July 2023 - Medbionode - MedUniGraz Mailing Lists

slurm configuration issue solved
by Trajanoski, Slave 31 Jul '23

31 Jul '23

Dear MedBioNode users, I have good news for you. IT department managed to solve the slurm configuration issue and sbatch is working normally again. 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>

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slurm issue
by Trajanoski, Slave 28 Jul '23

28 Jul '23

Dear MedbioNode users, IT department is working on the slurm configuration issue and latest on Monday it'll be fixed. If you urgently need to run some jobs use "srun" instead. 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>

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MedBioNode change in slurm configuration
by Trajanoski, Slave 26 Jul '23

26 Jul '23

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

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maintenance and upgrade finished
by Trajanoski, Slave 25 Jul '23

25 Jul '23

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>

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Reminder: Maintenance and upgrade of MedBioNode
by Trajanoski, Slave 19 Jul '23

19 Jul '23

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>

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