install CFDEM issues

Submitted by yyu on Tue, 11/19/2013 - 22:59

Hi everyone,

I tried to install liggghts and openfoam on multicore computer. I followed the instruction from the forum: http://cfdem.dcs-computing.com/?q=node/1575 and it works on my one core computer. When i did on 4core computer. some thing wrong:

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/yyu/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: yyu-Precision-WorkStation-T3400

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 19 2013
Time : 14:50:32
Host : "yyu-Precision-WorkStation-T3400"
PID : 7624
Case : /home/yyu/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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Octave was configured for "x86_64-pc-linux-gnu".

Additional information about Octave is available at http://www.octave.org.

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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:7627): WARNING **: Error when getting information for file '/home/yyu/CFDEM/CFDEMcoupling-PUBLIC-2.2.x/tutorials/cfdemSolverPiso/settlingTestMPI/CFD/octave/cfdemSolverPiso_settlingTestMPI.eps': No such file or directory

** (evince:7627): WARNING **: Error setting file metadata: No such file or directory

** (evince:7627): WARNING **: Error setting file metadata: No such file or directory

** (evince:7627): WARNING **: Error setting file metadata: No such file or directory

** (evince:7627): WARNING **: Error setting file metadata: No such file or directory

** (evince:7627): WARNING **: Error setting file metadata: No such file or directory

** (evince:7627): WARNING **: Error setting file metadata: No such file or directory

** (evince:7627): WARNING **: Error setting file metadata: No such file or directory

** (evince:7627): WARNING **: Error setting file metadata: No such file or directory

** (evince:7627): WARNING **: Error setting file metadata: No such file or directory

I googled the wrongs and found in the link: http://cfdem.dcs-computing.com/?q=node/1575
Alice and kunzhang both thought re installing cfdem carefully and following the manual.
and the wrongs happened, I checked the separate work of openfoam and liggghts and found
the liggghts didnot work either. the wrong in liggghts is:
yyu@yyu-Precision-WorkStation-T3400:~/LIGGGHTS/LIGGGHTS-PUBLIC/examples/LIGGGHTS/Tutorials_public/conveyor$ cd post
yyu@yyu-Precision-WorkStation-T3400:~/LIGGGHTS/LIGGGHTS-PUBLIC/examples/LIGGGHTS/Tutorials_public/conveyor/post$ lpp dump*.conveyor
aborting due to errors: Invalid or no argument given for cpunum

my question is: is there different istalling method for multcore computer? or any comments on my problems will be appreciated. thanks. look forward to any reply.

best regards,
yyu

Forums:

alice's picture

alice | Wed, 11/20/2013 - 13:04

Hello yyu,
the error messages start at the line that says:
"mpirun was unable to launch the specified application as it could not find an executable:

Executable: cfdemSolverPiso
Node: yyu-Precision-WorkStation-T3400

while attempting to start process rank 0."
Generally there is no difference in installing the software on one or multicore machines. As stated by "richie83" in one of the neighbouring threads, the current version of the coupling doesn't compile with OpenFOAM 2.2.x. (http://cfdem.dcs-computing.com/?q=comment/4464#comment-4464) Combining it with 2.1.x should work fine.
Cheers,
Alice

yyu | Wed, 11/20/2013 - 22:00

thanks for your reply.

I found one very funny phenomenon: I made openfoam 2.2.x with liggghts works together. but the liggghts cannot run separately in the coupling of openfoam and liggghts. When i run liggghts, the following wrong:

yyu@yyu-Precision-WorkStation-T3400:~/LIGGGHTS/LIGGGHTS-PUBLIC/examples/LIGGGHTS/Tutorials_public/conveyor/post$ lpp dump*.conveyor

aborting due to errors: Invalid or no argument given for cpunum

after I delete "cfdem env vars" in .bashrc file (by gedit ~/.bashrc in terminal) , the liggghts works. but at this moment, CFDEM cannot work.

