OpenFOAM and Code-Saturne problem

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7 years 8 months ago #7317 by Pranav
OpenFOAM and Code-Saturne problem was created by Pranav
Greetings All,

I'm having trouble and need to resolve this error.


Error:

****************
Create time

Processing tag:2411
Starting reading points at line 3.
Read 2955092 points.

Processing tag:2412
Starting reading cells at line 5910190.
First occurrence of element type 11 for cell 1 at line 5910191
First occurrence of element type 44 for cell 70456 at line 6121556
First occurrence of element type 41 for cell 70476 at line 6121596
Read 0 cells and 3005090 boundary faces.

Processing tag:2467
Starting reading patches at line 12139181.
For group 1 named Walls trying to read 148 patch face indices.
For group 2 named Inlet trying to read 36 patch face indices.
For group 3 named Outlet trying to read 245 patch face indices.

ideasUnvToFoam: ideasUnvToFoam.C:881: int main(int, char**): Assertion `nrFaceCells[faceI] == 1 || nrFaceCells[faceI] == 2' failed.
sh: line 1: 3931 Aborted

****************

While in Code-Saturne the error is

Error:

******
SIGSEGV signal (access to forbidden memory area) intercepted !

Call stack
1: 0x7f9b4238dcd9 (libc.so.6)
2: 0x7f9b42cb5b6d (libhdf5.so.7)
3: 0x7f9b42e7ba95 (libhdf5.so.7)
4: 0x7f9b42cb50e0 (libhdf5.so.7)
5: 0x7f9b42cc4bbc (libhdf5.so.7)
6: 0x7f9b42cc53ed (libhdf5.so.7)
7: 0x7f9b42cb4d8d (libhdf5.so.7)
8: 0x7f9b42cc0e8b (libhdf5.so.7)
9: 0x7f9b42cc12f7 (libhdf5.so.7)
10: 0x7f9b42a11104 (libmedC.so.1)
11: 0x7f9b429b36ce (libmedC.so.1)
12: 0x7f9b4298988d (libmedC.so.1)
13: 0x7f9b4297f94d (libmedC.so.1)
14: 0x4304e6 (cs_preprocess)
15: 0x40ebeb (cs_preprocess)
16: 0x409fd0 (cs_preprocess)
17: 0x7f9b42325c4d (libc.so.6)
18: 0x404209 (cs_preprocess)
End of stack
******

How do I proceed?

Thanks!
Best Regards
Pranav

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7 years 8 months ago #7328 by Pranav
Replied by Pranav on topic Re: OpenFOAM and Code-Saturne problem
Hey All,

I was using a surface mesh and that could be the cause of the error. Now, trying hard to volume mesh but memory allocation error can't seem to be resolved. Physical RAM - 4GB, virtual- 10GB in Windows and 26Gb swap in ubuntu don't seem to be sufficient. Any suggestions?

Best Regards,
Pranav

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7 years 8 months ago #7330 by Joël Cugnoni
Replied by Joël Cugnoni on topic Re: OpenFOAM and Code-Saturne problem
Hi,

First of all, try to change the meshing algorithm to Netgen 1/2/3D in SALOME, I seems the most appropriate for CFD in my opinion and may be more efficient...

Then try to partition your domain to better control the mesh size: 18 million cells is big, so you could increase the mesh size on edges/faces that are far enough from the surface to get a coarser mesh in region that don't show a strong gradient of velocity.

Another option would be to partition the domain into sub volumes and mesh each volume separately. At least , I know that Code-Saturne can easily stitch multiple meshes to reassemble the full domain even if the faces are not meshed in the same way.

Or another strategy could be to mesh the domain with a different tool, like for example Netgen or GMSH for tetrahedra, Engrid for mixed tet / prisms, or OpenFOAM snappy/HexMesh (or one of its GUI like HelyxOS / Discretizer) for Hexahedral dominant meshes (need to convert geometry to STL).

