error in running CFDEM after installation

Submitted by tala on Thu, 12/22/2016 - 22:14

Dear all
I have newly installed CFDEM and I want to know if my installation is correct.
I tried to run one of examples of tutorial via Allrun.sh in following directory:
~/CFDEM/CFDEMcoupling-PUBLIC-3.0.1/tutorials/cfdemSolverIB
but I have encountered these errors:

error: load: unable to find file ../../DEM/post/position_particle_1.txt
error: called from
postproc.m at line 11 column 5

** (evince:2351): WARNING **: Error when getting information for file '/home/talat/CFDEM/CFDEMcoupling-PUBLIC-3.0.1/tutorials/cfdemSolverIB/twoSpheresGlowinskiMPI/CFD/octave/pos_y_two_part_rec_glow.eps': No such file or directory

** (evince:2351): WARNING **: Error setting file metadata: No such file or directory

** (evince:2351): WARNING **: Error setting file metadata: No such file or directory

** (evince:2351): WARNING **: Error setting file metadata: No such file or directory

** (evince:2351): WARNING **: Error setting file metadata: No such file or directory

** (evince:2351): WARNING **: Error setting file metadata: No such file or directory

** (evince:2351): WARNING **: Error setting file metadata: No such file or directory

** (evince:2351): WARNING **: Error setting file metadata: No such file or directory

** (evince:2351): WARNING **: Error setting file metadata: No such file or directory

** (evince:2351): WARNING **: Error setting file metadata: No such file or directory

** (evince:2351): WARNING **: Error setting file metadata: No such file or directory

** (evince:2351): WARNING **: Error setting file metadata: No such file or directory

I would be grateful if somebody could help me.
Regarads

Forums:

j-kerbl's picture

j-kerbl | Thu, 12/29/2016 - 10:27

Hi Tala,

obviously the simulation didn't run properly.
Within the tutorial folder there should be a file like "log_run_parallel_cfdemSolverIB_twoSpheresGlowinskiMPI_CFDDEM" which should contain actual errors of the simulation.
You can also check if the executable cfdemSolverIB has been created and is witin the PATH environment by just typing cfdemSolverIB. If this fails you can go through the compilation logs of cfdemSolverIB and cfdemParticle in $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/log/ .

Regards,
Josef

tala | Fri, 01/06/2017 - 12:46

Dear Josef
After a little investigation I found that I was running in wrong directory, (in tutorial directory) instead of my case directory in /home/talat/CFDEM/talat-PUBLIC-3.0.1/run/ErgunTestMPI
after running in my case directory (for example ErgunTestMPI)
the error was:

// run_parallel_cfdemSolverPiso_ErgunTestMPI_CFDDEM //

/home/talat/CFDEM/talat-PUBLIC-3.0.1/run/ErgunTestMPI/CFD

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

Executable: cfdemSolverPiso
Node: talat-X555LD

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

then, I had run (cfdemSysTest) in run directory and the following result upcome:
*********************************************
* C F D E M (R) c o u p l i n g *
* *
* by DCS Computing GmbH *
* www.dcs-computing.com *
*********************************************

*********************************
CFDEM(R)coupling system settings:
*********************************
CFDEM_VERSION=PUBLIC
couple to OF_VERSION=3.0.1
compile option=Opt

