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The job will be started using MPI processes, by default 24 processes are placed on each compute node using all of the physical cores available.
The bolt job submission script creation tool will create job submission scripts with the correct settings for the aprun flags for parallel jobs on ARCHER.
Please use man aprun and aprun -h to query further options. The placement of processes and threads is controlled aprun options. Examples of these options are provided in the sections below.
A simple MPI job submission script to submit a job using 64 compute nodes maximum of physical cores for 20 minutes would look like:.
PBS will allocate 64 nodes to your job and place 24 MPI processes on each node one per physical core. A simple MPI job submission script to submit a job using 64 large memory compute nodes with GB of memory per node for 20 minutes would look like:.
PBS will allocate 64 large memory nodes to your job and place 24 MPI processes on each node one per physical core.
The following example job submission script uses a single node to run an OpenMP code with 12 threads for 12 hours. This means that the number of shared memory threads should be a factor of In the example below, we are using nodes physical processors for 6 hours.
If you are performing mixed mode hybrid simulations with MPI communications from threads i. This environment variable should be set to single , funneled , serialized or multiple :.
The nature of the job submission system on ARCHER does not lend itself to developing or debugging code as the queues are primarily set up for production jobs.
When you are developing or debugging code you often want to run many short jobs with a small amount of editing the code between runs.
An interactive job allows you to issue ' aprun ' commands directly from the command line without using a job submission script, and to see the output from your program directly in the terminal.
The following screencast demonstrates starting an interactive job and running a parallel program on the compute nodes from within the job.
To submit a request for an interactive job reserving 8 nodes cores for 1 hour you would issue the following qsub command from the command line:.
It may take some time for your interactive job to start. Once it runs you will enter a standard interactive terminal session. Whilst the interactive session lasts you will be able to run parallel jobs by issuing the ' aprun ' command directly at your command prompt using the same syntax as you would inside a job script.
The maximum number of nodes you can use is limited by the value of select you specify when you submit a request for the interactive job.
To reduce the amount of time spent waiting for your interactive job to start you may find it useful to use the short queue, though this has restrictions on job length and size.
Alternatively if you know you will be doing a lot of intensive debugging you may find it useful to request an interactive session lasting the expected length of your working session, say a full day.
To take maximum advantage of an interactive session submitted to the short queue longest job length 20 minutes it can be useful to set up an email alert so that the batch system mails you as soon your interactive session starts.
This can be achieved by using the -m and -M options with qsub when you request your interactive job as follows:. This should make it easier to do other tasks away from the terminal yet still be ready to use the interactive session as soon as it is available.
Please be aware that any command not prepended with aprun will be running directly on a job launcher node, rather than on a compute node. As the job launcher nodes are a shared resources for all users you are requested not to run any intensive computations without prepending the command with aprun in order to execute it on the compute node s you've reserved for the job.
The same applies for commands within job scripts submitted to the batch system. When using X-forward whilst working on the ARCHER login nodes, it is possible to enable further X-forwarding from the parallel nodes being used in an interactive job.
To do this simply add the -X flag to the qsub command, as shown below:. An array style job involves running multiple jobs at once using the same submission script.
Each job is subject to the same resource restrictions i. The number of array elements has been capped at 32 per job. This still allows any user to submit jobs at a time.
For most of the jobs people run on ARCHER the desired behaviour for node allocation is that only one job at a time has access to any given compute node.
However, sometimes people may wish to run shared-memory jobs such as OpenMP programs on a node that do not utilise all of the available cores.
In that circumstance it can be useful to be able to run another job on the same node to use the cores that have been left inactive by the first job.
The utility needed to run multiple jobs on a single node can be downloaded here. The utility is currently only setup to run two programs on a node, one on each of the processors.
If you need to run a different number of applications on a node, or have other requirements to vary how programs run, please get in touch with the helpdesk and we can provide different versions of this utility for you.
There is a utility available on ARCHER for running serial python programs as a task farm a task farm is a mechanism for running multiple copies of a program on a parallel system.
A readme file and example submission script is available in the ptf module for the location of the module files use the module show ptf command.
It requires that the name of the file containing the python program is provided as the first argument to the ptf executable when it is run.
The utility is currently only setup to run a separate instance of the python program on each core requested when the job is run.
