SUMA ERROR

Liumengxing · November 27, 2016, 9:24am

Hi afni group,
Everything works fine until yesterday, but I cannot call what I have done could make suma crashed…
When I start suma in terminal with command : suma
the error pops up:



oo     Warning SUMA_XErrHandler (SUMA_display.c:4147):
Intercepted X11 error: GLXBadContext
Will attempt to proceed but trouble might ensue.
++     Notice SUMA_XErrHandler (SUMA_display.c:4148 @17:45:47):
Trace At Xerr
     SUMA_XErrHandler
    SUMA_glXMakeCurrent
   SUMA_handleRedisplay
  suma
 Bottom of Debug Stack
oo     Warning SUMA_XErrHandler (SUMA_display.c:4147):
Intercepted X11 error: 0
Will attempt to proceed but trouble might ensue.
++     Notice SUMA_XErrHandler (SUMA_display.c:4148 @17:45:47):
Trace At Xerr
     SUMA_XErrHandler
    SUMA_glXMakeCurrent
   SUMA_handleRedisplay
  suma
 Bottom of Debug Stack
--     Error SUMA_glXMakeCurrent (SUMA_display.c:341):
Failed in glXMakeCurrent.

SUMA_glXMakeCurrent (via SUMA_GL_ERRS): Looking for OpenGL errors ...
SUMA_glXMakeCurrent: No errors found.
--     Error SUMA_glXMakeCurrent (SUMA_display.c:343):
Called from SUMA_glXMakeCurrent
    SUMA_glXMakeCurrent
   SUMA_handleRedisplay
  suma
 Bottom of Debug Stack
--     Error SUMA_handleRedisplay (SUMA_display.c:428):
Failed in SUMA_glXMakeCurrent.

oo     Warning SUMA_XErrHandler (SUMA_display.c:4147):
Intercepted X11 error: GLXBadContext
Will attempt to proceed but trouble might ensue.
++     Notice SUMA_XErrHandler (SUMA_display.c:4148 @17:45:47):
Trace At Xerr
     SUMA_XErrHandler
    SUMA_glXMakeCurrent
   SUMA_handleRedisplay
  suma
 Bottom of Debug Stack
oo     Warning SUMA_XErrHandler (SUMA_display.c:4147):
Intercepted X11 error: 0
Will attempt to proceed but trouble might ensue.
++     Notice SUMA_XErrHandler (SUMA_display.c:4148 @17:45:47):
Trace At Xerr
     SUMA_XErrHandler
    SUMA_glXMakeCurrent
   SUMA_handleRedisplay
  suma
 Bottom of Debug Stack
--     Error SUMA_glXMakeCurrent (SUMA_display.c:341):
Failed in glXMakeCurrent.

SUMA_glXMakeCurrent (via SUMA_GL_ERRS): Looking for OpenGL errors ...
SUMA_glXMakeCurrent: No errors found.
--     Error SUMA_glXMakeCurrent (SUMA_display.c:343):
Called from SUMA_glXMakeCurrent
    SUMA_glXMakeCurrent
   SUMA_handleRedisplay
  suma
 Bottom of Debug Stack
--     Error SUMA_handleRedisplay (SUMA_display.c:428):
Failed in SUMA_glXMakeCurrent.

oo     Warning SUMA_XErrHandler (SUMA_display.c:4147):
Intercepted X11 error: GLXBadContext
Will attempt to proceed but trouble might ensue.
++     Notice SUMA_XErrHandler (SUMA_display.c:4148 @17:45:47):
Trace At Xerr
     SUMA_XErrHandler
    SUMA_glXMakeCurrent
   SUMA_handleRedisplay
  suma
 Bottom of Debug Stack
oo     Warning SUMA_XErrHandler (SUMA_display.c:4147):
Intercepted X11 error: 0
Will attempt to proceed but trouble might ensue.
++     Notice SUMA_XErrHandler (SUMA_display.c:4148 @17:45:47):
Trace At Xerr
     SUMA_XErrHandler
    SUMA_glXMakeCurrent
   SUMA_handleRedisplay
  suma
 Bottom of Debug Stack
--     Error SUMA_glXMakeCurrent (SUMA_display.c:341):
Failed in glXMakeCurrent.

