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[OpenFOAM.org] OF2.3.1 + OS13.2 - Trying to use the dummy Pstream library

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Old   December 30, 2014, 10:05
Default OF2.3.1 + OS13.2 - Trying to use the dummy Pstream library
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Hi Foamers,

I've upgraded OpenSuse to 13.2 and OF to 2.3.1.
mpirun lead to that (already posted) error but I can't get rid of it:

Code:
--> FOAM FATAL ERROR: 
Trying to use the dummy Pstream library.
This dummy library cannot be used in parallel mode
Code:
echo $WM_COMPILER
Gcc
gcc version is 4.8.3
FOAM_MPI=openmpi-system
MPI_ARCH_PATH=/usr
mpi: /usr/lib64/mpi/gcc/openmpi/lib64

Ayla
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Old   December 30, 2014, 11:29
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Greetings Ayla,

Quick questions:
  1. Which installation instructions did you follow?
  2. Did you do anything differently from said instructions?
Best regards,
Bruno
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Old   December 30, 2014, 11:58
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Hi Bruno,

first I've followed the instructions on OpenFOAMWiki (can't load the website right now). Since I could not start paraview I switched to http://www.openfoam.org/download/source.php and recompilied paraview from the ThirdParty-2.3.1.tgz source pack with the result, that everything worked beside parallel runs using openmpi.

Then I've started from the beginning with downloading and compiling according to ://www.openfoam.org/download/source.php and ended up with the same error message.

Best regards,
Ayla
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Old   December 30, 2014, 12:57
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Hi Ayla,

If you Google this page:
Code:
http://openfoamwiki.net/index.php/Installation/Linux/OpenFOAM-2.3.1/openSUSE
it should be able to give you a cached link in the associated drop-down menu.

As for the problem, please tell me what are the lines you have in the file "$HOME/.bashrc" that are associated to OpenFOAM. To see this, the easiest is to run:
Code:
grep "OpenFOAM" $HOME/.bashrc
Best regards,
Bruno
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Old   December 30, 2014, 14:22
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Hi Bruno,

I still can't load the openfoamwiki.net.


OpenFOAM amendments of my ~/.bashrc file:

Code:
export PATH=$PATH:~/OpenFOAM/ayla-2.3.0/newApp/:/opt/Qt/Tools/QtCreator/bin/
export PATH=$PATH:~/OpenFOAM/ayla-2.3.0/run/987_C++/C++/
PYTHONPATH=$PYTHONPATH:/home/ayla/OpenFOAM/ThirdParty-2.3.0/platforms/linux64Gcc/ParaView-4.1.0/lib/paraview-4.1/site-packages/vtk
LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:~/OpenFOAM/ThirdParty-2.3.0/build/linux64Gcc/ParaView-4.1.0/lib/"
alias of='cd ~/OpenFOAM'
alias of22x='source $HOME/OpenFOAM/OpenFOAM-2.2.x/etc/bashrc WM_NCOMPPROCS=24 WM_MPLIB=SYSTEMOPENMPI WM_ARCH_OPTION=64'
alias of230='source $HOME/OpenFOAM/OpenFOAM-2.3.0/etc/bashrc WM_NCOMPPROCS=24 WM_MPLIB=SYSTEMOPENMPI'
alias of230d='source $HOME/OpenFOAM/OpenFOAM-2.3.0/etc/bashrc-d WM_NCOMPPROCS=24 WM_MPLIB=SYSTEMOPENMPI'
alias of231='source $HOME/OpenFOAM/OpenFOAM-2.3.1/etc/bashrc WM_NCOMPPROCS=24 WM_MPLIB=SYSTEMOPENMPI'
Best regards,
Ayla
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Old   December 31, 2014, 03:14
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I've restart the computer and tried to start two cases.

