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[foam-extend.org] core dumped for foam extended 3.2 on Ubuntu 16.04

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Old   September 15, 2016, 08:26
Default core dumped for foam extended 3.2 on Ubuntu 16.04
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Janry
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Hi Foamers,

Recently I've install the foam -extended 3.2 on Ubuntu 16.04.
However, when I run the cases and tutorials, all of them crashed with no reason core dumped.
For example:

Code:
uqjqi@uqjqi:~/Desktop/work/11_09_2016_Stage$ icoFoam 
/*---------------------------------------------------------------------------*\
| =========                 |                                                 |
| \\      /  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     : icoFoam
Date     : Sep 15 2016
Time     : 22:13:06
Host     : uqjqi
PID      : 12610
CtrlDict : "/home/uqjqi/Desktop/work/11_09_2016_Stage/system/controlDict"
Case     : /home/uqjqi/Desktop/work/11_09_2016_Stage
nProcs   : 1
SigFpe   : Enabling floating point exception trapping (FOAM_SIGFPE).

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

Create mesh for time = 1.653947e-06

Floating point exception (core dumped)

and


Code:
uqjqi@uqjqi:~/Desktop/work/11_09_2016_Stage$ steadyCompressibleMRFFoam 
/*---------------------------------------------------------------------------*\
| =========                 |                                                 |
| \\      /  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     : steadyCompressibleMRFFoam
Date     : Sep 15 2016
Time     : 22:12:55
Host     : uqjqi
PID      : 12606
CtrlDict : "/home/uqjqi/Desktop/work/11_09_2016_Stage/system/controlDict"
Case     : /home/uqjqi/Desktop/work/11_09_2016_Stage
nProcs   : 1
SigFpe   : Enabling floating point exception trapping (FOAM_SIGFPE).

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

Create mesh for time = 1.653947e-06

Floating point exception (core dumped)

can anybody help me out?

Thanks!
Janry
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Old   September 17, 2016, 08:39
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Quick answer: Your description is a bit inconsistent, because you mentioned that the tutorial cases crash, but then you provide the output for a case that is not part of the tutorials.

Please provide the output you get when you run one of the foam-extend 3.2 tutorials cases.

And/or please provide the file "system/controlDict", in which I'm guessing that you have a "libs" entry there that is forcing to load libraries that were last built for another version of foam-extend or OpenFOAM.
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Old   September 17, 2016, 08:49
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Quote:
Originally Posted by wyldckat View Post
Quick answer: Your description is a bit inconsistent, because you mentioned that the tutorial cases crash, but then you provide the output for a case that is not part of the tutorials.

Please provide the output you get when you run one of the foam-extend 3.2 tutorials cases.

And/or please provide the file "system/controlDict", in which I'm guessing that you have a "libs" entry there that is forcing to load libraries that were last built for another version of foam-extend or OpenFOAM.

Hi Bruno,

Thanks for your reply!
The following is the tutorial for the axialTurbin_mixingPlane:

Code:
uqjqi@uqjqi:~/foam/foam-extend-3.2/tutorials/incompressible/MRFSimpleFoam/axialTurbine_mixingPlane$ ./Allrun 
Running blockMesh on /home/uqjqi/foam/foam-extend-3.2/tutorials/incompressible/MRFSimpleFoam/axialTurbine_mixingPlane
/*---------------------------------------------------------------------------*\
| =========                 |                                                 |
| \\      /  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     : transformPoints -scale (1 20 1)
Date     : Sep 17 2016
Time     : 22:44:15
Host     : uqjqi
PID      : 7592
CtrlDict : "/home/uqjqi/foam/foam-extend-3.2/tutorials/incompressible/MRFSimpleFoam/axialTurbine_mixingPlane/system/controlDict"
Case     : /home/uqjqi/foam/foam-extend-3.2/tutorials/incompressible/MRFSimpleFoam/axialTurbine_mixingPlane
nProcs   : 1
SigFpe   : Enabling floating point exception trapping (FOAM_SIGFPE).

