Slicer 4.5 stable on Linux crash on startup

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Slicer 4.5 stable on Linux crash on startup

Alejo C.S.
Dear list, I'm trying to run Slicer 4.5 stable r24735 on Linux amd64 and it crash every time:

Session start time .......: 2015-11-18 08:35:58
Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 - installed
Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
Memory ...................: 7889 MB physical, 1999 MB virtual 
CPU ......................: GenuineIntel 3.339 MHz, 1 cores
Developer mode enabled ...: no
Prefer executable CLI ....: no
Additional module paths ..: (none)
Number of registered modules: 141 
error: [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real] exit abnormally - Report the problem.


Any help?

Thanks in advance!


PD: There is no problem running Slicer 4.4 



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Re: Slicer 4.5 stable on Linux crash on startup

Andrey Fedorov-2
Alejo,

I've just tried, and could not reproduce this crash on Ubuntu 14.04 LTS.

Can you try removing the settings or moving those files to another
location and check if this resolves the issue? There may be some
compatibility issues with the older settings, or with the extra
modules, if you have any.

http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/FAQ#How_to_uninstall_Slicer.3F

Note that this will reset all of your Slicer user settings.

AF

On Wed, Nov 18, 2015 at 6:41 AM, Alejo C.S. <[hidden email]> wrote:

> Dear list, I'm trying to run Slicer 4.5 stable r24735 on Linux amd64 and it
> crash every time:
>
> Session start time .......: 2015-11-18 08:35:58
> Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 - installed
> Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian
> 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
> Memory ...................: 7889 MB physical, 1999 MB virtual
> CPU ......................: GenuineIntel 3.339 MHz, 1 cores
> Developer mode enabled ...: no
> Prefer executable CLI ....: no
> Additional module paths ..: (none)
> Number of registered modules: 141
> error:
> [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real] exit
> abnormally - Report the problem.
>
>
> Any help?
>
> Thanks in advance!
>
>
> PD: There is no problem running Slicer 4.4
>
>
>
> _______________________________________________
> 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
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
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Re: Slicer 4.5 stable on Linux crash on startup

Andrey Fedorov-2
In reply to this post by Alejo C.S.
Interesting. Not sure what is going on.

cc'ing the list (please make sure you include the list next time)

On Wed, Nov 18, 2015 at 1:05 PM, Alejo C.S. <[hidden email]> wrote:

> Thanks for your response. I had remove the folder ~/.config/NA-MIC and still
> when I run ./Slicer crash on startup with same error:
>
> $ ~/Programas/Slicer-4.5.0-1-linux-amd64$ ./Slicer
> Session start time .......: 2015-11-18 15:04:38
> Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 - installed
> Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian
> 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
> Memory ...................: 7889 MB physical, 1999 MB virtual
> CPU ......................: GenuineIntel 3.398 MHz, 1 cores
> Developer mode enabled ...: no
> Prefer executable CLI ....: no
> Additional module paths ..: (none)
> Number of registered modules: 141
> error:
> [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real] exit
> abnormally - Report the problem.
> marmo@ANET:~/Programas/Slicer-4.5.0-1-linux-amd64$
>
>
>
> 2015-11-18 14:22 GMT-03:00 Andrey Fedorov <[hidden email]>:
>>
>> Alejo,
>>
>> I've just tried, and could not reproduce this crash on Ubuntu 14.04 LTS.
>>
>> Can you try removing the settings or moving those files to another
>> location and check if this resolves the issue? There may be some
>> compatibility issues with the older settings, or with the extra
>> modules, if you have any.
>>
>>
>> http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/FAQ#How_to_uninstall_Slicer.3F
>>
>> Note that this will reset all of your Slicer user settings.
>>
>> AF
>>
>> On Wed, Nov 18, 2015 at 6:41 AM, Alejo C.S. <[hidden email]> wrote:
>> > Dear list, I'm trying to run Slicer 4.5 stable r24735 on Linux amd64 and
>> > it
>> > crash every time:
>> >
>> > Session start time .......: 2015-11-18 08:35:58
>> > Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 -
>> > installed
>> > Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian
>> > 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
>> > Memory ...................: 7889 MB physical, 1999 MB virtual
>> > CPU ......................: GenuineIntel 3.339 MHz, 1 cores
>> > Developer mode enabled ...: no
>> > Prefer executable CLI ....: no
>> > Additional module paths ..: (none)
>> > Number of registered modules: 141
>> > error:
>> > [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real]
>> > exit
>> > abnormally - Report the problem.
>> >
>> >
>> > Any help?
>> >
>> > Thanks in advance!
>> >
>> >
>> > PD: There is no problem running Slicer 4.4
>> >
>> >
>> >
>> > _______________________________________________
>> > 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
>> >
>> >
>> > The information in this e-mail is intended only for the person to whom
>> > it is
>> > addressed. If you believe this e-mail was sent to you in error and the
>> > e-mail
>> > contains patient information, please contact the Partners Compliance
>> > HelpLine at
>> > http://www.partners.org/complianceline . If the e-mail was sent to you
>> > in
>> > error
>> > but does not contain patient information, please contact the sender and
>> > properly
>> > dispose of the e-mail.
>> >
>
>
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Re: Slicer 4.5 stable on Linux crash on startup

Alejo C.S.
In reply to this post by Alejo C.S.
Thanks Andrey, missed the list.

Thanks for your response. I had remove the folder ~/.config/NA-MIC and still when I run ./Slicer crash on startup with same error:
$ ~/Programas/Slicer-4.5.0-1-linux-amd64$ ./Slicer 
Session start time .......: 2015-11-18 15:04:38
Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 - installed
Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
Memory ...................: 7889 MB physical, 1999 MB virtual 
CPU ......................: GenuineIntel 3.398 MHz, 1 cores
Developer mode enabled ...: no
Prefer executable CLI ....: no
Additional module paths ..: (none)
Number of registered modules: 141 
error: [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real] exit abnormally - Report the problem.

2015-11-18 15:07 GMT-03:00 Andrey Fedorov <[hidden email]>:
Interesting. Not sure what is going on.

cc'ing the list (please make sure you include the list next time)

On Wed, Nov 18, 2015 at 1:05 PM, Alejo C.S. <[hidden email]> wrote:
> Thanks for your response. I had remove the folder ~/.config/NA-MIC and still
> when I run ./Slicer crash on startup with same error:
>
> $ ~/Programas/Slicer-4.5.0-1-linux-amd64$ ./Slicer
> Session start time .......: 2015-11-18 15:04:38
> Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 - installed
> Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian
> 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
> Memory ...................: 7889 MB physical, 1999 MB virtual
> CPU ......................: GenuineIntel 3.398 MHz, 1 cores
> Developer mode enabled ...: no
> Prefer executable CLI ....: no
> Additional module paths ..: (none)
> Number of registered modules: 141
> error:
> [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real] exit
> abnormally - Report the problem.
> marmo@ANET:~/Programas/Slicer-4.5.0-1-linux-amd64$
>
>
>
> 2015-11-18 14:22 GMT-03:00 Andrey Fedorov <[hidden email]>:
>>
>> Alejo,
>>
>> I've just tried, and could not reproduce this crash on Ubuntu 14.04 LTS.
>>
>> Can you try removing the settings or moving those files to another
>> location and check if this resolves the issue? There may be some
>> compatibility issues with the older settings, or with the extra
>> modules, if you have any.
>>
>>
>> http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/FAQ#How_to_uninstall_Slicer.3F
>>
>> Note that this will reset all of your Slicer user settings.
>>
>> AF
>>
>> On Wed, Nov 18, 2015 at 6:41 AM, Alejo C.S. <[hidden email]> wrote:
>> > Dear list, I'm trying to run Slicer 4.5 stable r24735 on Linux amd64 and
>> > it
>> > crash every time:
>> >
>> > Session start time .......: 2015-11-18 08:35:58
>> > Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 -
>> > installed
>> > Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian
>> > 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
>> > Memory ...................: 7889 MB physical, 1999 MB virtual
>> > CPU ......................: GenuineIntel 3.339 MHz, 1 cores
>> > Developer mode enabled ...: no
>> > Prefer executable CLI ....: no
>> > Additional module paths ..: (none)
>> > Number of registered modules: 141
>> > error:
>> > [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real]
>> > exit
>> > abnormally - Report the problem.
>> >
>> >
>> > Any help?
>> >
>> > Thanks in advance!
>> >
>> >
>> > PD: There is no problem running Slicer 4.4
>> >
>> >
>> >
>> > _______________________________________________
>> > 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
>> >
>> >
>> > The information in this e-mail is intended only for the person to whom
>> > it is
>> > addressed. If you believe this e-mail was sent to you in error and the
>> > e-mail
>> > contains patient information, please contact the Partners Compliance
>> > HelpLine at
>> > http://www.partners.org/complianceline . If the e-mail was sent to you
>> > in
>> > error
>> > but does not contain patient information, please contact the sender and
>> > properly
>> > dispose of the e-mail.
>> >
>
>


_______________________________________________
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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
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Re: Slicer 4.5 stable on Linux crash on startup

Jean-Christophe Fillion-Robin
Hi Alejo,

Thanks for the report.

Could you try the following and report which one are working/failing:

(1) ./Slicer --disable-settings

(2) ./Slicer --disable-modules --disable-modules


Then, you could also try using these flags:

 --disable-cli-modules
 --disable-loadable-modules
 --disable-scripted-loadable-modules

Hth
Jc



On Wed, Nov 18, 2015 at 1:10 PM, Alejo C.S. <[hidden email]> wrote:
Thanks Andrey, missed the list.

Thanks for your response. I had remove the folder ~/.config/NA-MIC and still when I run ./Slicer crash on startup with same error:
$ ~/Programas/Slicer-4.5.0-1-linux-amd64$ ./Slicer 
Session start time .......: 2015-11-18 15:04:38
Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 - installed
Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
Memory ...................: 7889 MB physical, 1999 MB virtual 
CPU ......................: GenuineIntel 3.398 MHz, 1 cores
Developer mode enabled ...: no
Prefer executable CLI ....: no
Additional module paths ..: (none)
Number of registered modules: 141 
error: [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real] exit abnormally - Report the problem.

2015-11-18 15:07 GMT-03:00 Andrey Fedorov <[hidden email]>:
Interesting. Not sure what is going on.

cc'ing the list (please make sure you include the list next time)

On Wed, Nov 18, 2015 at 1:05 PM, Alejo C.S. <[hidden email]> wrote:
> Thanks for your response. I had remove the folder ~/.config/NA-MIC and still
> when I run ./Slicer crash on startup with same error:
>
> $ ~/Programas/Slicer-4.5.0-1-linux-amd64$ ./Slicer
> Session start time .......: 2015-11-18 15:04:38
> Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 - installed
> Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian
> 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
> Memory ...................: 7889 MB physical, 1999 MB virtual
> CPU ......................: GenuineIntel 3.398 MHz, 1 cores
> Developer mode enabled ...: no
> Prefer executable CLI ....: no
> Additional module paths ..: (none)
> Number of registered modules: 141
> error:
> [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real] exit
> abnormally - Report the problem.
> marmo@ANET:~/Programas/Slicer-4.5.0-1-linux-amd64$
>
>
>
> 2015-11-18 14:22 GMT-03:00 Andrey Fedorov <[hidden email]>:
>>
>> Alejo,
>>
>> I've just tried, and could not reproduce this crash on Ubuntu 14.04 LTS.
>>
>> Can you try removing the settings or moving those files to another
>> location and check if this resolves the issue? There may be some
>> compatibility issues with the older settings, or with the extra
>> modules, if you have any.
>>
>>
>> http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/FAQ#How_to_uninstall_Slicer.3F
>>
>> Note that this will reset all of your Slicer user settings.
>>
>> AF
>>
>> On Wed, Nov 18, 2015 at 6:41 AM, Alejo C.S. <[hidden email]> wrote:
>> > Dear list, I'm trying to run Slicer 4.5 stable r24735 on Linux amd64 and
>> > it
>> > crash every time:
>> >
>> > Session start time .......: 2015-11-18 08:35:58
>> > Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 -
>> > installed
>> > Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian
>> > 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
>> > Memory ...................: 7889 MB physical, 1999 MB virtual
>> > CPU ......................: GenuineIntel 3.339 MHz, 1 cores
>> > Developer mode enabled ...: no
>> > Prefer executable CLI ....: no
>> > Additional module paths ..: (none)
>> > Number of registered modules: 141
>> > error:
>> > [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real]
>> > exit
>> > abnormally - Report the problem.
>> >
>> >
>> > Any help?
>> >
>> > Thanks in advance!
>> >
>> >
>> > PD: There is no problem running Slicer 4.4
>> >
>> >
>> >
>> > _______________________________________________
>> > 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
>> >
>> >
>> > The information in this e-mail is intended only for the person to whom
>> > it is
>> > addressed. If you believe this e-mail was sent to you in error and the
>> > e-mail
>> > contains patient information, please contact the Partners Compliance
>> > HelpLine at
>> > http://www.partners.org/complianceline . If the e-mail was sent to you
>> > in
>> > error
>> > but does not contain patient information, please contact the sender and
>> > properly
>> > dispose of the e-mail.
>> >
>
>


_______________________________________________
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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.




--
+1 919 869 8849

_______________________________________________
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To unsubscribe: send email to [hidden email] with unsubscribe as the subject
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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Re: Slicer 4.5 stable on Linux crash on startup

Andras Lasso-2

It would help a lot to know in which shared library the crash occurs. Can you run Slicer in gdb? (you need to run gdb with the launcher: Slicer, and then in gdb run the actual application: SlicerApp-real)

 

You may also try to upgrade/downgrade your graphics card driver.

 

Andras

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Jean-Christophe Fillion-Robin
Sent: Wednesday, November 18, 2015 1:49 PM
To: Alejo C.S. <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Slicer 4.5 stable on Linux crash on startup

 

Hi Alejo,

Thanks for the report.

Could you try the following and report which one are working/failing:

(1) ./Slicer --disable-settings

(2) ./Slicer --disable-modules --disable-modules

Then, you could also try using these flags:

 --disable-cli-modules
 --disable-loadable-modules
 --disable-scripted-loadable-modules

 

Hth

Jc

 

 

On Wed, Nov 18, 2015 at 1:10 PM, Alejo C.S. <[hidden email]> wrote:

Thanks Andrey, missed the list.

 

Thanks for your response. I had remove the folder ~/.config/NA-MIC and still when I run ./Slicer crash on startup with same error:
$ ~/Programas/Slicer-4.5.0-1-linux-amd64$ ./Slicer 
Session start time .......: 2015-11-18 15:04:38
Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 - installed
Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
Memory ...................: 7889 MB physical, 1999 MB virtual 
CPU ......................: GenuineIntel 3.398 MHz, 1 cores
Developer mode enabled ...: no
Prefer executable CLI ....: no
Additional module paths ..: (none)
Number of registered modules: 141 
error: [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real] exit abnormally - Report the problem.

 

2015-11-18 15:07 GMT-03:00 Andrey Fedorov <[hidden email]>:

Interesting. Not sure what is going on.

cc'ing the list (please make sure you include the list next time)


On Wed, Nov 18, 2015 at 1:05 PM, Alejo C.S. <[hidden email]> wrote:
> Thanks for your response. I had remove the folder ~/.config/NA-MIC and still
> when I run ./Slicer crash on startup with same error:
>
> $ ~/Programas/Slicer-4.5.0-1-linux-amd64$ ./Slicer
> Session start time .......: 2015-11-18 15:04:38
> Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 - installed
> Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian
> 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
> Memory ...................: 7889 MB physical, 1999 MB virtual
> CPU ......................: GenuineIntel 3.398 MHz, 1 cores
> Developer mode enabled ...: no
> Prefer executable CLI ....: no
> Additional module paths ..: (none)
> Number of registered modules: 141
> error:
> [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real] exit
> abnormally - Report the problem.
> [hidden email]
>
>
>
> 2015-11-18 14:22 GMT-03:00 Andrey Fedorov <[hidden email]>:
>>
>> Alejo,
>>
>> I've just tried, and could not reproduce this crash on Ubuntu 14.04 LTS.
>>
>> Can you try removing the settings or moving those files to another
>> location and check if this resolves the issue? There may be some
>> compatibility issues with the older settings, or with the extra
>> modules, if you have any.
>>
>>
>> http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/FAQ#How_to_uninstall_Slicer.3F
>>
>> Note that this will reset all of your Slicer user settings.
>>
>> AF
>>
>> On Wed, Nov 18, 2015 at 6:41 AM, Alejo C.S. <[hidden email]> wrote:

>> > Dear list, I'm trying to run Slicer 4.5 stable r24735 on Linux amd64 and
>> > it
>> > crash every time:
>> >
>> > Session start time .......: 2015-11-18 08:35:58
>> > Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 -
>> > installed
>> > Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian
>> > 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
>> > Memory ...................: 7889 MB physical, 1999 MB virtual
>> > CPU ......................: GenuineIntel 3.339 MHz, 1 cores
>> > Developer mode enabled ...: no
>> > Prefer executable CLI ....: no
>> > Additional module paths ..: (none)
>> > Number of registered modules: 141
>> > error:
>> > [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real]
>> > exit
>> > abnormally - Report the problem.
>> >
>> >
>> > Any help?
>> >
>> > Thanks in advance!
>> >
>> >
>> > PD: There is no problem running Slicer 4.4
>> >
>> >
>> >

>> > _______________________________________________
>> > 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
>> >
>> >
>> > The information in this e-mail is intended only for the person to whom
>> > it is
>> > addressed. If you believe this e-mail was sent to you in error and the
>> > e-mail
>> > contains patient information, please contact the Partners Compliance
>> > HelpLine at
>> > http://www.partners.org/complianceline . If the e-mail was sent to you
>> > in
>> > error
>> > but does not contain patient information, please contact the sender and
>> > properly
>> > dispose of the e-mail.
>> >
>
>

 


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Re: Slicer 4.5 stable on Linux crash on startup

Alejo C.S.
In reply to this post by Jean-Christophe Fillion-Robin
Ok, the results with each settings are:


./Slicer --disable-settings 
Crash all times

./Slicer --disable-modules --disable-modules
Starts on all attempts

./Slicer  --disable-cli-modules
Crash all times

./Slicer --disable-loadable-modules
Crash all times

./Slicer --disable-scripted-loadable-modules
Starts on all attempts


In gdb mode Running Slicer and SlicerApp-real this shows up:

Starting program: /home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real 
/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real: error while loading shared libraries: libqSlicerApp.so: cannot open shared object file: No such file or directory
[Inferior 1 (process 13519) exited with code 0177]


Starting program: /home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real bin/SlicerApp-real
/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real: error while loading shared libraries: libqSlicerApp.so: cannot open shared object file: No such file or directory
[Inferior 1 (process 13553) exited with code 0177]
(gdb) 


ls -l on ./lib/Slicer-4.5/libqSlicerApp.so

-rw-r--r-- 1 marmo marmo 810K 12/11/2015 17:06:23 ./lib/Slicer-4.5/libqSlicerApp.so

Hope this is useful.

Thanks in advance.

Alejo



2015-11-18 16:13 GMT-03:00 Andras Lasso <[hidden email]>:

It would help a lot to know in which shared library the crash occurs. Can you run Slicer in gdb? (you need to run gdb with the launcher: Slicer, and then in gdb run the actual application: SlicerApp-real)

 

You may also try to upgrade/downgrade your graphics card driver.

