problem with QValueAxis during compile #10
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This code needs QtCharts to run, but some default packages do not have it.
Frank
…On Fri, Nov 8, 2019 at 8:50 AM andregouws ***@***.***> wrote:
Debian stretch g++ 8 gcc 8
In both group_connectometry.cpp and nn_connectometry.cpp I get errors
during compile when the attributes setTickType and setTickInterval are
being set. e.g.
connectometry/group_connectometry.cpp: In member function ‘void
group_connectometry::show_fdr_report()’:
connectometry/group_connectometry.cpp:169:60: error: ‘class
QtCharts::QValueAxis’ has no member named ‘setTickType’; did you mean
‘setTickCount’?
((QValueAxis*)fdr_chart->axes(Qt::Horizontal).back())->setTickType(QValueAxis::TicksDynamic);
^~~~~~~~~~~
setTickCount
connectometry/group_connectometry.cpp:169:84: error: ‘TicksDynamic’ is not
a member of ‘QtCharts::QValueAxis’
((QValueAxis*)fdr_chart->axes(Qt::Horizontal).back())->setTickType(QValueAxis::TicksDynamic);
^~~~~~~~~~~~
.. which ulitmately results in:
make: *** [Makefile:5051: group_connectometry.o] Error 1
I have worked around this by simply commneting out any lines in
group_connectometry.cpp and nn_connectometry.cpp that make calls to
setTickType and setTickInterval. The package then compiles and runs, but
obviously this is not ideal.
Thanks for your help.
Andre'
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I was getting QtCharts errors earlier in the compile process but thought I had resolved those - I stopped getting errors after successfully running:
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Maybe the version is different?
' setTickType' needs QtCharts 5.13.2
Frank
…On Fri, Nov 8, 2019 at 8:57 AM andregouws ***@***.***> wrote:
I was getting QtCharts errors earlier in the compile process but thought I
had resolved those - I stopped getting errors after successfully running:
sudo apt-get install libqt5charts5 libqt5charts5-dev
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That'll be it - thanks Frank. |
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For the record (and anyone else searching) - at this point in time Debian Stretch current libqt5charts5 and libqt5charts5-dev are at stable version 5.11.3 and 5.12 is only just in testing. |
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Thanks for the information, and sorry for the hassle!
Frank
…On Fri, Nov 8, 2019 at 9:09 AM andregouws ***@***.***> wrote:
For the record (and anyone else searching) - at this point in time Debian Stretch current libqt5charts5 and libqt5charts5-dev are at stable version 5.11.3 and 5.12 is only just in testing.
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Sorry, how do we upgrade our version of qtcharts to the right one? |
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It is included in the Qt. 5.12.2
…On Wed, May 13, 2020 at 10:36 PM Angela Zhang ***@***.***> wrote:
Sorry, how do we upgrade our version of qtcharts to the right one?
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I would suggest you use Docker or Singularity to run DSI Studio:
http://dsi-studio.labsolver.org/dsi-studio-download
…On Wed, May 13, 2020 at 10:45 PM Fang-Cheng Yeh ***@***.***> wrote:
It is included in the Qt. 5.12.2
On Wed, May 13, 2020 at 10:36 PM Angela Zhang ***@***.***> wrote:
>
> Sorry, how do we upgrade our version of qtcharts to the right one?
>
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Sorry, I have Ubuntu 18.04. It looks like the Docker or Singularity options are for Mac. I'm not sure Qt above 5.9 is available for that in a stable release... is there a way to get around this? Sorry for the trouble! |
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I'm attempting to install Qt 12 now. I'll update when it finishes, thanks! |
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… On Wed, May 13, 2020 at 10:52 PM Angela Zhang ***@***.***> wrote:
I'm attempting to install Qt 12 now. I'll update when it finishes, thanks!
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Oh, I didn't realize the container was cross platform. Singularity worked well. Thank you very much :) |
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Hi Frank, I am trying to visualize fibers, but get this error when running the module on singularity with Linux: Please advise. Thank you! |
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It is a problem with Qt 5.12, and currently there seems no solution yet.
