[foam-extend.org] foam-extend 3.2 on Ubuntu 12.04, Floating point exception for tutorials

arsalan.dryi · November 10, 2016, 20:26

Dear Foamers,
Recently I've installed foam extend 3.2 on Ubuntu 12.04, a long time installation procedure!
But I get floating point exception (core dumped) when I run tutorial cases in the surfaceTracking folder!
Also I'd installed foam-extend 3.1 a long time ago and I didn't have this problem!
For example, here is the results of hydrofoil tutorial after Allrun executation:

log.makeFaMesh:

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-a4e7bf3b15c0
Exec     : makeFaMesh
Date     : Nov 11 2016
Time     : 03:34:02
Host     : arsalan-VPCSE2EFX
PID      : 6655
CtrlDict : "/home/arsalan/foam/arsalan-3.2/run/hydrofoil/system/controlDict"
Case     : /home/arsalan/foam/arsalan-3.2/run/hydrofoil
nProcs   : 1
SigFpe   : Enabling floating point exception trapping (FOAM_SIGFPE).

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

Create mesh for time = 0

Floating point exception (core dumped)

log.interTrackFoam:

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-a4e7bf3b15c0
Exec     : interTrackFoam
Date     : Nov 11 2016
Time     : 03:34:02
Host     : arsalan-VPCSE2EFX
PID      : 6657
CtrlDict : "/home/arsalan/foam/arsalan-3.2/run/hydrofoil/system/controlDict"
Case     : /home/arsalan/foam/arsalan-3.2/run/hydrofoil
nProcs   : 1
SigFpe   : Enabling floating point exception trapping (FOAM_SIGFPE).

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

Create dynamic mesh for time = 0

Selecting dynamicFvMesh dynamicMotionSolverFvMesh
Floating point exception (core dumped)

For more detailed information, here is the result of "ldd $(which interTrackFoam)" command:

Code:

	linux-vdso.so.1 =>  (0x00007ffe944ec000)
	libfreeSurface.so => /home/arsalan/foam/foam-extend-3.2/lib/linux64Gcc49DPOpt/libfreeSurface.so (0x00007fd32c97e000)
	libdynamicFvMesh.so => /home/arsalan/foam/foam-extend-3.2/lib/linux64Gcc49DPOpt/libdynamicFvMesh.so (0x00007fd32c618000)
	libdynamicMesh.so => /home/arsalan/foam/foam-extend-3.2/lib/linux64Gcc49DPOpt/libdynamicMesh.so (0x00007fd32c1e8000)
	libmeshTools.so => /home/arsalan/foam/foam-extend-3.2/lib/linux64Gcc49DPOpt/libmeshTools.so (0x00007fd32bd8f000)
	libfiniteVolume.so => /home/arsalan/foam/foam-extend-3.2/lib/linux64Gcc49DPOpt/libfiniteVolume.so (0x00007fd329e8d000)
	libfiniteArea.so => /home/arsalan/foam/foam-extend-3.2/lib/linux64Gcc49DPOpt/libfiniteArea.so (0x00007fd329837000)
	liblduSolvers.so => /home/arsalan/foam/foam-extend-3.2/lib/linux64Gcc49DPOpt/liblduSolvers.so (0x00007fd3295d3000)
	libmesquite.so.0 => /home/arsalan/foam/foam-extend-3.2/ThirdParty/packages/mesquite-2.1.2/platforms/linux64Gcc49DPOpt/lib/libmesquite.so.0 (0x00007fd32921d000)
	libfoam.so => /home/arsalan/foam/foam-extend-3.2/lib/linux64Gcc49DPOpt/libfoam.so (0x00007fd3284d5000)
	libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007fd3282d1000)
	librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007fd3280c9000)
	libstdc++.so.6 => /home/arsalan/foam/foam-extend-3.2/ThirdParty/packages/gcc-4.9.2/platforms/linux64Gcc49DPOpt/lib64/libstdc++.so.6 (0x00007fd327d9d000)
	libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007fd327aa1000)
	libgcc_s.so.1 => /home/arsalan/foam/foam-extend-3.2/ThirdParty/packages/gcc-4.9.2/platforms/linux64Gcc49DPOpt/lib64/libgcc_s.so.1 (0x00007fd32788b000)
	libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fd3274cd000)
	libtetFiniteElement.so => /home/arsalan/foam/foam-extend-3.2/lib/linux64Gcc49DPOpt/libtetFiniteElement.so (0x00007fd326e92000)
	libtetMotionSolver.so => /home/arsalan/foam/foam-extend-3.2/lib/linux64Gcc49DPOpt/libtetMotionSolver.so (0x00007fd326c28000)
	libdecompositionMethods.so => /home/arsalan/foam/foam-extend-3.2/lib/linux64Gcc49DPOpt/libdecompositionMethods.so (0x00007fd3269fd000)
	libsolidBodyMotion.so => /home/arsalan/foam/foam-extend-3.2/lib/linux64Gcc49DPOpt/libsolidBodyMotion.so (0x00007fd3267bd000)
	libfvMotionSolver.so => /home/arsalan/foam/foam-extend-3.2/lib/linux64Gcc49DPOpt/libfvMotionSolver.so (0x00007fd3263d9000)
	libRBFMotionSolver.so => /home/arsalan/foam/foam-extend-3.2/lib/linux64Gcc49DPOpt/libRBFMotionSolver.so (0x00007fd3261c7000)
	liblagrangian.so => /home/arsalan/foam/foam-extend-3.2/lib/linux64Gcc49DPOpt/liblagrangian.so (0x00007fd325fa6000)
	libmpi.so.1 => /home/arsalan/foam/foam-extend-3.2/ThirdParty/packages/openmpi-1.6.5/platforms/linux64Gcc49DPOpt/lib/libmpi.so.1 (0x00007fd325c06000)
	libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007fd3259ef000)
	/lib64/ld-linux-x86-64.so.2 (0x00007fd32cde1000)
	libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007fd3257d2000)
	libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x00007fd3255cf000)