 

Andras

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Jean-Christophe Fillion-Robin
Sent: Wednesday, November 18, 2015 1:49 PM
To: Alejo C.S. <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Slicer 4.5 stable on Linux crash on startup

 

Hi Alejo,

Thanks for the report.

Could you try the following and report which one are working/failing:

(1) ./Slicer --disable-settings

(2) ./Slicer --disable-modules --disable-modules

Then, you could also try using these flags:

 --disable-cli-modules
 --disable-loadable-modules
 --disable-scripted-loadable-modules

 

Hth

Jc

 

 

On Wed, Nov 18, 2015 at 1:10 PM, Alejo C.S. <[hidden email]> wrote:

Thanks Andrey, missed the list.

 

Thanks for your response. I had remove the folder ~/.config/NA-MIC and still when I run ./Slicer crash on startup with same error:
$ ~/Programas/Slicer-4.5.0-1-linux-amd64$ ./Slicer 
Session start time .......: 2015-11-18 15:04:38
Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 - installed
Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
Memory ...................: 7889 MB physical, 1999 MB virtual 
CPU ......................: GenuineIntel 3.398 MHz, 1 cores
Developer mode enabled ...: no
Prefer executable CLI ....: no
Additional module paths ..: (none)
Number of registered modules: 141 
error: [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real] exit abnormally - Report the problem.

 

2015-11-18 15:07 GMT-03:00 Andrey Fedorov <[hidden email]>:

Interesting. Not sure what is going on.

cc'ing the list (please make sure you include the list next time)


On Wed, Nov 18, 2015 at 1:05 PM, Alejo C.S. <[hidden email]> wrote:
> Thanks for your response. I had remove the folder ~/.config/NA-MIC and still
> when I run ./Slicer crash on startup with same error:
>
> $ ~/Programas/Slicer-4.5.0-1-linux-amd64$ ./Slicer
> Session start time .......: 2015-11-18 15:04:38
> Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 - installed
> Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian
> 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
> Memory ...................: 7889 MB physical, 1999 MB virtual
> CPU ......................: GenuineIntel 3.398 MHz, 1 cores
> Developer mode enabled ...: no
> Prefer executable CLI ....: no
> Additional module paths ..: (none)
> Number of registered modules: 141
> error:
> [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real] exit
> abnormally - Report the problem.
> [hidden email]
>
>
>
> 2015-11-18 14:22 GMT-03:00 Andrey Fedorov <[hidden email]>:
>>
>> Alejo,
>>
>> I've just tried, and could not reproduce this crash on Ubuntu 14.04 LTS.
>>
>> Can you try removing the settings or moving those files to another
>> location and check if this resolves the issue? There may be some
>> compatibility issues with the older settings, or with the extra
>> modules, if you have any.
>>
>>
>> http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/FAQ#How_to_uninstall_Slicer.3F
>>
>> Note that this will reset all of your Slicer user settings.
>>
>> AF
>>
>> On Wed, Nov 18, 2015 at 6:41 AM, Alejo C.S. <[hidden email]> wrote:

>> > Dear list, I'm trying to run Slicer 4.5 stable r24735 on Linux amd64 and
>> > it
>> > crash every time:
>> >
>> > Session start time .......: 2015-11-18 08:35:58
>> > Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 -
>> > installed
>> > Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian
>> > 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
>> > Memory ...................: 7889 MB physical, 1999 MB virtual
>> > CPU ......................: GenuineIntel 3.339 MHz, 1 cores
>> > Developer mode enabled ...: no
>> > Prefer executable CLI ....: no
>> > Additional module paths ..: (none)
>> > Number of registered modules: 141
>> > error:
>> > [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real]
>> > exit
>> > abnormally - Report the problem.
>> >
>> >
>> > Any help?
>> >
>> > Thanks in advance!
>> >
>> >
>> > PD: There is no problem running Slicer 4.4
>> >
>> >
>> >

>> > _______________________________________________
>> > 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
>> >
>> >
>> > The information in this e-mail is intended only for the person to whom
>> > it is
>> > addressed. If you believe this e-mail was sent to you in error and the
>> > e-mail
>> > contains patient information, please contact the Partners Compliance
>> > HelpLine at
>> > http://www.partners.org/complianceline . If the e-mail was sent to you
>> > in
>> > error
>> > but does not contain patient information, please contact the sender and
>> > properly
>> > dispose of the e-mail.
>> >
>
>

 


_______________________________________________
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[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.




--

+1 919 869 8849



_______________________________________________
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The information in this e-mail is intended only for the person to whom it is
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Re: Slicer 4.5 stable on Linux crash on startup

Alejo C.S.
Any news on this? Same crash on last build (revision 24775 built 2015-11-26) with same error on 

"libqSlicerApp.so: cannot open shared object file: No such file or directory"

Regards

2015-11-18 17:03 GMT-03:00 Alejo C.S. <[hidden email]>:
Ok, the results with each settings are:


./Slicer --disable-settings 
Crash all times

./Slicer --disable-modules --disable-modules
Starts on all attempts

./Slicer  --disable-cli-modules
Crash all times

./Slicer --disable-loadable-modules
Crash all times

./Slicer --disable-scripted-loadable-modules
Starts on all attempts


In gdb mode Running Slicer and SlicerApp-real this shows up:

Starting program: /home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real 
/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real: error while loading shared libraries: libqSlicerApp.so: cannot open shared object file: No such file or directory
[Inferior 1 (process 13519) exited with code 0177]


Starting program: /home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real bin/SlicerApp-real
/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real: error while loading shared libraries: libqSlicerApp.so: cannot open shared object file: No such file or directory
[Inferior 1 (process 13553) exited with code 0177]
(gdb) 


ls -l on ./lib/Slicer-4.5/libqSlicerApp.so

-rw-r--r-- 1 marmo marmo 810K 12/11/2015 17:06:23 ./lib/Slicer-4.5/libqSlicerApp.so

Hope this is useful.

Thanks in advance.

Alejo



2015-11-18 16:13 GMT-03:00 Andras Lasso <[hidden email]>:

It would help a lot to know in which shared library the crash occurs. Can you run Slicer in gdb? (you need to run gdb with the launcher: Slicer, and then in gdb run the actual application: SlicerApp-real)

 

You may also try to upgrade/downgrade your graphics card driver.

 

Andras

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Jean-Christophe Fillion-Robin
Sent: Wednesday, November 18, 2015 1:49 PM
To: Alejo C.S. <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Slicer 4.5 stable on Linux crash on startup

 

Hi Alejo,

Thanks for the report.

Could you try the following and report which one are working/failing:

(1) ./Slicer --disable-settings

(2) ./Slicer --disable-modules --disable-modules

Then, you could also try using these flags:

 --disable-cli-modules
 --disable-loadable-modules
 --disable-scripted-loadable-modules

 

Hth

Jc

 

 

On Wed, Nov 18, 2015 at 1:10 PM, Alejo C.S. <[hidden email]> wrote:

Thanks Andrey, missed the list.

 

Thanks for your response. I had remove the folder ~/.config/NA-MIC and still when I run ./Slicer crash on startup with same error:
$ ~/Programas/Slicer-4.5.0-1-linux-amd64$ ./Slicer 
Session start time .......: 2015-11-18 15:04:38
Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 - installed
Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
Memory ...................: 7889 MB physical, 1999 MB virtual 
CPU ......................: GenuineIntel 3.398 MHz, 1 cores
Developer mode enabled ...: no
Prefer executable CLI ....: no
Additional module paths ..: (none)
Number of registered modules: 141 
error: [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real] exit abnormally - Report the problem.

 

2015-11-18 15:07 GMT-03:00 Andrey Fedorov <[hidden email]>:

Interesting. Not sure what is going on.

cc'ing the list (please make sure you include the list next time)


On Wed, Nov 18, 2015 at 1:05 PM, Alejo C.S. <[hidden email]> wrote:
> Thanks for your response. I had remove the folder ~/.config/NA-MIC and still
> when I run ./Slicer crash on startup with same error:
>
> $ ~/Programas/Slicer-4.5.0-1-linux-amd64$ ./Slicer
> Session start time .......: 2015-11-18 15:04:38
> Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 - installed
> Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian
> 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
> Memory ...................: 7889 MB physical, 1999 MB virtual
> CPU ......................: GenuineIntel 3.398 MHz, 1 cores
> Developer mode enabled ...: no
> Prefer executable CLI ....: no
> Additional module paths ..: (none)
> Number of registered modules: 141
> error:
> [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real] exit
> abnormally - Report the problem.
> [hidden email]
>
>
>
> 2015-11-18 14:22 GMT-03:00 Andrey Fedorov <[hidden email]>:
>>
>> Alejo,
>>
>> I've just tried, and could not reproduce this crash on Ubuntu 14.04 LTS.
>>
>> Can you try removing the settings or moving those files to another
>> location and check if this resolves the issue? There may be some
>> compatibility issues with the older settings, or with the extra
>> modules, if you have any.
>>
>>
>> http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/FAQ#How_to_uninstall_Slicer.3F
>>
>> Note that this will reset all of your Slicer user settings.
>>
>> AF
>>
>> On Wed, Nov 18, 2015 at 6:41 AM, Alejo C.S. <[hidden email]> wrote:

>> > Dear list, I'm trying to run Slicer 4.5 stable r24735 on Linux amd64 and
>> > it
>> > crash every time:
>> >
>> > Session start time .......: 2015-11-18 08:35:58
>> > Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 -
>> > installed
>> > Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian
>> > 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
>> > Memory ...................: 7889 MB physical, 1999 MB virtual
>> > CPU ......................: GenuineIntel 3.339 MHz, 1 cores
>> > Developer mode enabled ...: no
>> > Prefer executable CLI ....: no
>> > Additional module paths ..: (none)
>> > Number of registered modules: 141
>> > error:
>> > [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real]
>> > exit
>> > abnormally - Report the problem.
>> >
>> >
>> > Any help?
>> >
>> > Thanks in advance!
>> >
>> >
>> > PD: There is no problem running Slicer 4.4
>> >
>> >
>> >

>> > _______________________________________________
>> > 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
>> >
>> >
>> > The information in this e-mail is intended only for the person to whom
>> > it is
>> > addressed. If you believe this e-mail was sent to you in error and the
>> > e-mail
>> > contains patient information, please contact the Partners Compliance
>> > HelpLine at
>> > http://www.partners.org/complianceline . If the e-mail was sent to you
>> > in
>> > error
>> > but does not contain patient information, please contact the sender and
>> > properly
>> > dispose of the e-mail.
>> >
>
>

 


_______________________________________________
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
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.




--

+1 919 869 8849



_______________________________________________
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The information in this e-mail is intended only for the person to whom it is
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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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Re: Slicer 4.5 stable on Linux crash on startup

Jean-Christophe Fillion-Robin
In reply to this post by Jean-Christophe Fillion-Robin
Hi Alejo,

Thanks for reporting back.

This is helpful. It seems on of the scripted module (or one of its dependencies) is the culprit.

Before creating a script that would allow us to find out which one is the culprit.

You could try attaching gdb.

In a nutshell, you start Slicer using:

   ./Slicer --attach-process

and then attach the debugger.

More details are posted here:

  http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/Debug_Instructions#GDB_debug_by_attaching_to_running_process_.5BRECOMMENDED.5D

That should help identify which library is causing trouble.

Hth
Jc

On Wed, Nov 18, 2015 at 3:03 PM, Alejo C.S. <[hidden email]> wrote:
Ok, the results with each settings are:


./Slicer --disable-settings 
Crash all times

./Slicer --disable-modules --disable-modules
Starts on all attempts

./Slicer  --disable-cli-modules
Crash all times

./Slicer --disable-loadable-modules
Crash all times

./Slicer --disable-scripted-loadable-modules
Starts on all attempts


In gdb mode Running Slicer and SlicerApp-real this shows up:

Starting program: /home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real 
/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real: error while loading shared libraries: libqSlicerApp.so: cannot open shared object file: No such file or directory
[Inferior 1 (process 13519) exited with code 0177]


Starting program: /home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real bin/SlicerApp-real
/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real: error while loading shared libraries: libqSlicerApp.so: cannot open shared object file: No such file or directory
[Inferior 1 (process 13553) exited with code 0177]
(gdb) 


ls -l on ./lib/Slicer-4.5/libqSlicerApp.so

-rw-r--r-- 1 marmo marmo 810K 12/11/2015 17:06:23 ./lib/Slicer-4.5/libqSlicerApp.so

Hope this is useful.

Thanks in advance.

Alejo



2015-11-18 16:13 GMT-03:00 Andras Lasso <[hidden email]>:

It would help a lot to know in which shared library the crash occurs. Can you run Slicer in gdb? (you need to run gdb with the launcher: Slicer, and then in gdb run the actual application: SlicerApp-real)

 

You may also try to upgrade/downgrade your graphics card driver.

 

Andras

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Jean-Christophe Fillion-Robin
Sent: Wednesday, November 18, 2015 1:49 PM
To: Alejo C.S. <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Slicer 4.5 stable on Linux crash on startup

 

Hi Alejo,

Thanks for the report.

Could you try the following and report which one are working/failing:

(1) ./Slicer --disable-settings

(2) ./Slicer --disable-modules --disable-modules

Then, you could also try using these flags:

 --disable-cli-modules
 --disable-loadable-modules
 --disable-scripted-loadable-modules

 

Hth

Jc

 

 

On Wed, Nov 18, 2015 at 1:10 PM, Alejo C.S. <[hidden email]> wrote:

Thanks Andrey, missed the list.

 

Thanks for your response. I had remove the folder ~/.config/NA-MIC and still when I run ./Slicer crash on startup with same error:
$ ~/Programas/Slicer-4.5.0-1-linux-amd64$ ./Slicer 
Session start time .......: 2015-11-18 15:04:38
Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 - installed
Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
Memory ...................: 7889 MB physical, 1999 MB virtual 
CPU ......................: GenuineIntel 3.398 MHz, 1 cores
Developer mode enabled ...: no
Prefer executable CLI ....: no
Additional module paths ..: (none)
Number of registered modules: 141 
error: [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real] exit abnormally - Report the problem.

 

2015-11-18 15:07 GMT-03:00 Andrey Fedorov <[hidden email]>:

Interesting. Not sure what is going on.

cc'ing the list (please make sure you include the list next time)


On Wed, Nov 18, 2015 at 1:05 PM, Alejo C.S. <[hidden email]> wrote:
> Thanks for your response. I had remove the folder ~/.config/NA-MIC and still
> when I run ./Slicer crash on startup with same error:
>
> $ ~/Programas/Slicer-4.5.0-1-linux-amd64$ ./Slicer
> Session start time .......: 2015-11-18 15:04:38
> Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 - installed
> Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian
> 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
> Memory ...................: 7889 MB physical, 1999 MB virtual
> CPU ......................: GenuineIntel 3.398 MHz, 1 cores
> Developer mode enabled ...: no
> Prefer executable CLI ....: no
> Additional module paths ..: (none)
> Number of registered modules: 141
> error:
> [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real] exit
> abnormally - Report the problem.
> [hidden email]
>
>
>
> 2015-11-18 14:22 GMT-03:00 Andrey Fedorov <[hidden email]>:
>>
>> Alejo,
>>
>> I've just tried, and could not reproduce this crash on Ubuntu 14.04 LTS.
>>
>> Can you try removing the settings or moving those files to another
>> location and check if this resolves the issue? There may be some
>> compatibility issues with the older settings, or with the extra
>> modules, if you have any.
>>
>>
>> http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/FAQ#How_to_uninstall_Slicer.3F
>>
>> Note that this will reset all of your Slicer user settings.
>>
>> AF
>>
>> On Wed, Nov 18, 2015 at 6:41 AM, Alejo C.S. <[hidden email]> wrote:

>> > Dear list, I'm trying to run Slicer 4.5 stable r24735 on Linux amd64 and
>> > it
>> > crash every time:
>> >
>> > Session start time .......: 2015-11-18 08:35:58
>> > Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 -
>> > installed
>> > Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian
>> > 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
>> > Memory ...................: 7889 MB physical, 1999 MB virtual
>> > CPU ......................: GenuineIntel 3.339 MHz, 1 cores
>> > Developer mode enabled ...: no
>> > Prefer executable CLI ....: no
>> > Additional module paths ..: (none)
>> > Number of registered modules: 141
>> > error:
>> > [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real]
>> > exit
>> > abnormally - Report the problem.
>> >
>> >
>> > Any help?
>> >
>> > Thanks in advance!
>> >
>> >
>> > PD: There is no problem running Slicer 4.4
>> >
>> >
>> >

>> > _______________________________________________
>> > 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
>> >
>> >
>> > The information in this e-mail is intended only for the person to whom
>> > it is
>> > addressed. If you believe this e-mail was sent to you in error and the
>> > e-mail
>> > contains patient information, please contact the Partners Compliance
>> > HelpLine at
>> > http://www.partners.org/complianceline . If the e-mail was sent to you
>> > in
>> > error
>> > but does not contain patient information, please contact the sender and
>> > properly
>> > dispose of the e-mail.
>> >
>
>

 


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http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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The information in this e-mail is intended only for the person to whom it is
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Re: Slicer 4.5 stable on Linux crash on startup

Alejo C.S.
In reply to this post by Jean-Christophe Fillion-Robin
Hi Jean-Christophe, the results of gdb are the following:

Program received signal SIGSEGV, Segmentation fault.
0x00007f9c34974626 in vtkSubjectHelper::InvokeEvent(unsigned long, void*, vtkObject*) ()
   from /home/ar/Programas/Slicer-4.5.0-1-linux-amd64/./lib/Slicer-4.5/libvtkCommon-6.3.so.1
(gdb) 

Hope it helps

Regards,

A.


2015-11-26 16:14 GMT-03:00 Jean-Christophe Fillion-Robin <[hidden email]>:
Hi Alejo,

Thanks for reporting back.

This is helpful. It seems on of the scripted module (or one of its dependencies) is the culprit.

Before creating a script that would allow us to find out which one is the culprit.

You could try attaching gdb.

In a nutshell, you start Slicer using:

   ./Slicer --attach-process

and then attach the debugger.

More details are posted here:

  http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/Debug_Instructions#GDB_debug_by_attaching_to_running_process_.5BRECOMMENDED.5D

That should help identify which library is causing trouble.

Hth
Jc

On Wed, Nov 18, 2015 at 3:03 PM, Alejo C.S. <[hidden email]> wrote:
Ok, the results with each settings are:


./Slicer --disable-settings 
Crash all times

./Slicer --disable-modules --disable-modules
Starts on all attempts

./Slicer  --disable-cli-modules
Crash all times

./Slicer --disable-loadable-modules
Crash all times

./Slicer --disable-scripted-loadable-modules
Starts on all attempts


In gdb mode Running Slicer and SlicerApp-real this shows up:

Starting program: /home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real 
/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real: error while loading shared libraries: libqSlicerApp.so: cannot open shared object file: No such file or directory
[Inferior 1 (process 13519) exited with code 0177]


Starting program: /home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real bin/SlicerApp-real
/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real: error while loading shared libraries: libqSlicerApp.so: cannot open shared object file: No such file or directory
[Inferior 1 (process 13553) exited with code 0177]
(gdb) 


ls -l on ./lib/Slicer-4.5/libqSlicerApp.so

-rw-r--r-- 1 marmo marmo 810K 12/11/2015 17:06:23 ./lib/Slicer-4.5/libqSlicerApp.so

Hope this is useful.

