Hi Martin,
I thought we fixed this problem with the latest release. I am checking
into this.
--Lilla
---------- Forwarded message ----------
Date: Fri, 15 Oct 2010 14:38:29 +0200
From: Martin Kavec <martin.ka...@gmail.com>
To: Freesurfer mailing list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Potential memory leak in mri_cvs_register
Hi,
I am trying to do a mri_cvs_register two subjects analyzed with FS-5.0.0 on
a 64-bit Gentoo linux with 4GB memory and another 4GB of swap space. I am
running a signle mri_cvs_register and after certain time the PC starts using
swap intensively and finally the process terminates.
My commandline is:
mri_cvs_register --mov S2 --template S1 --outdir /home/me/CVS/S2 --nocleanup
Thanks,
Martin
I am pasting the last couple of tens of lines of the
trace_el_reg_to_S1_S2.txt below:
***************************************************************************************************
compressing morph
dcds mesh direct image = 0 0 0
dir img for computed transform = 2.08004e-317 2.122e-314 2.122e-314
dir img for compressed = 2.08004e-317 2.122e-314 2.122e-314
dcds total image for source point = 2.08004e-317 2.122e-314 2.122e-314
name = compressed_step_3
Initial transform
name = compressed_step_4
Initial transform
name = compressed_step_5
Initial transform
name = compressed_step_6
Initial transform
name = compressed_step_7
Initial transform
name = compressed_step_8
Initial transform
name = compressed_step_9
Initial transform
name = compressed_step_10
Initial transform
name = compressed_step_11
Initial transform
name = compressed_step_12
Initial transform
name = compressed_step_13
Initial transform
name = compressed_step_14
Initial transform
name = compressed_step_15
Initial transform
name = compressed_step_16
Initial transform
name = compressed_step_17
Initial transform
name =
FEM error
Initial displacement = 7.25836
Final displacement = 1.36008
Max after displacement = 24.2243
Error points = 0
======================
step = 2
===============
elt_vol= 5.3125
Constructing Delaunay tetrahedralization.
Delaunay seconds: 0.33
Creating surface mesh.
Perturbing vertices.
Delaunizing segments.
Constraining facets.
Segment and facet seconds: 4.17
Removing unwanted tetrahedra.
Hole seconds: 0.2
Repairing mesh.
Repair seconds: 0.09
Adding Steiner points to enforce quality.
Quality seconds: 38.28
Smoothing mesh.
Smooth seconds: 2.6
Writing nodes.
Writing elements.
Writing faces.
Output seconds: 0.22
Total running seconds: 46.58
Statistics:
Input points: 8
Input facets: 6
Input holes: 0
Input regions: 0
Mesh points: 216665
Mesh tetrahedra: 1330756
Mesh faces: 2685486
Mesh subfaces: 47948
Mesh subsegments: 733
Saving nodes to iteration.node
Saving elements to iteration.ele
Saving faces to iteration.face
mesh nodes = 216665 mesh elts = 1330756
building index src
done building the list
count inserted = 0 elapsed = 0.026 seconds element count = 1
count inserted = 100000 elapsed = 61.096 seconds element count =
554226
count inserted = 200000 elapsed = 4.754 seconds element count =
1587360
count inserted = 300000 elapsed = 40.398 seconds element count =
2754998
count inserted = 400000 elapsed = 20.41 seconds element count =
3851406
count inserted = 500000 elapsed = 1.861 seconds element count =
4890326
count inserted = 600000 elapsed = 1.384 seconds element count =
5917866
count inserted = 700000 elapsed = 1.302 seconds element count =
6942363
count inserted = 800000 elapsed = 0.495 seconds element count =
7957496
count inserted = 900000 elapsed = 0.377 seconds element count =
8967778
count inserted = 1000000 elapsed = 0.45 seconds element count =
9982380
count inserted = 1100000 elapsed = 0.175 seconds element count =
11004521
count inserted = 1200000 elapsed = 0.813 seconds element count =
12022297
count inserted = 1300000 elapsed = 0.176 seconds element count =
13050507
done building octree - total elements = 13367338
penalty_weight = 1000
setting bc 206.321 180.221 209.482 -> 0 0 0
instead 206.311 180.211 209.472 -> norm = 0.0173205
setting bc 206.321 180.221 15.2289 -> 0 0 0
instead 206.311 180.211 15.2389 -> norm = 0.0173205
setting bc 206.321 46.9577 209.482 -> 0 0 0
instead 206.311 46.9677 209.472 -> norm = 0.0173205
setting bc 206.321 46.9577 15.2289 -> 0 0 0
instead 206.311 46.9677 15.2389 -> norm = 0.0173205
setting bc 48.9912 180.221 209.482 -> 0 0 0
instead 49.0012 180.211 209.472 -> norm = 0.0173205
setting bc 48.9912 180.221 15.2289 -> 0 0 0
instead 49.0012 180.211 15.2389 -> norm = 0.0173205
setting bc 48.9912 46.9577 209.482 -> 0 0 0
instead 49.0012 46.9677 209.472 -> norm = 0.0173205
setting bc 48.9912 46.9577 15.2289 -> 0 0 0
instead 49.0012 46.9677 15.2389 -> norm = 0.0173205
computing statistics for the displacement application error
average norm of error in placement = 0.0173205
iterating
done with candidates
Active BCs = 179269
Total BCs = 563742
no-eqs = 649995
[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 -2147483648
[0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info.
[0]PETSC ERROR: Memory requested 782593984!
[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 k2 by kavec Sat Sep 25
17:52:24 2010
[0]PETSC ERROR: Libraries linked from
/autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
[0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
[0]PETSC ERROR: Configure options --with-debugging=no --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]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 linux-gnu named k2 by kavec Sat Sep 25
17:52:24 2010
[0]PETSC ERROR: Libraries linked from
/autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
[0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
[0]PETSC ERROR: Configure options --with-debugging=no --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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