GUI socket disconnected

5 posts / 0 new
Last post
erikklontz
GUI socket disconnected

Hi, 

I've seen similar threads posted on these forums but perhaps none that address my situation. During 2D classification (with my dataset) and/or ab-initio 3D reconstruction (with the tutorial dataset), the cisTEM GUI randomly crashes and terminal states that the GUI socket disconnected. Here are a few lines leading up to the crash during my last 2D classification:

"Dumping intermediate files...

Total logP = -789.116

Refine2D: Normal termination

Total logP = -1326.15

Refine2D: Normal termination

JOB CONTROL: Master Socket Disconnected!!

Running...

JOB CONTROL: Trying to connect to 10.0.2.15:3000 (Timeout = 4 sec)...

JOB CONTROL: Succeeded-Connection established!!

JOB CONTROL: GUI Socket Disconnected!!"

 

I don't have access to a dedicated linux box or cluster yet, so I am running cisTEM on a personal workstation:

  • Intel Core i5-7600K Processor 3.80GHz
  • NVIDIA GeForce GTX1070 8GB GDDR5 VR Ready
  • 16GB DDR4-3000 RAM

I have Windows 10 with VirtualBox running Ubuntu, and cisTEM installed as recommended in the tutorial (cistem-1.0.0-beta-intel-linux.tar.gz)

Any ideas how to prevent this?

Thanks!

Erik

 

 

erikklontz
I'm not sure if this is

I'm not sure if this is related, but the "canberra-gtk-module" fails to load when launching cisTEM.

Erik

timgrant
Hi Erik,

Hi Erik,

I don't have any experience running in VirtualBox, how much memory/disk space are you giving the virtual machine?   

Cheers,

Tim

erikklontz
Hi Tim,

Hi Tim,

I'm giving it 14GB of memory, and I've allocated 25GB of dedicated disk space. However, I'm running cisTEM out of a folder that is shared with the entire hard drive, so it shouldn't be able to run out of storage.

Thanks,

Erik

timgrant
Hi Erik,

Hi Erik,

Sorry you're having trouble. One way to get to the bottom of this, is if you could run a debug version and give us the backtrace output. Can you download a debug version of the cisTEM gui from here :-

http://grigoriefflab.janelia.org/sites/default/files/timgrant_18-07-12_5...

unzip it with :-

gzip -d cisTEM_debug.gz

then run it in GDB :-

gdb ./cisTEM_debug

At this point you need to type "run".  The gui should then run, and you should be able to open your project.  When it crashes, please type "bt" in the window and post the output.

Thanks!

Tim

 

Log in or register to post comments