High Performance Computing Center North
This is a quickstart guide to using the compute clusters on HPC2N.
Follow the instructions below to log on to 'Abisko' or 'Kebnekaise'.
If this is the first time you are using any of the HPC2N facilities, please change your password after you have logged in. See Login and password at HPC2N for more information.
Access to our systems is possible by using SSH. The example below uses SSH with standard interactive password login. For information on using Kerberos/GSSAPI for passwordless logins, see the section about Login/password.
If you are using Linux or Mac, you should just open a terminal and:
If you are using Windows, you need to use something like PuTTY or CygWin to connect. You can read a short introduction here.
Storing your files in the right location is essential when working with the batch system. See the section about the different filessystems at HPC2N for more information.
If unsure, start by using the parallel file system 'pfs'.
A set of computing tasks submitted to a batch system is called a job. Jobs can be submitted in two ways: a) from a command line or b) using a job script. We recommend using a job script as it makes troubleshooting easier and also allows you to keep track of batch system parameters you used in the past.
Abisko and Kebnekaise both run the batch system SLURM.
To create a new job script (also called a submit script or a submit file) you need to:
There are several examples, and more information, about using the batch system and writing scripts in the subsection for the batch system.
Here we will demonstrate the usage of the batch system directives on the following simple submit file example.
#!/bin/bash #SBATCH -A <account> #SBATCH -n 6 #SBATCH --time=01:00:00 # Load compiler toolchain module for MPI, compiler, libraries, etc. as needed/desired. This loads foss, which # is GCC, OpenMPI, OpenBLAS/LAPACK, FFTW, and ScaLAPACK module add foss # Use mpirun on Kebnekaise. Change to srun on Abisko mpirun ./mpi_program
Batch system directives start with #SBATCH. The first line says that Linux shell bash will be used to interpret the job script. Here are some of the most common directives.
In order to see how much of your allocation you have used up, use the command projinfo.
There is a set of batch system commands available to users for managing their jobs. The following is a list of commands useful to end-users:
More information on batch systems can be found on the Internet. We recommend visiting the following pages (keep in mind that some information may not apply to the HPC2N environment):
Follow the instructions below to compile a parallel program
$ module add foss
For availability of other compilers write:
$ module avail
$ make -f makefile