Frank
…On Wed, Jun 10, 2020 at 7:37 PM Angela Zhang ***@***.***> wrote:
Hi Frank,
I am trying to visualize fibers, but get this error when running the
module on singularity with Linux:
No XVisualInfo for format QSurfaceFormat(version 2.0, options QFlags<QSurfaceFormat::FormatOption>(), depthBufferSize 0, redBufferSize 1, greenBufferSize 1, blueBufferSize 1, alphaBufferSize -1, stencilBufferSize 0, samples 1, swapBehavior QSurfaceFormat::SingleBuffer, swapInterval -1, colorSpace QSurfaceFormat::DefaultColorSpace, profile QSurfaceFormat::NoProfile)
Falling back to using screens root_visual.
qt.glx: qglx_findConfig: Failed to finding matching FBConfig (8 8 8 0)
qt.glx: qglx_findConfig: Failed to finding matching FBConfig (1 8 8 0)
qt.glx: qglx_findConfig: Failed to finding matching FBConfig (1 1 8 0)
qt.glx: qglx_findConfig: Failed to finding matching FBConfig (1 1 1 0)
qt.glx: qglx_findConfig: Failed to finding matching FBConfig (1 1 1 0)
qt.glx: qglx_findConfig: Failed to finding matching FBConfig (1 1 1 0)
qt.glx: qglx_findConfig: Failed to finding matching FBConfig (1 1 1 0)
qt.glx: qglx_findConfig: Failed to finding matching FBConfig (1 1 1 0)
qt.glx: qglx_findConfig: Failed to finding matching FBConfig (1 1 1 0)
qt.glx: qglx_findConfig: Failed to finding matching FBConfig (8 8 8 0)
qt.glx: qglx_findConfig: Failed to finding matching FBConfig (1 8 8 0)
qt.glx: qglx_findConfig: Failed to finding matching FBConfig (1 1 8 0)
qt.glx: qglx_findConfig: Failed to finding matching FBConfig (1 1 1 0)
qt.glx: qglx_findConfig: Failed to finding matching FBConfig (1 1 1 0)
qt.glx: qglx_findConfig: Failed to finding matching FBConfig (1 1 1 0)
qt.glx: qglx_findConfig: Failed to finding matching FBConfig (1 1 1 0)
qt.glx: qglx_findConfig: Failed to finding matching FBConfig (1 1 1 0)
qt.glx: qglx_findConfig: Failed to finding matching FBConfig (1 1 1 0)
Could not initialize GLX
Aborted (core dumped)
Please advise. Thank you!
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I see. So there is not a way to visualize the fibers right now? Thanks! |
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It seems so. I am sorry about that.
Frank
…On Wed, Jun 10, 2020 at 7:49 PM Angela Zhang ***@***.***> wrote:
I see. So there is not a way to visualize the fibers right now? Thanks!
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Okay I see. Thank you and please let me know if there's a solution. |
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Dear both, |
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Singularity or docker container can now handle this problem.
We don't need to compile code to run DSI Studio on Linux systems.
Frank
…On Wed, Nov 25, 2020 at 3:32 AM barbrakr ***@***.***> wrote:
Dear both,
Do you happen to know if there's a solution to this yet - I've seen a new
QT version out - can that be used with dsistudio singularity?
Thanks,
Kind wishes,
Barbara
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oh, great, thanks! |
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Oh - actually, I just tried it out - it results in a Nov 3rd build and when loading a fib.gz file I get this in the Terminal (repeatedly) |
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The error is caused by the openGL library.
There may be additional configuration needed to get a correct openGL with
singularity or docker container.
Frank
…On Wed, Nov 25, 2020 at 11:13 AM barbrakr ***@***.***> wrote:
Oh - actually, I just tried it out - it results in a Nov 3rd build and
when loading a fib.gz file I get this in the Terminal (repeatedly)
GL_INVALID_OPERATION
begin
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when loading a fib.gz file I get this in the Terminal (repeatedly)
GL_INVALID_OPERATION
begin
Same here with latest docker instance
On Wed, Nov 25, 2020 at 4:18 PM Fang-Cheng (Frank) Yeh <
notifications@github.com> wrote:
… The error is caused by the openGL library.
There may be additional configuration needed to get a correct openGL with
singularity or docker container.
Frank
On Wed, Nov 25, 2020 at 11:13 AM barbrakr ***@***.***>
wrote:
> Oh - actually, I just tried it out - it results in a Nov 3rd build and
> when loading a fib.gz file I get this in the Terminal (repeatedly)
> GL_INVALID_OPERATION
> begin
>
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I am sorry to hear this and wish I knew how to fix.
