Job Scripts on Saga

This page documents how to specify the queue system parameters for the different job types on Saga. See Saga Job Types for information about the different job types on Saga.

Normal

The basic type of job on Saga is the normal job.

Normal jobs must specify account (--account), walltime limit (--time) and how much memory is needed. Usually, they will also specify the number of tasks (i.e., processes) to run (--ntasks - the default is 1), and they can also specify how many cpus each task should get (--cpus-per-task - the default is 1).

The jobs can also specify how man tasks should be run per node (--ntasks-per-node), or how many nodes the tasks should be distributed over (--nodes). Without any of these two specifications, the tasks will be distributed on any available resources.

Memory usage is specified with --mem-per-cpu, in MiB (--mem-per-cpu=3600M) or GiB (--mem-per-cpu=4G).

If a job tries to use more (resident) memory on a compute node than it requested, it will be killed. Note that it is the total memory usage on each node that counts, not the usage per task or cpu. So, for instance, if your job has two single-cpu tasks on a node and asks for 2 GiB RAM per cpu, the total limit on that node will be 4 GiB. The queue system does not care if one of the tasks uses more than 2 GiB, as long as the total usage on the node is not more than 4 GiB.

A typical job specification for a normal job would be

#SBATCH --account=MyProject
#SBATCH --job-name=MyJob
#SBATCH --time=1-0:0:0
#SBATCH --mem-per-cpu=3G
#SBATCH --ntasks=16

This will start 16 tasks (processes), each one getting one cpu and 3 GiB RAM. The tasks can be distributed on any number of nodes (up to 16, of course).

To run multithreaded applications, use --cpus-per-task to allocate the right number of cpus to each task. --cpus-per-task sets the environment variable $OMP_NUM_THREADS so that OpenMP programs by default will use the right number of threads. (It is possible to override this number by setting $OMP_NUM_THREADS in the job script.) For instance:

#SBATCH --account=MyProject
#SBATCH --job-name=MyJob
#SBATCH --time=1-0:0:0
#SBATCH --mem-per-cpu=4G
#SBATCH --ntasks=8 --cpus-per-task=10 --ntasks-per-node=4

This job will get 2 nodes, and run 4 processes on each of them, each process getting 10 cpus. All in all, that will be two whole nodes on Saga.

All jobs on Saga are allocated the requested cpus and memory exclusively, but share nodes with other jobs. Also note that they are bound to the cpu cores they are allocated. However, the tasks and threads are free to use all cores the job has access to on the node.

Note that the more restrictive one is in specifying how tasks are placed on nodes, the longer the job might have to wait in the job queue: In this example, for instance, there might be eight nodes with 10 idle cpus, but not two whole idle nodes. Without the --ntasks-per-node specification, the job could have started, but with the specification, it will have to wait.

The Saga Sample MPI Job page has an example of a normal MPI job.

Bigmem

Bigmem jobs are specified exactly like the normal jobs except that you also have to specify --partition=bigmem.

Here is an example that asks for 2 tasks, 4 cpus per task, and 32 GiB RAM per cpu:

#SBATCH --account=MyProject --job-name=MyJob
#SBATCH --partition=bigmem
#SBATCH --time=1-0:0:0
#SBATCH --ntasks=2 --cpus-per-task=4
#SBATCH --mem-per-cpu=32G

Accel

Accel jobs are specified just like normal jobs except that they also have to specify --partition=accel. Also, they must also specify how many GPUs to use, with --gres=gpu:N, where N is 1, 2, 3 or 4.

Here is an example that asks for 2 tasks and 2 gpus on one gpu node:

#SBATCH --account=MyProject --job-name=MyJob
#SBATCH --partition=accel --gres=gpu:2
#SBATCH --time=1-0:0:0
#SBATCH --ntasks-per-node=2 --nodes=1
#SBATCH --mem-per-cpu=8G

Optimist

Optimist jobs are specified just like normal jobs, except that they also must must specify --qos=optimist, and should not specify wall time limit. They can on any node on Saga.

An optimist job can be scheduled if there are free resources at least 30 minutes when the job is considered for scheduling. However, it can be requeued before 30 minutes have passed, so there is no gurarantee of a minimum run time. When an optimist job is requeued, it is first sent a SIGTERM signal. This can be trapped in order to trigger a checkpoint. After 30 seconds, the job receives a SIGKILL signal, which cannot be trapped.

A simple optimist job specification might be:

#SBATCH --account=MyProject
#SBATCH --job-name=MyJob
#SBATCH --partition=optimist
#SBATCH --mem-per-cpu=3G
#SBATCH --ntasks=16

Devel

Devel jobs must specify --qos=devel. A devel job is like a normal job, except that it has restrictions on job length and size.

For instance:

#SBATCH --account=MyProject
#SBATCH --job-name=MyJob
#SBATCH --qos=devel
#SBATCH --time=00:30:00
#SBATCH --ntasks=16

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