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[Other] Compiling hacFoam (Ubuntu 10.04)(OF2.0.0)(LAMMPS13Jul2010))

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Old   September 15, 2016, 04:33
Default Compiling hacFoam (Ubuntu 10.04)(OF2.0.0)(LAMMPS13Jul2010))
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Henrik Esche
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Hi,

I installed OpenFOAM-2.0.0 on a fresh Ubuntu 10.04 machine. I run some turorials (with mpi), everything is working well.
Then I installed LAMMPS and run some tutorials (with mpi), this also worked well.
Afterwards I tried to install a OpenFOAM solver called hacFoam. I had to solve some issues regarding fftw. Then the building of hacFoam could be finished without errors.

When I tried a tutorial (distributed with the hacFoam solver), it breaks with some errors:

Code:
hacfoam@HacFoam:~/Hac_Foam/aepc_v1_0/example_couette_esche$ mpirun -np 8 hacFoam -parallel
[HacFoam:24009] [[20734,1],1] ORTE_ERROR_LOG: Not found in file ess_env_module.c at line 225
[HacFoam:24009] [[20734,1],1] ORTE_ERROR_LOG: Not found in file ess_env_module.c at line 225
[HacFoam:24009] [[20734,1],1] ORTE_ERROR_LOG: Not found in file ess_env_module.c at line 225
[HacFoam:24009] [[20734,1],1] ORTE_ERROR_LOG: Not found in file ess_env_module.c at line 225
[HacFoam:24009] [[20734,1],1] ORTE_ERROR_LOG: Not found in file ess_env_module.c at line 225
[HacFoam:24009] [[20734,1],1] ORTE_ERROR_LOG: Not found in file ess_env_module.c at line 225
[HacFoam:24009] [[20734,1],1] ORTE_ERROR_LOG: Not found in file ess_env_module.c at line 225
[HacFoam:24010] [[20734,1],2] ORTE_ERROR_LOG: Not found in file ess_env_module.c at line 225
[HacFoam:24010] [[20734,1],2] ORTE_ERROR_LOG: Not found in file ess_env_module.c at line 225
[HacFoam:24010] [[20734,1],2] ORTE_ERROR_LOG: Not found in file ess_env_module.c at line 225
[HacFoam:24010] [[20734,1],2] ORTE_ERROR_LOG: Not found in file ess_env_module.c at line 225
[HacFoam:24010] [[20734,1],2] ORTE_ERROR_LOG: Not found in file ess_env_module.c at line 225
[HacFoam:24010] [[20734,1],2] ORTE_ERROR_LOG: Not found in file ess_env_module.c at line 225
[HacFoam:24010] [[20734,1],2] ORTE_ERROR_LOG: Not found in file ess_env_module.c at line 225
[HacFoam:24012] [[20734,1],4] ORTE_ERROR_LOG: Not found in file ess_env_module.c at line 225
[HacFoam:24012] [[20734,1],4] ORTE_ERROR_LOG: Not found in file ess_env_module.c at line 225
[HacFoam:24012] [[20734,1],4] ORTE_ERROR_LOG: Not found in file ess_env_module.c at line 225
[HacFoam:24012] [[20734,1],4] ORTE_ERROR_LOG: Not found in file ess_env_module.c at line 225
[HacFoam:24012] [[20734,1],4] ORTE_ERROR_LOG: Not found in file ess_env_module.c at line 225
[HacFoam:24012] [[20734,1],4] ORTE_ERROR_LOG: Not found in file ess_env_module.c at line 225
[HacFoam:24012] [[20734,1],4] ORTE_ERROR_LOG: Not found in file ess_env_module.c at line 225
[HacFoam:24011] [[20734,1],3] ORTE_ERROR_LOG: Not found in file ess_env_module.c at line 225
[HacFoam:24011] [[20734,1],3] ORTE_ERROR_LOG: Not found in file ess_env_module.c at line 225
[HacFoam:24011] [[20734,1],3] ORTE_ERROR_LOG: Not found in file ess_env_module.c at line 225
[HacFoam:24011] [[20734,1],3] ORTE_ERROR_LOG: Not found in file ess_env_module.c at line 225
[HacFoam:24011] [[20734,1],3] ORTE_ERROR_LOG: Not found in file ess_env_module.c at line 225
[HacFoam:24011] [[20734,1],3] ORTE_ERROR_LOG: Not found in file ess_env_module.c at line 225
[HacFoam:24011] [[20734,1],3] ORTE_ERROR_LOG: Not found in file ess_env_module.c at line 225
[HacFoam:24008] [[20734,1],0] ORTE_ERROR_LOG: Not found in file ess_env_module.c at line 225
[HacFoam:24008] [[20734,1],0] ORTE_ERROR_LOG: Not found in file ess_env_module.c at line 225
[HacFoam:24008] [[20734,1],0] ORTE_ERROR_LOG: Not found in file ess_env_module.c at line 225
[HacFoam:24008] [[20734,1],0] ORTE_ERROR_LOG: Not found in file ess_env_module.c at line 225
[HacFoam:24008] [[20734,1],0] ORTE_ERROR_LOG: Not found in file ess_env_module.c at line 225
[HacFoam:24008] [[20734,1],0] ORTE_ERROR_LOG: Not found in file ess_env_module.c at line 225
[HacFoam:24008] [[20734,1],0] ORTE_ERROR_LOG: Not found in file ess_env_module.c at line 225
[HacFoam:24013] [[20734,1],5] ORTE_ERROR_LOG: Not found in file ess_env_module.c at line 225
[HacFoam:24013] [[20734,1],5] ORTE_ERROR_LOG: Not found in file ess_env_module.c at line 225
[HacFoam:24013] [[20734,1],5] ORTE_ERROR_LOG: Not found in file ess_env_module.c at line 225
[HacFoam:24013] [[20734,1],5] ORTE_ERROR_LOG: Not found in file ess_env_module.c at line 225
[HacFoam:24013] [[20734,1],5] ORTE_ERROR_LOG: Not found in file ess_env_module.c at line 225
[HacFoam:24013] [[20734,1],5] ORTE_ERROR_LOG: Not found in file ess_env_module.c at line 225
[HacFoam:24013] [[20734,1],5] ORTE_ERROR_LOG: Not found in file ess_env_module.c at line 225
[HacFoam:24009] *** Process received signal ***
[HacFoam:24009] Signal: Segmentation fault (11)
[HacFoam:24009] Signal code: Address not mapped (1)
[HacFoam:24009] Failing at address: (nil)
[HacFoam:24009] [ 0] /lib/libc.so.6(+0x338c0) [0x7fa935ad08c0]
[HacFoam:24009] *** End of error message ***
--------------------------------------------------------------------------
mpirun noticed that process rank 1 with PID 24009 on node HacFoam exited on signal 11 (Segmentation fault).
With the help of google I got the information, that this could be an mpi problem.
Google also brought some hints to solve this, for centOS. But they don't work for me.