The first with OF2.3.0. BlockMesh gives this error:

Code:
Creating block mesh from
    "/home/ayla/OpenFOAM/ayla-2.3.0/run/510_LES_TESTCASE_90x120x80_1101_04m01m02m_symm/constant/polyMesh/blockMeshDict"
Creating curved edges
Creating topology blocks
Creating topology patches

Creating block mesh topology

Check topology

        Basic statistics
                Number of internal faces : 0
                Number of boundary faces : 6
                Number of defined boundary faces : 6
                Number of undefined boundary faces : 0
        Checking patch -> block consistency
#0  Foam::error::printStack(Foam::Ostream&) at ??:?
#1  Foam::sigSegv::sigHandler(int) at ??:?
#2   in "/lib64/libc.so.6"
#3  Foam::blockMesh::checkBlockMesh(Foam::polyMesh const&) const at ??:?
#4  Foam::blockMesh::createTopology(Foam::IOdictionary const&, Foam::word const&) at ??:?
#5  Foam::blockMesh::blockMesh(Foam::IOdictionary const&, Foam::word const&) at ??:?
#6  
 at ??:?
#7  __libc_start_main in "/lib64/libc.so.6"
#8  
 at /home/abuild/rpmbuild/BUILD/glibc-2.18/csu/../sysdeps/x86_64/start.S:125
Speicherzugriffsfehler
The second case with OF2.3.1. I get this message:
Code:
-----------------------------------------------------------------------------
It seems that there is no lamd running on the host linux-3tg7.

This indicates that the LAM/MPI runtime environment is not operating.
The LAM/MPI runtime environment is necessary for the "mpirun" command.

Please run the "lamboot" command the start the LAM/MPI runtime
environment.  See the LAM/MPI documentation for how to invoke
"lamboot" across multiple machines.
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
It seems that there is no lamd running on the host linux-3tg7.

This indicates that the LAM/MPI runtime environment is not operating.
The LAM/MPI runtime environment is necessary for the "mpirun" command.

Please run the "lamboot" command the start the LAM/MPI runtime
environment.  See the LAM/MPI documentation for how to invoke
"lamboot" across multiple machines.
-----------------------------------------------------------------------------
If I start lamboot this error (already posted above) appears:
Code:
--> FOAM FATAL ERROR: 
Trying to use the dummy Pstream library.
This dummy library cannot be used in parallel mode


    From function UPstream::init(int& argc, char**& argv)
    in file UPstream.C at line 37.


FOAM exiting
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Old   December 31, 2014, 03:33
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If I start lamboot first and source then OpenFOAM-2.3.1/etc/bashrc I get:

Code:
pimpleFoam: error while loading shared libraries: libincompressibleTransportModels.so: cannot open shared object file: No such file or directory
pimpleFoam: error while loading shared libraries: libincompressibleTransportModels.so: cannot open shared object file: No such file or directory
pimpleFoam: error while loading shared libraries: libincompressibleTransportModels.so: cannot open shared object file: No such file or directory
pimpleFoam: error while loading shared libraries: libincompressibleTransportModels.so: cannot open shared object file: No such file or directory                                                                                                                          
pimpleFoam: error while loading shared libraries: libincompressibleTransportModels.so: cannot open shared object file: No such file or directory                                                                                                                          
pimpleFoam: error while loading shared libraries: libincompressibleTransportModels.so: cannot open shared object file: No such file or directory
pimpleFoam: error while loading shared libraries: libincompressibleTransportModels.so: cannot open shared object file: No such file or directory
-----------------------------------------------------------------------------
It seems that [at least] one of the processes that was started with
mpirun did not invoke MPI_INIT before quitting (it is possible that
more than one process did not invoke MPI_INIT -- mpirun was only
notified of the first one, which was on node n0).

mpirun can *only* be used with MPI programs (i.e., programs that
invoke MPI_INIT and MPI_FINALIZE).  You can use the "lamexec" program
to run non-MPI programs over the lambooted nodes.
-----------------------------------------------------------------------------
Ayla
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Old   December 31, 2014, 10:09
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Hi Ayla,

Sorry, yesterday I was already too tired and didn't manage to properly think of a reason why this is happening.
In addition, the wiki was down, but it's up again, as reported here: http://www.cfd-online.com/Forums/ope...tml#post525668 - post #178

