Dear MedBioNode users,
we've received the additional HP Apollo chassis for the HW reconfiguration of the current GPU node sx138 and already scheduled date for this task. Therefore all users of the GPU node should finish their jobs until the end of this week. I'll put the node in drain mode on Wednesday 27.11.2023 (no new slurm jobs will be accepted for execution) and on Friday 01.12.2023 still running jobs have to be canceled.
Please take in consideration your plans and running time of your jobs adequately.
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 User!
We would like to ask you to participate in our evaluation of your satisfaction with the services offered by the ZMF and Core Facilities.
Only the comprehensive knowledge of your opinion about our services is the prerequisite for the continuous improvement of our performance. You can answer this questionnaire in a few minutes.
This survey is anonymous. No personal information about you will be stored in the survey responses unless a question explicitly asks for it (here you decide freely whether you want to disclose data or not).
Thank you for your participation and time!
Link to the online survey
https://survey.medunigraz.at/index.php/972413?lang=en<https://urldefense.com/v3/__https:/survey.medunigraz.at/index.php/972413?la…>
Kind regards,
Andrea Groselj-Strele
Mag. Dr. Andrea Groselj-Strele
Head Core Facility Computational Bioanalytics
2. Stv. des Leiters der Abteilung ZMF - Zuständigkeit Core Facilities
[zmf-sublogo]
Zentrum für Medizinische Forschung
Core Facility Computational Bioanalytics
Neue Stiftingtalstraße 6 Turm West, Stiege P, 4. OG, A-8010 Graz
Tel: 0316/ 385 73012
E-Mail: andrea.groselj-strele(a)medunigraz.at<mailto:andrea.groselj-strele@medunigraz.at>
Dear MedBioNode users,
herewith I'd like to remind you about storage space policies for the MedBioNode cluster:
1. GPFS Volume (user home directories under /home/gpfs/o_xxxxxx) standard limitation 250GB, exceptions allowed with approval up to 500GB. This location is not appropriate for storing data, because of the size. Important for RStudio users to take care about the size of their R objects and other data type, which by default is stored under this location. If RStudio users need more space, they just need to use the other volumes.
2. Isilon Volume (user data folder under /home/isilon/users/o_xxxxx) standard limitation 4TB.
3. CEPH Volume (user data folder under /home/cluster/o_xxxxx) standard limitation 5TB. Currently limited amount of space, until some data is removed.
!!!!All users exciding this limitations should take immediate action, so that other users can use their space up to the given limitation.!!!
If you have any questions don't hesitate to contact us.
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,
since yesterday CEPH (/home/cluster and /home/data) is out of space and no data can be stored there anymore. To keep this volume operational you'll need to remove unneeded/old data immediately, otherwise we'll have to run our scripts to delete oldest data automatically.
I was already announcing that this year we're moving to the new Isilon storage system, so herewith from today we're providing 4TB of storage space for each user under /home/Isilon/users/o_xxxxxx. If you need more space, each research group needs to take care for this by contacting IT department and requesting certain amount of disk space.
Important: be advised to avoid coping/transferring huge data at once, since this will not work and can lead to issues. Use rsync data bandwith limitation (--bwlimit=KBPS) for this purpose.
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,
Please monitor the execution of your tasks and the amount of resources (CPUs & RAM) you are using while using any of our login nodes (primary sx036 and sj211, which you should only use if sx036 is not available!). Adjust your tasks as necessary to leave some resources available for the others as well, especially when running R code in Rstudio Server or uploading data using SFTP (FileZilla). To view CPU load while uploading data, enable the Remote monitoring option in MobXTerm (see below), as these processes are not easily accessible via the htop command.
As you can see, we presently have a large number of people online (hopefully the most of them utilize Slurm), therefore it would be great to share the cluster fairly without interfering with one another.
I appreciate your understanding and co-operation.
Best,
Marija
[cid:image003.jpg@01D9CB80.3CE2A8C0]
Marija Đurđević, MSc
PhD, Diagnostic & Research Center for Molecular BioMedicine
Institute of Pathology
Bioinformatician, Core Facility Computational Bioanalytics
Center for Medical Research
Medical University Graz
Center for Medical Research
Neue Stiftingtalstraße 6-West, Turm/Stiege:P, 4.Stock
A-8010 Graz
Austria
We’re starting the day with great news. Thanks to the support from IT department the problem with the booting of the login node sx036 could be quickly resolved and you can proceed with your work normally. RStudio server is also functioning 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
Tel. +43 316 385 73024
E-Mail: slave.trajanoski(a)medunigraz.at<mailto:slave.trajanoski@medunigraz.at>
Dear MedBioNode users,
please use temporarily sj211.medunigraz.at as login node, until sx036 is online again. I'm looking for some solution regarding RStudio server.
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,
unfortunately since today in the morning login node sx036 is down. This involves also RStudio Server, because it runs on the same machine. The issue is already reported to the IT department, but we cannot estimate how long it'll take until the server is repaired.
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,
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>
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>
