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[foam-extend.org] Problems installing foam-extend-3.2 on Ubuntu 12.04

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Old   June 21, 2016, 09:47
Default Problems installing foam-extend-3.2 on Ubuntu 12.04
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Johan Roenby
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Hello

I have followed the instructions here:

https://openfoamwiki.net/index.php/I...oam-extend-3.2
https://openfoamwiki.net/index.php/I...u#Ubuntu_12.04

to install foam-extend-3.2 on my updated and restarted Ubuntu 12.04 system machine. The compilation appears to succeed without errors including the download and installation of gcc-4.9.2.

The foamInstallationTest script reports no errors.

The problem is that a lot of the tutorials crash with a "Floating point exception (core dumped)". Others, e.g. damBreak, run fine without problems. An example of a crashing case is basic/scalarTransportFoam/pitzDaily, where the blockMesh is successfully run, but the scalarTransportFoam crashes. A checkMesh also crashes with the floating point exception, but the produced mesh looks fine in Paraview.

I have double-checked that I am not sourcing any of my OpenFOAM (vanilla) installations in my ~/.bashrc file.

When I run scalarTransportFoam with gdb, this is what I get:

Code:
dhi@argos3:~/foam/foam-extend-3.2/tutorials/basic/scalarTransportFoam/pitzDaily$ gdb scalarTransportFoam
GNU gdb (Ubuntu/Linaro 7.4-2012.04-0ubuntu2.1) 7.4-2012.04
Copyright (C) 2012 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-linux-gnu".
For bug reporting instructions, please see:
<http://bugs.launchpad.net/gdb-linaro/>...
Reading symbols from /home/dhi/foam/foam-extend-3.2/applications/bin/linux64Gcc49DPOpt/scalarTransportFoam...(no debugging symbols found)...done.
(gdb) run
Starting program: /home/dhi/foam/foam-extend-3.2/applications/bin/linux64Gcc49DPOpt/scalarTransportFoam 
warning: no loadable sections found in added symbol-file system-supplied DSO at 0x7ffff7ffa000
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
/*---------------------------------------------------------------------------*\
| =========                 |                                                 |
| \\      /  F ield         | foam-extend: Open Source CFD                    |
|  \\    /   O peration     | Version:     3.2                                |
|   \\  /    A nd           | Web:         http://www.foam-extend.org         |
|    \\/     M anipulation  | For copyright notice see file Copyright         |
\*---------------------------------------------------------------------------*/
Build    : 3.2-334ba0562a2c
Exec     : /home/dhi/foam/foam-extend-3.2/applications/bin/linux64Gcc49DPOpt/scalarTransportFoam
Date     : Jun 21 2016
Time     : 15:36:27
Host     : argos3
PID      : 5662
CtrlDict : "/home/dhi/foam/foam-extend-3.2/tutorials/basic/scalarTransportFoam/pitzDaily/system/controlDict"
Case     : /home/dhi/foam/foam-extend-3.2/tutorials/basic/scalarTransportFoam/pitzDaily
nProcs   : 1
SigFpe   : Enabling floating point exception trapping (FOAM_SIGFPE).

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Create time

Create mesh for time = 0


Program received signal SIGFPE, Arithmetic exception.
0x00007ffff52a97e1 in Foam::operator>>(Foam::Istream&, double&) () from /home/dhi/foam/foam-extend-3.2/lib/linux64Gcc49DPOpt/libfoam.so
Please, can anyone make any sense of this? I am lost and without ideas about what to try. I have tried 3 times now to compile a freshly downloaded foam-extend-3.2 using the above instructions. I would love to provide more information, but I simply don't know what to provide.

Please help!

Kind regards,
Johan

Last edited by wyldckat; September 11, 2016 at 12:36. Reason: Changed [QUOTE][/QUOTE] to [CODE][/CODE]
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Old   August 10, 2016, 08:18
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Hi Johan,

Did you find what the problem was ?

I think I've got the same issue with the compilation of foam-extend-3.2

Thanks,
Fabien
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Old   August 10, 2016, 09:17
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Hi Fabian

No, I never got it to work with Ubuntu 12.04.
I ended up upgrading my ubuntu to 14.04, in which the problem did not occur (not necessarily a painless process either - for instance getting my thinlinc remote desktop to work again in 14.04 cost me several days of work and despair until I realised that ubuntu had reverted to using the NVIDIA graphics driver which messed up my thinlinc for some reason).

