Errors about running the tutorials

kunzhang's picture
Submitted by kunzhang on Mon, 07/30/2012 - 22:41

Hi everyone,

I have installed the CFDEM, and I want to check whether it has been installed correctly. I typed cfdemTestTUT in my terminal, and it shows:

This routine will execute the CFDEMcoupling tutorial cases specified in tutorial-list.txt
Are the variables CFDEM_TUT_DIR=/home/kun/CFDEM/CFDEMcoupling-PUBLIC-2.1.x/tutorials
and CFDEM_SRC_DIR=/home/kun/CFDEM/CFDEMcoupling-PUBLIC-2.1.x/src/lagrangian/cfdemParticle correct? (y/n)

Then, I type y and Enter.

Another terminal is opened, and error happens:

--> FOAM FATAL ERROR:
No times selected

From function reconstructPar
in file reconstructPar.C at line 139.

FOAM exiting

rm: cannot remove `cfdemSolverPiso_settlingTestMPI.eps': No such file or directory
/home/kun/CFDEM/CFDEMcoupling-PUBLIC-2.1.x/tutorials/cfdemSolverPiso/settlingTestMPI/parCFDDEMrun.sh: line 42: octave: command not found

** (evince:18604): WARNING **: Error stating file '/home/kun/CFDEM/CFDEMcoupling-PUBLIC-2.1.x/tutorials/cfdemSolverPiso/settlingTestMPI/CFD/octave/cfdemSolverPiso_settlingTestMPI.eps': No such file or directory

** (evince:18604): WARNING **: Error setting file metadata: No such file or directory

Is there something wrong during my installation? and How could this problem be resolved?
Looking forward to your help. Thanks

Forums:

alice's picture

alice | Tue, 07/31/2012 - 08:57

Good morning kunzhang,
the error indicates that your case has been decomposed, but the computation hasn't been carried out. Go to the CFD directory in cfdemTut: /cfdemSolverPiso/settlingTestMPI/CFD, run the case manually (mpirun -np 2 cfdemSolverPiso -parallel) and see what happens. If you get "End Finalising parallel run" then your installation went right and you need to double check the setting of the paths..
For postprocessing you still need to get the open source software octave (sudo apt-get install octave should do on ubuntu).
Cheers,
Alice

kunzhang's picture

kunzhang | Tue, 07/31/2012 - 18:11

Hello Alice, Thanks for your kind reply.

I went to the directory of .../cfdemSolverPiso/settlingTestMPI/CFD, and run the case as your instructions. And the error shows like this:
mpirun was unable to launch the specified application as it could not find an executable:

Executable: cfdemSolverPiso
Node: kun-laptop

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

And, I have already installed the software octave and evince following the CFDEMcoupling_Manual. Then I run the cfdemTestTUT in the terminal, errors shows like this:

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

** (evince:2342): WARNING **: Error stating file '/home/kun/CFDEM/CFDEMcoupling-PUBLIC-2.1.x/tutorials/cfdemSolverPiso/settlingTestMPI/CFD/octave/cfdemSolverPiso_settlingTestMPI.eps': No such file or directory

** (evince:2342): WARNING **: Error setting file metadata: No such file or directory

What is the file of cfdemSolverPiso_settlingTestMPI.eps? Is this file created automatically during installation?
Looking forward to your help, Alice.
Have a great day. Thanks

kunzhang

alice's picture

alice | Tue, 07/31/2012 - 23:29

Hey,
apparently something went wrong with the installation. The problem is that the executable cfdemSolverPiso was not found. Try to reinstall cfdemCoupling and see if any error-messages appear there.
The files that are missing were meant to be created during the calculation (velocity.txt) or while postprocessing (cfdemSolverPiso_settlingTestMPI.eps), but as the computation never took place, this couldn't happen either. Don't worry about their absence at this stage!
Cheers,
Alice

kunzhang's picture

kunzhang | Wed, 08/01/2012 - 00:47

Hi Alice, I am confused about the installation instructions of

To specify the paths of pizza, please check the setting in $CFDEM_SRC_DIR/etc/bashrc.

