Error using "General registration (BRAINS)" module

classic Classic list List threaded Threaded
4 messages Options
Reply | Threaded
Open this post in threaded view
|

Error using "General registration (BRAINS)" module

Andrey Fedorov-2
Hi,

with the today's nightly, I am unable to run "General registration
(BRAINS)". The error says:

ModuleType: SharedObjectModule
Failed to load "/Applications/Slicer.app/Contents/lib/Slicer-4.5/cli-modules/libBRAINSFitLib.dylib"
QLibrary error message(s):
("Cannot load library
/Applications/Slicer.app/Contents/lib/Slicer-4.5/cli-modules/libBRAINSFitLib.dylib:
(dlopen(/Applications/Slicer.app/Contents/lib/Slicer-4.5/cli-modules/libBRAINSFitLib.dylib,
5): Library not loaded:
/Users/kitware/Dashboards/Nightly/Slicer-0-build/ITKv4-build/lib/libITKIOBMP-4.10.1.dylib
  Referenced from:
/Applications/Slicer.app/Contents/lib/Slicer-4.5/cli-modules/libBRAINSFitLib.dylib
  Reason: image not found)", "Cannot load library
/Applications/Slicer.app/Contents/lib/Slicer-4.5/cli-modules/libBRAINSFitLib.dylib:
(dlopen(/Applications/Slicer.app/Contents/lib/Slicer-4.5/cli-modules/libBRAINSFitLib.dylib,
5): Library not loaded:
/Users/kitware/Dashboards/Nightly/Slicer-0-build/ITKv4-build/lib/libITKIOBMP-4.10.1.dylib

The workaround is to check "Prefer Executable CLIs" in App settings > Modules.

AF
_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
Reply | Threaded
Open this post in threaded view
|

Re: Error using "General registration (BRAINS)" module

inorton
This was the motivation for: https://github.com/Slicer/Slicer/pull/550 to get actionable error messages.

The dylib files in `Slicer.app/Contents/lib/Slicer-4.5/cli-modules/` have hard-coded RPATHs. There is a second copy one directory up ("Slicer-4.5/") which has the correct `@rpath/...` designations. You can actually copy these to `cli-modules` and they will then work fine as SharedObjectModule.

This appears to have been an issue for a while now, see: http://www.na-mic.org/Bug/view.php?id=4041#c13339

However, some more recent change led to the runtime load failure. Of nightly versions I have installed, 5/8 works, 6/8 and later do not. Unfortunately, I haven't been able to exactly reproduce this in a local build so not sure about a solution. Hopefully Jc will weigh in.

(In local release build, the objects `dlopen` fine, but then fail in ITK iterator code with a region size error that "may" be related to shared object loading: http://public.kitware.com/pipermail/community/2015-October/010057.html)

On Fri, Jul 15, 2016 at 5:46 PM, Andrey Fedorov <[hidden email]> wrote:
Hi,

with the today's nightly, I am unable to run "General registration
(BRAINS)". The error says:

ModuleType: SharedObjectModule
Failed to load "/Applications/Slicer.app/Contents/lib/Slicer-4.5/cli-modules/libBRAINSFitLib.dylib"
QLibrary error message(s):
("Cannot load library
/Applications/Slicer.app/Contents/lib/Slicer-4.5/cli-modules/libBRAINSFitLib.dylib:
(dlopen(/Applications/Slicer.app/Contents/lib/Slicer-4.5/cli-modules/libBRAINSFitLib.dylib,
5): Library not loaded:
/Users/kitware/Dashboards/Nightly/Slicer-0-build/ITKv4-build/lib/libITKIOBMP-4.10.1.dylib
  Referenced from:
/Applications/Slicer.app/Contents/lib/Slicer-4.5/cli-modules/libBRAINSFitLib.dylib
  Reason: image not found)", "Cannot load library
/Applications/Slicer.app/Contents/lib/Slicer-4.5/cli-modules/libBRAINSFitLib.dylib:
(dlopen(/Applications/Slicer.app/Contents/lib/Slicer-4.5/cli-modules/libBRAINSFitLib.dylib,
5): Library not loaded:
/Users/kitware/Dashboards/Nightly/Slicer-0-build/ITKv4-build/lib/libITKIOBMP-4.10.1.dylib

The workaround is to check "Prefer Executable CLIs" in App settings > Modules.

