CTFTILT segmentation fault

Submitted by wimhagen on Sun, 2012-09-23 14:57

Forums

ctffind & ctftilt

Hi,

I get segmentation faults when running CTFTILT on tilted 2K and 1K CCD images. With a box size of 128 everything runs fine, but when I try box size 256 I get segmentation faults on most (but not all) of the images.

CTFTILT version is 1.5 from December 3 2010. I found a couple of threads regarding this error, but am not sure what to do, so before I start bugging our IT guy: Would a newer version make a difference or am I using weird parameters?

#!/bin/csh -x
ctftilt << eof
$1
$2
2.7,200,0.07,1,0.0003007,1
256,100.0,5.0,10000,50000,1000,$3,5
eof
#

Best,

Wim Hagen
EMBL Heidelberg

niko Sun, 2012-09-23 20:10

I would try running the latest version before doing anything else. It is easy enough to download and install.

Also, you parameters seem to be a bit unusual. You seem to have entered 0.0003007 for the magnification. For the high-resolution limit of the CTF fit, you have entered 5.0. At 5 Angstrom resolution I doubt that you have any useful signal for the CTF fit. I would limit it to 10 Angstroms or so. Please download the latest version of CTFTILT and carefully go through all the parameters in the example script.

wimhagen Sat, 2012-10-06 18:39

I am trying to install latest version on my macbook running 10.7.5, gcc 4.6.2:

gfortran -O3 -s -fomit-frame-pointer -Wall -falign-functions=4 \
-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE \
-w -c ctffind3.f
gfortran -O3 -s -fomit-frame-pointer -Wall -falign-functions=4 \
-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE \
-w -c iof.f
gcc -O3 -DPROTOTYPE -Dalliant -D_FILE_OFFSET_BITS=64 \
-D_LARGEFILE_SOURCE -w -c ioc.c
gfortran -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE \
ctffind3.o iof.o ioc.o -o ctffind3.exe
Undefined symbols for architecture x86_64:
"_omp_get_num_procs_", referenced from:
_MAIN__ in ctffind3.o
"_omp_set_num_threads_", referenced from:
_MAIN__ in ctffind3.o
ld: symbol(s) not found for architecture x86_64
collect2: ld returned 1 exit status
make: *** [ctffind3.exe] Error 1

I read a number of threads on the forum but simply have no clue about all this, any advice or help is appreciated.

Best,
Wim

niko Sun, 2012-10-07 09:25

It looks like the compiler cannot find the library for OpenMP parallelization. The code inside ctffind3 and ctftilt that uses OpenMP should only be used by the compiler if the option -fopenmp is specified. Please check that this option does not appear in the Makefile you are using. Alternatively, delete the following lines in CTFFIND3:

#ifdef _OPENMP
      CALL GETENV('OMP_NUM_THREADS',NCPUS)
      READ(NCPUS,*,ERR=111,END=111)IMP
111   CONTINUE
      IF (IMP.LE.0) THEN
        CALL GETENV('NCPUS',NCPUS)
        READ(NCPUS,*,ERR=112,END=112)IMP
112     CONTINUE
      ENDIF
      IF (IMP.LE.0) THEN
        IMP=OMP_GET_NUM_PROCS()
      ENDIF
      CALL OMP_SET_NUM_THREADS(IMP)
#endif

Also delete the following lines in CTFTILT:

#ifdef _OPENMP
      CALL GETENV('OMP_NUM_THREADS',NCPUS)
      READ(NCPUS,*,ERR=111,END=111)IMP
111   CONTINUE
      IF (IMP.LE.0) THEN
        CALL GETENV('NCPUS',NCPUS)
        READ(NCPUS,*,ERR=112,END=112)IMP
112     CONTINUE
      ENDIF
      IF (IMP.LE.0) THEN
        IMP=OMP_GET_NUM_PROCS()
      ENDIF
#endif

Then try to compile CTFFIND3 and CTFTILT again.