and then I type cfdemSysTest in my terminal, lines show like this,

check if paths are set correctly
valid:yes critical:yes - $CFDEM_LIGGGHTS_SRC_DIR = /home/kun/LIGGGHTS/LIGGGHTS-PUBLIC/src
valid:yes critical:yes - $CFDEM_PROJECT_DIR = /home/kun/CFDEM/CFDEMcoupling-PUBLIC-2.1.x
valid:yes critical:no - $CFDEM_PROJECT_USER_DIR = /home/kun/CFDEM/kun-PUBLIC-2.1.x
valid:yes critical:yes - $CFDEM_SRC_DIR = /home/kun/CFDEM/CFDEMcoupling-PUBLIC-2.1.x/src/lagrangian/cfdemParticle
valid:NO critical:yes - $CFDEM_LPP_DIR = /home/kun/LIGGGHTS/mylpp/src does not exist
valid:NO critical:no - $CFDEM_PIZZA_DIR = /home/kun/LIGGGHTS/PIZZA/gran_pizza_17Aug10/src does not exist
valid:yes critical:no - $CFDEM_TEST_HARNESS_PATH = /home/kun/CFDEM/kun-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/kun/OpenFOAM/ThirdParty-2.1.x/platforms/linux64Gcc/paraview-3.12.0/lib/paraview-3.12:/home/kun/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/lib/openmpi-1.5.3:/home/kun/OpenFOAM/ThirdParty-2.1.x/platforms/linux64GccDPOpt/lib/openmpi-1.5.3:/home/kun/OpenFOAM/ThirdParty-2.1.x/platforms/linux64Gcc/openmpi-1.5.3/lib:/home/kun/OpenFOAM/ThirdParty-2.1.x/platforms/linux64Gcc/openmpi-1.5.3/lib64:/home/kun/OpenFOAM/kun-2.1.x/platforms/linux64GccDPOpt/lib:/home/kun/OpenFOAM/site/2.1.x/platforms/linux64GccDPOpt/lib:/home/kun/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/lib:/home/kun/OpenFOAM/ThirdParty-2.1.x/platforms/linux64GccDPOpt/lib:/home/kun/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/lib/dummy
*******************
g++:
/usr/bin/g++
g++ (Ubuntu 4.4.3-4ubuntu5.1) 4.4.3
Copyright (C) 2009 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 4.4.3-4ubuntu5.1) 4.4.3
Copyright (C) 2009 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/kun/OpenFOAM/ThirdParty-2.1.x/platforms/linux64Gcc/openmpi-1.5.3/bin/mpic++
g++ (Ubuntu 4.4.3-4ubuntu5.1) 4.4.3
Copyright (C) 2009 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.

I think some problems happened in this step since $CFDEM_PIZZA_DIR = /home/kun/LIGGGHTS/PIZZA/gran_pizza_17Aug10/src does not exist.
I am not sure whether the openfoam is installed correctly. However, it could be run in the terminal and checked the results in Paraview.

Thanks for your patients. I am new to those software, and I am really eager to learn and use them correctly.

kunzhang

cgoniva's picture

cgoniva | Wed, 08/01/2012 - 08:07

Hi,

did you run the "cfdemCompLIG" and "cfdemCompCFDEM" routines to compile LIGGGHTS and CFDEMcoupling?
What messages do you get when running these commands?

Cheers,
Chris

kunzhang's picture

kunzhang | Wed, 08/01/2012 - 17:45

Hi,

After running the cfdemCompLIG, some warning shows like this:

read_data.cpp:322: warning: deprecated conversion from string constant to ‘char*’
pppm.cpp:153: warning: deprecated conversion from string constant to ‘char*’
pair_airebo.cpp:3410: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result
read_restart.cpp:649: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result
thermo.cpp:259: warning: format not a string literal and no format arguments
thermo.cpp: In member function ‘void LAMMPS_NS::Thermo::compute(int)’

After running the cfdemCompCFDEM,

/home/kun/OpenFOAM/OpenFOAM-2.1.x/src/finiteVolume/lnInclude/readPISOControls.H: In function ‘int main(int, char**)’:
/home/kun/OpenFOAM/OpenFOAM-2.1.x/src/finiteVolume/lnInclude/readPISOControls.H:3: warning: unused variable ‘nOuterCorr’
/home/kun/OpenFOAM/OpenFOAM-2.1.x/src/finiteVolume/lnInclude/readPISOControls.H:15: warning: unused variable ‘transonic’
make: *** [/home/kun/OpenFOAM/kun-2.1.x/platforms/linux64GccDPOpt/bin/cfdemSolverPisoScalar] Error 1
Note: the list of solvers compiled might be incomplete.
please check /home/kun/CFDEM/CFDEMcoupling-PUBLIC-2.1.x/applications/solvers for more solvers available

Is it possible that the OpenFOAM is not installed correctly?

kunzhang

cgoniva's picture

cgoniva | Wed, 08/01/2012 - 19:29

Hi,

could you please post the complete of cfdemCompLIG and cfdemCompCFDEM, probably something went wrong with the compilation, so the testcases cannot run correctly.