Good luck, and let us know if you find a solution.

Best,
Johan
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Old   September 11, 2016, 12:52
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Greetings to all! Sorry for the late response.

I haven't tried building again foam-extend 3.2 inside an Ubuntu 12.04 VM, because I suspect that I'll simply will not be able to reproduce the same error.

Therefore, I'm guessing that this:
Quote:
Originally Posted by roenby View Post
Code:
Program received signal SIGFPE, Arithmetic exception.
0x00007ffff52a97e1 in Foam::operator>>(Foam::Istream&, double&) () from /home/dhi/foam/foam-extend-3.2/lib/linux64Gcc49DPOpt/libfoam.so
is the best hint we have so far.

May I ask you two which localization options did you choose when installing or changed preferences in Ubuntu?
I ask this because the choices of localization (keyboard settings, system language, timing and number values) may be the ones affecting the installation of foam-extend, in the sense that the mathematical operations could have been affected.


There are a few other possibilities:
  1. The shell environment might be contaminated from other environment variables. After activating the foam-extend 3.2 shell environment, please run:
    Code:
    export > log.export
    gzip < log.export > log.export.gz
    and attach the file "log.export.gz" to your next post. I would like to examine for any potential suspects, such as "LD_PRELOAD".
    You may want to first check the contents of the file "log.export" first, in case there is any sensitive data there and then run the last command again.
  2. The other possibility is whether there a library being incorrectly loaded in. Try running:
    Code:
    ldd $(which scalarTransportFoam)
    and please post what it gives you.
    • On my installation, that I have on Ubuntu 16.04, gives me this:
      Code:
          linux-vdso.so.1 =>  (0x00007ffe7850a000)
          libfiniteVolume.so => /home/ofuser/foam/foam-extend-3.2/lib/linux64Gcc49DPOpt/libfiniteVolume.so (0x00007f43a7a78000)
          liblduSolvers.so => /home/ofuser/foam/foam-extend-3.2/lib/linux64Gcc49DPOpt/liblduSolvers.so (0x00007f43a7818000)
          libfoam.so => /home/ofuser/foam/foam-extend-3.2/lib/linux64Gcc49DPOpt/libfoam.so (0x00007f43a6b00000)
          libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f43a68b8000)
          librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f43a66b0000)
          libstdc++.so.6 => /home/ofuser/foam/foam-extend-3.2/ThirdParty/packages/gcc-4.9.2/platforms/linux64Gcc49DPOpt/lib64/libstdc++.so.6 (0x00007f43a6380000)
          libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f43a6070000)
          libgcc_s.so.1 => /home/ofuser/foam/foam-extend-3.2/ThirdParty/packages/gcc-4.9.2/platforms/linux64Gcc49DPOpt/lib64/libgcc_s.so.1 (0x00007f43a5e58000)
          libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f43a5a88000)
          libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f43a5868000)
          libmeshTools.so => /home/ofuser/foam/foam-extend-3.2/lib/linux64Gcc49DPOpt/libmeshTools.so (0x00007f43a5420000)
          libmpi.so.1 => /home/ofuser/foam/foam-extend-3.2/ThirdParty/packages/openmpi-1.6.5/platforms/linux64Gcc49DPOpt/lib/libmpi.so.1 (0x00007f43a5070000)
          libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f43a4e50000)
          /lib64/ld-linux-x86-64.so.2 (0x000055973108c000)
          libdecompositionMethods.so => /home/ofuser/foam/foam-extend-3.2/lib/linux64Gcc49DPOpt/libdecompositionMethods.so (0x00007f43a4c20000)
          liblagrangian.so => /home/ofuser/foam/foam-extend-3.2/lib/linux64Gcc49DPOpt/liblagrangian.so (0x00007f43a49f8000)
          libnsl.so.1 => /lib/x86_64-linux-gnu/libnsl.so.1 (0x00007f43a47d8000)
          libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x00007f43a45d0000)
  3. Yet another possibility has to do with "libiberty", which may be contaminating the binaries somehow. Follow the steps given on this post: http://www.cfd-online.com/Forums/ope...tml#post588535 - post #7
Best regards,
Bruno
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Old   September 13, 2016, 03:01
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Johan Roenby
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Hi Bruno

Thank you very much for your suggestions. Since I worked around the problem by installing Ubuntu 14.04 (cf. post #3), I no longer have an environment for investigating the error.

Best regards,
Johan
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