Also the attachment contains result of "export" command.

Finally, the installation procedure which I've passed is as follows:
1)

Code:

sudo apt-get update

2)

Code:

sudo apt-get install git-core build-essential binutils-dev flex \
bison zlib1g-dev qt4-dev-tools libqt4-dev libncurses5-dev \
libxt-dev rpm mercurial graphviz python python-dev

3)

Code:

cd ~/foam/foam-extend-3.2
 
echo export WM_COMPILER=Gcc49 >> etc/prefs.sh
echo export WM_THIRD_PARTY_USE_GCC_492=1  >> etc/prefs.sh
echo export compilerInstall=FOAM >> etc/prefs.sh
 
source etc/bashrc

4)

Code:

cd ~
mkdir foam
cd foam
git clone git://git.code.sf.net/p/foam-extend/foam-extend-3.2 foam-extend-3.2

5)

Code:

cd ~/foam/foam-extend-3.2
source etc/bashrc
 
echo "alias fe32='source \$HOME/foam/foam-extend-3.2/etc/bashrc'" >> $HOME/.bashrc

6)

Code:

export QT_BIN_DIR=/usr/bin/qmake-qt4
echo "export QT_BIN_DIR=$QT_BIN_DIR" >> etc/prefs.sh

7)

Code:

export CUDA_ARCH=sm_30
echo "export CUDA_ARCH=sm_30" >> etc/prefs.sh

8)

Code:

./Allwmake.firstInstall

Sorry for the long post, but I tried to give a detailed information about my problem for a better solution.

Any help will be appreciated,
Regards,
Arsalan.

wyldckat · November 13, 2016, 13:52

Quick answer: This seemed fairly familiar... the following thread accounts something very similar: http://www.cfd-online.com/Forums/ope...u-16-04-a.html

Many thanks for all of the details! Nonetheless, my best guess is that the foam-extend 3.1 was still partially loaded in when you build foam-extend 3.2?
Did you start with a clean shell environment (no OpenFOAM/foam-extend environment loaded in)?

