
Set the number of requested nodes:
Set the number of processes to start:
Optionally, you can specify how many threads each process would open with the directive:
The number of cores assigned to the job will be the total_tasks number * cpus_per_task number.
Set the number of tasks assigned to a node:
Set the number of tasks assigned to a socket:
Set the reservation name where your jobs will be allocated (assuming that your account has access to that reservation):
Sometimes, node reservations can be granted for executions where only a set of accounts can run jobs. Useful for courses.
Those two directives are presented as a set because they need to be used at the same time. They will enable e-mail notifications that are triggered when a job starts its execution (begin), ends its execution (end) or both (all):
Example (notified at the end of the job execution):
The "none" option doesn't trigger any e-mail, it is the same as not putting the directives. The only requisite is that the e-mail specified is valid and also the same one that you use for the HPC User Portal (what is the HPC User Portal, you ask? Excellent question, check it out here!
Select which configuration to run your job with:
For example, use "fat" to run the job on a high memory node with 8 GB per core.REMARK
- Without this directive the jobs will be sent to standard nodes that have 4GB of RAM per core.
- There are only a limited number of high memory nodes available, 7 nodes out of 48 nodes in total. Therefore when requesting these nodes you can expect significantly longer queueing times to fulfil the resource request before your job can start.
The accounting for one core hour in standard and highmem nodes is the same, e.g. 1 core hour per core per hour will be budgeted. For faster turnaround times in the queues you can also use standard nodes and run less processes per node. For this you will need to use more cores per task, as every cores requested comes with its 4 GB RAM. You can do this by specifying the flag #SBATCH --cpus-per-task=number and your budget will get charged for all cores requested.
By default, Slurm tries to schedule a job in order to use the minimum amount of switches. However, a user can request a maximum of switches for your job:
Slurm will try to schedule the job for timeout minutes. If it is not possible to request number switches after timeout minutes, Slurm will schedule the job by default.
Submit a job array, multiple jobs to be executed with identical parameters:
The indexes specification identifies what array index values should be used. Multiple values may be specified using a comma separated list and/or a range of values with a "-" separator.info
Job arrays will have two additional environment variable set. SLURM_ARRAY_JOB_ID will be set to the first job ID of the array. SLURM_ARRAY_TASK_ID will be set to the job array index value.
sbatch --array=1-3 job.cmd
Submitted batch job 36
Will generate a job array containing three jobs and then the environment variables will be set as follows:
# Job 1
# Job 2
# Job 3
Some useful Slurm's environment variables
|SLURM_JOBID||Specifies the job ID of the executing job|
|SLURM_NPROCS||Specifies the total number of processes in the job|
|SLURM_NNODES||Is the actual number of nodes assigned to run your job|
|SLURM_PROCID||Specifies the MPI rank (or relative process ID) for the current process. The range is from 0-(SLURM_NPROCS-1)|
|SLURM_NODEID||Specifies relative node ID of the current job. The range is from 0-(SLURM_NNODES-1)|
|SLURM_LOCALID||Specifies the node-local task ID for the process within a job|
Example for a sequential job:
./serial_binary > serial.out
Examples for a parallel job:
Running a pure OpenMP job on one SL node using 40 cores on the xlong queue:
Running on two SL nodes using a pure MPI job
Running a hybrid MPI+OpenMP job on two SL nodes with 20 MPI tasks (10 per node), each using 4 cores via OpenMP:
srun ./parallel_binary > parallel.output
It is currently not possible to be notified about the status of jobs via email. To check if your jobs are being executed or have finished you will need to connect to the system and verify their status manually. For the future it is being planned to enable automatic notifications.
Interpreting job status and reason codes
When using squeue, Slurm will report back the status of your launched jobs. If they are still waiting to enter execution, they will be followed by the reason. Slurm uses codes to display this information, so in this section we will be covering the meaning of the most relevant ones.
Job state codes
This list contains the usual state codes for jobs that have been submitted:
- COMPLETED (CD): The job has completed the execution.
- COMPLETING (CG): The job is finishing, but some processes are still active.
- FAILED (F): The job terminated with a non-zero exit code.
- PENDING (PD): The job is waiting for resource allocation. The most common state after running "sbatch", it will run eventually.
- PREEMPTED (PR): The job was terminated because of preemption by another job.
- RUNNING (R): The job is allocated and running.
- SUSPENDED (S): A running job has been stopped with its cores released to other jobs.
- STOPPED (ST): A running job has been stopped with its cores retained.
Job reason codes
This list contains the most common reason codes of the jobs that have been submitted and are still not in the running state:
- Priority: One or more higher priority jobs is in queue for running. Your job will eventually run.
- Dependency: This job is waiting for a dependent job to complete and will run afterwards.
- Resources: The job is waiting for resources to become available and will eventually run.
- InvalidAccount: The job’s account is invalid. Cancel the job and resubmit with correct account.
- InvaldQoS: The job’s QoS is invalid. Cancel the job and resubmit with correct account.
- QOSGrpCpuLimit: All CPUs assigned to your job’s specified QoS are in use; job will run eventually.
- QOSGrpMaxJobsLimit: Maximum number of jobs for your job’s QoS have been met; job will run eventually.
- QOSGrpNodeLimit: All nodes assigned to your job’s specified QoS are in use; job will run eventually.
- PartitionCpuLimit: All CPUs assigned to your job’s specified partition are in use; job will run eventually.
- PartitionMaxJobsLimit: Maximum number of jobs for your job’s partition have been met; job will run eventually.
- PartitionNodeLimit: All nodes assigned to your job’s specified partition are in use; job will run eventually.
- AssociationCpuLimit: All CPUs assigned to your job’s specified association are in use; job will run eventually.
- AssociationMaxJobsLimit: Maximum number of jobs for your job’s association have been met; job will run eventually.
- AssociationNodeLimit: All nodes assigned to your job’s specified association are in use; job will run eventually.