I checked, that OpenFOAM uses openmpi which is installed with the third party package. I build LAMMPS also with this openmpi.

Has anyone a hint regarding this?
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Old   September 17, 2016, 08:46
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Bruno Santos
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Quick answer: After a quick search, that error message is apparently consistent with using different versions of Open-MPI.

To diagnose the problem, please run the following commands, which hopefully will give some insight into the installation:
Code:
ldd $(which hacFoam)

which mpirun
which mpicc
Furthermore, I've never installed LAMMPS myself, so I'm not familiar with the build procedure. Which installation instructions did you follow?
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Old   September 19, 2016, 10:45
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Henrik Esche
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Hello wyldckat,

thanks for your reply.

The answers to the commands of you are as follows:
Code:
hacfoam@HacFoam:~$ ldd $(which hacFoam)
    linux-vdso.so.1 =>  (0x00007fffeebf8000)
    libmpi_cxx.so.0 => /usr/lib/libmpi_cxx.so.0 (0x00007f8390cfb000)
    libfiniteVolume.so => /home/hacfoam/OpenFOAM/OpenFOAM-2.0.0/platforms/linux64GccDPOpt/lib/libfiniteVolume.so (0x00007f838fd53000)
    libOpenFOAM.so => /home/hacfoam/OpenFOAM/OpenFOAM-2.0.0/platforms/linux64GccDPOpt/lib/libOpenFOAM.so (0x00007f838f66f000)
    libdl.so.2 => /lib/libdl.so.2 (0x00007f838f46b000)
    libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x00007f838f156000)
    libm.so.6 => /lib/libm.so.6 (0x00007f838eed3000)
    libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00007f838ecbc000)
    libc.so.6 => /lib/libc.so.6 (0x00007f838e932000)
    libmpi.so.0 => /usr/lib/libmpi.so.0 (0x00007f838e682000)
    libpthread.so.0 => /lib/libpthread.so.0 (0x00007f838e465000)
    libPstream.so => /home/hacfoam/OpenFOAM/OpenFOAM-2.0.0/platforms/linux64GccDPOpt/lib/openmpi-1.5.3/libPstream.so (0x00007f838e25a000)
    libnsl.so.1 => /lib/libnsl.so.1 (0x00007f838e040000)
    libutil.so.1 => /lib/libutil.so.1 (0x00007f838de3d000)
    libtriSurface.so => /home/hacfoam/OpenFOAM/OpenFOAM-2.0.0/platforms/linux64GccDPOpt/lib/libtriSurface.so (0x00007f838dbcc000)
    libmeshTools.so => /home/hacfoam/OpenFOAM/OpenFOAM-2.0.0/platforms/linux64GccDPOpt/lib/libmeshTools.so (0x00007f838d7cc000)
    libz.so.1 => /lib/libz.so.1 (0x00007f838d5b5000)
    /lib64/ld-linux-x86-64.so.2 (0x00007f8390f32000)
    libopen-rte.so.0 => /usr/lib/libopen-rte.so.0 (0x00007f838d368000)
    libmpi.so.1 => /home/hacfoam/OpenFOAM/ThirdParty-2.0.0/platforms/linux64Gcc/openmpi-1.5.3/lib/libmpi.so.1 (0x00007f838d003000)
    libfileFormats.so => /home/hacfoam/OpenFOAM/OpenFOAM-2.0.0/platforms/linux64GccDPOpt/lib/libfileFormats.so (0x00007f838cdfa000)
    libopen-pal.so.0 => /usr/lib/libopen-pal.so.0 (0x00007f838cb86000)
hacfoam@HacFoam:~$ which mpirun
/home/hacfoam/OpenFOAM/ThirdParty-2.0.0/platforms/linux64Gcc/openmpi-1.5.3/bin/mpirun
hacfoam@HacFoam:~$ which mpicc
/home/hacfoam/OpenFOAM/ThirdParty-2.0.0/platforms/linux64Gcc/openmpi-1.5.3/bin/mpicc
hacfoam@HacFoam:~$
lammps can be build with some make files (for different machine types)
I chose make openmpi to build lammps.
These days I checked the makefile again, and found some lines to specify the location of mpi. They look like this:
Code:
# MPI library, can be src/STUBS dummy lib
# INC = path for mpi.h, MPI compiler settings
# PATH = path for MPI library
# LIB = name of MPI library

