Re: [Freesurfer] XQuartz 2.7.9 update results in errors -- possible solution

2016-07-15 Thread Z K
Sorry for the late response... It would be great if its fixed so as to 
avoid being pigeon holed into specific versions. Thanks for submitting 
the report.

On 07/14/2016 12:42 PM, Robert C Welsh wrote:
> Hi Zeke,
>
> After I created a bugzilla issue, it was identified as a previous issue
> and they submitted a work around. It has to do with changes made to iglx.
>
> See the report:
>
> https://bugs.freedesktop.org/show_bug.cgi?id=96260
>
> I’ve NOT tested it yet.
>
> -Robert
>
> 
> Robert C. Welsh, Ph.D.
> Associate Professor
> Department of Radiology
> Department of Psychiatry
> University of Michigan
> rcwe...@umich.edu 
>
> Associate Director, VA-fMRI Research, VA Ann Arbor
>
>
>
>> On Jul 7, 2016, at 1:05 PM, Robert C Welsh > > wrote:
>>
>> Hi Zeke,
>>
>> I’m seeing the same issue (running xquartz 2.7.9 on MacBooPro10,1). XQuartz 
>> 2.7.8 works, 2.7.9 breaks both freeview, tkmedit, qdec
>>
>> I’ve also submitted bug report to 
>> xquartz,https://bugs.freedesktop.org/show_bug.cgi?id=96849
>>
>> The errors thrown are:
>>
>>
>> *rcwelsh@mnemosyne:/home/Software/fs_install/bin$ qdec *X Error of
>> failed request: BadValue (integer parameter out of range for
>> operation) Major opcode of failed request: 150 (GLX) Minor opcode of
>> failed request: 3 (X_GLXCreateContext) Value in failed request: 0x0
>> Serial number of failed request: 1184 Current serial number in output
>> stream: 1185
>>
>>
>> *rcwelsh@mnemosyne:/home/Software/fs_install/bin$ tkmedit*
>> X Error of failed request:  GLXBadContext
>>   Major opcode of failed request:  150 (GLX)
>>   Minor opcode of failed request:  6 (X_GLXIsDirect)
>>   Serial number of failed request:  26
>>   Current serial number in output stream:  25
>>
>>
>> *rcwelsh@mnemosyne:/home/Software/fs_install/bin$ freeview*
>> X Error: BadValue (integer parameter out of range for operation) 2
>>   Extension:150 (Uknown extension)
>>   Minor opcode: 3 (Unknown request)
>>   Resource id:  0x0
>> X Error: GLXBadContext 160
>>   Extension:150 (Uknown extension)
>>   Minor opcode: 5 (Unknown request)
>>   Resource id:  0x18001d8
>> [0]PETSC ERROR:
>> 
>> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
>> probably memory access out of range
>> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>> [0]PETSC ERROR: or see
>> http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
>> ERROR: or try http://valgrind.org  on linux or
>> man libgmalloc on Apple to find memory corruption errors
>> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link,
>> and run
>> [0]PETSC ERROR: to get more information on the crash.
>> [0]PETSC ERROR: - Error Message
>> 
>> [0]PETSC ERROR: Signal received!
>> [0]PETSC ERROR:
>> 
>> [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15
>> 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
>> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
>> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
>> [0]PETSC ERROR: See docs/index.html for manual pages.
>> [0]PETSC ERROR:
>> 
>> [0]PETSC ERROR: Unknown Name on a linux-gnu named mnemosyne by rcwelsh
>> Thu Jul  7 14:56:12 2016
>> [0]PETSC ERROR: Libraries linked from
>> /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
>> [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
>> [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc
>> --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1
>> --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0
>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
>> [0]PETSC ERROR:
>> 
>> [0]PETSC ERROR: User provided function() line 0 in unknown directory
>> unknown file
>> [unset]: aborting job:
>> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
>> X Error: GLXBadContextTag 164
>>   Extension:150 (Uknown extension)
>>   Minor opcode: 1 (Unknown request)
>>   Resource id:  0x960005
>> *
>> *
>>
>> -Robert
>>
>> --
>>
>> Hello Kate,
>>
>> Thanks for the information. We have seen similar behavior with previous
>> XQuartz releases in the past as well. This tends to "freeze" certain
>> vesion of OSX with certain versions of XQuartz. I will take a closer
>> look but this is usually something that 

Re: [Freesurfer] XQuartz 2.7.9 update results in errors -- possible solution

2016-07-14 Thread Robert C Welsh
Hi Zeke,

After I created a bugzilla issue, it was identified as a previous issue and 
they submitted a work around. It has to do with changes made to iglx.