If I add "cfdem env vars (#- source cfdem env vars
export LD_LIBRARY_PATH=/home/yyu/OpenFOAM/ThirdParty-2.2.x/platforms/linux64Gcc/gperftools-svn/lib:/home/yyu/OpenFOAM/ThirdParty-2.2.x/platforms/linux64Gcc/paraview-3.12.0/lib/paraview-3.12:/home/yyu/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/openmpi-1.6.3:/home/yyu/OpenFOAM/ThirdParty-2.2.x/platforms/linux64GccDPOpt/lib/openmpi-1.6.3:/home/yyu/OpenFOAM/ThirdParty-2.2.x/platforms/linux64Gcc/openmpi-1.6.3/lib:/home/yyu/OpenFOAM/ThirdParty-2.2.x/platforms/linux64Gcc/openmpi-1.6.3/lib64:/home/yyu/OpenFOAM/yyu-2.2.x/platforms/linux64GccDPOpt/lib:/home/yyu/OpenFOAM/site/2.2.x/platforms/linux64GccDPOpt/lib:/home/yyu/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib:/home/yyu/OpenFOAM/ThirdParty-2.2.x/platforms/linux64GccDPOpt/lib:/home/yyu/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/dummy
export CFDEM_VERSION=PUBLIC
export CFDEM_PROJECT_DIR=$HOME/CFDEM/CFDEMcoupling-$CFDEM_VERSION-$WM_PROJECT_VERSION
export CFDEM_SRC_DIR=$CFDEM_PROJECT_DIR/src/lagrangian/cfdemParticle
export CFDEM_SOLVER_DIR=$CFDEM_PROJECT_DIR/applications/solvers
export CFDEM_DOC_DIR=$CFDEM_PROJECT_DIR/doc
export CFDEM_UT_DIR=$CFDEM_PROJECT_DIR/applications/utilities
export CFDEM_TUT_DIR=$CFDEM_PROJECT_DIR/tutorials
export CFDEM_PROJECT_USER_DIR=$HOME/CFDEM/$LOGNAME-$CFDEM_VERSION-$WM_PROJECT_VERSION
export CFDEM_bashrc=$CFDEM_SRC_DIR/etc/bashrc
export CFDEM_LIGGGHTS_SRC_DIR=$HOME/LIGGGHTS/LIGGGHTS-PUBLIC/src
export CFDEM_LIGGGHTS_MAKEFILE_NAME=fedora_fpic
export CFDEM_LPP_DIR=$HOME/LIGGGHTS/mylpp/src
export CFDEM_PIZZA_DIR=$HOME/LIGGGHTS/PIZZA/gran_pizza_17Aug10/src
. $CFDEM_bashrc
)"

back , The CFDEM works again. Really funny ???

Everytime, When I need liggght only, I should delet the "cfdem env vars". If need CFDEm, the cfdem env vars goes back again. by the way, I googled the wrong information, there is no such thing happened to other. Really interesting!!!

best regards,
yaowei yu

alice's picture

alice | Thu, 11/21/2013 - 08:29

Hello Yaowei,
this sounds interesting indeed... Have you tried using liggghts using the command "CFDEM_LIGGGHTS_SRC_DIR/$CFDEM_LIGGGHTS_LIB_NAME" instead of just "liggghts"?
With that command you make sure that you really call the liggghts grom the PFM-version...
Cheers,
Alice

yyu | Fri, 11/22/2013 - 00:22

I tried it which did not work. I donot know the reason. But I expect that the reason will be found out in the short future after having more experience, then share with your guys.
cheers,
yyu

cgoniva's picture

cgoniva | Tue, 02/04/2014 - 15:01

Hi,

seems like you execute several versions of liggghts being installed on your computer.

I recommend to use cfdemLiggghtsPar command which uses liggghts compiled as library which is the same as it is used for the coupling.

KR,
Chris

ndeen | Wed, 01/22/2014 - 08:13

Hello Alice and Yaowei,

I have the same issue as described by Yaowei. After a pain-staking installation I believe everything is installed correctly (using OpenFOAM 2.1.0 on Scientific Linux 6.5). Yet, I get the error below.

Does anyone have an idea how to fix this? Do I suffer from a compatibility issue between OpenFOAM, LIGGGHTS and/or CFDEM?

