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 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#Sig... 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 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 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 rcwelsh@umich.edu
Associate Director, VA-fMRI Research, VA Ann Arbor
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 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 rcwelsh@umich.edu
Associate Director, VA-fMRI Research, VA Ann Arbor
On Jul 7, 2016, at 1:05 PM, Robert C Welsh rcwelsh@umich.edu 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 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#Sig... http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC ERROR: or try http://valgrind.org 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 mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 rcwelsh@umich.edu mailto:rcwelsh@umich.edu
Associate Director, VA-fMRI Research, VA Ann Arbor
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 rcwelsh@umich.edu mailto:rcwelsh@umich.edu
Associate Director, VA-fMRI Research, VA Ann Arbor
On Jul 7, 2016, at 1:05 PM, Robert C Welsh <rcwelsh@umich.edu mailto:rcwelsh@umich.edu> 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#Sig... ERROR: or try http://valgrind.org 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 mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 rcwelsh@umich.edu mailto:rcwelsh@umich.edu
Associate Director, VA-fMRI Research, VA Ann Arbor
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Robert C Welsh -
Z K