Hi Peter, Could you attach the log files from your process?
Lilla On Mon, 5 Dec 2011, Peter J. Molfese wrote: > All, > > I've been trying to use mri_cvs_register on a 64-bit mac and received the > following error (below). Google found a couple of hits that others are > having this problem but no solution. I'm running the most recent version > from version 5.1 with the patch on the release notes page ($Id: > mri_cvs_register,v 1.15.2.9 2011/05/26 14:03:26 lzollei Exp $). Running the > process on a Mac Pro running 10.6.7 with 40GB of RAM (10.8.0 Darwin Kernel > Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; > root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64). I've tried the process on > several different Macs. Previous emails thought it was because the Mac > wasn't running a 64-bit version of freesurfer, but there don't appear to be > 64-bit binaries available for Mac yet. Any help would be appreciated. > > Peter > > > surf2vol(98451) 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 duke.haskins.lab by pete Mon > Dec 5 13:21:35 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]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 darwin9.8 named duke.haskins.lab by pete Mon > Dec 5 13:21:35 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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