OpenFOAM 5 source pack installation on Ubuntu 16.04
 

Hello FOAMers,
I tried to install the source pack in the first place ,but failed. Later I used the method in the following link, and it worked out.
https://openfoam.org/download/5-0-ubuntu/

Now I try to change the cloud type from reactingCloud to sprayCloud in the reactingParcelFilmFoam to build a new solver, following errors appeared,there error messages appeared before in the source pack installation:

-lm -o /opt/openfoam5/platforms/linux64GccDPInt32Opt/bin/sprayFilmFoam
/opt/openfoam5/platforms/linux64GccDPInt32Opt/lib/openmpi-system/libPstream.so: undefined reference to `ompi_mpi_comm_null'
/opt/openfoam5/platforms/linux64GccDPInt32Opt/lib/openmpi-system/libPstream.so: undefined reference to `ompi_mpi_group_null'
/opt/openfoam5/platforms/linux64GccDPInt32Opt/lib/openmpi-system/libPstream.so: undefined reference to `ompi_mpi_byte'
/opt/openfoam5/platforms/linux64GccDPInt32Opt/lib/openmpi-system/libPstream.so: undefined reference to `ompi_mpi_double'
/opt/openfoam5/platforms/linux64GccDPInt32Opt/lib/openmpi-system/libPstream.so: undefined reference to `ompi_mpi_op_min'
/opt/openfoam5/platforms/linux64GccDPInt32Opt/lib/openmpi-system/libPstream.so: undefined reference to `ompi_mpi_comm_world'
/opt/openfoam5/platforms/linux64GccDPInt32Opt/lib/openmpi-system/libPstream.so: undefined reference to `ompi_mpi_op_sum'
collect2: error: ld returned 1 exit status
/opt/openfoam5/wmake/makefiles/general:140: recipe for target '/opt/openfoam5/platforms/linux64GccDPInt32Opt/bin/sprayFilmFoam' failed
make: *** [/opt/openfoam5/platforms/linux64GccDPInt32Opt/bin/sprayFilmFoam] Error 1

Could anyone help me with this? Thank you very much.

Quick answer: I suspect that the problem has to do with the default version of MPI that is defined in your Ubuntu installation. That would also explain why you were not able to install from source code.

In order to have the correct MPI version being used for the Deb package of OpenFOAM, run the following command:
The command above is from one of the solutions given in the "Installation Problems" section on that page: https://openfoam.org/download/5-0-ub...ation-problems

Thanks Bruno, based on the suggestion on the website
I check whether MPICH is installed by
and it returns:
if I use
still get the same results, and the solver still can not be correct complied.
Do you have any more suggetion?

Quick answer: I forgot to mention that it would be preferable to start a new terminal after that, so that it would refresh the shell environment. Don't forget to activate OpenFOAM's shell environment as well, in case it's not done automatically:
You can check which MPI version you have currently loaded in by running:
The second command will try to should where exactly mpirun is installed.

This is so that we can confirm if the correct version and location is being used.

Thanks, Bruno

Based on your suggestion, I opened a new terminal, sourced the $FOAM_ETC/bashrc and type the following

I am a little confused about the different results between readlink -f $(which mpirun) and
which mpirun. Is this corrected installed or not? If not, how to point to the right folder?

and then I type
and it returns:
then I open a new terminal, source the $FOAM_ETC/bashrc file, the application still can not be compiled.

Any idea about this?

Quick answers:

1. "orterun" is one of the names used by Open-MPI, while "mpirun" is a more common name among MPI toolboxes.
2. "readlink" is telling us that "mpirun" is just a symbolic link to "orterun".
3. When in doubt, use the full list command "ls -l", like this:
   
   Code:

   ---

   ls -l $(which mpirun)

   ---

4. I need to see the complete output for when you try to build the custom solver. You can send the complete output by running the following command within the source code folder for that solver:
   
   Code:

   ---

   wmake > log.make 2>&1

   ---

   1. You may want to edit the file "log.make" and search+replace any sensitive information names.
   2. Then you can compress the file by running:
      
      Code:

      ---

      gzip < log.make > log.make.gz

      ---

   3. Then attach the file "log.make.gz" to your next post.
   Hopefully having this complete output will tell us the whole story of what and where it's looking for the MPI library that is missing.

Thanks Bruno,
Attached is the log file you mentioned, hope it could help out.