There are also, currently, some restrictions on the size and complexity of python program it can execute. If you need to assign different numbers of cores to each python program, or have other requirements to vary how the python programs run, please get in touch with the helpdesk and we can work on providing different versions of this utility for you.
The scheduling system is laid out so that all you need to do is request the number of nodes you need and the time for your job. The scheduling system will then schedule the jobs to ensure fair access.
Jobs which fall outside these limits may be accommodated via a reservation. Principally, the system attempts to place the largest jobs possible within the available space, and then tile the remaining nodes with the largest jobs that will fit, until the system is full.
Obviously, small jobs are easier to place than large ones - but the system will attempt, where possible, to place the largest it can. There is also degree of additional scheduling in place to try and prevent jobs from ageing too much in the queue.
The system will deploy the backfill scheduler to try and minimise the time that a large job will have to wait for resources, and this can mean that nodes appear to be free when they are actually being reserved in advance you can use the command qstat -wT to get snapshot and general idea of what jobs have been scheduled to run, when.
Under those circumstances, shorter jobs may have an enhanced chance of being released since they might be able to run and terminate before the large job that is being backfilled for is scheduled to run.
The system is configured to try and maximise the chances of large jobs running - but it is also true that very small jobs will also have a high likelihood of getting in to fill a small gap.
The checkScript tool has been written to allow users to validate their job submission scripts before submitting their jobs.
The tool will read your job submission script and try to identify errors, problems or inconsistencies. Note that tool currently only validates parallel job submission scripts.
Serial and low priority jobs are not included. If you want to leave time at the end of the job to do tidying up, e.
The usage is. This can be trapped in the program to do tidying up within the program, e. If the time limit is reached, the exit status will be even if SIGTERM is trapped by the program , otherwise the exit status will be the exit status of the program.
Low priority jobs are not charged against your allocation, although you do require a valid budget in your job script to allow the job to run.
Jobs can range from nodes cores and can have a maximum walltime of 3 hours. Only 1 low priority job per user can be run at any one time and only 3 jobs can be queued by any one user.
You submit low priority jobs to the queue "low" on the system. For example, if your job submission script is called "submit. The low priority access queue will be opened when the backlog in the queue system drops below 3 hours.
You submit weekend jobs to the queue "weekend" on the system. Long Jobs can run for a maximum of 48 hours. The second way to make use of the "long" queue on the system is to specify the queue in your submission script, as follows:.
Note: A job must require more than 24 hours to be accepted onto the long queue; jobs that take 24 hours or less should be submitted to the standard queue.
Jobs can range from nodes cores and can have a maximum walltime of 20 minutes. You can submit debug jobs to the queue short on ths system.
These allow users to reserve a number of nodes for a specified length of time starting at a particular time on the system. Reservations require justification.
They will only be approved if the request could not be fulfilled with the standard queues. Possible uses for a reservation would be:.
Note: Reservation requests must be submitted at least 60 Hours in advance of the reservation start time. If requesting a reservation for a Monday at , please ensure this is received by the Friday at the latest.
The same applies over Service Holidays. Reservations will be charged at 1. In addition, you will not be refunded the AUs if you fail to use them due to a job crash unless this crash is due to a system failure.
To request a reservation please use the form on your main SAFE page. You need to provide the following:. Your request will be checked by the Helpdesk and if approved you will be provided a reservation ID which can be used on the system.
You submit jobs to a reservation using the qsub command in the following way:. They should be used for jobs which do not require parallel processing but which would have an adverse impact on the operation of the login nodes if they were run interactively.
Example uses include: compressing large data files, visualising large datasets, large compilations and transferring large amounts of data off the system.
Please note you cannot run a serial job on the large memory bigmem compute nodes i. Direct interactive access to the PP nodes is also available.
This means that you do not need to submit a job to access the PP nodes interactively. For example, to submit a 1-hour interactive postprocessing job you would use:.
Remember to replace 'budget' with your budget code. When you submit this job your terminal will display something like:.
To do this simply add the -X flag to the qsub command as shown below:. When the job runs, you will be able to launch applications with a GUI and the interface will appear on your local machine.
Applications that attempt to access more memory than is available on a node 64GB for normal nodes, GB for high-memory nodes will abort producing an error similar to the following:.
If this happens to your code, you will need to run it using more nodes. There are two ways to do this:. See Parallel job launcher section for details on specifiying number of nodes.
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