Thanks in advance.

Alejo



2015-11-18 16:13 GMT-03:00 Andras Lasso <[hidden email]>:

It would help a lot to know in which shared library the crash occurs. Can you run Slicer in gdb? (you need to run gdb with the launcher: Slicer, and then in gdb run the actual application: SlicerApp-real)

 

You may also try to upgrade/downgrade your graphics card driver.

 

Andras

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Jean-Christophe Fillion-Robin
Sent: Wednesday, November 18, 2015 1:49 PM
To: Alejo C.S. <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Slicer 4.5 stable on Linux crash on startup

 

Hi Alejo,

Thanks for the report.

Could you try the following and report which one are working/failing:

(1) ./Slicer --disable-settings

(2) ./Slicer --disable-modules --disable-modules

Then, you could also try using these flags:

 --disable-cli-modules
 --disable-loadable-modules
 --disable-scripted-loadable-modules

 

Hth

Jc

 

 

On Wed, Nov 18, 2015 at 1:10 PM, Alejo C.S. <[hidden email]> wrote:

Thanks Andrey, missed the list.

 

Thanks for your response. I had remove the folder ~/.config/NA-MIC and still when I run ./Slicer crash on startup with same error:
$ ~/Programas/Slicer-4.5.0-1-linux-amd64$ ./Slicer 
Session start time .......: 2015-11-18 15:04:38
Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 - installed
Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
Memory ...................: 7889 MB physical, 1999 MB virtual 
CPU ......................: GenuineIntel 3.398 MHz, 1 cores
Developer mode enabled ...: no
Prefer executable CLI ....: no
Additional module paths ..: (none)
Number of registered modules: 141 
error: [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real] exit abnormally - Report the problem.

 

2015-11-18 15:07 GMT-03:00 Andrey Fedorov <[hidden email]>:

Interesting. Not sure what is going on.

cc'ing the list (please make sure you include the list next time)


On Wed, Nov 18, 2015 at 1:05 PM, Alejo C.S. <[hidden email]> wrote:
> Thanks for your response. I had remove the folder ~/.config/NA-MIC and still
> when I run ./Slicer crash on startup with same error:
>
> $ ~/Programas/Slicer-4.5.0-1-linux-amd64$ ./Slicer
> Session start time .......: 2015-11-18 15:04:38
> Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 - installed
> Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian
> 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
> Memory ...................: 7889 MB physical, 1999 MB virtual
> CPU ......................: GenuineIntel 3.398 MHz, 1 cores
> Developer mode enabled ...: no
> Prefer executable CLI ....: no
> Additional module paths ..: (none)
> Number of registered modules: 141
> error:
> [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real] exit
> abnormally - Report the problem.
> [hidden email]
>
>
>
> 2015-11-18 14:22 GMT-03:00 Andrey Fedorov <[hidden email]>:
>>
>> Alejo,
>>
>> I've just tried, and could not reproduce this crash on Ubuntu 14.04 LTS.
>>
>> Can you try removing the settings or moving those files to another
>> location and check if this resolves the issue? There may be some
>> compatibility issues with the older settings, or with the extra
>> modules, if you have any.
>>
>>
>> http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/FAQ#How_to_uninstall_Slicer.3F
>>
>> Note that this will reset all of your Slicer user settings.
>>
>> AF
>>
>> On Wed, Nov 18, 2015 at 6:41 AM, Alejo C.S. <[hidden email]> wrote:

>> > Dear list, I'm trying to run Slicer 4.5 stable r24735 on Linux amd64 and
>> > it
>> > crash every time:
>> >
>> > Session start time .......: 2015-11-18 08:35:58
>> > Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 -
>> > installed
>> > Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian
>> > 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
>> > Memory ...................: 7889 MB physical, 1999 MB virtual
>> > CPU ......................: GenuineIntel 3.339 MHz, 1 cores
>> > Developer mode enabled ...: no
>> > Prefer executable CLI ....: no
>> > Additional module paths ..: (none)
>> > Number of registered modules: 141
>> > error:
>> > [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real]
>> > exit
>> > abnormally - Report the problem.
>> >
>> >
>> > Any help?
>> >
>> > Thanks in advance!
>> >
>> >
>> > PD: There is no problem running Slicer 4.4
>> >
>> >
>> >

>> > _______________________________________________
>> > 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
>> >
>> >
>> > The information in this e-mail is intended only for the person to whom
>> > it is
>> > addressed. If you believe this e-mail was sent to you in error and the
>> > e-mail
>> > contains patient information, please contact the Partners Compliance
>> > HelpLine at
>> > http://www.partners.org/complianceline . If the e-mail was sent to you
>> > in
>> > error
>> > but does not contain patient information, please contact the sender and
>> > properly
>> > dispose of the e-mail.
>> >
>
>

 


_______________________________________________
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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.




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<a href="tel:%2B1%20919%20869%208849" value="&#43;19198698849" target="_blank">+1 919 869 8849





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+1 919 869 8849


_______________________________________________
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
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Re: Slicer 4.5 stable on Linux crash on startup

Andras Lasso-2
Could you please also send the stack trace? (I think the command to print it is: bt)

Andras

From: [hidden email]
Sent: ‎2015-‎11-‎27 08:12
To: [hidden email]
Subject: Re: [slicer-users] Slicer 4.5 stable on Linux crash on startup

Hi Jean-Christophe, the results of gdb are the following:

Program received signal SIGSEGV, Segmentation fault.
0x00007f9c34974626 in vtkSubjectHelper::InvokeEvent(unsigned long, void*, vtkObject*) ()
   from /home/ar/Programas/Slicer-4.5.0-1-linux-amd64/./lib/Slicer-4.5/libvtkCommon-6.3.so.1
(gdb) 

Hope it helps

Regards,

A.


2015-11-26 16:14 GMT-03:00 Jean-Christophe Fillion-Robin <[hidden email]>:
Hi Alejo,

Thanks for reporting back.

This is helpful. It seems on of the scripted module (or one of its dependencies) is the culprit.

Before creating a script that would allow us to find out which one is the culprit.

You could try attaching gdb.

In a nutshell, you start Slicer using:

   ./Slicer --attach-process

and then attach the debugger.

More details are posted here:

  http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/Debug_Instructions#GDB_debug_by_attaching_to_running_process_.5BRECOMMENDED.5D

That should help identify which library is causing trouble.

Hth
Jc

On Wed, Nov 18, 2015 at 3:03 PM, Alejo C.S. <[hidden email]> wrote:
Ok, the results with each settings are:


./Slicer --disable-settings 
Crash all times

./Slicer --disable-modules --disable-modules
Starts on all attempts

./Slicer  --disable-cli-modules
Crash all times

./Slicer --disable-loadable-modules
Crash all times

./Slicer --disable-scripted-loadable-modules
Starts on all attempts


In gdb mode Running Slicer and SlicerApp-real this shows up:

Starting program: /home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real 
/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real: error while loading shared libraries: libqSlicerApp.so: cannot open shared object file: No such file or directory
[Inferior 1 (process 13519) exited with code 0177]


Starting program: /home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real bin/SlicerApp-real
/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real: error while loading shared libraries: libqSlicerApp.so: cannot open shared object file: No such file or directory
[Inferior 1 (process 13553) exited with code 0177]
(gdb) 


ls -l on ./lib/Slicer-4.5/libqSlicerApp.so

-rw-r--r-- 1 marmo marmo 810K 12/11/2015 17:06:23 ./lib/Slicer-4.5/libqSlicerApp.so

Hope this is useful.

Thanks in advance.

Alejo



2015-11-18 16:13 GMT-03:00 Andras Lasso <[hidden email]>:

It would help a lot to know in which shared library the crash occurs. Can you run Slicer in gdb? (you need to run gdb with the launcher: Slicer, and then in gdb run the actual application: SlicerApp-real)

 

You may also try to upgrade/downgrade your graphics card driver.

 

Andras

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Jean-Christophe Fillion-Robin
Sent: Wednesday, November 18, 2015 1:49 PM
To: Alejo C.S. <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Slicer 4.5 stable on Linux crash on startup

 

Hi Alejo,

Thanks for the report.

Could you try the following and report which one are working/failing:

(1) ./Slicer --disable-settings

(2) ./Slicer --disable-modules --disable-modules

Then, you could also try using these flags:

 --disable-cli-modules
 --disable-loadable-modules
 --disable-scripted-loadable-modules

 

Hth

Jc

 

 

On Wed, Nov 18, 2015 at 1:10 PM, Alejo C.S. <[hidden email]> wrote:

Thanks Andrey, missed the list.

 

Thanks for your response. I had remove the folder ~/.config/NA-MIC and still when I run ./Slicer crash on startup with same error:
$ ~/Programas/Slicer-4.5.0-1-linux-amd64$ ./Slicer 
Session start time .......: 2015-11-18 15:04:38
Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 - installed
Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
Memory ...................: 7889 MB physical, 1999 MB virtual 
CPU ......................: GenuineIntel 3.398 MHz, 1 cores
Developer mode enabled ...: no
Prefer executable CLI ....: no
Additional module paths ..: (none)
Number of registered modules: 141 
error: [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real] exit abnormally - Report the problem.

 

2015-11-18 15:07 GMT-03:00 Andrey Fedorov <[hidden email]>:

Interesting. Not sure what is going on.

cc'ing the list (please make sure you include the list next time)


On Wed, Nov 18, 2015 at 1:05 PM, Alejo C.S. <[hidden email]> wrote:
> Thanks for your response. I had remove the folder ~/.config/NA-MIC and still
> when I run ./Slicer crash on startup with same error:
>
> $ ~/Programas/Slicer-4.5.0-1-linux-amd64$ ./Slicer
> Session start time .......: 2015-11-18 15:04:38
> Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 - installed
> Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian
> 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
> Memory ...................: 7889 MB physical, 1999 MB virtual
> CPU ......................: GenuineIntel 3.398 MHz, 1 cores
> Developer mode enabled ...: no
> Prefer executable CLI ....: no
> Additional module paths ..: (none)
> Number of registered modules: 141
> error:
> [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real] exit
> abnormally - Report the problem.
> [hidden email]
>
>
>
> 2015-11-18 14:22 GMT-03:00 Andrey Fedorov <[hidden email]>:
>>
>> Alejo,
>>
>> I've just tried, and could not reproduce this crash on Ubuntu 14.04 LTS.
>>
>> Can you try removing the settings or moving those files to another
>> location and check if this resolves the issue? There may be some
>> compatibility issues with the older settings, or with the extra
>> modules, if you have any.
>>
>>
>> http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/FAQ#How_to_uninstall_Slicer.3F
>>
>> Note that this will reset all of your Slicer user settings.
>>
>> AF
>>
>> On Wed, Nov 18, 2015 at 6:41 AM, Alejo C.S. <[hidden email]> wrote:

>> > Dear list, I'm trying to run Slicer 4.5 stable r24735 on Linux amd64 and
>> > it
>> > crash every time:
>> >
>> > Session start time .......: 2015-11-18 08:35:58
>> > Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 -
>> > installed
>> > Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian
>> > 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
>> > Memory ...................: 7889 MB physical, 1999 MB virtual
>> > CPU ......................: GenuineIntel 3.339 MHz, 1 cores
>> > Developer mode enabled ...: no
>> > Prefer executable CLI ....: no
>> > Additional module paths ..: (none)
>> > Number of registered modules: 141
>> > error:
>> > [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real]
>> > exit
>> > abnormally - Report the problem.
>> >
>> >
>> > Any help?
>> >
>> > Thanks in advance!
>> >
>> >
>> > PD: There is no problem running Slicer 4.4
>> >
>> >
>> >

>> > _______________________________________________
>> > 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
>> >
>> >
>> > The information in this e-mail is intended only for the person to whom
>> > it is
>> > addressed. If you believe this e-mail was sent to you in error and the
>> > e-mail
>> > contains patient information, please contact the Partners Compliance
>> > HelpLine at
>> > http://www.partners.org/complianceline . If the e-mail was sent to you
>> > in
>> > error
>> > but does not contain patient information, please contact the sender and
>> > properly
>> > dispose of the e-mail.
>> >
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>

 


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Re: Slicer 4.5 stable on Linux crash on startup

Alejo C.S.
In reply to this post by Alejo C.S.
Hi Andras, I re run Slicer and gdb for send you request and now shows the following (I run three more times and this error is showed every time now):



Program received signal SIGSEGV, Segmentation fault.
0x00007ff944a17347 in std::string::assign(std::string const&) () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6
(gdb) bt
#0  0x00007ff944a17347 in std::string::assign(std::string const&) () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6
#1  0x00007ff823b5221c in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so
#2  0x00007ff823b525b1 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so
#3  0x00007ff823b529e9 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so
#4  0x00007ff81ca114f3 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so
#5  0x00007ff81c975a5e in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so
#6  0x00007ff823c3e796 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so
#7  0x0000000000000000 in ?? ()


Regards,

A.

2015-11-27 10:16 GMT-03:00 Andras Lasso <[hidden email]>:
Could you please also send the stack trace? (I think the command to print it is: bt)

Andras

From: [hidden email]
Sent: ‎2015-‎11-‎27 08:12
To: [hidden email]

Subject: Re: [slicer-users] Slicer 4.5 stable on Linux crash on startup

Hi Jean-Christophe, the results of gdb are the following:

Program received signal SIGSEGV, Segmentation fault.
0x00007f9c34974626 in vtkSubjectHelper::InvokeEvent(unsigned long, void*, vtkObject*) ()
   from /home/ar/Programas/Slicer-4.5.0-1-linux-amd64/./lib/Slicer-4.5/libvtkCommon-6.3.so.1
(gdb) 

Hope it helps

Regards,

A.


2015-11-26 16:14 GMT-03:00 Jean-Christophe Fillion-Robin <[hidden email]>:
Hi Alejo,

Thanks for reporting back.

This is helpful. It seems on of the scripted module (or one of its dependencies) is the culprit.

Before creating a script that would allow us to find out which one is the culprit.

You could try attaching gdb.

In a nutshell, you start Slicer using:

   ./Slicer --attach-process

and then attach the debugger.

More details are posted here:

  http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/Debug_Instructions#GDB_debug_by_attaching_to_running_process_.5BRECOMMENDED.5D

That should help identify which library is causing trouble.

Hth
Jc

On Wed, Nov 18, 2015 at 3:03 PM, Alejo C.S. <[hidden email]> wrote:
Ok, the results with each settings are:


./Slicer --disable-settings 
Crash all times

./Slicer --disable-modules --disable-modules
Starts on all attempts

./Slicer  --disable-cli-modules
Crash all times

./Slicer --disable-loadable-modules
Crash all times

./Slicer --disable-scripted-loadable-modules
Starts on all attempts


In gdb mode Running Slicer and SlicerApp-real this shows up:

Starting program: /home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real 
/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real: error while loading shared libraries: libqSlicerApp.so: cannot open shared object file: No such file or directory
[Inferior 1 (process 13519) exited with code 0177]


Starting program: /home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real bin/SlicerApp-real
/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real: error while loading shared libraries: libqSlicerApp.so: cannot open shared object file: No such file or directory
[Inferior 1 (process 13553) exited with code 0177]
(gdb) 


ls -l on ./lib/Slicer-4.5/libqSlicerApp.so

-rw-r--r-- 1 marmo marmo 810K 12/11/2015 17:06:23 ./lib/Slicer-4.5/libqSlicerApp.so

Hope this is useful.

Thanks in advance.

Alejo



2015-11-18 16:13 GMT-03:00 Andras Lasso <[hidden email]>:

It would help a lot to know in which shared library the crash occurs. Can you run Slicer in gdb? (you need to run gdb with the launcher: Slicer, and then in gdb run the actual application: SlicerApp-real)

 

You may also try to upgrade/downgrade your graphics card driver.

 

Andras

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Jean-Christophe Fillion-Robin
Sent: Wednesday, November 18, 2015 1:49 PM
To: Alejo C.S. <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Slicer 4.5 stable on Linux crash on startup

 

Hi Alejo,

Thanks for the report.

Could you try the following and report which one are working/failing:

(1) ./Slicer --disable-settings

(2) ./Slicer --disable-modules --disable-modules

Then, you could also try using these flags:

 --disable-cli-modules
 --disable-loadable-modules
 --disable-scripted-loadable-modules

 

Hth

Jc

 

 

On Wed, Nov 18, 2015 at 1:10 PM, Alejo C.S. <[hidden email]> wrote:

Thanks Andrey, missed the list.

 

Thanks for your response. I had remove the folder ~/.config/NA-MIC and still when I run ./Slicer crash on startup with same error:
$ ~/Programas/Slicer-4.5.0-1-linux-amd64$ ./Slicer 
Session start time .......: 2015-11-18 15:04:38
Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 - installed
Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
Memory ...................: 7889 MB physical, 1999 MB virtual 
CPU ......................: GenuineIntel 3.398 MHz, 1 cores
Developer mode enabled ...: no
Prefer executable CLI ....: no
Additional module paths ..: (none)
Number of registered modules: 141 
error: [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real] exit abnormally - Report the problem.

 

2015-11-18 15:07 GMT-03:00 Andrey Fedorov <[hidden email]>:

Interesting. Not sure what is going on.

cc'ing the list (please make sure you include the list next time)


On Wed, Nov 18, 2015 at 1:05 PM, Alejo C.S. <[hidden email]> wrote:
> Thanks for your response. I had remove the folder ~/.config/NA-MIC and still
> when I run ./Slicer crash on startup with same error:
>
> $ ~/Programas/Slicer-4.5.0-1-linux-amd64$ ./Slicer
> Session start time .......: 2015-11-18 15:04:38
> Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 - installed
> Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian
> 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
> Memory ...................: 7889 MB physical, 1999 MB virtual
> CPU ......................: GenuineIntel 3.398 MHz, 1 cores
> Developer mode enabled ...: no
> Prefer executable CLI ....: no
> Additional module paths ..: (none)
> Number of registered modules: 141
> error:
> [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real] exit
> abnormally - Report the problem.
> [hidden email]
>
>
>
> 2015-11-18 14:22 GMT-03:00 Andrey Fedorov <[hidden email]>:
>>
>> Alejo,
>>
>> I've just tried, and could not reproduce this crash on Ubuntu 14.04 LTS.
>>
>> Can you try removing the settings or moving those files to another
>> location and check if this resolves the issue? There may be some
>> compatibility issues with the older settings, or with the extra
>> modules, if you have any.
>>
>>
>> http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/FAQ#How_to_uninstall_Slicer.3F
>>
>> Note that this will reset all of your Slicer user settings.
>>
>> AF
>>
>> On Wed, Nov 18, 2015 at 6:41 AM, Alejo C.S. <[hidden email]> wrote:

>> > Dear list, I'm trying to run Slicer 4.5 stable r24735 on Linux amd64 and
>> > it
>> > crash every time:
>> >
>> > Session start time .......: 2015-11-18 08:35:58
>> > Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 -
>> > installed
>> > Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian
>> > 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
>> > Memory ...................: 7889 MB physical, 1999 MB virtual
>> > CPU ......................: GenuineIntel 3.339 MHz, 1 cores
>> > Developer mode enabled ...: no
>> > Prefer executable CLI ....: no
>> > Additional module paths ..: (none)
>> > Number of registered modules: 141
>> > error:
>> > [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real]
>> > exit
>> > abnormally - Report the problem.
>> >
>> >
>> > Any help?
>> >
>> > Thanks in advance!
>> >
>> >
>> > PD: There is no problem running Slicer 4.4
>> >
>> >
>> >

>> > _______________________________________________
>> > 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
>> >
>> >
>> > The information in this e-mail is intended only for the person to whom
>> > it is
>> > addressed. If you believe this e-mail was sent to you in error and the
>> > e-mail
>> > contains patient information, please contact the Partners Compliance
>> > HelpLine at
>> > http://www.partners.org/complianceline . If the e-mail was sent to you
>> > in
>> > error
>> > but does not contain patient information, please contact the sender and
>> > properly
>> > dispose of the e-mail.
>> >
>
>

 


_______________________________________________
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
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.




