Re: [Freesurfer] PETSC ERROR WHEN TRYING TO OPEN FREEVIEW

2020-10-16 Thread Wang, Ruopeng 
Would it be possible for you to try the freeview build from FS v7:

https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview

Best,
Ruopeng

On Oct 16, 2020, at 2:47 PM, Álvaro Deleglise 
mailto:alvarodelegl...@gmail.com>> wrote:


External Email - Use Caution

Hi everybody,
I've just installed FreeSurfer v6 in my ubuntu 20.04 SO, but I can't open 
freeview due to PETSC errors. I executed "freeview" in the console, and then 
the following messages appear:

[0]PETSC ERROR: 

[0]PETSC ERROR: Caught signal number 8 FPE: Floating Point Exception,probably 
divide by zero
[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 adeleglise by adeleglise Fri 
Oct 16 15:46:03 2020
[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


I have seen other people with the same problem in the mail archive, but I 
didn't found any effective solution.
Does anybody knows how can I solve it?
Thanks in advance.
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[Freesurfer] PETSC ERROR WHEN TRYING TO OPEN FREEVIEW

2020-10-16 Thread Álvaro Deleglise 
External Email - Use Caution

Hi everybody,
I've just installed FreeSurfer v6 in my ubuntu 20.04 SO, but I can't open
freeview due to PETSC errors. I executed "freeview" in the console, and
then the following messages appear:

[0]PETSC ERROR:

[0]PETSC ERROR: Caught signal number 8 FPE: Floating Point
Exception,probably divide by zero
[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 adeleglise by adeleglise
Fri Oct 16 15:46:03 2020
[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


I have seen other people with the same problem in the mail archive, but I
didn't found any effective solution.
Does anybody knows how can I solve it?
Thanks in advance.
___
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Re: [Freesurfer] Petsc Error in Freesurfer v6.0

2017-04-05 Thread Chris Adamson 
I get these pincher errors as well in VirtualBox.
One thing that may fix it is to disable 3D acceleration for the graphics in the 
VM settings.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Michael ONeill
Sent: Thursday, 23 March 2017 11:56 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Petsc Error in Freesurfer v6.0

Hello Freesurfer Developers,

I've just installed Freesurfer v6.0 and attempted to run the commands printed 
below in order to test the installation:

freeview -v \

bert/mri/T1.mgz \

bert/mri/wm.mgz \

bert/mri/brainmask.mgz \

bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \

-f \

bert/surf/lh.white:edgecolor=blue \

bert/surf/lh.pial:edgecolor=red \

bert/surf/rh.white:edgecolor=blue \

bert/surf/rh.pial:edgecolor=red

Running this resulted in the a PETSC error which i have attached in .txt file.
I'm running Ubuntu 16.04 64bit in virtual box on a windows host.
I've tried numerous solutions including using the latest dev build of 
freesurfer v6.0 (as of 23/03/2017), installing the latest version of PETSC and 
doubling the amount of RAM available to the guest OS from 12GB to 24GB.
But unfortunately none of these approaches worked and the issue still persists.

I'm very eager to start using Freesurfer v6.0 and this seems to, hopefully, be 
the last rock in the road.
Any help you could offer would be appreciated.

Kind Regards,

Michael




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[Freesurfer] Petsc Error in Freesurfer v6.0

2017-03-23 Thread Michael ONeill 
This problem has been resolved by installing Freesurfer v6.0 on a Ubuntu 16.04 
64-bit guest OS with "fixed disk space" instead of "Dynamically allocated".

