Error message during AutoRefine

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rasmuskf
Error message during AutoRefine

Dear cisTEAM,

During an AutoRefine run in iteration 5 out of 20 I got an error message after the "calculating reconstruction step" saying,

error: mode 32618 MRC files currently not supported. 

The GUI then immediately aborted. When trying to open the already calculated volumes in chimera I get an error message saying that "file size is too small for grid size". Any suggestion if the already calculated volume can be used? Or should I retry the AutoRefine run?

Best,

Rasmus

timgrant
Hi Rasmus, 

Hi Rasmus, 

This sounds like something went wrong and the volume was not correctly written (is it possible you ran out of disk space in the scratch directory?)

I think you will have to retry the run - sorry!

Tim

rasmuskf
Hi Tim,

Hi Tim,

Disk space shouldn't be a problem. But out of curiosity, is there a way to see cisTEM's memory requirements for 3D refinements/classifications? The box sizes I use for my particles are in the 512-700 pixel range (1.1 Å/pix) and especially when I ask for multiple 3D classes it happens to me that the GUI suddenly aborts without providing any error messages.

Best,

Rasmus

timgrant
Hi Rasmus,

Hi Rasmus,

I think the memory usage should be less than 4 * the 3D size at most PER process.  So for 700 pixels, it would be ~5.2GB per process.

Tim

zz2629
error message during 3d refine

Error: File '/dev/null' couldn't be removed (error 13: Permission denied)

timgrant
This error can be ignored in

This error can be ignored in linux.

Thanks,

Tim

zz2629
error in 3d refine

Hi Tim,

Thank you very much for the reply. I am using OpenSuse 15.0. When I run 3d refine I get this error msg:

Refine3D: Normal termination

   100% [=================] done! (1h:32m22s)                      

Refine3D: Normal termination

JOB CONTROL : Master Socket Disconnected!!
Running...

 JOB CONTROL: Trying to connect to 192.168.8.3:3000 (timeout = 4 sec) ...
 JOB CONTROL: Succeeded - Connection established!

We read 31240 bytes
We read 31240 bytes

 327888 data lines read

 327888 data lines read

 327888 data lines read

 327888 data lines read
17:17:19: Error: File '/dev/null' couldn't be removed (error 13: Permission denied)
17:17:19: Error: File '/dev/null' couldn't be removed (error 13: Permission denied)
17:17:19: Error: File '/dev/null' couldn't be removed (error 13: Permission denied)
17:17:19: Error: File '/dev/null' couldn't be removed (error 13: Permission denied)

 327888 data lines read
17:17:19: Error: File '/dev/null' couldn't be removed (error 13: Permission denied)

 327888 data lines read
17:17:19: Error: File '/dev/null' couldn't be removed (error 13: Permission denied)

 327888 data lines read

 327888 data lines read
17:17:20: Error: File '/dev/null' couldn't be removed (error 13: Permission denied)

 327888 data lines read

 327888 data lines read

 327888 data lines read
17:17:20: Error: File '/dev/null' couldn't be removed (error 13: Permission denied)
17:17:20: Error: File '/dev/null' couldn't be removed (error 13: Permission denied)
17:17:20: Error: File '/dev/null' couldn't be removed (error 13: Permission denied)

 327888 data lines read
17:17:20: Error: File '/dev/null' couldn't be removed (error 13: Permission denied)
17:17:20: Error: File '/dev/null' couldn't be removed (error 13: Permission denied)
Connection Timer Fired

 327888 data lines read
17:17:21: Error: File '/dev/null' couldn't be removed (error 13: Permission denied)

 327888 data lines read

 327888 data lines read

 327888 data lines read
17:17:21: Error: File '/dev/null' couldn't be removed (error 13: Permission denied)
17:17:21: Error: File '/dev/null' couldn't be removed (error 13: Permission denied)
17:17:21: Error: File '/dev/null' couldn't be removed (error 13: Permission denied)
Connection Timer Fired
JOB  : Master Socket Disconnected!!
JOB  : Master Socket Disconnected!!
JOB  : Master Socket Disconnected!!
JOB  : Master Socket Disconnected!!
JOB  : Master Socket Disconnected!!
JOB  : Master Socket Disconnected!!
JOB  : Master Socket Disconnected!!
JOB  : Master Socket Disconnected!!
JOB  : Master Socket Disconnected!!
JOB  : Master Socket Disconnected!!
JOB  : Master Socket Disconnected!!
JOB  : Master Socket Disconnected!!
JOB  : Master Socket Disconnected!!
JOB  : Master Socket Disconnected!!
JOB  : Master Socket Disconnected!!
JOB  : Master Socket Disconnected!!
Calculation thread has been waiting for something to do for 30.000000.2 seconds - going to finish
Running...

 JOB CONTROL: Trying to connect to 192.168.8.3:3000 (timeout = 4 sec) ...
 JOB CONTROL: Succeeded - Connection established!

We read 3934 bytes
We read 3934 bytes
Connection Timer Fired
Connection Timer Fired
JOB  : Master SoJOB  : Master SoJOB  : Master Socket Disconnectecket Disconnected!!
cket Disconnected!!
d!!
JOB  : Master SoJOB  : Master SoJOB  : Master Socket Disconnectecket Disconnectecket Disconnected!!
d!!
d!!
JOB  : Master Socket DisconnecteJOB  : Master Sod!!
cket DisconnecteJOB  : Master SoJOB  : Master Sod!!
cket Disconnectecket DisconnecteJOB  : Master SoJOB  : Master SoJOB  : Master Sod!!
cket Disconnected!!
d!!
cket Disconnectecket Disconnected!!
d!!
JOB  : Master SoJOB  : Master SoJOB  : Master Socket Disconnectecket Disconnectecket Disconnected!!
d!!
d!!
JOB  : Master Socket Disconnected!!
JOB  : Master Socket Disconnected!!
JOB  : Master Socket Disconnected!!

Best regards,

Zhening

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