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mapFields : mpirun gives segmentation fault

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Old   August 27, 2015, 10:38
Unhappy mapFields : mpirun gives segmentation fault
  #1
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Abhinav R
Join Date: Aug 2015
Posts: 1
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vanihba2000 is on a distinguished road
I want to run mapFields in parallel. I am using the following commands to do so :

First,
Code:
<targetdirectory>$ decomposePar
Then,

Code:
<targetdirectory>$ mpirun -np 8 mapFields <sourcedirectory> -consistent -parallel
And I get the following error :
Code:
/*---------------------------------------------------------------------------*\
| =========                 |                                                 |
| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
|  \\    /   O peration     | Version:  2.3.0                                 |
|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
|    \\/     M anipulation  |                                                 |
\*---------------------------------------------------------------------------*/
Build  : 2.3.0-f5222ca19ce6
Exec   : mapFields -consistent ../chevron_v2_2p0_U25/ -parallel
Date   : Aug 27 2015
Time   : 18:44:37
Host   : "admin2-B85M-D3H"
PID    : 24985
Case   : /home/admin2/Chevron_Work/cases_of/chevron_v2/chevron_U25/chevron_U25_k0.01/chevron_v2_2p5_U25
nProcs : 8
Slaves : 
7
(
"admin2-B85M-D3H.24986"
"admin2-B85M-D3H.24987"
"admin2-B85M-D3H.24988"
"admin2-B85M-D3H.24989"
"admin2-B85M-D3H.24990"
"admin2-B85M-D3H.24991"
"admin2-B85M-D3H.24992"
)

Pstream initialized with:
    floatTransfer      : 0
    nProcsSimpleSum    : 0
    commsType          : nonBlocking
    polling iterations : 0
sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).
fileModificationChecking : Monitoring run-time modified files using timeStampMaster
allowSystemOperations : Disallowing user-supplied system call operations

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Source: "../chevron_v2_2p0_U25" ""
Target: "/home/admin2/Chevron_Work/cases_of/chevron_v2/chevron_U25/chevron_U25_k0.01" "chevron_v2_2p5_U25"

Create databases as time
Case   : ../chevron_v2_2p0_U25
nProcs : 8
Slaves : 
7
(
"admin2-B85M-D3H.24986"
"admin2-B85M-D3H.24987"
"admin2-B85M-D3H.24988"
"admin2-B85M-D3H.24989"
"admin2-B85M-D3H.24990"
"admin2-B85M-D3H.24991"
"admin2-B85M-D3H.24992"
)

Pstream initialized with:
    floatTransfer      : 0
    nProcsSimpleSum    : 0
    commsType          : nonBlocking
    polling iterations : 0

