shapeworks-users - [shapeworks-users] segfault

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[shapeworks-users] segfault

From: Wei Liu <weiliu620@gmail.com>
To: Shapeworks-users@sci.utah.edu
Subject: [shapeworks-users] segfault
Date: Tue, 1 Jul 2014 16:01:27 -0600

Dear shapeworks users,

Today I got a segmentation fault when running ShapeWorksRun on my CT image of 5 volumes. From the screen log, it seems the segfault happened at the "optimization step". Below I attached the log, the xml configuration file and the files that have been generated before the segfault happens.

I was monitoring the memory usage and found the allocated memory was within the limit of my physical memory.

Any insights on this issue? Or any flag to turn on to print more debug information?

Thanks in advance,

Wei

========= ShapeWorksRun log ===================

weiliu@lando:/scratch/experiments/shapeworks> /scratch/packages/shapeworks.git/build/ShapeWorksRun/ShapeWorksRun lung.correspondence.xml

m_processing_mode = 3

m_number_of_particles = 256

m_optimization_iterations = 200

m_output_points_prefix = lung

m_output_transform_file = output_transform_file

m_domains_per_shape = 1

m_timepts_per_subject = 1

m_starting_regularization = 10

m_ending_regularization = 0.1

m_iterations_per_split = 200

m_relative_weighting = 1

m_norm_penalty_weighting = 0

m_initial_relative_weighting = 0.05

m_initial_norm_penalty_weighting = 0

m_adaptivity_strength = 0

m_attributes_per_domain = 0

m_checkpointing_interval = 20

m_transform_file =

m_prefix_transform_file =

m_procrustes_interval = 0

m_recompute_regularization_interval = 1

m_procrustes_scaling = 1

m_adaptivity_mode = 0

m_keep_checkpoints = 0

m_optimization_iterations_completed = 0

Procrustes scaling is on

Mean curvature magnitude = 0.0410644

Std deviation = 0.0386809

Mean curvature magnitude = 0.0483452

Std deviation = 0.0401311

Mean curvature magnitude = 0.0528453

Std deviation = 0.0415891

Mean curvature magnitude = 0.0442168

Std deviation = 0.0440822

Mean curvature magnitude = 0.039068

Std deviation = 0.0368917

------------------------------

*** Initialize Step

------------------------------

Particle count: 2

Performing global step

..........Performing global step

..........Writing lung.0.wpts with 2points

Writing lung.1.wpts with 2points

Writing lung.2.wpts with 2points

Writing lung.3.wpts with 2points

Writing lung.4.wpts with 2points

Particle count: 4

Performing global step

..........Performing global step

..........Writing lung.0.wpts with 4points

Writing lung.1.wpts with 4points

Writing lung.2.wpts with 4points

Writing lung.3.wpts with 4points

Writing lung.4.wpts with 4points

Particle count: 8

Performing global step

..........Performing global step

..........Writing lung.0.wpts with 8points

Writing lung.1.wpts with 8points

Writing lung.2.wpts with 8points

Writing lung.3.wpts with 8points

Writing lung.4.wpts with 8points

Particle count: 16

Performing global step

..........Performing global step

..........Writing lung.0.wpts with 16points

Writing lung.1.wpts with 16points

Writing lung.2.wpts with 16points

Writing lung.3.wpts with 16points

Writing lung.4.wpts with 16points

Particle count: 32

Performing global step

..........Performing global step

..........Writing lung.0.wpts with 32points

Writing lung.1.wpts with 32points

Writing lung.2.wpts with 32points

Writing lung.3.wpts with 32points

Writing lung.4.wpts with 32points

Particle count: 64

Performing global step

..........Performing global step

..........Writing lung.0.wpts with 64points

Writing lung.1.wpts with 64points

Writing lung.2.wpts with 64points

Writing lung.3.wpts with 64points

Writing lung.4.wpts with 64points

Particle count: 128

Performing global step

..........Performing global step

..........Writing lung.0.wpts with 128points

Writing lung.1.wpts with 128points

Writing lung.2.wpts with 128points

Writing lung.3.wpts with 128points

Writing lung.4.wpts with 128points

Particle count: 256

Performing global step

..........Performing global step

..........Writing lung.0.wpts with 256points

Writing lung.1.wpts with 256points

Writing lung.2.wpts with 256points

Writing lung.3.wpts with 256points

Writing lung.4.wpts with 256points

Writing lung.0.wpts with 256points

Writing lung.1.wpts with 256points

Writing lung.2.wpts with 256points

Writing lung.3.wpts with 256points

Writing lung.4.wpts with 256points

------------------------------

*** AddAdaptivity Step

------------------------------

*** Optimize Step

------------------------------

Optimizing correspondences.

