Leginon Segmentation Fault during Navigator
Added by Long Gui about 12 years ago
To whom it may concern,
We have finished the installation of Leginon on the Ubuntu desktop as well as the TEM computer. The connection between the Leginon server and client went well and we took the calibrations as the followings.
All the calibrations went fine but when we carried out the checking step with "Navigator", the Leginon suddenly crashed and exit with a warning "Segmentation Fault".
Then we restarted the Leginon and run "Navigator" again, this time the Leginon did not crash but it lost response and freeze. The command windows shows "Memory Error".
At last, we had to restart the Ubuntu operation system and Leginon could work after restarting.
Here are our questions: Could the Calibrations results be saved if the Leginon crashes during the process? Do we have to repeat all the Calibrations steps?
Also, the desktop we are using is Dell PowerEdge T310, Intel Core i3 CPU 3.2GHz X4, Memory 1.9GB. Do you think it is possible that the hardware induces the instability of Leginon?
Thanks a lot in advance!
Long Gui,
Lee Lab, University of Washington
Replies (3)
RE: Leginon Segmentation Fault during Navigator - Added by Anchi Cheng about 12 years ago
I suppose the Error Checking is on in Navigator node.
The memory you have on the computer is too small. You will have to use smaller camera dimension after binning to do anything related to correlation such as Error Checking in Navigation, Drift monitoring, and Target Adjustment. Correlation is memory intensive. Leginon needs to Fourier transform two images, multiply in the Fourier space and back-Fourier transform to give the correlation map, and these are all done in memory, not saved until it is completed. We have the same error doing correlation on 4kx4k image on computer with 4 GB memory. If you can't buy more memory on this computer, use 512x512 binned by 8 where we say to use 1024x1024 binned by 4, you should be able to get through it.
Anchi
RE: Leginon Segmentation Fault during Navigator - Added by Long Gui about 12 years ago
Hi Anchi,
Thank you so much for your reply! I will consider increase the memory to at least 8GB.
I am wondering how Leginon saves the Calibrations? Do these matrix and stage shifts save automatically after each step or they save after the entire calibration?
Thanks a lot!
Long
RE: Leginon Segmentation Fault during Navigator - Added by Anchi Cheng about 12 years ago
Goniometer modeling saves shifts between each move in the database as it happens, which is why there is a separate "calibrate" step from "measure". Other calibrations if not having separate tool does not save the shifts, only the final calibration matrix.
Even if you get 8 GB memory, 4kx4k correlation is still not recommended. Even in tomography, you can take images at 4kx4k but the tracking that does the correlation will bin it down first before performing the task to increase signal to noise ratio. It is better to bin and do subpixel fit than correlat with noisy large image.
Anchi