This page describes the part of the job script that actually does the useful work and runs the programs you want to run.

When your job is started by the scheduler and the resource manager, your job script will run as a regular script on the first core of the first node assigned to the job. The script runs in your home directory, which is not the directory where you will do your work, and with the standard user environment. So before you can actually start your program(s), you need to set up a proper environment. On a cluster, this is a bit more involved than on your PC, partly also because multiple versions of the same program may be present on the cluster, or there may be conflicting programs that make it impossible to offer a single set-up that suits all users.

Setting up the environment

Changing the working directory

As explained above, the job script will start in your home directory, which is not the place where you should run programs. So the first step will almost always be to switch to the actual working directory (the bash cd command).

  • In most cases, you simply want to start your job in the directory from which you submitted your job. Torque offers the environment variable PBS_O_WORKDIR for that purpose. So for most users, all you need is simply cd $PBS_O_WORKDIR as the first actual command in your job script.
  • On all VSC clusters we also define a number of environment variables that point to different file systems that you have access to. They may also be useful in job scripts, and may help to make your job script more portable to other VSC clusters. An overview of environment variables that point to various file systems is given on the page "where should which data be stored?".

Loading modules

The next step consists of loading the appropriate modules. This is no different from loading the modules on the login nodes to prepare for your job or when running programs on interactive nodes, so we refer to the "Modules" page in the "Running software" section.

Useful Torque environment variables

Torque defines a lot of environment variables on the compute nodes on which your job runs, They can be very useful in your job scripts. Some of the more important ones are:

  • PBS_O_WORKDIR : The directory from which your job was submitted.
  • PBS_JOBNAME : The name of the job
  • PBS_JOBID : The unique jobid. This is very useful when constructing, e.g., unique file names.
  • PBS_NUM_NODES : The number of nodes you requested.
  • PBS_NUM_PPN : The number of cores per node requested.
  • PBS_NP : The total number of cores requested.
  • PBS_NODEFILE : This variable is used by several MPI implementation to get the node list from the resource manager when starting a MPI program. It will contain $PBS_NP lines.

There are also some variables that are useful if you use the Torque command pbsdsh to execute a command on another node/core of your allocation. We mention them here for completeness, but they will also be elaborated on in the paragraph on "Starting a single core program on each assinged core" further down this page.

  • PBS_NODENUM : The number of the node in your allocation. E.g., when starting a job with -l nodes=3:ppn=5, $PBS_NODENUM will be 0, 1 or 2 if the job script has actually been scheduled on three physically distinct nodes. As the job script executes on the first core of the allocation, its value will always be 0 in your job script.
  • PBS_VNODENUM : The number of the physical core or hyperthread in your allocation. The numbering continues across the nodes in the allocation, so in case of a job started with -l nodes=3:ppn=5, $PBS_VNODENUM will be a number between 0 and 14 (0 and 14 included). In your job script, its value will be 0.
  • PBS_TASKNUM : Number of the task. The numbering starts from 1 but continues across calls of pbsdsh. The login script runs with PBS_TASKNUM set to 1. The first call to pbsdsh will start its numbering from 2, and so on.

Starting programs

We show some very common start scenarios for programs on a cluster:

  • Shared memory programs with OpenMP as an example
  • Distributed memory programs with MPI programs as an example
  • An embarrassingly parallel job consisting of independent single-core runs combined in a single job script

Starting a single multithreaded program (e.g., an OpenMP program)

Starting a multithreaded program is easy. In principle, all you need to do is call its executable as you would do with any program at the command line.

However, often the program needs to be told how many threads to use. The default behaviour depends on the program. Most programs will either use only one thread unless told otherwise, or use one thread per core it can detect. The problem with programs that do the latter is that if you have requested only a subset of the cores on the node, the program will still detect the total number of cores or hyperthreads on the node and start that number of threads. Depending on the cluster you are using, these threads will swarm out over the whole node and sit in the way of other programs (often the case on older clusters) or will be contained in the set of cores/hyperthreads allocated to the job and sit in each others way (e.g., because they compete for the same limited cache space). In both cases, the program will run way slower than it could.

You will also need to experiment a bit with the number of cores that can actually be used in a useful way. This depends on the code and the size of the problem you are trying to solve. The same code may scale to only 4 threads for a small problem yet be able to use all cores on a node well when solving a much larger problem.

How to tell the program the number of threads to use, also differs between programs. Typical ways are through an environment variable or a command line option, though for some programs this is actually a parameter in the input file. Many scientific shared memory programs are developed using OpenMP directives. For these programs, the number of threads can be set through the environment variable OMP_NUM_THREADS. The line

export OMP_NUM_THREADS=$PBS_NUM_PPN

will set the number of threads to the value of ppn used in your job script.