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The information in this e-mail is intended only for the person to whom it is
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Re: Slicer 4.5 stable on Linux crash on startup

Andras Lasso-2

Thank you, this information is very helpful. It seems that the crash is related to SimpleITK. Your previous emails indicate that the error may be caused by a scripted module.

 

I’ve found only a few scripted modules that use SimpleITK. Could you please try deleting them one by one and see if the problem goes away when a particular one is deleted?

 

Slicer-4.5\qt-scripted-modules\SimpleFilters.py

Slicer-4.5\qt-scripted-modules\RegistrationLib\LocalSimpleITKPlugin.py

Slicer 4.5.0-1\lib\Slicer-4.5\qt-scripted-modules\EditorLib\WatershedFromMarkerEffect.py

 

Andras

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Alejo C.S.
Sent: Friday, November 27, 2015 10:06 AM
To: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Slicer 4.5 stable on Linux crash on startup

 

Hi Andras, I re run Slicer and gdb for send you request and now shows the following (I run three more times and this error is showed every time now):

 

 

 

Program received signal SIGSEGV, Segmentation fault.

0x00007ff944a17347 in std::string::assign(std::string const&) () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6

(gdb) bt

#0  0x00007ff944a17347 in std::string::assign(std::string const&) () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6

#1  0x00007ff823b5221c in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#2  0x00007ff823b525b1 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#3  0x00007ff823b529e9 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#4  0x00007ff81ca114f3 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#5  0x00007ff81c975a5e in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#6  0x00007ff823c3e796 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#7  0x0000000000000000 in ?? ()

 

 

Regards,

 

A.

 

2015-11-27 10:16 GMT-03:00 Andras Lasso <[hidden email]>:

Could you please also send the stack trace? (I think the command to print it is: bt)

Andras


From: [hidden email]
Sent: ‎2015-‎11-‎27 08:12
To: [hidden email]


Subject: Re: [slicer-users] Slicer 4.5 stable on Linux crash on startup

Hi Jean-Christophe, the results of gdb are the following:

 

Program received signal SIGSEGV, Segmentation fault.

0x00007f9c34974626 in vtkSubjectHelper::InvokeEvent(unsigned long, void*, vtkObject*) ()

   from /home/ar/Programas/Slicer-4.5.0-1-linux-amd64/./lib/Slicer-4.5/libvtkCommon-6.3.so.1

(gdb) 

 

Hope it helps

 

Regards,

 

A.

 

 

2015-11-26 16:14 GMT-03:00 Jean-Christophe Fillion-Robin <[hidden email]>:

Hi Alejo,

Thanks for reporting back.

This is helpful. It seems on of the scripted module (or one of its dependencies) is the culprit.

Before creating a script that would allow us to find out which one is the culprit.

You could try attaching gdb.

In a nutshell, you start Slicer using:

   ./Slicer --attach-process

and then attach the debugger.

More details are posted here:

  http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/Debug_Instructions#GDB_debug_by_attaching_to_running_process_.5BRECOMMENDED.5D

That should help identify which library is causing trouble.

 

Hth

Jc

 

On Wed, Nov 18, 2015 at 3:03 PM, Alejo C.S. <[hidden email]> wrote:

Ok, the results with each settings are:

 

 

./Slicer --disable-settings 

Crash all times

 

./Slicer --disable-modules --disable-modules

Starts on all attempts

 

./Slicer  --disable-cli-modules

Crash all times

 

./Slicer --disable-loadable-modules

Crash all times

 

./Slicer --disable-scripted-loadable-modules

Starts on all attempts

 

 

In gdb mode Running Slicer and SlicerApp-real this shows up:

 

Starting program: /home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real 

/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real: error while loading shared libraries: libqSlicerApp.so: cannot open shared object file: No such file or directory

[Inferior 1 (process 13519) exited with code 0177]

 

 

Starting program: /home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real bin/SlicerApp-real

/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real: error while loading shared libraries: libqSlicerApp.so: cannot open shared object file: No such file or directory

[Inferior 1 (process 13553) exited with code 0177]

(gdb) 

 

 

ls -l on ./lib/Slicer-4.5/libqSlicerApp.so

 

-rw-r--r-- 1 marmo marmo 810K 12/11/2015 17:06:23 ./lib/Slicer-4.5/libqSlicerApp.so

 

Hope this is useful.

 

Thanks in advance.

 

Alejo

 

 

 

2015-11-18 16:13 GMT-03:00 Andras Lasso <[hidden email]>:

It would help a lot to know in which shared library the crash occurs. Can you run Slicer in gdb? (you need to run gdb with the launcher: Slicer, and then in gdb run the actual application: SlicerApp-real)

 

You may also try to upgrade/downgrade your graphics card driver.

 

Andras

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Jean-Christophe Fillion-Robin
Sent: Wednesday, November 18, 2015 1:49 PM
To: Alejo C.S. <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Slicer 4.5 stable on Linux crash on startup

 

Hi Alejo,

Thanks for the report.

Could you try the following and report which one are working/failing:

(1) ./Slicer --disable-settings

(2) ./Slicer --disable-modules --disable-modules

Then, you could also try using these flags:

 --disable-cli-modules
 --disable-loadable-modules
 --disable-scripted-loadable-modules

 

Hth

Jc

 

 

On Wed, Nov 18, 2015 at 1:10 PM, Alejo C.S. <[hidden email]> wrote:

Thanks Andrey, missed the list.

 

Thanks for your response. I had remove the folder ~/.config/NA-MIC and still when I run ./Slicer crash on startup with same error:
$ ~/Programas/Slicer-4.5.0-1-linux-amd64$ ./Slicer 
Session start time .......: 2015-11-18 15:04:38
Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 - installed
Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
Memory ...................: 7889 MB physical, 1999 MB virtual 
CPU ......................: GenuineIntel 3.398 MHz, 1 cores
Developer mode enabled ...: no
Prefer executable CLI ....: no
Additional module paths ..: (none)
Number of registered modules: 141 
error: [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real] exit abnormally - Report the problem.

 

2015-11-18 15:07 GMT-03:00 Andrey Fedorov <[hidden email]>:

Interesting. Not sure what is going on.

cc'ing the list (please make sure you include the list next time)


On Wed, Nov 18, 2015 at 1:05 PM, Alejo C.S. <[hidden email]> wrote:
> Thanks for your response. I had remove the folder ~/.config/NA-MIC and still
> when I run ./Slicer crash on startup with same error:
>
> $ ~/Programas/Slicer-4.5.0-1-linux-amd64$ ./Slicer
> Session start time .......: 2015-11-18 15:04:38
> Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 - installed
> Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian
> 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
> Memory ...................: 7889 MB physical, 1999 MB virtual
> CPU ......................: GenuineIntel 3.398 MHz, 1 cores
> Developer mode enabled ...: no
> Prefer executable CLI ....: no
> Additional module paths ..: (none)
> Number of registered modules: 141
> error:
> [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real] exit
> abnormally - Report the problem.
> [hidden email]
>
>
>
> 2015-11-18 14:22 GMT-03:00 Andrey Fedorov <[hidden email]>:
>>
>> Alejo,
>>
>> I've just tried, and could not reproduce this crash on Ubuntu 14.04 LTS.
>>
>> Can you try removing the settings or moving those files to another
>> location and check if this resolves the issue? There may be some
>> compatibility issues with the older settings, or with the extra
>> modules, if you have any.
>>
>>
>> http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/FAQ#How_to_uninstall_Slicer.3F
>>
>> Note that this will reset all of your Slicer user settings.
>>
>> AF
>>
>> On Wed, Nov 18, 2015 at 6:41 AM, Alejo C.S. <[hidden email]> wrote:

>> > Dear list, I'm trying to run Slicer 4.5 stable r24735 on Linux amd64 and
>> > it
>> > crash every time:
>> >
>> > Session start time .......: 2015-11-18 08:35:58
>> > Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 -
>> > installed
>> > Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian
>> > 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
>> > Memory ...................: 7889 MB physical, 1999 MB virtual
>> > CPU ......................: GenuineIntel 3.339 MHz, 1 cores
>> > Developer mode enabled ...: no
>> > Prefer executable CLI ....: no
>> > Additional module paths ..: (none)
>> > Number of registered modules: 141
>> > error:
>> > [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real]
>> > exit
>> > abnormally - Report the problem.
>> >
>> >
>> > Any help?
>> >
>> > Thanks in advance!
>> >
>> >
>> > PD: There is no problem running Slicer 4.4
>> >
>> >
>> >

>> > _______________________________________________
>> > 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
>> >
>> >
>> > The information in this e-mail is intended only for the person to whom
>> > it is
>> > addressed. If you believe this e-mail was sent to you in error and the
>> > e-mail
>> > contains patient information, please contact the Partners Compliance
>> > HelpLine at
>> > http://www.partners.org/complianceline . If the e-mail was sent to you
>> > in
>> > error
>> > but does not contain patient information, please contact the sender and
>> > properly
>> > dispose of the e-mail.
>> >
>
>

 


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Re: Slicer 4.5 stable on Linux crash on startup

Alejo C.S.
In reply to this post by Alejo C.S.
Dear Andras, I deleted the three scripts:

Slicer-4.5\qt-scripted-modules\SimpleFilters.py
Slicer-4.5\qt-scripted-modules\RegistrationLib\LocalSimpleITKPlugin.py
Slicer 4.5.0-1\lib\Slicer-4.5\qt-scripted-modules\EditorLib\WatershedFromMarkerEffect.py
 
But still the program crash:


Continuing.
[New Thread 0x7fe58b7c4700 (LWP 12760)]
[New Thread 0x7fe58afc3700 (LWP 12761)]
[New Thread 0x7fe56365f700 (LWP 12763)]
[New Thread 0x7fe4e28ff700 (LWP 12764)]
[New Thread 0x7fe4e20fe700 (LWP 12765)]
[New Thread 0x7fe4e18fd700 (LWP 12766)]
[New Thread 0x7fe4e0ffc700 (LWP 12767)]
[New Thread 0x7fe483152700 (LWP 12770)]

Program received signal SIGSEGV, Segmentation fault.
0x00007fe599a95347 in std::string::assign(std::string const&) () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6
(gdb) bt
#0  0x00007fe599a95347 in std::string::assign(std::string const&) () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6
#1  0x00007fe47895b21c in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so
#2  0x00007fe47895b5b1 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so
#3  0x00007fe47895b9e9 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so
#4  0x00007fe47181a4f3 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so
#5  0x00007fe47177ea5e in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so
#6  0x00007fe478a47796 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so
#7  0x0000000000000000 in ?? ()
(gdb) 

Could be a problem with my SimpleITK? There is a way to reinstall SimpleITK? I tried with pip but  no success.

Regards,

A.



2015-11-27 12:14 GMT-03:00 Andras Lasso <[hidden email]>:

Thank you, this information is very helpful. It seems that the crash is related to SimpleITK. Your previous emails indicate that the error may be caused by a scripted module.

 

I’ve found only a few scripted modules that use SimpleITK. Could you please try deleting them one by one and see if the problem goes away when a particular one is deleted?

 

Slicer-4.5\qt-scripted-modules\SimpleFilters.py

Slicer-4.5\qt-scripted-modules\RegistrationLib\LocalSimpleITKPlugin.py

Slicer 4.5.0-1\lib\Slicer-4.5\qt-scripted-modules\EditorLib\WatershedFromMarkerEffect.py

 

Andras

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Alejo C.S.
Sent: Friday, November 27, 2015 10:06 AM
To: SPL Slicer Users <[hidden email]>


Subject: Re: [slicer-users] Slicer 4.5 stable on Linux crash on startup

 

Hi Andras, I re run Slicer and gdb for send you request and now shows the following (I run three more times and this error is showed every time now):

 

 

 

Program received signal SIGSEGV, Segmentation fault.

0x00007ff944a17347 in std::string::assign(std::string const&) () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6

(gdb) bt

#0  0x00007ff944a17347 in std::string::assign(std::string const&) () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6

#1  0x00007ff823b5221c in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#2  0x00007ff823b525b1 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#3  0x00007ff823b529e9 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#4  0x00007ff81ca114f3 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#5  0x00007ff81c975a5e in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#6  0x00007ff823c3e796 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#7  0x0000000000000000 in ?? ()

 

 

Regards,

 

A.

 

2015-11-27 10:16 GMT-03:00 Andras Lasso <[hidden email]>:

Could you please also send the stack trace? (I think the command to print it is: bt)

Andras


From: [hidden email]
Sent: ‎2015-‎11-‎27 08:12
To: [hidden email]


Subject: Re: [slicer-users] Slicer 4.5 stable on Linux crash on startup

Hi Jean-Christophe, the results of gdb are the following:

 

Program received signal SIGSEGV, Segmentation fault.

0x00007f9c34974626 in vtkSubjectHelper::InvokeEvent(unsigned long, void*, vtkObject*) ()

   from /home/ar/Programas/Slicer-4.5.0-1-linux-amd64/./lib/Slicer-4.5/libvtkCommon-6.3.so.1

(gdb) 

 

Hope it helps

 

Regards,

 

A.

 

 

2015-11-26 16:14 GMT-03:00 Jean-Christophe Fillion-Robin <[hidden email]>:

Hi Alejo,

Thanks for reporting back.

This is helpful. It seems on of the scripted module (or one of its dependencies) is the culprit.

Before creating a script that would allow us to find out which one is the culprit.

You could try attaching gdb.

In a nutshell, you start Slicer using:

   ./Slicer --attach-process

and then attach the debugger.

More details are posted here:

  http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/Debug_Instructions#GDB_debug_by_attaching_to_running_process_.5BRECOMMENDED.5D

That should help identify which library is causing trouble.

 

Hth

Jc

 

On Wed, Nov 18, 2015 at 3:03 PM, Alejo C.S. <[hidden email]> wrote:

Ok, the results with each settings are:

 

 

./Slicer --disable-settings 

Crash all times

 

./Slicer --disable-modules --disable-modules

Starts on all attempts

 

./Slicer  --disable-cli-modules

Crash all times

 

./Slicer --disable-loadable-modules

Crash all times

 

./Slicer --disable-scripted-loadable-modules

Starts on all attempts

 

 

In gdb mode Running Slicer and SlicerApp-real this shows up:

 

Starting program: /home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real 

/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real: error while loading shared libraries: libqSlicerApp.so: cannot open shared object file: No such file or directory

[Inferior 1 (process 13519) exited with code 0177]

 

 

Starting program: /home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real bin/SlicerApp-real

/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real: error while loading shared libraries: libqSlicerApp.so: cannot open shared object file: No such file or directory

[Inferior 1 (process 13553) exited with code 0177]

(gdb) 

 

 

ls -l on ./lib/Slicer-4.5/libqSlicerApp.so

 

-rw-r--r-- 1 marmo marmo 810K 12/11/2015 17:06:23 ./lib/Slicer-4.5/libqSlicerApp.so

 

Hope this is useful.

 

Thanks in advance.

 

Alejo

 

 

 

2015-11-18 16:13 GMT-03:00 Andras Lasso <[hidden email]>:

It would help a lot to know in which shared library the crash occurs. Can you run Slicer in gdb? (you need to run gdb with the launcher: Slicer, and then in gdb run the actual application: SlicerApp-real)

 

You may also try to upgrade/downgrade your graphics card driver.

 

Andras

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Jean-Christophe Fillion-Robin
Sent: Wednesday, November 18, 2015 1:49 PM
To: Alejo C.S. <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Slicer 4.5 stable on Linux crash on startup

 

Hi Alejo,

Thanks for the report.

Could you try the following and report which one are working/failing:

(1) ./Slicer --disable-settings

(2) ./Slicer --disable-modules --disable-modules

Then, you could also try using these flags:

 --disable-cli-modules
 --disable-loadable-modules
 --disable-scripted-loadable-modules

 

Hth

Jc

 

 

On Wed, Nov 18, 2015 at 1:10 PM, Alejo C.S. <[hidden email]> wrote:

Thanks Andrey, missed the list.

 

Thanks for your response. I had remove the folder ~/.config/NA-MIC and still when I run ./Slicer crash on startup with same error:
$ ~/Programas/Slicer-4.5.0-1-linux-amd64$ ./Slicer 
Session start time .......: 2015-11-18 15:04:38
Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 - installed
Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
Memory ...................: 7889 MB physical, 1999 MB virtual 
CPU ......................: GenuineIntel 3.398 MHz, 1 cores
Developer mode enabled ...: no
Prefer executable CLI ....: no
Additional module paths ..: (none)
Number of registered modules: 141 
error: [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real] exit abnormally - Report the problem.

 

2015-11-18 15:07 GMT-03:00 Andrey Fedorov <[hidden email]>:

Interesting. Not sure what is going on.

cc'ing the list (please make sure you include the list next time)


On Wed, Nov 18, 2015 at 1:05 PM, Alejo C.S. <[hidden email]> wrote:
> Thanks for your response. I had remove the folder ~/.config/NA-MIC and still
> when I run ./Slicer crash on startup with same error:
>
> $ ~/Programas/Slicer-4.5.0-1-linux-amd64$ ./Slicer
> Session start time .......: 2015-11-18 15:04:38
> Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 - installed
> Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian
> 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
> Memory ...................: 7889 MB physical, 1999 MB virtual
> CPU ......................: GenuineIntel 3.398 MHz, 1 cores
> Developer mode enabled ...: no
> Prefer executable CLI ....: no
> Additional module paths ..: (none)
> Number of registered modules: 141
> error:
> [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real] exit
> abnormally - Report the problem.
> [hidden email]
>
>
>
> 2015-11-18 14:22 GMT-03:00 Andrey Fedorov <[hidden email]>:
>>
>> Alejo,
>>
>> I've just tried, and could not reproduce this crash on Ubuntu 14.04 LTS.
>>
>> Can you try removing the settings or moving those files to another
>> location and check if this resolves the issue? There may be some
>> compatibility issues with the older settings, or with the extra
>> modules, if you have any.
>>
>>
>> http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/FAQ#How_to_uninstall_Slicer.3F
>>
>> Note that this will reset all of your Slicer user settings.
>>
>> AF
>>
>> On Wed, Nov 18, 2015 at 6:41 AM, Alejo C.S. <[hidden email]> wrote:

>> > Dear list, I'm trying to run Slicer 4.5 stable r24735 on Linux amd64 and
>> > it
>> > crash every time:
>> >
>> > Session start time .......: 2015-11-18 08:35:58
>> > Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 -
>> > installed
>> > Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian
>> > 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
>> > Memory ...................: 7889 MB physical, 1999 MB virtual
>> > CPU ......................: GenuineIntel 3.339 MHz, 1 cores
>> > Developer mode enabled ...: no
>> > Prefer executable CLI ....: no
>> > Additional module paths ..: (none)
>> > Number of registered modules: 141
>> > error:
>> > [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real]
>> > exit
>> > abnormally - Report the problem.
>> >
>> >
>> > Any help?
>> >
>> > Thanks in advance!
>> >
>> >
>> > PD: There is no problem running Slicer 4.4
>> >
>> >
>> >

>> > _______________________________________________
>> > 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
>> >
>> >
>> > The information in this e-mail is intended only for the person to whom
>> > it is
>> > addressed. If you believe this e-mail was sent to you in error and the
>> > e-mail
>> > contains patient information, please contact the Partners Compliance
>> > HelpLine at
>> > http://www.partners.org/complianceline . If the e-mail was sent to you
>> > in
>> > error
>> > but does not contain patient information, please contact the sender and
>> > properly
>> > dispose of the e-mail.
>> >
>
>

 


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http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
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Re: Slicer 4.5 stable on Linux crash on startup

Andras Lasso-2
It seems that your local Python and SimpleITK is used instead of those bundled with Slicer. Have you intentionally configured Slicer to use your local Python and SimpleITK?

