Slurm error?

[Jonas MR]

Hello,

I have used the Raxml BlackBox tool on cipres for a couple of years now, so I was surprised when it stopped working for me. As soon as I begin the job it automatically terminates it with the following error:

srun: error: exp-7-39: task 0: Exited with exit code 255

 and scheduler.stderror file:

/cm/local/apps/slurm/var/spool/job275047/slurm_script: line 22: genmap: command not found % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 3 100 3 0 0 46 0 --:--:-- --:--:-- --:--:-- 46 chmod: changing permissions of '_JOBINFO.TXT': Operation not permitted chmod: changing permissions of 'scheduler.conf': Operation not permitted % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 3 100 3 0 0 65 0 --:--:-- --:--:-- --:--:-- 65  

A quick google search seemed to suggest this had to do with SLURM. I am fairly sure it has nothing to do with my phylip alignment as I have double checked it and can't find anything out of the ordinary. I've requested many raxml runs on cipres using similar data without issues in the past.

Any insights?

Thank you,

[Alexandros Stamatakis]

Hi Jonas,

Our colleagues from SDSC on the BCC might be able to help you with this.

Alexis

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Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology

www.exelixis-lab.org

[Miller, Mark]

Hi there,

We just moved that code from Comet to the new machine EXPANSE.
I made some mistakes during the transition, and in the last couple of days there have been some issues with certain submitted jobs.

I believe that these are all repaired now, and if you clone and resubmit that job, it will work correctly. If it does not, there is a bug I have not caught yet. If you send me the file _jobinfo.txt for any failed jobs at mmi...@sdsc.edu
I will give you prompt resolution.

Best,
Mark

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Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology

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[Jonas MR]

This problem has been resolved.

Thank you