Let us know how you proceed.

Cheers

Joel

Joël Cugnoni - a.k.a admin
www.caelinux.com
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7 years 8 months ago - 7 years 8 months ago #7331 by Pranav
Replied by Pranav on topic Re: OpenFOAM and Code-Saturne problem
Hey!

This is my final year engineering project and I'm dealing with a fabric which is 0.5mm. I did use Netgen 1D-2D-3D in Salome. The algorithm does a neat job optimizing lenghts of elements along the edges. My model is a flexible wing with a missing nose to facilitate RAM air inflation just like parachutes hence meshing is bound to get tricky.

I simplified the problem, decided to permute with gemoetric parametersin 2D analysis. Unfortunately the geometry couldn't be reparied in Salome (despite editing tolerences to 1e-20). Now going for a infinite-wing wind tunnel setting. The flow field is 50mx50mx0.02m (z-x-y in standard convention). Now I get another error while running the code in OpenFOAM.

Error:
"..."

Processor 0
Number of cells = 270661
Number of faces shared with processor 1 = 157
Number of faces shared with processor 2 = 277
Number of processor patches = 2
Number of processor faces = 434
Number of boundary faces = 84914

Processor 1
Number of cells = 249098
Number of faces shared with processor 0 = 157
Number of faces shared with processor 2 = 82
Number of faces shared with processor 3 = 127
Number of processor patches = 3
Number of processor faces = 366
Number of boundary faces = 119600

Processor 2
Number of cells = 272807
Number of faces shared with processor 0 = 277
Number of faces shared with processor 1 = 82
Number of processor patches = 2
Number of processor faces = 359
Number of boundary faces = 84173

Processor 3
Number of cells = 250035
Number of faces shared with processor 1 = 127
Number of processor patches = 1
Number of processor faces = 127
Number of boundary faces = 43029

Number of processor faces = 643
Max number of cells = 272807 (4.66401% above average 260650)
Max number of processor patches = 3 (50% above average 2)
Max number of faces between processors = 434 (34.9922% above average 321.5)

Time = 0


--> FOAM FATAL IO ERROR:
keyword defaultFaces is undefined in dictionary "/home/..."

file: /home/.../p::boundaryField from line 25 to line 34.

From function dictionary::subDict(const word& keyword) const
in file db/dictionary/dictionary.C at line 461.

FOAM exiting

"..."

Create time

Create mesh for time = 0

Reading field p
[1]
[1] [2]

[2]
[2] --> FOAM FATAL IO ERROR:
[2] cannot find file
[2]
[2] file: /home/.../p at line 0.
[2]
[2] From function regIOobject::readStream()
[2] in file db/regIOobject/regIOobjectRead.C at line 73.
[2]
FOAM parallel run exiting
[2]
[1] --> FOAM FATAL IO ERROR: [3]
[3]
[3] --> FOAM FATAL IO ERROR:
[3] cannot find file
[3]
[3] file: /home/.../p at line 0.
[3]
[3] From function regIOobject::readStream()
[3] in file db/regIOobject/regIOobjectRead.C at line 73.
[3]
FOAM parallel run exiting
[3]


[1] [0]
[0]
[0] --> FOAM FATAL IO ERROR:
[0] cannot find file
[0]
[0] file: /home/.../p at line 0.
[0]
[0] From function regIOobject::readStream()
[0] in file db/regIOobject/regIOobjectRead.C at line 73.
[0]
FOAM parallel run exiting
[0]
cannot find file
[1]
[1] file: /home/.../p at line 0.
[1]
[1] From function regIOobject::readStream()
[1] in file db/regIOobject/regIOobjectRead.C at line 73.
[1]
FOAM parallel run exiting
[1]
MPI_ABORT was invoked on rank 3 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.