Andras

From: [hidden email]
Sent: ‎2015-‎11-‎30 09:17
To: [hidden email]
Subject: Re: [slicer-users] Slicer 4.5 stable on Linux crash on startup

Dear Andras, I deleted the three scripts:

Slicer-4.5\qt-scripted-modules\SimpleFilters.py
Slicer-4.5\qt-scripted-modules\RegistrationLib\LocalSimpleITKPlugin.py
Slicer 4.5.0-1\lib\Slicer-4.5\qt-scripted-modules\EditorLib\WatershedFromMarkerEffect.py
 
But still the program crash:


Continuing.
[New Thread 0x7fe58b7c4700 (LWP 12760)]
[New Thread 0x7fe58afc3700 (LWP 12761)]
[New Thread 0x7fe56365f700 (LWP 12763)]
[New Thread 0x7fe4e28ff700 (LWP 12764)]
[New Thread 0x7fe4e20fe700 (LWP 12765)]
[New Thread 0x7fe4e18fd700 (LWP 12766)]
[New Thread 0x7fe4e0ffc700 (LWP 12767)]
[New Thread 0x7fe483152700 (LWP 12770)]

Program received signal SIGSEGV, Segmentation fault.
0x00007fe599a95347 in std::string::assign(std::string const&) () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6
(gdb) bt
#0  0x00007fe599a95347 in std::string::assign(std::string const&) () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6
#1  0x00007fe47895b21c in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so
#2  0x00007fe47895b5b1 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so
#3  0x00007fe47895b9e9 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so
#4  0x00007fe47181a4f3 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so
#5  0x00007fe47177ea5e in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so
#6  0x00007fe478a47796 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so
#7  0x0000000000000000 in ?? ()
(gdb) 

Could be a problem with my SimpleITK? There is a way to reinstall SimpleITK? I tried with pip but  no success.

Regards,

A.



2015-11-27 12:14 GMT-03:00 Andras Lasso <[hidden email]>:

Thank you, this information is very helpful. It seems that the crash is related to SimpleITK. Your previous emails indicate that the error may be caused by a scripted module.

 

I’ve found only a few scripted modules that use SimpleITK. Could you please try deleting them one by one and see if the problem goes away when a particular one is deleted?

 

Slicer-4.5\qt-scripted-modules\SimpleFilters.py

Slicer-4.5\qt-scripted-modules\RegistrationLib\LocalSimpleITKPlugin.py

Slicer 4.5.0-1\lib\Slicer-4.5\qt-scripted-modules\EditorLib\WatershedFromMarkerEffect.py

 

Andras

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Alejo C.S.
Sent: Friday, November 27, 2015 10:06 AM
To: SPL Slicer Users <[hidden email]>


Subject: Re: [slicer-users] Slicer 4.5 stable on Linux crash on startup

 

Hi Andras, I re run Slicer and gdb for send you request and now shows the following (I run three more times and this error is showed every time now):

 

 

 

Program received signal SIGSEGV, Segmentation fault.

0x00007ff944a17347 in std::string::assign(std::string const&) () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6

(gdb) bt

#0  0x00007ff944a17347 in std::string::assign(std::string const&) () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6

#1  0x00007ff823b5221c in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#2  0x00007ff823b525b1 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#3  0x00007ff823b529e9 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#4  0x00007ff81ca114f3 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#5  0x00007ff81c975a5e in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#6  0x00007ff823c3e796 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#7  0x0000000000000000 in ?? ()

 

 

Regards,

 

A.

 

2015-11-27 10:16 GMT-03:00 Andras Lasso <[hidden email]>:

Could you please also send the stack trace? (I think the command to print it is: bt)

Andras


From: [hidden email]
Sent: ‎2015-‎11-‎27 08:12
To: [hidden email]


Subject: Re: [slicer-users] Slicer 4.5 stable on Linux crash on startup

Hi Jean-Christophe, the results of gdb are the following:

 

Program received signal SIGSEGV, Segmentation fault.

0x00007f9c34974626 in vtkSubjectHelper::InvokeEvent(unsigned long, void*, vtkObject*) ()

   from /home/ar/Programas/Slicer-4.5.0-1-linux-amd64/./lib/Slicer-4.5/libvtkCommon-6.3.so.1

(gdb) 

 

Hope it helps

 

Regards,

 

A.

 

 

2015-11-26 16:14 GMT-03:00 Jean-Christophe Fillion-Robin <[hidden email]>:

Hi Alejo,

Thanks for reporting back.

This is helpful. It seems on of the scripted module (or one of its dependencies) is the culprit.

Before creating a script that would allow us to find out which one is the culprit.

You could try attaching gdb.

In a nutshell, you start Slicer using:

   ./Slicer --attach-process

and then attach the debugger.

More details are posted here:

  http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/Debug_Instructions#GDB_debug_by_attaching_to_running_process_.5BRECOMMENDED.5D

That should help identify which library is causing trouble.

 

Hth

Jc

 

On Wed, Nov 18, 2015 at 3:03 PM, Alejo C.S. <[hidden email]> wrote:

Ok, the results with each settings are:

 

 

./Slicer --disable-settings 

Crash all times

 

./Slicer --disable-modules --disable-modules

Starts on all attempts

 

./Slicer  --disable-cli-modules

Crash all times

 

./Slicer --disable-loadable-modules

Crash all times

 

./Slicer --disable-scripted-loadable-modules

Starts on all attempts

 

 

In gdb mode Running Slicer and SlicerApp-real this shows up:

 

Starting program: /home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real 

/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real: error while loading shared libraries: libqSlicerApp.so: cannot open shared object file: No such file or directory

[Inferior 1 (process 13519) exited with code 0177]

 

 

Starting program: /home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real bin/SlicerApp-real

/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real: error while loading shared libraries: libqSlicerApp.so: cannot open shared object file: No such file or directory

[Inferior 1 (process 13553) exited with code 0177]

(gdb) 

 

 

ls -l on ./lib/Slicer-4.5/libqSlicerApp.so

 

-rw-r--r-- 1 marmo marmo 810K 12/11/2015 17:06:23 ./lib/Slicer-4.5/libqSlicerApp.so

 

Hope this is useful.

 

Thanks in advance.

 

Alejo

 

 

 

2015-11-18 16:13 GMT-03:00 Andras Lasso <[hidden email]>:

It would help a lot to know in which shared library the crash occurs. Can you run Slicer in gdb? (you need to run gdb with the launcher: Slicer, and then in gdb run the actual application: SlicerApp-real)

 

You may also try to upgrade/downgrade your graphics card driver.

 

Andras

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Jean-Christophe Fillion-Robin
Sent: Wednesday, November 18, 2015 1:49 PM
To: Alejo C.S. <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Slicer 4.5 stable on Linux crash on startup

 

Hi Alejo,

Thanks for the report.

Could you try the following and report which one are working/failing:

(1) ./Slicer --disable-settings

(2) ./Slicer --disable-modules --disable-modules

Then, you could also try using these flags:

 --disable-cli-modules
 --disable-loadable-modules
 --disable-scripted-loadable-modules

 

Hth

Jc

 

 

On Wed, Nov 18, 2015 at 1:10 PM, Alejo C.S. <[hidden email]> wrote:

Thanks Andrey, missed the list.

 

Thanks for your response. I had remove the folder ~/.config/NA-MIC and still when I run ./Slicer crash on startup with same error:
$ ~/Programas/Slicer-4.5.0-1-linux-amd64$ ./Slicer 
Session start time .......: 2015-11-18 15:04:38
Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 - installed
Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
Memory ...................: 7889 MB physical, 1999 MB virtual 
CPU ......................: GenuineIntel 3.398 MHz, 1 cores
Developer mode enabled ...: no
Prefer executable CLI ....: no
Additional module paths ..: (none)
Number of registered modules: 141 
error: [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real] exit abnormally - Report the problem.

 

2015-11-18 15:07 GMT-03:00 Andrey Fedorov <[hidden email]>:

Interesting. Not sure what is going on.

cc'ing the list (please make sure you include the list next time)


On Wed, Nov 18, 2015 at 1:05 PM, Alejo C.S. <[hidden email]> wrote:
> Thanks for your response. I had remove the folder ~/.config/NA-MIC and still
> when I run ./Slicer crash on startup with same error:
>
> $ ~/Programas/Slicer-4.5.0-1-linux-amd64$ ./Slicer
> Session start time .......: 2015-11-18 15:04:38
> Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 - installed
> Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian
> 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
> Memory ...................: 7889 MB physical, 1999 MB virtual
> CPU ......................: GenuineIntel 3.398 MHz, 1 cores
> Developer mode enabled ...: no
> Prefer executable CLI ....: no
> Additional module paths ..: (none)
> Number of registered modules: 141
> error:
> [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real] exit
> abnormally - Report the problem.
> [hidden email]
>
>
>
> 2015-11-18 14:22 GMT-03:00 Andrey Fedorov <[hidden email]>:
>>
>> Alejo,
>>
>> I've just tried, and could not reproduce this crash on Ubuntu 14.04 LTS.
>>
>> Can you try removing the settings or moving those files to another
>> location and check if this resolves the issue? There may be some
>> compatibility issues with the older settings, or with the extra
>> modules, if you have any.
>>
>>
>> http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/FAQ#How_to_uninstall_Slicer.3F
>>
>> Note that this will reset all of your Slicer user settings.
>>
>> AF
>>
>> On Wed, Nov 18, 2015 at 6:41 AM, Alejo C.S. <[hidden email]> wrote:

>> > Dear list, I'm trying to run Slicer 4.5 stable r24735 on Linux amd64 and
>> > it
>> > crash every time:
>> >
>> > Session start time .......: 2015-11-18 08:35:58
>> > Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 -
>> > installed
>> > Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian
>> > 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
>> > Memory ...................: 7889 MB physical, 1999 MB virtual
>> > CPU ......................: GenuineIntel 3.339 MHz, 1 cores
>> > Developer mode enabled ...: no
>> > Prefer executable CLI ....: no
>> > Additional module paths ..: (none)
>> > Number of registered modules: 141
>> > error:
>> > [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real]
>> > exit
>> > abnormally - Report the problem.
>> >
>> >
>> > Any help?
>> >
>> > Thanks in advance!
>> >
>> >
>> > PD: There is no problem running Slicer 4.4
>> >
>> >
>> >

>> > _______________________________________________
>> > 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
>> >
>> >
>> > The information in this e-mail is intended only for the person to whom
>> > it is
>> > addressed. If you believe this e-mail was sent to you in error and the
>> > e-mail
>> > contains patient information, please contact the Partners Compliance
>> > HelpLine at
>> > http://www.partners.org/complianceline . If the e-mail was sent to you
>> > in
>> > error
>> > but does not contain patient information, please contact the sender and
>> > properly
>> > dispose of the e-mail.
>> >
>
>

 


_______________________________________________
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http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.




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<a href="tel:%2B1%20919%20869%208849" target="_blank">+1 919 869 8849

 




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+1 919 869 8849

 

 



_______________________________________________
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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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Re: Slicer 4.5 stable on Linux crash on startup

Alejo C.S.
In reply to this post by Alejo C.S.
I have changed LD_LIBRARY_PATH and SlicerLauncherSettings.ini with no luck. Slicer still crash on startup. I'm stuck with 4.4

2015-12-18 12:28 GMT-03:00 Alejo C.S. <[hidden email]>:
I have changed LD_LIBRARY_PATH and SlicerLauncherSettings.ini with no luck. Slicer still crash on startup. I'm stuck with 4.4

2015-11-30 23:09 GMT-03:00 Andras Lasso <[hidden email]>:

If you start Slicer using the launcher (./Slicer) then it sets up LD_LIBRARY_PATH with all the Python, SimpleITK, etc. paths. This seems to fail on some linux computers (see https://www.na-mic.org/Mantis/view.php?id=3218). You may try to change your LD_LIBRARY_PATH and/or SlicerLauncherSettings.ini to remove your local Python/SimpleITK and add the Slicer’s Python/SimpleITK paths.

 

Andras

 

 

From: Alejo C.S. [mailto:[hidden email]]
Sent: November 30, 2015 1:00 PM
To: Andras Lasso <[hidden email]>


Subject: Re: [slicer-users] Slicer 4.5 stable on Linux crash on startup

 

Not at all, I just uncompress the tar.gz and run ./Slicer. 

 

is there a way to force slicer to use the bundled SimpleITK?

 

thanks!

 

2015-11-30 11:37 GMT-03:00 Andras Lasso <[hidden email]>:

It seems that your local Python and SimpleITK is used instead of those bundled with Slicer. Have you intentionally configured Slicer to use your local Python and SimpleITK?

Andras


From: [hidden email]
Sent: ‎2015-‎11-‎30 09:17


To: [hidden email]
Subject: Re: [slicer-users] Slicer 4.5 stable on Linux crash on startup

Dear Andras, I deleted the three scripts:

 

Slicer-4.5\qt-scripted-modules\SimpleFilters.py

Slicer-4.5\qt-scripted-modules\RegistrationLib\LocalSimpleITKPlugin.py

Slicer 4.5.0-1\lib\Slicer-4.5\qt-scripted-modules\EditorLib\WatershedFromMarkerEffect.py

 

But still the program crash:

 

 

Continuing.

[New Thread 0x7fe58b7c4700 (LWP 12760)]

[New Thread 0x7fe58afc3700 (LWP 12761)]

[New Thread 0x7fe56365f700 (LWP 12763)]

[New Thread 0x7fe4e28ff700 (LWP 12764)]

[New Thread 0x7fe4e20fe700 (LWP 12765)]

[New Thread 0x7fe4e18fd700 (LWP 12766)]

[New Thread 0x7fe4e0ffc700 (LWP 12767)]

[New Thread 0x7fe483152700 (LWP 12770)]

 

Program received signal SIGSEGV, Segmentation fault.

0x00007fe599a95347 in std::string::assign(std::string const&) () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6

(gdb) bt

#0  0x00007fe599a95347 in std::string::assign(std::string const&) () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6

#1  0x00007fe47895b21c in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#2  0x00007fe47895b5b1 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#3  0x00007fe47895b9e9 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#4  0x00007fe47181a4f3 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#5  0x00007fe47177ea5e in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#6  0x00007fe478a47796 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#7  0x0000000000000000 in ?? ()

(gdb) 

 

Could be a problem with my SimpleITK? There is a way to reinstall SimpleITK? I tried with pip but  no success.

 

Regards,

 

A.

 

 

 

2015-11-27 12:14 GMT-03:00 Andras Lasso <[hidden email]>:

Thank you, this information is very helpful. It seems that the crash is related to SimpleITK. Your previous emails indicate that the error may be caused by a scripted module.

 

I’ve found only a few scripted modules that use SimpleITK. Could you please try deleting them one by one and see if the problem goes away when a particular one is deleted?

 

Slicer-4.5\qt-scripted-modules\SimpleFilters.py

Slicer-4.5\qt-scripted-modules\RegistrationLib\LocalSimpleITKPlugin.py

Slicer 4.5.0-1\lib\Slicer-4.5\qt-scripted-modules\EditorLib\WatershedFromMarkerEffect.py

 

Andras

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Alejo C.S.
Sent: Friday, November 27, 2015 10:06 AM
To: SPL Slicer Users <[hidden email]>


Subject: Re: [slicer-users] Slicer 4.5 stable on Linux crash on startup

 

Hi Andras, I re run Slicer and gdb for send you request and now shows the following (I run three more times and this error is showed every time now):

 

 

 

Program received signal SIGSEGV, Segmentation fault.

0x00007ff944a17347 in std::string::assign(std::string const&) () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6

(gdb) bt

#0  0x00007ff944a17347 in std::string::assign(std::string const&) () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6

#1  0x00007ff823b5221c in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#2  0x00007ff823b525b1 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#3  0x00007ff823b529e9 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#4  0x00007ff81ca114f3 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#5  0x00007ff81c975a5e in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#6  0x00007ff823c3e796 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#7  0x0000000000000000 in ?? ()

 

 

Regards,

 

A.

 

2015-11-27 10:16 GMT-03:00 Andras Lasso <[hidden email]>:

Could you please also send the stack trace? (I think the command to print it is: bt)

Andras


From: [hidden email]
Sent: ‎2015-‎11-‎27 08:12
To: [hidden email]


Subject: Re: [slicer-users] Slicer 4.5 stable on Linux crash on startup

Hi Jean-Christophe, the results of gdb are the following:

 

Program received signal SIGSEGV, Segmentation fault.

0x00007f9c34974626 in vtkSubjectHelper::InvokeEvent(unsigned long, void*, vtkObject*) ()

   from /home/ar/Programas/Slicer-4.5.0-1-linux-amd64/./lib/Slicer-4.5/libvtkCommon-6.3.so.1

(gdb) 

 

Hope it helps

 

Regards,

 

A.

 

 

2015-11-26 16:14 GMT-03:00 Jean-Christophe Fillion-Robin <[hidden email]>:

Hi Alejo,

Thanks for reporting back.

This is helpful. It seems on of the scripted module (or one of its dependencies) is the culprit.

Before creating a script that would allow us to find out which one is the culprit.

You could try attaching gdb.

In a nutshell, you start Slicer using:

   ./Slicer --attach-process

and then attach the debugger.

More details are posted here:

  http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/Debug_Instructions#GDB_debug_by_attaching_to_running_process_.5BRECOMMENDED.5D

That should help identify which library is causing trouble.