Have you tried the simpler tutorial cases? For example "incompressible/icoFoam/cavity".

In addition, what do the following commands give you when you have foam-extend 3.2 environment loaded?

Code:

gcc --version
g++ --version

And do you really have the CUDA compiler stack installed?

arsalan.dryi · November 13, 2016, 19:04

Dear Bruno,
Thanks for your replay. About the problem,

Quote:

Originally Posted by wyldckat

Many thanks for all of the details! Nonetheless, my best guess is that the foam-extend 3.1 was still partially loaded in when you build foam-extend 3.2?
Did you start with a clean shell environment (no OpenFOAM/foam-extend environment loaded in)?

Mmm, I don't remember this, usually I use a clean shell environment for new purposes, but I can't say this with certainty.

Quote:

Originally Posted by wyldckat

Have you tried the simpler tutorial cases? For example "incompressible/icoFoam/cavity".

I tried them after your suggestion, some of them works likes:
cavity (icoFoam), damBreak (interFoam), sloshingTank2D (interDyMFoam), sloshing2D and ramp (interTrackFoam)
and some not, for example:
mixerVessel2D (MRFInterFoam), hydrofoil (interTrackFoam), bubble2D (bubbleInterTrackFoam).

Quote:

Originally Posted by wyldckat

In addition, what do the following commands give you when you have foam-extend 3.2 environment loaded?

Code:

gcc --version
g++ --version

Both of them says the same version of 4.9.2 for gcc and g++.

Quote:

Originally Posted by wyldckat

And do you really have the CUDA compiler stack installed?

Nope, just put this step since it's set to optionally in the wiki installation page.

Thanks for your time and helps.
Regards,
Arsalan.

wyldckat · November 13, 2016, 19:48

Hi Arsalan,

It feels like something is missing in your description or maybe I'm not seeing a clue that is already present in the details you've given.

A few more questions:

Did you need to run Allwmake.firstInstall more than once?
How much RAM does your machine have? When in doubt, you can run:
Code:
```
free -h
```
- Along with this, how many cores? You can check by running:
  Code:
```
lscpu
```
  E.g. the following lines tells us the main details about core distribution:
  Code:
```
CPU(s):                4
On-line CPU(s) list:   0-3
Thread(s) per core:    2
Core(s) per socket:    2
Socket(s):             1
NUMA node(s):          1
```
When you described the installation steps, did you really do steps #3 and #4 in that order? Or did you do #4 before #3?
Did you notice or have any other problems when trying to build foam-extend 3.2?

I ask these questions, because any of these can have a considerable impact on the resulting build as well, because the system's GCC may have been used to build at least part of foam-extend, which would conflict with the remaining build that was done with GCC 4.9.

Best regards,
Bruno

arsalan.dryi · November 14, 2016, 04:05

Hi Bruno,
Many thanks for your fast replay.

Quote:

Originally Posted by wyldckat

Hi Arsalan,
1. Did you need to run Allwmake.firstInstall more than once?

No I ran it only once, maybe I should run it for a second time if helps?

Quote:

2. How much RAM does your machine have? When in doubt, you can run:

Code:

free -h

Actually --h is an invalid option for free in my machine, the results of free --m (m for show output in MB) is as follows:

Code:

             total       used       free     shared    buffers     cached
Mem:          5885       1840       4045          0        120        807
-/+ buffers/cache:        912       4973
Swap:         5243          0       5243

Quote:

Along with this, how many cores? You can check by running:

Code:

lscpu

Well, the output of lscpu is shown below:

Code:

Architecture:          x86_64
CPU op-mode(s):        32-bit, 64-bit
Byte Order:            Little Endian
CPU(s):                4
On-line CPU(s) list:   0-3
Thread(s) per core:    2
Core(s) per socket:    2
Socket(s):             1
NUMA node(s):          1
Vendor ID:             GenuineIntel
CPU family:            6
Model:                 42
Stepping:              7
CPU MHz:               2801.000
BogoMIPS:              5587.04
Virtualization:        VT-x
L1d cache:             32K
L1i cache:             32K
L2 cache:              256K
L3 cache:              4096K
NUMA node0 CPU(s):     0-3

Quote:

3. When you described the installation steps, did you really do steps #3 and #4 in that order? Or did you do #4 before #3?
4. Did you notice or have any other problems when trying to build foam-extend 3.2?

