CFDEM Tutorial tests not running

Hi Alexander,

I get no output from which cfdemSolverPiso, either before or after I enter the OpenFOAM alias.

I also get a message whenever I open a new terminal that my version of OpenFOAM is not supported, but I think that is because when I initially open a terminal I have not yet entered the OpenFOAM-4.x alias that I have set.

Also I have now just found that when I scroll up in a new terminal that there is a message that has been there hidden away! It is:

************************************
using default CFDEM_ADD_LIBS_DIR=/home/robert/CFDEM/CFDEMcoupling-PUBLIC-4.x/src/lagrangian/cfdemParticle/etc/addLibs_universal
using default CFDEM_ADD_LIBS_NAME=additionalLibs_
!!! ERROR !!!: CFDEM_ADD_LIBS_DIR/CFDEM_ADD_LIBS_NAME=/home/robert/CFDEM/CFDEMcoupling-PUBLIC-4.x/src/lagrangian/cfdemParticle/etc/addLibs_universal/additionalLibs_ does not exist.
[3;J
************************************

(followed by the OpenFOAM error which I was seeing before)

ERROR from your CFDEM code!
ERROR: your OpenFOAM(R) version is not supported!
Please use a version that is supported, i.e., see the bashrc file in the source directory!
************************************
************************************

So its looking for the CFD_ADD_LIBS, of which there are many in the addLibs_universal directory (inc additionalLibs_4.x), however there is no additionalLibs_ (with nothing after the underscore). I'm not sure if it is looking for the incorrect file, or if is looking for the correct one and it does not exist.

Also, there is no bashrc file in the source directory (I assume it means ~/CFDEM/CFDEMcoupling-PUBLIC-4.x/src). Perhaps this is because it is not compiling properly as you suggest? Any help would be appreciated,

Regards,

Rob

So I have done a bit of fiddling, and the error messages I was getting in my last comment about the CFD_ADD_LIBS is sorted I think, as it is now looking for the correct files and is finding them.

I also had a closer look at the log files from cfdemCompCFDEM (which I can't seem to attach to this comment). It appears that the header files are not being found as defined in the [solver].c files.

Ok the log files all say pretty much the same thing:

// log_compileCFDEMcoupling_cfdemSolverPiso_cfdemSolverPiso-2017-07-11-14:00 //

/home/robert/CFDEM/CFDEMcoupling-PUBLIC-4.x/applications/solvers/cfdemSolverPiso

removing all .dep files ...
Make/linux64GccDPInt32Opt/options:54: /home/robert/CFDEM/CFDEMcoupling-PUBLIC-4.x/src/lagrangian/cfdemParticle/etc/addLibs_universal/additionalLibs_: No such file or directory
make: *** No rule to make target '/home/robert/CFDEM/CFDEMcoupling-PUBLIC-4.x/src/lagrangian/cfdemParticle/etc/addLibs_universal/additionalLibs_'. Stop.
Make/linux64GccDPInt32Opt/options:54: /home/robert/CFDEM/CFDEMcoupling-PUBLIC-4.x/src/lagrangian/cfdemParticle/etc/addLibs_universal/additionalLibs_: No such file or directory
make: *** No rule to make target '/home/robert/CFDEM/CFDEMcoupling-PUBLIC-4.x/src/lagrangian/cfdemParticle/etc/addLibs_universal/additionalLibs_'. Stop.
wmake error: file 'Make/linux64GccDPInt32Opt/sourceFiles' could not be created in /home/robert/CFDEM/CFDEMcoupling-PUBLIC-4.x/applications/solvers/cfdemSolverPiso

where the relevant names are as seen in the log file names below.

log_compileCFDEMcoupling_cfdemSolverPisoScalar
log_compileCFDEMcoupling_cfdemParticle
log_compileCFDEMcoupling_cfdemSolverPisoSTM
log_compileCFDEMcoupling_cfdemPostproc
log_compileCFDEMcoupling_fvOptionsCFDEM
log_compileCFDEMcoupling_cfdemSolverIB
log_compileCFDEMcoupling_scalarTransportModelsCFDEM
log_compileCFDEMcoupling_cfdemSolverPiso
log_compile_results_success

The final log file says that there were 4 successful compiles:
cfdemSolverPiso
cfdemSolverIB
cfdemSolverPisoScalar
cfdemSolverPisoSTM

but which (whatever solver) does not give any output.