 

Hth

Jc

 

On Wed, Nov 18, 2015 at 3:03 PM, Alejo C.S. <[hidden email]> wrote:

Ok, the results with each settings are:

 

 

./Slicer --disable-settings 

Crash all times

 

./Slicer --disable-modules --disable-modules

Starts on all attempts

 

./Slicer  --disable-cli-modules

Crash all times

 

./Slicer --disable-loadable-modules

Crash all times

 

./Slicer --disable-scripted-loadable-modules

Starts on all attempts

 

 

In gdb mode Running Slicer and SlicerApp-real this shows up:

 

Starting program: /home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real 

/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real: error while loading shared libraries: libqSlicerApp.so: cannot open shared object file: No such file or directory

[Inferior 1 (process 13519) exited with code 0177]

 

 

Starting program: /home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real bin/SlicerApp-real

/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real: error while loading shared libraries: libqSlicerApp.so: cannot open shared object file: No such file or directory

[Inferior 1 (process 13553) exited with code 0177]

(gdb) 

 

 

ls -l on ./lib/Slicer-4.5/libqSlicerApp.so

 

-rw-r--r-- 1 marmo marmo 810K 12/11/2015 17:06:23 ./lib/Slicer-4.5/libqSlicerApp.so

 

Hope this is useful.

 

Thanks in advance.

 

Alejo

 

 

 

2015-11-18 16:13 GMT-03:00 Andras Lasso <[hidden email]>:

It would help a lot to know in which shared library the crash occurs. Can you run Slicer in gdb? (you need to run gdb with the launcher: Slicer, and then in gdb run the actual application: SlicerApp-real)

 

You may also try to upgrade/downgrade your graphics card driver.

 

Andras

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Jean-Christophe Fillion-Robin
Sent: Wednesday, November 18, 2015 1:49 PM
To: Alejo C.S. <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Slicer 4.5 stable on Linux crash on startup

 

Hi Alejo,

Thanks for the report.

Could you try the following and report which one are working/failing:

(1) ./Slicer --disable-settings

(2) ./Slicer --disable-modules --disable-modules

Then, you could also try using these flags:

 --disable-cli-modules
 --disable-loadable-modules
 --disable-scripted-loadable-modules

 

Hth

Jc

 

 

On Wed, Nov 18, 2015 at 1:10 PM, Alejo C.S. <[hidden email]> wrote:

Thanks Andrey, missed the list.

 

Thanks for your response. I had remove the folder ~/.config/NA-MIC and still when I run ./Slicer crash on startup with same error:
$ ~/Programas/Slicer-4.5.0-1-linux-amd64$ ./Slicer 
Session start time .......: 2015-11-18 15:04:38
Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 - installed
Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
Memory ...................: 7889 MB physical, 1999 MB virtual 
CPU ......................: GenuineIntel 3.398 MHz, 1 cores
Developer mode enabled ...: no
Prefer executable CLI ....: no
Additional module paths ..: (none)
Number of registered modules: 141 
error: [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real] exit abnormally - Report the problem.

 

2015-11-18 15:07 GMT-03:00 Andrey Fedorov <[hidden email]>:

Interesting. Not sure what is going on.

cc'ing the list (please make sure you include the list next time)


On Wed, Nov 18, 2015 at 1:05 PM, Alejo C.S. <[hidden email]> wrote:
> Thanks for your response. I had remove the folder ~/.config/NA-MIC and still
> when I run ./Slicer crash on startup with same error:
>
> $ ~/Programas/Slicer-4.5.0-1-linux-amd64$ ./Slicer
> Session start time .......: 2015-11-18 15:04:38
> Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 - installed
> Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian
> 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
> Memory ...................: 7889 MB physical, 1999 MB virtual
> CPU ......................: GenuineIntel 3.398 MHz, 1 cores
> Developer mode enabled ...: no
> Prefer executable CLI ....: no
> Additional module paths ..: (none)
> Number of registered modules: 141
> error:
> [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real] exit
> abnormally - Report the problem.
> [hidden email]
>
>
>
> 2015-11-18 14:22 GMT-03:00 Andrey Fedorov <[hidden email]>:
>>
>> Alejo,
>>
>> I've just tried, and could not reproduce this crash on Ubuntu 14.04 LTS.
>>
>> Can you try removing the settings or moving those files to another
>> location and check if this resolves the issue? There may be some
>> compatibility issues with the older settings, or with the extra
>> modules, if you have any.
>>
>>
>> http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/FAQ#How_to_uninstall_Slicer.3F
>>
>> Note that this will reset all of your Slicer user settings.
>>
>> AF
>>
>> On Wed, Nov 18, 2015 at 6:41 AM, Alejo C.S. <[hidden email]> wrote:

>> > Dear list, I'm trying to run Slicer 4.5 stable r24735 on Linux amd64 and
>> > it
>> > crash every time:
>> >
>> > Session start time .......: 2015-11-18 08:35:58
>> > Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 -
>> > installed
>> > Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian
>> > 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
>> > Memory ...................: 7889 MB physical, 1999 MB virtual
>> > CPU ......................: GenuineIntel 3.339 MHz, 1 cores
>> > Developer mode enabled ...: no
>> > Prefer executable CLI ....: no
>> > Additional module paths ..: (none)
>> > Number of registered modules: 141
>> > error:
>> > [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real]
>> > exit
>> > abnormally - Report the problem.
>> >
>> >
>> > Any help?
>> >
>> > Thanks in advance!
>> >
>> >
>> > PD: There is no problem running Slicer 4.4
>> >
>> >
>> >

>> > _______________________________________________
>> > 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
>> >
>> >
>> > The information in this e-mail is intended only for the person to whom
>> > it is
>> > addressed. If you believe this e-mail was sent to you in error and the
>> > e-mail
>> > contains patient information, please contact the Partners Compliance
>> > HelpLine at
>> > http://www.partners.org/complianceline . If the e-mail was sent to you
>> > in
>> > error
>> > but does not contain patient information, please contact the sender and
>> > properly
>> > dispose of the e-mail.
>> >
>
>

 


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Re: Slicer 4.5 stable on Linux crash on startup

Steve Pieper-2
Hi Alejo -

I've used Slicer 4.5.0-1 on ubuntu 14.04 with no problems - I wonder if you have configured something like an ld_preload or something else that bypasses the regular slicer startup process.  Maybe you could try strace to see that only slicer-provided shared libraries are being loaded.  People here won't be able to help you unless you provide a lot more context about your system.

-Steve

On Fri, Dec 18, 2015 at 10:29 AM, Alejo C.S. <[hidden email]> wrote:
I have changed LD_LIBRARY_PATH and SlicerLauncherSettings.ini with no luck. Slicer still crash on startup. I'm stuck with 4.4

2015-12-18 12:28 GMT-03:00 Alejo C.S. <[hidden email]>:
I have changed LD_LIBRARY_PATH and SlicerLauncherSettings.ini with no luck. Slicer still crash on startup. I'm stuck with 4.4

2015-11-30 23:09 GMT-03:00 Andras Lasso <[hidden email]>:

If you start Slicer using the launcher (./Slicer) then it sets up LD_LIBRARY_PATH with all the Python, SimpleITK, etc. paths. This seems to fail on some linux computers (see https://www.na-mic.org/Mantis/view.php?id=3218). You may try to change your LD_LIBRARY_PATH and/or SlicerLauncherSettings.ini to remove your local Python/SimpleITK and add the Slicer’s Python/SimpleITK paths.

 

Andras

 

 

From: Alejo C.S. [mailto:[hidden email]]
Sent: November 30, 2015 1:00 PM
To: Andras Lasso <[hidden email]>


Subject: Re: [slicer-users] Slicer 4.5 stable on Linux crash on startup

 

Not at all, I just uncompress the tar.gz and run ./Slicer. 

 

is there a way to force slicer to use the bundled SimpleITK?

 

thanks!

 

2015-11-30 11:37 GMT-03:00 Andras Lasso <[hidden email]>:

It seems that your local Python and SimpleITK is used instead of those bundled with Slicer. Have you intentionally configured Slicer to use your local Python and SimpleITK?

Andras


From: [hidden email]
Sent: ‎2015-‎11-‎30 09:17


To: [hidden email]
Subject: Re: [slicer-users] Slicer 4.5 stable on Linux crash on startup

Dear Andras, I deleted the three scripts:

 

Slicer-4.5\qt-scripted-modules\SimpleFilters.py

Slicer-4.5\qt-scripted-modules\RegistrationLib\LocalSimpleITKPlugin.py

Slicer 4.5.0-1\lib\Slicer-4.5\qt-scripted-modules\EditorLib\WatershedFromMarkerEffect.py

 

But still the program crash:

 

 

Continuing.

[New Thread 0x7fe58b7c4700 (LWP 12760)]

[New Thread 0x7fe58afc3700 (LWP 12761)]

[New Thread 0x7fe56365f700 (LWP 12763)]

[New Thread 0x7fe4e28ff700 (LWP 12764)]

[New Thread 0x7fe4e20fe700 (LWP 12765)]

[New Thread 0x7fe4e18fd700 (LWP 12766)]

[New Thread 0x7fe4e0ffc700 (LWP 12767)]

[New Thread 0x7fe483152700 (LWP 12770)]

 

Program received signal SIGSEGV, Segmentation fault.

0x00007fe599a95347 in std::string::assign(std::string const&) () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6

(gdb) bt

#0  0x00007fe599a95347 in std::string::assign(std::string const&) () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6

#1  0x00007fe47895b21c in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#2  0x00007fe47895b5b1 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#3  0x00007fe47895b9e9 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#4  0x00007fe47181a4f3 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#5  0x00007fe47177ea5e in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#6  0x00007fe478a47796 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#7  0x0000000000000000 in ?? ()

(gdb) 

 

Could be a problem with my SimpleITK? There is a way to reinstall SimpleITK? I tried with pip but  no success.

 

Regards,

 

A.

 

 

 

2015-11-27 12:14 GMT-03:00 Andras Lasso <[hidden email]>:

Thank you, this information is very helpful. It seems that the crash is related to SimpleITK. Your previous emails indicate that the error may be caused by a scripted module.

 

I’ve found only a few scripted modules that use SimpleITK. Could you please try deleting them one by one and see if the problem goes away when a particular one is deleted?

 

Slicer-4.5\qt-scripted-modules\SimpleFilters.py

Slicer-4.5\qt-scripted-modules\RegistrationLib\LocalSimpleITKPlugin.py

Slicer 4.5.0-1\lib\Slicer-4.5\qt-scripted-modules\EditorLib\WatershedFromMarkerEffect.py

 

Andras

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Alejo C.S.
Sent: Friday, November 27, 2015 10:06 AM
To: SPL Slicer Users <[hidden email]>


Subject: Re: [slicer-users] Slicer 4.5 stable on Linux crash on startup

 

Hi Andras, I re run Slicer and gdb for send you request and now shows the following (I run three more times and this error is showed every time now):

 

 

 

Program received signal SIGSEGV, Segmentation fault.

0x00007ff944a17347 in std::string::assign(std::string const&) () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6

(gdb) bt

#0  0x00007ff944a17347 in std::string::assign(std::string const&) () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6

#1  0x00007ff823b5221c in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#2  0x00007ff823b525b1 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#3  0x00007ff823b529e9 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#4  0x00007ff81ca114f3 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#5  0x00007ff81c975a5e in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#6  0x00007ff823c3e796 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#7  0x0000000000000000 in ?? ()

 

 

Regards,

 

A.

 

2015-11-27 10:16 GMT-03:00 Andras Lasso <[hidden email]>:

Could you please also send the stack trace? (I think the command to print it is: bt)

Andras


From: [hidden email]
Sent: ‎2015-‎11-‎27 08:12
To: [hidden email]


Subject: Re: [slicer-users] Slicer 4.5 stable on Linux crash on startup

Hi Jean-Christophe, the results of gdb are the following:

 

Program received signal SIGSEGV, Segmentation fault.

0x00007f9c34974626 in vtkSubjectHelper::InvokeEvent(unsigned long, void*, vtkObject*) ()

   from /home/ar/Programas/Slicer-4.5.0-1-linux-amd64/./lib/Slicer-4.5/libvtkCommon-6.3.so.1

(gdb) 

 

Hope it helps

 

Regards,

 

A.

 

 

2015-11-26 16:14 GMT-03:00 Jean-Christophe Fillion-Robin <[hidden email]>:

Hi Alejo,

Thanks for reporting back.

This is helpful. It seems on of the scripted module (or one of its dependencies) is the culprit.

Before creating a script that would allow us to find out which one is the culprit.

You could try attaching gdb.

In a nutshell, you start Slicer using:

   ./Slicer --attach-process

and then attach the debugger.

More details are posted here:

  http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/Debug_Instructions#GDB_debug_by_attaching_to_running_process_.5BRECOMMENDED.5D

That should help identify which library is causing trouble.

 

Hth

Jc

 

On Wed, Nov 18, 2015 at 3:03 PM, Alejo C.S. <[hidden email]> wrote:

Ok, the results with each settings are:

 

 

./Slicer --disable-settings 

Crash all times

 

./Slicer --disable-modules --disable-modules

Starts on all attempts

 

./Slicer  --disable-cli-modules

Crash all times

 

./Slicer --disable-loadable-modules

Crash all times

 

./Slicer --disable-scripted-loadable-modules

Starts on all attempts

 

 

In gdb mode Running Slicer and SlicerApp-real this shows up:

 

Starting program: /home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real 

/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real: error while loading shared libraries: libqSlicerApp.so: cannot open shared object file: No such file or directory

[Inferior 1 (process 13519) exited with code 0177]

 

 

Starting program: /home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real bin/SlicerApp-real

/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real: error while loading shared libraries: libqSlicerApp.so: cannot open shared object file: No such file or directory

[Inferior 1 (process 13553) exited with code 0177]

(gdb) 

 

 

ls -l on ./lib/Slicer-4.5/libqSlicerApp.so

 

-rw-r--r-- 1 marmo marmo 810K 12/11/2015 17:06:23 ./lib/Slicer-4.5/libqSlicerApp.so

 

Hope this is useful.

 

Thanks in advance.

 

Alejo

 

 

 

2015-11-18 16:13 GMT-03:00 Andras Lasso <[hidden email]>:

It would help a lot to know in which shared library the crash occurs. Can you run Slicer in gdb? (you need to run gdb with the launcher: Slicer, and then in gdb run the actual application: SlicerApp-real)

 

You may also try to upgrade/downgrade your graphics card driver.

 

Andras

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Jean-Christophe Fillion-Robin
Sent: Wednesday, November 18, 2015 1:49 PM
To: Alejo C.S. <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Slicer 4.5 stable on Linux crash on startup

 

Hi Alejo,

Thanks for the report.

Could you try the following and report which one are working/failing:

(1) ./Slicer --disable-settings

(2) ./Slicer --disable-modules --disable-modules

Then, you could also try using these flags:

 --disable-cli-modules
 --disable-loadable-modules
 --disable-scripted-loadable-modules

 

Hth

Jc

 

 

On Wed, Nov 18, 2015 at 1:10 PM, Alejo C.S. <[hidden email]> wrote:

Thanks Andrey, missed the list.

 

Thanks for your response. I had remove the folder ~/.config/NA-MIC and still when I run ./Slicer crash on startup with same error:
$ ~/Programas/Slicer-4.5.0-1-linux-amd64$ ./Slicer 
Session start time .......: 2015-11-18 15:04:38
Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 - installed
Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
Memory ...................: 7889 MB physical, 1999 MB virtual 
CPU ......................: GenuineIntel 3.398 MHz, 1 cores
Developer mode enabled ...: no
Prefer executable CLI ....: no
Additional module paths ..: (none)
Number of registered modules: 141 
error: [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real] exit abnormally - Report the problem.

 

2015-11-18 15:07 GMT-03:00 Andrey Fedorov <[hidden email]>:

Interesting. Not sure what is going on.

cc'ing the list (please make sure you include the list next time)


On Wed, Nov 18, 2015 at 1:05 PM, Alejo C.S. <[hidden email]> wrote:
> Thanks for your response. I had remove the folder ~/.config/NA-MIC and still
> when I run ./Slicer crash on startup with same error:
>
> $ ~/Programas/Slicer-4.5.0-1-linux-amd64$ ./Slicer
> Session start time .......: 2015-11-18 15:04:38
> Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 - installed
> Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian
> 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
> Memory ...................: 7889 MB physical, 1999 MB virtual
> CPU ......................: GenuineIntel 3.398 MHz, 1 cores
> Developer mode enabled ...: no
> Prefer executable CLI ....: no
> Additional module paths ..: (none)
> Number of registered modules: 141
> error:
> [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real] exit
> abnormally - Report the problem.
> [hidden email]
>
>
>
> 2015-11-18 14:22 GMT-03:00 Andrey Fedorov <[hidden email]>:
>>
>> Alejo,
>>
>> I've just tried, and could not reproduce this crash on Ubuntu 14.04 LTS.
>>
>> Can you try removing the settings or moving those files to another
>> location and check if this resolves the issue? There may be some
>> compatibility issues with the older settings, or with the extra
>> modules, if you have any.
>>
>>
>> http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/FAQ#How_to_uninstall_Slicer.3F
>>
>> Note that this will reset all of your Slicer user settings.
>>
>> AF
>>
>> On Wed, Nov 18, 2015 at 6:41 AM, Alejo C.S. <[hidden email]> wrote:

>> > Dear list, I'm trying to run Slicer 4.5 stable r24735 on Linux amd64 and
>> > it
>> > crash every time:
>> >
>> > Session start time .......: 2015-11-18 08:35:58
>> > Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 -
>> > installed
>> > Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian
>> > 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
>> > Memory ...................: 7889 MB physical, 1999 MB virtual
>> > CPU ......................: GenuineIntel 3.339 MHz, 1 cores
>> > Developer mode enabled ...: no
>> > Prefer executable CLI ....: no
>> > Additional module paths ..: (none)
>> > Number of registered modules: 141
>> > error:
>> > [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real]
>> > exit
>> > abnormally - Report the problem.
>> >
>> >
>> > Any help?
>> >
>> > Thanks in advance!
>> >
>> >
>> > PD: There is no problem running Slicer 4.4
>> >
>> >
>> >

>> > _______________________________________________
>> > 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
>> >
>> >
>> > The information in this e-mail is intended only for the person to whom
>> > it is
>> > addressed. If you believe this e-mail was sent to you in error and the
>> > e-mail
>> > contains patient information, please contact the Partners Compliance
>> > HelpLine at
>> > http://www.partners.org/complianceline . If the e-mail was sent to you
>> > in
>> > error
>> > but does not contain patient information, please contact the sender and
>> > properly
>> > dispose of the e-mail.
>> >
>
>

 


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Re: Slicer 4.5 stable on Linux crash on startup

Andras Lasso-2
In reply to this post by Alejo C.S.

You have to set up the dynamic loader on your computer to not override loading of Slicer libraries. Just as a test, could you temporarily remove your local Python installation from home/ar/.local/lib/python2.7 to see if Slicer can start successfully then?

Andras

 


From: [hidden email]
Sent: December 18, 2015 10:29
To: [hidden email]
Subject: Re: [slicer-users] Slicer 4.5 stable on Linux crash on startup

 

I have changed LD_LIBRARY_PATH and SlicerLauncherSettings.ini with no luck. Slicer still crash on startup. I'm stuck with 4.4

 

2015-12-18 12:28 GMT-03:00 Alejo C.S. <[hidden email]>:

I have changed LD_LIBRARY_PATH and SlicerLauncherSettings.ini with no luck. Slicer still crash on startup. I'm stuck with 4.4

 

2015-11-30 23:09 GMT-03:00 Andras Lasso <[hidden email]>:

If you start Slicer using the launcher (./Slicer) then it sets up LD_LIBRARY_PATH with all the Python, SimpleITK, etc. paths. This seems to fail on some linux computers (see https://www.na-mic.org/Mantis/view.php?id=3218). You may try to change your LD_LIBRARY_PATH and/or SlicerLauncherSettings.ini to remove your local Python/SimpleITK and add the Slicer’s Python/SimpleITK paths.