AF
_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ


_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
Reply | Threaded
Open this post in threaded view
|

Re: Error using "General registration (BRAINS)" module

Andrey Fedorov-2
In reply to this post by Andrey Fedorov-2
Isaiah,

Thanks for the reply.

Do you know if any application really benefits seriously from this
in-memory communication? There are many important tasks and I wonder
if fixing this shared lib issue is of sufficiently high priority.

>
> This appears to have been an issue for a while now, see:
> http://www.na-mic.org/Bug/view.php?id=4041#c13339
>

Alas, mantis times out on me.

Perhaps we should change the default to executable only.

On the other hand, no-one else complained so far.

AF


On Sun, Jul 17, 2016 at 8:34 AM, Isaiah Norton <[hidden email]> wrote:

> This was the motivation for: https://github.com/Slicer/Slicer/pull/550 to
> get actionable error messages.
>
> The dylib files in `Slicer.app/Contents/lib/Slicer-4.5/cli-modules/` have
> hard-coded RPATHs. There is a second copy one directory up ("Slicer-4.5/")
> which has the correct `@rpath/...` designations. You can actually copy these
> to `cli-modules` and they will then work fine as SharedObjectModule.
>
> This appears to have been an issue for a while now, see:
> http://www.na-mic.org/Bug/view.php?id=4041#c13339
>
> However, some more recent change led to the runtime load failure. Of nightly
> versions I have installed, 5/8 works, 6/8 and later do not. Unfortunately, I
> haven't been able to exactly reproduce this in a local build so not sure
> about a solution. Hopefully Jc will weigh in.
>
> (In local release build, the objects `dlopen` fine, but then fail in ITK
> iterator code with a region size error that "may" be related to shared
> object loading:
> http://public.kitware.com/pipermail/community/2015-October/010057.html)
>
> On Fri, Jul 15, 2016 at 5:46 PM, Andrey Fedorov <[hidden email]>
> wrote:
>>
>> Hi,
>>
>> with the today's nightly, I am unable to run "General registration
>> (BRAINS)". The error says:
>>
>> ModuleType: SharedObjectModule
>> Failed to load
>> "/Applications/Slicer.app/Contents/lib/Slicer-4.5/cli-modules/libBRAINSFitLib.dylib"
>> QLibrary error message(s):
>> ("Cannot load library
>>
>> /Applications/Slicer.app/Contents/lib/Slicer-4.5/cli-modules/libBRAINSFitLib.dylib:
>>
>> (dlopen(/Applications/Slicer.app/Contents/lib/Slicer-4.5/cli-modules/libBRAINSFitLib.dylib,
>> 5): Library not loaded:
>>
>> /Users/kitware/Dashboards/Nightly/Slicer-0-build/ITKv4-build/lib/libITKIOBMP-4.10.1.dylib
>>   Referenced from:
>>
>> /Applications/Slicer.app/Contents/lib/Slicer-4.5/cli-modules/libBRAINSFitLib.dylib
>>   Reason: image not found)", "Cannot load library
>>
>> /Applications/Slicer.app/Contents/lib/Slicer-4.5/cli-modules/libBRAINSFitLib.dylib:
>>
>> (dlopen(/Applications/Slicer.app/Contents/lib/Slicer-4.5/cli-modules/libBRAINSFitLib.dylib,
>> 5): Library not loaded:
>>
>> /Users/kitware/Dashboards/Nightly/Slicer-0-build/ITKv4-build/lib/libITKIOBMP-4.10.1.dylib
>>
>> The workaround is to check "Prefer Executable CLIs" in App settings >
>> Modules.
>>
>> AF
>> _______________________________________________
>> slicer-users mailing list
>> [hidden email]
>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
>> To unsubscribe: send email to [hidden email] with
>> unsubscribe as the subject
>> http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
>
>
_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
Reply | Threaded
Open this post in threaded view
|

Re: Error using "General registration (BRAINS)" module

Steve Pieper-2
Switching to use executables by default makes a lot of sense if the shared library issue isn't easy to fix, at least on mac.

