[3dem] Re: processchunks error with tilt_sirt (Toni Uusim?ki)

Tobias Starborg tobias.starborg at manchester.ac.uk
Fri Feb 19 12:23:07 PST 2010


Toni,  Firstly, you should try posting this question on the IMOD mailing 
list, which you can join here 
(http://bio3d.colorado.edu/imod/joinlist.html).  You should get some 
good pointers from users on that list.

I have to admit that I don't know enough about IMOD to answer your 
particular problem.  I can tell you that the error about not being able 
to use the GPU is fairly standard.  It should switch to using your 
CPU(s) at this point.  The volume sizes don't look too bad either, as 
IMOD actually reconstructs the volume XZY, rather than XYZ.  Etomo 
automatically flips the data so that you view it as you would expect.  
At the end of the reconstruction process there is an option to rotate 
the volume (which is more accurate than flipping).

There was a bug in IMOD 4.0.22 that used to stop the reconstruction 
after the first set of sync files.  You state that 4.0.23 gave the GPU 
error (which is normal).  Have you checked that the process wasn't 
actually carrying on in the background?  You could use task manager 
(CTRL-ALT-DELETE) in Windows, or top in cygwin.  Look for a process 
(multiple if you're using multiple CPUs) called "tilt".

Other than this I can't really help.  I'd ask the IMOD community and 
hopefully you'll get a better answer.

Oh and if you're running on multiple computers then did you upgrade them 
all to 4.0.23?


That's my four peneth.

Toby S

Oh and its just occurred to me that you may need to re-run sirtsetup 
with 4.0.23, rather than continuing from the point it last crashed.  TS

----------

Hello all,

i have been trying now for a long time to get sirt reconstruction out of 
IMOD.
I have tried it with the cpu.adoc file with all necessary enviromental 
variables and
directly setting the cpus and gpu in the etomo settings, but neither 
works. The processchunks
fails all the time in around tilt_sirt-025. I am using windows XP and 
with IMOD 4.0.23 it
says that cannot use GPU, using CPU instead -when it fails. The GPU 
reconstruction in etomo
works well thought. With IMOD 4.0.22 it says CHUNK ERROR: (last line) - 
--------------- ...
There is two things i am concerned about:
1. when running processchunks, it says w: command not found -before 
starting the routine
2. the output from log file is 1024,60,1024 althought from etomo it is 
1024,1024,60

I have tried it with switches from sirtsetup -ch -pc -st ... and none work.
Also the switches from Processchunks -g -P -n 1 won't work.
Also settting x tilt to 0 won't work.

I think there is just a small thing i have not realized because i
am not so experienced with IMOD.

Thanks for any help!!!

Sincerely,

Toni


-- 
Dr T Starborg
FLS, University of Manchester, Michael Smith Building, Oxford Road, Manchester. M13 9PT
Tel: +44(0)1612751557
Fax: +44(0)1612751505
http://manchesterpolara.org.uk

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