The same code works on Windows and Mac, but for some Linux systems
(not all Linux systems have this problem), the container does not work
with the OpenGL library. "GL_INVALID_OPERATION" is the error code when
openGL library failed to execute the function requested by DSI Studio.
Googling this error message with docker container or singularity leads
to a variety of possibilities. Some could be fixed at the OS level.
I will keep track of this issue and fix it if there is a solution.
Frank
…On Wed, Nov 25, 2020 at 1:15 PM andregouws ***@***.***> wrote:
> when loading a fib.gz file I get this in the Terminal (repeatedly)
> GL_INVALID_OPERATION
> begin
Same here with latest docker instance
On Wed, Nov 25, 2020 at 4:18 PM Fang-Cheng (Frank) Yeh <
***@***.***> wrote:
> The error is caused by the openGL library.
> There may be additional configuration needed to get a correct openGL with
> singularity or docker container.
> Frank
>
> On Wed, Nov 25, 2020 at 11:13 AM barbrakr ***@***.***>
> wrote:
>
> > Oh - actually, I just tried it out - it results in a Nov 3rd build and
> > when loading a fib.gz file I get this in the Terminal (repeatedly)
> > GL_INVALID_OPERATION
> > begin
> >
> > —
> > You are receiving this because you modified the open/close state.
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Don't be sorry!! You do sooo much hard work!! .. I'll keep debugging and
see what I can come up with...
On Wed, 25 Nov 2020, 18:41 Fang-Cheng (Frank) Yeh, <notifications@github.com>
wrote:
… I am sorry to hear this and wish I knew how to fix.
The same code works on Windows and Mac, but for some Linux systems
(not all Linux systems have this problem), the container does not work
with the OpenGL library. "GL_INVALID_OPERATION" is the error code when
openGL library failed to execute the function requested by DSI Studio.
Googling this error message with docker container or singularity leads
to a variety of possibilities. Some could be fixed at the OS level.
I will keep track of this issue and fix it if there is a solution.
Frank
On Wed, Nov 25, 2020 at 1:15 PM andregouws ***@***.***>
wrote:
>
> > when loading a fib.gz file I get this in the Terminal (repeatedly)
> > GL_INVALID_OPERATION
> > begin
>
> Same here with latest docker instance
>
> On Wed, Nov 25, 2020 at 4:18 PM Fang-Cheng (Frank) Yeh <
> ***@***.***> wrote:
>
> > The error is caused by the openGL library.
> > There may be additional configuration needed to get a correct openGL
with
> > singularity or docker container.
> > Frank
> >
> > On Wed, Nov 25, 2020 at 11:13 AM barbrakr ***@***.***>
> > wrote:
> >
> > > Oh - actually, I just tried it out - it results in a Nov 3rd build
and
> > > when loading a fib.gz file I get this in the Terminal (repeatedly)
> > > GL_INVALID_OPERATION
> > > begin
> > >
> > > —
> > > You are receiving this because you modified the open/close state.
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Hi both, |
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Dear all, so we have tried something based on this: with cuda-drivers and the --nv flag |
|
googling the error message will lead to some solutions:
CoatiSoftware/Sourcetrail#891
…On Fri, Nov 27, 2020 at 10:03 AM barbrakr ***@***.***> wrote:
Dear all, so we have tried something based on this: with cuda-drivers and
the --nv flag
dsi_studio outputs this - not sure if this is some hint to some of you...
dsi_studio: symbol lookup error: /.singularity.d/libs/libGL.so.1:
undefined symbol: _glapi_tls_Current
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So I got this working finally on Deb 10 (buster) - both on a personal
laptop and on my work PC.
Turns out there are a few authority/permissions challenges to expose the
display and opengl / other libraries to the docker session.
