Software of the cluster

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Access to the cluster software is via the module system. To display graphical user interfaces, you need an "X11 forwarding". Read the chapter Starting programs interactively. The following software is installed on the cluster:

Abaqus

Interactive working with Abaqus in the Linux cluster:

uk00123@its-cs1:/home/users/000/uk00123>
salloc -N1 -t 1:00:00 salloc: Granted job allocation 5404733
uk00123@its-cs1:/home/users/000/uk00123> srun xterm

To display the graphical user interface, an SSH connection with X11 forwarding is required.

A node is requested with salloc for one hour and then a terminal is started on the assigned node with srun xterm. You can now work interactively in the terminal with the abaqus command.

The graphical interface of Abaqus is started with abaqus cae -mesa. This can lead to a semi-transparent display of the GUI. The following variable can be set before the abaqus command in the xterm terminal to remedy this:

export XLIB_SKIP_ARGB_VISUALS=1 && abaqus cae -mesa

 

SubmitScript for Abaqus:

In order for an Abaqus job to run without errors in the batch system, the command

unset SLURM_GTIDS

must be inserted before calling Abaqus, otherwise an error "abaqus illegal memory reference (signal 11)" may occur.

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ACML 4.1.0

The use of the AMD Core Math Library is recommended for optimizing vector-based calculations. This combines libraries for

  • highly optimized BLAS (Basic Linear Algebra Subroutines)
  • LAPACK (Linear Algebra Pack)
  • FFT (Fast Fourier Transforms)

The software is available on all machines of the cluster for the respective compiler ($compiler) under

/opt/acml/$compiler

Further information.

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CalculiX

CalculiX is a finite element program for the simulation of three-dimensional flow processes.

cgx_2.5 -b examples/compressor/lavff.fbd

To use the graphical user interface, you must use an X11 redirect.

DALTON and LSDALTON

To use the software, please send the signed and scanned license agreement by e-mail. You will then be given access to the software.

Erlang/OTP

Erlang is used for concurrent, distributed and parallel programming and is available in version 18.0 on the Linux cluster.

To use the module, the following command must be executed:

module load erlang/18.0

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jrMan

jrMan is an open-source Java implementation of the RenderMan standard (Reyes algorithm). To use jrMan, environment variables must be adapted. This is done in the Kornshell (ksh) with the command:

module load jrman

(RenderMan (R) Interface Procedures and RIB Protocol: Copyright 1988, 1989, Pixar.)

Matlab

  • Version R2017a
  • License: 13 academic licenses (Matlab, Simulink, Symbolic Math) - in future campus license
  • Toolboxes: Optimization Toolbox (3 licenses), Statistics Toolbox (2 licenses)
  • Official website

Mathematica

The mathematical and scientific program package Mathematica is installed on all machines in the Linux cluster.

Working with Mathematica in the Linux cluster:

uk00123@its-cs1:/home/users/000/uk00123> salloc -N1 -t 1:00:00
salloc: Granted job allocation 5404733
uk00123@its-cs1:/home/users/000/uk00123> srun Mathematica

A computer system is requested for one hour. The graphical user interface is then started with srun Mathematica. For batch operation, Mathematica is started by calling math in command line mode. Further information is available via man math (mcc, mathematica) .

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Maple

The computer algebra system Maple is installed on all machines in the Linux cluster. Maple is used in algebra, analysis, discrete mathematics and numerics. Maple offers programming interfaces and visualization of mathematical structures.

Working with Maple in the Linux cluster with graphical user interface:

uk00123@its-cs1:/home/users/000/uk00123> salloc -N1 -t 1:00:00
salloc: Granted job allocation 5404733
uk00123@its-cs1:/home/users/000/uk00123> srun xmaple

The call reserves a computer system in the Linux cluster for a period of 1 hour and starts the Maple graphical environment on the reserved system. For batch operation, Maple is started via the maple call in command line mode. Further information is available via man maple .

OpenFOAM

OpenFOAM is a software for solving problems in continuum mechanics.

 

Working with OpenFOAM in the Linux cluster:

uk00123@its-cs1:/home/users/000/uk00123> module load openfoam
uk00123@its-cs1:/home/users/000/uk00123> salloc -N1 -t 1:00:00
salloc: Granted job allocation 5404733
uk00123@its-cs1:/home/users/000/uk00123> srun xterm

The environment variables for working with OpenFOAM are set with the module load openfoam command. A computer system is then requested for one hour with srun and an Xterm is started there. OpenFOAM is used in the Xterm.

