Job Scripts on Fram
This page documents how to specify the queue system parameters for the different job types on Fram. See Job Types on Fram for information about the different job types on Fram.
The basic type of job on Fram is the normal job. Most of the other job types are “variants” of a normal job.
Normal jobs must specify account (
--account), walltime limit
--time) and number of nodes (
--nodes). The jobs can specify how
many tasks should run per node and how many CPUs should be used by
A typical job specification for a normal job would be
#SBATCH --account=MyProject #SBATCH --job-name=MyJob #SBATCH --time=1-0:0:0 #SBATCH --nodes=10 --ntasks-per-node=32
This will start 32 tasks (processes) on each node, one for each cpu on the node.
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 59 GiB, but it can change. If a job would require more memory per task than the given 59 GiB split by 32 tasks, the trick is to limit the number of tasks per node the following way:
#SBATCH --account=MyProject #SBATCH --job-name=MyJob #SBATCH --time=1-0:0:0 #SBATCH --nodes=10 --ntasks-per-node=4
This example above will use only 4 tasks per node, giving each task 15 GiB. Note that is the total memory usage on each node that counts, so one of the tasks can use more than 15 GiB, as long as the total is less than 59 GiB.
If your job needs more than 59 GiB per task, the only option on Fram is to use a bigmem job (see below).
To run multithreaded applications, use
--cpus-per-task to allocate
the right number of cpus to each task. For instance:
#SBATCH --account=MyProject #SBATCH --job-name=MyJob #SBATCH --time=1-0:0:0 #SBATCH --nodes=4 --ntasks-per-node=2 --cpus-per-task=16
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 Fram Sample MPI Job page has an example of a normal MPI job.
See Fram Job Placement for optional parameters for controlling which nodes a normal job is run on.
Bigmem jobs must specify
--partition=bigmem. In addition, they
must specify wall time limit, the number of tasks and the amount of
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, 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 --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 normal jobs, 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).
Here is a simpler example, which only asks for 16 tasks (of 1 cpu each) and 32 GiB RAM per task; it does not care how the tasks are allocated on the nodes:
#SBATCH --account=MyProject --job-name=MyJob #SBATCH --partition=bigmem #SBATCH --time=1-0:0:0 #SBATCH --ntasks=16 #SBATCH --mem-per-cpu=32G
devel jobs must specify
--qos=devel. A devel job is like a normal
job, except that it has restrictions on job length and size.
#SBATCH --account=MyProject #SBATCH --job-name=MyJob #SBATCH --qos=devel #SBATCH --time=00:30:00 #SBATCH --nodes=2 --ntasks-per-node=32
short jobs must specify
--qos=short. A short job is like a normal
job, except that it has restrictions on job length and size. It
differs from devel jobs in that it allows somewhat longer and larger
jobs, but typically have longer wait time.
#SBATCH --account=MyProject #SBATCH --job-name=MyJob #SBATCH --qos=short #SBATCH --time=2:00:00 #SBATCH --nodes=8 --ntasks-per-node=32
Optimist jobs are specified just like normal jobs, except that
they also must must specify
--qos=optimist. They run on the same
nodes as normal jobs.
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
signal, which cannot be trapped.
A simple optimist job specification might be:
#SBATCH --account=MyProject #SBATCH --job-name=MyJob #SBATCH --partition=optimist #SBATCH --nodes=4 --ntasks-per-node=32 #SBATCH --time=2:00:00