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[foam-extend.org] Foam-extend-3.1 on RHEL: mesh problem

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Old   February 24, 2017, 13:10
Post Foam-extend-3.1 on RHEL: mesh problem
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Lee
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Dear foamers,

I am now trying to compile foam-extend 3.1 on RHEL cluster (Red Hat Enterprise Linux Workstation release 6.7 (Santiago)). I followed the installation tutorial on the wiki as below. I did check all the required system packages and they have already been installed in the cluster.

https://openfoamwiki.net/index.php/I...oam-extend-3.1

I tried to download foam-extend-3.1 from both source code and binary package, but I still suffered from a lot of errors and warnings during compilation, e.g. "variables unused", "couldn't open files", etc. I was thinking maybe I could ignore these warnings, as the compilation came to the last step (finished stage 5) and I can successfully run a tutorial case in serial. However, if I want to decompose the domain and run in parallel, the job abort. Although the mesh can be "block" and "decompose", some errors are returned which make me very confused.

log.blockMesh:
Code:
Create time


Creating block mesh from
    "/home/xul15103/foam/xul15103-3.1/run/ras/damBreakFine/constant/polyMesh/blockMeshDict"

Creating curved edges
Creating topology blocks
Creating topology patches

Creating block mesh topology
--> FOAM Warning :
    From function polyMesh::polyMesh(... construct from shapes...)
    in file meshes/polyMesh/polyMeshFromShapeMesh.C at line 903
    Found 10 undefined faces in mesh; adding to default patch.

Check topology

        Basic statistics
                Number of internal faces : 4
                Number of boundary faces : 22
                Number of defined boundary faces : 22
                Number of undefined boundary faces : 0
        Checking patch -> block consistency

Creating block offsets
Creating merge list .

Creating polyMesh from blockMesh
Creating patches
Creating cells
Creating points with scale 0.146
    Block 0 cell size :
        i : 0.00634783 .. 0.00634783
        j : 0.0047999 .. 0.0047999
        k : 0.0146 .. 0.0146

    Block 1 cell size :
        i : 0.00670001 .. 0.00670001
        j : 0.0047999 .. 0.0047999
        k : 0.0146 .. 0.0146

    Block 2 cell size :
        i : 0.00634783 .. 0.00634783
        j : 0.00488593 .. 0.00977187
        k : 0.0146 .. 0.0146

    Block 3 cell size :
        i : 0.00599987 .. 0.00599987
        j : 0.00488593 .. 0.00977187
        k : 0.0146 .. 0.0146

    Block 4 cell size :
        i : 0.00670001 .. 0.00670001
        j : 0.00488593 .. 0.00977187
        k : 0.0146 .. 0.0146


Writing polyMesh
----------------
Mesh Information
----------------
  boundingBox: (0 0 0) (0.584 0.584 0.0146)
  nPoints: 15774
  nCells: 7700
  nFaces: 30986
  nInternalFaces: 15214
----------------
Patches
----------------
  patch 0 (start: 15214 size: 86) name: leftWall
  patch 1 (start: 15300 size: 86) name: rightWall
  patch 2 (start: 15386 size: 110) name: lowerWall
  patch 3 (start: 15496 size: 90) name: atmosphere
  patch 4 (start: 15586 size: 15400) name: defaultFaces

End
log.decomposePar
Code:
Create time

Time = 0
Create mesh for region region0

Calculating distribution of cells
--> FOAM Warning :
    From function dlLibraryTable::open(const fileName& functionLibName)
    in file db/dlLibraryTable/dlLibraryTable.C at line 85
    could not load libscotch.so: cannot open shared object file: No such file or directory
--> FOAM Warning :
    From function decompositionMethod::loadExternalLibraries()
    in file decompositionMethod/decompositionMethod.C at line 453
    Loading of decomposition library libscotchDecomp.so unsuccesful. Some decomposition methods may not be  available
--> FOAM Warning :
    From function dlLibraryTable::open(const fileName& functionLibName)
    in file db/dlLibraryTable/dlLibraryTable.C at line 85
    could not load libmetisDecomp.so: cannot open shared object file: No such file or directory
--> FOAM Warning :
    From function decompositionMethod::loadExternalLibraries()
    in file decompositionMethod/decompositionMethod.C at line 453
    Loading of decomposition library libmetisDecomp.so unsuccesful. Some decomposition methods may not be  available
--> FOAM Warning :
    From function dlLibraryTable::open(const fileName& functionLibName)
    in file db/dlLibraryTable/dlLibraryTable.C at line 85
    could not load libparMetisDecomp.so: cannot open shared object file: No such file or directory
--> FOAM Warning :
    From function decompositionMethod::loadExternalLibraries()
    in file decompositionMethod/decompositionMethod.C at line 453
    Loading of decomposition library libparMetisDecomp.so unsuccesful. Some decomposition methods may not be  available
Selecting decompositionMethod simple

