[Shijian-20]

Hi all,

I am new to 3D simulations in SU2. My problem is how to define the volumes in mesh I created. Several test cases are operated but got stuck on geometry processing. Looks like I missed something in volume markers setup. Please offer some help if possible.

Attached zip includes my configuration files and Gmsh mesh script.

Following are the error massage.

Last login: Mon May 29 11:47:48 on ttys003
ccp@MaverickdeMacBookPro ~ % cd ~/desktop/laminar_test
ccp@MaverickdeMacBookPro laminar_test % mpirun -n 6 SU2_CFD lam_NS_cylinder.cfg

-------------------------------------------------------------------------
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-------------------------------------------------------------------------

Parsing config file for zone 0

----------------- Physical Case Definition ( Zone 0 ) -------------------
Compressible Laminar Navier-Stokes' equations.
Mach number: 3.
Angle of attack (AoA): 0 deg, and angle of sideslip (AoS): 0 deg.
Reynolds number: 600000. Reference length 0.012.
No restart solution, use the values at infinity (freestream).
Dimensional simulation.
The reference area will be computed using y(2D) or z(3D) projection.
The semi-span will be computed using the max y(3D) value.
The reference length is 0 m.
Reference origin for moment evaluation is (0, 0, 0).
Surface(s) where the force coefficients are evaluated: wall.

Surface(s) plotted in the output file: wall.
Input mesh file name: 12mm_3D.su2

--------------- Space Numerical Integration ( Zone 0 ) ------------------
Roe (with entropy fix = 0.001) solver for the flow inviscid terms.
Standard Roe without low-dissipation function.
Second order integration in space, with slope limiter.
Venkatakrishnan slope-limiting method, with constant: 0.5.
The reference element size is: 1.
Average of gradients with correction (viscous flow terms).
Gradient for upwind reconstruction: Green-Gauss.
Gradient for viscous and source terms: Green-Gauss.

--------------- Time Numerical Integration ( Zone 0 ) ------------------
Unsteady simulation, dual time stepping strategy (second order in time).
Unsteady time step provided by the user (s): 1e-05.
Runge-Kutta explicit method for the flow equations.
Number of steps: 3
Alpha coefficients: 0.66667 0.66667 1
No CFL adaptation.
Courant-Friedrichs-Lewy number: 0.5

------------------ Convergence Criteria ( Zone 0 ) ---------------------
Maximum number of solver subiterations: 100.
Maximum number of physical time-steps: 100.
Begin convergence monitoring at iteration 10.
Residual minimum value: 1e-12.
Cauchy series min. value: 1e-06.
Number of Cauchy elements: 100.
Begin windowed time average at iteration 500.
Begin time convergence monitoring at iteration 510.
Time cauchy series min. value: 1e-08.
Number of Cauchy elements: 100.

-------------------- Output Information ( Zone 0 ) ----------------------
File writing frequency:
+------------------------------------+
| File| Frequency|
+------------------------------------+
| PARAVIEW| 1|
| SURFACE_PARAVIEW| 1|
+------------------------------------+
Writing the convergence history file every 0 inner iterations.
Writing the convergence history file every 1 time iterations.
Writing the screen convergence history every 1 inner iterations.
Writing the screen convergence history every 1 time iterations.
The tabular file format is CSV (.csv).
Convergence history file name: history.
Forces breakdown file name: forces_breakdown.dat.
Surface file name: surface_flow.
Volume file name: flow.
Restart file name: restart_flow.dat.

------------- Config File Boundary Information ( Zone 0 ) ---------------
+-----------------------------------------------------------------------+
| Marker Type| Marker Name|
+-----------------------------------------------------------------------+
| Far-field| inlet|
| | outlet|
| | farfield|
+-----------------------------------------------------------------------+
| Internal boundary| Fluid|
+-----------------------------------------------------------------------+
| Heat flux wall| wall|
+-----------------------------------------------------------------------+

-------------------- Output Preprocessing ( Zone 0 ) --------------------

WARNING: SURFACE_PRESSURE_DROP can only be computed for at least 2 surfaces (outlet, inlet, ...)