It looks like from the log files that it is still trying to locate the additionalLibs_ folder instead of the additionalLibs_4.x folder. I thought I had fixed that problem as I said in the above comment, but perhaps there is more than one place I need to define additionalLibs_4.x?

I tried commenting out the functions part of the cfdemSolverPiso/ErgunTestMPI/CFD/system/controlDict but continued to fail to run past the mesh generation and distribution across the multiple cores:

/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 4.x |
| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
Build : 4.x-b5331fdc8656
Exec : blockMesh
Date : Jul 11 2017
Time : 14:20:29
Host : "XPS15"
PID : 10600
Case : /home/robert/CFDEM/CFDEMcoupling-PUBLIC-4.x/tutorials/cfdemSolverPiso/ErgunTestMPI/CFD
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 entry::getKeyword(keyType&, Istream&)
in file db/dictionary/entry/entryIO.C at line 80
Reading /home/robert/CFDEM/CFDEMcoupling-PUBLIC-4.x/tutorials/cfdemSolverPiso/ErgunTestMPI/CFD/system/controlDict
found on line 162 the punctuation token ')'
expected either } or EOF
Creating block mesh from
"/home/robert/CFDEM/CFDEMcoupling-PUBLIC-4.x/tutorials/cfdemSolverPiso/ErgunTestMPI/CFD/constant/polyMesh/blockMeshDict"
Creating curved edges
Creating topology blocks
Creating topology patches

Reading patches section

Creating block mesh topology

Reading physicalType from existing boundary file

Default patch type set to empty

Check topology

Basic statistics
Number of internal faces : 8
Number of boundary faces : 14
Number of defined boundary faces : 14
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 1
Block 0 cell size :
i : 0.001725 .. 0.001725
j : 0.001725 .. 0.001725
k : 0.00230417 .. 0.00230417

Block 1 cell size :
i : 0.001725 .. 0.001725
j : 0.00101048 .. 0.00101048
k : 0.00230417 .. 0.00230417

Block 2 cell size :
i : 0.00101048 .. 0.00101048
j : 0.00270527 .. 0.00270527
k : 0.00230417 .. 0.00230417

Block 3 cell size :
i : 0.00270527 .. 0.00270527
j : 0.00101048 .. 0.00101048
k : 0.00230417 .. 0.00230417

Block 4 cell size :
i : 0.00101048 .. 0.00101048
j : 0.001725 .. 0.001725
k : 0.00230417 .. 0.00230417

Writing polyMesh
----------------
Mesh Information
----------------
boundingBox: (-0.0138 -0.0138 0) (0.0138 0.0138 0.0553)
nPoints: 5225
nCells: 4608
nFaces: 14400
nInternalFaces: 13248
----------------
Patches
----------------
patch 0 (start: 13248 size: 192) name: inlet
patch 1 (start: 13440 size: 192) name: outlet
patch 2 (start: 13632 size: 768) name: wall

End

starting DEM run in parallel...
rm: cannot remove '/home/robert/CFDEM/CFDEMcoupling-PUBLIC-4.x/tutorials/cfdemSolverPiso/ErgunTestMPI/log_run_liggghts_init_DEM': No such file or directory

// run_liggghts_init_DEM //

/home/robert/CFDEM/CFDEMcoupling-PUBLIC-4.x/tutorials/cfdemSolverPiso/ErgunTestMPI/DEM

