CGNS: error checking file type

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mmagain
Posts: 10
Joined: Mon Jan 15, 2024 9:20 pm

CGNS: error checking file type

Post by mmagain »

Hi,

I am following the "full domain" tutorial. More specifically, the first case. When I arrive at the computation stage. I get the following error displayed :

Code: Select all

                      code_saturne
                      ============

Version:   7.0.6-patch
Path:      /home/fuxin/Code_Saturne/7.0.6-patch/code_saturne-7.0.6-patch/arch/Linux_x86_64

Result directory:
  /home/fuxin/Desktop/Code_Saturne_Tutorials/full_domain/case1/RESU/20240412-0235

Copying base setup data
-----------------------

Compiling and linking user-defined functions
--------------------------------------------

Preparing calculation data
--------------------------

 Single processor code_saturne simulation.

Preprocessing calculation
-------------------------

Post-calculation operations
---------------------------

Error running the preprocessor.
Check the preprocessor.log file for details.

Error in preprocessing stage.

Error in preprocessing stage.
Inspecting the logs, I see this :

Code: Select all

/home/fuxin/Code_Saturne/7.0.6-patch/code_saturne-7.0.6-patch/arch/Linux_x86_64/libexec/code_saturne/cs_preprocess 
--out mesh_input/mesh_03.csm --log preprocessor_03.log --case preprocessor_03 
/home/fuxin/Desktop/Code_Saturne_Tutorials/full_domain/MESH/vessel.cgns 

  .------------------------------.
  |                              |
  |   Code_Saturne Preprocessor  |
  |                              |
  `------------------------------'

  code_saturne version 7.0.6-patch   (built Thu Jan 11 18:43:35 2024)

  CGNS 4.1.0 file format support
  MED 4.1.1 (HDF5 1.10.6) file format support
  Reading of compressed files ('.gz') with Zlib 1.2.11



Case configuration
------------------

  Date                : Fri Apr 12 02:35:31 2024
  System              : Linux 5.15.0-102-generic
  Machine             : fuxin
  Processor           : AMD Ryzen 7 5800X 8-Core Processor
  Memory              : 16275496
  User                : fuxin (fuxin)
  Directory           : /home/fuxin/Desktop/Code_Saturne_Tutorials/full_domain/case1/RESU/20240412-0235

  Case name           : preprocessor_03
  Mesh file           : /home/fuxin/Desktop/Code_Saturne_Tutorials/full_domain/MESH/vessel.cgns



Reading mesh from file in CGNS format
----------------------
  Mesh file: /home/fuxin/Desktop/Code_Saturne_Tutorials/full_domain/MESH/vessel.cgns



Error in preprocessor execution
===============================

/home/fuxin/Documents/saturne-src/code_saturne/preprocessor/pre-post/ecs_pre_cgns.c:250: Fatal error.

CGNS: error checking file type "/home/fuxin/Desktop/Code_Saturne_Tutorials/full_domain/MESH/vessel.cgns":
no CGNS error reported


Call stack 
   1: 0x563e1a52017f <ecs_pre_cgns__lit_maillage+0x41af> (cs_preprocess)
   2: 0x563e1a5175b3 <ecs_pre__lit_maillage+0x103>    (cs_preprocess)
   3: 0x563e1a50f390 <main+0xa0>                      (cs_preprocess)
   4: 0x7fdb647b3083 <__libc_start_main+0xf3>         (libc.so.6)
   5: 0x563e1a50fbde <_start+0x2e>                    (cs_preprocess)
End of stack
Any idea on how to solve this problem? I haven't seen anything related to this issue on this forum. The other two meshes in .med file type are preprocessing correctly. Only vessel.cgns seems to cause the issue.

If it can be of any information, I did the simple junction tutorial without any problems.

Thank you in advance,

Michael
Yvan Fournier
Posts: 4107
Joined: Mon Feb 20, 2012 3:25 pm

Re: CGNS: error checking file type

Post by Yvan Fournier »

Hello,

This error means a CGNS library call (cg_is_cgns) checking that the file is indeed a CGNS file has failed.

This could be a bug in the CGNS library (we have tested 4.1.2, 4.4.0, and some 4.3 versions I think, but I am not sure about 4.1.0), and install issue (if CGNS is not built with HDF5 support), or a corrupted file.

If you have the CGNS tools installed, can you open the file using cgnsview or cgnscheck) ? That would help guide further checks.

Best regards,

Yvan
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