macos_10.12_local on Catalina

AFNI Message Board
1

Hi AFNI experts,

I have a Mac mini with new installation of Catalina. I downloaded the precompiled macos_10.12_local.tgz and unpacked it to /usr/local/.
When I try to start afni, this is what I get. Please help.

Fatal Signal 11 (SIGSEGV) received
ISQ_record_button
open_MCW_imseq
SPLASH_popup_image
AFNI_splashup
MAIN_workprocess
AFNI:main
Bottom of Debug Stack
** AFNI version = AFNI_19.3.13 Compile date = Nov 19 2019
** [[Precompiled binary macos_10.12_local: Nov 19 2019]]
** Program Death **
** If you report this crash to the AFNI message board,
** please copy the error messages EXACTLY, and give
** the command line you used to run the program, and
** any other information needed to repeat the problem.
** You may later be asked to upload data to help debug.
** Crash log is appended to file /Users/hnladmin/.afni.crashlog

And here is what in the crashlog:------ CRASH LOG ------------------------------**
Fatal Signal 11 (SIGSEGV) received
… recent internal history …
-------AFNI_process_environ [7]: EXIT} (file=afni_environ.c line=175) to open_MCW_imseq {84 ms}
+++++++mri_free [7]: {ENTRY (file=mri_free.c line=49) from open_MCW_imseq {84 ms}
mri_free – call killpurge {84 ms}
++++++++mri_killpurge [8]: {ENTRY (file=mri_purger.c line=259) from mri_free {84 ms}
mri_killpurge – check if im==NULL ptr=0x7fbaf3406e20
mri_killpurge – can’t killpurge NULL fname! {84 ms}
--------mri_killpurge [8]: EXIT} (file=mri_purger.c line=270) to mri_free {84 ms}
mri_free – free ptr {84 ms}
mri_free – free im {84 ms}
-------mri_free [7]: EXIT} (file=mri_free.c line=67) to open_MCW_imseq {84 ms}
+++++++AFNI_process_environ [7]: {ENTRY (file=afni_environ.c line=155) from open_MCW_imseq {84 ms}
++++++++AFNI_suck_file [8]: {ENTRY (file=afni_environ.c line=64) from AFNI_process_environ {84 ms}
--------AFNI_suck_file [8]: EXIT} (file=afni_environ.c line=73) to AFNI_process_environ {84 ms}
-------AFNI_process_environ [7]: EXIT} (file=afni_environ.c line=175) to open_MCW_imseq {84 ms}
+++++++AFNI_process_environ [7]: {ENTRY (file=afni_environ.c line=155) from open_MCW_imseq {84 ms}
++++++++AFNI_suck_file [8]: {ENTRY (file=afni_environ.c line=64) from AFNI_process_environ {84 ms}
--------AFNI_suck_file [8]: EXIT} (file=afni_environ.c line=73) to AFNI_process_environ {84 ms}
-------AFNI_process_environ [7]: EXIT} (file=afni_environ.c line=175) to open_MCW_imseq {84 ms}
+++++++AFNI_process_environ [7]: {ENTRY (file=afni_environ.c line=155) from open_MCW_imseq {84 ms}
++++++++AFNI_suck_file [8]: {ENTRY (file=afni_environ.c line=64) from AFNI_process_environ {84 ms}
--------AFNI_suck_file [8]: EXIT} (file=afni_environ.c line=73) to AFNI_process_environ {84 ms}
-------AFNI_process_environ [7]: EXIT} (file=afni_environ.c line=175) to open_MCW_imseq {84 ms}
+++++++AFNI_process_environ [7]: {ENTRY (file=afni_environ.c line=155) from open_MCW_imseq {90 ms}
++++++++AFNI_suck_file [8]: {ENTRY (file=afni_environ.c line=64) from AFNI_process_environ {90 ms}
--------AFNI_suck_file [8]: EXIT} (file=afni_environ.c line=73) to AFNI_process_environ {90 ms}
-------AFNI_process_environ [7]: EXIT} (file=afni_environ.c line=175) to open_MCW_imseq {90 ms}
+++++++AFNI_process_environ [7]: {ENTRY (file=afni_environ.c line=155) from open_MCW_imseq {90 ms}
++++++++AFNI_suck_file [8]: {ENTRY (file=afni_environ.c line=64) from AFNI_process_environ {90 ms}
--------AFNI_suck_file [8]: EXIT} (file=afni_environ.c line=73) to AFNI_process_environ {90 ms}
-------AFNI_process_environ [7]: EXIT} (file=afni_environ.c line=175) to open_MCW_imseq {90 ms}
+++++++ISQ_record_button [7]: {ENTRY (file=imseq.c line=10986) from open_MCW_imseq {91 ms}
…
ISQ_record_button
open_MCW_imseq
SPLASH_popup_image
AFNI_splashup
MAIN_workprocess
AFNI:main
** AFNI compile date = Nov 19 2019
** [[Precompiled binary macos_10.12_local: Nov 19 2019]]
** Program Crash **

Thanks,
George

2

Hi-

We haven’t been able to look in detail at changes that Mac OS 10.15 (Catalina) might have made, with regards to running/loading AFNI. There do tend to be some fun surprises with each of their updates…

However, in terms of installing AFNI, have you gone through the instructions here? These have been validated for Mac versions up through 10.14, but this would be the best place to start, esp. in terms of dependencies:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/install_instructs/steps_mac.html

Also, could you send the results of your system check:


afni_system_check.py -check_all

?

thanks,
pt

3

Hi pt,
I think it’s the DYLD_LIBRARY_PATH… it runs after I set it correctly.
Thanks.
George

4

Hi, George-

Great, glad that sorted it. Please let us know if you run into any quirks using AFNI on Catalina (and if you don’t run into any in the near-ish future, that would also be useful feedback).

thanks,
pt