Ab-initio 3D Crash (How to prevent/recover)

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Stephen
Ab-initio 3D Crash (How to prevent/recover)

Hi Tim,

The Ab-initio 3D run crashed, with the following message on the terminal

     0% [                              ] ???h:??m:??s  
Number of global search views = 184 (best_parameters to keep = 184)

Average sigma noise = 42.846611, average LogP = 11.391157
Average ShiftX = -0.564679, average ShiftY = -0.384859
Sigma ShiftX = 16.473682, sigma ShiftY = 16.191534
Number of particles to refine = 13246

     0% [                              ] ???h:??m:??s  
Number of global search views = 184 (best_parameters to keep = 184)

Average sigma noise = 42.846611, average LogP = 11.391157
Average ShiftX = -0.564679, average ShiftY = -0.384859
Sigma ShiftX = 16.473682, sigma ShiftY = 16.191534
Number of particles to refine = 13245

JOB CONTROL : Master Socket Disconnected!!h:32m22s                
JOB  : Master Socket Disconnected!!
JOB  : Master Socket Disconnected!!
JOB  : Master Socket Disconnected!!
JOB  : Master Socket Disconnected!!
03:41:51: Debug: In file ./src/unix/threadpsx.cpp at line 261: 'pthread_mutex_destroy()' failed with error 0x00000010 (Device or resource busy).
    47% [==============                ] 1h:33m16s       

 

cisTEM version 1.0.0-beta Running on Red Hat Enterprise Linux 6.10 (Santiago)

Looking in ./Assets/Parameters

I can see the files startup_input_stats_33_1.txt, startup_input_par_33_1.par & output_par_33_1.par. Is there a way to restart from where it left off (i.e. Cycle 33).

Thanks,

Stephen

Stephen
Update

Update -  Re-ran with 15 Cycles (instead of 40), and a resoltuion of 8 Ang. (instead of 6), and it ran to completion, although the reconstruction was not that good.

timgrant
Hi Stephen,

Hi Stephen,

Sorry for the late reply - does it always crash with 40 cycles?  Is it possible you are running out of disk space?

Tim

Stephen
Thanks Tim,

Thanks Tim,
The crash happens between cycles 33-36 when running 40 cycles. It only crashes with this dataset (works fine with beta-gal test dataset). There is enough space on the disk.
Stephen

timgrant
Hmm, that is weird, I'm

Hmm, that is weird, I'm afraid I am not sure what could be causing it.

We're working on getting the new release out in the next few months - it has many changes so I hope this will be fixed by that.

Tim

Stephen
Computer setup

Hi Tim,

I am starting to suspect that there is something amiss with our local computer setup.

Even during simple jobs like Align Movies, sometimes the GUI suddenly shuts down. 

Are there any common reasons that could cause cisTEM GUI to shutdown. I have not noticed any pattern to when this happens, but happens somewhat randomly.

Thanks,

Stephen

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