Cheers,
Chris

ghaffari_ali | Wed, 08/01/2012 - 20:05

Hi Chris
I have installed the LIGGGHTS and CFDEMcoupling according to the procedure illustrated in Dtx.Osrgs.pdf file, which is available in CFDEM.com site. It seems that installation proceeded correctly because when I typed cfdemSysTest command, there was no error. But problem is: when I type cfdemCompLIG command in terminal in order to compiling LIGGGHTS, it proceeds at first but computer hangs after some minutes for no apparent reason. I take it enough time but it doesn’t proceed anyway. I don’t know what should I do?! How could this problem be resolved? Looking forward to your help. Thanks

kunzhang's picture

kunzhang | Wed, 08/01/2012 - 17:51

I type the foamInstallationTest in my terminal, and messages are:

Checking basic setup...
-------------------------------------------------------------------------------
Shell: bash
Host: kun-laptop
OS: Linux version 2.6.32-41-generic
-------------------------------------------------------------------------------

Checking main OpenFOAM env variables...
-------------------------------------------------------------------------------
Environment_variable Set_to_file_or_directory Valid Crit
-------------------------------------------------------------------------------
$WM_PROJECT_INST_DIR /home/kun/OpenFOAM yes yes
$WM_PROJECT_USER_DIR /home/kun/OpenFOAM/kun-2.1.x yes no
$WM_THIRD_PARTY_DIR /home/kun/OpenFOAM/ThirdParty-2.1.x yes yes
-------------------------------------------------------------------------------

Checking the OpenFOAM env variables set on the PATH...
-------------------------------------------------------------------------------
Environment_variable Set_to_file_or_directory Valid Path Crit
-------------------------------------------------------------------------------
$WM_PROJECT_DIR /home/kun/OpenFOAM/OpenFOAM-2.1.x yes yes yes

$FOAM_APPBIN ...-2.1.x/platforms/linux64GccDPOpt/bin yes yes yes
$FOAM_SITE_APPBIN .../2.1.x/platforms/linux64GccDPOpt/bin no no
$FOAM_USER_APPBIN ...-2.1.x/platforms/linux64GccDPOpt/bin yes yes no
$WM_DIR /home/kun/OpenFOAM/OpenFOAM-2.1.x/wmake yes yes yes
-------------------------------------------------------------------------------

Checking the OpenFOAM env variables set on the LD_LIBRARY_PATH...
-------------------------------------------------------------------------------
Environment_variable Set_to_file_or_directory Valid Path Crit
-------------------------------------------------------------------------------
$FOAM_LIBBIN ...-2.1.x/platforms/linux64GccDPOpt/lib yes yes yes
$FOAM_SITE_LIBBIN .../2.1.x/platforms/linux64GccDPOpt/lib no no
$FOAM_USER_LIBBIN ...-2.1.x/platforms/linux64GccDPOpt/lib yes yes no
$MPI_ARCH_PATH ...x/platforms/linux64Gcc/openmpi-1.5.3 yes yes yes
-------------------------------------------------------------------------------

Third party software
-------------------------------------------------------------------------------
Software Version Location
-------------------------------------------------------------------------------
flex 2.5.35 /usr/bin/flex
gcc 4.4.3 /usr/bin/gcc
gzip 1.3.12 /bin/gzip
tar 1.22 /bin/tar
icoFoam 2.1.x ...M/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/bin/icoFoam
-------------------------------------------------------------------------------

Summary
-------------------------------------------------------------------------------
Base configuration ok.
Critical systems ok.

Done

I noticed two environment variables are not valid
$FOAM_SITE_APPBIN .../2.1.x/platforms/linux64GccDPOpt/bin no no
$FOAM_SITE_LIBBIN .../2.1.x/platforms/linux64GccDPOpt/lib no no
How could I solve these problems? Thanks for your help.

kunzhang

ghaffari_ali | Wed, 08/01/2012 - 19:44

Hi Chris
I have installed the LIGGGHTS and CFDEMcoupling according to the procedure illustrated in Dtx.Osrgs.pdf file, which is available in CFDEM.com site. It seems that installation proceeded correctly because when I typed cfdemSysTest command, there was no error. But problem is: when I type cfdemCompLIG command in terminal in order to compiling LIGGGHTS, it proceeds at first but computer hangs after some minutes for no apparent reason. I take it enough time but it doesn’t proceed anyway. I don’t know what should I do?! How could this problem be resolved? Looking forward to your help. Thanks

kunzhang's picture

kunzhang | Wed, 08/01/2012 - 23:25

Hi Chris, I update the software of paraview through "sudo apt-get install paraview", and install mpirun through "sudo apt-get install openmpi-dev". Then, cfdemCompLIG and cfdemCompCFDEM are run. And after that, I typed cfdemTestTUT in my terminal, the case runs, and two figures are showed in my computer directly.
One is titled with cfdemSolverPiso_settlingTestMPI.eps