mpirun has exited due to process rank 1 with PID 2835 on
node ... exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
[...:02833] 3 more processes have sent help message help-mpi-api.txt / mpi-abort
[...:02833] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
/*
*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 2.1.1 |
| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*
*/
Build : 2.1.1-221db2718bbb
Exec : reconstructPar
Date : Dec 30 2013
Time : 22:44:12
Host : "..."
PID : 2839
Case : /home/....
nProcs : 1
sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).
fileModificationChecking : Monitoring run-time modified files using timeStampMaster
allowSystemOperations : Disallowing user-supplied system call operations

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



--> FOAM FATAL ERROR:
No times selected

From function reconstructPar
in file reconstructPar.C at line 139.

FOAM exiting


And in CodeSaturne

Error
Code_Saturne is running
***********************

Version: 3.0.0
Path: /opt/saturne-3.0

Result directory:
/home/..../RESU/20131231-0113


Parallel code_saturne on 4 processes.


****************************
Preparing calculation data
****************************


***************************
Preprocessing calculation
***************************


**********************
Starting calculation
**********************

MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.

mpiexec.openmpi has exited due to process rank 0 with PID 4680 on
node ... exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpiexec.openmpi (as reported here).
solver script exited with status 1.

Error running the calculation.

Check code_saturne log (listing) and error* files for details.


****************************
Saving calculation results
****************************

What could be wrong?

Best Regards,
Pranav

PS:
"..." means I haven't pasted those lines here.
Last edit: 7 years 8 months ago by Pranav.

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7 years 8 months ago #7333 by Yvan Fournier
Replied by Yvan Fournier on topic Re: OpenFOAM and Code-Saturne problem
Hello,

In the case of Code_Saturne, could you post the listing an error* files, as mentioned in the error message you posted ? Could you also post the preprocessor.log file ?

Regards,

Yvan

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7 years 8 months ago - 7 years 8 months ago #7335 by Pranav
Replied by Pranav on topic Re: OpenFOAM and Code-Saturne problem
Greetings Yvan,

The error file mentioned a boundary condition error. The root of the error was that I created a geometric group -Inlet- with two faces and subsequently used this group to create a mesh group from geometry. The two aforementioned faces formed the inlet face of my rectangular flow field. The error was corrected by making each surface an inlet and greating mesh groups from gemoetry unique to each face.

However, now I hit another error,.
Error Log:

cs_sles.c:2583: Fatal error.

Jacobi: error (divergence) solving for TurbEner


Call stack:
1: 0x7f10ceb9e70b <reslin_+0x4bb> (libsaturne.so.0)
2: 0x7f10cebbd996 <invers_+0x1f6> (libsaturne.so.0)
3: 0x7f10ce9a89ed <codits_+0x14a9> (libsaturne.so.0)
4: 0x7f10cec93bf0 <turbke_+0x5e8c> (libsaturne.so.0)
5: 0x7f10ceaac8e7 <tridim_+0x4d17> (libsaturne.so.0)
6: 0x7f10ce988834 <caltri_+0x30e0> (libsaturne.so.0)
7: 0x7f10ce95f125 <cs_run+0xa35> (libsaturne.so.0)
8: 0x7f10ce95e60a <main+0x14a> (libsaturne.so.0)
9: 0x7f10ce35376d <__libc_start_main+0xed> (libc.so.6)
10: 0x4006c9 <> (cs_solver)
End of stack

preprocessor log
/opt/.../

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

code_saturne version 3.0.0 (built Thu 02 May 2013 08:04:15 AM IST)

CGNS 3.1.3 file format support
MED 3.0.6 (HDF5 1.8.9) file format support
Reading of compressed files ('.gz') with Zlib 1.2.3.4



Case configuration

Date : Tue 31 Dec 2013 06:01:46 PM IST
System : Linux 3.2.0-57-generic
Machine :
Processor : Intel(R) Core(TM) i5 CPU M 460 @ 2.53GHz
Memory : 3911508
User :
Directory : /home/...