I'm now more rested and thanks to the latest information you've provided, I think I now have a clear understanding of what's happening:
  1. Regarding the contents of the ".bashrc" file, there are two things I suggest you change:
    1. This part looks dangerous:
      Code:
      export PATH=$PATH:~/OpenFOAM/ayla-2.3.0/newApp/:/opt/Qt/Tools/QtCreator/bin/
      export PATH=$PATH:~/OpenFOAM/ayla-2.3.0/run/987_C++/C++/
      The reason why I say this isn't because of QtCreator, it's because of the other paths that present there. It's possible that they are interfering with other installations of OpenFOAM, other than 2.3.0. It's advisable to change this to an alias as well, such as:
      Code:
      export PATH=$PATH:/opt/Qt/Tools/QtCreator/bin/
      alias otherapps='export PATH=$PATH:~/OpenFOAM/ayla-2.3.0/newApp/:~/OpenFOAM/ayla-2.3.0/run/987_C++/C++/'
      and run only when you need them.
    2. Code:
      PYTHONPATH=$PYTHONPATH:/home/ayla/OpenFOAM/ThirdParty-2.3.0/platforms/linux64Gcc/ParaView-4.1.0/lib/paraview-4.1/site-packages/vtk
      LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:~/OpenFOAM/ThirdParty-2.3.0/build/linux64Gcc/ParaView-4.1.0/lib/"
      This has an even higher reason for concern, because of two reasons:
      1. The export command is not used, which means that it will only affect the current environment and will not pass onto the scripts that are executed in the terminal you're using.
      2. You're loading to the "LD_LIBRARY_PATH" environment variable a hard-coded path to the ParaView installation in ThirdParty-2.3.0, which can go into conflict with the other two installations, namely 2.2.x and 2.3.1. My advice would be to change to something like this:
        Code:
        alias aux230='export PYTHONPATH=$PYTHONPATH:/home/ayla/OpenFOAM/ThirdParty-2.3.0/platforms/linux64Gcc/ParaView-4.1.0/lib/paraview-4.1/site-packages/vtk; export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:~/OpenFOAM/ThirdParty-2.3.0/build/linux64Gcc/ParaView-4.1.0/lib/"'
        I know, it's one very long line, but it reduces impact on the other OpenFOAM versions. Then call aux230 only when you load up one of the versions for OpenFOAM 2.3.0 versions.
  2. LAM-MPI shouldn't be necessary. My guess is that you have more than one MPI toolbox installed and that the default being used is LAM-MPI. This can be confirmed if you run this command:
    Code:
    mpi-selector --list
    If you can choose Open-MPI, it would be preferable. Then start a new terminal and/or run:
    Code:
    source /etc/profile.d/mpi-selector.sh
  3. In addition to the previous point, check which mpirun version you're using, by running these two commands:
    Code:
    mpirun --version
    ls -l $(which mpirun)
That's all I can think of right now. The use of loading certain applications to each shell environment should be done carefully, since if they are hard-coded to work with a specific version of OpenFOAM, you will run into problems when trying to use another version of OpenFOAM.


If you want, you can also create a file on each OpenFOAM version that will load automatically for that version only, namely if you create the file "etc/prefs.sh", as explained here: http://openfoamwiki.net/index.php/In...eference_files


Best regards,
Bruno
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Old   December 31, 2014, 13:22
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Hi Bruno,

I've changed these points but still have the same problem.

That is the current content of the bashrc file:

Code:
export PATH=$PATH:/opt/Qt/Tools/QtCreator/bin/
alias otherapps='export PATH=$PATH:~/OpenFOAM/ayla-2.3.0/newApp/:~/OpenFOAM/ayla-2.3.0/run/987_C++/C++/'


PYTHONPATH=$PYTHONPATH:/usr/lib64/python2.7/site-packages
alias aux230='export PYTHONPATH=$PYTHONPATH:/home/ayla/OpenFOAM/ThirdParty-2.3.0/platforms/linux64Gcc/ParaView-4.1.0/lib/paraview-4.1/site-packages/vtk; export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:~/OpenFOAM/ThirdParty-2.3.0/build/linux64Gcc/ParaView-4.1.0/lib/"'

export PATH=$PATH:/home/ayla/foam/ParaView-4.2.0-Linux-64bit/bin/

#CUDA
export PATH=/usr/local/cuda-6.5/bin:$PATH
export LD_LIBRARY_PATH=/usr/local/cuda-6.5/lib64:$LD_LIBRARY_PATH