Source time: 0
Target time: 0

Create meshes

Source mesh size: 93771	Target mesh size: 152552


Consistently creating and mapping fields for time 0

Creating mesh-to-mesh addressing for region0 and region0 regions using cellVolumeWeight
[6] #0  Foam::error::printStack(Foam::Ostream&)[2] #0  Foam::error::printStack(Foam::Ostream&)[3] #0  Foam::error::printStack(Foam::Ostream&)[7] #0  Foam::error::printStack(Foam::Ostream&) at ??:?
[6] #1  Foam::sigSegv::sigHandler(int) at ??:?
[7] #1  Foam::sigSegv::sigHandler(int) at ??:?
[2] #1  Foam::sigSegv::sigHandler(int) at ??:?
[3] #1  Foam::sigSegv::sigHandler(int) at ??:?
[2] #2   at ??:?
[3] #2   at ??:?
[6] #2   at ??:?
[7] #2  [5] #0  Foam::error::printStack(Foam::Ostream&) in "/lib/x86_64-linux-gnu/libc.so.6"
[6] #3  cfree in "/lib/x86_6 in "/lib/x86_64-linux-gnu/libc.so.6"
[2] #3  cfree4-linux-gnu/libc.so.6"
[3] #3  cfree[4] [0] #0  Foam::error::printStack(Foam::Ostream&) in "/lib/x86_64-linux-gnu/libc.so.6"
[6] #4  Foam::List<int>::operator=(Foam::List<int> const&) at ??:?
[5] #1  Foam::sigSegv::sigHandler(int)#0  Foam::error::printStack(Foam::Ostream&) in "/lib/x86_64-linux-gnu/libc.so.6"
[7] #3  cfree in "/lib/x86_64-linux-gnu/libc.so.6"
[3] #4  Foam::List<int>::operator=(Foam::List<int> const&) in "/lib/x86_64-linux-gnu/libc.so.6"
[2] #4  Foam::List<int>::operator=(Foam::List<int> const&)[1] #0  Foam::error::printStack(Foam::Ostream&) in "/lib/x86_64-linux-gnu/libc.so.6"
[7] #4  Foam::List<int>::operator=(Foam::List<int> const&) at ??:?
[2] #5  Foam::meshToMesh::distributeAndMergeCells(Foam::mapDistribute const&, Foam::polyMesh const&, Foam::globalIndex const&, Foam::Field<Foam::Vector<double> >&, Foam::List<Foam::face>&, Foam::List<int>&, Foam::List<int>&, Foam::List<int>&) const at ??:?
[6] #5  Foam::meshToMesh::distributeAndMergeCells(Foam::mapDistribute const&, Foam::polyMesh const&, Foam::globalIndex const&, Foam::Field<Foam::Vector<double> >&, Foam::List<Foam::face>&, Foam::List<int>&, Foam::List<int>&, Foam::List<int>&) const at ??:?
[3] #5  Foam::meshToMesh::distributeAndMergeCells(Foam::mapDistribute const&, Foam::polyMesh const&, Foam::globalIndex const&, Foam::Field<Foam::Vector<double> >&, Foam::List<Foam::face>&, Foam::List<int>&, Foam::List<int>&, Foam::List<int>&) const at ??:?
[5] #2   at ??:?
[4] #1  Foam::sigSegv::sigHandler(int) at ??:?
[1] #1  Foam::sigSegv::sigHandler(int) at ??:?
[6] #6  Foam::meshToMesh::calculate() at ??:?
[3] #6  Foam::meshToMesh::calculate() at ??:?
[0] #1  Foam::sigSegv::sigHandler(int) at ??:?
[2] #6  Foam::meshToMesh::calculate() in "/lib/x86_64-linux-gnu/libc.so.6"
[5] #3  cfree at ??:?
[3] #7  Foam::meshToMesh::meshToMesh(Foam::polyMesh const&, Foam::polyMesh const&, Foam::meshToMesh::interpolationMethod const&, bool) at ??:?
[2] #7  Foam::meshToMesh::meshToMesh(Foam::polyMesh const&, Foam::polyMesh const&, Foam::meshToMesh::interpolationMethod const&, bool) at ??:?
[7] #5  Foam::meshToMesh::distributeAndMergeCells(Foam::mapDistribute const&, Foam::polyMesh const&, Foam::globalIndex const&, Foam::Field<Foam::Vector<double> >&, Foam::List<Foam::face>&, Foam::List<int>&, Foam::List<int>&, Foam::List<int>&) const at ??:?
[0] #2   at ??:?
[4] #2   at ??:?
[6] #7  Foam::meshToMesh::meshToMesh(Foam::polyMesh const&, Foam::polyMesh const&, Foam::meshToMesh::interpolationMethod const&, bool) at ??:?
[7] #6  Foam::meshToMesh::calculate() in "/lib/x86_64-linux-gnu/libc.so.6"
[5] #4  Foam::List<int>::operator=(Foam::List<int> const&) at ??:?
[1] #2   at ??:?
[2] #8   at ??:?
[3] #8   in "/lib/x86_64-linux-gnu/libc.so.6"
[4] #3  cfree at ??:?
[7] #7  Foam::meshToMesh::meshToMesh(Foam::polyMesh const&, Foam::polyMesh const&, Foam::meshToMesh::interpolationMethod const&, bool) at ??:?
[5] #5  Foam::meshToMesh::distributeAndMergeCells(Foam::mapDistribute const&, Foam::polyMesh const&, Foam::globalIndex const&, Foam::Field<Foam::Vector<double> >&, Foam::List<Foam::face>&, Foam::List<int>&, Foam::List<int>&, Foam::List<int>&) const at ??:?
[6] #8  
 in "/lib/x86_64-linux-gnu/libc.so.6"
[0] #3  cfree
 in "/lib/x86_64-linux-gnu/libc.so.6"
[4] #4  Foam::List<int>::operator=(Foam::List<int> const&) at ??:?
[5] #6  Foam::meshToMesh::calculate()[2]  at ??:?
[2] #9   in "/lib/x86_64-linux-gnu/libc.so.6"
[1] #3  cfree
 at ??:?
[7] #8  [3]  at ??:?
[3] #9   in "/lib/x86_64-linux-gnu/libc.so.6"
[0] #4  Foam::List<int>::operator=(Foam::List<int> const&) at ??:?
[5] #7  Foam::meshToMesh::meshToMesh(Foam::polyMesh const&, Foam::polyMesh const&, Foam::meshToMesh::interpolationMethod const&, bool) in "/lib/x86_64-linux-gnu/libc.so.6"
[1] #4  Foam::List<int>::operator=(Foam::List<int> const&)[6]  at ??:?
[6] #9   at ??:?
[4] #5  Foam::meshToMesh::distributeAndMergeCells(Foam::mapDistribute const&, Foam::polyMesh const&, Foam::globalIndex const&, Foam::Field<Foam::Vector<double> >&, Foam::List<Foam::face>&, Foam::List<int>&, Foam::List<int>&, Foam::List<int>&) const
 at ??:?
[0] #5  Foam::meshToMesh::distributeAndMergeCells(Foam::mapDistribute const&, Foam::polyMesh const&, Foam::globalIndex const&, Foam::Field<Foam::Vector<double> >&, Foam::List<Foam::face>&, Foam::List<int>&, Foam::List<int>&, Foam::List<int>&) const at ??:?
[5] #8  


