Hi there. I am trying to install AFNI on behalf of a user of our HPC cluster. Apologies in advance because our setup has quite a few layers, and I'm guessing relies on a strong understanding of how afni interacts with an apptainer container.
In short, I have pulled the existing AFNI_24.1.22 Docker container using Apptainer instead of Docker. We offer remote desktops via noVNC. These desktops run on Rocky 9.2.
Here comes the weird part. If I run afni by first shelling into the container, then it works as expected. The windows pop up and persist. My commands and output are below:
[lexg@m3t106 blah]$ apptainer shell $AFNI_SIF
Apptainer> afni
Precompiled binary linux_ubuntu_16_64_glw_local_shared: Jun 21 2024 (Version AFNI_24.1.22 'Publius Septimius Geta')
** Version check disabled: AFNI_VERSION_CHECK forbids
Thanks go to A Clark for awe-inspiring caffeine binging
Initializing: X11[TigerVNC v 11400000].
++++++++ IMAGE SAVE SETUP WARNINGS ++++++++
++ Can't find program ffmpeg for Save to MPEG-1
++ To disable these warnings, set environment
++ variable AFNI_IMSAVE_WARNINGS to 'NO'.
+++++++++++++++++++++++++++++++++++++++++++++
. Widgets.
++ WARNING: Can't find default atlas (Brodmann_Pijn_AFNI) dataset for 'whereami_afni'!
++--------- See https://afni.nimh.nih.gov/pub/dist/data/
..... Input files:
** Searching subdirectories of './' for data
** No datasets found -- making up something **
Timeseries.1D = 0 files read
.[tc]sv data = 0 files read
Path(s) to be searched for plugins:
/opt/afni/install /opt/afni/install/../lib
Plugins = 49 libraries read
write compress= GZIP
++ AFNI is detached from terminal.
Apptainer>
++ NOTE: This version of AFNI was built Jun 21 2024 ++
++ NOTE: 'Define Markers' is hidden: right-click 'DataDir' to see it
++ NOTE: Use '-seehidden' option to see which plugins are hidden
------------------------- AFNI Startup Tip (44/112)----------------------------
Left-click in the square right of 'Etc->' in an AFNI controller will
popup a copy of the splash screen again. Another left-click there will
pop the splash window down again. Clicking in the reincarnated splash screen
may give funny results.
Right-click in that square will give a menu with some fun choices.
Middle-click in that square will popup a random insult.
-------------------------------------------------------------------------------
However, if I then run afni directly by using apptainer exec instead of apptainer shell, the windows pop up for a few seconds, but then the program crashes:
[lexg@m3t106 blah]$ apptainer exec $AFNI_SIF afni
Precompiled binary linux_ubuntu_16_64_glw_local_shared: Jun 21 2024 (Version AFNI_24.1.22 'Publius Septimius Geta')
** Version check disabled: AFNI_VERSION_CHECK forbids
Thanks go to EA DeYoe for many suggestions
Initializing: X11[TigerVNC v 11400000].
++++++++ IMAGE SAVE SETUP WARNINGS ++++++++
++ Can't find program ffmpeg for Save to MPEG-1
++ To disable these warnings, set environment
++ variable AFNI_IMSAVE_WARNINGS to 'NO'.
+++++++++++++++++++++++++++++++++++++++++++++
. Widgets.
++ WARNING: Can't find default atlas (Brodmann_Pijn_AFNI) dataset for 'whereami_afni'!
++--------- See https://afni.nimh.nih.gov/pub/dist/data/
..... Input files:
** Searching subdirectories of './' for data
** No datasets found -- making up something **
Timeseries.1D = 0 files read
.[tc]sv data = 0 files read
Path(s) to be searched for plugins:
/opt/afni/install /opt/afni/install/../lib
Plugins = 49 libraries read
write compress= GZIP
++ AFNI is detached from terminal.
[lexg@m3t106 blah]$
++ NOTE: This version of AFNI was built Jun 21 2024 ++
++ NOTE: 'Define Markers' is hidden: right-click 'DataDir' to see it
++ NOTE: Use '-seehidden' option to see which plugins are hidden
------------------------- AFNI Startup Tip (80/112)----------------------------
Fatal Signal 7 (SIGBUS) received
Last STATUS: splashed down
AFNI_startup_timeout_CB
AFNI:main
Bottom of Debug Stack
** AFNI version = AFNI_24.1.22 Compile date = Jun 21 2024
** [[Precompiled binary linux_ubuntu_16_64_glw_local_shared: Jun 21 2024]]
** 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 /home/lexg/.afni.crashlog
The crash log is:
*********------ CRASH LOG ------------------------------***********
Fatal Signal 7 (SIGBUS) received
.......... recent internal history .........................................