#Openmpi
export LD_LIBRARY_PATH=/usr/lib64/mpi/gcc/openmpi/lib64:$LD_LIBRARY_PATH


alias of='cd ~/OpenFOAM'
alias of22x='source $HOME/OpenFOAM/OpenFOAM-2.2.x/etc/bashrc WM_NCOMPPROCS=24 WM_MPLIB=SYSTEMOPENMPI WM_ARCH_OPTION=64'
alias of230='source $HOME/OpenFOAM/OpenFOAM-2.3.0/etc/bashrc WM_NCOMPPROCS=24 WM_MPLIB=SYSTEMOPENMPI'
alias of230d='source $HOME/OpenFOAM/OpenFOAM-2.3.0/etc/bashrc-d WM_NCOMPPROCS=24 WM_MPLIB=SYSTEMOPENMPI'
alias of231='source $HOME/OpenFOAM/OpenFOAM-2.3.1/etc/bashrc WM_NCOMPPROCS=24 WM_MPLIB=SYSTEMOPENMPI'
#alias fe30='source $HOME/foam/foam-extend-3.0/etc/bashrc'
#alias fe31='source $HOME/foam/foam-extend-3.1/etc/bashrc'
alias thumb='mogrify -format gif -path thumbs/ -thumbnail 800x600 *'
#alias qtcreator='/opt/Qt/Tools/QtCreator/bin/qtcreator'
alias fe30='source $HOME/foam/foam-extend-3.0/etc/bashrc'
Code:
mpi-selector --list
openmpi-1.7.2
Code:
mpirun --version 
ls -l $(which mpirun)
mpirun (Open MPI) 1.7.2


Before changing the bashrc file I could not start mpi, neither with openFoam nor directly (mpirun -np 2 ls). I've received the same error in both cases.
Now, if I try
Code:
mpirun -np 2 ls
it works.
Still not within OpenFoam :-(

Ayla
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Old   December 31, 2014, 14:19
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Hi Ayla,

OK, then now try these steps:
Code:
of231
foam
./Allwmake > log.make 2>&1

#and do it a second time, to get a summary of the build
./Allwmake > log.make 2>&1
Best regards,
Bruno
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Old   January 2, 2015, 04:34
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Hello Bruno,

I wish you a happy New Year!


I've installed OpenSUSE 13.2 from the live CD to start from a completely new system:


1) open mpi
-----------------------------------------------------------------------------------------------------------------
First I've tested mpi which gave me the same error as before:
Code:
-----------------------------------------------------------------------------
It seems that there is no lamd running on the host linux-ivta.

This indicates that the LAM/MPI runtime environment is not operating.
The LAM/MPI runtime environment is necessary for the "mpirun" command.

Please run the "lamboot" command the start the LAM/MPI runtime
environment.  See the LAM/MPI documentation for how to invoke
"lamboot" across multiple machines.
-----------------------------------------------------------------------------
If I
Code:
source /etc/profile.d/mpi-selector.sh
I can use mpi in that terminal.
I've add this line to my ~/.bashrc file. Otherwise I need to retype the line each time I open a new terminal.


2) paraview
-----------------------------------------------------------------------------------------------------------------
Next I've installed OpenFOAM 2.3.1 and the ThirdParty package according to: http://www.openfoam.org/download/source.php

Following:
Code:
cd $FOAM_RUN/tutorials/incompressible/icoFoam/cavity 
blockMesh 
icoFoam 
paraFoam
paraFoam does not start. I get:

Code:
Please build the reader module before continuing:
cd $FOAM_UTILITIES/postProcessing/graphics/PV4Readers
./Allwclean
./Allwmake
./Allwmake gives me an
Code:
ERROR: ParaView not found in /home/elisabeth/OpenFOAM/ThirdParty-2.3.1/platforms/linux64Gcc/ParaView-4.1.0
because there are no compilied paraview libs, neither in ~/OpenFOAM/ThirdParty-2.3.1/platforms/linux64GccDPOpt/lib nor in ~/OpenFOAM/ThirdParty-2.3.1/platforms/linux64Gcc

