CFD Online Discussion Forums - Segmentation fault with particleTracks

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Segmentation fault with particleTracks

Hello,
I'm trying to generate particle tracks using the particleTracks utility from trajectories obtained from solidParticleFoam.
The output ends with the following:

Code:

...

Time = 39400.897

    Reading particle positions

    Read 682 particles

Time = 39400.898

    Reading particle positions

    Read 682 particles

Time = 39400.899

    Reading particle positions

    Read 682 particles

Time = 39400.9

    Reading particle positions

    Read 682 particles



Particle statistics:

    Found 0 particles originating from processor 0







Generating 0 particle tracks for cloud defaultCloud



Time = 39400

    Reading particle positions

    Constructing tracks



#0  Foam::error::printStack(Foam::Ostream&) in "/opt/openfoam210/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"

#1  Foam::sigSegv::sigHandler(int) in "/opt/openfoam210/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"

#2   in "/lib/libc.so.6"

#3  

 in "/opt/openfoam210/platforms/linux64GccDPOpt/bin/particleTracks"

#4  __libc_start_main in "/lib/libc.so.6"

#5  

 in "/opt/openfoam210/platforms/linux64GccDPOpt/bin/particleTracks"

Segmentation fault

This is using 1 processor and OpenFoam 2.1.0.

My particleTracksProperties file:

Code:



/*--------------------------------*- C++ -*----------------------------------*\

| =========                 |                                                 |

| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |

|  \\    /   O peration     | Version:  2.1.0                                 |

|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |

|    \\/     M anipulation  |                                                 |

\*---------------------------------------------------------------------------*/

FoamFile

{

    version     2.0;

    format      ascii;

    class       dictionary;

    object      particleTrackProperties;

}

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //



cloudName       defaultCloud;



sampleFrequency 1;



maxPositions    1000000;  



// ************************************************************************* //

Any tips in figuring out what I might be doing wrong are appreciated.

I can try to provide any additional information that would help in diagnosing the problem.

Thanks in advance,
Greg

I have just now tried to run this using the gdb debugger. The results aren't particularly informative to me (looks like the crash is in the main() function), but my hope is that they will be meaningful to someone else:

Code:

...

Particle statistics:

    Found 0 particles originating from processor 0







Generating 0 particle tracks for cloud defaultCloud



Time = 39400

    Reading particle positions

    Constructing tracks





Program received signal SIGSEGV, Segmentation fault.

0x00000000004098f0 in main ()

(gdb) where

#0  0x00000000004098f0 in main ()

I think I've figured out the problem and came up with a way to address this.

I added some debugging lines to determined that was related to insufficient origId information; the code was storing -1 for all the IDs and the code was crashing on the line "if (allTracks[trackId].size() < maxPositions)" with trackId equal to -1. It turns out that I wasn't aware of the need for origId and origProcId files when I ran solidParticleFoam (which I used to generate the trajectories); solidParticleFoam didn't seem to require origID or origProcID in the 0/lagrangian/defaultCloud directory (actually, technically, I'm using 39400 as starting time here), and when I ran solidParticleFoam, it filled subsequent time directories with "1000{-1}" and "1000{0}" for these files, respectively.

If I instead put origID and origProcID in the 0/lagrangian/defaultCloud directory, filled with contents like shown below, before running solidParticleFoam, then subsequent use of particleTracks works fine, and without error.

Code:

/*--------------------------------*- C++ -*----------------------------------*\

| =========                 |                                                 |

| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |

|  \\    /   O peration     | Version:  2.1.0                                 |

|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |

|    \\/     M anipulation  |                                                 |

\*---------------------------------------------------------------------------*/

FoamFile

{

    version     2.0;

    format      ascii;

    class       labelField;

    location    "39400";

    object      origId;

}

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //



1000

(

0

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

...

Code:

/*--------------------------------*- C++ -*----------------------------------*\

| =========                 |                                                 |

| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |

|  \\    /   O peration     | Version:  2.1.0                                 |

|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |

|    \\/     M anipulation  |                                                 |

\*---------------------------------------------------------------------------*/

FoamFile

{

    version     2.0;

    format      ascii;

    class       labelField;

    location    "39400";

    object      origProcId;

}

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //



1000

(

0

0

0

0

0

0

0

0

0

...

For context, there seems to be a similar issue that can be encountered when changing the number of processors that are used (http://www.openfoam.org/mantisbt/view.php?id=419), but this is unrelated, and wasn't an issue in my case.

Hi,

I have a similar problem.
But your solution didn't work on mine.

I am using DPMFoam on OF 2.3.
neither it worked on my own solver in which I added particle tracking library into icoFoam.

In both serial and parallel runs I get the following error:

Code:

#0  Foam::error::printStack(Foam::Ostream&) at ??:?

#1  Foam::sigSegv::sigHandler(int) at ??:?

#2   in "/lib/x86_64-linux-gnu/libc.so.6"

#3  Foam::coordSet::scalarCoord(int) const at ??:?

#4  Foam::writer<double>::writeTable(Foam::coordSet const&, Foam::List<Foam::List<double> const*> const&, Foam::Ostream&) const at ??:?

#5  Foam::rawSetWriter<double>::write(bool, Foam::PtrList<Foam::coordSet> const&, Foam::List<Foam::word> const&, Foam::List<Foam::List<Foam::Field<double> > > const&, Foam::Ostream&) const at ??:?

#6  

 at ??:?

#7  __libc_start_main in "/lib/x86_64-linux-gnu/libc.so.6"

#8  

 at ??:?

Segmentation fault (core dumped)

origId and origProcId are as follows for a sample time step:

origId:

Code:

9(0 1 2 3 4 5 6 7 8)

origProcId:

Code:

9{0}

I even added both "origId" and "origProcId" into the "0" time step, but no success.

Here is my particleTrackProperties file:

Code:

cloudName       kinematicCloud;



sampleFrequency 1;



maxPositions    9;



setFormat       csv;    // see sampleDict for set formats

Thanks.

I think I found a solution.

Changing the setFormat into vtk seems to solve the problem.
However I don't know why raw or csv formats don't work yet.