Skip to content

Applications

R 4.3.0 in r-env, 20.6.2023

R version 4.3.0 is now available in r-env and is set as the default version. The new version will also be available in RStudio in the Puhti web interface shortly.

Gromacs 2023.1 available on LUMI, 7.6.2023

CPU and GPU versions of Gromacs 2023.1 have been installed on LUMI. Notably, the GPU-enabled module is the official hipSYCL version, which has improved significantly in terms of performance since the previous releases. The LUMI-G instructions on the Gromacs application page have also been updated and the tutorial on running multi-simulations using the built-in multidir feature extended and adapted for LUMI-G.

R 4.2.2 in r-env, 26.5.2023

R version 4.2.2 is now available in r-env and is set as the default version. The new version will also be available in RStudio in the Puhti web interface shortly.

Schrödinger Maestro 2023.2, 25.5.2023

Schrödinger Maestro version 2023.2 has been installed and set as the default module on Puhti and Mahti. See release notes for a list of new features and improvements.

NoMachine will no longer be available on CSC's supercomputers, 9.5.2023

The NoMachine remote desktop service will be discontinued on 25th May 2023, at the end of the current licensing period. The service is superseded by web interfaces on CSC's supercomputers. The first of them, Puhti web interface, has been liked by the researchers, the number of users is still rapidly increasing and now represents 36% of all users. Similar web interfaces will be opened for both Mahti and LUMI, in the near future. For replacements in specific use cases, please see the application page for NoMachine.

Gromacs and CP2K now available on LUMI, 19.4.2023

CPU and GPU-enabled versions of Gromacs and CP2K have been installed on LUMI. Before loading the modules, first take the CSC module tree into use with module use /appl/local/csc/modulefiles. Note that the GPU-enabled Gromacs version is an unofficial HIPified fork of the software by AMD and hence unsupported by the upstream developers.

PyTorch 2.0 and TensorFlow 2.12, 27.3.2023

PyTorch 2.0 and TensorFlow 2.12 are now available on Puhti and Mahti. See PyTorch 2.0 blog post or the TensorFlow 2.12 release notes.

Turbomole 7.7, 3.3.2023

Turbomole 7.7 has been installed and set as the default module on Puhti and Mahti. See release notes here.

Schrödinger Maestro 2023.1 and module removal policy, 10.2.2023

  • The latest version of Schrödinger Maestro (v2023.1) has been installed and set as the default module on CSC supercomputers. See release notes for a list of new features and improvements.
  • Henceforth, a two-year cleaning cycle is applied on the Maestro modules on CSC supercomputers. Specifically, module versions older than two years will be removed in order to free up disk space and encourage use of the latest versions which tend to be more performant and have less bugs.

CSC software collection on LUMI, 31.1.2023

Applications pre-installed by CSC on the LUMI supercomputer can now be viewed in the application list grouped by availability. For a comprehensive list of available EasyBuild recipes for personal or project-specific installations, see the LUMI Software Library.

CP2K 2023.1, 30.1.2023

CP2K 2023.1 has been installed and set as the default module on Puhti and Mahti. See release notes here.

Gromacs 2022.4, 16.1.2023

Gromacs 2022.4 has been installed and set as the default module on Puhti and Mahti. See release notes here.

License for Materials and Discovery Studio no longer available, 3.1.2023

The national Materials Studio and Discovery Studio licenses provided by CSC ended at the end of 2022. Please consider using, e.g., Maestro or AMS instead.

sbatch-hq, 19.12.2022

A wrapper for HyperQueue called sbatch-hq has been created to enable easy and efficient task farming, i.e. high-throughput computing workflows where the intention is to run many similar (non-MPI parallel, independent) commands/programs. See the HyperQueue page for more details.

PyTorch 1.13, 9.12.2022

PyTorch 1.13.0 is now available in the pytorch/1.13 module on Puhti and Mahti, and has been set as the default version. See the PyTorch 1.13 release blog post, and CSC's PyTorch module documentation.

Amber22 installed on Puhti, 16.11.2022

Amber version 22 has been installed on Puhti and set as the default module. See here for a list of major new features.

Maestro 2022.3 and 2022.4 installed on Puhti, 15.11.2022

Schrödinger Maestro 2022.3 and 2022.4 have been installed on Puhti and the latter version set as the default module. See release notes here.

CP2K 2022.2, 10.11.2022

CP2K 2022.2 has been installed and set as the default module on Puhti and Mahti. See release notes here.

Gromacs 2022.3, 7.11.2022

Gromacs 2022.3 has been installed and set as the default module on Puhti and Mahti. See release notes here.