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

Scaling points by (1 20 1)
Writing points into directory "/home/uqjqi/foam/foam-extend-3.2/tutorials/incompressible/MRFSimpleFoam/axialTurbine_mixingPlane/constant/polyMesh"

/*---------------------------------------------------------------------------*\
| =========                 |                                                 |
| \\      /  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     : transformPoints -cylToCart ((0 0 0) (0 0 1) (1 0 0))
Date     : Sep 17 2016
Time     : 22:44:15
Host     : uqjqi
PID      : 7593
CtrlDict : "/home/uqjqi/foam/foam-extend-3.2/tutorials/incompressible/MRFSimpleFoam/axialTurbine_mixingPlane/system/controlDict"
Case     : /home/uqjqi/foam/foam-extend-3.2/tutorials/incompressible/MRFSimpleFoam/axialTurbine_mixingPlane
nProcs   : 1
SigFpe   : Enabling floating point exception trapping (FOAM_SIGFPE).

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

Writing points into directory "/home/uqjqi/foam/foam-extend-3.2/tutorials/incompressible/MRFSimpleFoam/axialTurbine_mixingPlane/constant/polyMesh"

Running setSet on /home/uqjqi/foam/foam-extend-3.2/tutorials/incompressible/MRFSimpleFoam/axialTurbine_mixingPlane
Running setsToZones on /home/uqjqi/foam/foam-extend-3.2/tutorials/incompressible/MRFSimpleFoam/axialTurbine_mixingPlane
Running MRFSimpleFoam on /home/uqjqi/foam/foam-extend-3.2/tutorials/incompressible/MRFSimpleFoam/axialTurbine_mixingPlane
uqjqi@uqjqi:~/foam/foam-extend-3.2/tutorials/incompressible/MRFSimpleFoam/axialTurbine_mixingPlane$
And the log for the solvers:

Code:
/*---------------------------------------------------------------------------*\
| =========                 |                                                 |
| \\      /  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     : MRFSimpleFoam
Date     : Sep 17 2016
Time     : 22:44:16
Host     : uqjqi
PID      : 7599
CtrlDict : "/home/uqjqi/foam/foam-extend-3.2/tutorials/incompressible/MRFSimpleFoam/axialTurbine_mixingPlane/system/controlDict"
Case     : /home/uqjqi/foam/foam-extend-3.2/tutorials/incompressible/MRFSimpleFoam/axialTurbine_mixingPlane
nProcs   : 1
SigFpe   : Enabling floating point exception trapping (FOAM_SIGFPE).

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

Create mesh for time = 0

Floating point exception (core dumped)
Same conditions occuring everywhere...
Another is the axialTurbin_ggi:

Code:
uqjqi@uqjqi:~/foam/foam-extend-3.2/tutorials/incompressible/MRFSimpleFoam/axialTurbine_ggi$ ./Allrun 
Running blockMesh on /home/uqjqi/foam/foam-extend-3.2/tutorials/incompressible/MRFSimpleFoam/axialTurbine_ggi
/*---------------------------------------------------------------------------*\
| =========                 |                                                 |
| \\      /  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     : transformPoints -scale (1 20 1)
Date     : Sep 17 2016
Time     : 22:48:16
Host     : uqjqi
PID      : 7811
CtrlDict : "/home/uqjqi/foam/foam-extend-3.2/tutorials/incompressible/MRFSimpleFoam/axialTurbine_ggi/system/controlDict"
Case     : /home/uqjqi/foam/foam-extend-3.2/tutorials/incompressible/MRFSimpleFoam/axialTurbine_ggi
nProcs   : 1
SigFpe   : Enabling floating point exception trapping (FOAM_SIGFPE).

