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[snappyHexMesh] Problem with parallel run of snappyHexMesh

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Old   April 11, 2016, 06:15
Default Problem with parallel run of snappyHexMesh
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Lorenzo
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Hi everyone,

my problem is the following: I have to run SHM on a given geometry and I wanted to execute it in a parallel run with mpirun.
After the meshing is successfully done , I use reconstructPar -latestTime but when I perform this stage I get to a rather long list of warnings concerning lacking directories and libraries , which eventually end up with a Fatal Error.
It is quite strange since when the very same meshing is performed without parallelization, then no error occurs.
I would be grateful if anyone can give me a hint on what is going on, and maybe help me sort it out.
Thanks

Here the copy of the error statement after meshing on two processors has been terminated:

Finished meshing without any errors
Finished meshing in = 321.52 s.
End

Finalising parallel run
/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 2.4.0 |
| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
Build : 2.4.0-f0842aea0e77
Exec : reconstructPar -latestTime
Date : Apr 10 2016
Time : 14:25:37
Host : "user-X555LAB"
PID : 2716
Case : /home/user/Documenti/Lorenzo/Materie_quinto_anno/Tesi_Les_Naso/Manara_Copia/DeltaPTot
nProcs : 1
sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).
fileModificationChecking : Monitoring run-time modified files using timeStampMaster
allowSystemOperations : Allowing user-supplied system call operations

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

--> FOAM Warning :
From function dlOpen(const fileName&, const bool)
in file POSIX.C at line 1179
dlopen error : libswak4FoamParsers.so: cannot open shared object file: No such file or directory
--> FOAM Warning :
From function dlLibraryTable:open(const fileName&, const bool)
in file db/dynamicLibrary/dlLibraryTable/dlLibraryTable.C at line 99
could not load "libswak4FoamParsers.so"
--> FOAM Warning :
From function dlOpen(const fileName&, const bool)
in file POSIX.C at line 1179
dlopen error : libsimpleSwakFunctionObjects.so: cannot open shared object file: No such file or directory
--> FOAM Warning :
From function dlLibraryTable:open(const fileName&, const bool)
in file db/dynamicLibrary/dlLibraryTable/dlLibraryTable.C at line 99
could not load "libsimpleSwakFunctionObjects.so"
--> FOAM Warning :
From function dlOpen(const fileName&, const bool)
in file POSIX.C at line 1179
dlopen error : libswakFunctionObjects.so: cannot open shared object file: No such file or directory
--> FOAM Warning :
From function dlLibraryTable:open(const fileName&, const bool)
in file db/dynamicLibrary/dlLibraryTable/dlLibraryTable.C at line 99
could not load "libswakFunctionObjects.so"
--> FOAM Warning :
From function dlOpen(const fileName&, const bool)
in file POSIX.C at line 1179
dlopen error : libgroovyBC.so: cannot open shared object file: No such file or directory
--> FOAM Warning :
From function dlLibraryTable:open(const fileName&, const bool)
in file db/dynamicLibrary/dlLibraryTable/dlLibraryTable.C at line 99
could not load "libgroovyBC.so"
--> FOAM Warning :
From function dlOpen(const fileName&, const bool)
in file POSIX.C at line 1179
dlopen error : libswak4FoamParsers.so: cannot open shared object file: No such file or directory
--> FOAM Warning :
From function dlLibraryTable:open(const fileName&, const bool)
in file db/dynamicLibrary/dlLibraryTable/dlLibraryTable.C at line 99
could not load "libswak4FoamParsers.so"
--> FOAM Warning :
From function dlOpen(const fileName&, const bool)
in file POSIX.C at line 1179
dlopen error : libsimpleSwakFunctionObjects.so: cannot open shared object file: No such file or directory
--> FOAM Warning :
From function dlLibraryTable:open(const fileName&, const bool)
in file db/dynamicLibrary/dlLibraryTable/dlLibraryTable.C at line 99
could not load "libsimpleSwakFunctionObjects.so"
--> FOAM Warning :
From function dlOpen(const fileName&, const bool)
in file POSIX.C at line 1179
dlopen error : libswakFunctionObjects.so: cannot open shared object file: No such file or directory
--> FOAM Warning :
From function dlLibraryTable:open(const fileName&, const bool)
in file db/dynamicLibrary/dlLibraryTable/dlLibraryTable.C at line 99
could not load "libswakFunctionObjects.so"
--> FOAM Warning :
From function dlOpen(const fileName&, const bool)
in file POSIX.C at line 1179
dlopen error : libgroovyBC.so: cannot open shared object file: No such file or directory
--> FOAM Warning :
From function dlLibraryTable:open(const fileName&, const bool)
in file db/dynamicLibrary/dlLibraryTable/dlLibraryTable.C at line 99
could not load "libgroovyBC.so"
--> FOAM Warning :
From function dlOpen(const fileName&, const bool)
in file POSIX.C at line 1179
dlopen error : libswak4FoamParsers.so: cannot open shared object file: No such file or directory
--> FOAM Warning :
From function dlLibraryTable:open(const fileName&, const bool)
in file db/dynamicLibrary/dlLibraryTable/dlLibraryTable.C at line 99
could not load "libswak4FoamParsers.so"
--> FOAM Warning :
From function dlOpen(const fileName&, const bool)
in file POSIX.C at line 1179
dlopen error : libsimpleSwakFunctionObjects.so: cannot open shared object file: No such file or directory
--> FOAM Warning :
From function dlLibraryTable:open(const fileName&, const bool)
in file db/dynamicLibrary/dlLibraryTable/dlLibraryTable.C at line 99
could not load "libsimpleSwakFunctionObjects.so"
--> FOAM Warning :
From function dlOpen(const fileName&, const bool)
in file POSIX.C at line 1179
dlopen error : libswakFunctionObjects.so: cannot open shared object file: No such file or directory
--> FOAM Warning :
From function dlLibraryTable:open(const fileName&, const bool)
in file db/dynamicLibrary/dlLibraryTable/dlLibraryTable.C at line 99
could not load "libswakFunctionObjects.so"
--> FOAM Warning :
From function dlOpen(const fileName&, const bool)
in file POSIX.C at line 1179
dlopen error : libgroovyBC.so: cannot open shared object file: No such file or directory
--> FOAM Warning :
From function dlLibraryTable:open(const fileName&, const bool)
in file db/dynamicLibrary/dlLibraryTable/dlLibraryTable.C at line 99
could not load "libgroovyBC.so"