--------------------------------------------------------------------------
mpirun was unable to launch the specified application as it could not access
or execute an executable:

Executable: /home/robert/LIGGGHTS-PUBLIC3.6.0/src/lmp_fedora_fpic
Node: XPS15

while attempting to start process rank 0.
--------------------------------------------------------------------------
4 total processes failed to start
rm: cannot remove '/home/robert/CFDEM/CFDEMcoupling-PUBLIC-4.x/tutorials/cfdemSolverPiso/ErgunTestMPI/log_run_parallel_cfdemSolverPiso_ErgunTestMPI_CFDDEM': No such file or directory
Decomposing case.
/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 4.x |
| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
Build : 4.x-b5331fdc8656
Exec : decomposePar -force
Date : Jul 11 2017
Time : 14:20:30
Host : "XPS15"
PID : 10625
Case : /home/robert/CFDEM/CFDEMcoupling-PUBLIC-4.x/tutorials/cfdemSolverPiso/ErgunTestMPI/CFD
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 entry::getKeyword(keyType&, Istream&)
in file db/dictionary/entry/entryIO.C at line 80
Reading /home/robert/CFDEM/CFDEMcoupling-PUBLIC-4.x/tutorials/cfdemSolverPiso/ErgunTestMPI/CFD/system/controlDict
found on line 162 the punctuation token ')'
expected either } or EOF

Decomposing mesh region0

Create mesh

Calculating distribution of cells
Selecting decompositionMethod simple

Finished decomposition in 0 s

Calculating original mesh data

Distributing cells to processors

Distributing faces to processors

Distributing points to processors

Constructing processor meshes
--> FOAM Warning :
From function entry::getKeyword(keyType&, Istream&)
in file db/dictionary/entry/entryIO.C at line 80
Reading /home/robert/CFDEM/CFDEMcoupling-PUBLIC-4.x/tutorials/cfdemSolverPiso/ErgunTestMPI/CFD/system/controlDict
found on line 162 the punctuation token ')'
expected either } or EOF

Processor 0
Number of cells = 1152
Number of faces shared with processor 1 = 192
Number of faces shared with processor 2 = 192
Number of processor patches = 2
Number of processor faces = 384
Number of boundary faces = 288
--> FOAM Warning :
From function entry::getKeyword(keyType&, Istream&)
in file db/dictionary/entry/entryIO.C at line 80
Reading /home/robert/CFDEM/CFDEMcoupling-PUBLIC-4.x/tutorials/cfdemSolverPiso/ErgunTestMPI/CFD/system/controlDict
found on line 162 the punctuation token ')'
expected either } or EOF

Processor 1
Number of cells = 1152
Number of faces shared with processor 0 = 192
Number of faces shared with processor 3 = 192
Number of processor patches = 2
Number of processor faces = 384
Number of boundary faces = 288
--> FOAM Warning :
From function entry::getKeyword(keyType&, Istream&)
in file db/dictionary/entry/entryIO.C at line 80
Reading /home/robert/CFDEM/CFDEMcoupling-PUBLIC-4.x/tutorials/cfdemSolverPiso/ErgunTestMPI/CFD/system/controlDict
found on line 162 the punctuation token ')'
expected either } or EOF

Processor 2
Number of cells = 1152
Number of faces shared with processor 0 = 192
Number of faces shared with processor 3 = 192
Number of processor patches = 2
Number of processor faces = 384
Number of boundary faces = 288
--> FOAM Warning :
From function entry::getKeyword(keyType&, Istream&)
in file db/dictionary/entry/entryIO.C at line 80
Reading /home/robert/CFDEM/CFDEMcoupling-PUBLIC-4.x/tutorials/cfdemSolverPiso/ErgunTestMPI/CFD/system/controlDict
found on line 162 the punctuation token ')'
expected either } or EOF