.../linux64Gcc contains only scotch_6.0.0
.../linux64GccDPOpt/lib contains dll files from scotch and openmpi

In ~/OpenFOAM/ThirdParty-2.3.1/ there is a /build/linux64Gcc folder containing two folders:
CGAL-4.3
ParaView-4.1.0
~/OpenFOAM/ThirdParty-2.3.1/build/linux64Gcc/ParaView-4.1.0/lib contains dynamic library files of ParaView
To me it seems that this folder should be in ~/OpenFOAM/OpenFOAM-2.3.1/applications/utilities/postProcessing/graphics/PV4Readers
I am confused because of different places of the lib folders.


3)blockMesh
-----------------------------------------------------------------------------------------------------------------
If i go to ~/OpenFOAM/OpenFOAM-2.3.1/tutorials/incompressible/icoFoam/cavity
and do blockMesh the utility works.

I've copied one of my own cases in $FOAM_RUN. This case was already running in OF2.3.0 but delivers an ERROR in OF2.3.1.
blockMesh gives:
Code:
/*---------------------------------------------------------------------------*\
| =========                 |                                                 |
| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
|  \\    /   O peration     | Version:  2.3.1                                 |
|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
|    \\/     M anipulation  |                                                 |
\*---------------------------------------------------------------------------*/
Build  : 2.3.1-262087cdf8db
Exec   : blockMesh
Date   : Jan 02 2015
Time   : 10:19:38
Host   : "linux-ivta"
PID    : 2682
Case   : /home/elisabeth/OpenFOAM/elisabeth-2.3.1/run/610_LES_1101_04m01m02m_symmetric_ATHENE
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

Inconsistency detected by ld.so: dl-version.c: 224: _dl_check_map_versions: Assertion `needed != ((void *)0)' failed!
elisabeth@linux-ivta:~/OpenFOAM/elisabeth-2.3.1/run/610_LES_1101_04m01m02m_symmetric_ATHENE>
I have not changed that case at all and also don't get this error if I start blockMesh in the tutorial cavity case.
Yesterday I've installed Ubuntu 14.10 on another hard disk and run this case without any problems.

Best regards,
Ayla
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Old   January 2, 2015, 06:35
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Hi Ayla,

Took me a while to deduce what's going on... and I think I've figured it out. In your case, check the contents of the file "system/controlDict" and look for the entry "libs", which lists the libraries to be loaded.
On that list is a library that is being loaded when it shouldn't, because the object payload is incompatible with the build you're using right now of OpenFOAM 2.3.1.

if you comment out completely that list "libs", then blockMesh should work properly.

Best regards,
Bruno
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Old   January 2, 2015, 14:05
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Hi Bruno,


blockMesh
-------------------
I've followed your instructions and blockMesh works. But it works with the original controlDict too. In the meantime I've recompilied swak4foam and PyFoam.

open mpi
-------------------
your instructions solved the open mpi problem too!
1.)
source /etc/profile.d/mpi-selector.sh
2.)
of231 foam ./Allwmake > log.make 2>&1

paraview
-------------------
I've recompilied paraview again and ended up with the same problem and your
advice helped again: post480510

cd $WM_THIRD_PARTY_DIR
./makeParaView4
worked after installing the missing libraries you've mentioned.

Thanks a lot!

Best regards,
Ayla
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Old   January 19, 2015, 13:11
Default OF2.3.x + OS13.2 -- Scotch decomposition
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Hello Ayla,

Have you managed to run decomposePar with scotch decomposition on OpenSUSE 13.2?

I'm trying to decompose the ./tutorials/incompressible/pimpleDyMFoam/oscillatingInletACMI2D test case with scotch, but I get a segmentation fault.

I suspect it might be due to the ACMI cyclic boundary though, as scotch appears to be working with "normal" test cases. (I decomposed the ./tutorials/incompressible/pisoFoam/les/pitzDailyMapped test case without issues.)

