Applications
We provide a wide range of centrally installed commercial and open source applications and libraries to our cluster users.
Central installations
Applications and libraries that are used by many people from different departments of ETH (e.g. MATLAB, Comsol, Ansys, etc.) or that are explicitly requested by a shareholder group will be installed centrally in /cluster/apps. Providing a software stack of centrally installed applications and libraries gives the users certain advantages.
- Applications and libraries are visible and accessible to all users via environment modules.
- They are maintained by the ID SIS HPC group (or in a few cases also by users).
- Commercial licenses are provided by the central license administration of ETH (IT shop).
If an application or library is only used by a few people, then we recommend the users to install it locally in their home directory. In case you need help to install an application or library locally, please do not hesitate to contact cluster support.
Software stacks
On our clusters we provide multiple software stacks.
- The old software stack on Euler uses environment modules
- The new software stack on Euler and the software stack on Leonahrd Open uses LMOD modules
On the Euler cluster, we are in the transition phase from the old software stack to the new software stack. Currently when users login, the old software stack is still set as the default. It will be kept on an as-is basis to allow reproducing older results. New software is only installed in the new software stack. It is set up with the package manager SPACK on Euler using the LMOD module system. The new software stack has 4 basic toolchains (GCC 4.8.5, GCC 6.3.0, GCC 8.2.0 and Intel 18.0.1). A toolchain is a combination of compiler, MPI and BLAS/LAPACK library. For each of the toolchains, several hundred packages are available.
For an overview on all installed packages, please have a look at the following wiki pages:
Commercial/Open source
Please find below a selection of centrally installed applications that covers a wide range of research fields
| Bioinformatics |
|---|
| Bamtools, BLAST, Bowtie, CLC Genomics Server, RAxML, Relion, TopHat |
| Finite element methods |
| Ansys, Abaqus, FEniCS |
| Machine learning |
| PyTorch, Scikit-Learn, TensorFlow, Theano |
| Multi-physics phenomena |
| Ansys EDT, COMSOL Multiphysics, STAR-CCM+ |
| Quantum chemistry and molecular dynamics |
| ADF, Ambertools, Gaussian, Molcas, Octopus, Orca, Qbox, Turbomole |
| Symbolic, numberical and statistical mathematics |
| Gurobi, Mathematica, MATLAB, R, Stata |
| Visualization |
| Ffmpeg, ParaView, VisIT, VTK |
Development
We also provide a range of programs or libraries for the development of software, in order to allow users to write their own codes and to run and profile them on the cluster.
| Compiler |
|---|
| GCC, Intel |
| Programming languages |
| C, C++, Fortran, Go, Java, Julia, Perl, Python, Ruby, Scala |
| Scientific libraries |
| Boost, Eigen, FFTW, GMP, GSL, HDF5, MKL, NetCDF, NumPy, OpenBLAS, SciPy |
| MPI libraries |
| Open MPI, Intel MPI, MPICH |
| Build systems |
| GNU Autotools, CMake, QMake, Make, SCons |
| Version control |
| SVN, Git, Mercurial, CVS |
