MOTD.txt

TAB-separated lines are used to display metaMOTD / Tip-of-the-day during login on frontend nodes. Create the file touch ~/.hushmotd to test it. Avoid using URLs, bold/italic, special characters or formatting. You can check the result using:

wget -q https://wiki.metacentrum.cz/wiki/MOTD -O - | grep "<li>" | sed -e "s/.*<li>/%/g" -e "s/<\/li>.*//g" -e "s/%/%\n/g"

  


General tips
    Do not use frontends for intensive workloads. Allocate a node using an interactive job (qsub -I ...)
    You can check allocated/available storage in the table above.
    Something's not working? Before reporting it, please check the Outages section on metavo.metacentrum.cz
    Most of our storages are not backed up. Please double-check where you store critical data!
    Home directories are readable for everyone by default - consider protecting your sensitive data with appropriate ACLs.
    Statistics of usage available at https://metavo.metacentrum.cz/cs/state/stats/2025/index.html
    Have you tried our AI Chat and LLM (AI‑as‑a‑Service) yet? Discover how it works and get started here: https://docs.cerit‑sc.cz/en/docs/ai-as-a-service/introduction
    Looking for the latest updates? Visit our blog at https://blog.e‑infra.cz

PBS
    Do you know you can request a minimum processor speed? (i.e. qsub -l select=1:spec=4.8)
    Do you know you can request a minimum GPU memory? (i.e. qsub -l select=1:gpu_mem=10gb)
    Use the 'pbs-get-job-history' command to get a wealth of information about pbs jobs, including historical ones.
    You can avoid submitting to the faulty node using qsub -l select=1:vnode=^short_hostname
    You can avoid submitting at an unwanted cluster using qsub -l select=1:cluster=^cluster_name
    Did you know the qextend utility can be used for an additional extension of the walltime for your calculations? Call the 'qextend' command to see the manual.
    The data quota in /tmp is quite small, about 1 GB. If you need more, set "export TMPDIR=$SCRATCHDIR" in the job.

SW
    Are you missing any SW in the Metacentre? Feel free to ask us (meta@cesnet.cz) to install it!
    Did you only find an old version of the SW? Feel free to ask us (meta@cesnet.cz) for an update.
    Do you need some system package (.deb)? Feel free to ask us (meta@cesnet.cz) to install it!
    Have you ever heard about a Chipster? Chipster is a web-based interactive analysis software for NGS and microarray data. More information at https://docs.metacentrum.cz/en/docs/related/chipster.

Singularity
    For the large /tmp directory inside the Singularity image, set SINGULARITY_TMPDIR=$SCRATCHDIR and SINGULARITY_CACHEDIR=$SCRATCHDIR

Storage
    Need more storage space? Let us know (meta@cesnet.cz).
    NFS is complex and, unfortunately, buggy. If you run into any problems, please let us know.
    You can download external data using various protocols/commands, i.e. scp, s3cmd, wget...
    Do you need to back up or archive large amounts of data? Visit web du.cesnet.cz
    Do you need object storage? Look at web du.cesnet.cz
    You can quickly move data between our storages using the scp command (e.g. scp storage-plzen1:~/file storage-praha1:~)
    Need to work with large data stored in /home? Copying them directly from storage hosts can be vastly faster than using NFS mounted /storage
    You can check your quota on a local disk (typically /tmp or /var/spool/pbs) by using the "check-local-quota" command on the compute node of interest.

GUI
    Need a graphical user interface? Try ondemand.grid.cesnet.cz, which offers launching PBS tasks, accessing persistent terminals, copying files between our storages, or launching multiple graphical applications in the browser.
    Have you explored the Galaxy portal (usegalaxy.cz) yet? Find out how to get started and make the most of its graphical tools: https://docs.metacentrum.cz/en/docs/graphical/usegalaxy
    Have you tried AlphaFold through a graphical interface? Give Foldify a spin – the web‑app that lets you run AlphaFold with just a few clicks: https://docs.cerit.io/en/docs/web-apps/foldify
    

HW
    Need more GPU/RAM/storage/CPU? Give us feedback in our annual surveys, we try to buy new HW according to our users' needs.
    With great computational power comes great responsibility. Be sure that your calculations use dedicated hardware as efficiently as possible.

Courses
    Are you interested in the hands-on course or tailored theoretical lecture for a small group of users? Let us know (meta@cesnet.cz), and we can discuss your needs and possibilities.
    Explore our past seminars, lectures and hands-on courses with many valuable tips and tricks (https://docs.metacentrum.cz/en/docs/tutorials).