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CSC Computing environment Q&A session 26.4.2022
tags:
puhti
mahti
allas
This is the place to ask questions about the workshop content! We use the Zoom chat only for posting links, reporting Zoom problems and such.
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Learn More →`
) for thecode blocks
. Otherwise, it's like a Google doc: it allows simultaneous editing.Code of conduct
We strive to follow the Code of Conduct developed by The Carpentries organisation to foster a welcoming environment for everyone. In short:
TO DO before the course
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Learn More →You can type your questions here. We will answer them, and this document will store the answers for you for later use!
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Learn More →General and practical matters
Q1: I have difficulty pasting my questions into HackMD (here). Do you have some instructions on how to write here?
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Learn More →Q2: I cannot access most of the slides from the course page. These are marked with an earth logo.
Q5: Do we get ECTS credits from this course for our university transcripts?
Q6: Should I get my "own" project for the course, can't I just use a project you provide?
Q7: So many credendials… Which ones do I need and where?!?
Q: How long are the course materials available online? Tutorials, slides etc.?
Q: To whom (what level student) should the CSC services be recommended?
Q: Tykky container service. How to install python / local packages?
Q: I registered as a student but I can't found COMSOL multiphysics software. are available softwares are limited for student?
Q: How to access huge data (very big! :) from ALLAS to work with Matlab from cPouta? Are there examples online (I couldn't find them)?
Q: Hi, I have a basic question. I used to get email notif when my batch job status is failed. But now I only get notified when it successfully ran. Is there some changes in csc with this?
Great! You're asking
--mail-type=END
i.e. send email when the job ends. If you want mail also when it starts –>--mail-type=BEGIN,END
. If you also want notification when job fails, also specifyFAIL
–>--mail-type=BEGIN,END,FAIL
Q: I am trying to run a batch job, basically doing a diamond blast to one database (non-redundant, nr). Previously I do it with swiss-prot, which took around 16min/sample and between 8-10G of memory. But with nr database the job is cancelled after 10h because exceeds the maximum memory (16G), which cannot be increased. I checked and any output file of the 40 desired was created before the job was cancelled. How can I run the job? How can I by-pass the memory limitation? I send this question by email hpcplatforms #538239
Try sinfo command to learn about partitions, and about max mem
Check chapters 5 and 6 from the self-learning course, there we are talking about this! It's a common difficulty!
A good tutorial, where the memory runs out, and how to figure that out: https://csc-training.github.io/csc-env-eff/hands-on/batch_resources/tutorial_sacct_and_seff.html
How much memory is available? List of Puhti's partitions (queues) https://docs.csc.fi/computing/running/batch-job-partitions/
Try:
#SBATCH --mem-per-cpu=32G
Don't use max mem, if you don't need that much -the "why" for this is explained in the training material
Q: Does the '#SBATCH –time' starts when the job starts or when you submit the batch job?
Q:
Action points: