Compilation works fine but the cases won't run

Submitted by blais.bruno on Tue, 10/01/2013 - 15:54
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Plain text icon cfdcompcfdem.txt111.79 KB
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Hello everyone,

I have been trying to install cfdem in the past few days but I have had little success.

I am running Ubuntu 13.04. I already had OpenFOAM installed and I have been using extensively, so this should not be a problem. I have installed Ubuntu using the deb pack online using this procedure :
http://www.openfoam.org/download/ubuntu.php

I have installed LIGGGHTS and LPP and have been able to run the test cases without any problem and visualize the results.

However, when compiling the coupling using the cfdemCompCFDEM command I get the following (see attached file cfdcompcfdem).

Although the beggining of the file appears to be weird, it seems compilation goes fine and I do not get any critical error that break down compilation.

However, whenever i go to run a case, I get the following (see attached file). Furthermore, I get the following error to stdout :

rm: cannot remove ‘couplingFiles/*’: No such file or directory

--> FOAM FATAL ERROR:
No times selected

From function reconstructPar
in file reconstructPar.C at line 178.

FOAM exiting

and a bunch of "cannot remove".

I am pretty sure something is wrong with my installation, but I cannot pinpoint what it is... Could anyone lend me a hand with this issue?

Thank you very much,
Bruno

alice's picture

alice | Wed, 10/02/2013 - 10:51

Hey Bruno,
did you already try to run the cases manually? (i.e. start off with
>> blockMesh
if necessary, then make a
>> decomposePar
and then run the solver with the command
>> mpirun -np 4 cfdemSolverPiso -parallel
(in this case the process is run with 4 processors and the solver in use is cfdemSolverPiso. In case you are working with another solver, please adjust it). If the calculation runs through you can go to post-processing:
I already encountered cases where the reconstructPar didn't work for my case, as there are troubles with the reconstruction of the lagrangian fields. This is not much of a problem, there's at least one simple work-around: just create an empty file in your CFD-directory that has a name ending with ".foam" (e.g. type
>> touch visual.foam
), open paraview by typing
>> paraview visual.foam
and then choose "Decomposed Case" as case type before loading the data. Starting from the second time step you will see the lagrangian particles as well as the mesh...
Cheers,
Alice

blais.bruno | Wed, 10/02/2013 - 15:00

Dear Alice,

First of all, thank you very much for your fast answer. I did as you have told me and everything seems to work fine. I only have a last problem. For instance, in the case twoSpheresGlowinskiMPI, I cannot use reconstructPar without errors. Following your advice, I have been able to post-process the data. However, I cannot find a way to access the lagrangian data (in order to use the point sprite renderer on them for instance). At iteration 2 I can see the r and v fields for the particles, but I cannot seem to find a way to be able to use those as an unstructured lagrangian data set.

Thank you again, you have been most helpfull.
Bruno

alice's picture

alice | Thu, 10/03/2013 - 09:39

Hello Bruno,
always happy to help ;)
reconstructPar hast troubles with reconstructing a mesh that changes over time as soon as particles are around. That's the reason why it cannot be used for twoSpheresGlowinskiMPI. But again there is a workaround: you can load your dataset twice, in one case you just unselect the internal mesh data. Starting from the second iteration you then can display the particles, e.g. as points or even spheres if you add a glyph...
Cheers,
Alice

blais.bruno | Thu, 10/03/2013 - 16:44

Dear Alice,

Thank you very much. Everything is functionnal now. I must say the solution was simpler than I first imagined it would be.

I wish you the best of luck in your endeavours.

Best regards,
Bruno

shahabgol | Mon, 11/18/2013 - 16:18

Dear all,
I had the same problem and error:

rm: cannot remove ‘couplingFiles/*’: No such file or directory

when I entered >>blockMesh in terminal the following error occured:

--> FOAM FATAL IO ERROR:
cannot find file

file: /home/shahab14/system/controlDict at line 0.

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

FOAM exiting
---------------------------------------------
By the way, I have tried >>blockMesh and >>icoFoam and >>paraFoam before installation of LIGGGHTS and CFDEM and they worked properly but now this error happens.

could u please help me?? I had this problem before, so I reinstalled ubuntu and all the programs again but the problem remains.

Best Regards,
Shahab Golshan

alice's picture

alice | Tue, 11/19/2013 - 12:15

Hello Shahab,
are you sure that you were in the right directory when typing blockMesh? The error message indicates that you were in your home directory and not in the case directory when tying to mesh...
Cheers,
Alice

shahabgol | Tue, 11/19/2013 - 12:31

Hello Alice,
Thank you for your kind answer. You are right, I am very amateur in using Ubuntu. Can you please help me fix this error? Here is the error appears in terminal when I type cfdemTestTUT:
-------------------------------------------------------------------------------------------------------------------------------
Create time

Decomposing mesh region0

Create mesh

Calculating distribution of cells
Selecting decompositionMethod simple

Finished decomposition in 0.01 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 = 4000
Number of faces shared with processor 1 = 400
Number of processor patches = 1
Number of processor faces = 400
Number of boundary faces = 1200

Processor 1
Number of cells = 4000
Number of faces shared with processor 0 = 400
Number of processor patches = 1
Number of processor faces = 400
Number of boundary faces = 1200

Number of processor faces = 400
Max number of cells = 4000 (0% above average 4000)
Max number of processor patches = 1 (0% above average 1)
Max number of faces between processors = 400 (0% above average 400)

Time = 0

Processor 0: field transfer
Processor 1: field transfer

End.

// run_parallel_cfdemSolverPiso_settlingTestMPI_CFDDEM //

/home/shahab14/CFDEM/CFDEMcoupling-PUBLIC-2.2.x/tutorials/cfdemSolverPiso/settlingTestMPI/CFD

rm: cannot remove `couplingFiles/*': No such file or directory
--------------------------------------------------------------------------
mpirun was unable to launch the specified application as it could not find an executable:

Executable: cfdemSolverPiso
Node: shahab14-System-Product-Name

while attempting to start process rank 0.
--------------------------------------------------------------------------
2 total processes failed to start
/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 2.2.x |
| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
Build : 2.2.x-ab211bf15d63
Exec : reconstructPar
Date : Nov 20 2013
Time : 14:52:05
Host : "shahab14-System-Product-Name"
PID : 2515
Case : /home/shahab14/CFDEM/CFDEMcoupling-PUBLIC-2.2.x/tutorials/cfdemSolverPiso/settlingTestMPI/CFD
nProcs : 1
sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).
fileModificationChecking : Monitoring run-time modified files using timeStampMaster
allowSystemOperations : Disallowing user-supplied system call operations

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

--> FOAM FATAL ERROR:
No times selected

From function reconstructPar
in file reconstructPar.C at line 178.

FOAM exiting

rm: cannot remove `cfdemSolverPiso_settlingTestMPI.eps': No such file or directory
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This is free software; see the source code for copying conditions.
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http://www.octave.org/bugs.html to learn how to write a helpful report).

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error: load: unable to find file ../../DEM/post/velocity.txt
error: called from:
error: settlingVelocity.m at line 9, column 6

** (evince:2518): WARNING **: Error when getting information for file '/home/shahab14/CFDEM/CFDEMcoupling-PUBLIC-2.2.x/tutorials/cfdemSolverPiso/settlingTestMPI/CFD/octave/cfdemSolverPiso_settlingTestMPI.eps': No such file or directory

** (evince:2518): WARNING **: Error setting file metadata: No such file or directory

** (evince:2518): WARNING **: Error setting file metadata: No such file or directory

** (evince:2518): WARNING **: Error setting file metadata: No such file or directory

** (evince:2518): WARNING **: Error setting file metadata: No such file or directory

** (evince:2518): WARNING **: Error setting file metadata: No such file or directory

** (evince:2518): WARNING **: Error setting file metadata: No such file or directory

** (evince:2518): WARNING **: Error setting file metadata: No such file or directory

** (evince:2518): WARNING **: Error setting file metadata: No such file or directory

** (evince:2518): WARNING **: Error setting file metadata: No such file or directory

** (evince:2518): WARNING **: Error setting file metadata: No such file or directory

** (evince:2518): WARNING **: Error setting file metadata: No such file or directory

** (evince:2518): WARNING **: Error setting file metadata: No such file or directory
--------------------------------------------------------------------------------------------------------------
What should I exactly do now??

Regards,
Sh.G

alice's picture

alice | Tue, 11/19/2013 - 14:13

Hi Shahab,
the message "mpirun was unable to launch the specified application as it could not find an executable: cfdemSolverPiso" inidicates that the solvers are not installed. Please try to recompile CFDEMcoupling.
Cheers,
Alice

shahabgol | Wed, 11/20/2013 - 08:51

Dear Alice,
Thank you very much again, I tried again these codes : ">> cfdemCompLIG >> cfdemCompCFDEM" to recompile, but the error remains.
I reached this folder: "/home/shahab14/CFDEM/CFDEMcoupling-PUBLIC-2.2.x/src/lagrangian/cfdemParticle/etc" and entered >>bash testTutorials.sh
But everytime I try to run a case this message appears in my terminal:
---------------------------------------------------------------------------------------
This routine will execute the CFDEMcoupling tutorial cases specified in tutorial-list.txt

Are the variables CFDEM_TUT_DIR=/home/shahab14/CFDEM/CFDEMcoupling-PUBLIC-2.2.x/tutorials
and CFDEM_SRC_DIR=/home/shahab14/CFDEM/CFDEMcoupling-PUBLIC-2.2.x/src/lagrangian/cfdemParticle correct? (y/n)
----------------------------------------------------------------------------------------
My friends did not encounter any similar messsages in their works. I thought it might relate this error.

shahabgol | Wed, 11/20/2013 - 11:54

By the way, after entring >>cfdemCompCFDEM these errors appear in terminal:
-----------------------------------------------------------------------------------------------------
removing all .dep files ...
wmakeLnInclude: linking include files to ./lnInclude
Making dependency list for source file cfdemCloud/cfdemCloud.C
could not open file RASModel.H for source file cfdemCloud/cfdemCloud.C
Making dependency list for source file derived/cfdemCloudIB/cfdemCloudIB.C
could not open file RASModel.H for source file derived/cfdemCloudIB/cfdemCloudIB.C
Making dependency list for source file subModels/forceModel/forceModel/forceModel.C
could not open file RASModel.H for source file subModels/forceModel/forceModel/forceModel.C
Making dependency list for source file subModels/forceModel/forceModel/newForceModel.C
could not open file RASModel.H for source file subModels/forceModel/forceModel/newForceModel.C
Making dependency list for source file subModels/forceModel/noDrag/noDrag.C
could not open file RASModel.H for source file subModels/forceModel/noDrag/noDrag.C
Making dependency list for source file subModels/forceModel/checkCouplingInterval/checkCouplingInterval.C
could not open file RASModel.H for source file subModels/forceModel/checkCouplingInterval/checkCouplingInterval.C
could not open file omp.h for source file subModels/forceModel/checkCouplingInterval/checkCouplingInterval.C
could not open file openmpi/ompi/mpi/cxx/mpicxx.h for source file subModels/forceModel/checkCouplingInterval/checkCouplingInterval.C
Making dependency list for source file subModels/forceModel/DiFeliceDrag/DiFeliceDrag.C
could not open file RASModel.H for source file subModels/forceModel/DiFeliceDrag/DiFeliceDrag.C
Making dependency list for source file subModels/forceModel/GidaspowDrag/GidaspowDrag.C
could not open file RASModel.H for source file subModels/forceModel/GidaspowDrag/GidaspowDrag.C
Making dependency list for source file subModels/forceModel/SchillerNaumannDrag/SchillerNaumannDrag.C
could not open file RASModel.H for source file subModels/forceModel/SchillerNaumannDrag/SchillerNaumannDrag.C
Making dependency list for source file subModels/forceModel/Archimedes/Archimedes.C
could not open file RASModel.H for source file subModels/forceModel/Archimedes/Archimedes.C
Making dependency list for source file subModels/forceModel/ArchimedesIB/ArchimedesIB.C
could not open file RASModel.H for source file subModels/forceModel/ArchimedesIB/ArchimedesIB.C
lnInclude/cfdemCloud.H:72:7: error: forward declaration of ‘struct Foam::meshMotionModel’
make: *** [Make/linuxGccDPOpt/cfdemCloudIB.o] Error 1

// log_compileCFDEMcoupling_cfdemSolverPiso_cfdemSolverPiso-2013-11-21-14:14 //

/home/shahab14/CFDEM/CFDEMcoupling-PUBLIC-2.2.x/applications/solvers/cfdemSolverPiso

removing all .dep files ...
Making dependency list for source file cfdemSolverPiso.C
could not open file RASModel.H for source file cfdemSolverPiso.C
SOURCE=cfdemSolverPiso.C ; g++ -m32 -Dlinux -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -O3 -DNoRepository -ftemplate-depth-100 -I/home/shahab14/OpenFOAM/OpenFOAM-2.2.x/src/turbulenceModels/incompressible/turbulenceModel -I/home/shahab14/OpenFOAM/OpenFOAM-2.2.x/src/transportModels -I/home/shahab14/OpenFOAM/OpenFOAM-2.2.x/src/transportModels/incompressible/singlePhaseTransportModel -I/home/shahab14/OpenFOAM/OpenFOAM-2.2.x/src/finiteVolume/lnInclude -I/home/shahab14/CFDEM/CFDEMcoupling-PUBLIC-2.2.x/src/lagrangian/cfdemParticle/lnInclude -I/home/shahab14/CFDEM/CFDEMcoupling-PUBLIC-2.2.x/src/lagrangian/cfdemParticle/cfdTools -IlnInclude -I. -I/home/shahab14/OpenFOAM/OpenFOAM-2.2.x/src/OpenFOAM/lnInclude -I/home/shahab14/OpenFOAM/OpenFOAM-2.2.x/src/OSspecific/POSIX/lnInclude -fPIC -c $SOURCE -o Make/linuxGccDPOpt/cfdemSolverPiso.o
/home/shahab14/CFDEM/CFDEMcoupling-PUBLIC-2.2.x/src/lagrangian/cfdemParticle/lnInclude/cfdemCloud.H:72:7: error: forward declaration of ‘struct Foam::meshMotionModel’
make: *** [Make/linuxGccDPOpt/cfdemSolverIB.o] Error 1
--------------------------------------------------------------------
and the last part of error is very strange for me because it says command "make" is undefuned!! here it is:
--------------------------------------------------------------------
make: *** [Make/linuxGccDPOpt/cfdemPostproc.o] Error 1
Note: the list of utilities compiled might be incomplete.
please check /home/shahab14/CFDEM/CFDEMcoupling-PUBLIC-2.2.x/applications/utilities for more utilities available
shahab14@shahab14-System-Product-Name:~$ lnInclude/cfdemCloud.H:72:7: error: forward declaration of ‘struct Foam::meshMotionModel’
bash: lnInclude/cfdemCloud.H:72:7:: No such file or directory
shahab14@shahab14-System-Product-Name:~$ make: *** [Make/linuxGccDPOpt/cfdemCloudIB.o] Error 1
No command 'make:' found, did you mean:
Command 'makeg' from package 'xutils-dev' (main)
Command 'make' from package 'make' (main)
make:: command not found
shahab14@shahab14-System-Product-Name:~$
shahab14@shahab14-System-Product-Name:~$ // log_compileCFDEMcoupling_cfdemSolverPiso_cfdemSolverPiso-2013-11-21-14:14 //
bash: //: Is a directory
shahab14@shahab14-System-Product-Name:~$
shahab14@shahab14-System-Product-Name:~$ /home/shahab14/CFDEM/CFDEMcoupling-PUBLIC-2.2.x/applications/solvers/cfdemSolverPiso
bash: /home/shahab14/CFDEM/CFDEMcoupling-PUBLIC-2.2.x/applications/solvers/cfdemSolverPiso: Is a directory
shahab14@shahab14-System-Product-Name:~$
shahab14@shahab14-System-Product-Name:~$ removing all .dep files ...
removing: command not found
shahab14@shahab14-System-Product-Name:~$ Making dependency list for source file cfdemSolverPiso.C
Making: command not found
shahab14@shahab14-System-Product-Name:~$ could not open file RASModel.H for source file cfdemSolverPiso.C
could: command not found
shahab14@shahab14-System-Product-Name:~$ SOURCE=cfdemSolverPiso.C ; g++ -m32 -Dlinux -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -O3 -DNoRepository -ftemplate-depth-100 -I/home/shahab14/OpenFOAM/OpenFOAM-2.2.x/src/turbulenceModels/incompressible/turbulenceModel -I/home/shahab14/OpenFOAM/OpenFOAM-2.2.x/src/transportModels -I/home/shahab14/OpenFOAM/OpenFOAM-2.2.x/src/transportModels/incompressible/singlePhaseTransportModel -I/home/shahab14/OpenFOAM/OpenFOAM-2.2.x/src/finiteVolume/lnInclude -I/home/shahab14/CFDEM/CFDEMcoupling-PUBLIC-2.2.x/src/lagrangian/cfdemParticle/lnInclude -I/home/shahab14/CFDEM/CFDEMcoupling-PUBLIC-2.2.x/src/lagrangian/cfdemParticle/cfdTools -IlnInclude -I. -I/home/shahab14/OpenFOAM/OpenFOAM-2.2.x/src/OpenFOAM/lnInclude -I/home/shahab14/OpenFOAM/OpenFOAM-2.2.x/src/OSspecific/POSIX/lnInclude -fPIC -c $SOURCE -o Make/linuxGccDPOpt/cfdemSolverPiso.o
g++: error: cfdemSolverPiso.C: No such file or directory
g++: fatal error: no input files
--------------------------------------------------------------------
You are right, CFDEM is not compiled correctly.
What should I do now?

Regards,
Shahab

alice's picture

alice | Wed, 11/20/2013 - 12:13

Hi Shahab,
I just noticed that you are using OpenFOAM 2.2.x. I am still using 2.1.x, and haven't tried 2.2.x so far. It's possible that the new OpenFOAM version causes these error messages. (Btw. the OpenFOAM version is defined in the file .../etc/OFversion in the cfdemParticle-folder, right now there is no switch for 2.2.x).
If possible try to compile the solvers along with OF 2.1.x, this should work for now.
Cheers,
Alice

shahabgol | Sun, 11/24/2013 - 12:59

Thank you so much again. I am trying to install OF2.1.1. Do you have installation tutorial for OF2.1.1 and LIGGGGTS and CFDEM that explains the installation process step by step?

Regards,
Sh.G

shahabgol | Sun, 11/24/2013 - 16:16

By the way, what do these errors mean?

mkdir: cannot create directory `linuxGccDPOpt': Permission denied
/bin/sh: 1: cannot create linuxGccDPOpt/options: Directory nonexistent
make[2]: *** [linuxGccDPOpt/options] Error 2
/opt/openfoam211/wmake/MakefileFiles:40: linuxGccDPOpt/options: No such file or directory
make[2]: *** No rule to make target `linuxGccDPOpt/options'. Stop.
wmake error: file 'Make/linuxGccDPOpt/objectFiles' could not be created in /opt/openfoam211/applications/solvers/stressAnalysis/solidEquilibriumDisplacementFoam
make[1]: *** [solidEquilibriumDisplacementFoam] Error 1
make[1]: Target `application' not remade because of errors.
make[1]: Leaving directory `/opt/openfoam211/applications/solvers/stressAnalysis'
make: *** [stressAnalysis] Error 2
make: Target `application' not remade because of errors.

richti83's picture

richti83 | Mon, 11/25/2013 - 13:14

Hi shahabgol,

about the 1st one: I followed this instruction:
http://www.openfoam.org/download/source.php
but replaces the tar archives with
http://sourceforge.net/projects/foam/files/foam/2.2.1/ those ones DO NOT USE ANY VERSION BIGGER THAN 2.2.1

about the second: you accidently created the openfoam folder as superuser.
I would do a fresh start

cd $HOME
sudo rm -rf OpenFOAM
mkdir OpenFOAM (WITHOUT SUDO!!!!)
cd OpenFOAM
wget http://optimate.dl.sourceforge.net/project/foam/foam/2.2.1/OpenFOAM-2.2.1.tgz
wget http://optimate.dl.sourceforge.net/project/foam/foam/2.2.1/ThirdParty-2.2.1.tgz
tar -xf OpenFOAM*
tar -xf ThirdParty*
cd OpenFOAM-2.2.1
source $HOME/OpenFOAM/OpenFOAM-2.2.1/etc/bashrc
.Allwmake

SuperUser rights are only neccessary for apt-get commands, all others should work as normal user.

After the OpenFoam examples are working start to compile cfdem.

I'm not an associate of DCS GmbH and not a core developer of LIGGGHTS®
but I have 7 years user experience using LIGGGHTS®, ParaView and LINUX

shahabgol | Mon, 11/25/2013 - 14:24

Thank you very much. I couldn't accomplish it without your help.