Frontend

From MetaCentrum
Jump to navigation Jump to search

(Czech version)


Metacentrum wiki is deprecated after March 2023
Dear users, due to integration of Metacentrum into https://www.e-infra.cz/en (e-INFRA CZ service), the documentation for users will change format and site.
The current wiki pages won't be updated after end of March 2023. They will, however, be kept for a few months for backwards reference.
The new documentation resides at https://docs.metacentrum.cz.

Frontend in MetaCentrum is a machine, to which users can log in directly, without reservation.

Frontends are the following machines:

Machine name System Home directory PBS server Note
skirit.ics.muni.cz Debian 11 /storage/brno2/home/ meta-pbs.metacentrum.cz
alfrid.meta.zcu.cz Debian 11 /storage/plzen1/home/ meta-pbs.metacentrum.cz
tarkil.grid.cesnet.cz Debian 11 /storage/praha1/home/ meta-pbs.metacentrum.cz
nympha.zcu.cz Debian 11 /storage/plzen1/home/ meta-pbs.metacentrum.cz
charon.nti.tul.cz Debian 11 /storage/liberec3-tul/home/ meta-pbs.metacentrum.cz
minos.zcu.cz Debian 11 /storage/plzen1/home/ meta-pbs.metacentrum.cz alias for nympha.zcu.cz
perian.grid.cesnet.cz Debian 11 /storage/brno2/home/ meta-pbs.metacentrum.cz
onyx.metacentrum.cz Debian 11 /storage/brno2/home/ meta-pbs.metacentrum.cz alias for perian.grid.cesnet.cz
tilia.ibot.cas.cz Debian 11 /storage/pruhonice1-ibot/home/ meta-pbs.metacentrum.cz Cluster of the Institute of Botany, CAS
zuphux.cerit-sc.cz CentOS 7.9 /storage/brno3-cerit/home/ cerit-pbs.cerit-sc.cz
elmo.elixir-czech.cz Debian 11 /storage/praha5-elixir/home/ elixir-pbs.elixir-czech.cz

The same names are also aliased to the metacentrum.cz domain, e.g. skirit.metacentrum.cz.


ZarovkaMala.png Note: Actual SSH keys can be found at https://metavo.metacentrum.cz/ssh_known_hosts


ZarovkaMala.png Note: SHA256 fingerprints of the SSH keys can be verified at https://metavo.metacentrum.cz/ssh_known_hosts.fp

Home directory

On every frontend the /home directory is mapped onto one of the /storage volumes as /home ---> /storage/CITY_XY/home. This means that depending on your location, it is advisable to log onto a frontend in the same location, as it should guarantee the fastest access to data on disk arrays. If, however, the frontend's reponse is too slow (e.g. due to overload), do not hesitate to access your data from another one. Just keep in mind you have to change explicitly into your home directory where you keep your data.

ssh melounova@skirit.ics.muni.cz # suppose the frontend skirit in Brno does not respond
ssh melounova@alfrid.meta.zcu.cz # let's try frontend tarkil in Plzen
(STRETCH)melounova@alfrid:~$ pwd # where am I?
/storage/plzen1/home/melounova # but my data are on /storage/brno2/home/melounova !
(STRETCH)melounova@alfrid:~$ cd /storage/brno2/home/melounova/
(STRETCH)melounova@alfrid:/storage/brno2/home/melounova$ 

Usage of frontends

Please consider that frontends are shared among all users. If you need to run interactively some demanding activity, like working with huge amount of data or software compilation, please don't use the frontend but rather reserve some computing node for an interactive jobs. Such operations could slow down the frontend and bother other users.

Warning.gif Warning: Use the direct access to data storages to manipulate with huge amounts of data.

Batch system

cd /storage/brno3-cerit/home/$LOGNAME
export PBS_SERVER=meta-pbs.metacentrum.cz

Login notes

  • You should use the ssh protocol for remote access to clusters because it encrypts all communication.
  • For login you can use all SSH possibilities such as password, Kerberos or the ssh key. You should use so called Kerberos tickets for working with machines. Without them you cannot submit jobs via qsub command and the NFS4 directories, such as all /storage directories connected from non-local cities.
    • You will automatically obtain the Kerberos tickets while login with password. The ticket is valid for 10 hours.
kinit 'META username'@META #You will be asked to fill in password
klist #Will show actual tickets.

    • You should delegate the tickets in Kerberos client while using local Kerberos authentication. Just edit the file /etc/ssh/ssh_config or ~/.ssh/config and change the value of variable GSSAPIDelegateCredentials to yes (default is no).
    • You can not delegate the Kerberos tickets while using ssh key. After the login via ssh key you have to abotain tickets via kinit command.
  • Frontend tarkil.metacentrum.cz supports AES (Advanced Encryption Standard) working with Mac OS. To log on MetaCentrum from Mac OS use
 ssh -K <$LOGNAME>@tarkil.metacentrum.cz

Node for master/submitting jobs

If you would like to automatically submit jobs to planning system PBS with diferent inputs, or automatically set inputs or steps of a new jobs according to results of a previous job, you can use special computational node oven.ics.muni.cz. On this node you can run long-term jobs which are able to manage other jobs.