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Old   July 15, 2016, 12:19
Default Error while running sample utility
  #1
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Join Date: Sep 2015
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Dear all,

I am trying to use the sample utility to get a cross section of my 3D case. Here is my sampleDict:
Code:
FoamFile
{
    version     2.0;
    format      ascii;
    class       dictionary;
    object      sampleDict;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //

setFormat raw;

surfaceFormat vtk;

formatOptions { }

interpolationScheme cellPoint;

fields ( p U );

sets ( );

surfaces
(
    xNormal
    {
        type            plane;
        basePoint       (0 0 0);
        normalVector    (1 0 0);
        interpolate     true;
    }
);

// *********************************************************************** //
It has been working fine on my PC until recently. The process keeps getting 'Killed' most likely due to insufficient memory. But I am not sure why it worked fine earlier though...

So, I tried running it in a HPC and it resulted in the following error:

Code:
Build  : 2.4.0-dcea1e13ff76
Exec   : sample -latestTime
Date   : Jul 15 2016
Time   : 22:55:33
Host   : "std1621"
PID    : 20741
Case   : /home/users/ntu/m150086/OpenFOAM/JET/atmosphere/ref_1
nProcs : 1
sigFpe : Floating point exception trapping - not supported on this platform
fileModificationChecking : Monitoring run-time modified files using timeStampMaster
allowSystemOperations : Allowing user-supplied system call operations

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Create time

Create mesh for time = 0.002

Reading surface description:
    xNormal

Time = 0.002

#0  Foam::error::printStack(Foam::Ostream&) at ??:?
#1  Foam::sigSegv::sigHandler(int) at ??:?
#2  ? in "/lib64/libc.so.6"
#3  Foam::cuttingPlane::calcCutCells(Foam::primitiveMesh const&, Foam::Field<double> const&, Foam::UList<int> const&) at ??:?
#4  Foam::cuttingPlane::reCut(Foam::primitiveMesh const&, bool, Foam::UList<int> const&) at ??:?
#5  Foam::sampledPlane::update() at ??:?
#6  Foam::sampledSurfaces::update() at ??:?
#7  Foam::sampledSurfaces::write() at ??:?
#8  ? at ??:?
#9  __libc_start_main in "/lib64/libc.so.6"
#10  ? at ??:?
[std1621:20741:0] Caught signal 11 (Segmentation fault)
==== backtrace ====
 2 0x0000000000059e9c mxm_handle_error()  /var/tmp/OFED_topdir/BUILD/mxm-3.4.3065/src/mxm/util/debug/debug.c:641
 3 0x000000000005a00c mxm_error_signal_handler()  /var/tmp/OFED_topdir/BUILD/mxm-3.4.3065/src/mxm/util/debug/debug.c:616
 4 0x0000003b84a326a0 killpg()  ??:0
 5 0x0000003b84a32625 raise()  ??:0
 6 0x0000003b84a326a0 killpg()  ??:0
 7 0x00000000001ebc65 _ZN4Foam12cuttingPlane12calcCutCellsERKNS_13primitiveMeshERKNS_5FieldIdEERKNS_5UListIiEE()  ??:0
 8 0x00000000001eb72d _ZN4Foam12cuttingPlane5reCutERKNS_13primitiveMeshEbRKNS_5UListIiEE()  ??:0
 9 0x0000000000232cad _ZN4Foam12sampledPlane6updateEv()  ??:0
10 0x0000000000342c81 _ZN4Foam15sampledSurfaces6updateEv()  ??:0
11 0x0000000000343a03 _ZN4Foam15sampledSurfaces5writeEv()  ??:0
12 0x00000000004067a9 main()  ??:0
13 0x0000003b84a1ed5d __libc_start_main()  ??:0
14 0x0000000000405ad9 _start()  ??:0
===================
I am not sure what to make of the error. Any help would be appreciated.

Thanks to everyone.
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Old   November 16, 2018, 10:06
Default
  #2
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Ehsan Asgari
Join Date: Apr 2010
Posts: 471
Rep Power: 16
syavash is on a distinguished road
Quote:
Originally Posted by usv001 View Post
Dear all,

I am trying to use the sample utility to get a cross section of my 3D case. Here is my sampleDict:
Code:
FoamFile
{
    version     2.0;
    format      ascii;
    class       dictionary;
    object      sampleDict;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //

setFormat raw;

surfaceFormat vtk;

formatOptions { }

interpolationScheme cellPoint;

fields ( p U );

sets ( );

surfaces
(
    xNormal
    {
        type            plane;
        basePoint       (0 0 0);
        normalVector    (1 0 0);
        interpolate     true;
    }
);

// *********************************************************************** //
It has been working fine on my PC until recently. The process keeps getting 'Killed' most likely due to insufficient memory. But I am not sure why it worked fine earlier though...