check if paths are set correctly
valid:yes critical:yes - $CFDEM_PROJECT_DIR = /home/talat/CFDEM/CFDEMcoupling-PUBLIC-3.0.1
valid:yes critical:no - $CFDEM_PROJECT_USER_DIR = /home/talat/CFDEM/talat-PUBLIC-3.0.1
valid:yes critical:yes - $CFDEM_SRC_DIR = /home/talat/CFDEM/CFDEMcoupling-PUBLIC-3.0.1/src
valid:yes critical:yes - $CFDEM_SOLVER_DIR = /home/talat/CFDEM/CFDEMcoupling-PUBLIC-3.0.1/applications/solvers
valid:yes critical:yes - $CFDEM_TUT_DIR = /home/talat/CFDEM/CFDEMcoupling-PUBLIC-3.0.1/tutorials
valid:yes critical:yes - $CFDEM_LIGGGHTS_SRC_DIR = /home/talat/LIGGGHTS/LIGGGHTS-PUBLIC/src
valid:NO critical:yes - $CFDEM_LPP_DIR = /home/talat/LIGGGHTS/mylpp/src does not exist
valid:yes critical:yes - $CFDEM_ADD_LIBS_DIR = /home/talat/CFDEM/CFDEMcoupling-PUBLIC-3.0.1/src/lagrangian/cfdemParticle/etc
valid:NO critical:no - $CFDEM_PIZZA_DIR = /home/talat/LIGGGHTS/PIZZA/gran_pizza_17Aug10/src does not exist
valid:yes critical:no - $CFDEM_TEST_HARNESS_PATH = /home/talat/CFDEM/talat-PUBLIC-3.0.1/log/logFilesCFDEM-PUBLIC-3.0.1
valid:NO critical:no - $C3PO_SRC_DIR = /home/talat/CFDEM/CFDEMcoupling-PUBLIC-3.0.1/src/c3po does not exist

library names
$CFDEM_LIGGGHTS_LIB_NAME = lmp_fedora_fpic
$CFDEM_LIB_NAME = lagrangianCFDEM-PUBLIC-3.0.1
$LD_LIBRARY_PATH = /opt/ThirdParty-3.0.1/platforms/linux64Gcc/gperftools-svn/lib:/opt/paraviewopenfoam44/lib/paraview-4.4:/opt/openfoam30/platforms/linux64GccDPInt32Opt/lib/openmpi-system:/opt/ThirdParty-3.0.1/platforms/linux64GccDPInt32Opt/lib/openmpi-system:/usr/lib/openmpi/lib:/home/talat/OpenFOAM/talat-3.0.1/platforms/linux64GccDPInt32Opt/lib:/opt/site/3.0.1/platforms/linux64GccDPInt32Opt/lib:/opt/openfoam30/platforms/linux64GccDPInt32Opt/lib:/opt/ThirdParty-3.0.1/platforms/linux64GccDPInt32Opt/lib:/opt/openfoam30/platforms/linux64GccDPInt32Opt/lib/dummy
$WM_NCOMPPROCS =
$WM_LABEL_SIZE = 32
*******************
g++:
/usr/bin/g++
g++ (Ubuntu 5.2.1-22ubuntu2) 5.2.1 20151010
Copyright (C) 2015 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 (Ubuntu 5.2.1-22ubuntu2) 5.2.1 20151010
Copyright (C) 2015 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++:
/usr/bin/mpic++
g++ (Ubuntu 5.2.1-22ubuntu2) 5.2.1 20151010
Copyright (C) 2015 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:
/usr/bin/mpirun
mpirun (Open MPI) 1.6.5

Report bugs to http://www.open-mpi.org/community/help/
**********************
additional packages...
c3po does not exist.

may pls tell me what is wrong? and what to do?
Thanks a lot
Talat

alice's picture

alice | Mon, 01/09/2017 - 10:49

Hi Talat,
the error message indicates that your compilation did not work out correctly (cfdemSolverPiso not found). The system test indicates that te system settings seem to be okay. Please have a look at the log files that were generated during your installation ($CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/log). First look into log_compileCFDEMcoupling_cfdemParticle. If the last line says "is up to date" the cloud compiled correctly, and something went wrong when installing the solver. (Have a look at the log file for cfdemSolverPiso in that case). Otherwise have a closer look at the cfdemParticle log file to find out what went wrong (or post the file here).
Best regards,
Alice

tala | Mon, 01/09/2017 - 21:11

Dear Alice
Thank you for the reply, I had a look at (log_compileCFDEMcoupling_cfdemParticle), the last line don't say "is up to date" and this file contains:

