MrBayes task getting stuck at seed command

[Natalie Finnegan]

Hi!

I have wracked my brain trying to fix this on my own, but I can't seem to figure out what I might be doing wrong. I have tried to run a few jobs using the mrbayes on access tool with different mrbayes blocks, using interleaved or not interleaved nexus files, trying to change things around, not using a mrBayes block but using the interface given in the tool, but in my STDOUT file it seems to keep stalling on the seed line. I have inspected my nexus and there doesn't seem to be anything wrong with it that I can see, but I may be missing something. I am using an identical mrbayes block to an earlier job with fewer samples (7 instead of 23) that worked well.

The job may be listed under nrfi...@ucla.edu (instead of nrfi...@g.ucla.edu).

Any help you can offer would be greatly appreciated!

Sincerely,

Natalie Finnegan

[Mark Miller]

Hi Natalie,

There are many jobs that I see that were stopped when they reached the time limit of 30 minutes.

You can use the restart button to restart them, and you can add more time when you restart, if you need a longer run.

There are two ways to tell is it is a time issue.

The output line says:

MRBAYES_XSEDE-723C9245014D4E1DB7E2A70EFB849C81 reached its maximum allowed run time before completing. This job can be restarted, but only if you act within 14 days. If you need help configuring your run, please contact me at mmi...@sdsc.edu

And the file _scheduler_stderr.txt says:

srun: Job step aborted: Waiting up to 62 seconds for job step to finish. slurmstepd: error: *** STEP 2013801.0 ON pcn-4-01 CANCELLED AT 2024-10-29T12:40:14 DUE TO TIME LIMIT ***

If there is another that I did not see, just let me know, and paste in the contents of the file _JOBINFO.TXT so I can locate it.

Best.

Mark

[Natalie Finnegan]

Hi Mark!

Thank you for getting back to me! I was using the smaller time limits because I didn't want to waste hours while trying to figure out this issue of why it kept stopping at the same line multiple times. So you think I should run it for a longer time and it could just be that generating the next line (calling where to save the files) is just a rather intense command that takes a good amount of time to complete? There was one job that ran a lot longer and still stopped there. I am worried about running it for a long time and it still stops at that line, but I am out hours (I plan on buying more hours but still am tentative to expend them on accident!)

Natalie

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[Miller, Mark]

Ah, ok.

 

Can you send me the identifier for that job, and I will investigate?

That would be very helpful to me.

 

Mark