trouble compiling cfMesh-cfdof on linux

A subforum specific to the development of the OpenFoam-based workbenches ( Cfd https://github.com/qingfengxia/Cfd and CfdOF https://github.com/jaheyns/CfdOF )

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peob
Posts: 4
Joined: Sat Jun 08, 2019 5:02 pm

trouble compiling cfMesh-cfdof on linux

Post by peob » Sat Jun 08, 2019 5:29 pm

I'm new to this forum and hope that someone can help me out...

I've been using cfMesh-cfdof for almost a year now without any problems. I'm using it with OpenFOAM v6 and am running on two different systems. One is using SUSE Linux Enterprise Server 12 SP3, release 12.3. The other is Ubuntu 16.04.6 LTS, release 16.04.

I recently downloaded the latest snapshot of the code from the github and tried to compile it but I got a number of messages I hadn't seen before...

for example...

wmakeLnInclude error: base directory /opt/OpenFOAM/OpenFOAM-6/src/edgeMesh/ does not exist
wmakeLnInclude: linking include files to ./lnInclude
Making dependency list for source file workflowControls.C
could not open file UList.T.H for source file utilities/workflowControls/workflowControls.C due to No such file or directory
could not open file Istream.T.H for source file utilities/workflowControls/workflowControls.C due to No such file or directory

I let the Allwmake script run its course and copied the /bin/* and /lib/* files to the respective locations in the OpenFoam-6 folders, and then gave it a try on a small, simple problem (less than 1 million cells, intersecting pipes). This ran without problems and gave me a decent grid. However, when I went to a larger, more complex problem (10 million cells, two air-swirlers), the run terminated with the following error...

Finished creating polyMesh
Mesh has :
8538693 vertices
22041902 faces
6764126 cells
Finished extracting polyMesh
Checking for irregular surface connections
Checking cells connected to surface vertices
Found 1747360 boundary faces
#0 Foam::error::printStack(Foam::Ostream&) at ??:?
#1 Foam::sigSegv::sigHandler(int) at ??:?
#2 ? in "/lib/x86_64-linux-gnu/libc.so.6"
#3 ? at checkIrregularSurfaceConnectionsFunctions.C:?
#4 ? in "/usr/lib/x86_64-linux-gnu/libgomp.so.1"
#5 ? in "/lib/x86_64-linux-gnu/libpthread.so.0"
#6 clone in "/lib/x86_64-linux-gnu/libc.so.6"
Segmentation fault
Done running cfmesh:cartesianMesh


I'm not sure what is going on here.

Any thoughts would be greatly appreciated.
BTW, I don't yet use FreeCAD. I'm currently running OpenFOAM v6 in a stand-alone mode.

thanks.
Phil

chrisb
Posts: 16858
Joined: Tue Mar 17, 2015 9:14 am

Re: trouble compiling cfMesh-cfdof on linux

Post by chrisb » Sat Jun 08, 2019 10:09 pm

Hi and welcome. I'm no CFD expert, but it may help the experts if you attach your full FreeCAD info as explained in the forum guidelines, and if you can provide a file showing this behaviour; preferably you should attach it here to the post, but if it is too large you can provide a link to a publicly available file hosting service.

peob
Posts: 4
Joined: Sat Jun 08, 2019 5:02 pm

Re: trouble compiling cfMesh-cfdof on linux

Post by peob » Sun Jun 09, 2019 1:56 am

chrisb,

Thanks for the helpful suggestions.

I'm not a FreeCAD user, so I'm not running FreeCAD and can't get the FreeCAD info. I do, however, use Oliver Oxtoby's fork of cfMesh from SourceForge, because it is the only version of cfMesh which (at the time) compiled with OpenFOAM versions 5 and 6. It also appears to be the only version on sourceforge that is regularly updated.

The files might be too big to post here, so I'll have to look into a public hosting site. I was hoping that I included the relevant sections of the files in my prior post, but perhaps I should post the entire files.

Thanks again.

Phil.

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oliveroxtoby
Posts: 279
Joined: Fri Dec 23, 2016 9:43 am
Location: South Africa

Re: trouble compiling cfMesh-cfdof on linux

Post by oliveroxtoby » Sun Jun 09, 2019 8:10 am

peob wrote:
Sat Jun 08, 2019 5:29 pm
I'm new to this forum and hope that someone can help me out...

I've been using cfMesh-cfdof for almost a year now without any problems. I'm using it with OpenFOAM v6 and am running on two different systems. One is using SUSE Linux Enterprise Server 12 SP3, release 12.3. The other is Ubuntu 16.04.6 LTS, release 16.04.