----MCW_popup_message [4]: EXIT} (file=xutil.c line=644) to AFNI_startup_timeout_CB {2688 ms}
++++AFNI_vedit_CB [4]: {ENTRY (file=afni_widg.c line=7702) from AFNI_startup_timeout_CB {4552 ms}
+++++AFNI_misc_CB [5]: {ENTRY (file=afni_func.c line=7265) from AFNI_vedit_CB {4552 ms}
++++++AFNI_controller_index [6]: {ENTRY (file=afni_widg.c line=6333) from AFNI_misc_CB {4552 ms}
------AFNI_controller_index [6]: EXIT} (file=afni_widg.c line=6338) to AFNI_misc_CB {4552 ms}
++++++AFNI_controller_index [6]: {ENTRY (file=afni_widg.c line=6333) from AFNI_misc_CB {4552 ms}
------AFNI_controller_index [6]: EXIT} (file=afni_widg.c line=6338) to AFNI_misc_CB {4552 ms}
-----AFNI_misc_CB [5]: EXIT} (file=afni_func.c line=7707) to AFNI_vedit_CB {4552 ms}
----AFNI_vedit_CB [4]: EXIT} (file=afni_widg.c line=7772) to AFNI_startup_timeout_CB {4552 ms}
++++AFNI_set_cursor [4]: {ENTRY (file=afni.c line=13478) from AFNI_startup_timeout_CB {4753 ms}
----AFNI_set_cursor [4]: EXIT} (file=afni.c line=13554) to AFNI_startup_timeout_CB {4758 ms}
++++AFNI_quit_CB [4]: {ENTRY (file=afni.c line=3322) from AFNI_startup_timeout_CB {4758 ms}
----AFNI_quit_CB [4]: EXIT} (file=afni.c line=3337) to AFNI_startup_timeout_CB {4758 ms}
++++AFNI_controller_index [4]: {ENTRY (file=afni_widg.c line=6333) from AFNI_startup_timeout_CB {4758 ms}
----AFNI_controller_index [4]: EXIT} (file=afni_widg.c line=6338) to AFNI_startup_timeout_CB {4758 ms}
++++AFNI_coord_filer_setup [4]: {ENTRY (file=afni_filer.c line=49) from AFNI_startup_timeout_CB {4758 ms}
+++++AFNI_controller_index [5]: {ENTRY (file=afni_widg.c line=6333) from AFNI_coord_filer_setup {4758 ms}
-----AFNI_controller_index [5]: EXIT} (file=afni_widg.c line=6338) to AFNI_coord_filer_setup {4758 ms}
----AFNI_coord_filer_setup [4]: EXIT} (file=afni_filer.c line=57) to AFNI_startup_timeout_CB {4758 ms}
++++AFNI_splashdown [4]: {ENTRY (file=afni_splash.c line=95) from AFNI_startup_timeout_CB {4758 ms}
+++++SPLASH_popup_image [5]: {ENTRY (file=afni_splash.c line=539) from AFNI_splashdown {4758 ms}
SPLASH_popup_image -- unrealizing splash window {4758 ms}
++++++drive_MCW_imseq [6]: {ENTRY (file=imseq.c line=8144) from SPLASH_popup_image {4758 ms}
+++++++ISQ_timer_stop [7]: {ENTRY (file=imseq.c line=13366) from drive_MCW_imseq {4758 ms}
-------ISQ_timer_stop [7]: EXIT} (file=imseq.c line=13370) to drive_MCW_imseq {4758 ms}
------drive_MCW_imseq [6]: EXIT} (file=imseq.c line=9068) to SPLASH_popup_image {4758 ms}
-----SPLASH_popup_image [5]: EXIT} (file=afni_splash.c line=550) to AFNI_splashdown {4758 ms}
+++++mri_free [5]: {ENTRY (file=mri_free.c line=49) from AFNI_splashdown {4758 ms}
-----mri_free [5]: EXIT} (file=mri_free.c line=50) to AFNI_splashdown {4758 ms}
----AFNI_splashdown [4]: EXIT} (file=afni_splash.c line=121) to AFNI_startup_timeout_CB {4758 ms}
AFNI_startup_timeout_CB -- splashed down {4758 ms}
............................................................................
