[shreyash08@]

Hi,

I am trying to run the same SU2 files after a long time. The files were originally run successfully using SU2 version 7.2.0. Now I am trying to run the files using the version 7.5.1 (configuration file is attached below). When I do that, the SU2 process gets killed after "Initialize Jacobian structure (Navier-Stokes). MG level:0." I would appreciate any help in fixing this issue. Here is what I get on the screen when I run the files:

-------------------------------------------------------------------------
| ___ _ _ ___ |
| / __| | | |_ ) Release 7.5.1 "Blackbird" |
| \__ \ |_| |/ / |
| |___/\___//___| Suite (Computational Fluid Dynamics Code) |
| |
-------------------------------------------------------------------------
| SU2 Project Website: https://su2code.github.io |
| |
| The SU2 Project is maintained by the SU2 Foundation |
| (http://su2foundation.org) |
-------------------------------------------------------------------------
| Copyright 2012-2023, SU2 Contributors |
| |
| SU2 is free software; you can redistribute it and/or |
| modify it under the terms of the GNU Lesser General Public |
| License as published by the Free Software Foundation; either |
| version 2.1 of the License, or (at your option) any later version. |
| |
| SU2 is distributed in the hope that it will be useful, |
| but WITHOUT ANY WARRANTY; without even the implied warranty of |
| MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
| Lesser General Public License for more details. |
| |
| You should have received a copy of the GNU Lesser General Public |
| License along with SU2. If not, see <http://www.gnu.org/licenses/>. |
-------------------------------------------------------------------------

Parsing config file for zone 0

----------------- Physical Case Definition ( Zone 0 ) -------------------
Compressible RANS equations.
Turbulence model: Spalart-Allmaras-noft2
Hybrid RANS/LES: No Hybrid RANS/LES
Mach number: 0.745.
Angle of attack (AoA): 0 deg, and angle of sideslip (AoS): 0 deg.
Reynolds number: 5.8622e+06. Reference length 1.
No restart solution, use the values at infinity (freestream).
Dimensional simulation.
The reference area is 1 m^2.
The semi-span will be computed using the max y(3D) value.
The reference length is 1 m.
Reference origin for moment evaluation is (0.25, 0, 0).
Surface(s) where the force coefficients are evaluated: wall.

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

--------------- Space Numerical Integration ( Zone 0 ) ------------------
Jameson-Schmidt-Turkel scheme (2nd order in space) for the flow inviscid terms.
JST viscous coefficients (2nd & 4th): 0.5, 0.02.
The method includes a grid stretching correction (p = 0.3).
Scalar upwind solver for the turbulence model.
First order integration in space.
Average of gradients with correction (viscous flow terms).
Average of gradients with correction (viscous turbulence terms).
Gradient for upwind reconstruction: Green-Gauss.
Gradient for viscous and source terms: Green-Gauss.

--------------- Time Numerical Integration ( Zone 0 ) ------------------
Local time stepping (steady state simulation).
Euler implicit method for the flow equations.
FGMRES is used for solving the linear system.
Using a ILU(0) preconditioning.
Convergence criteria of the linear solver: 1e-12.
Max number of linear iterations: 3.
No CFL adaptation.
Courant-Friedrichs-Lewy number: 20
Euler implicit time integration for the turbulence model.

------------------ Convergence Criteria ( Zone 0 ) ---------------------
Maximum number of solver subiterations: 80000.
Begin convergence monitoring at iteration 10.
Residual minimum value: 1e-8.
Cauchy series min. value: 1e-10.
Number of Cauchy elements: 1000.
Begin windowed time average at iteration 0.

-------------------- Output Information ( Zone 0 ) ----------------------
File writing frequency:
+------------------------------------+
| File| Frequency|
+------------------------------------+
| RESTART| 250|
| PARAVIEW| 250|
| SURFACE_PARAVIEW| 250|
+------------------------------------+
Writing the convergence history file every 1 inner iterations.
Writing the screen convergence history every 1 inner iterations.
The tabular file format is Tecplot (.dat).
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.dat.

------------- Config File Boundary Information ( Zone 0 ) ---------------
+-----------------------------------------------------------------------+
| Marker Type| Marker Name|
+-----------------------------------------------------------------------+
| Far-field| far_field|
+-----------------------------------------------------------------------+
| Inlet boundary| fan_outlet|
| | core_outlet|
+-----------------------------------------------------------------------+
| Outlet boundary| fan_inlet|
+-----------------------------------------------------------------------+
| Heat flux wall| wall|
+-----------------------------------------------------------------------+

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

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

Screen output fields: INNER_ITER, RMS_DENSITY, RMS_NU_TILDE, LIFT, DRAG
History output group(s): ITER, RMS_RES
Convergence field(s): RMS_DENSITY
Warning: No (valid) fields chosen for time convergence monitoring. Time convergence monitoring inactive.
Volume output fields: COORDINATES, SOLUTION, PRIMITIVE

