Free Tier - Software
- Edward Ferguson
The current Unix (Linux) version on a cluster node can be retrieved with the following command:
cat /etc/redhat-release
The command 'uname -a' returns the version and release of the Unix kernel.
For equivalent info along with specification of the version of the installed gcc (GNU Compiler Collection), type:
cat /proc/version
The table below shows software already installed on the cluster system-wide. The last two columns in it indicate whether the corresponding software is available on a given type of Free Tier node.
The list may be partial and not totally up-to-date at any given time. Use one of the following commands to verify whether unlisted software/packages can be found on Free Tier otherwise:
module avail
rpm -qa <packageName>
locate <name>
Name | Version | Location / Module | RPM / files | Category |
|---|---|---|---|---|
anaconda 2 2019.03 | python 2.7.16 | module load anaconda/2-2019.03 | /rigel/opt/anaconda2-2019.03 | Python for Scientific Computing |
anaconda 3 2021.11 | python 3.9.7 | module load anaconda/3-2021.11 | /rigel/opt/anaconda3-2021.11 | Python for Scientific Computing |
cuda | 11.2.2 | module load cuda11.2/toolkit | /cm/shared/apps/cuda11.2.2/toolkit | GPU Computing |
| cudnn | 8.0 | module load cudnn8.0-cuda11.2 | /cm/shared/apps/cudnn8.0-cuda11.2 | CUDA Deep Neural Network |
cudnn | 8.1 | module load cudnn8.1-cuda11.2 | /cm/shared/apps/cudnn8.1-cuda11.2 | CUDA Deep Neural Network |
deal.ii | 8.4.0 | module load deal.II/8.4.0 | /rigel/opt/deal.II | Library - Scientific |
fftw2 | 2.1.5 | module load fftw2/openmpi/gcc/64/double/2.1.5 | /cm/shared/apps/fftw/openmpi/gcc/64/2.1.5/double | Library - Scientific |
fftw3 | 3.3.4 | module load fftw3/openmpi/gcc/64/3.3.4 | /cm/shared/apps/fftw/openmpi/gcc/64/3.3.4 | Library - Scientific |
gcc | 10.3.0 | module load gcc/10.3.0 | /bin/gcc | Compiler - C, C++ |
gcc | 4.8.5 | module load gcc/4.8.5 | /bin/gcc | Compiler - C, C++ |
git | 1.8.3.1 | /usr/bin/git | /usr/bin/git | Revision control |
gromacs | 5.1.4 | module load gromacs/5.1.4-nongpu | /rigel/opt/gromacs-5.1.4-nongpu | Molecular Dynamics |
gromacs gpu | 5.1.4 | /rigel/opt/gromacs-5.1.4 | /rigel/opt/gromacs-5.1.4 | Molecular Dynamics |
gsl | 1.15 | /usr/bin/gsl-histogram | /usr/bin/gsl-histogram | Library - Scientific |
idl | 8.4 | module load idl/8.4 | /rigel/opt/exelis/idl84 | Library - Scientific |
intel-parallel-studio | 2020 | module load intel-parallel-studio/2020 | /rigel/opt/parallel_studio_xe_2020 | Intel Compiler |
java | 1.8.0 | module load java/1.8.0 | /usr/bin/java | Java |
knitro | 13.2.0 | module load knitro/13.2.0 | /rigel/opt/knitro-13.2.0-Linux-64 | Solving large scale nonlinear mathematical optimization problems |
matlab | R2019b | module load matlab/2019b | /rigel/opt/matlab/R2019b | Numerical Computing |
netcdf-fortran | 4.4.4 | module load netcdf-fortran/4.4.4 | /rigel/opt/netcdf-fortran-4.4.4 | Library - Scientific |
| paraview | 5.7.0 | module load paraview/5.7.0 | /rigel/opt/ParaView-5.7.0/bin/paraview | Visualization |
parallel hdf5 | 1.8.18 | module load hdf5p/1.8.18 | /rigel/opt/hdf5p-1.8.18 | Library - Scientific |
Quantum Espresso | 7.1 | module load QE/7.1 | /rigel/opt/QE/7.1/bin | Computer codes for electronic-structure calculations and materials modeling at the nanoscale |
R | 4.2.2 | module load R/4.2.2 | /rigel/opt/R-4.2.2 | Programming language |
| Shrodinger | 2021-2 | module load schrodinger/2021-2 | /rigel/opt/schrodinger/2021-2 | Physics-based computational platform |
| Singularity | 3.2.0 | module load singularity | /rigel/opt/singularity-3.2.0 | Run Docker-like Containers |
| spark | 2.3.2 | module load spark/2.3.2 | /rigel/opt/spark-2.3.2 | Distributed computing |
| Stata | 15 | module load stata | /rigel/opt/stata15 | General-purpose Statistical Software |
Paraview 5.7.0
If you are using a Mac with XQuartz, starting with Paraview version 5.7.0 in order to access the Mesa 3D Graphics Library you now launch ParaView with an auxilliary executable that sets up library paths so that Mesa is used, e.g.,
paraview-mesa paraview --backend llvmpipe
Otherwise you will run into errors such as:
( 4.099s) [paraview ]vtkOpenGLRenderWindow.c:761 ERR| vtkXOpenGLRenderWindow (0x4044040): Unable to find a valid OpenGL 3.2 or later implementation.
Please update your video card driver to the latest version. If you are using Mesa please make sure you have version 11.2 or later and make sure your driver in
Mesa supports OpenGL 3.2 such as llvmpipe or openswr. If you are on windows and using Microsoft remote desktop note that it only supports OpenGL 3.2 with nvidia
quadro cards. You can use other remoting software such as nomachine to avoid this issue.
Loguru caught a signal: SIGSEGV
Stack trace:
0 0x2aaaaad03250 /lib64/libc.so.6(+0x35250) [0x2aaaaad03250]
( 4.131s) [paraview ] :0 FATL| Signal: SIGSEGV