SUMA_glXMakeCurrent (via SUMA_GL_ERRS): Looking for OpenGL errors ...
SUMA_glXMakeCurrent: No errors found.
--     Error SUMA_glXMakeCurrent (SUMA_display.c:343):
Called from SUMA_glXMakeCurrent
    SUMA_glXMakeCurrent
   SUMA_handleRedisplay
  suma
 Bottom of Debug Stack
--     Error SUMA_handleRedisplay (SUMA_display.c:428):
Failed in SUMA_glXMakeCurrent.

oo     Warning SUMA_XErrHandler (SUMA_display.c:4147):
Intercepted X11 error: GLXBadContext
Will attempt to proceed but trouble might ensue.
++     Notice SUMA_XErrHandler (SUMA_display.c:4148 @17:45:47):
Trace At Xerr
     SUMA_XErrHandler
    SUMA_glXMakeCurrent
   SUMA_handleRedisplay
  suma
 Bottom of Debug Stack
oo     Warning SUMA_XErrHandler (SUMA_display.c:4147):
Intercepted X11 error: 0
Will attempt to proceed but trouble might ensue.
++     Notice SUMA_XErrHandler (SUMA_display.c:4148 @17:45:47):
Trace At Xerr
     SUMA_XErrHandler
    SUMA_glXMakeCurrent
   SUMA_handleRedisplay
  suma
 Bottom of Debug Stack
--     Error SUMA_glXMakeCurrent (SUMA_display.c:341):
Failed in glXMakeCurrent.

SUMA_glXMakeCurrent (via SUMA_GL_ERRS): Looking for OpenGL errors ...
SUMA_glXMakeCurrent: No errors found.
--     Error SUMA_glXMakeCurrent (SUMA_display.c:343):
Called from SUMA_glXMakeCurrent
    SUMA_glXMakeCurrent
   SUMA_handleRedisplay
  suma
 Bottom of Debug Stack
--     Error SUMA_handleRedisplay (SUMA_display.c:428):
Failed in SUMA_glXMakeCurrent.

oo     Warning SUMA_XErrHandler (SUMA_display.c:4147):
Intercepted X11 error: GLXBadContext
Will attempt to proceed but trouble might ensue.
++     Notice SUMA_XErrHandler (SUMA_display.c:4148 @17:45:47):
Trace At Xerr
     SUMA_XErrHandler
    SUMA_glXMakeCurrent
   SUMA_handleRedisplay
  suma
 Bottom of Debug Stack
oo     Warning SUMA_XErrHandler (SUMA_display.c:4147):
Intercepted X11 error: 0
Will attempt to proceed but trouble might ensue.
++     Notice SUMA_XErrHandler (SUMA_display.c:4148 @17:45:47):
Trace At Xerr
     SUMA_XErrHandler
    SUMA_glXMakeCurrent
   SUMA_handleRedisplay
  suma
 Bottom of Debug Stack
--     Error SUMA_glXMakeCurrent (SUMA_display.c:341):
Failed in glXMakeCurrent.