Last STATUS: splashed down
AFNI_startup_timeout_CB
AFNI:main
** AFNI compile date = Jun 21 2024
** [[Precompiled binary linux_ubuntu_16_64_glw_local_shared: Jun 21 2024]]
** Program Crash **
Here is the output of a system check:
[lexg@m3t106 blah]$ apptainer exec $AFNI_SIF afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit ELF
cpu type: x86_64
system: Linux
release: 5.14.0-284.25.1.el9_2.x86_64
version: #1 SMP PREEMPT_DYNAMIC Wed Aug 2 14:53:30 UTC 2023
distribution: Ubuntu 18.04 bionic
number of CPUs: 4
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni :
: AFNI_24.1.22 'Publius Septimius Geta'
AFNI_version.txt : AFNI_24.1.22, linux_ubuntu_16_64_glw_local_shared, Jun 21 2024, local
which python :
which R :
instances of various programs found in PATH:
afni : 1 (/opt/afni/install/afni)
R : 1 (/usr/bin/R)
python : 1 (/usr/bin/python3.6)
python2 : 0
python3 : 1 (/usr/bin/python3.6)
** have python3 but not python2
testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success
uber_subject.py : success
3dMVM : FAILURE
Error in library(data.table) : there is no package called \u2018data.table\u2019
Calls: source ... suppressPackageStartupMessages -> withCallingHandlers -> library
Execution halted
have failures, testing programs under implied /opt/afni/install...
afni : success
suma : success
3dSkullStrip : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success
uber_subject.py : success
3dMVM : FAILURE
Error in library(data.table) : there is no package called \u2018data.table\u2019
Calls: source ... suppressPackageStartupMessages -> withCallingHandlers -> library
Execution halted
------------------------ dependent program tests -------------------------
checking for dependent programs...
which tcsh :
which Xvfb :
checking for R packages...
rPkgsInstall -pkgs ALL -check : FAILURE
oo Warning:
These packages are not installed on the computer: afex!
These packages are not installed on the computer: phia!
These packages are not installed on the computer: snow!
These packages are not installed on the computer: lme4!
These packages are not installed on the computer: lmerTest!
These packages are not installed on the computer: gamm4!
These packages are not installed on the computer: data.table!
These packages are not installed on the computer: paran!
These packages are not installed on the computer: psych!
These packages are not installed on the computer: brms!
These packages are not installed on the computer: corrplot!
These packages are not installed on the computer: metafor!
R RHOME : /usr/lib/R
------------------------------ python libs -------------------------------
++ module loaded: matplotlib.pyplot
module file : /opt/user_pip_packages/lib/python3.6/site-packages/matplotlib/pyplot.py
matplotlib version : 3.3.4
** failed to load module flask
-- flask is not required, but is desirable
** failed to load module flask_cors
-- flask_cors is not required, but is desirable
-------------------------------- env vars --------------------------------
PATH = /opt/afni/src/../install:/opt/cmake/cmake-3.14.7-Linux-x86_64/bin:/opt/user_pip_packages/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
PYTHONPATH = /usr/local/strudel2/submit
R_LIBS =
LD_LIBRARY_PATH = /.singularity.d/libs
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =
CONDA_SHLVL =
CONDA_DEFAULT_ENV =
----------------------------- eval dot files -----------------------------
----------- AFNI $HOME files -----------
.afnirc : found
.sumarc : missing
.afni/help/all_progs.COMP : missing
--------- shell startup files ----------
** error: have no found abin, so please use -dir_bin
------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : missing afni_handouts
atlas : did not find TT_N27+tlrc
------------------------------ OS specific -------------------------------
have Ubuntu system: Ubuntu 18.04 bionic
========================= summary, please fix: =========================
* just be aware: login shell 'bash', but our code examples use 'tcsh'
* missing program: afni
* missing program: python
* missing program: R
* failure under initial "AFNI and related program tests"
* AFNI programs show FAILURE
* consider adding /opt/afni/install to your PATH
* missing program: tcsh
* missing program: Xvfb
* missing R packages (see rPkgsInstall)
* please run: "suma -update_env" for .sumarc
* please run: apsearch -update_all_afni_help
* failure running init_user_dotfiles.py -test
* insufficient data for AFNI bootcamp
(see "Prepare for Bootcamp" on install pages)
* possibly missing atlases
There is zero difference between running this check with exec vs shell.