------------------- Geometry Preprocessing ( Zone 0 ) -------------------
Three dimensional problem.
1750175 grid points.
5135379 volume elements.
5 surface markers.
8470 boundary elements in index 0 (Marker = core_outlet).
4274 boundary elements in index 1 (Marker = fan_inlet).
5622 boundary elements in index 2 (Marker = fan_outlet).
5046 boundary elements in index 3 (Marker = far_field).
30992 boundary elements in index 4 (Marker = wall).
3857962 tetrahedra.
945713 hexahedra.
263615 prisms.
68089 pyramids.
Setting point connectivity.
Renumbering points (Reverse Cuthill McKee Ordering).
Recomputing point connectivity.
Setting element connectivity.
Checking the numerical grid orientation.
All volume elements are correctly orientend.
All surface elements are correctly orientend.
Identifying edges and vertices.
Setting the control volume structure.
Volume of the computational grid: 245.266.
Searching for the closest normal neighbors to the surfaces.
Storing a mapping from global to local point index.
Compute the surface curvature.
Max K: 25401.4. Mean K: 158.444. Standard deviation K: 1112.79.
Checking for periodicity.
Computing mesh quality statistics for the dual control volumes.
+--------------------------------------------------------------+
| Mesh Quality Metric| Minimum| Maximum|
+--------------------------------------------------------------+
| Orthogonality Angle (deg.)| 9.42382| 90|
| CV Face Area Aspect Ratio| 1.03699| 193585|
| CV Sub-Volume Ratio| 1| 1667.18|
+--------------------------------------------------------------+
Finding max control volume width.
Semi-span length = 1.06909 m.
Wetted area = 49.9468 m^2.
Area projection in the x-plane = 2.64922 m^2, y-plane = 15.6722 m^2, z-plane = 15.6569 m^2.
Max. coordinate in the x-direction = 4.30887 m, y-direction = 1.06909 m, z-direction = 1.04735 m.
Min. coordinate in the x-direction = -0.679988 m, y-direction = -1.0762 m, z-direction = -1.09807 m.
Computing wall distances.

-------------------- Solver Preprocessing ( Zone 0 ) --------------------
Viscous flow: Computing pressure using the ideal gas law
based on the free-stream temperature and a density computed
from the Reynolds number.
Force coefficients computed using free-stream values.

-- Models:
+------------------------------------------------------------------------------+
| Viscosity Model| Conductivity Model| Fluid Model|
+------------------------------------------------------------------------------+
| SUTHERLAND| CONSTANT_PRANDTL| STANDARD_AIR|
+------------------------------------------------------------------------------+
-- Fluid properties:
+------------------------------------------------------------------------------+
| Name| Dim. value| Ref. value| Unit|Non-dim. value|
+------------------------------------------------------------------------------+
| Ref. Viscosity| 1.716e-05| 1| N.s/m^2| 1.716e-05|
| Sutherland Temp.| 273.15| 1| K| 273.15|
| Sutherland Const.| 110.4| 1| K| 110.4|
+------------------------------------------------------------------------------+
| Prandtl (Lam.)| -| -| -| 0.72|
| Prandtl (Turb.)| -| -| -| 0.9|
+------------------------------------------------------------------------------+
| Gas Constant| 287.058| 1| N.m/kg.K| 287.058|
| Spec. Heat Ratio| -| -| -| 1.4|
+------------------------------------------------------------------------------+
-- Initial and free-stream conditions:
+------------------------------------------------------------------------------+
| Name| Dim. value| Ref. value| Unit|Non-dim. value|
+------------------------------------------------------------------------------+
| Static Pressure| 23907.1| 1| Pa| 23907.1|
| Density| 0.38042| 1| kg/m^3| 0.38042|
| Temperature| 218.924| 1| K| 218.924|
| Total Energy| 181526| 1| m^2/s^2| 181526|
| Velocity-X| 220.98| 1| m/s| 220.98|
| Velocity-Y| 0| 1| m/s| 0|
| Velocity-Z| 0| 1| m/s| 0|
| Velocity Magnitude| 220.98| 1| m/s| 220.98|
+------------------------------------------------------------------------------+
| Viscosity| 1.43402e-05| 1| N.s/m^2| 1.43402e-05|
| Conductivity| -| 1| W/m^2.K| -|
| Turb. Kin. Energy| 183.12| 1| m^2/s^2| 183.12|
| Spec. Dissipation| 485785| 1| 1/s| 485785|
+------------------------------------------------------------------------------+
| Mach Number| -| -| -| 0.745|
| Reynolds Number| -| -| -| 5.8622e+06|
+------------------------------------------------------------------------------+
Initialize Jacobian structure (Navier-Stokes). MG level: 0.
Killed

[bigfootedrockmidget]

Can you try with the latest version, and if that doesn't work, can you then also provide the mesh so we can reproduce the issue?


https://su2code.github.io/download.html

[joshkellyjak]

Are you running in parallel? I remember encountering this issue on a very old version of the code, the way I handled it was to change the number of partitions I requested from mpi.

[shreyash08@]

Thanks @bigfootedrockmidget and @joshkellyjak! I did try running it on the latest version that was on the cluster (v 8.0.1). Still got the same error.
But I did find the solution! The mesh file that I am using is too big. So, the memory that I was requesting for the job (11 GB) was not enough to run this simulation. Increasing the requested memory to something huge like 256 GB solved this issue!

[bigfootedrockmidget]

Great to hear that this problem is solved!

That is a lot of memory :-) I hope you do not actually need all of that.
Usually after your run is finished you get a log file from the hpc submit system that tells you the maximum amount of memory used. You can use a slightly higher value next time because 1. your job will start faster from the queue because it needs to allocate less resources and 2. all that memory is reserved for your job even if you do not use it. Other users might not be able to start their job because the memory is not available. Looking forward to seeing some nice results :-)