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Hi d.m.,

I'm not entirely sure then. There is an idle loop in FSLeyes, but it runs once every 200 millseconds most of the time, so that would not explain it. I guess it could be something to do with the software GL driver.

Cheers,

Paul

On 30 August 2017 at 08:42, d m <[log in to unmask]> wrote:

Paul,


Thanks. Despite choosing option 1, 2 or 3, I still see above normal CPU usage for an application when fsleyes is idle with just the window open. CPU percentage is around 25-30% whle not in use, just open. Strange, since other applications on our server such as Matlab, emacs, etc. or even the older fslview. They don't use CPU this much when idle, more like 1%-2%. Just wondering if this has something to do with software rendering, the fsleyes is configure, or something else?


Also, i have Ubuntu 14.04 and fsl is installed via Neurodebian. I couldn't install fsleyes using:


sudo apt-get install fsleyes

Reading package lists... Done
Building dependency tree       
Reading state information... Done
Package fsleyes is not available, but is referred to by another package.
This may mean that the package is missing, has been obsoleted, or
is only available from another source

E: Package 'fsleyes' has no installation candidate


Right now, I have it installed using the direct installer from here:

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSLeyes


Will fsleyes be available using Neurodebian eventually for 14.04?


Thanks,


d.m.


From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of paul mccarthy <[log in to unmask]>
Sent: Monday, August 28, 2017 2:55:42 PM

To: [log in to unmask]
Subject: Re: [FSL] fsleyes installation in Ubuntu 14.04
 
Hi d.m.

The performance setting is in the "view settings panel" - this is accessed through the spanner button on the toolbar.

Cheers,

Paul

On 28 August 2017 at 10:31, d m <[log in to unmask]> wrote:

Paul,

I tried to locate the 'Performance' option in the view settings panel, but I could not find it. I've attached a picture.

I'm running Ubuntu 14.04 and I have fsl installed via neurodebian. I downloaded FSLeyes from here:

Thanks.

d.m.


From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of paul mccarthy <[log in to unmask]>
Sent: Sunday, August 27, 2017 2:04:30 PM

To: [log in to unmask]
Subject: Re: [FSL] fsleyes installation in Ubuntu 14.04
 
Hi D.m.,

(Thanks Kristian!)

FSLeyes may have defaulted to running in a lower performance mode, where it pre-renders slices for all of your loaded images. You can check this via the 'Performance' option in the view settings panel (the spanner button). 

If it is set to 'Fastest', then FSLeyes will work pre-generate images in the background. If you get acceptable performance with either of the other two choices (Better or 'Best looking'), then you can configure FSLeyes to default to them via the '-p' command line flag ('-p 2' for better, or '-p 3' for best looking).

Cheers,

Paul

On 25 August 2017 at 13:00, d m <[log in to unmask]> wrote:

Kristian.


Thank You!


That workaround helped a great deal. I followed the steps described in the wiki, and it worked.


The OpenGL version string is now 2.1, and I no longer receive error messages.


The only additional steps were to place that mesa directory in a selected path,e.g.,/path/mesa-10.1.3/. Substitute that path for `pwd` in this line:


export LD_LIBRARY_PATH=`pwd`/build/linux-x86_64-debug/gallium/targets/libgl-xlib/:${LD_LIBRARY_PATH}
becomes


export LD_LIBRARY_PATH=/path/mesa-10.1.3/build/linux-x86_64-debug/gallium/targets/libgl-xlib/:${LD_LIBRARY_PATH}


Added the above line with the modified path to my .bashrc file.


Works fine now each time I call fsleyes from the command line.


One thing I noticed is that fsleyes used about 23% CPU power even while open, but idle. Is this normal?


Thanks again.


d.m.



From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Kristian Loewe <[log in to unmask]>
Sent: Wednesday, August 23, 2017 4:33:59 PM
To: [log in to unmask]
Subject: Re: [FSL] fsleyes installation in Ubuntu 14.04
 
Hi d.m. and Paul,

I think, x2go only supports GLX 1.2.

Have you tried this workaround:
http://wiki.x2go.org/doku.php/wiki:development:glx-xlib-workaround ?