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

Scaling points by (1 20 1)
Writing points into directory "/home/uqjqi/foam/foam-extend-3.2/tutorials/incompressible/MRFSimpleFoam/axialTurbine_ggi/constant/polyMesh"

/*---------------------------------------------------------------------------*\
| =========                 |                                                 |
| \\      /  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     : transformPoints -cylToCart ((0 0 0) (0 0 1) (1 0 0))
Date     : Sep 17 2016
Time     : 22:48:16
Host     : uqjqi
PID      : 7812
CtrlDict : "/home/uqjqi/foam/foam-extend-3.2/tutorials/incompressible/MRFSimpleFoam/axialTurbine_ggi/system/controlDict"
Case     : /home/uqjqi/foam/foam-extend-3.2/tutorials/incompressible/MRFSimpleFoam/axialTurbine_ggi
nProcs   : 1
SigFpe   : Enabling floating point exception trapping (FOAM_SIGFPE).

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

Floating point exception (core dumped)
Running setSet on /home/uqjqi/foam/foam-extend-3.2/tutorials/incompressible/MRFSimpleFoam/axialTurbine_ggi
Running setsToZones on /home/uqjqi/foam/foam-extend-3.2/tutorials/incompressible/MRFSimpleFoam/axialTurbine_ggi
Running MRFSimpleFoam on /home/uqjqi/foam/foam-extend-3.2/tutorials/incompressible/MRFSimpleFoam/axialTurbine_ggi
Thanks!
Janry
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Old   September 17, 2016, 09:28
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Quick answer: Please run this command:
Code:
ldd $(which MRFSimpleFoam)
and let me know of what it outputs.

In addition, the output of the following command is also useful:
Code:
export
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Old   September 17, 2016, 22:26
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Quote:
Originally Posted by wyldckat View Post
Quick answer: Please run this command:
Code:
ldd $(which MRFSimpleFoam)
and let me know of what it outputs.

In addition, the output of the following command is also useful:
Code:
export
Hi Bruno,
Thanks for your reply.
The following is the output when running the ldd $(which MRFSimpleFoam):
Code:
uqjqi@uqjqi:~/foam/foam-extend-3.2/tutorials/incompressible/MRFSimpleFoam/axialTurbine_ggi$ ldd $(which MRFSimpleFoam)        linux-vdso.so.1 =>  (0x00007f0f492e1000)
    libincompressibleRASModels.so => /home/uqjqi/foam/foam-extend-3.2/lib/linux64GccDPOpt/libincompressibleRASModels.so (0x00007f0f48d85000)
    libincompressibleTransportModels.so => /home/uqjqi/foam/foam-extend-3.2/lib/linux64GccDPOpt/libincompressibleTransportModels.so (0x00007f0f48b03000)
    libfiniteVolume.so => /home/uqjqi/foam/foam-extend-3.2/lib/linux64GccDPOpt/libfiniteVolume.so (0x00007f0f46c03000)
    liblduSolvers.so => /home/uqjqi/foam/foam-extend-3.2/lib/linux64GccDPOpt/liblduSolvers.so (0x00007f0f4699e000)
    libfoam.so => /home/uqjqi/foam/foam-extend-3.2/lib/linux64GccDPOpt/libfoam.so (0x00007f0f45c58000)
    libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f0f45a29000)
    librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f0f45820000)
    libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f0f4549e000)
    libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f0f45195000)
    libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f0f44f7e000)
    libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f0f44bb5000)
    libincompressibleTurbulenceModel.so => /home/uqjqi/foam/foam-extend-3.2/lib/linux64GccDPOpt/libincompressibleTurbulenceModel.so (0x00007f0f4495a000)
    libmeshTools.so => /home/uqjqi/foam/foam-extend-3.2/lib/linux64GccDPOpt/libmeshTools.so (0x00007f0f444ff000)
    libmpi.so.1 => /home/uqjqi/foam/foam-extend-3.2/ThirdParty/packages/openmpi-1.6.5/platforms/linux64GccDPOpt/lib/libmpi.so.1 (0x00007f0f4415f000)
    libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f0f43f44000)
    libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f0f43d27000)
    /lib64/ld-linux-x86-64.so.2 (0x000055c53f341000)
    libdecompositionMethods.so => /home/uqjqi/foam/foam-extend-3.2/lib/linux64GccDPOpt/libdecompositionMethods.so (0x00007f0f43afb000)
    liblagrangian.so => /home/uqjqi/foam/foam-extend-3.2/lib/linux64GccDPOpt/liblagrangian.so (0x00007f0f438da000)
    libnuma.so.1 => /usr/lib/x86_64-linux-gnu/libnuma.so.1 (0x00007f0f436cf000)
    libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x00007f0f434cb000)
Thanks again!
Janry
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Old   September 18, 2016, 16:17
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Quick answer: ldd did not show anything out of the ordinary. It's linking to "libnuma.so", which I wasn't familiar with, but I guess it's due to the machine you have, namely if you have a multi-socket workstation/server.