Starting a distributed memory program (e.g., a MPI program)

Starting a distributed memory program is a bit more involved as they always involve more than one Linux proces. Most distributed memory programs in scientific computing are written using the the Single Program Multiple Data paradigm: A single executable is ran on each core, but each cores works on a different part of the data. And the most popular technique for developing such programs is by using the MPI (Message Passing Interface) library.

Distributed memory programs are usually started through a starter command. For MPI programs, this is mpirun or mpiexec (often one is an alias for the other). The command line arguments for mpirun differ between MPI implementations. We refer to the documentation on toolchains in the "Software development" section of this web site for more information on the implementations supported at the VSC. As most MPI implementations in use at the VSC recognise our resource manager software and get their information about the number of nodes and cores directly from the resource manager, it is usually sufficient to start your MPI program using

mpirun <mpi-program>

where <mpi-program> is your MPI program and its command line arguments. This will start one instance of your MPI program on each core or hyperthread assigned to the job.

Programs using different distributed memory libraries may use a different starter program, and some programs come with a script that will call mpirun for you, so you can start those as a regular program.

Some programs use a mix of MPI and OpenMP (or a combination of another distributed and shared memory programming technique). Examples are some programs in Gromacs and QuantumESPRESSO. The rationale is that a single node on a cluster may not be enough, so you need distributed memory, while a shared memory paradigm is often more efficient in exploiting parallelism in the node. You'll need additional implementation-dependent options to mpirun to start such programs and also to define how many threads each instance can use. There is some information specifically for hybrid MPI/OpenMP programs on the "Hybrid MPI/OpenMP programs" page in the software development section. We advise you to contact user support to help you figuring out the right options and values for those options if you are not sure which options and values to use.

Starting a single-core program on each assigned core

A rather common use case on a cluster is running many copies of the same program independently on a different data set. It is not uncommon that those programs are not or very poorly parallelised and run on only a single core. Rather than submitting a lot of single core jobs, it is easier for the scheduler if those jobs are bundled in a single job that fills a whole node. Our job scheduler will try to fill a whole node using multiple of your jobs, but this doesn't always work right. E.g., assume a cluster with 20-core nodes where some nodes have 3 GB per core available for user jobs and some nodes have 6 GB available. If your job needs 5 GB per core (and you specify that using the mem or pmem parameters), but you don\t explicitly tell that you want to use the nodes with 6 GB per core, the scheduler may still schedule the first job on a node with only 3 GB per core, then try to fill up that node further with jobs from you, but once half the node is filled discover that there is not enough memory left to start more jobs, leaving half of the CPU capacity unused.

To ease combining jobs in a single larger job, we advise to have a look at the Worker framework. It helps you to organise the input to the various instances of your program for many common scenarios.

Should you decide to start the instances of your program yourself, we advise to have a look at the Torque pbsdsh command rather than ssh. This assures that all programs will execute under the full control of the resource manager on the cores allocated to your job. The variables PBS_NODENUM, PBS_VNODENUM and PBS_TASKNUM can be used to determine on which core you are running and to select the appropriate input files. Note that in most cases, it will actually be necessary to write a second script besides your job script. That second script then uses these variables to compute the names of the input and the output files and start the actual program you want to run on that core.

To further explore the meaning of PBS_NODENUM, PBS_VNODENUM and PBS_TASKNUM and to illustrate the use of pbsdsh, consider the job script

#! /bin/bash
cd $PBS_O_WORKDIR
echo "Started with nodes=$PBS_NUM_NODES:ppn=$PBS_NUM_PPN"
echo "First call of pbsdsh"
pbsdsh bash -c 'echo "Hello from node $PBS_NODENUM ($HOSTNAME) vnode $PBS_VNODENUM task $PBS_TASKNUM"'
echo "Second call of pbsdsh"
pbsdsh bash -c 'echo "Hello from node $PBS_NODENUM ($HOSTNAME) vnode $PBS_VNODENUM task $PBS_TASKNUM"'

Save this script as "testscript.pbs" and execute it for different numbers of nodes and cores-per-node using

qsub -l nodes=4:ppn=5 testscript.pbs

(so using 4 nodes and 5 cores per node in this example). When calling qsub, it will return a job number, and when the job ends you will find a file testscript.pbs.o<number_of_the_job> in the directory where you executed qsub.

For more information on the pbsdsh command, we refer to the the Torque manual on the Adaptive Computing documentation web site.

or to the manual page ("man pbsdsh").