SUMA_glXMakeCurrent (via SUMA_GL_ERRS): Looking for OpenGL errors ...
SUMA_glXMakeCurrent: No errors found.
--     Error SUMA_glXMakeCurrent (SUMA_display.c:343):
Called from SUMA_glXMakeCurrent
    SUMA_glXMakeCurrent
   SUMA_handleRedisplay
  suma
 Bottom of Debug Stack
--     Error SUMA_handleRedisplay (SUMA_display.c:428):
Failed in SUMA_glXMakeCurrent.

oo     Warning SUMA_XErrHandler (SUMA_display.c:4147):
Intercepted X11 error: GLXBadContext
Will attempt to proceed but trouble might ensue.
++     Notice SUMA_XErrHandler (SUMA_display.c:4148 @17:45:47):
Trace At Xerr
     SUMA_XErrHandler
    SUMA_glXMakeCurrent
   SUMA_handleRedisplay
  suma
 Bottom of Debug Stack
oo     Warning SUMA_XErrHandler (SUMA_display.c:4147):
Intercepted X11 error: 0
Will attempt to proceed but trouble might ensue.
++     Notice SUMA_XErrHandler (SUMA_display.c:4148 @17:45:47):
Trace At Xerr
     SUMA_XErrHandler
    SUMA_glXMakeCurrent
   SUMA_handleRedisplay
  suma
 Bottom of Debug Stack
--     Error SUMA_glXMakeCurrent (SUMA_display.c:341):
Failed in glXMakeCurrent.

SUMA_glXMakeCurrent (via SUMA_GL_ERRS): Looking for OpenGL errors ...
SUMA_glXMakeCurrent: No errors found.
--     Error SUMA_glXMakeCurrent (SUMA_display.c:343):
Called from SUMA_glXMakeCurrent
    SUMA_glXMakeCurrent
   SUMA_handleRedisplay
  suma
 Bottom of Debug Stack
--     Error SUMA_handleRedisplay (SUMA_display.c:428):
Failed in SUMA_glXMakeCurrent.

ptaylor · November 27, 2016, 1:45pm

Hi-

It would help to know what system you are using and your exact input command (I’m not sure if it was only “$ suma” or something else). The first part can best be answered by pasting the results of afni_system_check:


$ afni_system_check.py -check_all

Note that if you are using Mac Sierra, then this might be of use:
https://afni.nimh.nih.gov/afni/community/board/read.php?1,152998,152999#msg-152999
but it would be good to see the system check.

–pt

Liumengxing · November 27, 2016, 2:12pm

the input command is only “suma”, and “suma -spec xx.spec -sv xxxx.nii.gz” also report the same error
I’m using ssh to running suma in a remote server here are the stdout of afni_system_check.py
[max@admin1 ~]$ afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 3.10.0-327.el7.x86_64
version: #1 SMP Thu Nov 19 22:10:57 UTC 2015
distribution: CentOS Linux 7.2.1511 Core
number of CPUs: 12
apparent login shell: csh
shell RC file: .cshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /public/software/afni/afni
afni version : Precompiled binary linux_openmp_64: Nov 23 2016
AFNI_version.txt : AFNI_16.3.13, linux_openmp_64, Nov 23 2016
which python : /usr/bin/python
python version : 2.7.5
which R : /public/software/R/3.3.0/gnu/bin/R
R version : R version 3.3.0 (2016-05-03) – “Supposedly Educational”
which tcsh : /usr/bin/tcsh

instances of various programs found in PATH:
afni : 1 (/public/software/afni/afni)
R : 1 (/public/software/R/3.3.0/gnu/bin/R)
python : 1 (/usr/bin/python2.7)

testing ability to start various programs…
afni : success
suma : success
3dSkullStrip : success
uber_subject.py : success
3dAllineate : success
3dRSFC : success
SurfMesh : success

checking for R packages…
rPkgsInstall -pkgs ALL -check : FAILURE

    oo Warning: 
       These packages are not installed on the computer: paran!
    These packages are not installed on the computer: psych!

checking for $HOME files…
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : missing

------------------------------ python libs -------------------------------
++ module ‘PyQt4’ found at /usr/lib64/python2.7/site-packages/PyQt4
++ module loaded: PyQt4

