GRID FEUP documentation:software

ABAQUS

Anonymous (anonymous@undisclosed.example.com) — 2020-05-21T09:27:23+00:00

ABAQUS Licensing Abaqus is licensed software which you must configure to use the correct license server before you can use it. Previously it was possible to configure Abaqus to use either “FLEXLM” or “DSLS” for licensing, but now only the DSLS method is available. If you were previously using the FLEXLM method, you must change your configuration to use DSLS.

ANSYS FLUENT

Anonymous (anonymous@undisclosed.example.com) — 2018-07-06T16:22:48+00:00

ANSYS FLUENT ANSYS FLUENT is available on the cluster nodes but because of space constraints it's not available on the submit host. It can be invoked as fluent after using the module load ansys command. Documentation Documentation for ANSYS FLUENT is available via the

Compiling software on the user profile

Anonymous (anonymous@undisclosed.example.com) — 2022-01-04T13:24:14+00:00

Compiling software on the user profile This section aims at helping the users compile the software they need. They are mere guidelines! Incompact3d Following instructions from salloc git clone cd Incompact3d/ git checkout v3.0 module load mpi/openmpi-x86_64

Hadoop

Anonymous (anonymous@undisclosed.example.com) — 2016-05-25T16:34:57+00:00

Hadoop Hadoop is an Apache project which develops eponymous software for analyzing “big data” over many systems in a hadoop cluster. Because Hadoop clusters assume that they are dedicated to the purpose of running hadoop jobs, they don't interact well with the existing cluster system - because the two scheduling systems aren't aware of each other, they can both run jobs and cause nodes to become over occupied, reducing overall performance.

February 2021 - Note - Interactive Graphics Slurm

Anonymous (anonymous@undisclosed.example.com) — 2021-10-13T14:37:12+00:00

February 2021 - Note - Interactive Graphics Slurm We have detected a problem running Interactive graphics. We suspect that to correct the error we will have to update the grid slurm, which will take some time. However, we have an alternative solution that will allow you to use the grid interactively, until the problem is resolved.

Licensing

Anonymous (anonymous@undisclosed.example.com) — 2024-01-22T16:22:09+00:00

Licensing Some of the software installed on the cluster is not free and requires licenses to run. These licenses are normally bought by FEUP (or members of FEUP) for the use of the whole campus and normally they restrict the number of running programs to a certain number. For example, on the 3rd of June 2013, only 100 copies of Matlab can run within FEUP at the same time.

Matlab

Anonymous (anonymous@undisclosed.example.com) — 2018-06-25T18:16:49+00:00

Matlab Detailed documentation about Matlab can be found on the vendor's website. Licensing Matlab is a licensed product that requires free licenses to execute, the licenses for Matlab are shared between all of FEUPs users. It's therefore possible for jobs on the cluster to fail because there are no free licenses. This can be avoided by using the Matlab compiler to compile your Matlab code into an executable. Running this executable doesn't require a license. Matlab has parallelization support…

MPI

Anonymous (anonymous@undisclosed.example.com) — 2018-07-11T12:52:31+00:00

MPI MPI (or Message Passing Interface) is a standard for passing messages between processes running on the same or different computers. The standard can be found at the MPI Forum website. There are various implementations of the MPI standard, the two main open implementations (as opposed to commercial ones) are:

OpenFOAM

Anonymous (anonymous@undisclosed.example.com) — 2018-06-25T18:12:28+00:00

OpenFOAM OpenFOAM versions 2.3.0 and 17.12 are available on the cluster nodes. To use them, use the following commands: module load openfoam/v1712 source $FOAM If you wish to use OpenFOAM 2.3.0, replace v1712 with 2.3.0 After running these command the OpenFOAM commands are available for use.

R

Anonymous (anonymous@undisclosed.example.com) — 2019-01-09T17:54:03+00:00

R Batch jobs If you have a R script called job.r, you can run it from your submit script with the following command: R CMD BATCH -q job.r job.out The job.out determines where printed output from job.r goes. If you have multiple jobs running at the same time this will cause your jobs to overwrite each others output. In this case, replace the command with the following: