Is there a reason that the Mac binaries are not available in 64-bit versions?

On Jun 21, 2011, at 3:11 PM, freesurfer-request@nmr.mgh.harvard.edu wrote:

Date: Tue, 21 Jun 2011 21:11:54 +0200
From: Martin Kavec <martin.kavec@gmail.com>
Subject: Re: [Freesurfer] error during mri_cvs_register
To: David Brang <dbrang@gmail.com>
Cc: freesurfer@nmr.mgh.harvard.edu, rspriti@nmr.mgh.harvard.edu
Message-ID: <BANLkTi=4zCQWpzUam0oLpmzGW6mO5fkb4A@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Hi David,

FreeSurfer's binaries for MAC are still 32-bit and apparently cvs
tries to allocate more that is possible. The lines of the error code
below suggest that. I had the same problem and had to opt for x86_64
linux binaries, where the cvs runs fine. It needs ~ 6 GB of memory and
takes ~ 2 days to finish.

Regards,

Martin

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

On Mon, Jun 20, 2011 at 11:34 PM, David Brang <dbrang@gmail.com> wrote:
Thanks for the advice Priti,
I deleted the old cvs files and re-ran but still no luck. I also tried a new
subject on a different Mac (still 10.6.7) and received the same error.
Thanks
David

On Mon, Jun 20, 2011 at 12:56 PM, <rspriti@nmr.mgh.harvard.edu> wrote:

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
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