Installing software with Spack, 28.10.2022

Users can now install software on CSC supercomputers using the Spack package manager. See here for a short tutorial on how to use the user Spack module at CSC.

Installing packages from Bioconda using Tykky, 10.10.2022

A new tutorial on how to install packages from the Bioconda channel using the Tykky container wrapper tool has been published. This tutorial outlines the recommended way to install software packages related to bioinformatics and biomedical research. Note that CSC has deprecated the direct (non-containerized) usage of Conda installations on our supercomputers due to file system performance issues.

Available applications can now be viewed as grouped by license type, 7.10.2022

In addition to alphabetical ordering, grouped by discipline or by availability, applications can now be viewed as grouped by license type. Some information about each of the license categories is provided. See Applications by license. (The page can also be reached from the side navigation: Applications > By license)

Python Data 3.10-22.09, 7.10.2022

Coinciding with the Red Hat 8 update of Puhti, a new Python Data module has been installed (on both Puhti and Mahti). In addition, old conda-based modules have been removed, and the naming of modules has changed. Modules are now named according to the Python version (PV) and the year (YY) and month (MM) of the installation, as PV-YY.MM. Typically the module will include the newest versions of libraries at installation time, to the extent software dependencies allow. Modules can also be loaded simply with the Python version, and you will get the most recent installation with that version of Python, for example: module load python-data/3.9.

r-env-singularity renamed to r-env and update to R 4.2.1 coinciding with RHEL8 update, 14.9.2022

Following the RHEL8 update on Puhti, the r-env-singularity module has been renamed to r-env. The R version has been updated to 4.2.1, along with several other version updates for installations included in the module. Due to the RHEL8 update requiring modifications to the r-env module setup, older R versions are currently unavailable.

Discovery Studio and Material Studio license discontinued in 2023, 25.8.2022

CSC has been providing a national academic license for Discovery Studio and Materials Studio. Due to small usage and the availability of overlapping tools (Maestro), the license will not be continued after this year. This means that in 2023 these molecular modeling tools can't be used any more at CSC nor on users' own computers. Please contact Service Desk if you need help in moving your molecular modeling work to other modeling environments.

PyTorch 1.12, 8.7.2022

PyTorch 1.12.0 is now available in the pytorch/1.12 module on Puhti and Mahti. See the official PyTorch 1.12 release notes, and CSC's PyTorch module documentation.

CP2K modules on Mahti recompiled, 5.7.2022

Due to an issue related to OpenBLAS, the CP2K modules on Mahti have been recompiled and linked to another linear algebra library (AMD BLIS). The old versions were in some cases using up to seven times as much memory as before, while matrix diagonalizations were not benefiting from the ELPA library as expected.

Python Data 3.9-3 and RAPIDS 22.04, 5.5.2022

New versions of Python Data and RAPIDS are now available on both Puhti and Mahti. The default versions have been changed to these new versions.

CP2K 9.1 linked to Gromacs 2022, 19.4.2022

CP2K 9.1 has been linked to Gromacs 2022 for QM/MM in the module gromacs-env/2022-cp2k on Mahti. This option was previously available under the CP2K module cp2k/8.1-gmx, which has now been deprecated. Please use gromacs-env/2022-cp2k for QM/MM simulations from now on.

PyTorch 1.11, 8.4.2022

PyTorch 1.11.0 is now available in the pytorch/1.11 module on Puhti and Mahti, and has been set as the default module. See the official PyTorch 1.11 release notes, and CSC's PyTorch module documentation.

LUE released on Puhti, 5.4.2022

An approximate tool called LUE (Lustre Usage Explorer) for reporting amount of data in folders has been released on Puhti. LUE is significantly faster than standard tools like stat or du while being nicer on the file system. Please use LUE to keep track of how much data/files you have on the disk and perform clean-ups in a timely manner to ensure a more performant filesystem for all users.

Tykky 0.2.2, 31.3.2022

Tykky, a brand new tool for wrapping Conda/pip environments inside a Singularity container, has been released. Containerization will considerably improve startup times and decrease IO load with less files on the shared parallel filesystem. We recommend wrapping all existing Conda environments within containers using Tykky as the direct usage of Conda on CSC supercomputers has been deprecated.

TensorFlow 2.8, 17.3.2022

TensorFlow 2.8.0 is now available in the tensorflow/2.8 module on Puhti and Mahti, and has been set as the default module. See the TensorFlow 2.8 release notes on GitHub for more details.

Gromacs 2022, 9.3.2022

Gromacs 2022 has been installed on Puhti and Mahti and is available on both systems with module load gromacs-env/2022. A list of new features and changes is found in the Gromacs manual. gromacs-env/2021 is now the default.

