repeated afni crash

krasmussn · September 8, 2016, 1:33pm

Good morning,
I have been having afni crash on me at various stages of viewing and attempting to save images since late yesterday evening. I have attached the terminal output and crash log from the most recent failure below. Any ideas you have on getting this fixed would be much appreciated.
Thanks!
Kate

Precompiled binary linux_xorg7_64: Jan 27 2016 (Version AFNI_16.0.01)

Thanks go to JA Bobholz for inspiration

Initializing: X11.++ AFNI is detached from terminal.
[krasmussn@ipl5 preop]$
++++++++ IMAGE SAVE SETUP WARNINGS ++++++++
++ Can’t find program mpeg_encode for Save to MPEG-1
++ Can’t find program gifsicle OR whirlgif for Save to Animated GIF
++ To disable these warnings, set environment
++ variable AFNI_IMSAVE_WARNINGS to ‘NO’.
+++++++++++++++++++++++++++++++++++++++++++
. Widgets… Input files:
session # 1 = fromCLI ==> 2 datasets
dataset count = 2
Time series = 0 files read
NLfit & NLerr= Optimizer (AFNI_NLFIM_METHOD) is SIMPLEX
NLfit & NLerr= Found 28 models
Plugins = 52 libraries read

++ WARNING: ~/.afni.log is now 43,674,857 (44 million [mega]) bytes long!

```
     (Is that you, Kevin?)
```

++ NOTE: This version of AFNI was built Jan 27 2016 ++
++ NOTE: ‘Define Markers’ is hidden: right-click ‘DataDir’ to see it
++ NOTE: you may want to consider creating a ‘.afnirc’ file in your home
directory, to control AFNI’s setup. For more details, see
http://afni.nimh.nih.gov/pub/dist/doc/program_help/README.environment.html
++ Writing one 229x193 image to file test.ppm
*+ WARNING: No whereami program in Unix path ==> no WamI button in Clusterize!

Fatal Signal 11 (SIGSEGV) received
AFNI:main
Bottom of Debug Stack
** AFNI version = AFNI_16.0.01 Compile date = Jan 27 2016
** [[Precompiled binary linux_xorg7_64: Jan 27 2016]]
** Program Death **

------ CRASH LOG ------------------------------**
Fatal Signal 11 (SIGSEGV) received
… recent internal history …
++++++drive_MCW_grapher [6]: {ENTRY (file=afni_graph.c line=4829) from AFNI_set_viewpoint
------drive_MCW_grapher [6]: EXIT} (file=afni_graph.c line=4831) to AFNI_set_viewpoint
++++++drive_MCW_grapher [6]: {ENTRY (file=afni_graph.c line=4829) from AFNI_set_viewpoint
------drive_MCW_grapher [6]: EXIT} (file=afni_graph.c line=4831) to AFNI_set_viewpoint
++++++drive_MCW_grapher [6]: {ENTRY (file=afni_graph.c line=4829) from AFNI_set_viewpoint
------drive_MCW_grapher [6]: EXIT} (file=afni_graph.c line=4831) to AFNI_set_viewpoint
++++++AFNI_process_redisplay [6]: {ENTRY (file=afni_receive.c line=645) from AFNI_set_viewpoint
------AFNI_process_redisplay [6]: EXIT} (file=afni_receive.c line=669) to AFNI_set_viewpoint
-----AFNI_set_viewpoint [5]: EXIT} (file=afni.c line=7552) to AFNI_crosshair_visible_CB
+++++AFNI_quit_CB [5]: {ENTRY (file=afni.c line=2624) from AFNI_crosshair_visible_CB
-----AFNI_quit_CB [5]: EXIT} (file=afni.c line=2639) to AFNI_crosshair_visible_CB
----AFNI_crosshair_visible_CB [4]: EXIT} (file=afni.c line=6176) to AVOPT_press_CB
—AVOPT_press_CB [3]: EXIT} (file=bbox.c line=1793) to AFNI:main
+++ISQ_drawing_EV [3]: {ENTRY (file=imseq.c line=5594) from AFNI:main
++++ISQ_show_image [4]: {ENTRY (file=imseq.c line=5267) from ISQ_drawing_EV
ISQ_show_image – putting sized_xim to screen
+++++ISQ_draw_winfo [5]: {ENTRY (file=imseq.c line=5374) from ISQ_show_image
-----ISQ_draw_winfo [5]: EXIT} (file=imseq.c line=5465) to ISQ_show_image
----ISQ_show_image [4]: EXIT} (file=imseq.c line=5361) to ISQ_drawing_EV
—ISQ_drawing_EV [3]: EXIT} (file=imseq.c line=6153) to AFNI:main
+++ISQ_drawing_EV [3]: {ENTRY (file=imseq.c line=5594) from AFNI:main
—ISQ_drawing_EV [3]: EXIT} (file=imseq.c line=6153) to AFNI:main
+++ISQ_drawing_EV [3]: {ENTRY (file=imseq.c line=5594) from AFNI:main
—ISQ_drawing_EV [3]: EXIT} (file=imseq.c line=6153) to AFNI:main
+++ISQ_drawing_EV [3]: {ENTRY (file=imseq.c line=5594) from AFNI:main
—ISQ_drawing_EV [3]: EXIT} (file=imseq.c line=6153) to AFNI:main
+++ISQ_drawing_EV [3]: {ENTRY (file=imseq.c line=5594) from AFNI:main
++++ISQ_show_bar [4]: {ENTRY (file=imseq.c line=5540) from ISQ_drawing_EV
ISQ_show_bar – putting sized_xbar to screen
----ISQ_show_bar [4]: EXIT} (file=imseq.c line=5579) to ISQ_drawing_EV
—ISQ_drawing_EV [3]: EXIT} (file=imseq.c line=6153) to AFNI:main
…
AFNI:main
** AFNI compile date = Jan 27 2016
** [[Precompiled binary linux_xorg7_64: Jan 27 2016]]
** Program Crash **

dglen · September 8, 2016, 4:05pm

A few oddities there that you might try to fix.

image conversion tools not installed
sudo yum install -y netpbm-progs libpng12
Large afni command log - delete the history
rm ~/.afni.log
whereami is missing - this is strange. See if it is really in your afni directory
ls ~/abin/whereami
If whereami is there, then your path needs to be updated to include that directory. If it isn’t, try redownloading or using another linux package (@update.afni.binaries -package linux_openmp_64)

krasmussn · September 8, 2016, 4:18pm

Thank you - it seems to be working now. I appreciate the help!

dglen · September 8, 2016, 4:28pm

Which part worked for you?

krasmussn · September 9, 2016, 1:27pm

I believe deleting the large afni command log was the trigger.

rwcox · September 9, 2016, 1:31pm

You can set environment variable AFNI_DONT_LOGFILE to YES to turn off the logging. This trick is useful in scripts if you are running a program thousands of times to test something (as I am doing right now).

krasmussn · September 9, 2016, 2:20pm

That is excellent, thank you!