See the report:

https://bugs.freedesktop.org/show_bug.cgi?id=96260 


I’ve NOT tested it yet.

-Robert


Robert C. Welsh, Ph.D.
Associate Professor
Department of Radiology
Department of Psychiatry
University of Michigan
rcwe...@umich.edu

Associate Director, VA-fMRI Research, VA Ann Arbor



> On Jul 7, 2016, at 1:05 PM, Robert C Welsh  wrote:
> 
> Hi Zeke,
> 
> I’m seeing the same issue (running xquartz 2.7.9 on MacBooPro10,1). XQuartz 
> 2.7.8 works, 2.7.9 breaks both freeview, tkmedit, qdec
> 
> I’ve also submitted bug report to xquartz, 
> https://bugs.freedesktop.org/show_bug.cgi?id=96849 
> 
> 
> The errors thrown are:
> 
> 
> rcwelsh@mnemosyne:/home/Software/fs_install/bin$ qdec
> X Error of failed request:  BadValue (integer parameter out of range for 
> operation)
>   Major opcode of failed request:  150 (GLX)
>   Minor opcode of failed request:  3 (X_GLXCreateContext)
>   Value in failed request:  0x0
>   Serial number of failed request:  1184
>   Current serial number in output stream:  1185
> 
> 
> rcwelsh@mnemosyne:/home/Software/fs_install/bin$ tkmedit
> X Error of failed request:  GLXBadContext
>   Major opcode of failed request:  150 (GLX)
>   Minor opcode of failed request:  6 (X_GLXIsDirect)
>   Serial number of failed request:  26
>   Current serial number in output stream:  25
> 
> 
> rcwelsh@mnemosyne:/home/Software/fs_install/bin$ freeview
> X Error: BadValue (integer parameter out of range for operation) 2
>   Extension:150 (Uknown extension)
>   Minor opcode: 3 (Unknown request)
>   Resource id:  0x0
> X Error: GLXBadContext 160
>   Extension:150 (Uknown extension)
>   Minor opcode: 5 (Unknown request)
>   Resource id:  0x18001d8
> [0]PETSC ERROR: 
> 
> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, 
> probably memory access out of range
> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [0]PETSC ERROR: or see 
> http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
>  
> 
>  ERROR: or try http://valgrind.org  on linux or man 
> libgmalloc on Apple to find memory corruption errors
> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and 
> run 
> [0]PETSC ERROR: to get more information on the crash.
> [0]PETSC ERROR: - Error Message 
> 
> [0]PETSC ERROR: Signal received!
> [0]PETSC ERROR: 
> 
> [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 
> CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> [0]PETSC ERROR: See docs/index.html for manual pages.
> [0]PETSC ERROR: 
> 
> [0]PETSC ERROR: Unknown Name on a linux-gnu named mnemosyne by rcwelsh Thu 
> Jul  7 14:56:12 2016
> [0]PETSC ERROR: Libraries linked from 
> /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
> [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
> [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc 
> --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 
> --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 
> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
> [0]PETSC ERROR: 
> 
> [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown 
> file
> [unset]: aborting job:
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
> X Error: GLXBadContextTag 164
>   Extension:150 (Uknown extension)
>   Minor opcode: 1 (Unknown request)
>   Resource id:  0x960005
> 
> 
> -Robert
> 
> --
> 
> Hello Kate,
> 
> Thanks for the information. We have seen similar behavior with previous 
> XQuartz releases in the past as well. This tends to "freeze" certain 
> vesion of OSX with certain versions of XQuartz. I will take a closer 
> look but this is usually something that we have to deal with.
> -Zeke
> 
> On 06/20/2016 08:34 PM, Kate Mills wrote:
> > Hi All,
> >
> > My lab is having difficulty loading the 