If I would need to start all over, what OS would you recommend; Ubuntu? I am most interested in an easy installation and a system that works in the end :-)

Thanks for your help,

Niels

// run_parallel_cfdemSolverPiso_settlingTestMPI_CFDDEM //

/home/ndeen/CFDEM/CFDEMcoupling-PUBLIC-2.1.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: SnelleJelle

while attempting to start process rank 0.
--------------------------------------------------------------------------
2 total processes failed to start

ndeen | Wed, 01/22/2014 - 09:27

I found out that CFDEM didn't install properly (I previously ignored all the error messages in the compilation, which of course I shouldn't have :-(). Now, I entirely removed CFDEM and started all over, but now I'm stuck with the command cfdemSysTest, which is looking in a very odd path (no clue where it found the *double* subdir "lagrangian/cfdemParticle"):

bash: /home/ndeen/CFDEM/CFDEMcoupling-PUBLIC-2.1.x/src/lagrangian/cfdemParticle/lagrangian/cfdemParticle/etc/cfdemSystemTest.sh: No such file or directory

Anyone a comment on this one? Cheers,

Niels

cgoniva's picture

cgoniva | Tue, 02/04/2014 - 15:08

Hello Niels,

all of the settings for the env paths are done in ~/.bashrc . Once they work togeher everything else is consistent (except I make an error with a new release).

So most probably somehing in your ~/.bashrc is wrong.
The cfdemSysTest checks if the paths exist (still not bullet proof that everything is correct.

Please not that there was a change in this nomenclature of the paths just for the last (not announced) release.

Kind Regards,
Chris

ndeen | Wed, 01/22/2014 - 13:52

It turns out there was an error in the paths. The following information should be CHANGED in ~/.bashrc

export CFDEM_SRC_DIR=$CFDEM_PROJECT_DIR/src
export CFDEM_bashrc=$CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/bashrc

After that I am ready for install, as you can see here:

[ndeen@SnelleJelle etc]$ cfdemSysTest
*******************
system settings:
*******************
CFDEM_VERSION=PUBLIC
couple to OF_VERSION=2.1.x
compile option=Opt

check if paths are set correctly
valid:yes critical:yes - $CFDEM_PROJECT_DIR = /home/ndeen/CFDEM/CFDEMcoupling-PUBLIC-2.1.x
valid:yes critical:no - $CFDEM_PROJECT_USER_DIR = /home/ndeen/CFDEM/ndeen-PUBLIC-2.1.x
valid:yes critical:yes - $CFDEM_SRC_DIR = /home/ndeen/CFDEM/CFDEMcoupling-PUBLIC-2.1.x/src
valid:yes critical:yes - $CFDEM_SOLVER_DIR = /home/ndeen/CFDEM/CFDEMcoupling-PUBLIC-2.1.x/applications/solvers
valid:yes critical:yes - $CFDEM_TUT_DIR = /home/ndeen/CFDEM/CFDEMcoupling-PUBLIC-2.1.x/tutorials
valid:yes critical:yes - $CFDEM_LIGGGHTS_SRC_DIR = /home/ndeen/LIGGGHTS/LIGGGHTS-PUBLIC/src
valid:yes critical:yes - $CFDEM_LPP_DIR = /home/ndeen/LIGGGHTS/mylpp/src
valid:NO critical:no - $CFDEM_PIZZA_DIR = /home/ndeen/LIGGGHTS/PIZZA/gran_pizza_17Aug10/src does not exist
valid:yes critical:no - $CFDEM_TEST_HARNESS_PATH = /home/ndeen/CFDEM/ndeen-PUBLIC-2.1.x/log/logFilesCFDEM-PUBLIC-2.1.x

library names
$CFDEM_LIGGGHTS_LIB_NAME = lmp_fedora_fpic
$CFDEM_LIB_NAME = lagrangianCFDEM-PUBLIC-2.1.x
$LD_LIBRARY_PATH = /home/ndeen/OpenFOAM/ThirdParty-2.1.x/platforms/linux64Gcc/paraview-3.12.0/lib/paraview-3.12:/home/ndeen/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/lib/openmpi-1.5.3:/home/ndeen/OpenFOAM/ThirdParty-2.1.x/platforms/linux64GccDPOpt/lib/openmpi-1.5.3:/home/ndeen/OpenFOAM/ThirdParty-2.1.x/platforms/linux64Gcc/openmpi-1.5.3/lib:/home/ndeen/OpenFOAM/ThirdParty-2.1.x/platforms/linux64Gcc/openmpi-1.5.3/lib64:/home/ndeen/OpenFOAM/ndeen-2.1.x/platforms/linux64GccDPOpt/lib:/home/ndeen/OpenFOAM/site/2.1.x/platforms/linux64GccDPOpt/lib:/home/ndeen/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/lib:/home/ndeen/OpenFOAM/ThirdParty-2.1.x/platforms/linux64GccDPOpt/lib:/home/ndeen/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/lib/dummy
*******************
g++:
/usr/bin/g++
g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4)
Copyright (C) 2010 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

gcc:
/usr/bin/gcc
gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4)
Copyright (C) 2010 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

mpic++:
/home/ndeen/OpenFOAM/ThirdParty-2.1.x/platforms/linux64Gcc/openmpi-1.5.3/bin/mpic++
g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4)
Copyright (C) 2010 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

mpirun:
/home/ndeen/OpenFOAM/ThirdParty-2.1.x/platforms/linux64Gcc/openmpi-1.5.3/bin/mpirun
mpirun (Open MPI) 1.5.3

