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Compiling with CGNS Support

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Old   January 24, 2014, 08:14
Default Compiling with CGNS Support
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Hey everybody,

I am trying to import an cgns file but keep receiving an error within the Geometry Preprocessing:
"------------------------- Geometry Preprocessing ------------------------
Setting local point and element connectivity.
Checking the numerical grid orientation.
Identifying edges and vertices.
Computing centers of gravity.
Setting the control volume structure.
Searching for the closest normal neighbors to the surfaces.
Segmentation fault (core dumped)"

the input/output information within the cfg file looks like that:
% ------------------------- INPUT/OUTPUT INFORMATION --------------------------%
%
% Mesh input file format (SU2, CGNS, NETCDF_ASCII)
MESH_FORMAT= CGNS
%
% Mesh input file
MESH_FILENAME= a.cgns
%
% Convert a CGNS mesh to SU2 format (YES, NO)
CGNS_TO_SU2= YES
%
% Converted SU2 mesh filename
NEW_SU2_FILENAME= new_mesh.su2
%
% Mesh output file
MESH_OUT_FILENAME= mesh_out.su2

But I actually don’t believe that the inp-file is the issue... Regarding to the instructions for cgns import I have installed cgnslib_3.1.4 within the SU2 directory.
(I am a noop when it comes to linux, but I am running Ubuntu and I was simple doing: ./configure -> make -> make install, which was so far that I can tell successful) and before that I have installed hdf5-1.8.12 in the root directory (same way).

Within the SU2_CFD/obj (there was no SU2_CFD/config/ directory) I have removed "-DNO_CGNS" from the Makefile but after checking Makefile.in I haven found that compiler within the c++-comp. list..

If anybody has any ideas where I went wrong I appreciate any ideas
Best Regards,
Josh
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Old   January 30, 2014, 02:17
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Francisco Palacios
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Quote:
Originally Posted by granbycools View Post
Hey everybody,

I am trying to import an cgns file but keep receiving an error within the Geometry Preprocessing:
"------------------------- Geometry Preprocessing ------------------------
Setting local point and element connectivity.
Checking the numerical grid orientation.
Identifying edges and vertices.
Computing centers of gravity.
Setting the control volume structure.
Searching for the closest normal neighbors to the surfaces.
Segmentation fault (core dumped)"

the input/output information within the cfg file looks like that:
% ------------------------- INPUT/OUTPUT INFORMATION --------------------------%
%
% Mesh input file format (SU2, CGNS, NETCDF_ASCII)
MESH_FORMAT= CGNS
%
% Mesh input file
MESH_FILENAME= a.cgns
%
% Convert a CGNS mesh to SU2 format (YES, NO)
CGNS_TO_SU2= YES
%
% Converted SU2 mesh filename
NEW_SU2_FILENAME= new_mesh.su2
%
% Mesh output file
MESH_OUT_FILENAME= mesh_out.su2

But I actually donít believe that the inp-file is the issue... Regarding to the instructions for cgns import I have installed cgnslib_3.1.4 within the SU2 directory.
(I am a noop when it comes to linux, but I am running Ubuntu and I was simple doing: ./configure -> make -> make install, which was so far that I can tell successful) and before that I have installed hdf5-1.8.12 in the root directory (same way).

Within the SU2_CFD/obj (there was no SU2_CFD/config/ directory) I have removed "-DNO_CGNS" from the Makefile but after checking Makefile.in I haven found that compiler within the c++-comp. list..

If anybody has any ideas where I went wrong I appreciate any ideas
Best Regards,
Josh
Could you please post the complete console output.

Best,
francisco
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Old   January 30, 2014, 13:01
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sure, please see attached file
Attached Files
File Type: txt SU2_log.txt (5.6 KB, 19 views)
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Old   February 12, 2014, 14:11
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Thomas D. Economon
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Hi,

It may be that the library is not correctly linked. Are you building SU2 using the ./configure -> make -> make install process? Within our configure process, we have an option to build with the CGNS library. The configure process will then create new makefiles for you automatically that have removed the -DNO_CGNS directive from all the pertinent makefiles.

Can you please verify that you are building with CGNS by checking the console output from configure or sharing your command line argument that you enter for the configure step (type './configure --help' to see all of the available configure options)?

Hope this helps,
Tom
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Old   March 25, 2014, 10:33
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you were absolutly right. I just linked one of the cgns library but finally succeeded! Thanks a lot for that

I was able to run an simple mesh (with low) quality, but when I am using a little bigger one with about 1 mio elements I receive the follwoing error:

"Successfully wrote the SU2 mesh file.
Three dimensional problem.
10346324 inner elements.
terminate called after throwing an instance of `st9bad_alloc`
what(): std::bad_alloc
Aborted (core dumped)"


any clues where that might comes from?

Last edited by granbycools; March 26, 2014 at 04:50.
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Old   March 27, 2014, 00:44
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Thomas D. Economon
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Quote:
Originally Posted by granbycools View Post
Three dimensional problem.
10346324 inner elements.
terminate called after throwing an instance of `st9bad_alloc`
what(): std::bad_alloc
Aborted (core dumped)"[/I]
Are you running on a single processor? Perhaps you have run out of memory?

Also, does the same error happen if you convert the mesh to SU2 format and then attempt the same simulation with the native SU2 mesh?
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Old   March 31, 2014, 06:52
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Hey,
does anybody know what that means when I am trying parallel computation?
best Regards,
granbycools

mpirun was unable to launch the specified application as it could not access
or execute an executable:

Executable: /home/josh/Documents/SU_CGNS/SU2/bin/SU2_DDC
Node: ubuntu

while attempting to start process rank 0.

Last edited by granbycools; April 2, 2014 at 10:01.
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