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[Other] Compiling hacFoam (Ubuntu 10.04)(OF2.0.0)(LAMMPS13Jul2010)) |
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September 15, 2016, 05:33 |
Compiling hacFoam (Ubuntu 10.04)(OF2.0.0)(LAMMPS13Jul2010))
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#1 |
New Member
Henrik Esche
Join Date: Sep 2016
Posts: 2
Rep Power: 0 |
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). 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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September 17, 2016, 09:46 |
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#2 |
Retired Super Moderator
Bruno Santos
Join Date: Mar 2009
Location: Lisbon, Portugal
Posts: 10,981
Blog Entries: 45
Rep Power: 128 |
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 $(which hacFoam) which mpirun which mpicc
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September 19, 2016, 11:45 |
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#3 |
New Member
Henrik Esche
Join Date: Sep 2016
Posts: 2
Rep Power: 0 |
Hello wyldckat,
thanks for your reply. The answers to the commands of you are as follows: Code:
hacfoam@HacFoam:~$ 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:~$ 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 = 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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September 29, 2016, 17:16 |
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#4 | ||
Retired Super Moderator
Bruno Santos
Join Date: Mar 2009
Location: Lisbon, Portugal
Posts: 10,981
Blog Entries: 45
Rep Power: 128 |
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:
Code:
/home/hacfoam/OpenFOAM/ThirdParty-2.0.0/platforms/linux64Gcc/openmpi-1.5.3/include/ As for the libraries that ldd revealed, here's the problem: Quote:
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:
Best regards, Bruno
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