Dear MedBioNode users,
please be aware that during the cluster maintenance, we've also changed the slurm configuration. Now there are two queues (partitions):
1. cpu partition
2. gpu partition for jobs requiring GPU processing
When submitting jobs you need to specify the partition and therefore adopt your scripts by adding the parameter partition = cpu.
Best regards,
Slave
Dear MedBioNode users,
the maintenance could be finished faster than planed thanks to the efforts from the IT department (special gratitude to Michi Fladischer).
Best regards,
Slave
--
Slave Trajanoski, Phd
Senior Scientist Bioinformatics
CF Computational Bioanalytics, Center for medical research
Medical University Graz
Neue Stiftingtalstraße 6-West, Turm/Stiege:P, 4.Stock
8010 Graz
Tel. +43 316 385 73024
E-Mail: slave.trajanoski(a)medunigraz.at<mailto:slave.trajanoski@medunigraz.at>
Dear MedBioNode users,
this is just a reminder about the MedBioNode cluster maintenance planed for next week, starting on Monday 24 July 20023. Please don't start high number of jobs or ones that need long execution time (more than few hours), otherwise we cannot finish the maintenance on time. Also cluster we'll be down for some time, when we need to upgrade the master/login node (sx036). This downtime includes RStudio Server, as it runs on the same server (sx036).
Thanks for your cooperation.
Best regards,
Slave
From: Trajanoski, Slave <slave.trajanoski(a)medunigraz.at>
Sent: Thursday, 29 June 2023 08:45
To: medbionode(a)lists.medunigraz.at
Subject: [Medbionode] FW: Maintenance and upgrade of MedBioNode
Dear MedBioNode users,
I apologize for this additional E-Mail, but I've just realized that I've put the wrong week in my writing. The correct one is CW30, end of July starting with 24 July 2023.
Sorry for any inconvenience caused by this mistake.
Regards,
Slave
From: Trajanoski, Slave <slave.trajanoski(a)medunigraz.at<mailto:slave.trajanoski@medunigraz.at>>
Sent: Wednesday, 28 June 2023 16:50
To: medbionode(a)lists.medunigraz.at<mailto:medbionode@lists.medunigraz.at>
Subject: [Medbionode] Maintenance and upgrade of MedBioNode
Dear MedBioNode users,
in the last week of July KW26 we're planning upgrade of the Debian operating system, as well as regular cluster maintenance. The upgrade will be performed gradually, so that we can minimize the downtime, nevertheless there will be interruption of the services including RStudio Server, Jupyter Hub and Galaxy currently operated on MedBioNode.
Please plan your work and job submission adequately and avoid starting any long execution jobs (more than 6 hours) before or during the upgrade.
Thanks for your understanding.
Kind regards,
Slave
--
Slave Trajanoski, Phd
Senior Scientist Bioinformatics
CF Computational Bioanalytics, Center for medical research
Medical University Graz
Neue Stiftingtalstraße 6-West, Turm/Stiege:P, 4.Stock
8010 Graz
Tel. +43 316 385 73024
E-Mail: slave.trajanoski(a)medunigraz.at<mailto:slave.trajanoski@medunigraz.at>
Dear MedBioNode users,
in the last week of July KW26 we're planning upgrade of the Debian operating system, as well as regular cluster maintenance. The upgrade will be performed gradually, so that we can minimize the downtime, nevertheless there will be interruption of the services including RStudio Server, Jupyter Hub and Galaxy currently operated on MedBioNode.
Please plan your work and job submission adequately and avoid starting any long execution jobs (more than 6 hours) before or during the upgrade.
Thanks for your understanding.
Kind regards,
Slave
--
Slave Trajanoski, Phd
Senior Scientist Bioinformatics
CF Computational Bioanalytics, Center for medical research
Medical University Graz
Neue Stiftingtalstraße 6-West, Turm/Stiege:P, 4.Stock
8010 Graz
Tel. +43 316 385 73024
E-Mail: slave.trajanoski(a)medunigraz.at<mailto:slave.trajanoski@medunigraz.at>
Dear MedBioNode cluster users,
our login node sx036 lost connection to CEPH (/home/cluster) and the server needs to be restarted. In the meantime you session will be canceled and you cannot login.