I should note that the user has reported that the non-GUI executables work just fine via apptainer exec. I compared printenv | sort when running with shell vs exec and saw no significant differences,
[lexg@m3-login3 blah]$ diff *.txt
15c15
< APPTAINER_COMMAND=exec
---
> APPTAINER_COMMAND=shell
43d42
< eval ${which_declare} ) | /usr/bin/which --tty-only --read-alias --read-functions --show-tilde --show-dot $@
44a44
> eval ${which_declare} ) | /usr/bin/which --tty-only --read-alias --read-functions --show-tilde --show-dot $@
100d99
< PROMPT_COMMAND=PS1="Apptainer> "; unset PROMPT_COMMAND
118c117
< SHLVL=3
---
> SHLVL=5
170c169
< _=/usr/bin/apptainer
---
> _=/usr/bin/printenv
and I don't believe the filesystem bindings should differ between the two.
I also set export AFNI_TRACE=Y and here is the tail of the output before it crashes:
++++++get_session_dset [6]: {ENTRY (file=thd_warp_tables.c line=48) from set_session_dset {4051 ms}
------get_session_dset [6]: EXIT} (file=thd_warp_tables.c line=67) to set_session_dset {4051 ms}
-----set_session_dset [5]: EXIT} (file=thd_warp_tables.c line=161) to AFNI_read_inputs {4051 ms}
+++++set_session_dset [5]: {ENTRY (file=thd_warp_tables.c line=81) from AFNI_read_inputs {4051 ms}
++++++get_session_dset [6]: {ENTRY (file=thd_warp_tables.c line=48) from set_session_dset {4051 ms}
------get_session_dset [6]: EXIT} (file=thd_warp_tables.c line=67) to set_session_dset {4051 ms}
-----set_session_dset [5]: EXIT} (file=thd_warp_tables.c line=161) to AFNI_read_inputs {4051 ms}
+++++set_session_dset [5]: {ENTRY (file=thd_warp_tables.c line=81) from AFNI_read_inputs {4051 ms}
-----set_session_dset [5]: EXIT} (file=thd_warp_tables.c line=141) to AFNI_read_inputs {4051 ms}
+++++set_session_dset [5]: {ENTRY (file=thd_warp_tables.c line=81) from AFNI_read_inputs {4051 ms}
++++++get_session_dset [6]: {ENTRY (file=thd_warp_tables.c line=48) from set_session_dset {4051 ms}
------get_session_dset [6]: EXIT} (file=thd_warp_tables.c line=67) to set_session_dset {4051 ms}
-----set_session_dset [5]: EXIT} (file=thd_warp_tables.c line=161) to AFNI_read_inputs {4051 ms}
+++++set_session_dset [5]: {ENTRY (file=thd_warp_tables.c line=81) from AFNI_read_inputs {4051 ms}
++++++get_session_dset [6]: {ENTRY (file=thd_warp_tables.c line=48) from set_session_dset {4051 ms}
------get_session_dset [6]: EXIT} (file=thd_warp_tables.c line=67) to set_session_dset {4051 ms}
-----set_session_dset [5]: EXIT} (file=thd_warp_tables.c line=161) to AFNI_read_inputs {4051 ms}
+++++set_session_dset [5]: {ENTRY (file=thd_warp_tables.c line=81) from AFNI_read_inputs {4051 ms}
-----set_session_dset [5]: EXIT} (file=thd_warp_tables.c line=141) to AFNI_read_inputs {4051 ms}
+++++set_session_dset [5]: {ENTRY (file=thd_warp_tables.c line=81) from AFNI_read_inputs {4051 ms}
++++++get_session_dset [6]: {ENTRY (file=thd_warp_tables.c line=48) from set_session_dset {4051 ms}
------get_session_dset [6]: EXIT} (file=thd_warp_tables.c line=67) to set_session_dset {4051 ms}
-----set_session_dset [5]: EXIT} (file=thd_warp_tables.c line=161) to AFNI_read_inputs {4051 ms}
+++++set_session_dset [5]: {ENTRY (file=thd_warp_tables.c line=81) from AFNI_read_inputs {4051 ms}
++++++get_session_dset [6]: {ENTRY (file=thd_warp_tables.c line=48) from set_session_dset {4051 ms}
------get_session_dset [6]: EXIT} (file=thd_warp_tables.c line=67) to set_session_dset {4051 ms}
-----set_session_dset [5]: EXIT} (file=thd_warp_tables.c line=161) to AFNI_read_inputs {4051 ms}
Fatal Signal 7 (SIGBUS) received
AFNI_read_inputs