// log_compileCFDEMcoupling_cfdemParticle-2016-12-19-21:56 //

/home/talat/CFDEM/CFDEMcoupling-PUBLIC-3.0.1/src/lagrangian/cfdemParticle

removing all .dep files ...
find: `./Make/linux64GccDPInt32Opt': No such file or directory
Make/linux64GccDPInt32Opt/options:60: /home/talat/CFDEM/CFDEMcoupling-PUBLIC-3.0.1/src/lagrangian/cfdemParticle/etc/additionalLibs_3.0.1: No such file or directory
make: *** No rule to make target '/home/talat/CFDEM/CFDEMcoupling-PUBLIC-3.0.1/src/lagrangian/cfdemParticle/etc/additionalLibs_3.0.1'. Stop.
Make/linux64GccDPInt32Opt/options:60: /home/talat/CFDEM/CFDEMcoupling-PUBLIC-3.0.1/src/lagrangian/cfdemParticle/etc/additionalLibs_3.0.1: No such file or directory
make: *** No rule to make target '/home/talat/CFDEM/CFDEMcoupling-PUBLIC-3.0.1/src/lagrangian/cfdemParticle/etc/additionalLibs_3.0.1'. Stop.
wmake error: file 'Make/linux64GccDPInt32Opt/sourceFiles' could not be created in /home/talat/CFDEM/CFDEMcoupling-PUBLIC-3.0.1/src/lagrangian/cfdemParticle

j-kerbl's picture

j-kerbl | Tue, 01/10/2017 - 11:25

Hi Talat,

When you type
echo $WM_PROJECT_VERSION
does it show you 3.0.1 ?
If so, please copy
/home/talat/CFDEM/CFDEMcoupling-PUBLIC-3.0.1/src/lagrangian/cfdemParticle/etc/additionalLibs_3.0.x
to
/home/talat/CFDEM/CFDEMcoupling-PUBLIC-3.0.1/src/lagrangian/cfdemParticle/etc/additionalLibs_3.0.1

Cheers
Josef

tala | Tue, 01/10/2017 - 12:05

Dear Josef
it shows 3.0.1
but i don't have such file in the mentioned directory: additionalLibs_3.0.1
I have file by this name: additionalLibs_3.0.x
Regards,
Talat

j-kerbl's picture

j-kerbl | Tue, 01/10/2017 - 14:58

Hi Talat,

yes please copy additionalLibs_3.0.x and give the new file the name additionalLibs_3.0.1 .

Cheers,
Josef

tala | Tue, 01/10/2017 - 15:39

Dear Josef
I have copied this: "/home/talat/CFDEM/CFDEMcoupling-PUBLIC-3.0.1/src/lagrangian/cfdemParticle/etc/additionalLibs_3.0.x" at the first line, and changed the file's name to "additionalLibs_3.0.1".
but the problem is not fixed. do I need to compile cfdem again?
sorry for asking so many questions, I am new to linux and cfdem.
Regards.
Talat

j-kerbl's picture

j-kerbl | Tue, 01/10/2017 - 16:44

Hi Talat,

yes you need to compile again. The problem is the compilation so far did not work, but with fingers crossed it should this time :)

Cheers,
josef

tala | Thu, 01/12/2017 - 09:14

Hi Josef
I have tried to compile CFDEM, the error for all solvers is:

// log_compileCFDEMcoupling_cfdemSolverPiso_cfdemSolverPiso-2017-01-12-11:17 //

/home/talat/CFDEM/CFDEMcoupling-PUBLIC-3.0.1/applications/solvers/cfdemSolverPiso

removing all .dep files ...
/home/talat/CFDEM/CFDEMcoupling-PUBLIC-3.0.1/src/lagrangian/cfdemParticle/etc/additionalLibs_3.0.1:1: *** missing separator (did you mean TAB instead of 8 spaces?). Stop.
/home/talat/CFDEM/CFDEMcoupling-PUBLIC-3.0.1/src/lagrangian/cfdemParticle/etc/additionalLibs_3.0.1:1: *** missing separator (did you mean TAB instead of 8 spaces?). Stop.
wmake error: file 'Make/linux64GccDPInt32Opt/sourceFiles' could not be created in /home/talat/CFDEM/CFDEMcoupling-PUBLIC-3.0.1/applications/solvers/cfdemSolverPiso

what is your idea about this?
Thanks a lot,
Regards,
Talat

j-kerbl's picture

j-kerbl | Mon, 01/16/2017 - 12:52

Hi Talat,

please post the contents of
/home/talat/CFDEM/CFDEMcoupling-PUBLIC-3.0.1/src/lagrangian/cfdemParticle/etc/additionalLibs_3.0.1

