Running Jobs

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.

IMPORTANT

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.

Queues

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:

bsc_queues

info

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.

Submitting jobs

A job is the execution unit for Slurm. 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.

info

For more information:

man sbatch
man srun
man salloc

IMPORTANT

The maximum amount of queued jobs (running or not) is 366.
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.

Important accounting changes

To ensure fair and reliable CPU usage accounting information, we've enforced the need to use at least 40 threads for each GPU requested. In your job scripts, make sure that the amount of threads used meet the requirements for your GPU needs. Note that Slurm does refer to each thread as if it was a physical CPU.

The value of "cpu-per-task" x "task-per-node" should amount to those 40 threads. Remember that, by default, the value of "cpu-per-task" is 1.

If you can't change the number of tasks in your job, you can edit the number of CPUs per task (#SBATCH --cpus-per-task=). In order to not affect your executions, you can choose the desired CPUs per task by setting the environment variable OMP_NUM_THREADS (this variable may not work for every application).

Otherwise, an error message will be displayed pointing out this issue:

sbatch: error: Minimum cpus requested should be (nodes * gpus/node * 40). 
Cpus requested: X. Gpus: Y, Required cpus: Z
sbatch: error: Batch job submission failed: CPU count specification invalid

SBATCH commands

These are the primary directives to submit jobs with sbatch:

Submit a job script to the queue system (see Job directives):
```
sbatch <job_script>
```
Show all the submitted jobs:
```
squeue
```
Remove a job from the queue system, canceling the execution of the processes (if they were still running):
```
scancel <job_id>
```
To set up X11 forwarding on a srun allocation (so that you will be able to execute a graphical command):
```
srun --x11
```
REMARK
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
```

Interactive Sessions

Allocation of an interactive session has to be done through Slurm:

salloc [ OPTIONS ] 

note

Some of the parameters you can use with salloc are the following (see also Job directives):

-p, --partition=<name>
-q, --qos=<name>
-t, --time=<time>
-n, --ntasks=<number>
-c, --cpus-per-task=<number>
-J, --job-name=<name>
--exclusive

Examples

Interactive session for 10 minutes, 1 task, 40 CPUs (cores) per task:

salloc -t 00:10:00 -n 1 -c 40 -J myjob

Interactive session for 80 CPUs (cores) + 2 GPUs:

$> salloc -c 80 --gres=gpu:2

Job directives

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 syntax is of the form:

#SBATCH --directive=value

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:

Request the queue for the job:
```
#SBATCH --qos=debug
```
REMARKS
- Slurm will use the user's default queue if it is not specified.
- The queue 'debug' is only intended for small tests.
Set the limit of wall clock time:
```
#SBATCH --time=HH:MM:SS
```
caution
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): If not specified, it is the current
```
#SBATCH -D pathname
```
caution
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:
```
#SBATCH --output=file
```
Set the name of the file to collect the standard error output (stderr) of the job:
```
#SBATCH --error=file
```
Set the number of processes to start:

#SBATCH --ntasks=number

Optionally, you can specify how many threads each process would open with the directive:
```
#SBATCH --cpus-per-task=number
```
info
The number of cpus assigned to the job will be the total_tasks number * cpus_per_task number.
Set the number of tasks assigned to a node:
```
#SBATCH --ntasks-per-node=number
```
Set the number of GPUs assigned to a node:
```
#SBATCH --gres=gpu:number
```
Request an exclusive use of a compute node without sharing the resources with other users:
```
#SBATCH --exclusive
```
Set the reservation name where you will allocate your jobs (assuming that your account has access to that reservation):
```
#SBATCH --reservation=reservation_name
```
REMARK
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):
```
#SBATCH --mail-type=[begin|end|all|none]
#SBATCH --mail-user=<your_email>
```
Example (notified at the end of the job execution):
```
#SBATCH --mail-type=end
#SBATCH --mail-user=dannydevito@bsc.es
```
REMARK
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).

Some useful Slurm's environment variables

Variable	Meaning
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

Examples

sbatch examples

Example for a sequential job:

#!/bin/bash
#SBATCH --job-name="test_serial"
#SBATCH -D .
#SBATCH --output=serial_%j.out
#SBATCH --error=serial_%j.err
#SBATCH --ntasks=1
#SBATCH --time=00:02:00

./serial_binary > serial.out

The job would be submitted using:

sbatch ptest.cmd

Example for a parallel job:

#!/bin/bash
#SBATCH --job-name=test_parallel
#SBATCH -D .
#SBATCH --output=mpi_%j.out
#SBATCH --error=mpi_%j.err
#SBATCH --ntasks=20
#SBATCH --cpus-per-task=4
#SBATCH --time=00:02:00
#SBATCH --gres=gpu:2

mpirun ./parallel_binary > parallel.output

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.

Running Jobs

Queues​

Submitting jobs​

Important accounting changes​

SBATCH commands​

Interactive Sessions​

Examples​

Job directives​

Some useful Slurm's environment variables​

Examples​

sbatch examples​

Interpreting job status and reason codes​

Job state codes​

Job reason codes​

Queues

Submitting jobs

Important accounting changes

SBATCH commands

Interactive Sessions

Examples

Job directives

Some useful Slurm's environment variables

Examples

sbatch examples

Interpreting job status and reason codes

Job state codes

Job reason codes