-------------------------------- env vars --------------------------------
PATH = /public/software/freesurfer/bin:/public/software/freesurfer/fsfast/bin:/public/software/freesurfer/tktools:/public/software/freesurfer/mni/bin:/usr/lib64/qt-3.3/bin:/public/home/max/perl5/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/public/software/MATLAB/R2015b/bin:/public/software/afni:/public/software/R/3.3.0/gnu/bin/

PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =

------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing suma_demo
data dir : missing FATCAT_DEMO
data dir : missing afni_handouts
atlas : found TT_N27+tlrc under /public/software/afni

------------------------------ OS specific -------------------------------
which yum : /usr/bin/yum
yum version : 3.4.3

============================ summary comments ============================

‘afni’ executable is owned by root
missing R packages (see rPkgsInstall)
consider running: apsearch -update_all_afni_help
insufficient data for AFNI bootcamp

[max@admin1 ~]$

dglen · November 29, 2016, 8:20am

If glxinfo doesn’t work also, but it does work with “sudo glxinfo”, try the simple recommendations here:

https://bbs.archlinux.org/viewtopic.php?id=199463

Liumengxing · November 29, 2016, 11:41am

I think my situation differs from that one
as max
[max@admin1 ~]$ glxinfo
name of display: localhost:12.0
libGL error: No matching fbConfigs or visuals found
libGL error: failed to load driver: swrast
X Error of failed request: GLXBadContext
Major opcode of failed request: 154 (GLX)
Minor opcode of failed request: 6 (X_GLXIsDirect)
Serial number of failed request: 46
Current serial number in output stream: 45

as root
[root@admin1 ~]# glxinfo
name of display: localhost:13.0
libGL error: No matching fbConfigs or visuals found
libGL error: failed to load driver: swrast
X Error of failed request: GLXBadContext
Major opcode of failed request: 154 (GLX)
Minor opcode of failed request: 6 (X_GLXIsDirect)
Serial number of failed request: 46
Current serial number in output stream: 45

sudo
[root@admin1 ~]# sudo glxinfo
name of display: localhost:13.0
libGL error: No matching fbConfigs or visuals found
libGL error: failed to load driver: swrast
X Error of failed request: GLXBadContext
Major opcode of failed request: 154 (GLX)
Minor opcode of failed request: 6 (X_GLXIsDirect)
Serial number of failed request: 46
Current serial number in output stream: 45

dglen · November 30, 2016, 9:24am

Try installing OpenGL drivers with these commands (use the package manager command for your system)

yum install mesa-libGL
yum install mesa-libGL-devel

Liumengxing · November 30, 2016, 11:09am

[root@admin1 ~]# yum install mesa-libGL
Loaded plugins: aliases, changelog, fastestmirror, kabi, langpacks, tmprepo,
: verify, versionlock
Loading support for Red Hat kernel ABI
Loading mirror speeds from cached hostfile
Package mesa-libGL-10.6.5-3.20150824.el7.x86_64 already installed and latest version
Nothing to do
[root@admin1 ~]# yum install mesa-libGL-devel
Loaded plugins: aliases, changelog, fastestmirror, kabi, langpacks, tmprepo,
: verify, versionlock
Loading support for Red Hat kernel ABI
Loading mirror speeds from cached hostfile
Package mesa-libGL-devel-10.6.5-3.20150824.el7.x86_64 already installed and latest version
Nothing to do
[root@admin1 ~]#

Liumengxing · November 30, 2016, 1:39pm

I have tried log in the server with MobaXterm in Windows, and SUMA works fine!!! ( I usually log in remote server in Ubuntu with system terminal, while suma failed couple days ago)
So now i am confused, whether the source of the problem is in remote server or in my local machine Ubuntu

Hope it will give some thoughts.

Liumengxing · November 30, 2016, 1:47pm

ok now i figured out it might be due to the graphic card driver in my local machine, when i switch to Intel GC, ssh to remote server and suma works fine!!! While if I use Nvi card, it doesn’t.
so now i will try to find a new driver for my Nvi graphic card.
Anyway, thanks for your time Daniel!!!