Quick answer: I've finally managed to take a quick look into this. Something seems to be misplaced in your Ubuntu and/or OpenFOAM installation.
Hopefully the following commands will help us diagnose the issue further:

1. The following commands should help confirm if the correct environment path is being used:
   
   Code:

   ---

   echo $FOAM_MPI
echo $MPI_ARCH_PATH

   ---

2. This command should help diagnose if all of the correct libraries are available for "libPstream.so":
   
   Code:

   ---

   ldd $FOAM_LIBBIN/openmpi-system/libPstream.so

   ---

   It should give the following output:
   
   Code:

   ---

       linux-vdso.so.1 =>  (0x00007ffe67f0c000)
    libmpi.so.12 => /usr/lib/libmpi.so.12 (0x00007f93cbe72000)
    libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f93cbaea000)
    libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f93cb7da000)
    libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f93cb5c2000)
    libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f93cb3a2000)
    libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f93cafd2000)
    libibverbs.so.1 => /usr/lib/libibverbs.so.1 (0x00007f93cadc2000)
    libopen-rte.so.12 => /usr/lib/libopen-rte.so.12 (0x00007f93cab42000)
    libopen-pal.so.13 => /usr/lib/libopen-pal.so.13 (0x00007f93ca8a2000)
    /lib64/ld-linux-x86-64.so.2 (0x00007f93cc35a000)
    libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f93ca69a000)
    libhwloc.so.5 => /usr/lib/x86_64-linux-gnu/libhwloc.so.5 (0x00007f93ca45a000)
    librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f93ca252000)
    libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x00007f93ca04a000)
    libnuma.so.1 => /usr/lib/x86_64-linux-gnu/libnuma.so.1 (0x00007f93c9e3a000)
    libltdl.so.7 => /usr/lib/x86_64-linux-gnu/libltdl.so.7 (0x00007f93c9c2a000)

   ---

3. It's possible that GNU LD Gold is being used by default, which would explain the problem, so please run the following commands to see which one it's using by default:
   
   Code:

   ---

   ls -l /usr/bin/ld*
ls -l /usr/bin/x86_64-linux-gnu-ld*

   ---

Hello, Bruno
Thank you very much for your time and help on fixing this problem.
It seems the libPsteam.so is not corrected installed.
Do you know how to fix this?

Thank you very much.

Quick note: There is an 'r' missing when you wrote "libPsteam", it should be "libPstream", like this:

sorry about that, the actual results should be

It seems to be the same with your results.Do you have any idea?

My apologies, but I haven't had time to look into this since we last exchanged messages.
Have you managed to solve this problem?

Hello Bruno,


I am facing the similar problem in 'libPstream.so' related to mpi. Will you please let me know the solution for it. Thanks.

Quick request: Please provide more details, namely:

1. Which Linux Distribution you are using?
2. Which OpenFOAM version you are using?
3. Which installation instructions did you follow?

Hi Bruno,



Thanks for the reply. I am installing OpenFoam 4.1 on Ubuntu 16.04 following the instructions at https://openfoamwiki.net/index.php/I...u#Ubuntu_16.04


My HPC system is shared by other users and has MPI installations like MPICH, along with open mpi.

Hi Abilash,

I was too much in a hurry and forgot to ask: Please provide the complete output that gave you the message about "libPstream.so".

This raises another question: How are you choosing which MPI toolbox to use, if there are several installed?

Best regards,
Bruno

Bruno,


Please find the attached log file generated. I am using the following symbolic links described in the installation procedure to link open mpi to OpenFoam.


ln -s /usr/bin/mpicc.openmpi OpenFOAM-4.1/bin/mpicc
ln -s /usr/bin/mpirun.openmpi OpenFOAM-4.1/bin/mpirun

I checked the commands that were mentioned in the post to verify the proper implementation of MPI and the output seemed to be okay.

Hi Bruno,

Please let me know if it is possible to solve this installation problem.


Thanks

Abilash

Quick answer:

The last line here implies that the MPI toolbox being used is not the system's own OpenMPI toolbox. This is why you are having problems compiling anything else.


There are two possible approaches that I can't go into much detail:

1. First approach is to remove the symbolic links:
   
   Code:

   ---

   rm OpenFOAM-4.1/bin/mpicc OpenFOAM-4.1/bin/mpirun

   ---

   then start a new terminal, run of41 to activate the OpenFOAM 4.1 shell environment, then rebuild the "Pstream" folder:
   
   Code:

   ---

   foam
wclean all src/Pstream
wmake all src/Pstream

   ---

   and hope it works. This is assuming that some version of Open-MPI is also the toolbox installed at "/usr/local", for which you should double-check by running on this new terminal:
   
   Code:

   ---

   which mpirun
mpirun --version
which mpiexec
mpiexec --version

   ---

2. The second approach is to remove any entries with "/usr/local" from the environment variables "PATH" and "LD_LIBRARY_PATH", then check what the "ldd" check gives you:
   
   Code:

   ---

   ldd $FOAM_LIBBIN/openmpi-system/libPstream.so

   ---

   although this may still require you to rebuild the "Pstream" folder.

Hi Bruno,


Thanks for the help. After following the steps, I am having this output. Although the I am successful in rebuilding the "Pstream" folder, I suppose the installation is incomplete as it is showing error when I tried to activate the OpenFoam shell environment with "of41".


Checking the version of Open-MPI toolbox resulted in following output.


In the new terminal I tried to see if the installation is complete, the following is the output. Please let me know if there is any solution for this.




Thanks


Abilash