 

Andras

 

 

From: Alejo C.S. [mailto:[hidden email]]
Sent: November 30, 2015 1:00 PM
To: Andras Lasso <[hidden email]>


Subject: Re: [slicer-users] Slicer 4.5 stable on Linux crash on startup

 

Not at all, I just uncompress the tar.gz and run ./Slicer. 

 

is there a way to force slicer to use the bundled SimpleITK?

 

thanks!

 

2015-11-30 11:37 GMT-03:00 Andras Lasso <[hidden email]>:

It seems that your local Python and SimpleITK is used instead of those bundled with Slicer. Have you intentionally configured Slicer to use your local Python and SimpleITK?

Andras

From: [hidden email]
Sent: ‎2015-‎11-‎30 09:17


To: [hidden email]
Subject: Re: [slicer-users] Slicer 4.5 stable on Linux crash on startup

Dear Andras, I deleted the three scripts:

 

Slicer-4.5\qt-scripted-modules\SimpleFilters.py

Slicer-4.5\qt-scripted-modules\RegistrationLib\LocalSimpleITKPlugin.py

Slicer 4.5.0-1\lib\Slicer-4.5\qt-scripted-modules\EditorLib\WatershedFromMarkerEffect.py

 

But still the program crash:

 

 

Continuing.

[New Thread 0x7fe58b7c4700 (LWP 12760)]

[New Thread 0x7fe58afc3700 (LWP 12761)]

[New Thread 0x7fe56365f700 (LWP 12763)]

[New Thread 0x7fe4e28ff700 (LWP 12764)]

[New Thread 0x7fe4e20fe700 (LWP 12765)]

[New Thread 0x7fe4e18fd700 (LWP 12766)]

[New Thread 0x7fe4e0ffc700 (LWP 12767)]

[New Thread 0x7fe483152700 (LWP 12770)]

 

Program received signal SIGSEGV, Segmentation fault.

0x00007fe599a95347 in std::string::assign(std::string const&) () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6

(gdb) bt

#0  0x00007fe599a95347 in std::string::assign(std::string const&) () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6

#1  0x00007fe47895b21c in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#2  0x00007fe47895b5b1 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#3  0x00007fe47895b9e9 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#4  0x00007fe47181a4f3 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#5  0x00007fe47177ea5e in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#6  0x00007fe478a47796 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#7  0x0000000000000000 in ?? ()

(gdb) 

 

Could be a problem with my SimpleITK? There is a way to reinstall SimpleITK? I tried with pip but  no success.

 

Regards,

 

A.

 

 

 

2015-11-27 12:14 GMT-03:00 Andras Lasso <[hidden email]>:

Thank you, this information is very helpful. It seems that the crash is related to SimpleITK. Your previous emails indicate that the error may be caused by a scripted module.

 

I’ve found only a few scripted modules that use SimpleITK. Could you please try deleting them one by one and see if the problem goes away when a particular one is deleted?

 

Slicer-4.5\qt-scripted-modules\SimpleFilters.py

Slicer-4.5\qt-scripted-modules\RegistrationLib\LocalSimpleITKPlugin.py

Slicer 4.5.0-1\lib\Slicer-4.5\qt-scripted-modules\EditorLib\WatershedFromMarkerEffect.py

 

Andras

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Alejo C.S.
Sent: Friday, November 27, 2015 10:06 AM
To: SPL Slicer Users <[hidden email]>


Subject: Re: [slicer-users] Slicer 4.5 stable on Linux crash on startup

 

Hi Andras, I re run Slicer and gdb for send you request and now shows the following (I run three more times and this error is showed every time now):

 

 

 

Program received signal SIGSEGV, Segmentation fault.

0x00007ff944a17347 in std::string::assign(std::string const&) () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6

(gdb) bt

#0  0x00007ff944a17347 in std::string::assign(std::string const&) () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6

#1  0x00007ff823b5221c in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#2  0x00007ff823b525b1 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#3  0x00007ff823b529e9 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#4  0x00007ff81ca114f3 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#5  0x00007ff81c975a5e in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#6  0x00007ff823c3e796 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#7  0x0000000000000000 in ?? ()

 

 

Regards,

 

A.

 

2015-11-27 10:16 GMT-03:00 Andras Lasso <[hidden email]>:

Could you please also send the stack trace? (I think the command to print it is: bt)

Andras

From: [hidden email]
Sent: ‎2015-‎11-‎27 08:12
To: [hidden email]


Subject: Re: [slicer-users] Slicer 4.5 stable on Linux crash on startup

Hi Jean-Christophe, the results of gdb are the following:

 

Program received signal SIGSEGV, Segmentation fault.

0x00007f9c34974626 in vtkSubjectHelper::InvokeEvent(unsigned long, void*, vtkObject*) ()

   from /home/ar/Programas/Slicer-4.5.0-1-linux-amd64/./lib/Slicer-4.5/libvtkCommon-6.3.so.1

(gdb) 

 

Hope it helps

 

Regards,

 

A.

 

 

2015-11-26 16:14 GMT-03:00 Jean-Christophe Fillion-Robin <[hidden email]>:

Hi Alejo,

Thanks for reporting back.

This is helpful. It seems on of the scripted module (or one of its dependencies) is the culprit.

Before creating a script that would allow us to find out which one is the culprit.

You could try attaching gdb.

In a nutshell, you start Slicer using:

   ./Slicer --attach-process

and then attach the debugger.

More details are posted here:

  http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/Debug_Instructions#GDB_debug_by_attaching_to_running_process_.5BRECOMMENDED.5D

That should help identify which library is causing trouble.

 

Hth

Jc

 

On Wed, Nov 18, 2015 at 3:03 PM, Alejo C.S. <[hidden email]> wrote:

Ok, the results with each settings are:

 

 

./Slicer --disable-settings 

Crash all times

 

./Slicer --disable-modules --disable-modules

Starts on all attempts

 

./Slicer  --disable-cli-modules

Crash all times

 

./Slicer --disable-loadable-modules

Crash all times

 

./Slicer --disable-scripted-loadable-modules

Starts on all attempts

 

 

In gdb mode Running Slicer and SlicerApp-real this shows up:

 

Starting program: /home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real 

/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real: error while loading shared libraries: libqSlicerApp.so: cannot open shared object file: No such file or directory

[Inferior 1 (process 13519) exited with code 0177]

 

 

Starting program: /home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real bin/SlicerApp-real

/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real: error while loading shared libraries: libqSlicerApp.so: cannot open shared object file: No such file or directory

[Inferior 1 (process 13553) exited with code 0177]

(gdb) 

 

 

ls -l on ./lib/Slicer-4.5/libqSlicerApp.so

 

-rw-r--r-- 1 marmo marmo 810K 12/11/2015 17:06:23 ./lib/Slicer-4.5/libqSlicerApp.so

 

Hope this is useful.

 

Thanks in advance.

 

Alejo

 

 

 

2015-11-18 16:13 GMT-03:00 Andras Lasso <[hidden email]>:

It would help a lot to know in which shared library the crash occurs. Can you run Slicer in gdb? (you need to run gdb with the launcher: Slicer, and then in gdb run the actual application: SlicerApp-real)

 

You may also try to upgrade/downgrade your graphics card driver.

 

Andras

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Jean-Christophe Fillion-Robin
Sent: Wednesday, November 18, 2015 1:49 PM
To: Alejo C.S. <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Slicer 4.5 stable on Linux crash on startup

 

Hi Alejo,

Thanks for the report.

Could you try the following and report which one are working/failing:

(1) ./Slicer --disable-settings

(2) ./Slicer --disable-modules --disable-modules

Then, you could also try using these flags:

 --disable-cli-modules
 --disable-loadable-modules
 --disable-scripted-loadable-modules

 

Hth

Jc

 

 

On Wed, Nov 18, 2015 at 1:10 PM, Alejo C.S. <[hidden email]> wrote:

Thanks Andrey, missed the list.

 

Thanks for your response. I had remove the folder ~/.config/NA-MIC and still when I run ./Slicer crash on startup with same error:
$ ~/Programas/Slicer-4.5.0-1-linux-amd64$ ./Slicer 
Session start time .......: 2015-11-18 15:04:38
Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 - installed
Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
Memory ...................: 7889 MB physical, 1999 MB virtual 
CPU ......................: GenuineIntel 3.398 MHz, 1 cores
Developer mode enabled ...: no
Prefer executable CLI ....: no
Additional module paths ..: (none)
Number of registered modules: 141 
error: [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real] exit abnormally - Report the problem.

 

2015-11-18 15:07 GMT-03:00 Andrey Fedorov <[hidden email]>:

Interesting. Not sure what is going on.

cc'ing the list (please make sure you include the list next time)


On Wed, Nov 18, 2015 at 1:05 PM, Alejo C.S. <[hidden email]> wrote:
> Thanks for your response. I had remove the folder ~/.config/NA-MIC and still
> when I run ./Slicer crash on startup with same error:
>
> $ ~/Programas/Slicer-4.5.0-1-linux-amd64$ ./Slicer
> Session start time .......: 2015-11-18 15:04:38
> Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 - installed
> Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian
> 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
> Memory ...................: 7889 MB physical, 1999 MB virtual
> CPU ......................: GenuineIntel 3.398 MHz, 1 cores
> Developer mode enabled ...: no
> Prefer executable CLI ....: no
> Additional module paths ..: (none)
> Number of registered modules: 141
> error:
> [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real] exit
> abnormally - Report the problem.
> marmo@ANET:~/Programas/Slicer-4.5.0-1-linux-amd64$
>
>
>
> 2015-11-18 14:22 GMT-03:00 Andrey Fedorov <[hidden email]>:
>>
>> Alejo,
>>
>> I've just tried, and could not reproduce this crash on Ubuntu 14.04 LTS.
>>
>> Can you try removing the settings or moving those files to another
>> location and check if this resolves the issue? There may be some
>> compatibility issues with the older settings, or with the extra
>> modules, if you have any.
>>
>>
>> http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/FAQ#How_to_uninstall_Slicer.3F
>>
>> Note that this will reset all of your Slicer user settings.
>>
>> AF
>>
>> On Wed, Nov 18, 2015 at 6:41 AM, Alejo C.S. <[hidden email]> wrote:

>> > Dear list, I'm trying to run Slicer 4.5 stable r24735 on Linux amd64 and
>> > it
>> > crash every time:
>> >
>> > Session start time .......: 2015-11-18 08:35:58
>> > Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 -
>> > installed
>> > Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian
>> > 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
>> > Memory ...................: 7889 MB physical, 1999 MB virtual
>> > CPU ......................: GenuineIntel 3.339 MHz, 1 cores
>> > Developer mode enabled ...: no
>> > Prefer executable CLI ....: no
>> > Additional module paths ..: (none)
>> > Number of registered modules: 141
>> > error:
>> > [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real]
>> > exit
>> > abnormally - Report the problem.
>> >
>> >
>> > Any help?
>> >
>> > Thanks in advance!
>> >
>> >
>> > PD: There is no problem running Slicer 4.4
>> >
>> >
>> >

>> > _______________________________________________
>> > 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
>> >
>> >
>> > The information in this e-mail is intended only for the person to whom
>> > it is
>> > addressed. If you believe this e-mail was sent to you in error and the
>> > e-mail
>> > contains patient information, please contact the Partners Compliance
>> > HelpLine at
>> > http://www.partners.org/complianceline . If the e-mail was sent to you
>> > in
>> > error
>> > but does not contain patient information, please contact the sender and
>> > properly
>> > dispose of the e-mail.
>> >
>
>

 


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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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Re: Slicer 4.5 stable on Linux crash on startup

Alejo C.S.
In reply to this post by Alejo C.S.
I get it started by renaming the Slicer folder. I had Slicer in the folder Slicer-4.5.0-2015-11-27-linux-amd64 and renamed to "Slicer" and now it starts ok. So it was a folder names issue?

Regards,

 

2015-12-18 12:36 GMT-03:00 Steve Pieper <[hidden email]>:
Hi Alejo -

I've used Slicer 4.5.0-1 on ubuntu 14.04 with no problems - I wonder if you have configured something like an ld_preload or something else that bypasses the regular slicer startup process.  Maybe you could try strace to see that only slicer-provided shared libraries are being loaded.  People here won't be able to help you unless you provide a lot more context about your system.

-Steve

On Fri, Dec 18, 2015 at 10:29 AM, Alejo C.S. <[hidden email]> wrote:
I have changed LD_LIBRARY_PATH and SlicerLauncherSettings.ini with no luck. Slicer still crash on startup. I'm stuck with 4.4

2015-12-18 12:28 GMT-03:00 Alejo C.S. <[hidden email]>:
I have changed LD_LIBRARY_PATH and SlicerLauncherSettings.ini with no luck. Slicer still crash on startup. I'm stuck with 4.4

2015-11-30 23:09 GMT-03:00 Andras Lasso <[hidden email]>:

If you start Slicer using the launcher (./Slicer) then it sets up LD_LIBRARY_PATH with all the Python, SimpleITK, etc. paths. This seems to fail on some linux computers (see https://www.na-mic.org/Mantis/view.php?id=3218). You may try to change your LD_LIBRARY_PATH and/or SlicerLauncherSettings.ini to remove your local Python/SimpleITK and add the Slicer’s Python/SimpleITK paths.

 

Andras

 

 

From: Alejo C.S. [mailto:[hidden email]]
Sent: November 30, 2015 1:00 PM
To: Andras Lasso <[hidden email]>


Subject: Re: [slicer-users] Slicer 4.5 stable on Linux crash on startup

 

Not at all, I just uncompress the tar.gz and run ./Slicer. 

 

is there a way to force slicer to use the bundled SimpleITK?

 

thanks!

 

2015-11-30 11:37 GMT-03:00 Andras Lasso <[hidden email]>:

It seems that your local Python and SimpleITK is used instead of those bundled with Slicer. Have you intentionally configured Slicer to use your local Python and SimpleITK?

Andras


From: [hidden email]
Sent: ‎2015-‎11-‎30 09:17


To: [hidden email]
Subject: Re: [slicer-users] Slicer 4.5 stable on Linux crash on startup

Dear Andras, I deleted the three scripts:

 

Slicer-4.5\qt-scripted-modules\SimpleFilters.py

Slicer-4.5\qt-scripted-modules\RegistrationLib\LocalSimpleITKPlugin.py

Slicer 4.5.0-1\lib\Slicer-4.5\qt-scripted-modules\EditorLib\WatershedFromMarkerEffect.py

 

But still the program crash:

 

 

Continuing.

[New Thread 0x7fe58b7c4700 (LWP 12760)]

[New Thread 0x7fe58afc3700 (LWP 12761)]

[New Thread 0x7fe56365f700 (LWP 12763)]

[New Thread 0x7fe4e28ff700 (LWP 12764)]

[New Thread 0x7fe4e20fe700 (LWP 12765)]

[New Thread 0x7fe4e18fd700 (LWP 12766)]

[New Thread 0x7fe4e0ffc700 (LWP 12767)]

[New Thread 0x7fe483152700 (LWP 12770)]

 

Program received signal SIGSEGV, Segmentation fault.

0x00007fe599a95347 in std::string::assign(std::string const&) () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6

(gdb) bt

#0  0x00007fe599a95347 in std::string::assign(std::string const&) () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6

#1  0x00007fe47895b21c in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#2  0x00007fe47895b5b1 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#3  0x00007fe47895b9e9 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#4  0x00007fe47181a4f3 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#5  0x00007fe47177ea5e in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#6  0x00007fe478a47796 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#7  0x0000000000000000 in ?? ()

(gdb) 

 

Could be a problem with my SimpleITK? There is a way to reinstall SimpleITK? I tried with pip but  no success.

 

Regards,

 

A.

 

 

 

2015-11-27 12:14 GMT-03:00 Andras Lasso <[hidden email]>:

Thank you, this information is very helpful. It seems that the crash is related to SimpleITK. Your previous emails indicate that the error may be caused by a scripted module.

 

I’ve found only a few scripted modules that use SimpleITK. Could you please try deleting them one by one and see if the problem goes away when a particular one is deleted?

 

Slicer-4.5\qt-scripted-modules\SimpleFilters.py

Slicer-4.5\qt-scripted-modules\RegistrationLib\LocalSimpleITKPlugin.py

Slicer 4.5.0-1\lib\Slicer-4.5\qt-scripted-modules\EditorLib\WatershedFromMarkerEffect.py

 

Andras

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Alejo C.S.
Sent: Friday, November 27, 2015 10:06 AM
To: SPL Slicer Users <[hidden email]>


Subject: Re: [slicer-users] Slicer 4.5 stable on Linux crash on startup

 

Hi Andras, I re run Slicer and gdb for send you request and now shows the following (I run three more times and this error is showed every time now):

 

 

 

Program received signal SIGSEGV, Segmentation fault.

0x00007ff944a17347 in std::string::assign(std::string const&) () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6

(gdb) bt

#0  0x00007ff944a17347 in std::string::assign(std::string const&) () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6

#1  0x00007ff823b5221c in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#2  0x00007ff823b525b1 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#3  0x00007ff823b529e9 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#4  0x00007ff81ca114f3 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#5  0x00007ff81c975a5e in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#6  0x00007ff823c3e796 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#7  0x0000000000000000 in ?? ()

 

 

Regards,

 

A.

 

2015-11-27 10:16 GMT-03:00 Andras Lasso <[hidden email]>:

Could you please also send the stack trace? (I think the command to print it is: bt)

Andras


From: [hidden email]
Sent: ‎2015-‎11-‎27 08:12
To: [hidden email]


Subject: Re: [slicer-users] Slicer 4.5 stable on Linux crash on startup

Hi Jean-Christophe, the results of gdb are the following:

 

Program received signal SIGSEGV, Segmentation fault.

0x00007f9c34974626 in vtkSubjectHelper::InvokeEvent(unsigned long, void*, vtkObject*) ()

   from /home/ar/Programas/Slicer-4.5.0-1-linux-amd64/./lib/Slicer-4.5/libvtkCommon-6.3.so.1

(gdb) 

 

Hope it helps

 

Regards,

 

A.

 

 

2015-11-26 16:14 GMT-03:00 Jean-Christophe Fillion-Robin <[hidden email]>:

Hi Alejo,

Thanks for reporting back.

This is helpful. It seems on of the scripted module (or one of its dependencies) is the culprit.

Before creating a script that would allow us to find out which one is the culprit.

You could try attaching gdb.

In a nutshell, you start Slicer using:

   ./Slicer --attach-process

and then attach the debugger.

More details are posted here:

  http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/Debug_Instructions#GDB_debug_by_attaching_to_running_process_.5BRECOMMENDED.5D

That should help identify which library is causing trouble.