Performing global step

BeforeIteration counter = 0

0: -1.95399e-12

1: 2233.63

2: 6109.69

3: 9130.2

4: 13024.7

ENERGY = 7.00618 MinimumVariance = 10

..........Performing global step

BeforeIteration counter = 0

0: 9.722e-12

1: 2632.27

2: 7232.2

3: 10060.2

4: 14207.3

ENERGY = 7.10904 MinimumVariance = 7.94328

..........Writing lung.0.wpts with 256points

Writing lung.1.wpts with 256points

Writing lung.2.wpts with 256points

Writing lung.3.wpts with 256points

Writing lung.4.wpts with 256points

Performing global step

BeforeIteration counter = 0

0: 1.0556e-11

1: 3094.51

2: 8472.64

3: 11077.3

4: 15777.5

ENERGY = 7.21294 MinimumVariance = 6.30957

..........Performing global step

BeforeIteration counter = 0

0: 2.98161e-12

1: 3625.51

2: 9820.69

3: 12145.6

4: 17588.4

ENERGY = 7.31406 MinimumVariance = 5.01187

..........Writing lung.0.wpts with 256points

Writing lung.1.wpts with 256points

Writing lung.2.wpts with 256points

Writing lung.3.wpts with 256points

Writing lung.4.wpts with 256points

Performing global step

BeforeIteration counter = 0

0: 1.29785e-11

1: 4217.28

2: 11188.9

3: 13313.2

4: 19565.2

ENERGY = 7.40989 MinimumVariance = 3.98107

..........Performing global step

BeforeIteration counter = 0

0: 1.87255e-11

1: 4865.53

2: 12485.8

3: 14779.8

4: 21615.6

ENERGY = 7.50115 MinimumVariance = 3.16228

.........Segmentation fault

============ end of ShapeWorksRun log ===========

============== files generated ==================

-rw-r--r-- 1 weiliu users 6825 Jul 1 14:45 lung.0.wpts

-rw-r--r-- 1 weiliu users 6825 Jul 1 14:45 lung.0.lpts

-rw-r--r-- 1 weiliu users 6790 Jul 1 14:45 lung.1.lpts

-rw-r--r-- 1 weiliu users 6790 Jul 1 14:45 lung.1.wpts

-rw-r--r-- 1 weiliu users 6820 Jul 1 14:45 lung.2.wpts

-rw-r--r-- 1 weiliu users 6820 Jul 1 14:45 lung.2.lpts

-rw-r--r-- 1 weiliu users 6807 Jul 1 14:45 lung.3.wpts

-rw-r--r-- 1 weiliu users 6807 Jul 1 14:45 lung.3.lpts

-rw-r--r-- 1 weiliu users 644 Jul 1 14:45 output_transform_file

-rw-r--r-- 1 weiliu users 6812 Jul 1 14:45 lung.4.wpts

-rw-r--r-- 1 weiliu users 6812 Jul 1 14:45 lung.4.lpts

-rw-r--r-- 1 weiliu users 6817 Jul 1 14:45 lung.d0.mean

-rw-r--r-- 1 weiliu users 6843 Jul 1 14:45 lung.d0.-3.0.mode

-rw-r--r-- 1 weiliu users 6829 Jul 1 14:45 lung.d0.-2.0.mode

-rw-r--r-- 1 weiliu users 6818 Jul 1 14:45 lung.d0.-1.0.mode

-rw-r--r-- 1 weiliu users 6809 Jul 1 14:45 lung.d0.2.0.mode

-rw-r--r-- 1 weiliu users 6814 Jul 1 14:45 lung.d0.1.0.mode

-rw-r--r-- 1 weiliu users 6791 Jul 1 14:45 lung.d0.3.0.mode

-rw-r--r-- 1 weiliu users 6793 Jul 1 14:45 lung.d0.-3.1.mode

-rw-r--r-- 1 weiliu users 6790 Jul 1 14:45 lung.d0.-2.1.mode

-rw-r--r-- 1 weiliu users 6805 Jul 1 14:45 lung.d0.-1.1.mode

-rw-r--r-- 1 weiliu users 6823 Jul 1 14:45 lung.d0.2.1.mode