Info: Ignoring the following screen output fields:
RMS_NU_TILDE
Screen output fields: TIME_ITER, INNER_ITER, RMS_DENSITY, LIFT, DRAG
History output group(s): ITER, RMS_RES
Convergence field(s): RMS_DENSITY
Time Convergence field(s): TAVG_DRAG, TAVG_LIFT
Info: Ignoring the following volume output fields/groups:
NONPHYSICAL_POINTS
Volume output fields: COORDINATES, SOLUTION, PRIMITIVE, VORTEX_IDENTIFICATION, MESH_QUALITY, TIME_AVERAGE

------------------- Geometry Preprocessing ( Zone 0 ) -------------------
Three dimensional problem.
3451250 grid points before partitioning.
3125000 volume elements before partitioning.
5 surface markers.
10000 boundary elements in index 0 (Marker = wall).
2500 boundary elements in index 1 (Marker = inlet).
2500 boundary elements in index 2 (Marker = outlet).
635000 boundary elements in index 3 (Marker = farfield).
3125000 boundary elements in index 4 (Marker = Fluid).
Executing the partitioning functions.
Building the graph adjacency structure.
Calling ParMETIS... graph partitioning complete (25808 edge cuts).
Distributing ParMETIS coloring.
Rebalancing vertices.
Rebalancing volume element connectivity.
Rebalancing markers and surface elements.
[MaverickdeMacBookPro:07887] *** Process received signal ***
[MaverickdeMacBookPro:07887] Signal: Segmentation fault: 11 (11)
[MaverickdeMacBookPro:07887] Signal code: Invalid permissions (2)
[MaverickdeMacBookPro:07887] Failing at address: 0x0
[MaverickdeMacBookPro:07887] [ 0] 0 libsystem_platform.dylib 0x000000019283ea84 _sigtramp + 56
[MaverickdeMacBookPro:07887] [ 1] 0 SU2_CFD 0x0000000105101568 _ZN17CPhysicalGeometry28PartitionSurfaceConnectivi tyEP7CConfigP9CGeometryt + 1076
[MaverickdeMacBookPro:07887] [ 2] 0 SU2_CFD 0x00000001050fd2a8 _ZN17CPhysicalGeometryC2EP9CGeometryP7CConfig + 924
[MaverickdeMacBookPro:07887] [ 3] 0 SU2_CFD 0x0000000104abb12c _ZN7CDriver29Geometrical_Preprocessing_FVMEP7CConf igRPP9CGeometry + 172
[MaverickdeMacBookPro:07887] [ 4] 0 SU2_CFD 0x0000000104aaff24 _ZN7CDriver25Geometrical_PreprocessingEP7CConfigRP P9CGeometryb + 632
[MaverickdeMacBookPro:07887] [ 5] 0 SU2_CFD 0x0000000104aaebc8 _ZN7CDriverC2EPctP19ompi_communicator_tb + 1020
[MaverickdeMacBookPro:07887] [ 6] 0 SU2_CFD 0x0000000104ae3878 _ZN17CSinglezoneDriverC1EPctP19ompi_communicator_t + 16
[MaverickdeMacBookPro:07887] [ 7] 0 SU2_CFD 0x00000001047788bc main + 1712
[MaverickdeMacBookPro:07887] [ 8] 0 dyld 0x00000001924b7f28 start + 2236
[MaverickdeMacBookPro:07887] *** End of error message ***
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 0 on node MaverickdeMacBookPro exited on signal 11 (Segmentation fault: 11).
--------------------------------------------------------------------------
ccp@MaverickdeMacBookPro laminar_test %

[Shijian-20]

No worries everybody, I've fixed this problem, it happens on Gmsh 4.11.1

[jeswinjo]

Hi,

I'm getting the same problem with Gmsh 4.11.1 and mpirun.
How did you solve it?

Thanks
Jeswin

-- (Edit) Problem solved when latest release of gmsh (4.12.2) was used.