Hi David, I usually get PETSC errors when I have files from a previous unsuccessful runs of cvs and mri_cvs_register is trying to overwrite the same set of files. I've always found that deleting all the cvs related files before starting mri_cvs_register from scratch usually solves the issue. You can try doing that to see if it works for you.
Thanks, Priti > Hi All > I'm receiving an error with mri_cvs_register from FS 5.1 on a 64-bit Mac > 10.6.7 system and was hoping for some help. It's the same error with the 3 > subjects I've tried it on, and occurs both before and after using the > mri_cvs_register that was updated on Jun 10th. I'm including the last few > lines of the log file. > Thanks > David > > ---------LOG---------- > > step = 12 > =============== > elt_vol= 15.0625 > Constructing Delaunay tetrahedralization. > Delaunay seconds: 7.9e-05 > Creating surface mesh. > Perturbing vertices. > Delaunizing segments. > Constraining facets. > Segment and facet seconds: 0.000686 > Removing unwanted tetrahedra. > Hole seconds: 3.3e-05 > Repairing mesh. > Repair seconds: 6.9e-05 > Adding Steiner points to enforce quality. > Quality seconds: 4.27942 > Smoothing mesh. > Smooth seconds: 0.299788 > > Writing nodes. > Writing elements. > Writing faces. > > Output seconds: 0.036639 > Total running seconds: 4.61682 > > Statistics: > > Input points: 8 > Input facets: 6 > Input holes: 0 > Input regions: 0 > > Mesh points: 81870 > Mesh tetrahedra: 491585 > Mesh faces: 995562 > Mesh subfaces: 24784 > Mesh subsegments: 530 > > Saving nodes to iteration.node > Saving elements to iteration.ele > Saving faces to iteration.face > mesh nodes = 81870 mesh elts = 491585 > building index src > done building the list > count inserted = 0 elapsed = 0 seconds element count = 1 > count inserted = 100000 elapsed = 0.302 seconds element count = > 1128168 > count inserted = 200000 elapsed = 0.496 seconds element count = > 3256402 > count inserted = 300000 elapsed = 0.411 seconds element count = > 5222879 > count inserted = 400000 elapsed = 0.343 seconds element count = > 7039018 > done building octree - total elements = 8705605 > 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 = 92200 > Total BCs = 548640 > no-eqs = 245610 > surf2vol(4634) malloc: *** mmap(size=295714816) failed (error code=12) > *** error: can't allocate region > *** set a breakpoint in malloc_error_break to debug > [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 0 > [0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info. > [0]PETSC ERROR: Memory requested 295714444! > [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 darwin9.8 named Psytechs-Mac-Pro.local by > dbrang Fri Jun 17 17:23:37 2011 > [0]PETSC ERROR: Libraries linked from > /usr/pubsw/packages/petsc/current/src/petsc-2.3.3-p13/lib/darwin9.8.0-c-opt > [0]PETSC ERROR: Configure run at Thu Feb 17 18:27:43 2011 > [0]PETSC ERROR: Configure options > --with-mpi-dir=/usr/pubsw/packages/petsc/current/src/mpilatestbuild/ > --with-shared=0 --with-debugging=0 --with-fc=gfortran --with-cc=gcc > [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 10 BUS: Bus Error, possibly illegal > memory access > [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]PETSCERROR: > 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 darwin9.8 named Psytechs-Mac-Pro.local by > dbrang Fri Jun 17 17:23:37 2011 > [0]PETSC ERROR: Libraries linked from > /usr/pubsw/packages/petsc/current/src/petsc-2.3.3-p13/lib/darwin9.8.0-c-opt > [0]PETSC ERROR: Configure run at Thu Feb 17 18:27:43 2011 > [0]PETSC ERROR: Configure options > --with-mpi-dir=/usr/pubsw/packages/petsc/current/src/mpilatestbuild/ > --with-shared=0 --with-debugging=0 --with-fc=gfortran --with-cc=gcc > [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 > _______________________________________________ > 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. 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