Michael



The opinions, conclusions and other information expressed in the above message, 
or contained within attachments to the above message, are not given or endorsed 
by Beaumont Hospital unless otherwise indicated by an authorised representative 
independent of this message. This e-mail message and any files transmitted with 
it are confidential and intended solely for the use of the individual or entity 
to whom they are addressed. This e-mail has been scanned for viruses. This 
e-mail and all attachments are confidential and may be privileged. If you have 
received this e-mail in error, notify the sender immediately. Do not use, 
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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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[Freesurfer] Petsc Error in Freesurfer v6.0

2017-03-23 Thread Michael ONeill 
Hello Freesurfer Developers,

I've just installed Freesurfer v6.0 and attempted to run the commands printed 
below in order to test the installation:

freeview -v \
bert/mri/T1.mgz \
bert/mri/wm.mgz \
bert/mri/brainmask.mgz \
bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \
-f \
bert/surf/lh.white:edgecolor=blue \
bert/surf/lh.pial:edgecolor=red \
bert/surf/rh.white:edgecolor=blue \
bert/surf/rh.pial:edgecolor=red

Running this resulted in the a PETSC error which i have attached in .txt file.
I'm running Ubuntu 16.04 64bit in virtual box on a windows host.
I've tried numerous solutions including using the latest dev build of 
freesurfer v6.0 (as of 23/03/2017), installing the latest version of PETSC and 
doubling the amount of RAM available to the guest OS from 12GB to 24GB.
But unfortunately none of these approaches worked and the issue still persists.

I'm very eager to start using Freesurfer v6.0 and this seems to, hopefully, be 
the last rock in the road.
Any help you could offer would be appreciated.

Kind Regards,

Michael




The opinions, conclusions and other information expressed in the above message, 
or contained within attachments to the above message, are not given or endorsed 
by Beaumont Hospital unless otherwise indicated by an authorised representative 
independent of this message. This e-mail message and any files transmitted with 
it are confidential and intended solely for the use of the individual or entity 
to whom they are addressed. This e-mail has been scanned for viruses. This 
e-mail and all attachments are confidential and may be privileged. If you have 
received this e-mail in error, notify the sender immediately. Do not use, 
disseminate, store or copy it in any way.

OpenGL Warning: No pincher, please call crStateSetCurrentPointers() in your SPU
[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 freesurfer-VirtualBox by 
freesurfer Thu Mar 23 12:41:03 2017
[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
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] PETSC ERROR

2011-06-22 Thread Lilla Zollei 


Hi David,

Have you downloaded the updates of mri_cvs_register from 
http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes ? We found some bugs 
in the orginial 5.1 release and put the fixed versions at the above.


Let me know if that still does not solve the problem.

--Lilla

On Tue, 21 Jun 2011, David Brang wrote:


Hi
I posted a couple days ago about a PETSC ERROR with while running 
mri_cvs_register but I seem to be having a more general problem. I'm receiving 
the same
error on two 10.6.7 macs as well as on a Windows running virtualbox, both while 
processing my own subjects and FS5.1 bert. I'm using the command
mri_cvs_register --mov bert --template cvs_avg35 and between step = 17 and step 
= 12 (break point is consistent within the individual but differs between
individuals) I receive the same PETSC error (end of log appended below).

In the VB I doubled the amount of memory allocated to the system and bert 
crashed as the same point in the process.

Thanks in advance
David


 step = 16
===
elt_vol= 19.8125
Constructing Delaunay tetrahedralization.
Delaunay seconds:  0
Creating surface mesh.
Perturbing vertices.
Delaunizing segments.
Constraining facets.
Segment and facet seconds:  0
Removing unwanted tetrahedra.
Hole seconds:  0
Repairing mesh.
Repair seconds:  0
Adding Steiner points to enforce quality.
Quality seconds:  6.32
Smoothing mesh.
Smooth seconds:  0.41

Writing nodes.
Writing elements.
Writing faces.

Output seconds:  0.03
Total running seconds:  6.76

Statistics:

  Input points: 8
  Input facets: 6
  Input holes: 0
  Input regions: 0

  Mesh points: 62502
  Mesh tetrahedra: 372867
  Mesh faces: 755978
  Mesh subfaces: 20488
  Mesh subsegments: 465

