largest possible image size

Submitted by Jamon on Thu, 2014-12-18 00:04

Forums

Frealign

I am wondering the largest the image size that frealign can handel. I have something that might exceed 1024*1024, is it possible.

niko Thu, 2014-12-18 00:24

I have not tried larger sizes but I think it may work, provided you have sufficient memory on your machine.

Jamon Thu, 2014-12-18 00:56

I get frealign8.11 started, it finish the first image, but somehow failed on the second one with message as follows.

##########Log file
NX, NY, NZ: 1248 1248 3254
MODE : real
Min, max : 0.000000 0.000000
Mean, RMS : 0.000000 0.000000
TITLE 1: EMAN 12/16/2014 20:46

Time before particle 1 was 13:48:51
Time before particle 2 was 13:52:43
Cannot use file - no file name. Open file first.

##########parameter file output
C PSI THETA PHI SHX SHY MAG FILM DF1 DF2 ANGAST PRESA DPRES
1 45.49 18.68 152.69 -8.43 -4.63 61718. 1 12931.9 13094.0 -15.50 77.59 77.59

niko Thu, 2014-12-18 07:35

Please use the new version, 9.09. Also note that this new version comes with new scripts to run Frealign.

Jamon Tue, 2014-12-23 04:48

Dear Niko,
I tried v9.09 with the new script for large particles(1080*1080), both refine and reconstruction failed at begining without any meaningful output. I suspect it may due to memory allocation. Is there some parameter I can tweak in the source code and recompile frealign.
My workstation has 256GB memory so it should not be the limitation.

Thanks and Regards,
Jian

Jamon Wed, 2014-12-24 14:08

Yes. Frealign 8/9 both works perfectly fine with examples and other dataset with smaller sizes. It looks around 1024 is the limits. Frealign will exit after reading in dataset and volume but before starting refining more than 1 particles. For reconstruction, it actually went through the whole dataset but no new volumes created and no resolution and statistics calculated. All ends without error messages and no clues.