I recently downloaded the latest snapshot of the code from the github and tried to compile it but I got a number of messages I hadn't seen before...

for example...

wmakeLnInclude error: base directory /opt/OpenFOAM/OpenFOAM-6/src/edgeMesh/ does not exist
wmakeLnInclude: linking include files to ./lnInclude
Making dependency list for source file workflowControls.C
could not open file UList.T.H for source file utilities/workflowControls/workflowControls.C due to No such file or directory
could not open file Istream.T.H for source file utilities/workflowControls/workflowControls.C due to No such file or directory

I let the Allwmake script run its course and copied the /bin/* and /lib/* files to the respective locations in the OpenFoam-6 folders, and then gave it a try on a small, simple problem (less than 1 million cells, intersecting pipes). This ran without problems and gave me a decent grid. However, when I went to a larger, more complex problem (10 million cells, two air-swirlers), the run terminated with the following error...

Finished creating polyMesh
Mesh has :
8538693 vertices
22041902 faces
6764126 cells
Finished extracting polyMesh
Checking for irregular surface connections
Checking cells connected to surface vertices
Found 1747360 boundary faces
#0 Foam::error::printStack(Foam::Ostream&) at ??:?
#1 Foam::sigSegv::sigHandler(int) at ??:?
#2 ? in "/lib/x86_64-linux-gnu/libc.so.6"
#3 ? at checkIrregularSurfaceConnectionsFunctions.C:?
#4 ? in "/usr/lib/x86_64-linux-gnu/libgomp.so.1"
#5 ? in "/lib/x86_64-linux-gnu/libpthread.so.0"
#6 clone in "/lib/x86_64-linux-gnu/libc.so.6"
Segmentation fault
Done running cfmesh:cartesianMesh


I'm not sure what is going on here.

Any thoughts would be greatly appreciated.
BTW, I don't yet use FreeCAD. I'm currently running OpenFOAM v6 in a stand-alone mode.

thanks.
Phil
The errors about .T.H files are nothing to worry about. These are files that are only used in the BlueCFD compilation.

It's impossible to tell what the segfault is caused by without your input data, but I recently (last week) fixed a subtle error affecting cfMesh with OpenFOAM 6, so please could you re-try with the latest version?

peob
Posts: 4
Joined: Sat Jun 08, 2019 5:02 pm

Re: trouble compiling cfMesh-cfdof on linux

Post by peob » Sun Jun 09, 2019 2:04 pm

Thanks for the help.

I'll download the latest version from sourceforge and give it a go.

BTW, thanks for all the effort you and the community are putting into this.
I'm an old-timer from the days of FORTRAN, and never learned C++ (I'm slowly working on it), so I am not able to contribute much to the effort. However, I greatly appreciate being able to use the software.

Phil.

peob
Posts: 4
Joined: Sat Jun 08, 2019 5:02 pm

Re: trouble compiling cfMesh-cfdof on linux

Post by peob » Mon Jun 17, 2019 4:55 pm

I just downloaded the latest version of cfMesh-cfdof from the github; compiled and ran it on my test case, and I got the same error as above.

My test case happens to be proprietary, so I'll have to make a generic one to make available for examination.

Is it possible that the failure is related to the error that I get when I compile cfmesh...

wmakeLnInclude error: base directory /opt/OpenFOAM/OpenFOAM-6/src/edgeMesh/ does not exist

I did notice that with OpenFOAM-6, the "edgeMesh" directory is not at the "src" level, but is down one level inside the "meshTools" directory. Before versions 5 & 6, the "edgeMesh" directory was at the "src" level (i.e. "../src/edgeMesh"), but for some reason it is now located inside "meshTools" (i.e. ".../src/meshTools/edgeMesh").

User avatar
oliveroxtoby
Posts: 279
Joined: Fri Dec 23, 2016 9:43 am
Location: South Africa

Re: trouble compiling cfMesh-cfdof on linux

Post by oliveroxtoby » Wed Jun 26, 2019 1:48 pm

peob wrote:
Sat Jun 08, 2019 5:29 pm

Finished creating polyMesh
Mesh has :
8538693 vertices
22041902 faces
6764126 cells
Finished extracting polyMesh
Checking for irregular surface connections
Checking cells connected to surface vertices
Found 1747360 boundary faces
#0 Foam::error::printStack(Foam::Ostream&) at ??:?
#1 Foam::sigSegv::sigHandler(int) at ??:?
#2 ? in "/lib/x86_64-linux-gnu/libc.so.6"
#3 ? at checkIrregularSurfaceConnectionsFunctions.C:?
#4 ? in "/usr/lib/x86_64-linux-gnu/libgomp.so.1"
#5 ? in "/lib/x86_64-linux-gnu/libpthread.so.0"
#6 clone in "/lib/x86_64-linux-gnu/libc.so.6"
Segmentation fault
Done running cfmesh:cartesianMesh

It's possible that this has now been fixed.

Thanks for the appreciation!

Regards
Oliver

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