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csc-training
GitHub Repository: csc-training/csc-env-eff
 Path: blob/master/_slides/00_study_tips.md
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theme: csc-eurocc-2019
lang: en
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Study tips and problem solving {.title}

How to use the material and how to solve common problems.

![](https://mirrors.creativecommons.org/presskit/buttons/88x31/png/by-sa.png)
All materials (c) 2020-2025 by CSC – IT Center for Science Ltd. This work is licensed under a **Creative Commons Attribution-ShareAlike** 4.0 Unported License, [http://creativecommons.org/licenses/by-sa/4.0/](http://creativecommons.org/licenses/by-sa/4.0/)

Using these materials

  • The material is organized by topics of increasing complexity

    • Feel free to jump if you know the basics already

  • Read the slides / watch the videos first

  • Complete the tutorials to make sure you've got the steps right

  • Try out one or more of the exercises to verify your new skills

  • If you get stuck, consult Docs CSC linked to the topic slides

  • Press shift to open links with additional information in a new window

  • Left-click on slides and you can then navigate them with the arrow keys

General problem solving

  1. Go to docs.csc.fi and check in the right section in the navigation

  2. Try the FAQ

  3. Try the search function in CSC Docs or search the web

    • Type a keyword in CSC Docs, copy/paste the error message in your favorite search engine

  4. Send an email to [email protected] containing:

Running a new application in Puhti 1/2

  • If it comes with tutorials, do at least one

    • This will likely be the fastest way forward

    • Naturally, read the manual/instructions

  • Check if there's a page about it in Docs CSC

    • If there is, use the batch script example from there

    • Otherwise, use a general template

  • Try first running interactively (not on a login node)

    • Perhaps it is easier to find the correct command line options

    • Use the top command to get rough estimate of memory use, etc.

    • If developers provide some test or example data, run it first and make sure results are correct

Running a new application in Puhti 2/2

  • You can use the test queue to check that your batch job script is correct

    • Limits : 15 min, 2 nodes

    • Job turnaround usually very fast even if machine is "full"

    • Can be useful to spot typos, missing files, etc. before submitting a job that will idle in the queue

  • Before large runs, it's a good idea to do a smaller trial run

    • Check that results are as expected

    • Check the resource usage after the test run and adjust accordingly

  • How many cores to allocate?

What if your job fails? Troubleshooting checklist 1/2

  1. Did the job run out of time?

  2. Did the job run out of memory?

  3. Did the job actually use the resources you specified?

    • Problems in the batch job script can cause parameters to be ignored and default values are used instead

  4. Did it fail immediately or did it run for some time?

    • Jobs failing immediately are often due to something simple like typos, missing inputs, bad parameters, etc.

What if your job fails? Troubleshooting checklist 2/2

  1. Check the error file captured by the batch job script

  2. Check any other error files and logs the your program may have produced

  3. Error messaged can sometimes be long, cryptic and a bit intimidating, but ...

    • Try skimming through them and see if you can spot something "human-readable"

    • Often you can spot the actual problem easily if you go through the whole message. Something like "required input file so-and-so missing" or "parameter X out of range", etc.

  4. Consult the FAQ on common Slurm issues in the CSC Docs

Document your discoveries

  • When you've successfully solved an issue, make it easy to rediscover it

  • Set up a file in your $HOME and add your commands there

    • It's quick to copy/paste from the screen to the end of the file

cat >> $HOME/vault
<copy/paste>
Ctrl-C

  • ... and finding them with grep later is quick (grep them $HOME/vault)

    • bash history is nice, but it keeps also the commands that didn't work...

    • Note, don't overwrite your vault file (e.g., with cat > $HOME/vault)

  • Store scripts in $HOME/bin and take backups