Kind regards,

Francois.
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Old   January 19, 2015, 14:31
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Quick answer: http://www.cfd-online.com/Forums/ope...tml#post391337 post #9
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Old   January 19, 2015, 14:39
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Hi Fransje,

I've tried scotch a couple of minutes before on my workstation (OpenFOAM 2.3.1) with a LES testcase and it worked without errors.
I've split the domain in 8 subdomains (probably not optimal, since I have two CPUs, each 6 cores) and will test the case on a Cluster to see what scotch does with 4 CPUs each 8 cores, compared with different hierarchical decompositions. My cases need to be start in a private queue at the moment, I've to wait for manual support.

I've started a couple of test cases and woke up with the same situation as lakeat.
Do you have experience with the optimization instructions from Eugene?

Ayla
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Old   January 20, 2015, 05:16
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Good morning Ayla and Bruno,

First of all, thank you for your quick replies!

Bruno, I already tried the preservePatches approach, but unfortunately it didn't seem to help.. What is strange is that I also get segfaults for some some combinations of processor decomposition with the simple method..

Ayla, if you have time, could you perhaps try to decompose the ./tutorials/incompressible/pimpleDyMFoam/oscillatingInletACMI2D test case with scotch and see if it works on your system? That would rule out some strange library problem on OpenSUSE 13.2..

Thank you for your help!

Kind regards,

Francois.
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Old   January 21, 2015, 10:50
Default scotchcle
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Hi Francois,


/run/tutorials/incompressible/pimpleDyMFoam/oscillatingInletACMI2D>
OpenSuse 13.2, OF2.3.1
decomposePar (scotch) results in:


Code:
/*---------------------------------------------------------------------------*\
| =========                 |                                                 |
| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
|  \\    /   O peration     | Version:  2.3.1                                 |
|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
|    \\/     M anipulation  |                                                 |
\*---------------------------------------------------------------------------*/
Build  : 2.3.1-262087cdf8db
Exec   : decomposePar
Date   : Jan 21 2015
Time   : 16:24:24
Host   : "linux-wgcv"
PID    : 3064
Case   : /home/ayla/OpenFOAM/ayla-2.3.1/run/tutorials/incompressible/pimpleDyMFoam/oscillatingInletACMI2D
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



Decomposing mesh region0

Create mesh
AMI: Creating addressing and weights between 40 source faces and 96 target faces
AMI: Patch source sum(weights) min/max/average = 1, 1, 1
AMI: Patch target sum(weights) min/max/average = 0, 1, 0.4

Calculating distribution of cells
Selecting decompositionMethod scotch

Finished decomposition in 0.02 s

Calculating original mesh data

Distributing cells to processors

Distributing faces to processors

Distributing points to processors

Constructing processor meshes
#0  Foam::error::printStack(Foam::Ostream&) at ??:?
#1  Foam::sigSegv::sigHandler(int) at ??:?
#2   in "/lib64/libc.so.6"
#3  Foam::cyclicACMIPolyPatch::setNeighbourFaceAreas() const at ??:?
#4  Foam::cyclicACMIPolyPatch::resetAMI(Foam::AMIInterpolation<Foam::PrimitivePatch<Foam::face, Foam::SubList, Foam::Field<Foam::Vector<double> > const&, Foam::Vector<double> >, Foam::PrimitivePatch<Foam::face, Foam::SubList, Foam::Field<Foam::Vector<double> > const&, Foam::Vector<double> > >::interpolationMethod const&) const at ??:?
#5  Foam::cyclicACMIPolyPatch::initGeometry(Foam::PstreamBuffers&) at ??:?
#6  Foam::polyBoundaryMesh::calcGeometry() at ??:?
#7  Foam::polyMesh::addPatches(Foam::List<Foam::polyPatch*> const&, bool) at ??:?
#8
 at ??:?
#9
 at ??:?
#10  __libc_start_main in "/lib64/libc.so.6"
#11
 at /home/abuild/rpmbuild/BUILD/glibc-2.19/csu/../sysdeps/x86_64/start.S:125
log.decomposePar of my test case:

Code:
/*---------------------------------------------------------------------------*\
| =========                 |                                                 |
| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
|  \\    /   O peration     | Version:  2.3.1                                 |
|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
|    \\/     M anipulation  |                                                 |
\*---------------------------------------------------------------------------*/
Build  : 2.3.1-262087cdf8db
Exec   : decomposePar
Date   : Jan 21 2015
Time   : 16:37:28
Host   : "linux-wgcv"
PID    : 5188
Case   : /home/ayla/OpenFOAM/ayla-2.3.1/run/610_LES_1101_04m01m02m_symmetric_ATHENE/610_LES_1101_04m01m02m_symmetric_ATHENE_v10
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 : /home/ayla/OpenFOAM/ayla-2.3.1/platforms/linux64GccDPOpt/lib/libdynamicSmagorinskyModel.so: undefined symbol: _ZTIN4Foam14incompressible9LESModels11GenEddyViscE
--> FOAM Warning : 
    From function dlLibraryTable::open(const fileName&, const bool)
    in file db/dynamicLibrary/dlLibraryTable/dlLibraryTable.C at line 99
    could not load "libdynamicSmagorinskyModel.so"


Decomposing mesh region0

Create mesh

Calculating distribution of cells
Selecting decompositionMethod scotch

Finished decomposition in 4.29 s

Calculating original mesh data

Distributing cells to processors

Distributing faces to processors

Distributing points to processors

Constructing processor meshes

Processor 0
    Number of cells = 108619
    Number of faces shared with processor 1 = 3875
    Number of faces shared with processor 1 = 206
    Number of faces shared with processor 1 = 9
    Number of faces shared with processor 2 = 557
    Number of faces shared with processor 2 = 14
    Number of faces shared with processor 3 = 109
    Number of faces shared with processor 4 = 6314
    Number of faces shared with processor 4 = 14
    Number of faces shared with processor 5 = 909
    Number of faces shared with processor 6 = 2642
    Number of faces shared with processor 6 = 15
    Number of faces shared with processor 7 = 3144
    Number of processor patches = 12
    Number of processor faces = 17808
    Number of boundary faces = 2272

Processor 1
    Number of cells = 108282
    Number of faces shared with processor 0 = 3875
    Number of faces shared with processor 0 = 206
    Number of faces shared with processor 0 = 9
    Number of faces shared with processor 3 = 4262
    Number of faces shared with processor 4 = 1255
    Number of faces shared with processor 5 = 3676
    Number of faces shared with processor 5 = 3
    Number of faces shared with processor 6 = 89
    Number of faces shared with processor 7 = 935
    Number of faces shared with processor 7 = 1
    Number of faces shared with processor 7 = 711
    Number of processor patches = 11
    Number of processor faces = 15022
    Number of boundary faces = 2632

Processor 2
    Number of cells = 108103
    Number of faces shared with processor 0 = 557
    Number of faces shared with processor 0 = 14
    Number of faces shared with processor 4 = 4492
    Number of faces shared with processor 4 = 1
    Number of faces shared with processor 5 = 32
    Number of faces shared with processor 5 = 1606
    Number of faces shared with processor 6 = 4533
    Number of faces shared with processor 6 = 22
    Number of processor patches = 8
    Number of processor faces = 11257
    Number of boundary faces = 6933

Processor 3
    Number of cells = 108090
    Number of faces shared with processor 0 = 109
    Number of faces shared with processor 1 = 4262
    Number of faces shared with processor 7 = 3161
    Number of faces shared with processor 7 = 1
    Number of faces shared with processor 7 = 2208
    Number of processor patches = 5
    Number of processor faces = 9741
    Number of boundary faces = 6871

Processor 4
    Number of cells = 106940
    Number of faces shared with processor 0 = 6314
    Number of faces shared with processor 0 = 14
    Number of faces shared with processor 1 = 1255
    Number of faces shared with processor 2 = 4492
    Number of faces shared with processor 2 = 1
    Number of faces shared with processor 5 = 73
    Number of faces shared with processor 5 = 3545
    Number of faces shared with processor 6 = 144
    Number of faces shared with processor 7 = 820
    Number of faces shared with processor 7 = 10
    Number of processor patches = 10
    Number of processor faces = 16668
    Number of boundary faces = 2870

