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 = 100000 elapsed = 0.307 seconds element count = 1457735 count inserted = 200000 elapsed = 0.44 seconds element count = 3996981 count inserted = 300000 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 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...: 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: 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: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
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 = 100000 elapsed = 0.307 seconds element count = 1457735 count inserted = 200000 elapsed = 0.44 seconds element count = 3996981 count inserted = 300000 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 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: 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: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
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 lzollei@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 = 100000 elapsed = 0.307 seconds element count = 1457735
count inserted = 200000 elapsed = 0.44 seconds element count = 3996981
count inserted = 300000 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 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: 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: 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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Lilla Zollei