Re: [Freesurfer] OpenGL link errors

[Hoopes, Andrew]

Hi, I’ve responded to your issue via the GitHub page, but I’ll post my response 
here for the records:

It looks like your compilation is missing the -lGLU -lGL library flags. You 
should check mris_show/Makefile to make sure that GL_LIBS and GLU_LIBS have 
been set:

grep -e GLU_LIBS -e GL_LIBS mris_show/Makefile

If not, it's possible that you just need to install these libs with "yum 
install mesa-libGL-devel mesa-libGLU-devel" and reconfigure. You can also check 
this by inspecting the configure output for "GL found" and "GLu found"

best,
Andrew

On Dec 22, 2017, at 12:04 PM, Melvin Robinson 
mailto:mrobin...@uttyler.edu>> wrote:

I posted this to the Freesurfer github site, but didn't exactly know if that 
was the most appropriate place.

The Freesurfer build fails at this command:
libtool: link: g++ -fdata-sections -ffunction-sections -Wl,--gc-sections 
-Wl,-Map -Wl,ld_map.txt -Wl,--no-demangle -o mris_show mris_show.o 
/usr/lib64/libuuid.so 
-L/home/melrobin/packages/centos6-x86_64-packages/qt/current/lib -L/usr/lib64
-L/usr/X11R6/lib64 
-L/home/melrobin/packages/centos6-x86_64-packages//mni/current/lib 
-L/home/melrobin/packages/centos6-x86_64-packages//vxl/current/lib 
-L/home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit
 ../utils/libutils.a ../minc_substitute/libminc_substitute.a 
../fsgdf/libfsgdf.a ../rgb/librgb.a ../unix/libunix.a ../dicom/libdicom.a 
../hipsstubs/libhipsstubs.a ../log/liblog.a ../xml2/libxml2.a ../jpeg/libjpeg.a 
../tiff/libtiff.a ../expat/libexpat.a ../glut/libglut.a -L/lib64 -lX11 -lXmu 
/home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libITKIO.a
 
/home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libITKAlgorithms.a
 
/home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libITKCommon.a
 
/home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libITKNumerics.a
 
/home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libITKMetaIO.a
 
/home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libITKniftiio.a
 
/home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libITKNrrdIO.a
 
/home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libitkpng.a
 
/home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libitksys.a
 
/home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libitktiff.a
 
/home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libitkv3p_netlib.a
 
/home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libitkzlib.a
 
/home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libitkgdcm.a
 
/home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libitkopenjpeg.a
 
/home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libitkjpeg8.a
 
/home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libitkjpeg12.a
 
/home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libitkjpeg16.a
 
/home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libITKDICOMParser.a
 -lz -lm -lcrypt -ldl -lpthread 
/home/melrobin/packages/centos6-x86_64-packages//mni/current/lib/libvolume_io.a 
/home/melrobin/packages/centos6-x86_64-packages//mni/current/lib/libminc.a 
/home/melrobin/packages/centos6-x86_64-packages//mni/current/lib/libnetcdf.a 
-lvnl_algo -lvnl -lvcl -lnetlib -lv3p_netlib
and produces lots of these types of errors
/home/melrobin/packages/freesurfer/mris_show/mris_show.c:878: undefined 
reference to glViewport' mris_show.o: In functionspecial_key_handler':
/home/melrobin/packages/freesurfer/mris_show/mris_show.c:923: undefined 
reference to glMatrixMode' 
/home/melrobin/packages/freesurfer/mris_show/mris_show.c:937: undefined 
reference toglRotatef'
/home/melrobin/packages/freesurfer/mris_show/mris_show.c:955: undefined 
reference to glRotatef' 
/home/melrobin/packages/freesurfer/mris_show/mris_show.c:945: undefined 
reference toglRotatef'
/home/melrobin/packages/freesurfer/mris_show/mris_show.c:951: undefined 
reference to glRotatef' 
/home/melrobin/packages/freesurfer/mris_show/mris_show.c:933: undefined 
reference toglRotatef'


The build seems not to include the OpenGL libraries when building mris_show as 
you can see from the link line. I'm trying to trace this up the Autotools 
chain, but need some help. I can work a little more on a fix with a little 
guidance telling me where to look.