CP2K 9.1, 4.3.2022

CP2K version 9.1 has been installed on Mahti and is available with module load cp2k/9.1-omp, given that gcc/10.3.0 and openmpi/4.1.0 are first loaded. A list of new features and changes is found on the CP2K website.

Schrödinger Maestro 2022.1, 25.2.2022

Schrödinger Maestro 2022.1 has been installed on Puhti and set as the default module. For a list of new features, see the Schrödinger website.

Gromacs 2021 now default version, 7.2.2022

Gromacs 2021.5 has been installed on Puhti and Mahti and set as the default module (gromacs-env).

Direct usage of Conda deprecated, 4.2.2022

CSC has deprecated the direct usage of Conda installations on our supercomputers' (Puhti and Mahti) shared file systems.

Python Data 3.9-2, 20.1.2022

A new version of Python Data is now available with module load python-data/3.9-2 on both Puhti and Mahti. It includes the most recent versions of Scikit-learn, SciPy, Pandas, JupyterLab and many other popular data analytics and machine learning packages for Python 3.9.

Python Data default module now uses Singularity, 26.11.2021

The default version of the python-data module has been changed to 3.9-1. This means that if you have been simply doing module load python-data you will now get this new version automatically. This version has been installed using Singularity which should make loading times much faster. Thanks to wrapper scripts this change should be mostly invisible to users. If you still encounter any problems, don't hesitate to report them to CSC's service desk.

Schrödinger Maestro 2021.4, 24.11.2021

Schrödinger Maestro 2021.4 has been installed on Puhti and set as the default module.

PyTorch 1.10, 10.11.2021

PyTorch 1.10.0 is now available in the pytorch/1.10 module on Puhti and Mahti, and has been set as the default module. See the official PyTorch 1.10 release notes for more details. CSC's module has the following improvements:

  • Jupyter Lab now works (previously only regular Jupyter Notebook UI worked)
  • DeepSpeed support built in (experimental support)

TensorFlow 2.7, 9.11.2021

TensorFlow 2.7.0 is now available in the tensorflow/2.7 module on Puhti and Mahti, and has been set as the default module. See the TensorFlow 2.7 release notes on GitHub for more details. CSC's module has the following improvements:

  • Jupyter Lab now works (previously only regular Jupyter Notebook UI worked)

Schrödinger Maestro 2021.3, 30.8.2021

Schrödinger Maestro 2021.3 has been installed on Puhti and set as the default module. The extended Maestro instructions have been appended with a section on how to speed up Quantum Espresso jobs. A bug in the script that generates the schrodinger.hosts file has also been fixed by setting the parallel HOST entry to use the large Slurm partition as intended.

Turbomole 7.5.1, 25.8.2021

Turbomole 7.5.1 is now available and the default module on Puhti. The most important change with this version is that the ricc2 module for performing 2nd order approximate coupled cluster calculations works appropriately, while older versions on Puhti have been recently reported to suffer from numerical instabilities. These issues do not apply to TM v7.5 installed on Mahti.

CP2K 8.2, 13.8.2021

CP2K version 8.2 has been installed on Mahti and is available with module load cp2k/8.2-omp. This requires that gcc/10.3.0 and openmpi/4.1.0 are first loaded. Version 7.1-elpa will remain the default module for now, but will be changed to 8.2-omp in the near future (despite the name, the ELPA diagonalization library is also linked to the new 8.2 version). The cp2k.psmp binary of version 8.2-omp has been tested and is roughly as efficient as 7.1-elpa.

A list of new features and changes is found on the CP2K website. Note that some keywords, such as MAP_CONSISTENT in the QS section, have been deprecated.

AMS 2021.102, 13.8.2021

AMS has been updated to version 2021.102 on both Mahti and Puhti and set as the default module. The AMS documentation has been updated accordingly to cover version 2021.102.

Molpro 2021.2, 10.8.2021

Molpro 2021.2 is now available and the default version on Puhti. List of recent changes are available on Molpro website. Our Molpro page also contains new scalability information and an example on how to use NVMe.

PyTorch 1.9, 2.7.2021

PyTorch 1.9.0 is now available in the pytorch/1.9 module on Puhti and Mahti. The module also includes the most recent versions of TorchVision, TorchAudio and TorchText. See the official release notes for more details.

Python Data 3.9, 22.6.2021

A new version of Python Data is now available with module load python-data/3.9-1 on Puhti. It includes the most recent versions of Scikit-learn, Pandas, JupyterLab and many other popular data analytics and machine learning packages for Python 3.9.

This is the first version of Python Data that has been installed using Singularity which should make loading times much faster. Thanks to wrapper scripts this change should be mostly invisible to users. If you still encounter any problems, don't hesitate to report them to CSC's service desk.