Bug #2256
closedCan not run Xmipp Reference Based Maximum Likelihood Alignment on emportal
0%
Description
Hi
I am using goby - emportal.scripps.edu/ to process my data.
After generating a few classes using Xmipp Maximum Likelihood Alignment (reference free) and creating templates, I tried to run Xmipp Reference Based Maximum Likelihood Alignment. It shows as a running job for a second and then quits.
I've tried a few times and the output is the same altering the number of classes. Below is the message.
Thanks a lot
I get the following messages in the mail
Message 5:
From adm@goby.amigroup.scripps.edu Tue Feb 19 13:48:05 2013
Date: Tue, 19 Feb 2013 13:48:05 -0800
From: adm <adm@goby.amigroup.scripps.edu>
To: jpluciano@goby.amigroup.scripps.edu
Subject: PBS JOB 23936.goby.amigroup.scripps.edu
Precedence: bulk
PBS Job Id: 23936.goby.amigroup.scripps.edu
Job Name: right_reference_alignmen3.appionsub.job
Exec host: node01/11+node01/10+node01/9+node01/8
Execution terminated
Exit_status=0
resources_used.cput=00:00:00
resources_used.mem=0kb
resources_used.vmem=0kb
resources_used.walltime=00:00:18
&
Message 6:
From adm@goby.amigroup.scripps.edu Tue Feb 19 13:48:09 2013
Date: Tue, 19 Feb 2013 13:48:09 -0800
From: adm <adm@goby.amigroup.scripps.edu>
To: jpluciano@goby.amigroup.scripps.edu
Subject: PBS JOB 23936.goby.amigroup.scripps.edu
Precedence: bulk
PBS Job Id: 23936.goby.amigroup.scripps.edu
Job Name: right_reference_alignmen3.appionsub.job
Exec host: node01/11+node01/10+node01/9+node01/8
An error has occurred processing your job, see below.
Post job file processing error; job 23936.goby.amigroup.scripps.edu on host node01/11+node01/10+node01/9+node01/8
- error from copy
Permission denied (publickey,gssapi-with-mic,password).
lost connection - end error output
Output retained on that host in: /var/spool/torque/undelivered/23936.goby.amigroup.scripps.edu.OU
Updated by Amber Herold almost 12 years ago
- Status changed from New to Assigned
- Assignee set to Sargis Dallakyan
Sargis,
It looks like Julia is having a similar issue on Goby to what I'm experiencing on Guppy, where the job output file can not be copied into the run directory. Any ideas?
Amber
Updated by Amber Herold almost 12 years ago
- Status changed from Assigned to In Test
- Affected Version changed from Appion/Leginon 2.1.0 to Appion/Leginon 2.2.0
Julia, I have found a bug in the code that was the main source of the issue.
I've checked in a fix, but we need to update the system for it to be available to you.
Sargis, I need you to update the goby appion 2.2 installation as soon as you can, then assign this to Julia to test.
Thanks.
A note on the fix. We were sending an argument of True to the init function for the script which was setting the params to true instead of the actual list of params. I think the function was supposed to be passing quiet=True, which would reduce the output from the routine. I just removed the parameter, so if the output is too much, we can add that in later.
Anchi code reviewed in person.
Updated by Sargis Dallakyan almost 12 years ago
- Assignee changed from Sargis Dallakyan to Julia Luciano
Thank you Amer and Julia. I build and updated the goby appion 2.2 installation on the head and work nodes with this new revision.
Assigning this issue to Julia to test.
Updated by Julia Luciano almost 12 years ago
Hello There
So far, so good.. It has been running for 2 hours without crashing.
I will update you when the run is over. Thanks
Updated by Julia Luciano almost 12 years ago
Xmipp Reference Based Maximum Likelihood Alignment ran fine multiple times with my data set. It looks like the bug has been fixed. Thanks
But now I get a lot of black boxes for my templates, and the description of this features mentions that such thing happens and that it is untested as to how much bias the reference gives you.
Any word as to further testing of this feature or how often the "back boxing" of unused templates happens?
Thanks again
Updated by Amber Herold almost 12 years ago
- Status changed from In Test to Closed
closing this out, and will look into the black box thing.