Processor 3
Number of cells = 1152
Number of faces shared with processor 1 = 192
Number of faces shared with processor 2 = 192
Number of processor patches = 2
Number of processor faces = 384
Number of boundary faces = 288

Number of processor faces = 768
Max number of cells = 1152 (0% above average 1152)
Max number of processor patches = 2 (0% above average 2)
Max number of faces between processors = 384 (0% above average 384)

Time = 0

Processor 0: field transfer
--> FOAM Warning :
From function entry::getKeyword(keyType&, Istream&)
in file db/dictionary/entry/entryIO.C at line 80
Reading /home/robert/CFDEM/CFDEMcoupling-PUBLIC-4.x/tutorials/cfdemSolverPiso/ErgunTestMPI/CFD/system/controlDict
found on line 162 the punctuation token ')'
expected either } or EOF
Processor 1: field transfer
--> FOAM Warning :
From function entry::getKeyword(keyType&, Istream&)
in file db/dictionary/entry/entryIO.C at line 80
Reading /home/robert/CFDEM/CFDEMcoupling-PUBLIC-4.x/tutorials/cfdemSolverPiso/ErgunTestMPI/CFD/system/controlDict
found on line 162 the punctuation token ')'
expected either } or EOF
Processor 2: field transfer
--> FOAM Warning :
From function entry::getKeyword(keyType&, Istream&)
in file db/dictionary/entry/entryIO.C at line 80
Reading /home/robert/CFDEM/CFDEMcoupling-PUBLIC-4.x/tutorials/cfdemSolverPiso/ErgunTestMPI/CFD/system/controlDict
found on line 162 the punctuation token ')'
expected either } or EOF
Processor 3: field transfer
--> FOAM Warning :
From function entry::getKeyword(keyType&, Istream&)
in file db/dictionary/entry/entryIO.C at line 80
Reading /home/robert/CFDEM/CFDEMcoupling-PUBLIC-4.x/tutorials/cfdemSolverPiso/ErgunTestMPI/CFD/system/controlDict
found on line 162 the punctuation token ')'
expected either } or EOF

End

do nothing.

// run_parallel_cfdemSolverPiso_ErgunTestMPI_CFDDEM //

/home/robert/CFDEM/CFDEMcoupling-PUBLIC-4.x/tutorials/cfdemSolverPiso/ErgunTestMPI/CFD

rm: cannot remove 'couplingFiles/*': No such file or directory
--------------------------------------------------------------------------
mpirun was unable to find the specified executable file, and therefore
did not launch the job. This error was first reported for process
rank 0; it may have occurred for other processes as well.

NOTE: A common cause for this error is misspelling a mpirun command
line parameter option (remember that mpirun interprets the first
unrecognized command line token as the executable).

Node: XPS15
Executable: cfdemSolverPiso
--------------------------------------------------------------------------
4 total processes failed to start
rm: cannot remove 'cfdemSolverPiso_ErgunTestMPI.png': No such file or directory

(octave-gui:10652): Gtk-WARNING **: Unable to locate theme engine in module_path: "adwaita",
rhoG = 10
error: load: unable to find file ../postProcessing/probes/0/p
error: called from
totalPressureDrop.m at line 12 column 6
cp: cannot stat 'cfdemSolverPiso_ErgunTestMPI.png': No such file or directory
deleting data at: /home/robert/CFDEM/CFDEMcoupling-PUBLIC-4.x/tutorials/cfdemSolverPiso/ErgunTestMPI ? otherwise press Ctrl-C:\n

Hi Alexander,

Yes I am using 4.x

I tried changing all "( )" to "{ }" under the functions within controlDict file, but nothing different is output.

Ok I deleted everything and decided to start again. I downloaded the newest versions of LIGGGHTS and CFDEMcoupling from github, and was following the instructions from https://www.cfdem.com/media/CFDEM/docu/CFDEMcoupling_Manual.html#install-2

Instead of running cfdemCompCFDEMall I ran the commands individually. cfdemComLIG seems to work, and it creates an lmp_auto executable.