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Re: [Freesurfer] OpenGL

[Nick Schmansky]

Dan,

The GUI apps all use Tcl/Tk, and scuba2 and qdec also use Vtk and
KWWidgets.  All the apps have wrapper scripts which call one or more of
the scripts tcl_setup, vtk_setup and kww_setup, which set paths to the
libraries, prior to calling the .bin.  So for example, 'tkmedit' is a
wrapper script which sources $FREESURFER_HOME/bin/tcl_setup, then calls
tkmedit.bin.  So probably what you need to do is call those wrapper
scripts (tcl_setup, etc).

Nick

> Hello,
>
> I am configuring a Freesurfer installation for two different types of
> computers (headless servers and workstations).  For both sets of
> computers we want any non-OpenGL commands that are run to first go
> through python scripts which load balance (these are working fine);
> however we have directly included the standard tkmedit* tksurfer*
> tkregister2* scuba* scuba2* and qdec* in the bin directory of freesurfer
> for the workstations.  We still do not seem able to get these
> applications to work.  Are there some dependencies, which I am missing
> for each of these besides tkmedit.bin etc.?
>
> Thank You,
> Dan
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>
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Re: [Freesurfer] OpenGL

[Rudolph Pienaar]

Hi Dan -

On Tuesday 06 November 2007 12:30, Daniel Wakeman wrote:
> We still do not seem able to get these
> applications to work.

When you say you can't get them to work, what exactly do you mean? Do you get 
any console error messages? Do you get nothing? Are the processes still 
lurking about in the process table...? What command line syntax (including 
arguments do you use)?

At the very least, you should get a "surfer.log" and "error.log" file in the 
directory from which you launch any of the graphical apps... Do these even 
appear?


-=R

-- 
Rudolph Pienaar, M.Eng, D.Eng / email: [EMAIL PROTECTED]
MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
149 (2301) 13th Street, Charlestown, MA 02129 USA
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Re: [Freesurfer] OpenGL, GLX, X11, VNC with FreeSurfer

[ppj]

Hi,

FreeSurfer rendering under VNC is very slow and sometimes not possible. You
may try UltraVNC (freeware - worked with me once) that has a better OpenGL
support.

I strongly recommend that you install a local copy of FreeSurfer and use it
to visualize the data.

Best Regards,

Pedro Paulo Oliveira Jr

On Fri, 14 Sep 2007 16:16:54 -0600, Troy Mcan <[EMAIL PROTECTED]>
wrote:
> Hi All,
> 
> I'm trying to connect to a computer remotely to use freesurfer. However,
> when I log in and try to load up a surface in freesurfer, I get the
> following message:
> 
> -No glx extension!
> -Surfer: failed, trying double buffered window
> -Xlib: extension "GLX" missing on display "computer name"
> -Window type not found!
> -Surfer: failed, no suitable display found
> 
> I am using a VNC viewer (from www.realvnc.com) to log into the computer.
> Are there any software rendering solutions for freesurfer so the VNC
> doesn't run into the openGL problems? Or, on the other hand, are there
any
> VNC clients that are known to work with freesurfer?
> 
> Thank you very much!
> 
> 
> 
> _
> Gear up for Halo® 3 with free downloads and an exclusive offer. It’s
> our way of saying thanks for using Windows Live™.
> http://gethalo3gear.com?ocid=SeptemberWLHalo3_WLHMTxt_2
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RE: [Freesurfer] OpenGL

[Satrajit Ghosh]

A further clarification. This has to do with the server end of things, not
the viewer end.

