Applications

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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.

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