Cheers,
Josef

tala | Tue, 01/17/2017 - 19:41

Hi Josef
it is as following

/home/talat/CFDEM/CFDEMcoupling-PUBLIC-3.0.1/src/lagrangian/cfdemParticle/etc/additionalLibs_3.0.x
# paths for additional libraries
CFDEM_ADD_LIB_PATHS = \

# additional libraries to be linked to solvers
CFDEM_ADD_LIBS = \

# additional static libraries to be linked to lagrangian library
CFDEM_ADD_STATICLIBS = \
-lmpi_cxx \

#################################################################
## SETTINGS FOR 3.0.x ##
#################################################################
#----------------------------------------------------------------
# incompressible turbulence model settings
#----------------------------------------------------------------
# paths for incompressible turbulence models to use
CFDEM_ADD_INCOMPTURBMOD_PATHS = \
-I$(LIB_SRC)/TurbulenceModels/turbulenceModels/lnInclude \
-I$(LIB_SRC)/TurbulenceModels/incompressible/lnInclude \
-I$(LIB_SRC)/fvOptions/lnInclude \

# libs for turbulence models to use
CFDEM_ADD_INCOMPTURBMOD_LIBS = \
-lturbulenceModels \
-lincompressibleTurbulenceModels \
-lfvOptions \

#----------------------------------------------------------------
# compressible turbulence model settings
#----------------------------------------------------------------
# paths for compressible turbulence models to use
CFDEM_ADD_COMPTURBMOD_PATHS = \
-I$(LIB_SRC)/TurbulenceModels/turbulenceModels/lnInclude \
-I$(LIB_SRC)/TurbulenceModels/compressible/lnInclude \
-I$(LIB_SRC)/transportModels/compressible/lnInclude \
-I$(LIB_SRC)/thermophysicalModels/radiation/lnInclude \

# libs for turbulence models to use
CFDEM_ADD_COMPTURBMOD_LIBS = \
-lturbulenceModels \
-lcompressibleTurbulenceModels \
#################################################################

Refards
Talat,

cgoniva's picture

cgoniva | Thu, 01/19/2017 - 12:50

Hello Talat,

in the CFDEM(R)coupling 3.6.0 the handling of additionalLibs was simplified a lot.

No need to specify CFDEM_ADD_LIBS_DIR and CFDEM_ADD_LIBS_NAME any more in your bashrc, and no need to care about VTK version installed or OF version used.

Please try to use version 3.6.0 and let us know if the compilation works fine for you.

Best regards,

Christoph Goniva

j-kerbl's picture

j-kerbl | Fri, 01/20/2017 - 10:00

Hi Talat,

of course an update isn't a bad idea, but you would still have to copy the 3.0.x to a 3.0.1 additionalLibs file.

The error you are getting is very weird. It complains about the first line in
/home/talat/CFDEM/CFDEMcoupling-PUBLIC-3.0.1/src/lagrangian/cfdemParticle/etc/additionalLibs_3.0.1

Just a quick question: In your post you stated
/home/talat/CFDEM/CFDEMcoupling-PUBLIC-3.0.1/src/lagrangian/cfdemParticle/etc/additionalLibs_3.0.x
Is this a part of the additionalLibs_3.0.1?
If so, please remove this line.
If not and you posted the contents of additionalLibs_3.0.x, please post the contents of additionalLibs_3.0.1.

Thanks,
Josef

tala | Fri, 01/20/2017 - 12:00

Hi josef
many many many thanks :)
I removed the first line that I had copied it in additionalLibs_3.0.1 and compilation done.
again I thank you for all your help.

regards,
Talat

Dhar | Tue, 02/01/2022 - 12:54

Hi JOSEF ,
These are the errors we are finding in simulation of first tutorial after installation first time . Can you help in this concern ?

trying to start paraview...
./Allrun.sh: line 81: /home/vivek/software/ParaView-4.3.1-Linux-64bit/bin/paraview: No such file or directory