Satra 

-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Satrajit Ghosh
Sent: Monday, July 17, 2006 1:36 PM
To: 'Joe Berens'; freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] OpenGL

Hi Joe,

You may want to try realvnc (www.realvnc.com). We have been trying their
enterprise edition and it works really well. The typical vnc server that's
installed does not support OpenGL. I do know that more recent editions of
realvnc do support the GLX extension.

Cheers,

Satra 

-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Joe Berens
Sent: Monday, July 17, 2006 11:46 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] OpenGL

Hello,

A user gets the following:

GLUT: Fatal Error in tkmedit: OpenGL GLX extension not supported by
display: :60.0

This is using tightvnc via ssh from a windows xp box to Redhat Enterprise 3.

Every thing else seems to work fine. Any Ideas?

-Joe
A

__
Joe Berens
Department of Electrical and Computer Engineering
University of Minnesota - Twin CitiesPhone: 612-625-4585
200 Union Street SE, Room 4-174  Email: [EMAIL PROTECTED]
Minneapolis, MN 55455Office: EE/CSsci 1-183

Department of Psychology
University of Minnesota - Twin CitiesPhone: 612-625-0644
75 East River Road   Email: [EMAIL PROTECTED]
Minneapolis, MN 55455Office: N219 Elliot Hall
__

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RE: [Freesurfer] OpenGL

[Satrajit Ghosh]

Hi Joe,

You may want to try realvnc (www.realvnc.com). We have been trying their
enterprise edition and it works really well. The typical vnc server that's
installed does not support OpenGL. I do know that more recent editions of
realvnc do support the GLX extension.

Cheers,

Satra 

-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Joe Berens
Sent: Monday, July 17, 2006 11:46 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] OpenGL

Hello,

A user gets the following:

GLUT: Fatal Error in tkmedit: OpenGL GLX extension not supported by
display: :60.0

This is using tightvnc via ssh from a windows xp box to Redhat Enterprise 3.

Every thing else seems to work fine. Any Ideas?

-Joe
A

__
Joe Berens
Department of Electrical and Computer Engineering
University of Minnesota - Twin CitiesPhone: 612-625-4585
200 Union Street SE, Room 4-174  Email: [EMAIL PROTECTED]
Minneapolis, MN 55455Office: EE/CSsci 1-183

Department of Psychology
University of Minnesota - Twin CitiesPhone: 612-625-0644
75 East River Road   Email: [EMAIL PROTECTED]
Minneapolis, MN 55455Office: N219 Elliot Hall
__

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Re: [Freesurfer] OpenGL

[Nick Schmansky]

Joe,

Does tkmedit work directly on the RH3 box?  If so, then it is the windows
box that does not have the GLX extensions built into its OpenGL driver. 
GLX allows running X windows apps (like tkmedit) to run using the OpenGL
calls locally on a machine (for performance).  I don't have experience
running tightvnc on windows xp, but I have successfully run tkmedit via
realvnc on win xp (using an Nvidia GeForce 2 card).

Nick


> Hello,
>
> A user gets the following:
>
> GLUT: Fatal Error in tkmedit: OpenGL GLX extension not supported by
> display: :60.0
>
> This is using tightvnc via ssh from a windows xp box to Redhat Enterprise
> 3.
>
> Every thing else seems to work fine. Any Ideas?
>
> -Joe
> A
>
> __
> Joe Berens
> Department of Electrical and Computer Engineering
> University of Minnesota - Twin CitiesPhone: 612-625-4585
> 200 Union Street SE, Room 4-174  Email: [EMAIL PROTECTED]
> Minneapolis, MN 55455Office: EE/CSsci 1-183
>
> Department of Psychology
> University of Minnesota - Twin CitiesPhone: 612-625-0644
> 75 East River Road   Email: [EMAIL PROTECTED]
> Minneapolis, MN 55455Office: N219 Elliot Hall
> __
>
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>

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