Re: [Freesurfer] XQuartz 2.7.9 update results in errors

2016-07-07 Thread Robert C Welsh
Hi Zeke,

I’m seeing the same issue (running xquartz 2.7.9 on MacBooPro10,1). XQuartz 
2.7.8 works, 2.7.9 breaks both freeview, tkmedit, qdec

I’ve also submitted bug report to xquartz, 
https://bugs.freedesktop.org/show_bug.cgi?id=96849 


The errors thrown are:


rcwelsh@mnemosyne:/home/Software/fs_install/bin$ qdec
X Error of failed request:  BadValue (integer parameter out of range for 
operation)
  Major opcode of failed request:  150 (GLX)
  Minor opcode of failed request:  3 (X_GLXCreateContext)
  Value in failed request:  0x0
  Serial number of failed request:  1184
  Current serial number in output stream:  1185


rcwelsh@mnemosyne:/home/Software/fs_install/bin$ tkmedit
X Error of failed request:  GLXBadContext
  Major opcode of failed request:  150 (GLX)
  Minor opcode of failed request:  6 (X_GLXIsDirect)
  Serial number of failed request:  26
  Current serial number in output stream:  25


rcwelsh@mnemosyne:/home/Software/fs_install/bin$ freeview
X Error: BadValue (integer parameter out of range for operation) 2
  Extension:150 (Uknown extension)
  Minor opcode: 3 (Unknown request)
  Resource id:  0x0
X Error: GLXBadContext 160
  Extension:150 (Uknown extension)
  Minor opcode: 5 (Unknown request)
  Resource id:  0x18001d8
[0]PETSC ERROR: 

[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably 
memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see 
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
 ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find 
memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run 
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: - Error Message 

[0]PETSC ERROR: Signal received!
[0]PETSC ERROR: 

[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 
2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR: 

[0]PETSC ERROR: Unknown Name on a linux-gnu named mnemosyne by rcwelsh Thu Jul  
7 14:56:12 2016
[0]PETSC ERROR: Libraries linked from 
/autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
[0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc 
--with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 
--with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 
CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
[0]PETSC ERROR: 

[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown 
file
[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
X Error: GLXBadContextTag 164
  Extension:150 (Uknown extension)
  Minor opcode: 1 (Unknown request)
  Resource id:  0x960005


-Robert

--

Hello Kate,

Thanks for the information. We have seen similar behavior with previous 
XQuartz releases in the past as well. This tends to "freeze" certain 
vesion of OSX with certain versions of XQuartz. I will take a closer 
look but this is usually something that we have to deal with.
-Zeke

On 06/20/2016 08:34 PM, Kate Mills wrote:
> Hi All,
>
> My lab is having difficulty loading the freeview gui after updating to
> the latest version of XQuartz (2.7.9). We were wondering if others have
> experienced this issue? We have reverted by to XQuartz 2.7.8 on our
> machines for now. In case relevant, this errors seems to span Mac OS
> versions.
>
> Thank you!
>
> Kate
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
> 
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 



Robert C. Welsh, Ph.D.
Associate Professor
Department of Radiology
Department of Psychiatry
University of Michigan
rcwe...@umich.edu

Associate 

Re: [Freesurfer] XQuartz 2.7.9 update results in errors

2016-06-21 Thread Z K
Hello Kate,

Thanks for the information. We have seen similar behavior with previous 
XQuartz releases in the past as well. This tends to "freeze" certain 
vesion of OSX with certain versions of XQuartz. I will take a closer 
look but this is usually something that we have to deal with.

-Zeke

On 06/20/2016 08:34 PM, Kate Mills wrote:
> Hi All,
>
> My lab is having difficulty loading the freeview gui after updating to
> the latest version of XQuartz (2.7.9). We were wondering if others have
> experienced this issue? We have reverted by to XQuartz 2.7.8 on our
> machines for now. In case relevant, this errors seems to span Mac OS
> versions.
>
> Thank you!
>
> Kate
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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.



[Freesurfer] XQuartz 2.7.9 update results in errors

2016-06-20 Thread Kate Mills
Hi All,

My lab is having difficulty loading the freeview gui after updating to the
latest version of XQuartz (2.7.9). We were wondering if others have
experienced this issue? We have reverted by to XQuartz 2.7.8 on our
machines for now. In case relevant, this errors seems to span Mac OS
versions.

Thank you!

Kate
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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.