Saving nodes to iteration.node
Saving elements to iteration.ele
Saving faces to iteration.face
 mesh nodes = 62502 mesh elts = 372867
 building index src
 done building the list
     count inserted = 0 elapsed = 0 seconds  element count = 1
     count inserted = 10 elapsed = 0.307 seconds  element count = 1457735
     count inserted = 20 elapsed = 0.44 seconds  element count = 3996981
     count inserted = 30 elapsed = 0.338 seconds  element count = 6263194
 done building octree - total elements = 7845082
 penalty_weight = 1000
setting bc 205.891 174.948 225.515 - 0 0 0
     instead 205.881 174.938 225.505 - norm = 0.0173205
setting bc 205.891 174.948 27.6148 - 0 0 0
     instead 205.881 174.938 27.6248 - norm = 0.0173205
setting bc 205.891 35.1985 225.515 - 0 0 0
     instead 205.881 35.2085 225.505 - norm = 0.0173205
setting bc 205.891 35.1985 27.6148 - 0 0 0
     instead 205.881 35.2085 27.6248 - norm = 0.0173205
setting bc 52.3002 174.948 225.515 - 0 0 0
     instead 52.3102 174.938 225.505 - norm = 0.0173205
setting bc 52.3002 174.948 27.6148 - 0 0 0
     instead 52.3102 174.938 27.6248 - norm = 0.0173205
setting bc 52.3002 35.1985 225.515 - 0 0 0
     instead 52.3102 35.2085 225.505 - norm = 0.0173205
setting bc 52.3002 35.1985 27.6148 - 0 0 0
     instead 52.3102 35.2085 27.6248 - norm = 0.0173205
 computing statistics for the displacement application error
 average norm of error in placement = 0.0173205
 iterating
 done with candidates
 Active BCs = 83286
 Total BCs = 548640
 no-eqs = 187506
[0]PETSC ERROR: - Error Message 

[0]PETSC ERROR: Out of memory. This could be due to allocating
[0]PETSC ERROR: too large an object or bleeding by not properly
[0]PETSC ERROR: destroying unneeded objects.
[0]PETSC ERROR: Memory allocated 0 Memory used by process 1973583872
[0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info.
[0]PETSC ERROR: Memory requested 225757228!
[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: surf2vol on a linux-gnu named FreeSurfer by virtualuser Tue Jun 
21 12:18:59 2011
[0]PETSC ERROR: Libraries linked from 
/autofs/space/lyon_006/pubsw/Linux2-2.3-i386/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
[0]PETSC ERROR: Configure run at Mon Jun 16 12:09:46 2008
[0]PETSC ERROR: Configure options --with-debugging=0 --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: PetscMallocAlign() line 61 in src/sys/memory/mal.c
[0]PETSC ERROR: MatSeqAIJSetPreallocation_SeqAIJ() line 2818 in

Re: [Freesurfer] PETSC ERROR

2011-06-22 Thread dbrang 

Hi Lilla,
Yes, sadly the problem still persists. The strangest part is that the same  
error occurred when I tried to process bert (mri_cvs_register --mov bert)  
using the VirtualBox Ubuntu package for FS on Windows. My only guess (as  
suggested by one of the other users) is that it's a problem with 32-bit  
binaries not having access to 4gigs of RAM, as both FS for the Virtual Box  
and for Mac are 32 bit. I've installed 64-bit Linux versions into virtual  
boxes on both my Windows and Mac computers and haven't received any errors  
yet (~24 hours of processing) so this will hopefully get around the  
problem. Has there been any movement compiling FS with 64-bit binaries for  
Mac?

Thanks for the help
David

On , Lilla Zollei lzol...@nmr.mgh.harvard.edu wrote:



Hi David,




Have you downloaded the updates of mri_cvs_register from  
http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes ? We found some  
bugs in the orginial 5.1 release and put the fixed versions at the above.





Let me know if that still does not solve the problem.





--Lilla





On Tue, 21 Jun 2011, David Brang wrote:






Hi


I posted a couple days ago about a PETSC ERROR with while running  
mri_cvs_register but I seem to be having a more general problem. I'm  
receiving the same


error on two 10.6.7 macs as well as on a Windows running virtualbox, both  
while processing my own subjects and FS5.1 bert. I'm using the command


mri_cvs_register --mov bert --template cvs_avg35 and between step = 17  
and step = 12 (break point is consistent within the individual but  
differs between



individuals) I receive the same PETSC error (end of log appended below).




