To ensure efficient use of the compute nodes and give users fair access to the resources, jobs are divided into different types, which determine where and how they are run. The different types are
- normal: The default type. Most jobs are
normaljobs. They run on between 4 and 32 standard nodes (but see below).
- bigmem: Jobs that require more memory (RAM).
bigmemjobs run on special nodes with more RAM.
- preproc: Short, 1-node jobs for things like preprocessing and postprocessing, that don't need many cpus.
- devel: Short jobs, meant for quick development and testing. They get higher priority to start sooner, but can only use upto 10 nodes each, and 16 in total.
- optimist : Low priority jobs that can start whenever there are free resources, but will be requeued when other jobs need the resources. Meant for jobs that use checkpointing. Projects need to make a request for using this job type, and will get a separate quota for it.
normal jobs must specify account (
--account), walltime limit (
and number of nodes (
--nodes). By default, they must use between 4 and 32
nodes, but a project can be allowed to use more nodes if needed. The jobs can
specify how many tasks should run per node and how many CPUs should be used by
If more than 32 nodes is needed, and the application in question can actually scale more than 32 nodes, please send a request to email@example.com.
All normal jobs gets exclusive access to whole nodes (all CPUs and memory). If a job tries to use more (resident) memory than is configured on the nodes, it will be killed. Currently, this limit is 60 GiB, but it can change. The maximal wall time limit for normal jobs is 7 days (168 hours).
Note that setting
--cpus-per-task does not bind the tasks to the given number of
CPUs for normal jobs; it merely sets
$OMP_NUM_THREADS so that OpenMP jobs 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.)
The Sample Batch Script page has an example of a normal job.
There are eight nodes with 512 GiB memory and two nodes with 6 TiB.
To use the large memory nodes, jobs must specify
addition, they must specify wall time limit, number of CPUs/nodes and
memory memory per CPU. A
bigmem job is assigned the requested CPUs and
memory exclusively, but shares nodes with other jobs. If a
bigmem job tries
to use more resident memory than requested, it gets killed. The maximal wall
time limit for bigmem jobs is 14 days.
Here is an example that asks for 2 nodes, 3 tasks per node, and 4 CPUs per task, and 32 GiB RAM per CPU:
#SBATCH --account=nn9999k --partition=bigmem #SBATCH --time=1-0:0:0 #SBATCH --nodes=2 --ntasks-per-node=3 --cpus-per-task=4 #SBATCH --mem-per-cpu=32G
Note that even though the memory specification is called
memory limit the job gets on the node is for the total usage by all processes
on the node, so in the above example, it would get a limit of 3 4 32 GiB =
384 GiB. The queue system doesn't care how the memory usage is divided between
the processes or threads, as long as the total usage on the node is below the
Also note that contrary to
bigmem jobs will be bound to the
CPU cores they are allocated, so the above sample job will have access to 12
cores on each node. However, the three tasks are free to use all cores the job
has access to on the node (12 in this example).
preproc jobs must specify
preproc job is allocated 1 node,
exclusively, and has a maximum walltime of 1 day. Otherwise, it is the same
as a normal job. The idea is that preprocessing, postprocessing or similar
doesn't need to use many nodes. Note that there is a limit of how many
preproc jobs a project can run at the same time.
Example of a general
preproc specification (1 node, 4 tasks with 8 CPUs/task):
#SBATCH --account=nn9999k --qos=preproc #SBATCH --time=1:0:0 #SBATCH --ntasks-per-node=4 --cpus-per-task=8
Here is a simpler
preproc job (one task on one node):
#SBATCH --account=nn9999k --qos=preproc #SBATCH --time=1:0:0
devel jobs must specify
devel job is like a
job, except that it can use between 1 and 10 nodes, and there is a limit of
how many nodes
devel jobs can use at the same time (currently 16).
jobs also have a maximum walltime of 1 hour. On the other hand, they get
higher priority than other jobs, in order to start as soon as possible.
If you have temporary development needs that cannot be fulfilled by the devel QoS, please contact us at firstname.lastname@example.org.
optimist jobs must specify
--qos=optimist, and should specify the
number of nodes needed (between 4 and 32), but they should not
specify wall time limit. They run on the same nodes as
They get lower priority than other jobs, but can start as soon as
there are free resources. However, when any other job needs its
optimist job is stopped and put back on the job
queue. Therefore, all
optimist jobs must use checkpointing, and
access to run
optimist jobs will only be given to projects that
demonstrate that they can use checkpointing.
optimist job will only 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.
To be able submit
optimist jobs the project has to send a request to
Sigma2 to get an optimist quota.
The priority setup has been designed to be as predictable and easy to understand as possible, while trying to maximize the utilisation of the cluster.
The principle is that a job's priority increases 1 point per minute the job is waiting in the queue, and once the priority reaches 20,000, the job gets a reservation in the future. It can start before that, and before it gets a reservation, but only if it does not delay any jobs with reservations.
The different job types start with different priorities:
develjobs start with 20,000, so get a reservation directly
preprocjobs start with 19,760, so get a reservation in 4 hours
preprocjobs(*) start with 19,040, so get a reservation in 16 hrs
optimistjobs start with 1 and end at 10,080, so they never get a reservation
The idea is that once a job has been in the queue long enough to get a reservation, no other lower priority job should be able delay it. But before it gets a reservation, the queue system backfiller is free to start any other job that can start now, even if that will delay the job. Note that there are still factors that can change the estimated start time, for instance running jobs that exit sooner than expected, or nodes failing.
(*) In some cases when a project applies for extra CPU hours because it has
spent its allocation, it will get "unprioritized" hours, meaning their jobs
will have lower priority than standard jobs (but still higher than