Case name : preprocess
Mesh file : /home/...



Reading mesh from file in MED (EDF/CEA) format
Mesh file: /home/...


Mesh name: 35_0(Infinite)

Number of vertices : 254413

Warning
=======
The MED mesh contains 14677 elements of type seg2
which are ignored by the Preprocessor.

Number of faces : 331716
Family 6 : 291120
Family 7 : 4000
Family 8 : 32596
Family 9 : 2000
Family 10 : 2000
Number of cells : 1042601
Family 0 : 1042601

Wall-clock time: 0.143587 s; CPU time: 0.144009 s


Done reading mesh
Theoretical mesh size: 20.971 Mb
Theoretical current memory: 26.794 Mb
Theoretical peak memory: 61.142 Mb
Total memory used: 107.641 Mb

Domain coordinate extents:

[-2.50000e+01, -1.00000e-02, -2.50000e+01]
[ 2.50000e+01, 1.00000e-02, 2.50000e+01]
Number of elements tria3 : 331716
Number of elements tetra4 : 1042601



Defining families


Element orientation check.


End of conversion to descending connectivity
Theoretical mesh size: 50.258 Mb
Theoretical current memory: 56.080 Mb
Theoretical peak memory: 162.332 Mb
Total memory used: 229.914 Mb


Main mesh properties

Number of cells: 1042601
Number of internal faces: 1919344
Number of boundary faces: 331716
Number of vertices: 254413


Definition of face and cell families

Family 1
Group "Inlet1"
Number of boundary faces : 2000
Family 2
Group "Inlet2"
Number of boundary faces : 2000
Family 3
Group "Outlet"
Number of boundary faces : 4000
Family 4
Group "Walls"
Number of boundary faces : 291120
Family 5
Group "Wing"
Number of boundary faces : 32596
Family 5
Default family
(no group)
Number of cells : 1042601
Number of internal faces : 1919344


Write output for Kernel

Opening file: mesh_input

Wrote: "start_block:dimensions"
Wrote: "n_cells" ; Type: "u8"; Size: 1
Wrote: "n_faces" ; Type: "u8"; Size: 1
Wrote: "n_vertices" ; Type: "u8"; Size: 1
Wrote: "face_vertices_size" ; Type: "u8"; Size: 1
Wrote: "n_group_classes" ; Type: "i4"; Size: 1
Wrote: "n_group_class_props_max" ; Type: "i4"; Size: 1
Wrote: "n_groups" ; Type: "u8"; Size: 1
Wrote: "group_name_index" ; Type: "i4"; Size: 6
Wrote: "group_name" ; Type: "c "; Size: 32
Wrote: "group_class_properties" ; Type: "i4"; Size: 6
Wrote: "end_block:dimensions"
Wrote: "start_block:data"
Wrote: "face_cells" ; Type: "i4"; Size: 4502120
Wrote: "cell_group_class_id" ; Type: "i4"; Size: 1042601
Wrote: "face_group_class_id" ; Type: "i4"; Size: 2251060
Wrote: "face_vertices_index" ; Type: "u8"; Size: 2251061
Wrote: "face_vertices" ; Type: "i4"; Size: 6753180
Wrote: "vertex_coords" ; Type: "r8"; Size: 763239
Wrote: "end_block:data"
Wrote: "EOF"

Closing file: mesh_input


Time and memory summary

User CPU time (sec) : 5.17
System CPU time (sec) : 0.82
Total time (sec) : 6.00
Total CPU time / Total time : 1.00

Memory use summary:

Total memory used: 229.914 Mb
Theoretical instrumented dynamic memory: 162.332 Mb


.
.
| |
| Preprocessor finish |
| |
`
'



I'm having trouble uploading the .tar file. When I hit open, the dialog box disappears and I don't see it listed in the attachements.
What must I do to upload?

Best Regards,
Pranav
Last edit: 7 years 8 months ago by Pranav.

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