In the VB I doubled the amount of memory allocated to the system and bert  
crashed as the same point in the process.





Thanks in advance



David







step = 16



===



elt_vol= 19.8125



Constructing Delaunay tetrahedralization.



Delaunay seconds: 0



Creating surface mesh.



Perturbing vertices.



Delaunizing segments.



Constraining facets.



Segment and facet seconds: 0



Removing unwanted tetrahedra.



Hole seconds: 0



Repairing mesh.



Repair seconds: 0



Adding Steiner points to enforce quality.



Quality seconds: 6.32



Smoothing mesh.



Smooth seconds: 0.41





Writing nodes.



Writing elements.



Writing faces.





Output seconds: 0.03



Total running seconds: 6.76





Statistics:





Input points: 8



Input facets: 6



Input holes: 0



Input regions: 0





Mesh points: 62502



Mesh tetrahedra: 372867



Mesh faces: 755978



Mesh subfaces: 20488



Mesh subsegments: 465





Saving nodes to iteration.node



Saving elements to iteration.ele



Saving faces to iteration.face



mesh nodes = 62502 mesh elts = 372867



building index src



done building the list



count inserted = 0 elapsed = 0 seconds element count = 1



count inserted = 10 elapsed = 0.307 seconds element count = 1457735



count inserted = 20 elapsed = 0.44 seconds element count = 3996981



count inserted = 30 elapsed = 0.338 seconds element count = 6263194



done building octree - total elements = 7845082



penalty_weight = 1000



setting bc 205.891 174.948 225.515 - 0 0 0



instead 205.881 174.938 225.505 - norm = 0.0173205



setting bc 205.891 174.948 27.6148 - 0 0 0



instead 205.881 174.938 27.6248 - norm = 0.0173205



setting bc 205.891 35.1985 225.515 - 0 0 0



instead 205.881 35.2085 225.505 - norm = 0.0173205



setting bc 205.891 35.1985 27.6148 - 0 0 0



instead 205.881 35.2085 27.6248 - norm = 0.0173205



setting bc 52.3002 174.948 225.515 - 0 0 0



instead 52.3102 174.938 225.505 - norm = 0.0173205



setting bc 52.3002 174.948 27.6148 - 0 0 0



instead 52.3102 174.938 27.6248 - norm = 0.0173205



setting bc 52.3002 35.1985 225.515 - 0 0 0



instead 52.3102 35.2085 225.505 - norm = 0.0173205



setting bc 52.3002 35.1985 27.6148 - 0 0 0



instead 52.3102 35.2085 27.6248 - norm = 0.0173205



computing statistics for the displacement application error



average norm of error in placement = 0.0173205



iterating



done with candidates



Active BCs = 83286



Total BCs = 548640



no-eqs = 187506


[0]PETSC ERROR: - Error Message  




[0]PETSC ERROR: Out of memory. This could be due to allocating



[0]PETSC ERROR: too large an object or bleeding by not properly



[0]PETSC ERROR: destroying unneeded objects.



[0]PETSC ERROR: Memory allocated 0 Memory used by process 1973583872



[0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info.



[0]PETSC ERROR: Memory requested 225757228!


[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

[Freesurfer] PETSC ERROR

2011-06-21 Thread David Brang 
Hi
I posted a couple days ago about a PETSC ERROR with while running
mri_cvs_register but I seem to be having a more general problem. I'm
receiving the same error on two 10.6.7 macs as well as on a Windows running
virtualbox, both while processing my own subjects and FS5.1 bert. I'm using
the command mri_cvs_register --mov bert --template cvs_avg35 and between
step = 17 and step = 12 (break point is consistent within the individual but
differs between individuals) I receive the same PETSC error (end of log
appended below).

In the VB I doubled the amount of memory allocated to the system and bert
crashed as the same point in the process.