Then my terminal shows:
did the case run correcty? - press enter to proceed.
I press enter, it went on,
The other figure is shown and titled with cfdemSolverPiso_ErgunTestMPI.eps

Then, I continue press enter, and no figure is shown.
Does it mean I install the CFDEM incompletely? Or CFDEM has been already installed correctly?
Also I want to know, If I did not want to proceed, how should I do? Just close the terminal?

Your time and help will be appreciated. Thanks.

kunzhang

kunzhang's picture

kunzhang | Wed, 08/01/2012 - 03:01

Alice, I install the mylpp and make file PIZZA under the file of LIGGGHTS, and I also download and unzip the gran_pizza_17Aug10 under the directory of PIZZA. Then type cfdemSysTest, lines in terminal show like this,

check if paths are set correctly
valid:yes critical:yes - $CFDEM_LIGGGHTS_SRC_DIR = /home/kun/LIGGGHTS/LIGGGHTS-PUBLIC/src
valid:yes critical:yes - $CFDEM_PROJECT_DIR = /home/kun/CFDEM/CFDEMcoupling-PUBLIC-2.1.x
valid:yes critical:no - $CFDEM_PROJECT_USER_DIR = /home/kun/CFDEM/kun-PUBLIC-2.1.x
valid:yes critical:yes - $CFDEM_SRC_DIR = /home/kun/CFDEM/CFDEMcoupling-PUBLIC-2.1.x/src/lagrangian/cfdemParticle
valid:yes critical:yes - $CFDEM_LPP_DIR = /home/kun/LIGGGHTS/mylpp/src
valid:yes critical:no - $CFDEM_PIZZA_DIR = /home/kun/LIGGGHTS/PIZZA/gran_pizza_17Aug10/src
valid:yes critical:no - $CFDEM_TEST_HARNESS_PATH = /home/kun/CFDEM/kun-PUBLIC-2.1.x/log/logFilesCFDEM-PUBLIC-2.1.x

All valid shows yes， however, after installation, cfdemTestTUT can not still run correctly. I think the step of set environment variables goes wrong during my installation. So Would you give me detailed instruction regarding the setting environment? Thanks a lot.

kunzhang

alice's picture

alice | Wed, 08/01/2012 - 08:09

hello kunzhang,
your environment-variables now seem all set correctly. What you have to do next is recompile (cfdemCompCFDEM). Make sure that the comliation of the solvers really worked out (as this was the problem before..)
Cheers,
Alice

kunzhang's picture

kunzhang | Wed, 08/01/2012 - 23:27

Hi Alice, I update the software of paraview through "sudo apt-get install paraview", and install mpirun through "sudo apt-get install openmpi-dev". Then, cfdemCompLIG and cfdemCompCFDEM are run. And after that, I typed cfdemTestTUT in my terminal, the case runs, and two figures are showed in my computer directly.
One is titled with cfdemSolverPiso_settlingTestMPI.eps

Then my terminal shows:
did the case run correcty? - press enter to proceed.
I press enter, it went on,
The other figure is shown and titled with cfdemSolverPiso_ErgunTestMPI.eps

Then, I continue press enter, and no figure is shown.
Does it mean I install the CFDEM incompletely? Or CFDEM has been already installed correctly?
Also I want to know, If I did not want to proceed, how should I do? Just close the terminal?

Your time and help will be appreciated. Thanks.

kunzhang

alice's picture

alice | Thu, 08/02/2012 - 09:29

Hello kunzhang,
congrats, you made it! :) CFDEM was installed correctly. The different tutorial cases come with different postprocessing tools, so no pic doesn't have to mean failiure. If you do not want to continue, Ctrl+C should help...
Next would be to have a closer look at the cases, see what they do, and adjust (one of) them to your needs!
Cheers,
Alice

kunzhang's picture

kunzhang | Thu, 08/02/2012 - 17:32

Hi Alice, Thanks a lot for those day's help. Your time and patients are really appreciated. I am going to learn CFDEM case in detail.

Warm Regards,

Kun

kunzhang