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We are preparing the transition to the new PBS - OpenPBS. Existing PBSPro servers will be decommissioned in the future because they cannot communicate directly with the new OpenPBS servers and utilities. At the same time as the migration to the new PBS we are upgrading the OS: Debian11 -> Debian12.
For testing purposes we have prepared a new OpenPBS environment pbs-m1.metacentrum.cz with new frontend zenith running on Debian12 OS:
- new frontend zenith.cerit-sc.cz (aka zenith.metacentrum.cz) running Debian12 OS
- new OpenPBS server pbs-m1.metacentrum.cz
- home /storage/brno12-cerit/
Gradually the new environment will be added to other clusters.
Overview of machines running Debian12: https://metavo.metacentrum.cz/pbsmon2/props?property=os%3Ddebian12
List of available frontends including the current OS: https://docs.metacentrum.cz/computing/frontends/
The new PBS can also be accessed from other frontends, but the openpbs module (module add openpbs) must be activated.
We are continuously solving compatibility problems of some applications with Debian12 OS by recompiling new software modules. If you encounter a problem with your application, try adding the debian11/compat module to the beginning of the startup script (module add debian11/compat). If problems persist (missing libraries, etc.), let us know at meta(at)cesnet.cz.
For more information, see the documentation at https://docs.metacentrum.cz/tutorials/debian-12/ (we will specify the migration procedure here).
We would like to remind you of the opportunity to share with us your experience with computing services of the large research infrastructure e-INFRA CZ, which consists of e-infrastructures CESNET, CERIT-SC and IT4Innovations. Please complete the questionnaire by 8 March 2024. Your answers will help us to adjust our services to better suit you.
If you have already completed the questionnaire, thank you for doing so! We greatly appreciate it.
The questionnaire is available at https://survey.e-infra.cz/compute
Matlab
We have acquired a new academic license for 200 instances of Matlab 9.14 and later (including a wide range of toolboxes), covering the computing environments of MetaCenter, CERIT-SC and IT4Innovations.
The new license comes with stricter conditions compared to the previous version. Please be aware that it is exclusively valid for use from MetaCenter/IT4Innovations IP addresses. Consequently, it cannot be utilized for running Matlab on personal computers or within university lecture rooms.
More information: https://docs.metacentrum.cz/software/sw-list/matlab/
Mathematica
Starting this year, MetaCentrum no longer holds a grid license for the general use of SW Mathematica (the supplier was unable to offer a suitable licensing model).
Currently, Mathematica 9 licenses are restricted to members of UK (Charles University) and JČU (University of South Bohemia) who have their own licenses for students and employees.
If you have your own (institutional) Mathematica software license, please contact us for more information at meta@cesnet.cz.
More information: https://docs.metacentrum.cz/software/sw-list/wolfram-math/
Chipster
MetaCenter has recently made its own instance of the Chipster tool available to users athttps://chipster.metacentrum.cz/.
Chipster is an open-source tool for analyzing genomic data. Its main purpose is to enable researchers and bioinformatics experts to perform advanced analyses on genomic data, including sequencing data, microarrays, and RNA-seq:
More information: https://docs.metacentrum.cz/related/chipster/
Galaxy for MetaCenter users
Galaxy is an open web platform designed for FAIR data analysis. Originally focused on biomedical research, it now covers various scientific domains. For MetaCentrum users, we have prepared two Galaxy environments for general use:
a) usegalaxy.cz
General portal at https://usegalaxy.cz/ mirrors the functionality (especially the set of available tools) of global services (usegalaxy.org, usegalaxy.eu). Additionally, it offers significantly higher user quotas (both computational and storage) for registered MetaCentrum users. Key features:
More information: https://docs.metacentrum.cz/related/galaxy/
b) RepeatExplorer Galaxy
In addition to the general-purpose Galaxy, we offer our users a dedicated Galaxy instance with the Repeat Explorer tool. You need to register for the service.
RepeatExplorer is a powerful data processing tool that is based on the Galaxy platform. Its main purpose is to characterize repetitive sequences in data obtained from sequencing. Key features:
More information: https://galaxy-elixir.cerit-sc.cz/
OnDemand
Open OnDemand https://ondemand.grid.cesnet.cz/ is a service that allows users to access computational resources through a web browser in graphical mode. The user can run common PBS jobs, access frontend terminals, copy files between repositories, or run multiple graphical applications directly in the browser.
Some of the features of Open OnDemand include:
More information: https://docs.metacentrum.cz/software/ondemand/
Kubernetes/Rancher
A number of graphical applications are also available in Kubernetes/Rancher https://rancher.cloud.e-infra.cz/dashboard/ under the management of CERIT-SC (Ansys, Remote Desktop, Matlab, RStudio, ...)
More information: https://docs.cerit.io/
JupyterNotebooks
Jupyter Notebooks is an "as a Service" environment based on Jupyter technology. It is a tool that is accessible via a web browser and allows users to combine code (mainly in Python), using Markdown output, text, math, calculations and rich media content.
MetaCenter users can use Jupyter Notebooks in three flavors:
a) CERIT-SC offers access to AlphaFold as a Service in a web browser (as a pre-built Jupyter Notebook).
More information: https://docs.cerit.io/docs/alphafold.html
b) in batch jobs in v OnDemand https://ondemand.grid.cesnet.cz/pun/sys/myjobs/workflows/new
c) in batch jobs using RemoteDesktop and pre-made containers for Singularity
More information: https://docs.metacentrum.cz/software/sw-list/alphafold/
The archive repository du4.cesnet.cz at MetaCenter connected as storage-du-cesnet.metacentrum.cz is out of warranty and is experiencing a number of technical problems in the tape library mechanics, which does not compromise the stored data itself, but complicates its availability. Colleagues at CESNET Data Storage are preparing to migrate the existing data to a new system (Object Storage).
We now need to dampen the traffic on this repository as much as possible, please
If you need the data stored here for calculations, please arrange a priority migration with our colleagues at du-support@cesnet.cz
If, on the other hand, you have data stored here that you no longer plan to use or move (for example, old backups), please also contact colleagues at du-support@cesnet.cz.