Thanks in advance
David


 step = 16
===
elt_vol= 19.8125
Constructing Delaunay tetrahedralization.
Delaunay seconds:  0
Creating surface mesh.
Perturbing vertices.
Delaunizing segments.
Constraining facets.
Segment and facet seconds:  0
Removing unwanted tetrahedra.
Hole seconds:  0
Repairing mesh.
Repair seconds:  0
Adding Steiner points to enforce quality.
Quality seconds:  6.32
Smoothing mesh.
Smooth seconds:  0.41

Writing nodes.
Writing elements.
Writing faces.

Output seconds:  0.03
Total running seconds:  6.76

Statistics:

  Input points: 8
  Input facets: 6
  Input holes: 0
  Input regions: 0

  Mesh points: 62502
  Mesh tetrahedra: 372867
  Mesh faces: 755978
  Mesh subfaces: 20488
  Mesh subsegments: 465

Saving nodes to iteration.node
Saving elements to iteration.ele
Saving faces to iteration.face
 mesh nodes = 62502 mesh elts = 372867
 building index src
 done building the list
 count inserted = 0 elapsed = 0 seconds  element count = 1
 count inserted = 10 elapsed = 0.307 seconds  element count =
1457735
 count inserted = 20 elapsed = 0.44 seconds  element count = 3996981
 count inserted = 30 elapsed = 0.338 seconds  element count =
6263194
 done building octree - total elements = 7845082
 penalty_weight = 1000
setting bc 205.891 174.948 225.515 - 0 0 0
 instead 205.881 174.938 225.505 - norm = 0.0173205
setting bc 205.891 174.948 27.6148 - 0 0 0
 instead 205.881 174.938 27.6248 - norm = 0.0173205
setting bc 205.891 35.1985 225.515 - 0 0 0
 instead 205.881 35.2085 225.505 - norm = 0.0173205
setting bc 205.891 35.1985 27.6148 - 0 0 0
 instead 205.881 35.2085 27.6248 - norm = 0.0173205
setting bc 52.3002 174.948 225.515 - 0 0 0
 instead 52.3102 174.938 225.505 - norm = 0.0173205
setting bc 52.3002 174.948 27.6148 - 0 0 0
 instead 52.3102 174.938 27.6248 - norm = 0.0173205
setting bc 52.3002 35.1985 225.515 - 0 0 0
 instead 52.3102 35.2085 225.505 - norm = 0.0173205
setting bc 52.3002 35.1985 27.6148 - 0 0 0
 instead 52.3102 35.2085 27.6248 - norm = 0.0173205
 computing statistics for the displacement application error
 average norm of error in placement = 0.0173205
 iterating
 done with candidates
 Active BCs = 83286
 Total BCs = 548640
 no-eqs = 187506
[0]PETSC ERROR: - Error Message

[0]PETSC ERROR: Out of memory. This could be due to allocating
[0]PETSC ERROR: too large an object or bleeding by not properly
[0]PETSC ERROR: destroying unneeded objects.
[0]PETSC ERROR: Memory allocated 0 Memory used by process 1973583872
[0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info.
[0]PETSC ERROR: Memory requested 225757228!
[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: surf2vol on a linux-gnu named FreeSurfer by virtualuser Tue
Jun 21 12:18:59 2011
[0]PETSC ERROR: Libraries linked from
/autofs/space/lyon_006/pubsw/Linux2-2.3-i386/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
[0]PETSC ERROR: Configure run at Mon Jun 16 12:09:46 2008
[0]PETSC ERROR: Configure options --with-debugging=0 --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: PetscMallocAlign() line 61 in src/sys/memory/mal.c
[0]PETSC ERROR: MatSeqAIJSetPreallocation_SeqAIJ() line 2818 in
src/mat/impls/aij/seq/aij.c
[0]PETSC ERROR: MatCreateSeqAIJ() line 2703 in src/mat/impls/aij/seq/aij.c
[0]PETSC ERROR: TSolver::setup_matrix() line 658 in
unknowndirectory/solver.h
[0]PETSC ERROR:

[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
probably memory access out