Best regards,
Slave
--
Slave Trajanoski, Phd
Senior Scientist Bioinformatics
CF Computational Bioanalytics, Center for medical research
Medical University Graz
Neue Stiftingtalstraße 6-West, Turm/Stiege:P, 4.Stock
8010 Graz
Tel. +43 316 385 73024
E-Mail: slave.trajanoski(a)medunigraz.at<mailto:slave.trajanoski@medunigraz.at>
Dear MedBioNode users,
on our last Bioinformatics round table there was a wish for establishing common cluster discussion channel. Human Genetics department already created such communication platform based on Discord and they will gladly share this instance with the other MedBioNode users. If you have interest on joining it please use the following link for your registration:
https://discord.gg/MJVZngC5
Best regards,
Slave
--
Slave Trajanoski, Phd
Senior Scientist Bioinformatics
CF Computational Bioanalytics, Center for medical research
Medical University Graz
Neue Stiftingtalstraße 6-West, Turm/Stiege:P, 4.Stock
8010 Graz
Tel. +43 316 385 73024
E-Mail: slave.trajanoski(a)medunigraz.at<mailto:slave.trajanoski@medunigraz.at>
Dear MedBioNode users,
Beginning this weekend (25.02.2023) and lasting through the middle of the next week (probably Wednesday 01.03.2023), some adjustments must be made for the new GPU node in the SLURM configuration.
Avoid starting any job that will take more than one day to complete, and try to finish long-running jobs before Monday, February 27, 2023.
The link https://rstudio.medunigraz.at will be used as the new secure connection (https) for RStudio login starting on Monday.
The RStudio server login page will only be accessible in the future via this link.
Thanks for your cooperation.
Best regards,
Slave
--
Slave Trajanoski, Phd
Senior Scientist Bioinformatics
CF Computational Bioanalytics, Center for medical research
Medical University Graz
Neue Stiftingtalstraße 6-West, Turm/Stiege:P, 4.Stock
8010 Graz
Tel. +43 316 385 73024
E-Mail: slave.trajanoski(a)medunigraz.at<mailto:slave.trajanoski@medunigraz.at>
Dear MedBioNode users,
we have to restart login node (sx036) immediately, because it lost its connection to CEPH storage (/home/cluster). Please logout from the login node and stop using RStudio server for the next one hour.
Thanks for your understanding.
Best regards,
Slave
--
Slave Trajanoski, Phd
Senior Scientist Bioinformatics
CF Computational Bioanalytics, Center for medical research
Medical University Graz
Neue Stiftingtalstraße 6-West, Turm/Stiege:P, 4.Stock
8010 Graz
Tel. +43 316 385 73024
E-Mail: slave.trajanoski(a)medunigraz.at<mailto:slave.trajanoski@medunigraz.at>
Dear MedBioNode/Rstudio users,
because of imminent issue with the CEPH client on the login node sx036 and therefore problems with accessing the shared storage (/home/cluster) we need to reboot this server immediately. Please close your sessions at once, since reboot will happen in 5 minutes.
Thanks for your understanding.
Best regards,
Slave
--
Slave Trajanoski, Phd
Senior Scientist Bioinformatics
CF Computational Bioanalytics, Center for medical research
Medical University Graz
Neue Stiftingtalstraße 6-West, Turm/Stiege:P, 4.Stock
8010 Graz
Tel. +43 316 385 73024
E-Mail: slave.trajanoski(a)medunigraz.at<mailto:slave.trajanoski@medunigraz.at>
Dear MedBioNode (RStudio Server) users,
since Friday 25 November 2022 Login node sx036 is online and operational, so don’t use sj211 anymore. In the next days users that are still present on sj211 will be automatically logged out. The same regulation applies also for RStudio server.
Thanks for your understanding.
Regards,
Slave
--
Slave Trajanoski, Phd
Senior Scientist Bioinformatics
CF Computational Bioanalytics, Center for medical research
Medical University Graz
Neue Stiftingtalstraße 6-West, Turm/Stiege:P, 4.Stock
8010 Graz
Tel. +43 316 385 73024
E-Mail: slave.trajanoski(a)medunigraz.at<mailto:slave.trajanoski@medunigraz.at>