Cheers,

Kristian


On 23.08.2017 11:23, paul mccarthy wrote:
> Hi d.m.,
>
> Currently the graphics hardware on your remote machines is not being
> used at all - GLX redirects all graphics calls to the local machine that
> you connect from. If you want to use the graphics cards on your server,
> then the only way I am aware of is via VirtualGL.
>
> If you want to continue using x2go/freenx, then unfortunately I don't
> know of a workaround for the problem you are experiencing. I have not
> been able to reproduce it. Hopefully Kristian or somebody else may be
> able to give some advice.
>
> Cheers,
>
> Paul
>
> On 22 August 2017 at 19:18, d m <[log in to unmask]
> <mailto:[log in to unmask]>> wrote:
>
>     Kristian and Paul, thank you for your feedback.
>
>
>     Yes, we do connect remotely to our server using x2go/freenx.
>
>
>     I tried clearing the LIBGL_ALWAYS_INDIRECT environment variable. It
>     still did not work. I think the problem is that I have more than one
>     graphics card on our machine. We have a Matrox VGA controller and
>     two NVIDIA 3-D controllers installed on the machine.
>
>
>     We have other servers with one card installed (the same VGA
>     controller ), and fsleyes works fine.
>
>
>     Somehow we are reduced to Opengl 1.2 and OpenGL renderer string:
>     Mesa GLX Indirect with our hybrid graphic card setup. Is there a
>     workaround or solution for this to get fsleyes running?
>
>
>     Thanks.
>
>
>     d.m.
>
>     ------------------------------------------------------------------------
>     *From:* FSL - FMRIB's Software Library <[log in to unmask]
>     <mailto:[log in to unmask]>> on behalf of Kristian Loewe
>     <[log in to unmask] <mailto:[log in to unmask]>>
>     *Sent:* Tuesday, August 8, 2017 4:03:02 PM
>     *To:* [log in to unmask] <mailto:[log in to unmask]>
>     *Subject:* Re: [FSL] fsleyes installation in Ubuntu 14.04
>     Hi,
>
>     If indirect rendering is not possible, another option is to use
>     VirtualGL. With VirtualGL, you can use the server's GPU for rendering
>     and have the rendered results sent to your local or virtual X server.
>     Depending on the graphics setup, the network speed, and the data size,
>     this approach may also give you noticably better performance than
>     indirect rendering.
>
>     Cheers,
>
>     Kristian
>
>     On 08.08.2017 20:10, paul mccarthy wrote:
>     > Hi d.m.,
>     >
>     > I guess you are running FSLeyes on a remote server, right? Try clearing
>     > the LIBGL_ALWAYS_INDIRECT environment variable, as documented here:
>     >
>     > https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/userdoc/latest/troubleshooting.html#opengl-1-4-or-newer-is-required-detected-version-1-2
>     <https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/userdoc/latest/troubleshooting.html#opengl-1-4-or-newer-is-required-detected-version-1-2>
>     >
>     > Unfortunately if this doesn't work, I have not yet figured out a
>     > solution for this problem.
>     >
>     > Cheers,
>     >
>     > Paul
>     >
>     > On 8 August 2017 at 17:45, d m <[log in to unmask] <mailto:[log in to unmask]>
>     > <mailto:[log in to unmask]>> wrote:
>     >
>     >     Michael,
>     >
>     >
>     >     Thanks for the suggestion.  That worked, but now I get the following
>     >     error message after typing "./fsleyes":
>     >
>     >
>     >     WARNING          __init__.py  595: create          - GLContext
>     >     callback function raised RuntimeError: OpenGL 1.4 or newer is
>     >     required (detected version: 1.2
>     >     Traceback (most recent call last):
>     >        File "fsleyes/gl/__init__.py", line 589, in create
>     >        File "fsleyes/main.py", line 377, in realCallback
>     >        File "fsleyes/gl/__init__.py", line 314, in bootstrap
>     >     RuntimeError: OpenGL 1.4 or newer is required (detected version: 1.2
>     >
>     >     Have you or anyone seen this message? If so, what was the solution?
>     >
>     >
>     >     Thanks.
>     >
>     >
>     >     d.m.
>     >
>     >     ------------------------------------------------------------------------
>     >     *From:* FSL - FMRIB's Software Library <[log in to unmask] <mailto:[log in to unmask]>
>     >     <mailto:[log in to unmask]>> on behalf of Michael Firbank
>     >     <[log in to unmask]UK <mailto:michael.firbank@NEWCASTLE.AC.UK>
>     >     <mailto:michael.firbank@NEWCASTLE.AC.UK
>     <mailto:michael.firbank@NEWCASTLE.AC.UK>>>
>     >     *Sent:* Friday, July 7, 2017 5:16:57 PM
>     >
>     >     *To:* [log in to unmask] <mailto:[log in to unmask]>
>     <mailto:[log in to unmask]>
>     >     *Subject:* Re: [FSL] fsleyes installation in Ubuntu 14.04
>     >
>     >     Hello
>     >
>     >
>     >     You can unzip the folder wherever you like. Probably the $FSLDIR/bin