-rw-r--r-- 1 weiliu users 6804 Jul 1 14:45 lung.d0.1.1.mode

-rw-r--r-- 1 weiliu users 6796 Jul 1 14:45 lung.d0.3.1.mode

-rw-r--r-- 1 weiliu users 6790 Jul 1 14:45 lung.d0.-3.2.mode

-rw-r--r-- 1 weiliu users 6775 Jul 1 14:45 lung.d0.-2.2.mode

-rw-r--r-- 1 weiliu users 6795 Jul 1 14:45 lung.d0.-1.2.mode

-rw-r--r-- 1 weiliu users 6818 Jul 1 14:45 lung.d0.1.2.mode

-rw-r--r-- 1 weiliu users 6808 Jul 1 14:45 lung.d0.3.2.mode

-rw-r--r-- 1 weiliu users 6829 Jul 1 14:45 lung.d0.2.2.mode

-rw-r--r-- 1 weiliu users 6827 Jul 1 14:45 lung.d0.-3.3.mode

-rw-r--r-- 1 weiliu users 6793 Jul 1 14:45 lung.d0.-2.3.mode

-rw-r--r-- 1 weiliu users 6801 Jul 1 14:45 lung.d0.-1.3.mode

-rw-r--r-- 1 weiliu users 6798 Jul 1 14:45 lung.d0.1.3.mode

-rw-r--r-- 1 weiliu users 6815 Jul 1 14:45 lung.d0.3.3.mode

-rw-r--r-- 1 weiliu users 6806 Jul 1 14:45 lung.d0.2.3.mode

-rw-r--r-- 1 weiliu users 6817 Jul 1 14:45 lung.d0.-3.4.mode

-rw-r--r-- 1 weiliu users 6817 Jul 1 14:45 lung.d0.-2.4.mode

-rw-r--r-- 1 weiliu users 6816 Jul 1 14:45 lung.d0.1.4.mode

-rw-r--r-- 1 weiliu users 6817 Jul 1 14:45 lung.d0.-1.4.mode

-rw-r--r-- 1 weiliu users 6817 Jul 1 14:45 lung.d0.2.4.mode

-rw-r--r-- 1 weiliu users 6816 Jul 1 14:45 lung.d0.3.4.mode

=============== configuration .xml file =====================

<?xml version="1.0" ?>

PE105B.nii.gz

PE900B.nii.gz

PE908B.nii.gz

PE916B.nii.gz

PE919B.nii.gz

</inputs>

<!--

OPTIONALLY we could specify a set of point files to initialize the optimization like this:

<point_files>

torusDT.00.lpts

torusDT.01.lpts

torusDT.19.lpts

</point_files>

-->

<!-- If point files are not specified, then the application will initialize particles

by splitting until each shape has this total number of particles. -->

<number_of_particles> 256 </number_of_particles>

<iterations_per_split> 200 </iterations_per_split>

<starting_regularization> 10.0 </starting_regularization>

<ending_regularization> 0.1 </ending_regularization>

<optimization_iterations> 200 </optimization_iterations>

<checkpointing_interval> 20 </checkpointing_interval>

<output_points_prefix> lung </output_points_prefix>

[shapeworks-users] segfault, Wei Liu, 07/01/2014
- Re: [shapeworks-users] segfault, Alan Morris, 07/02/2014
  - Re: [shapeworks-users] segfault, Wei Liu, 07/03/2014
    - Re: [shapeworks-users] segfault, Alan Morris, 07/03/2014
      - Re: [shapeworks-users] segfault, Wei Liu, 07/03/2014
        
        Re: [shapeworks-users] segfault, Alan Morris, 07/03/2014
        
        Re: [shapeworks-users] segfault, Alan Morris, 07/09/2014
        
        Re: [shapeworks-users] segfault, Wei Liu, 07/09/2014
        Re: [shapeworks-users] segfault, Josh Cates, 07/09/2014

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