Reconstructing fields for mesh region0

Time = 0.0003

--> FOAM Warning :
From function polyMesh::readUpdateState polyMesh::readUpdate()
in file meshes/polyMesh/polyMeshIO.C at line 207
Number of patches has changed. This may have unexpected consequences. Proceed with care.
--> FOAM Warning :
From function polyMesh::readUpdateState polyMesh::readUpdate()
in file meshes/polyMesh/polyMeshIO.C at line 207
Number of patches has changed. This may have unexpected consequences. Proceed with care.


--> FOAM FATAL IO ERROR:
cannot find file

file: /home/user/Documenti/Lorenzo/Materie_quinto_anno/Tesi_Les_Naso/Manara_Copia/DeltaPTot/processor0/0.0003/polyMesh/pointProcAddressing at line 0.

From function regIOobject::readStream()
in file db/regIOobject/regIOobjectRead.C at line 73.

FOAM exiting
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Old   April 12, 2016, 02:45
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Hi,

You might want to try first with reconstructParMesh and then use reconstructPar.

Hope this helps.

Cheers,
Antimony
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Old   April 12, 2016, 08:53
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Lorenzo
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It works now, thank you very much Antimony!
For the sake of clarity I just launched reconstructParMesh and then reconstructPar -latestTime.
But now I don't know what the two commands separately do, I thought to use reconstructPar-latestTime in order to reconstruct the meshes created by the two processors ( at the end of the latest time step, in my case correspondent to the layer addition). Please correct me if I'm wrong.
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Old   April 13, 2016, 02:07
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Hi,

You are welcome!

As far as I understand it and have used it, reconstructParMesh puts the meshes together, but not the fields, which is taken care of by reconstructPar.

(http://cfd.direct/openfoam/user-guid...ard-utilities/)

Cheers,
Antimony
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Old   April 14, 2016, 15:50
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So after having run my analysis in parallel mode I should reconstruct also the fields of pressure and velocity of course using reconstructPar.
Thanks a lot again!!
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Old   April 15, 2016, 04:12
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Hi,

You are welcome!

Actually, if you want you are going to analyze your results in Paraview, you don't need to reconstruct. You can simply choose the "Decomposed Case" in the Case Type and you are good to go.

Cheers,
Antimony
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