[Freesurfer] Potential memory leak in mri_cvs_register (fwd)

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.kavec@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#Sig...: 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

_______________________________________________

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edu

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer