ctffind 4 Segmentation fault

Submitted by JMedeiros on Thu, 2015-07-02 09:34

Forums

ctffind & ctftilt

Hello!

I've installed ctffind 4.0.16 on my OS X workstation (version 10.9.5) where I used gfortran (gcc5 5.1.0_1) to compile it.

The program works fine when I start it from terminal with no options, however when I use --old-school-input I get:

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0 0x103f05b26
#1 0x103f050c3
#2 0x7fff832065a9
#3 0x103f93dcf
#4 0x103d64b44
#5 0x103d651a3
#6 0x103daf0a2
#7 0x103db65de
Segmentation fault: 11

Upon further investigation I noticed that it only accepts the --omp-num-threads N option, giving out segmentation faults only when using any other flags. Do you have any idea of what the cause might be?

Otherwise the program works flawlessly, but I need it to run with Relion, the the old school input is required.

If you need any more information, just let me know.

Cheers!
João Medeiros

Alexis Sat, 2015-07-04 08:43

Hello João,

Thanks for the bug report. I can reproduce this on linux with gfortran.

It may take me a while to get to the bottom of this. For now, it seems that this problem is specific to gfortran builds. Do you have access to the Intel fortran compiler? If so, please try to compile with this compiler.

If not, perhaps you could run ctffind on a linux machine and use the binaries that are available from the website?

Thanks
Alexis

JMedeiros Mon, 2015-07-06 10:07

Dear Alexis,

I was able to get the Intel fortran compiler through an institutional license and by compiling the code with it solved the issue.

Thank you for your support. If you would like me to run any further tests just let me know.

Cheers!
João Medeiros