-Steve

On Mon, Jul 18, 2016 at 6:53 AM, Andrey Fedorov <[hidden email]> wrote:
Isaiah,

Thanks for the reply.

Do you know if any application really benefits seriously from this
in-memory communication? There are many important tasks and I wonder
if fixing this shared lib issue is of sufficiently high priority.

>
> This appears to have been an issue for a while now, see:
> http://www.na-mic.org/Bug/view.php?id=4041#c13339
>

Alas, mantis times out on me.

Perhaps we should change the default to executable only.

On the other hand, no-one else complained so far.

AF


On Sun, Jul 17, 2016 at 8:34 AM, Isaiah Norton <[hidden email]> wrote:
> This was the motivation for: https://github.com/Slicer/Slicer/pull/550 to
> get actionable error messages.
>
> The dylib files in `Slicer.app/Contents/lib/Slicer-4.5/cli-modules/` have
> hard-coded RPATHs. There is a second copy one directory up ("Slicer-4.5/")
> which has the correct `@rpath/...` designations. You can actually copy these
> to `cli-modules` and they will then work fine as SharedObjectModule.
>
> This appears to have been an issue for a while now, see:
> http://www.na-mic.org/Bug/view.php?id=4041#c13339
>
> However, some more recent change led to the runtime load failure. Of nightly
> versions I have installed, 5/8 works, 6/8 and later do not. Unfortunately, I
> haven't been able to exactly reproduce this in a local build so not sure
> about a solution. Hopefully Jc will weigh in.
>
> (In local release build, the objects `dlopen` fine, but then fail in ITK
> iterator code with a region size error that "may" be related to shared
> object loading:
> http://public.kitware.com/pipermail/community/2015-October/010057.html)
>
> On Fri, Jul 15, 2016 at 5:46 PM, Andrey Fedorov <[hidden email]>
> wrote:
>>
>> Hi,
>>
>> with the today's nightly, I am unable to run "General registration
>> (BRAINS)". The error says:
>>
>> ModuleType: SharedObjectModule
>> Failed to load
>> "/Applications/Slicer.app/Contents/lib/Slicer-4.5/cli-modules/libBRAINSFitLib.dylib"
>> QLibrary error message(s):
>> ("Cannot load library
>>
>> /Applications/Slicer.app/Contents/lib/Slicer-4.5/cli-modules/libBRAINSFitLib.dylib:
>>
>> (dlopen(/Applications/Slicer.app/Contents/lib/Slicer-4.5/cli-modules/libBRAINSFitLib.dylib,
>> 5): Library not loaded:
>>
>> /Users/kitware/Dashboards/Nightly/Slicer-0-build/ITKv4-build/lib/libITKIOBMP-4.10.1.dylib
>>   Referenced from:
>>
>> /Applications/Slicer.app/Contents/lib/Slicer-4.5/cli-modules/libBRAINSFitLib.dylib
>>   Reason: image not found)", "Cannot load library
>>
>> /Applications/Slicer.app/Contents/lib/Slicer-4.5/cli-modules/libBRAINSFitLib.dylib:
>>
>> (dlopen(/Applications/Slicer.app/Contents/lib/Slicer-4.5/cli-modules/libBRAINSFitLib.dylib,
>> 5): Library not loaded:
>>
>> /Users/kitware/Dashboards/Nightly/Slicer-0-build/ITKv4-build/lib/libITKIOBMP-4.10.1.dylib
>>
>> The workaround is to check "Prefer Executable CLIs" in App settings >
>> Modules.
>>
>> AF
>> _______________________________________________
>> slicer-users mailing list
>> [hidden email]
>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
>> To unsubscribe: send email to [hidden email] with
>> unsubscribe as the subject
>> http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
>
>
_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ


_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