## ------------ code starts here
## CAREFUL - you may not want to remove any docker install you already have
- I just started from fresh
sudo apt-get remove docker docker-engine docker.io containerd runc
sudo apt-get update
# some core libs we'll need (may already be installed
sudo apt-get install apt-transport-https ca-certificates curl
gnupg-agent software-properties-common
# this is Debian specific so may require alternatives in Ubuntu etc
sudo curl -fsSL https://download.docker.com/linux/debian/gpg | sudo apt-key
add
sudo apt-key fingerprint 0EBFCD88
sudo add-apt-repository "deb [arch=amd64]
https://download.docker.com/linux/debian \
(lsb_release -cs) \
stable"
sudo apt-get update
# get docker
sudo apt-get install docker-ce docker-ce-cli containerd.io
# set permissions (may already be set)
sudo groupadd docker
sudo usermod -aG docker $USER
# TEST that docker runs at least
docker run hello-world
# extra libs for dtistudio - you may or may not have these already
sudo apt-get install libxcb1-dev
sudo apt-get install libqt5opengl5
sudo apt-get install libqt5
sudo apt-get install libqt5charts5
sudo apt-get install libqt5core5a
sudo apt-get install libxcb1
sudo apt-get install xcb
# in case you need to check the xauth settings (debugging really)
xauth list
# --- READY TO GO - try one of the two options below
#sometimes we need this (usually on your personal laptop)
# NB replace the "/media/andre/disk/Common/dti/R1025" with the path to your
data folder (this is mounted as "data" in the docker instance file tree)
docker run -it --network=host --env DISPLAY=$DISPLAY --privileged
--volume="$HOME/.Xauthority:/root/.Xauthority:rw" -v
/tmp/.X11-unix:/tmp/.X11-unix -v /media/andre/disk/Common/dti/R1025/:/data
--rm dsistudio/dsistudio:latest
# on my networked PC with extra safety / firewalls at work I have to run it
this way
# NB replace the "/var/tmp/" with the path to your data folder (this is
mounted as "data" in the docker instance file tree)
docker run -it --network=host --env DISPLAY=$DISPLAY --privileged -v
/tmp/.X11-unix:/tmp/.X11-unix -v /var/tmp/:/data --rm
dsistudio/dsistudio:latest
### ----- code ends here
On Fri, Nov 27, 2020 at 3:54 PM Fang-Cheng (Frank) Yeh <
notifications@github.com> wrote:
… googling the error message will lead to some solutions:
CoatiSoftware/Sourcetrail#891
On Fri, Nov 27, 2020 at 10:03 AM barbrakr ***@***.***>
wrote:
> Dear all, so we have tried something based on this: with cuda-drivers and
> the --nv flag
> dsi_studio outputs this - not sure if this is some hint to some of you...
> dsi_studio: symbol lookup error: /.singularity.d/libs/libGL.so.1:
> undefined symbol: _glapi_tls_Current
>
> —
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Thanks! This is really helpful!
Frank
…On Wed, Dec 2, 2020 at 6:21 AM andregouws ***@***.***> wrote:
So I got this working finally on Deb 10 (buster) - both on a personal
laptop and on my work PC.
Turns out there are a few authority/permissions challenges to expose the
display and opengl / other libraries to the docker session.
## ------------ code starts here
## CAREFUL - you may not want to remove any docker install you already have
- I just started from fresh
sudo apt-get remove docker docker-engine docker.io containerd runc
sudo apt-get update
# some core libs we'll need (may already be installed
sudo apt-get install apt-transport-https ca-certificates curl
gnupg-agent software-properties-common
# this is Debian specific so may require alternatives in Ubuntu etc
sudo curl -fsSL https://download.docker.com/linux/debian/gpg | sudo
apt-key
add
sudo apt-key fingerprint 0EBFCD88
sudo add-apt-repository "deb [arch=amd64]
https://download.docker.com/linux/debian \
(lsb_release -cs) \
stable"
sudo apt-get update
# get docker
sudo apt-get install docker-ce docker-ce-cli containerd.io
# set permissions (may already be set)
sudo groupadd docker
sudo usermod -aG docker $USER
# TEST that docker runs at least
docker run hello-world
# extra libs for dtistudio - you may or may not have these already
sudo apt-get install libxcb1-dev
sudo apt-get install libqt5opengl5
sudo apt-get install libqt5
sudo apt-get install libqt5charts5
sudo apt-get install libqt5core5a
sudo apt-get install libxcb1
sudo apt-get install xcb
# in case you need to check the xauth settings (debugging really)
xauth list
# --- READY TO GO - try one of the two options below
#sometimes we need this (usually on your personal laptop)
# NB replace the "/media/andre/disk/Common/dti/R1025" with the path to your
data folder (this is mounted as "data" in the docker instance file tree)
docker run -it --network=host --env DISPLAY=$DISPLAY --privileged
--volume="$HOME/.Xauthority:/root/.Xauthority:rw" -v
/tmp/.X11-unix:/tmp/.X11-unix -v /media/andre/disk/Common/dti/R1025/:/data
--rm dsistudio/dsistudio:latest
# on my networked PC with extra safety / firewalls at work I have to run it
this way
# NB replace the "/var/tmp/" with the path to your data folder (this is
mounted as "data" in the docker instance file tree)
docker run -it --network=host --env DISPLAY=$DISPLAY --privileged -v
/tmp/.X11-unix:/tmp/.X11-unix -v /var/tmp/:/data --rm
dsistudio/dsistudio:latest
### ----- code ends here
On Fri, Nov 27, 2020 at 3:54 PM Fang-Cheng (Frank) Yeh <
***@***.***> wrote:
> googling the error message will lead to some solutions:
> CoatiSoftware/Sourcetrail#891
>
> On Fri, Nov 27, 2020 at 10:03 AM barbrakr ***@***.***>
> wrote:
>
> > Dear all, so we have tried something based on this: with cuda-drivers
and
> > the --nv flag
> > dsi_studio outputs this - not sure if this is some hint to some of
you...
