- Medbionode - MedUniGraz Mailing Lists

new login node and transfer of jupyterhub and rstudio server

by Trajanoski, Slave

Dear MedBioNode users, I have great news for you. IT department managed to issue new certificates for the two critical services much faster than expected: 1. jupyter.medunigraz.at 2. rstudio.medunigraz.at which are running on the new login node sx163. You can access them with any browser over https secure connection. Many thanks to the responsible person at the IT department. The new server has much better and faster hardware: 256 logical cores and 1.5TB working memory. Herewith you can also ignore my previous E-Mail. 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 Tel. +43 316 385 73024 E-Mail: slave.trajanoski(a)medunigraz.at<mailto:slave.trajanoski@medunigraz.at>

3 months, 3 weeks

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second login node jupyterhub and rstudio server

by Trajanoski, Slave

Dear MedBioNode users, I have good news. We're providing additional login node, RStudio Server and JupyterHub over the following links: 1. Second login node ssh sx163.medunigraz.at 2. RStudio server http://sx163.medunigraz.at:8787 3. JupyterHub https://sx163.medunigraz.at For RStudio server and JupyterHub you'll need to use Firefox and make exception for this address until IT department provides certificates for them. Since both services will run in your one and same user profile you must avoid opening sessions at the same time on current servers (jupyterhub.medunigraz.at and rstudio.medunigraz.at) and the new ones. If you have doubts, need support or just ask questions don't hesitate to contact me. 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>

3 months, 3 weeks

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private chat messenger with MedBioNode space for communication

by Trajanoski, Slave

Dear MedBioNode users, herewith we’re introducing new way for encrypted communication using save local server installed and administered by the IT departement. This is the documentation on how to install and configure your chat client: https://confluence.medunigraz.at/display/ITKB/Matrix+%28Element%29+Messenger and here the invitation for the MedBioNode space. https://matrix.to/#/#medbionode:medunigraz.at You can contact me also directly over this channel. The already existing Discord channel will not and should not be used in the future. 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 Tel. +43 316 385 73024 E-Mail: slave.trajanoski(a)medunigraz.at<mailto:slave.trajanoski@medunigraz.at>

5 months

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SLURM Workshop: Practical Use Cases for Data Analysis on MedBioNode

by Trajanoski, Slave

Dear MedBioNode users, I’d like to draw your attention to our new free course we’re organizing in spring to help you mastering your SLURM knowledge. Several regular proficient cluster users will share their SLURM experience with you and answer your questions, as well as try to solve your problems with data analysis on our MedBioNode. Register to get your place over the MERAG website under the topic MedBioNode. Below you’ll find the official inviation. https://zmf.medunigraz.at/merag SLURM Workshop: Practical Use Cases for Data Analysis on MedBioNode Join us for an engaging SLURM Workshop at the university, where experts will showcase how they leverage SLURM for data analysis on the MedBioNode cluster. This session, taking place from 13:00 to 16:00, will feature a series of presentations by researchers and professionals who use SLURM in their daily work. Through real-world use cases, you'll gain insights into efficient job scheduling, resource management, and performance optimization for computational workloads. Whether you're a beginner or an advanced user, this workshop will provide valuable knowledge and best practices to enhance your workflow on MedBioNode. For those who wish to practice or participate in hands-on exercises, please bring your own laptop with an operational University WiFi connection. 📍 Location: MedCampus 📅 Date: 09.04.2025 ⏰ Time: 13:00 – 16:00 Don't miss this opportunity to learn from experienced users and improve your SLURM skills! Best regards, Slave From: Trajanoski, Slave Sent: Monday, 27 January 2025 15:40 To: Plank, Gernot <gernot.plank(a)medunigraz.at<mailto:gernot.plank@medunigraz.at>>; marija.durdevic(a)medunigraz.at<mailto:marija.durdevic@medunigraz.at>; Diener, Christian <christian.diener(a)medunigraz.at<mailto:christian.diener@medunigraz.at>>; 'Isaac Lazzeri (isaac.lazzeri(a)medunigraz.at<mailto:isaac.lazzeri@medunigraz.at>)' <isaac.lazzeri(a)medunigraz.at<mailto:isaac.lazzeri@medunigraz.at>>; Sánchez Murcia, Pedro Alejandro <pedro.murcia(a)medunigraz.at<mailto:pedro.murcia@medunigraz.at>> Subject: SLURM Workshop poll for date and time Dear colleagues, first of all I’d like to thank you all for your participation to our MedBioNode SLURM Workshop. Herewith I’d like to find appropriate date and therefore I’ll need your input in the current meeting poll: https://www.termino.gv.at/meet/p/a6f702a57bf2853c8a9cea82511b2a07-411341 Please provide me your answers until Wednesday, 29.01.2025, so I can book the room and start with the further preparations. 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>

5 months

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using GPFS for wrtiting data

by Trajanoski, Slave

Dear MedBioNode users, I can report that the issue is not present anymore. Unfortunately we could detect the process causing this extreme GPFS IO operation, since this activity has stopped. Herewith I'd like just to emphasize the importance of avoiding high data writing on GPFS, since it affects all users in doing there normal work. GPFS is the home directory location for all MedBioNode users. In case you have such situations there are different solutions to accomplish this. Please contact me if you need some assistance. Thanks for your cooperation. 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>

8 months, 4 weeks

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using GPFS for wrtiting data

by Trajanoski, Slave

Dear MedBioNode users, we have currently issue that some user process puts heavy writing load in home directory (/home/gpfs) causing that it is impossible to work. 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>

8 months, 4 weeks

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GPU node sx138 downtime 18.10.2024 09.00 - 10.30

by Trajanoski, Slave

Dear MedBioNode users, since the scheduled maintenance work with external company on GPU node sx088 today was successfully finished, the same work is scheduled for the second node sx138 on Friday 18.10.2024 from 09.00 until 10.30 . Please plan your job execution on this node only accordingly, since the node will be shutdown during this time. 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>

9 months, 1 week

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GPU node sx088 downtime 14.10.2024 13.00-17.00

by Trajanoski, Slave

Just a reminder of the planned downtime for sx088. Thanks. From: Trajanoski, Slave Sent: Monday, 30 September 2024 13:24 To: medbionode(a)lists.medunigraz.at Subject: GPU node downtime 14.10.2024 13.00-17.00 Importance: High Dear MedBioNode users, we have scheduled maintenance work with external company on GPU node sx088 on 14.10.2024 from 13.00 until 17.00. Please plan your job execution on this node only accordingly, since the node will be shutdown during this time. 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>

9 months, 1 week

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GPU node downtime 14.10.2024 13.00-17.00

by Trajanoski, Slave

Dear MedBioNode users, we have scheduled maintenance work with external company on GPU node sx088 on 14.10.2024 from 13.00 until 17.00. Please plan your job execution on this node only accordingly, since the node will be shutdown during this time. 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>

9 months, 3 weeks

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new CPU node sy178 available

by Trajanoski, Slave

Dear MedBioNode users, great news for our cluster. Since today we have additional computational node sy178 as part of the CPU partition. 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>

10 months, 2 weeks

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