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I have a python program that runs inside a conda environment installed in a specific node of a cluster. I would like to submit it into qsub but just need help. My script is:

#!/bin/bash
source conda activate myenv
pyhton3.6 myprogram.py

I have already tried:

  • ssh **node** 'export SGE_ROOT=/usr/local/run/ge2011.11; /usr/local/run/ge2011.11/bin/linux-x64/qsub script.sh'

    but says

    Unable to run job: denied: host "**node**" is no submit hot. Exiting

  • qsub cwd -V qu=**node** script.sh

    but says

    Unable to read script because of error: error opening cwd;error opening qu=**node**

Thanks!

muru
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TYSH
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  • So what is installed on the node? AFAIR, your script must be installed on the submit host (on a disk accessible to the submit host), the particular environment and such may only be on the specific node as long as you ensure it only runs on that node. – Ott Toomet Dec 12 '20 at 21:35

1 Answers1

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Maybe this is a detour but I did:

  1. Login the node
  2. Include in myscript.py:
#!/anaconda3path/bin/python3.6
  1. Run as:
nohup python3.6 myprogram.py > NNp.out &

Problem solved!

TYSH
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