Problems setting environment

bastil · September 7, 2007, 02:33

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Hi all,

I have troubles to set the environment on a x86_64 machine. I use the alias:

alias OpenFOAM13='export WM_64=Y &&. $HOME/OpenFOAM/OpenFOAM-1.3/.OpenFOAM-1.3/bashrc'

to set environment for OF 1.3. Afterwards, I get the following message while trying to execute any OF program:

simpleFoam: /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.1' not found (required by /home/brblo/OpenFOAM/OpenFOAM-1.3/lib/linuxAMD64Gcc4DPOpt/libfiniteVolume.so)

This can by fixed by manually adding

/home/brblo/OpenFOAM/OpenFOAM-1.3/linuxAMD64/gcc-4.1.0/lib64

to my $PATH, but not for parallel runs. What is the intended way to switch from system compiler and libraries to the ones shiped with OF? I also get the warning of conflicting versions while installation check.

Thanks.

bastil · September 7, 2007, 02:37

EDIT:

I also have to add the path to $LD_LIBRARY_PATH.

msrinath80 · September 7, 2007, 02:46

Just recompile your solver. All will be fine.

bastil · September 7, 2007, 02:53

I wanted to avoid recompiling, is there no other way using the binaries?

Thanks

msrinath80 · September 7, 2007, 03:34

Just your solver. Not all of OpenFOAM. Go to ~/OpenFOAM/OpenFOAM-1.3/applications/solvers/your_solver_directory and run wclean && wmake there.

mattijs · September 7, 2007, 03:49

For parallel runs you'll have to make sure your default environment sets up 1.3 and all its paths (such as /home/brblo/OpenFOAM/OpenFOAM-1.3/linuxAMD64/gcc-4.1.0/lib64)

The problem is that mpirun uses 'ssh' to start processes which does not inherit any settings. It will execute .bashrc so that should be such that it sets up any Foam specifics.

gschaider · September 7, 2007, 04:23

Another possibility for parallel run would be to export a minimal environment via mpirun (this has worked for me in the past with OpenMPI):

Add the options
-x LD_LIBRARY_PATH -x WM_PROJECT_DIR -x FOAM_MPI_LIBBIN
to the mpirun-call. Of course this assumes that the paths are the same on all your machines

bastil · September 7, 2007, 04:28

Thanks for these tipps, I will try them out and get back to you. Nevertheless, I guess I am doing something wrong because I have to add a dictionary to the $LD_LIBRARY_PATH manually. What is wrong there?

September 7, 2007, 02:33	Hi all, I have troubles to	#1
bastil Senior Member BastiL Join Date: Mar 2009 Posts: 500 Rep Power: 13	Sponsored Links Hi all, I have troubles to set the environment on a x86_64 machine. I use the alias: alias OpenFOAM13='export WM_64=Y &&. $HOME/OpenFOAM/OpenFOAM-1.3/.OpenFOAM-1.3/bashrc' to set environment for OF 1.3. Afterwards, I get the following message while trying to execute any OF program: simpleFoam: /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.1' not found (required by /home/brblo/OpenFOAM/OpenFOAM-1.3/lib/linuxAMD64Gcc4DPOpt/libfiniteVolume.so) This can by fixed by manually adding /home/brblo/OpenFOAM/OpenFOAM-1.3/linuxAMD64/gcc-4.1.0/lib64 to my $PATH, but not for parallel runs. What is the intended way to switch from system compiler and libraries to the ones shiped with OF? I also get the warning of conflicting versions while installation check. Thanks.

September 7, 2007, 02:37	EDIT: I also have to add th	#2
bastil Senior Member BastiL Join Date: Mar 2009 Posts: 500 Rep Power: 13	EDIT: I also have to add the path to $LD_LIBRARY_PATH.

September 7, 2007, 02:46	Just recompile your solver. Al	#3
msrinath80 Senior Member Srinath Madhavan (a.k.a pUl\|) Join Date: Mar 2009 Location: Edmonton, AB, Canada Posts: 703 Rep Power: 14	Just recompile your solver. All will be fine.

September 7, 2007, 02:53	I wanted to avoid recompiling,	#4
bastil Senior Member BastiL Join Date: Mar 2009 Posts: 500 Rep Power: 13	I wanted to avoid recompiling, is there no other way using the binaries? Thanks

September 7, 2007, 03:34	Just your solver. Not all of O	#5
msrinath80 Senior Member Srinath Madhavan (a.k.a pUl\|) Join Date: Mar 2009 Location: Edmonton, AB, Canada Posts: 703 Rep Power: 14	Just your solver. Not all of OpenFOAM. Go to ~/OpenFOAM/OpenFOAM-1.3/applications/solvers/your_solver_directory and run wclean && wmake there.

September 7, 2007, 03:49	For parallel runs you'll have	#6
mattijs Super Moderator Mattijs Janssens Join Date: Mar 2009 Posts: 1,419 Rep Power: 18	For parallel runs you'll have to make sure your default environment sets up 1.3 and all its paths (such as /home/brblo/OpenFOAM/OpenFOAM-1.3/linuxAMD64/gcc-4.1.0/lib64) The problem is that mpirun uses 'ssh' to start processes which does not inherit any settings. It will execute .bashrc so that should be such that it sets up any Foam specifics.

September 7, 2007, 04:23	Another possibility for parall	#7
gschaider Assistant Moderator Bernhard Gschaider Join Date: Mar 2009 Posts: 4,008 Rep Power: 43	Another possibility for parallel run would be to export a minimal environment via mpirun (this has worked for me in the past with OpenMPI): Add the options -x LD_LIBRARY_PATH -x WM_PROJECT_DIR -x FOAM_MPI_LIBBIN to the mpirun-call. Of course this assumes that the paths are the same on all your machines __________________ Note: I don't use "Friend"-feature on this forum out of principle. Ah. And by the way: I'm not on Facebook either. So don't be offended if I don't accept your invitation/friend request

September 7, 2007, 04:28	Thanks for these tipps, I will	#8
bastil Senior Member BastiL Join Date: Mar 2009 Posts: 500 Rep Power: 13	Thanks for these tipps, I will try them out and get back to you. Nevertheless, I guess I am doing something wrong because I have to add a dictionary to the $LD_LIBRARY_PATH manually. What is wrong there?

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