Example:

uk000123@its-cs1:/home/users/000/uk000123> mkdir OpenFOAM
uk000123@its-cs1:/home/users/000/uk000123> cp -r $FOAM_TUTORIALS OpenFOAM
uk000123@its-cs1:/home/users/000/uk000123> cd
OpenFOAM/tutorials/incompressible/icoFoam/cavity
...icoFoam/cavity> blockMesh
...icoFoam/cavity> icoFoam ...icoFoam/cavity> paraFoam

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Pixie-2.2.4

Pixie is an open-source implementation of the RenderMan standard for creating photorealistic images. RenderMan is involved in the production of the visual effects of today's Hollywood films such as Star Wars and The Lord of the Rings. To use Pixie, environment variables must be adapted.

This is done in the Kornshell (ksh) with the command:

module add Pixie

Polymake

Mathematical software for studying the combinatorics and geometry of convex polytopes and polyhedra.

Working with Polymake in the Linux cluster:

First reserve resources in the Linux cluster with salloc and then start a shell on the assigned node with srun xterm. The program can be started here with the polymake command.

QEPCAD

QEPCAD is a program for quantifier elimination by partial cylindrical algebraic decomposition.

Working with qepcad in the Linux cluster:

uk00123@its-cs1:/home/users/000/uk00123> salloc -N1 -t 1:00:00
salloc: Granted job allocation 5404733
uk00123@its-cs1:/home/users/000/uk00123> srun xterm

This command reserves a machine in the Linux cluster for one hour and starts a shell window (xterm) on the reserved machine. The program is started in the shell window with the qepcad command.

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RStudio

The RStudio IDE is available on the its-cs10 node for the R statistics software. To access it, you must be in the university network or use the VPN client. RStudio can be accessed at the following address:

http://its-cs136.its.uni-kassel.de:8787

R

The free statistics software "R" is installed on all computers in the Linux cluster.

  • Version 3.6.0, 3.5.1 and 4.0.3, 4.2.1
  • License: GNU GENERAL PUBLIC LICENCE
  • Official website

 

You can either suggest package installations for R to the support of the Linux cluster "for all users" or carry out your own installation in your home directory without having to install R yourself:

mkdir ~/R_libs #create directory R_libs in your home directory
nano ~/.Renviron #create new file. Insert the following content:
R_LIBS_USER=~/R_libs/

It should now be possible to install within R using install.packages("PAKETNAME") on a node with direct Internet access on which direct computing is permitted (currently only its-cs136).

REDUCE (Free CSL Version)

OpenREDUCE is the open source version of the REDUCE computer algebra system

Using REDUCE in a Linux cluster:

First reserve resources in the Linux cluster with salloc and then start a shell on the assigned node with srun xterm. Here the program can be started with the reduce command.

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Sage

Sage is an open source math software

Working with Sage in the Linux cluster:

uk00123@its-cs1:/home/users/000/uk00123> salloc -N1 -t 1:00:00
salloc: Granted job allocation 5404733
uk00123@its-cs1:/home/users/000/uk00123> srun xterm

This command reserves a machine in the Linux cluster for one hour and starts a shell window (xterm) on the reserved machine. The program is started in the shell window with the command sage .

Vampire

The Vampir Performance Analyzer offers the possibility of a scalable result analysis of complex performance data in a graphical user interface. It visualizes the individual processes of parallel programs and their communication with each other.

This requires so-called trace files, which can be created with the help of a wrapper compiler(mpicc-vt, mpic++-vt, mpicxx-vt, mpif77-vt, mpif90-vt or mpifort-vt). After successful compilation and execution of the program, a trace file with the file extension.otf is created. This can be opened and analyzed with Vampir. An SSH connection with X11 forwarding to the cluster is required(ssh -X uk00123@its-cs10.its.uni-kassel.de).

Using Vampir in the Linux cluster:

uk00123@its-cs10:/home/users/000/uk00123>mpicc-vt -o hello_mpi hello_mpi.c
uk00123@its-cs10:/home/users/000/uk00123> mpirun -n 6 ./hello_mpi
uk00123@its-cs10:/home/users/000/uk00123> vampir hello_mpi.otf

X10 Programming language

x10 is a strongly typed, object-oriented programming language under an open-source license. A Java or C++ source code is generated from the programs, which is compiled with the appropriate backend (Java compiler or GCC from version 4.2). The code of the C++ backend uses OpenMPI and can be executed directly with mpirun distributed.

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