Frealign

Hello,

Trying to scale up my refinement, I have an error message "cannot close file". I don't know where it comes from. I have plenty of space on my hard drive and it was working fine when doing a test run with only 200 particles.
Any help welcome!

Amedee

Opening MRC/CCP4 file for READ...
File : /master.raid/home_master/frealign_v8.08_2/spiderinput/hr8_0.spi
NX, NY, NZ: 350 350 350
MODE : real
Min, max : -0.2297778E-02 0.2791442E-02
Mean, RMS : 0.2085688E-04 0.3075726E-03

Hello,

This is a very basic question, but when converting a spider stack to MRC, do you consider it to be a 3D volume or a set of 2D files?
Or do you first convert the stack to a volume, and then to MRC format?

I'm asking this only because I'm struggling since a few days to have images readable by frealign. Something must be wrong with my use of em2em..

Regards

Hi Niko,

I got this error message when reading the spider stack file:

............................

Opening SPIDER file for READ...
File : /home/spider/CryoEM_Software/Frealign/frealign_v8.09/examples/refinetest/../ENV06test_norm.spi
Non-native byte order
NX, NY, NZ: 200 200 1157
MODE : real
Min, max : 0.000000 0.000000
Mean, RMS : 0.000000 0.000000
TITLE 1:
TITLE 2:
TITLE 3: CREATED 13-AUG-2010 AT 18:22:39

Time before particle 1 was 18:25:22

I have problems compiling the GPU version of frealign on our system.

I updated the Makefile to the right gcc version, I tried it with gcc 3.4 and 4.3, but both will not work. When I use the nvcc string as provided in the Makefile (nvcc -arch sm_13 -lpthread --compiler-bindir /usr/bin/gcc) I get the following error:
gcc -O3 -DPROTOTYPE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o ioc.o ioc.c
ar r frealign_v8.a ioc.o
nvcc -arch sm_13 -lpthread --compiler-bindir /usr/bin/gcc -O3 -lg2c -lcufft -DPROTOTYPE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c a3d3_gpu.cu


Hello,

I get this error message at the start of my refinement run (mode 1):
-----------------------------
PGFIO-F-209/OPEN/unit=77/'OLD' specified for file which does not exist.
File name = /master.raid/home_master/hr80_0.par !FINPAR - Input parameter file if mode >=0

In source file card10.f, at line number 54

-----------------------------
The file is definitely there and has all the bits that I think it should have..

By advance, thank you for your help.

Hello,

I have about 200 micrographs (~200 GB) and want to do a frealign refinement on my cluster. Shall I group them all into one stack and one alignment file or is it better to keep them all in separate files and submit each of them on a separate node?
I guess it doesn't matter too much for the alignment part, but may matter quite a bit for the reconstruction part.. ?

By advance, many thanks.

Hi. I am currently using the latest non-GPU version of frealign 8 and I got an error when I was trying to do a reconstruction. The program randomly stopped at different points during the reconstruction process and gave a message "cannot seek in file.." before it terminated. I have checked the parameter file as well as the stack and they both look fine, and there is no problem when I use them in frealign 7. I am suspecting that there is actually a bug in the latest version?

Thank you very much.

Hi, I have a minor request that you put the README.txt online. I am finding myself constantly referring to it and then I have to find the frealign download directory and find the find. It would also be nice if google indexed it for people searching about frealign.

Hi,
I am trying to get the multiprocessor reconstruction to work on my cluster (just the reconstruction part, not the refinement part). In my testing, I haven't seen an appreciable improvement in the reconstruction time. I am using frealign_v8.08 with the precompiled binary frealign_v8_mp.exe. Below is my frealign job.
#!/bin/bash
#MOAB -l nodes=1:ppn=8
#MOAB -l walltime=4:00:00

export NCPUS=8

cd /panfs/storage.local/imb/stagg/sstagg/10mar29b/frealign_test

### START FREALIGN ###
frealign.exe << EOF > frealign.combine_1_8.out
I,1,F,F,F,F,0,T,F,F,0,T,4

Hi Niko,

I thought I'd try letting you know about this through this forum.

I've been setting up frealign_v8.08 for use on a new cluster. We generally use large stack files that have come from many different films. Therefore, our card 10b's might look like:

45,50000,1351,40961,41873,11.77,1
71,50000,1352,51021,51844,15.20,1
11,50000,1353,38316,39442,15.08,1
51,50000,1354,45028,45707,12.17,1
etc.
31,50000,1356,38205,39034,24.64,0