Report bugs to http://www.open-mpi.org/community/help/

However, when running cfdemCompCFDEM, I get the following error messages:

[ndeen@SnelleJelle etc]$ cfdemCompCFDEM

Please provide the libraries to be compiled in the //home/ndeen/CFDEM/CFDEMcoupling-PUBLIC-2.1.x/src/lagrangian/cfdemParticle/etc/library-list.txt file.
will change path...

// log_compileCFDEMcoupling_cfdemParticle-2014-01-22-13:50 //

/home/ndeen/CFDEM/CFDEMcoupling-PUBLIC-2.1.x/src/lagrangian/cfdemParticle

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

etc.

Anyone any clue? Thanks for your help!

Niels

vonboetticher | Mon, 01/27/2014 - 13:14

I have the same problem. Any news?

richti83's picture

richti83 | Mon, 01/27/2014 - 14:22

In the past there was a compiling issui with OF 2.1.X, sometime in august they changed something under the hood and since this the install instruction here doesnt work anymore.

You could try to go back in git to a date known to work (I don't know which commit has broken CFDEM coupling !), OR you use the tar.gz install procedure discribed here:
http://cfdem.dcs-computing.com/?q=comment/4615#comment-4615

Best,
Christian.

I'm not an associate of DCS GmbH and not a core developer of LIGGGHTS®
ResearchGate | Contact

vonboetticher | Mon, 01/27/2014 - 14:32

...well I had some success commenting out -lmpi_cxx \ from the cfdemParticle/Make/Options. cfdemSolverPiso works now, but cfdemSolverIB misses three files:
cfdemSolverIB.C:54:27: error: meshToMeshNew.H: No such file or directory
cfdemSolverIB.C:55:28: error: fvIOoptionList.H: No such file or directory
cfdemSolverIB.C:71:33: error: createFvOptions.H: No such file or directory

richti83's picture

richti83 | Wed, 02/05/2014 - 17:45

.. but I don't really remember the date, the other christoph told me he knows the exact commit in OF 2.2.x git repo which has broken compatibility with CFDEM Pakage when you were here in Magdeburg :-)

I'm not an associate of DCS GmbH and not a core developer of LIGGGHTS®
ResearchGate | Contact

vikultomar | Mon, 08/17/2015 - 09:16

Hello all,

I am using the ubuntu 12.04 for my work. I have installed OpenFoam -2.3.0, mpirun 1.4.3, LIGGGHTS and cfdem-coupling. OpenFoam and LIGGGHTS are working separately but the cfedm coupling is showing the same error as described by yyu
mpirun was unable to launch the specified application as it could not find an executable:

Executable: cfdemSolverPiso

What should I do? Please suggest.

j-kerbl's picture

j-kerbl | Mon, 08/17/2015 - 14:24

Hi vikultomar,

please check the compile logs in $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/log for errors.

Cheers
Josef

ritesh | Wed, 03/16/2016 - 10:51

hi all,
i am using ubuntu 14.04. i have installed cfdem coupling with OF-231 and LIGGGHTS-238. OF and liggghts are running seperatly, but in coupling i am facing the same problem as described by yyu.

anyone plz look into it and help us asap...

thanks,
ritesh

ritesh raman
IIT Bombay, India

alice's picture

alice | Wed, 03/16/2016 - 14:10

Hello Ritesh,
please make sure you use an OpenFOAM*.x version and not a precompiled binary. I'd for example recommend OpenFOAM-2.4.x.
Best regards,
Alice

manton | Tue, 04/19/2016 - 15:42

Hello everyone,
I m also facing similar probelm when running testcase of CFDEM coupling. Since i see this post dates way back to 2013. I believe someone could have solved this problem, could you please post what you have done to solve this problem. It would be helpful to me.