MPI_INC =       
MPI_PATH = 
MPI_LIB =
I thougt that there is only one mpi installation, so I left them empty up to now. Maybe I should spend some path there.
But I can't find mpi.h in the folders of
/home/hacfoam/OpenFOAM/ThirdParty-2.0.0/openmpi-1.5.3
Do I have to look on a different place?

Thanks a lot,
Henrik
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Old   September 29, 2016, 16:16
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Bruno Santos
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Greetings Henrik,

Sorry, it took me a while to manage to find the time and mind to properly check the information you've provided.

OK, there are 2 details that I've spotted so far, but let me first answer your question:
Quote:
Originally Posted by Henrik_E View Post
But I can't find mpi.h in the folders of
/home/hacfoam/OpenFOAM/ThirdParty-2.0.0/openmpi-1.5.3
Do I have to look on a different place?
It's actually inside this folder:
Code:
/home/hacfoam/OpenFOAM/ThirdParty-2.0.0/platforms/linux64Gcc/openmpi-1.5.3/include/
This is because only after building and installing, will the "mpi.h" file be ready to be used.

As for the libraries that ldd revealed, here's the problem:
Quote:
Originally Posted by Henrik_E View Post
Code:
hacfoam@HacFoam:~$ ldd $(which hacFoam)
[...]
    libmpi_cxx.so.0 => /usr/lib/libmpi_cxx.so.0 (0x00007f8390cfb000)
[...]
    libmpi.so.0 => /usr/lib/libmpi.so.0 (0x00007f838e682000)
[...]
    libopen-rte.so.0 => /usr/lib/libopen-rte.so.0 (0x00007f838d368000)
    libmpi.so.1 =>  /home/hacfoam/OpenFOAM/ThirdParty-2.0.0/platforms/linux64Gcc/openmpi-1.5.3/lib/libmpi.so.1  (0x00007f838d003000)
[...]
    libopen-pal.so.0 => /usr/lib/libopen-pal.so.0 (0x00007f838cb86000)
All of these libraries refer to components that Open-MPI uses, problem is that there is one that is being used from the wrong place, when it shouldn't... ironically, the one that was built with OpenFOAM is the odd-one-out.


Therefore, I believe the solution is fairly simple: to use only the system's Open-MPI and forget about the one in "ThirdParty-2.0.0". To do this, I don't know how exactly you installed OpenFOAM, but I guess the simplest steps would be:
  1. Edit this file:
    Code:
    /home/hacfoam/OpenFOAM/OpenFOAM-2.0.0/etc/bashrc
  2. Change this line:
    Code:
    export WM_MPLIB=OPENMPI
    to this:
    Code:
    export WM_MPLIB=SYSTEMOPENMPI
  3. Save and close the file.
  4. Start a new terminal, activate the OpenFOAM environment and then run:
    Code:
    foam
./Allwmake
  5. Will take a bit to build only the new libraries, most of them are unaffected.
  6. Then try again running your case.
If LAMMPS was built after OpenFOAM 2.0.0, then you might want to rebuild it as well, if the previous changes aren't enough to solve the problem.

Best regards,
Bruno
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