Nonetheless, you forgot to also post the output from the export command that I asked for. If the output is too long, you can run:
Code:
export > log.export
gzip < log.export > log.export.gz
and then attach the file "log.export.gz" to your next post.
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Old   September 18, 2016, 19:53
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Quote:
Originally Posted by wyldckat View Post
Quick answer: ldd did not show anything out of the ordinary. It's linking to "libnuma.so", which I wasn't familiar with, but I guess it's due to the machine you have, namely if you have a multi-socket workstation/server.

Nonetheless, you forgot to also post the output from the export command that I asked for. If the output is too long, you can run:
Code:
export > log.export
gzip < log.export > log.export.gz
and then attach the file "log.export.gz" to your next post.

Hi Bruno,

Thanks for your reply.
The export output is attached, please see the attachment.
log.export.gz
Thanks!
Janry
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Old   September 26, 2016, 18:34
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Quick answer: I took a look into this during this past weekend and I wasn't able to figure out a reason for this problem that you're getting.
My best guess right now is that there is something installed in the user folders.
Try the following commands, to see if they list any suspicious libraries of applications:
Code:
ls -l $FOAM_USER_LIBBIN
ls -l $FOAM_USER_APPBIN
Because beyond this, the only other thing that comes to mind is that the compiler messed up somehow...

Although, now that I think about it, what exact installation instructions did you follow?
And did you make any changes besides what the instructions indicated?
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Old   September 26, 2016, 21:19
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Quote:
Originally Posted by wyldckat View Post
Quick answer: I took a look into this during this past weekend and I wasn't able to figure out a reason for this problem that you're getting.
My best guess right now is that there is something installed in the user folders.
Try the following commands, to see if they list any suspicious libraries of applications:
Code:
ls -l $FOAM_USER_LIBBIN
ls -l $FOAM_USER_APPBIN
Because beyond this, the only other thing that comes to mind is that the compiler messed up somehow...

Although, now that I think about it, what exact installation instructions did you follow?
And did you make any changes besides what the instructions indicated?

Hi Bruno,

Thanks for your reply.
Yes I think I use multiple gcc version when I installed it.
Because the default gcc version for 16.04 is 5.4, but the SIG density based solver requires gcc 4.6 to compile it.

So, after I install foam extend 3.1, I shifted to gcc 4.6 to compile the SIG density based solver, then, failed.

I think all the foam extend or the third party solvers should be installed within constant version of gcc and g++...


Thanks very much!
Janry
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Old   September 27, 2016, 16:39
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Quote:
Originally Posted by qjh888 View Post
So, after I install foam extend 3.1, I shifted to gcc 4.6 to compile the SIG density based solver, then, failed.

I think all the foam extend or the third party solvers should be installed within constant version of gcc and g++...
Quick answer: Yes, it's strongly advisable to use the same GCC version for building everything... I had no way to diagnose that this was a possible reason, unless I had done some wild guessing ... out of a few more dozen possible reasons...

Anyway, it's excellent that you've managed to pick up the origin of the problem!
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