 at ??:?
[4] #6  Foam::meshToMesh::calculate() at ??:?
[0] #6  Foam::meshToMesh::calculate()
[6]  at ??:?
[6] #10  __libc_start_main at ??:?
[1] #5  Foam::meshToMesh::distributeAndMergeCells(Foam::mapDistribute const&, Foam::polyMesh const&, Foam::globalIndex const&, Foam::Field<Foam::Vector<double> >&, Foam::List<Foam::face>&, Foam::List<int>&, Foam::List<int>&, Foam::List<int>&) const[2]  at ??:?
[2] #10  __libc_start_main[3]  at ??:?
[3] #10  __libc_start_main[7]  at ??:?
[7] #9  [5]  at ??:?
[5] #9   in "/lib/x86_64-linux-gnu/libc.so.6"
[2] #11   in "/lib/x86_64-linux-gnu/libc.so.6"
[6] #11   at ??:?
[4] #7  Foam::meshToMesh::meshToMesh(Foam::polyMesh const&, Foam::polyMesh const&, Foam::meshToMesh::interpolationMethod const&, bool) at ??:?
[1] #6  Foam::meshToMesh::calculate()
 in "/lib/x86_64-linux-gnu/libc.so.6"
[3] #11   at ??:?
[4] #8   at ??:?
[0] #7  Foam::meshToMesh::meshToMesh(Foam::polyMesh const&, Foam::polyMesh const&, Foam::meshToMesh::interpolationMethod const&, bool)


[6]  at ??:?
[2]  at ??:?


[7]  at ??:?
[7] #10  __libc_start_main at ??:?
[1] #7  Foam::meshToMesh::meshToMesh(Foam::polyMesh const&, Foam::polyMesh const&, Foam::meshToMesh::interpolationMethod const&, bool) at ??:?
[0] #8  [5]  at ??:?
[5] #10  __libc_start_main[4]  at ??:?
[4] #9  
[3]  at ??:?
 in "/lib/x86_64-linux-gnu/libc.so.6"
[5] #11  
 at ??:?
[1] #8  [4]  at ??:?
[4] #10  __libc_start_main
 in "/lib/x86_64-linux-gnu/libc.so.6"
[7] #11  
[0]  at ??:?
[0] #9  [5]  at ??:?

[7]  at ??:?

[1]  at ??:?
[1] #9   in "/lib/x86_64-linux-gnu/libc.so.6"
[4] #11  

[4]  at ??:?
[0]  at ??:?
[0] #10  __libc_start_main[1]  at ??:?
[1] #10  __libc_start_main in "/lib/x86_64-linux-gnu/libc.so.6"
[1] #11  
 in "/lib/x86_64-linux-gnu/libc.so.6"
[0] #11  
[0]  at ??:?
[1]  at ??:?
--------------------------------------------------------------------------
mpirun noticed that process rank 6 with PID 24991 on node admin2-B85M-D3H exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
dmytro.iurashev likes this.
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Old   October 13, 2015, 13:07
Default
  #2
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Ryan Tunstall
Join Date: Sep 2013
Posts: 10
Rep Power: 13
rt08 is on a distinguished road
Abhinav, did you manage to solve this issue in the end?
rt08 is offline   Reply With Quote

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mapfields, mpirun, segmentation fault

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