Processor 5
    Number of cells = 108163
    Number of faces shared with processor 0 = 909
    Number of faces shared with processor 1 = 3676
    Number of faces shared with processor 1 = 3
    Number of faces shared with processor 2 = 32
    Number of faces shared with processor 2 = 1606
    Number of faces shared with processor 4 = 73
    Number of faces shared with processor 4 = 3545
    Number of faces shared with processor 6 = 6876
    Number of faces shared with processor 6 = 7
    Number of processor patches = 9
    Number of processor faces = 16727
    Number of boundary faces = 3409

Processor 6
    Number of cells = 106939
    Number of faces shared with processor 0 = 2642
    Number of faces shared with processor 0 = 15
    Number of faces shared with processor 1 = 89
    Number of faces shared with processor 2 = 4533
    Number of faces shared with processor 2 = 22
    Number of faces shared with processor 4 = 144
    Number of faces shared with processor 5 = 6876
    Number of faces shared with processor 5 = 7
    Number of processor patches = 8
    Number of processor faces = 14328
    Number of boundary faces = 5024

Processor 7
    Number of cells = 108864
    Number of faces shared with processor 0 = 3144
    Number of faces shared with processor 1 = 935
    Number of faces shared with processor 1 = 1
    Number of faces shared with processor 1 = 711
    Number of faces shared with processor 3 = 3161
    Number of faces shared with processor 3 = 1
    Number of faces shared with processor 3 = 2208
    Number of faces shared with processor 4 = 820
    Number of faces shared with processor 4 = 10
    Number of processor patches = 9
    Number of processor faces = 10991
    Number of boundary faces = 5933

Number of processor faces = 56271
Max number of cells = 108864 (0.8% above average 108000)
Max number of processor patches = 12 (33.3333% above average 9)
Max number of faces between processors = 17808 (26.5874% above average 14067.8)

Time = 0

Processor 0: field transfer
Processor 1: field transfer
Processor 2: field transfer
Processor 3: field transfer
Processor 4: field transfer
Processor 5: field transfer
Processor 6: field transfer
Processor 7: field transfer

End.
decomposeParDict

Code:
/*--------------------------------*- C++ -*----------------------------------*\
| =========                 |                                                 |
| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
|  \\    /   O peration     | Version:  2.0.0                                 |
|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
|    \\/     M anipulation  |                                                 |
\*---------------------------------------------------------------------------*/
FoamFile
{
    version     2.0;
    format      ascii;
    class       dictionary;
    note        "mesh decomposition control dictionary";
    location    "system";
    object      decomposeParDict;
}

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //

numberOfSubdomains  8;

method          scotch;

scotchCoeffs
{
  processorWeights
  (
    1 1 1 1 1 1 1 1
  );
}


hierarchicalCoeffs
{
    n ( 2 2 2 );
    delta 0.001;
    order xyz;
}
// ************************************************************************* //
Best regards,
Ayla
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Old   January 21, 2015, 12:17
Default Solution
  #19
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Francois
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Dear Ayla,

Thank you for your reply and for the effort! So that confirm that the problem does not come from my OpenSUSE installation, and that is good to know.

In the mean time I had some interaction with the OpenFOAM developers and the problem seems to come from here:
Code:
void Foam::cyclicACMIPolyPatch::initGeometry(PstreamBuffers& pBufs)
{
    // initialise the AMI so that base geometry (e.g. cell volumes) are
    // correctly evaluated
    resetAMI();

    cyclicAMIPolyPatch::initGeometry(pBufs);
}
As a temporary workaround to be able to decompose the domain using scotch, resetAMI() has to be commented out (and the code recompiled of course.).
After decomposition, the code should be restored to its original state and recompiled, and the test case can then be run with pimpleDyMFoam.

Kind regards,

Francois
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Old   February 14, 2015, 16:08
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  #20
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Bruno Santos
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Greetings to all!

Since the latest posts relate to this bug report: http://www.openfoam.org/mantisbt/view.php?id=1450 - I'm letting future readers know that in the 2nd comment is a one time modification for the source code for working around the problem. This way you won't have to compile the library over and over, whenever you need to decompose the case

Best regards,
Bruno
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