MAIN_workprocess
AFNI:main
Bottom of Debug Stack
** AFNI version = AFNI_24.1.22 Compile date = Jun 21 2024
** [[Precompiled binary linux_ubuntu_16_64_glw_local_shared: Jun 21 2024]]
** 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 /home/lexg/.afni.crashlog
Obviously when running with shell, it gets much further and I instead see
-----set_session_dset [5]: EXIT} (file=thd_warp_tables.c line=161) to AFNI_read_inputs {3932 ms}
+++++set_session_dset [5]: {ENTRY (file=thd_warp_tables.c line=81) from AFNI_read_inputs {3932 ms}
-----set_session_dset [5]: EXIT} (file=thd_warp_tables.c line=141) to AFNI_read_inputs {3932 ms}
+++++set_session_dset [5]: {ENTRY (file=thd_warp_tables.c line=81) from AFNI_read_inputs {3932 ms}
++++++get_session_dset [6]: {ENTRY (file=thd_warp_tables.c line=48) from set_session_dset {3932 ms}
------get_session_dset [6]: EXIT} (file=thd_warp_tables.c line=67) to set_session_dset {3932 ms}
-----set_session_dset [5]: EXIT} (file=thd_warp_tables.c line=161) to AFNI_read_inputs {3932 ms}
+++++set_session_dset [5]: {ENTRY (file=thd_warp_tables.c line=81) from AFNI_read_inputs {3932 ms}
++++++get_session_dset [6]: {ENTRY (file=thd_warp_tables.c line=48) from set_session_dset {3932 ms}
------get_session_dset [6]: EXIT} (file=thd_warp_tables.c line=67) to set_session_dset {3932 ms}
-----set_session_dset [5]: EXIT} (file=thd_warp_tables.c line=161) to AFNI_read_inputs {3932 ms}
+++++THD_dummy_N27 [5]: {ENTRY (file=thd_dumdset.c line=5858) from AFNI_read_inputs {3932 ms}
++++++EDIT_empty_copy [6]: {ENTRY (file=edt_emptycopy.c line=29) from THD_dummy_N27 {3932 ms}
+++++++THD_init_diskptr_names [7]: {ENTRY (file=thd_initdkptr.c line=27) from EDIT_empty_copy {3932 ms}
-------THD_init_diskptr_names [7]: EXIT} (file=thd_initdkptr.c line=148) to EDIT_empty_copy {3932 ms}
+++++++THD_init_datablock_brick [7]: {ENTRY (file=thd_initdblk.c line=1206) from EDIT_empty_copy {3932 ms}
THD_init_datablock_brick -- making dblk->brick_bytes {3932 ms}
THD_init_datablock_brick -- making dblk->brick_fac {3932 ms}
THD_init_datablock_brick -- making new dblk->brick {3932 ms}
THD_init_datablock_brick -- starting sub-brick creations {3932 ms}
++++++++mri_new_7D_generic [8]: {ENTRY (file=mri_new.c line=48) from THD_init_datablock_brick {3932 ms}
mri_new_7D_generic -- nx=2 ny=2 nz=2 kind=1 bytes=16 (null) {3932 ms}
--------mri_new_7D_generic [8]: EXIT} (file=mri_new.c line=143) to THD_init_datablock_brick {3932 ms}
THD_init_datablock_brick -- exiting {3932 ms}
-------THD_init_datablock_brick [7]: EXIT} (file=thd_initdblk.c line=1268) to EDIT_empty_copy {3932 ms}
------EDIT_empty_copy [6]: EXIT} (file=edt_emptycopy.c line=227) to THD_dummy_N27 {3932 ms}
I'm really at a loss for what's going wrong here or how to resolve it. Some ideas I've had are:
- I see that
afniis launching TigerVNC inside the container. I don't know how this interacts with noVNC outside the container. - I see that
afni"detaches from the terminal". I wondered if this could explain the difference betweenshellvsexec, since detaching inshellstill leaves me inside the container shell, whereas detaching inexecmay be taking me outside the container. I could not find any environment variables to disable this detachment though, and it may be irrelevant anyway. - The container still seems to be missing lots of dependencies, mainly R libraries, but this doesn't seem to explain the discrepancy between
shellandexec.
Apologies for the barrage of information, just trying to be thorough. Would very much appreciate anyone's input on this!