So, I tried running it in a HPC and it resulted in the following error:

Code:
Build  : 2.4.0-dcea1e13ff76
Exec   : sample -latestTime
Date   : Jul 15 2016
Time   : 22:55:33
Host   : "std1621"
PID    : 20741
Case   : /home/users/ntu/m150086/OpenFOAM/JET/atmosphere/ref_1
nProcs : 1
sigFpe : Floating point exception trapping - not supported on this platform
fileModificationChecking : Monitoring run-time modified files using timeStampMaster
allowSystemOperations : Allowing user-supplied system call operations

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Create time

Create mesh for time = 0.002

Reading surface description:
    xNormal

Time = 0.002

#0  Foam::error::printStack(Foam::Ostream&) at ??:?
#1  Foam::sigSegv::sigHandler(int) at ??:?
#2  ? in "/lib64/libc.so.6"
#3  Foam::cuttingPlane::calcCutCells(Foam::primitiveMesh const&, Foam::Field<double> const&, Foam::UList<int> const&) at ??:?
#4  Foam::cuttingPlane::reCut(Foam::primitiveMesh const&, bool, Foam::UList<int> const&) at ??:?
#5  Foam::sampledPlane::update() at ??:?
#6  Foam::sampledSurfaces::update() at ??:?
#7  Foam::sampledSurfaces::write() at ??:?
#8  ? at ??:?
#9  __libc_start_main in "/lib64/libc.so.6"
#10  ? at ??:?
[std1621:20741:0] Caught signal 11 (Segmentation fault)
==== backtrace ====
 2 0x0000000000059e9c mxm_handle_error()  /var/tmp/OFED_topdir/BUILD/mxm-3.4.3065/src/mxm/util/debug/debug.c:641
 3 0x000000000005a00c mxm_error_signal_handler()  /var/tmp/OFED_topdir/BUILD/mxm-3.4.3065/src/mxm/util/debug/debug.c:616
 4 0x0000003b84a326a0 killpg()  ??:0
 5 0x0000003b84a32625 raise()  ??:0
 6 0x0000003b84a326a0 killpg()  ??:0
 7 0x00000000001ebc65 _ZN4Foam12cuttingPlane12calcCutCellsERKNS_13primitiveMeshERKNS_5FieldIdEERKNS_5UListIiEE()  ??:0
 8 0x00000000001eb72d _ZN4Foam12cuttingPlane5reCutERKNS_13primitiveMeshEbRKNS_5UListIiEE()  ??:0
 9 0x0000000000232cad _ZN4Foam12sampledPlane6updateEv()  ??:0
10 0x0000000000342c81 _ZN4Foam15sampledSurfaces6updateEv()  ??:0
11 0x0000000000343a03 _ZN4Foam15sampledSurfaces5writeEv()  ??:0
12 0x00000000004067a9 main()  ??:0
13 0x0000003b84a1ed5d __libc_start_main()  ??:0
14 0x0000000000405ad9 _start()  ??:0
===================
I am not sure what to make of the error. Any help would be appreciated.

Thanks to everyone.

Hi,


I'm having the exactly same error when sampling a surface. Did you find any solution?


Thanks,
Syavash
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Old   November 16, 2018, 10:23
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  #3
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I didn't manage to find a solution. Thankfully, the HPC people had compiled OpenFOAM v3.0 which worked fine. I believe that there are some incompatibilities with my compilation of OpenFOAM v2.3 and the libraries in the HPC but I cannot be too sure.

USV
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Old   November 16, 2018, 13:51
Default
  #4
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Ehsan Asgari
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Quote:
Originally Posted by usv001 View Post
I didn't manage to find a solution. Thankfully, the HPC people had compiled OpenFOAM v3.0 which worked fine. I believe that there are some incompatibilities with my compilation of OpenFOAM v2.3 and the libraries in the HPC but I cannot be too sure.

USV

Thanks for your reply. As I am also using OF 2.3.1 I guess it should be a problem related to the old version.


Regards,
Syavash
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