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[foam-extend.org] Foam-extend-3.1 on RHEL: mesh problem |
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February 24, 2017, 13:10 |
Foam-extend-3.1 on RHEL: mesh problem
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#1 |
New Member
Lee
Join Date: Mar 2016
Posts: 22
Rep Power: 10 |
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 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. Code:
/home/xul15103/foam/foam-extend-3.1/bin/tools/RunFunctions: line 85: mpirun: command not found Can someone help with this problem? Any suggestion is appreciated! Lee |
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February 25, 2017, 15:31 |
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#2 |
Member
Joćo Ferreira
Join Date: Nov 2014
Location: Braga, Portugal
Posts: 53
Rep Power: 12 |
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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February 26, 2017, 00:02 |
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#3 |
New Member
Lee
Join Date: Mar 2016
Posts: 22
Rep Power: 10 |
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 Thanks, Lee |
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March 1, 2017, 15:23 |
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#4 |
Member
Joćo Ferreira
Join Date: Nov 2014
Location: Braga, Portugal
Posts: 53
Rep Power: 12 |
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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March 25, 2017, 17:10 |
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#5 |
Retired Super Moderator
Bruno Santos
Join Date: Mar 2009
Location: Lisbon, Portugal
Posts: 10,982
Blog Entries: 45
Rep Power: 128 |
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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