>     >     is not the best place.
>     >
>     >     In any case the fsleyes file needs to be in a directory on your path.
>     >
>     >     if you need to see what that is, type
>     >
>     >     echo $PATH
>     >
>     >
>     >     If you unzipped it in the $FSLDIR/bin directory, the actual
>     >     executable will be in
>     >
>     >     $FSLDIR/bin/FSLeyes
>     >
>     >     if you cd to that directory and type
>     >
>     >     ./fsleyes
>     >
>     >     then it should start.
>     >
>     >
>     >     you can create a link to the fsleyes program by changing directory
>     >     to $FSLDIR/bin and then
>     >
>     >     ln -s FSLEYESDIRECTORY/fsleyes fsleyes
>     >
>     >
>     >     where FSLEYESDIRECTORY is the directory where fsleyes is. so you
>     >     probably want
>     >
>     >     ln -s $FSLDIR/bin/FSLeyes/fsleyes  fsleyes
>     >
>     >
>     >     Hope that helps
>     >
>     >
>     >     Michael
>     >
>     >
>     >     ------------------------------------------------------------------------
>     >     *From:* FSL - FMRIB's Software Library <[log in to unmask] <mailto:[log in to unmask]>
>     >     <mailto:[log in to unmask]>> on behalf of d m <[log in to unmask]
>     <mailto:[log in to unmask]>
>     >     <mailto:[log in to unmask]>>
>     >     *Sent:* 07 July 2017 18:25
>     >     *To:* [log in to unmask] <mailto:[log in to unmask]>
>     <mailto:[log in to unmask]>
>     >     *Subject:* Re: [FSL] fsleyes installation in Ubuntu 14.04
>     >
>     >     Michael,
>     >
>     >
>     >     Thanks for the reply.
>     >
>     >
>     >     I'm still somewhat confused. Where exactly do I unzip the folder?
>     >
>     >
>     >     Is it the $FSLDIR/bin/ directory?
>     >
>     >
>     >     If so, I added the folder and nothing changed.
>     >
>     >
>     >     Are there any further steps to complete before using fsleyes? Is
>     >     fslview no longer usable by adding the FSLeyes folder?
>     >
>     >
>     >     One thing I noticed, the neurodebian page only shows FSLeyes listed
>     >     for 16.04 and 17.04. Nothing for 14.04? Maybe that is the issue?
>     >
>     >
>     >     http://neuro.debian.net/pkgs/fsleyes.html?highlight=fsleyes
>     <http://neuro.debian.net/pkgs/fsleyes.html?highlight=fsleyes>
>     >     <http://neuro.debian.net/pkgs/fsleyes.html?highlight=fsleyes
>     <http://neuro.debian.net/pkgs/fsleyes.html?highlight=fsleyes>>
>     >
>     >
>     >     Thanks.
>     >
>     >
>     >     d.m.
>     >
>     >     ------------------------------------------------------------------------
>     >     *From:* FSL - FMRIB's Software Library <[log in to unmask] <mailto:[log in to unmask]>
>     >     <mailto:[log in to unmask]>> on behalf of Michael Firbank
>     >     <[log in to unmask]UK <mailto:michael.firbank@NEWCASTLE.AC.UK>
>     >     <mailto:michael.firbank@NEWCASTLE.AC.UK
>     <mailto:michael.firbank@NEWCASTLE.AC.UK>>>
>     >     *Sent:* Friday, July 7, 2017 10:10:29 AM
>     >     *To:* [log in to unmask] <mailto:[log in to unmask]>
>     <mailto:[log in to unmask]>
>     >     *Subject:* Re: [FSL] fsleyes installation in Ubuntu 14.04
>     >
>     >     Hello
>     >
>     >     For 16.04 I just downloaded and unzipped the relevant  file from
>     >
>     >     https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSLeyes
>     <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSLeyes>
>     >     <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSLeyes
>     <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSLeyes>>
>     >
>     >     FSLeyes - FslWiki - fsl.fmrib.ox.ac.uk <http://fsl.fmrib.ox.ac.uk>
>     >     <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSLeyes
>     <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSLeyes>>
>     >     fsl.fmrib.ox.ac.uk <http://fsl.fmrib.ox.ac.uk>
>     <http://fsl.fmrib.ox.ac.uk>
>     >     FSLeyes (pronounced fossilise) is the new FSL image viewer, released
>     >     with FSL 5.0.10. FSLeyes can either be installed as a standalone
>     >     application, or can be installed ...
>     >
>     >     seems to work ok.
>     >
>     >     Michael
>     >
>     >     *From:*FSL - FMRIB's Software Library [mailto:[log in to unmask] <mailto:[log in to unmask]>
>     >     <mailto:[log in to unmask]>] *On Behalf Of *d m
>     >     *Sent:* 07 July 2017 15:03
>     >     *To:* [log in to unmask] <mailto:[log in to unmask]>
>     <mailto:[log in to unmask]>
>     >     *Subject:* [FSL] fsleyes installation in Ubuntu 14.04
>     >
>     >     Hello,
>     >
>     >     How does one install fsleyes with Ubuntu 14.04? We have installed
>     >     fsl using neurodebian.
>     >
>     >     Thanks.
>     >
>     >     d.m.
>     >
>     >
>
>