I did step #3 before step #4, I'm sure about this. And I didn't have other problems at the building procedure.
Anyway, I'm ready for starting a new clean installation if only this could fix the problem.

Thanks in advance.
Regards,
Arsalan.

wyldckat · November 14, 2016, 18:16

Quote:

Originally Posted by arsalan.dryi

I did step #3 before step #4, I'm sure about this. And I didn't have other problems at the building procedure.
Anyway, I'm ready for starting a new clean installation if only this could fix the problem.

Quick answer: I don't see any major limitations regarding RAM and CPU, therefore I'm guessing that the problem was because step #3 was done before #4, which resulted in the problem you're having right now.

I'm sad to say that it does seem to be best that you start over the build from a clean installation. It's safer that way.

arsalan.dryi · November 14, 2016, 18:27

Dear Bruno,

Quote:

Originally Posted by wyldckat

Quick answer: I don't see any major limitations regarding RAM and CPU, therefore I'm guessing that the problem was because step #3 was done before #4, which resulted in the problem you're having right now.

I'm sad to say that it does seem to be best that you start over the build from a clean installation. It's safer that way.

Okay, is there anything that I should do for a new clean installation?! Except for starting with a clean shell environment!

Many thanks for your endless helps, it's really warming for us to have you in the forum.
Regards,
Arsalan.

wyldckat · November 14, 2016, 18:33

Quote:

Originally Posted by arsalan.dryi

Okay, is there anything that I should do for a new clean installation?! Except for starting with a clean shell environment!

I wrote about that a few years ago here: http://openfoamwiki.net/index.php/FA...ve_OpenFOAM.3F

November 13, 2016, 13:52		#2
wyldckat Retired Super Moderator Bruno Santos Join Date: Mar 2009 Location: Lisbon, Portugal Posts: 10,981 Blog Entries: 45 Rep Power: 128	Quick answer: This seemed fairly familiar... the following thread accounts something very similar: http://www.cfd-online.com/Forums/ope...u-16-04-a.html Many thanks for all of the details! Nonetheless, my best guess is that the foam-extend 3.1 was still partially loaded in when you build foam-extend 3.2? Did you start with a clean shell environment (no OpenFOAM/foam-extend environment loaded in)? Have you tried the simpler tutorial cases? For example "incompressible/icoFoam/cavity". In addition, what do the following commands give you when you have foam-extend 3.2 environment loaded? Code: gcc --version g++ --version And do you really have the CUDA compiler stack installed? arsalan.dryi likes this. __________________ OpenFOAM: FAQ \| Getting started Forum: How to get help, to post code/output and forum guide Read this before sending me PM

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November 13, 2016, 19:48		#4
wyldckat Retired Super Moderator Bruno Santos Join Date: Mar 2009 Location: Lisbon, Portugal Posts: 10,981 Blog Entries: 45 Rep Power: 128	Hi Arsalan, It feels like something is missing in your description or maybe I'm not seeing a clue that is already present in the details you've given. A few more questions: Did you need to run Allwmake.firstInstall more than once? How much RAM does your machine have? When in doubt, you can run: Code: free -h Along with this, how many cores? You can check by running: Code: lscpu E.g. the following lines tells us the main details about core distribution: Code: CPU(s): 4 On-line CPU(s) list: 0-3 Thread(s) per core: 2 Core(s) per socket: 2 Socket(s): 1 NUMA node(s): 1 When you described the installation steps, did you really do steps #3 and #4 in that order? Or did you do #4 before #3? Did you notice or have any other problems when trying to build foam-extend 3.2? I ask these questions, because any of these can have a considerable impact on the resulting build as well, because the system's GCC may have been used to build at least part of foam-extend, which would conflict with the remaining build that was done with GCC 4.9. Best regards, Bruno