> > dsi_studio: symbol lookup error: /.singularity.d/libs/libGL.so.1:
> > undefined symbol: _glapi_tls_Current
> >
> > —
> > You are receiving this because you modified the open/close state.
> > Reply to this email directly, view it on GitHub
> > <#10 (comment)>,
or
> > unsubscribe
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okay, so for my situation the solution was to delete the /.singularity.d/libs from LD_LIBRARY_PATH , so instead I made these dependent on the libraries from my remote host system. |
Hello, |
|
@barbrakr I'd be curious how you accomplished this as well. I'm trying to do visualization on our HPC and get the GL_INVALID_OPERATION issue. I can obviously do the visualization on my Windows machine, but I'm trying to keep everything contained to one location if I can. |
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IT solved it for me on our system (see below). I guess there may be a different fix for other systems. The container will not run without these adjustments on our end (sorry some comments are still in German): #Kurz zum Hintergrund: Der Container läuft nicht so richtig. Ich habe jetzt alle Bibliotheken vom SCC bzw. ugpu in den Container verlinkt. Dann geht es. Das heißt, man hat 4 Zeilen, die man auf der Kommandozeile ausführen muss. Ich kann dir das gerne nochmal in einer ViKo zeigen/erklären. Das ganze zum laufen zu kriege ist aber relativ einfach: #go to some directory with fib-files module purge #make sure no other modules #Dann ein export LD_LIBRARY_PATH=/cm/local/apps/cuda-driver/libs/current/lib64:/cm/local/apps/gcc/8.2.0/lib64:/usr/lib64/VirtualGL:/lib64 #Dann mit einer shell den Container starten mit #Danach befindest du dich mit deiner bash im Container jetzt einmal #Beim starten der Shell fügt Singularity das Verzeichnis export LD_LIBRARY_PATH=/cm/local/apps/cuda-driver/libs/current/lib64:/cm/local/apps/gcc/8.2.0/lib64:/usr/lib64/VirtualGL:/lib64 #go and start dsi_studio |
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Debian stretch g++ 8 gcc 8
In both group_connectometry.cpp and nn_connectometry.cpp I get errors during compile when the attributes setTickType and setTickInterval are being set. e.g.
connectometry/group_connectometry.cpp: In member function ‘void group_connectometry::show_fdr_report()’:
connectometry/group_connectometry.cpp:169:60: error: ‘class QtCharts::QValueAxis’ has no member named ‘setTickType’; did you mean ‘setTickCount’?
((QValueAxis*)fdr_chart->axes(Qt::Horizontal).back())->setTickType(QValueAxis::TicksDynamic);
^~~~~~~~~~~
setTickCount
connectometry/group_connectometry.cpp:169:84: error: ‘TicksDynamic’ is not a member of ‘QtCharts::QValueAxis’
((QValueAxis*)fdr_chart->axes(Qt::Horizontal).back())->setTickType(QValueAxis::TicksDynamic);
^~~~~~~~~~~~
.. which ulitmately results in:
make: *** [Makefile:5051: group_connectometry.o] Error 1I have worked around this by simply commenting out any lines in group_connectometry.cpp and nn_connectometry.cpp that make calls to setTickType and setTickInterval. The package then compiles and runs, but obviously this is not ideal.
Thanks for your help.
Andre'
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