 

Hth

Jc

 

On Wed, Nov 18, 2015 at 3:03 PM, Alejo C.S. <[hidden email]> wrote:

Ok, the results with each settings are:

 

 

./Slicer --disable-settings 

Crash all times

 

./Slicer --disable-modules --disable-modules

Starts on all attempts

 

./Slicer  --disable-cli-modules

Crash all times

 

./Slicer --disable-loadable-modules

Crash all times

 

./Slicer --disable-scripted-loadable-modules

Starts on all attempts

 

 

In gdb mode Running Slicer and SlicerApp-real this shows up:

 

Starting program: /home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real 

/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real: error while loading shared libraries: libqSlicerApp.so: cannot open shared object file: No such file or directory

[Inferior 1 (process 13519) exited with code 0177]

 

 

Starting program: /home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real bin/SlicerApp-real

/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real: error while loading shared libraries: libqSlicerApp.so: cannot open shared object file: No such file or directory

[Inferior 1 (process 13553) exited with code 0177]

(gdb) 

 

 

ls -l on ./lib/Slicer-4.5/libqSlicerApp.so

 

-rw-r--r-- 1 marmo marmo 810K 12/11/2015 17:06:23 ./lib/Slicer-4.5/libqSlicerApp.so

 

Hope this is useful.

 

Thanks in advance.

 

Alejo

 

 

 

2015-11-18 16:13 GMT-03:00 Andras Lasso <[hidden email]>:

It would help a lot to know in which shared library the crash occurs. Can you run Slicer in gdb? (you need to run gdb with the launcher: Slicer, and then in gdb run the actual application: SlicerApp-real)

 

You may also try to upgrade/downgrade your graphics card driver.

 

Andras

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Jean-Christophe Fillion-Robin
Sent: Wednesday, November 18, 2015 1:49 PM
To: Alejo C.S. <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Slicer 4.5 stable on Linux crash on startup

 

Hi Alejo,

Thanks for the report.

Could you try the following and report which one are working/failing:

(1) ./Slicer --disable-settings

(2) ./Slicer --disable-modules --disable-modules

Then, you could also try using these flags:

 --disable-cli-modules
 --disable-loadable-modules
 --disable-scripted-loadable-modules

 

Hth

Jc

 

 

On Wed, Nov 18, 2015 at 1:10 PM, Alejo C.S. <[hidden email]> wrote:

Thanks Andrey, missed the list.

 

Thanks for your response. I had remove the folder ~/.config/NA-MIC and still when I run ./Slicer crash on startup with same error:
$ ~/Programas/Slicer-4.5.0-1-linux-amd64$ ./Slicer 
Session start time .......: 2015-11-18 15:04:38
Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 - installed
Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
Memory ...................: 7889 MB physical, 1999 MB virtual 
CPU ......................: GenuineIntel 3.398 MHz, 1 cores
Developer mode enabled ...: no
Prefer executable CLI ....: no
Additional module paths ..: (none)
Number of registered modules: 141 
error: [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real] exit abnormally - Report the problem.

 

2015-11-18 15:07 GMT-03:00 Andrey Fedorov <[hidden email]>:

Interesting. Not sure what is going on.

cc'ing the list (please make sure you include the list next time)


On Wed, Nov 18, 2015 at 1:05 PM, Alejo C.S. <[hidden email]> wrote:
> Thanks for your response. I had remove the folder ~/.config/NA-MIC and still
> when I run ./Slicer crash on startup with same error:
>
> $ ~/Programas/Slicer-4.5.0-1-linux-amd64$ ./Slicer
> Session start time .......: 2015-11-18 15:04:38
> Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 - installed
> Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian
> 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
> Memory ...................: 7889 MB physical, 1999 MB virtual
> CPU ......................: GenuineIntel 3.398 MHz, 1 cores
> Developer mode enabled ...: no
> Prefer executable CLI ....: no
> Additional module paths ..: (none)
> Number of registered modules: 141
> error:
> [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real] exit
> abnormally - Report the problem.
> [hidden email]
>
>
>
> 2015-11-18 14:22 GMT-03:00 Andrey Fedorov <[hidden email]>:
>>
>> Alejo,
>>
>> I've just tried, and could not reproduce this crash on Ubuntu 14.04 LTS.
>>
>> Can you try removing the settings or moving those files to another
>> location and check if this resolves the issue? There may be some
>> compatibility issues with the older settings, or with the extra
>> modules, if you have any.
>>
>>
>> http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/FAQ#How_to_uninstall_Slicer.3F
>>
>> Note that this will reset all of your Slicer user settings.
>>
>> AF
>>
>> On Wed, Nov 18, 2015 at 6:41 AM, Alejo C.S. <[hidden email]> wrote:

>> > Dear list, I'm trying to run Slicer 4.5 stable r24735 on Linux amd64 and
>> > it
>> > crash every time:
>> >
>> > Session start time .......: 2015-11-18 08:35:58
>> > Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 -
>> > installed
>> > Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian
>> > 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
>> > Memory ...................: 7889 MB physical, 1999 MB virtual
>> > CPU ......................: GenuineIntel 3.339 MHz, 1 cores
>> > Developer mode enabled ...: no
>> > Prefer executable CLI ....: no
>> > Additional module paths ..: (none)
>> > Number of registered modules: 141
>> > error:
>> > [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real]
>> > exit
>> > abnormally - Report the problem.
>> >
>> >
>> > Any help?
>> >
>> > Thanks in advance!
>> >
>> >
>> > PD: There is no problem running Slicer 4.4
>> >
>> >
>> >

>> > _______________________________________________
>> > 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
>> >
>> >
>> > The information in this e-mail is intended only for the person to whom
>> > it is
>> > addressed. If you believe this e-mail was sent to you in error and the
>> > e-mail
>> > contains patient information, please contact the Partners Compliance
>> > HelpLine at
>> > http://www.partners.org/complianceline . If the e-mail was sent to you
>> > in
>> > error
>> > but does not contain patient information, please contact the sender and
>> > properly
>> > dispose of the e-mail.
>> >
>
>

 


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Re: Slicer 4.5 stable on Linux crash on startup

Andras Lasso-2
In reply to this post by Alejo C.S.

We know that local python is loaded instead of Slicer’s – see the stack trace in the emails below.

Andras

 


From: [hidden email]
Sent: December 18, 2015 10:36
To: [hidden email]
Cc: [hidden email]
Subject: Re: [slicer-users] Slicer 4.5 stable on Linux crash on startup

 

Hi Alejo -

 

I've used Slicer 4.5.0-1 on ubuntu 14.04 with no problems - I wonder if you have configured something like an ld_preload or something else that bypasses the regular slicer startup process.  Maybe you could try strace to see that only slicer-provided shared libraries are being loaded.  People here won't be able to help you unless you provide a lot more context about your system.

 

-Steve

 

On Fri, Dec 18, 2015 at 10:29 AM, Alejo C.S. <[hidden email]> wrote:

I have changed LD_LIBRARY_PATH and SlicerLauncherSettings.ini with no luck. Slicer still crash on startup. I'm stuck with 4.4

 

2015-12-18 12:28 GMT-03:00 Alejo C.S. <[hidden email]>:

I have changed LD_LIBRARY_PATH and SlicerLauncherSettings.ini with no luck. Slicer still crash on startup. I'm stuck with 4.4

 

2015-11-30 23:09 GMT-03:00 Andras Lasso <[hidden email]>:

If you start Slicer using the launcher (./Slicer) then it sets up LD_LIBRARY_PATH with all the Python, SimpleITK, etc. paths. This seems to fail on some linux computers (see https://www.na-mic.org/Mantis/view.php?id=3218). You may try to change your LD_LIBRARY_PATH and/or SlicerLauncherSettings.ini to remove your local Python/SimpleITK and add the Slicer’s Python/SimpleITK paths.

 

Andras

 

 

From: Alejo C.S. [mailto:[hidden email]]
Sent: November 30, 2015 1:00 PM
To: Andras Lasso <[hidden email]>


Subject: Re: [slicer-users] Slicer 4.5 stable on Linux crash on startup

 

Not at all, I just uncompress the tar.gz and run ./Slicer. 

 

is there a way to force slicer to use the bundled SimpleITK?

 

thanks!

 

2015-11-30 11:37 GMT-03:00 Andras Lasso <[hidden email]>:

It seems that your local Python and SimpleITK is used instead of those bundled with Slicer. Have you intentionally configured Slicer to use your local Python and SimpleITK?

Andras

From: [hidden email]
Sent: ‎2015-‎11-‎30 09:17


To: [hidden email]
Subject: Re: [slicer-users] Slicer 4.5 stable on Linux crash on startup

Dear Andras, I deleted the three scripts:

 

Slicer-4.5\qt-scripted-modules\SimpleFilters.py

Slicer-4.5\qt-scripted-modules\RegistrationLib\LocalSimpleITKPlugin.py

Slicer 4.5.0-1\lib\Slicer-4.5\qt-scripted-modules\EditorLib\WatershedFromMarkerEffect.py

 

But still the program crash:

 

 

Continuing.

[New Thread 0x7fe58b7c4700 (LWP 12760)]

[New Thread 0x7fe58afc3700 (LWP 12761)]

[New Thread 0x7fe56365f700 (LWP 12763)]

[New Thread 0x7fe4e28ff700 (LWP 12764)]

[New Thread 0x7fe4e20fe700 (LWP 12765)]

[New Thread 0x7fe4e18fd700 (LWP 12766)]

[New Thread 0x7fe4e0ffc700 (LWP 12767)]

[New Thread 0x7fe483152700 (LWP 12770)]

 

Program received signal SIGSEGV, Segmentation fault.

0x00007fe599a95347 in std::string::assign(std::string const&) () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6

(gdb) bt

#0  0x00007fe599a95347 in std::string::assign(std::string const&) () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6

#1  0x00007fe47895b21c in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#2  0x00007fe47895b5b1 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#3  0x00007fe47895b9e9 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#4  0x00007fe47181a4f3 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#5  0x00007fe47177ea5e in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#6  0x00007fe478a47796 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#7  0x0000000000000000 in ?? ()

(gdb) 

 

Could be a problem with my SimpleITK? There is a way to reinstall SimpleITK? I tried with pip but  no success.

 

Regards,

 

A.

 

 

 

2015-11-27 12:14 GMT-03:00 Andras Lasso <[hidden email]>:

Thank you, this information is very helpful. It seems that the crash is related to SimpleITK. Your previous emails indicate that the error may be caused by a scripted module.

 

I’ve found only a few scripted modules that use SimpleITK. Could you please try deleting them one by one and see if the problem goes away when a particular one is deleted?

 

Slicer-4.5\qt-scripted-modules\SimpleFilters.py

Slicer-4.5\qt-scripted-modules\RegistrationLib\LocalSimpleITKPlugin.py

Slicer 4.5.0-1\lib\Slicer-4.5\qt-scripted-modules\EditorLib\WatershedFromMarkerEffect.py

 

Andras

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Alejo C.S.
Sent: Friday, November 27, 2015 10:06 AM
To: SPL Slicer Users <[hidden email]>


Subject: Re: [slicer-users] Slicer 4.5 stable on Linux crash on startup

 

Hi Andras, I re run Slicer and gdb for send you request and now shows the following (I run three more times and this error is showed every time now):

 

 

 

Program received signal SIGSEGV, Segmentation fault.

0x00007ff944a17347 in std::string::assign(std::string const&) () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6

(gdb) bt

#0  0x00007ff944a17347 in std::string::assign(std::string const&) () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6

#1  0x00007ff823b5221c in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#2  0x00007ff823b525b1 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#3  0x00007ff823b529e9 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#4  0x00007ff81ca114f3 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#5  0x00007ff81c975a5e in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#6  0x00007ff823c3e796 in ?? () from /home/ar/.local/lib/python2.7/site-packages/SimpleITK-0.9.0-py2.7-linux-x86_64.egg/SimpleITK/_SimpleITK.so

#7  0x0000000000000000 in ?? ()

 

 

Regards,

 

A.

 

2015-11-27 10:16 GMT-03:00 Andras Lasso <[hidden email]>:

Could you please also send the stack trace? (I think the command to print it is: bt)

Andras

From: [hidden email]
Sent: ‎2015-‎11-‎27 08:12
To: [hidden email]


Subject: Re: [slicer-users] Slicer 4.5 stable on Linux crash on startup

Hi Jean-Christophe, the results of gdb are the following:

 

Program received signal SIGSEGV, Segmentation fault.

0x00007f9c34974626 in vtkSubjectHelper::InvokeEvent(unsigned long, void*, vtkObject*) ()

   from /home/ar/Programas/Slicer-4.5.0-1-linux-amd64/./lib/Slicer-4.5/libvtkCommon-6.3.so.1

(gdb) 

 

Hope it helps

 

Regards,

 

A.

 

 

2015-11-26 16:14 GMT-03:00 Jean-Christophe Fillion-Robin <[hidden email]>:

Hi Alejo,

Thanks for reporting back.

This is helpful. It seems on of the scripted module (or one of its dependencies) is the culprit.

Before creating a script that would allow us to find out which one is the culprit.

You could try attaching gdb.

In a nutshell, you start Slicer using:

   ./Slicer --attach-process

and then attach the debugger.

More details are posted here:

  http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/Debug_Instructions#GDB_debug_by_attaching_to_running_process_.5BRECOMMENDED.5D

That should help identify which library is causing trouble.

 

Hth

Jc

 

On Wed, Nov 18, 2015 at 3:03 PM, Alejo C.S. <[hidden email]> wrote:

Ok, the results with each settings are:

 

 

./Slicer --disable-settings 

Crash all times

 

./Slicer --disable-modules --disable-modules

Starts on all attempts

 

./Slicer  --disable-cli-modules

Crash all times

 

./Slicer --disable-loadable-modules

Crash all times

 

./Slicer --disable-scripted-loadable-modules

Starts on all attempts

 

 

In gdb mode Running Slicer and SlicerApp-real this shows up:

 

Starting program: /home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real 

/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real: error while loading shared libraries: libqSlicerApp.so: cannot open shared object file: No such file or directory

[Inferior 1 (process 13519) exited with code 0177]

 

 

Starting program: /home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real bin/SlicerApp-real

/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/bin/SlicerApp-real: error while loading shared libraries: libqSlicerApp.so: cannot open shared object file: No such file or directory

[Inferior 1 (process 13553) exited with code 0177]

(gdb) 

 

 

ls -l on ./lib/Slicer-4.5/libqSlicerApp.so

 

-rw-r--r-- 1 marmo marmo 810K 12/11/2015 17:06:23 ./lib/Slicer-4.5/libqSlicerApp.so

 

Hope this is useful.

 

Thanks in advance.

 

Alejo

 

 

 

2015-11-18 16:13 GMT-03:00 Andras Lasso <[hidden email]>:

It would help a lot to know in which shared library the crash occurs. Can you run Slicer in gdb? (you need to run gdb with the launcher: Slicer, and then in gdb run the actual application: SlicerApp-real)

 

You may also try to upgrade/downgrade your graphics card driver.

 

Andras

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Jean-Christophe Fillion-Robin
Sent: Wednesday, November 18, 2015 1:49 PM
To: Alejo C.S. <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Slicer 4.5 stable on Linux crash on startup

 

Hi Alejo,

Thanks for the report.

Could you try the following and report which one are working/failing:

(1) ./Slicer --disable-settings

(2) ./Slicer --disable-modules --disable-modules

Then, you could also try using these flags:

 --disable-cli-modules
 --disable-loadable-modules
 --disable-scripted-loadable-modules

 

Hth

Jc

 

 

On Wed, Nov 18, 2015 at 1:10 PM, Alejo C.S. <[hidden email]> wrote:

Thanks Andrey, missed the list.

 

Thanks for your response. I had remove the folder ~/.config/NA-MIC and still when I run ./Slicer crash on startup with same error:
$ ~/Programas/Slicer-4.5.0-1-linux-amd64$ ./Slicer 
Session start time .......: 2015-11-18 15:04:38
Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 - installed
Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
Memory ...................: 7889 MB physical, 1999 MB virtual 
CPU ......................: GenuineIntel 3.398 MHz, 1 cores
Developer mode enabled ...: no
Prefer executable CLI ....: no
Additional module paths ..: (none)
Number of registered modules: 141 
error: [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real] exit abnormally - Report the problem.

 

2015-11-18 15:07 GMT-03:00 Andrey Fedorov <[hidden email]>:

Interesting. Not sure what is going on.

cc'ing the list (please make sure you include the list next time)


On Wed, Nov 18, 2015 at 1:05 PM, Alejo C.S. <[hidden email]> wrote:
> Thanks for your response. I had remove the folder ~/.config/NA-MIC and still
> when I run ./Slicer crash on startup with same error:
>
> $ ~/Programas/Slicer-4.5.0-1-linux-amd64$ ./Slicer
> Session start time .......: 2015-11-18 15:04:38
> Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 - installed
> Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian
> 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
> Memory ...................: 7889 MB physical, 1999 MB virtual
> CPU ......................: GenuineIntel 3.398 MHz, 1 cores
> Developer mode enabled ...: no
> Prefer executable CLI ....: no
> Additional module paths ..: (none)
> Number of registered modules: 141
> error:
> [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real] exit
> abnormally - Report the problem.
> marmo@ANET:~/Programas/Slicer-4.5.0-1-linux-amd64$
>
>
>
> 2015-11-18 14:22 GMT-03:00 Andrey Fedorov <[hidden email]>:
>>
>> Alejo,
>>
>> I've just tried, and could not reproduce this crash on Ubuntu 14.04 LTS.
>>
>> Can you try removing the settings or moving those files to another
>> location and check if this resolves the issue? There may be some
>> compatibility issues with the older settings, or with the extra
>> modules, if you have any.
>>
>>
>> http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/FAQ#How_to_uninstall_Slicer.3F
>>
>> Note that this will reset all of your Slicer user settings.
>>
>> AF
>>
>> On Wed, Nov 18, 2015 at 6:41 AM, Alejo C.S. <[hidden email]> wrote:

>> > Dear list, I'm trying to run Slicer 4.5 stable r24735 on Linux amd64 and
>> > it
>> > crash every time:
>> >
>> > Session start time .......: 2015-11-18 08:35:58
>> > Slicer version ...........: 4.5.0-1 (revision 24735) linux-amd64 -
>> > installed
>> > Operating system .........: Linux / 3.16.0-4-amd64 / #1 SMP Debian
>> > 3.16.7-ckt11-1+deb8u6 (2015-11-09) - 64-bit
>> > Memory ...................: 7889 MB physical, 1999 MB virtual
>> > CPU ......................: GenuineIntel 3.339 MHz, 1 cores
>> > Developer mode enabled ...: no
>> > Prefer executable CLI ....: no
>> > Additional module paths ..: (none)
>> > Number of registered modules: 141
>> > error:
>> > [/home/marmo/Programas/Slicer-4.5.0-1-linux-amd64/./bin/SlicerApp-real]
>> > exit
>> > abnormally - Report the problem.
>> >
>> >
>> > Any help?
>> >
>> > Thanks in advance!
>> >
>> >
>> > PD: There is no problem running Slicer 4.4
>> >
>> >
>> >

>> > _______________________________________________
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>> > To unsubscribe: send email to [hidden email] with
>> > unsubscribe as the subject
>> > http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
>> >
>> >
>> > The information in this e-mail is intended only for the person to whom
>> > it is
>> > addressed. If you believe this e-mail was sent to you in error and the
>> > e-mail
>> > contains patient information, please contact the Partners Compliance
>> > HelpLine at
>> > http://www.partners.org/complianceline . If the e-mail was sent to you
>> > in
>> > error
>> > but does not contain patient information, please contact the sender and
>> > properly
>> > dispose of the e-mail.
>> >
>
>

 


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12