Segmentation fault issue when plotting with sir_graph_ng

[julie_huang]

To whom it may concern,

The UNAFold tool is a wonderful help for my research and development.
I have recently encountered the following issue when plotting for ".ct" files using the command line. The issue happened for some ".ct" file, not all.

The linux terminal version of the tool I used is as below:
sir_graph: mfold_util 4.7

The command and error is here:

Code: Select all

/MYPATH/unafold/bin/sir_graph_ng -jpg 800 -f -lab 20 MY_SS_FILE.ct

Errors are similar to this:

Code: Select all

Input File: MY_SS_FILE.ct
Segmentation fault

Is there a way to solve the "Segmentation fault"? Especially when running multiple plotting tasks within a short period of time.

Thank you so much!

[nmarkham]

Hi Julie,

Can you post a ct file that shows this problem? I tried a few I had lying around, but none generated a SEGV even with the exact command line you used.

Thanks,
Nick

[julie_huang]

Thank you Nick for the reply!

Below is an example of a ".ct" file that had "Segmentation fault" issue

Code: Select all

22      dG = 0.376       align_fp
1       g       0       2       0       1       0       0
2       c       1       3       0       2       0       0
3       g       2       4       0       3       0       0
4       a       3       5       0       4       0       0
5       a       4       6       0       5       0       6
6       a       5       7       13      6       5       7
7       t       6       8       12      7       6       0
8       g       7       9       0       8       0       0
9       a       8       10      0       9       0       0
10      a       9       11      0       10      0       0
11      a       10      12      0       11      0       0
12      g       11      13      7       12      0       13
13      t       12      14      6       13      12      14
14      g       13      15      0       14      13      0
15      a       14      16      0       15      0       0
16      a       15      17      0       16      0       0
17      c       16      18      0       17      0       0
18      g       17      19      0       18      0       0
19      g       18      20      0       19      0       0
20      a       19      21      0       20      0       0
21      g       20      22      0       21      0       0
22      g       21      0       0       22      0       0

[nmarkham]

This is odd. I tried that file and it worked for me.

Can you tell me what version of UNAFold you have, and how you installed it?

[julie_huang]

Version as below
sir_graph: mfold_util 4.7
(UNAFold®) 3.9

Installed on a CentOS Linux release 7.9 cluster. Had to load `libgd/2.2.4` module to visualize ".ct" files.

The issue occurred when I run lots of plotting tasks in a short period of time by using a loop. Is there a restriction on how many plots can be generated in a certain period of time? Is there other ways I can by-pass this issue then?

[nmarkham]

This is puzzling. I should be clear that I am not the author of mfold_util, but I'm fairly confident there are no limitations like what you described.

I wonder if you can download this binary:

http://www.unafold.org/for-julie/sir_graph_ng

and try it in place of the one you have. It's statically linked and should produce a "core" file if it exits with a segmentation fault. (You may have to run "ulimit -c unlimited" first to get it to save the core.) If you can reproduce the error with this binary and get a core file, send it to me and I'll see if I can figure out what's going on.

[julie_huang]

Thank you so much! I am contacting our IT support department to install the binary.