Finished decomposition in 0.01 s

Calculating original mesh data

Distributing cells to processors

Distributing faces to processors

Calculating processor boundary addressing

Distributing points to processors

Constructing processor meshes

Processor 0
    Number of cells = 1935
    Number of faces shared with processor 1 = 44
    Number of faces shared with processor 2 = 46
    Number of processor patches = 2
    Number of processor faces = 90
    Number of boundary faces = 3958

Processor 1
    Number of cells = 1915
    Number of faces shared with processor 0 = 44
    Number of faces shared with processor 3 = 45
    Number of processor patches = 2
    Number of processor faces = 89
    Number of boundary faces = 3939

Processor 2
    Number of cells = 1915
    Number of faces shared with processor 0 = 46
    Number of faces shared with processor 3 = 43
    Number of processor patches = 2
    Number of processor faces = 89
    Number of boundary faces = 3917

Processor 3
    Number of cells = 1935
    Number of faces shared with processor 1 = 45
    Number of faces shared with processor 2 = 43
    Number of processor patches = 2
    Number of processor faces = 88
    Number of boundary faces = 3958

Number of processor faces = 178
Max number of processor patches = 2
Max number of faces between processors = 90

Processor 0: field transfer
Processor 1: field transfer
Processor 2: field transfer
Processor 3: field transfer

End.
log.interFoam
Code:
/home/xul15103/foam/foam-extend-3.1/bin/tools/RunFunctions: line 85: mpirun: command not found
I am not sure these problems are related to RHEL system or the cluster. If more details are needed, I can recompile the foam-extend-3.1 and upload the log.

Can someone help with this problem? Any suggestion is appreciated!

Lee
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Old   February 25, 2017, 15:31
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Joćo Ferreira
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Hi,

From the logs it seems that MPI was not compile or an error occurred while compile it. If it was compiled, check if your environment is setup correctly (i.e your PATH contains the mpirun binaries).
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Old   February 26, 2017, 00:02
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Lee
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Hi Joćo,

Thanks for your reply. I think the problem with MPI is due to I did not load the MPI environment module. However, I am still confusing about the warnings shown in the logs for blockMesh and decomposePar. I believe there is something wrong during the compilation for foam-extend-3.1, as there a lot of "variable not used" and "couldn't open file" in the log (attached below in the dropbox).

https://www.dropbox.com/sh/xzva3fg86...lHg-O7AOa?dl=0

I followed the installation tutorial on the wiki. I also checked the system packages requirement for Fedora (since RHEL is similar to Fedora) and found they were all installed in the server.
Code:
sudo yum groupinstall "Development Tools"
sudo yum install gcc-c++ binutils-devel cmake wget bison flex m4 zlib-devel \
qt-devel qtwebkit-devel mercurial graphviz
I have no idea about what is going on during the compilation. Is there still missing any system package or should I modify some files before compiling in RHEL 6.7?

Thanks,
Lee
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Old   March 1, 2017, 15:23
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Joćo Ferreira
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Hi,

Is openmpi installed in your system?
To be honest I usually compile all third party packages instead of using the system ones. However, that's a personal preference and it results in a bigger installation.
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Old   March 25, 2017, 17:10
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Greetings to all!

@Lee: Sorry for taking so long to look into this and since it has passed a month already, I have to ask you: have you managed to solve this problem or do you still need help with this?

Best regards,
Bruno
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