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#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: 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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>
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