The remaining 3 commands (cfdemCompCFDEMsrc/sol/uti) all constantly produce outputs like this:

// log_compileCFDEMcoupling_cfdemSolverPiso_cfdemSolverPiso-2017-07-13-12:28 //

/home/robert/CFDEM/CFDEMcoupling-PUBLIC-4.x/applications/solvers/cfdemSolverPiso

removing all .dep files ...
Making dependency list for source file cfdemSolverPiso.C
could not open file fvIOoptionList.H for source file cfdemSolverPiso.C due to No such file or directory
could not open file omp.h for source file cfdemSolverPiso.C due to No such file or directory
could not open file ompi/mpi/cxx/pmpicxx.h for source file cfdemSolverPiso.C due to No such file or directory
could not open file ompi/mpi/cxx/pop_inln.h for source file cfdemSolverPiso.C due to No such file or directory
could not open file ompi/mpi/cxx/pgroup_inln.h for source file cfdemSolverPiso.C due to No such file or directory
could not open file ompi/mpi/cxx/pstatus_inln.h for source file cfdemSolverPiso.C due to No such file or directory
could not open file ompi/mpi/cxx/prequest_inln.h for source file cfdemSolverPiso.C due to No such file or directory
could not open file math.h for source file cfdemSolverPiso.C due to No such file or directory
could not open file cfdemCloudRotation.H for source file cfdemSolverPiso.C due to No such file or directory
could not open file cfdemCloudRotationSuperquadric.H for source file cfdemSolverPiso.C due to No such file or directory
could not open file readPISOControls.H for source file cfdemSolverPiso.C due to No such file or directory
.
.
.

Is there something wrong with my openmpi installation? I'm not sure why this would be causing an issue though.

Ahhh thank you Alice, I had seen those files earlier (before I deleted the installation and started again) and there was a fail log.

I know have the following two success logs, which do contain the 4 solvers and 3 src:

log_compile_results_sol_success contains
cfdemSolverPiso
cfdemSolverIB
cfdemSolverPisoScalar
cfdemSolverPisoSTM

log_compile_results_src_success contains
cfdemParticle
scalarTransportModelsCFDEM
fvOptionsCFDEM

The last lines of the other log files you suggested are:

log_compileCFDEMcoupling_cfdemParticle
'/home/robert/CFDEM/CFDEMcoupling-PUBLIC-4.x/platforms/linux64GccDPInt32Opt/lib/liblagrangianCFDEM-PUBLIC-4.x.so' is up to date.
log_compileCFDEMcoupling_cfdemSolverIB
-lm -o /home/robert/CFDEM/CFDEMcoupling-PUBLIC-4.x/platforms/linux64GccDPInt32Opt/bin/cfdemSolverIB
log_compileCFDEMcoupling_cfdemSolverPiso
-lm -o /home/robert/CFDEM/CFDEMcoupling-PUBLIC-4.x/platforms/linux64GccDPInt32Opt/bin/cfdemSolverPiso
log_compileCFDEMcoupling_cfdemSolverPisoScalar
-lm -o /home/robert/CFDEM/CFDEMcoupling-PUBLIC-4.x/platforms/linux64GccDPInt32Opt/bin/cfdemSolverPisoScalar
log_compileCFDEMcoupling_cfdemSolverPisoSTM
-lm -o /home/robert/CFDEM/CFDEMcoupling-PUBLIC-4.x/platforms/linux64GccDPInt32Opt/bin/cfdemSolverPisoSTM

So it looks like everything has compiled correctly then, and it is only the octave post-processing that seems to be having an issue. I will try commenting out the functions in the controlDict and see if I can view the results with paraview, and I will also try this install at home and use OF-3.x and see if that fixes the issues. Perhaps using 4.x was just an unnecessary complication....

Rob.