Issues with IQ-Tree Run

17 views
Skip to first unread message

Rodolfo Probst

unread,
Feb 22, 2024, 8:41:36 PMFeb 22
to CIPRES Science Gateway Users
Dear all,


I am attempting to run a simple tree reconstruction on IQ-Tree 2.1.2 on ACCESS and I keep getting the following error message:

"Inactive Modules: 1) subversion/1.14.0 The following have been reloaded with a version change: 1) cpu/0.17.3b => cpu/0.15.4 /home/cipres/ngbw/contrib/tools/bin/iqtree2_2.1.2_expanse: line 14: 1009953 Killed $cmdline slurmstepd: error: Detected 1 oom_kill event in StepId=28886735.0. Some of the step tasks have been OOM Killed. srun: error: exp-1-34: task 0: Out Of Memory srun: Terminating StepId=28886735.0"

The runs have been killed after under a minute. Not sure what might be wrong since I have been running several similar runs with success. Any fdback would be highly appreciated.

All the best,
Rodolfo

Mark Miller

unread,
Feb 22, 2024, 9:33:24 PMFeb 22
to CIPRES Science Gateway Users
Hi Rodolfo,

Thanks for reporting the issue.
This almost certainly an out of memory error, but it is possible there is an issue with the machine, or the specific node your job landed on.
A couple of things:
1. It sounds like it is reproducible, which makes a specific node error seem less likely.
2. Have you tried increasing the available memory?  There are two more memory options. They make the run more costly, but may allow it to get through.
3. Is there really no difference between these runs and the ones that work in terms of expected memory footprint?
4. If you are stumped, you can send me the _JOBINFO.TXT file for a job that worked, and one that did not. I will investigate.

Mark

Rodolfo Probst

unread,
Feb 22, 2024, 10:57:15 PMFeb 22
to Mark Miller, CIPRES Science Gateway Users
Hi Mark,

Thank you very much for your prompt response and I appreciate the feedback. You were absolutely right about being a memory issue!
In any case, I am addressing your points 2-4:

2. I tried increasing memory, but with a free subscription I am unable to go over 998 hours at this time (but see my comment for #4);
3. Matter of fact, there is a small difference - I am adding a dozen or so terminals to this run compared to others that worked;
4. I attempted to decrease the run to 40 hours and selected the first "more memory" option - so to negotiate for the 998 quota I have left - and it is now working.

Thanks again for your help, Mark!

Best,
Rodolfo
________________________________
Postdoc at the Science Research Initiative (SRI)
College of Science
257 S 1400 E, University of Utah
Salt Lake City, UT 84112



--
You received this message because you are subscribed to the Google Groups "CIPRES Science Gateway Users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cipres-science-gatew...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/cipres-science-gateway-users/6e53a37f-6cee-4507-bd33-b7e81c97e25bn%40googlegroups.com.

Mark Miller

unread,
Feb 23, 2024, 11:51:08 AMFeb 23
to CIPRES Science Gateway Users
Thanks for letting me know Rodolfo.
I understand about the free tier and time issue; you found a good solution.
We recently added a tier to allow an additional 1000 hours for just $30 in case that helps.
The goal is to allow people to add more time from a grant if they need it.
We are trying to find ways to meet people's needs, and stay in business.
Let me know if you have any further issues.
Best,
Mark
Reply all
Reply to author
Forward
0 new messages