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Gmsh mesh to SU2 error : "corrupted size vs. prev_size" |
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July 29, 2017, 12:26
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Gmsh mesh to SU2 error : "corrupted size vs. prev_size"
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#1 |
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New Member
Chris McInally
Join Date: Jun 2017
Location: Scotland
Posts: 7
Rep Power: 8  |
Hi, I'm currently attempting to just simply run RANS solvet for a RAE2822 airfoil, meshed in gmesh. However I keep getting an error in SU2 that I don't recognize or am able to find a solution to.
Strangely SU2 seems to run fine until it comes to writing the solution file so depending on what iteration that is set to it will run up till that many iterations then exit with one of two errors, which it switches between one after the other each time I try and run it, either: Or: Code:
-------------------------- File Output Summary -------------------------- Writing comma-separated values (CSV) surface files. Loading solution output data locally on each rank. Sorting output data across all ranks. [Chrisub:08456] *** Process received signal *** [Chrisub:08456] Signal: Segmentation fault (11) [Chrisub:08456] Signal code: (128) [Chrisub:08456] Failing at address: (nil) [Chrisub:08456] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x11390)[0x7f8a6b674390] [Chrisub:08456] [ 1] SU2_CFD[0x87bbef] [Chrisub:08456] [ 2] SU2_CFD[0x8a1df5] [Chrisub:08456] [ 3] SU2_CFD[0x8035f3] [Chrisub:08456] [ 4] SU2_CFD[0x803d63] [Chrisub:08456] [ 5] SU2_CFD[0x407c04] [Chrisub:08456] [ 6] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7f8a6b2b9830] [Chrisub:08456] [ 7] SU2_CFD[0x7d1bf9] [Chrisub:08456] *** End of error message *** Segmentation fault (core dumped) Could it be to do with the splines in my gmsh file? Code:
//Define Foil Coordinates (128pts)
Point(1) = { 0, 0, 0 };
Point(2) = { 0.0006, 0.00323, 0 };
Point(3) = { 0.00241, 0.00642, 0 };
Point(4) = { 0.00541, 0.00945, 0 };
Point(5) = { 0.00961, 0.01269, 0 };
Point(6) = { 0.01498, 0.01579, 0 };
Point(7) = { 0.02153, 0.01875, 0 };
Point(8) = { 0.02923, 0.02163, 0 };
Point(9) = { 0.03806, 0.02445, 0 };
Point(10) = { 0.04801, 0.02726, 0 };
Point(11) = { 0.05904, 0.03004, 0 };
Point(12) = { 0.07114, 0.0328, 0 };
Point(13) = { 0.08427, 0.03552, 0 };
Point(14) = { 0.0984, 0.03817, 0 };
Point(15) = { 0.11349, 0.04073, 0 };
Point(16) = { 0.12952, 0.04321, 0 };
Point(17) = { 0.14645, 0.04558, 0 };
Point(18) = { 0.16422, 0.04778, 0 };
Point(19) = { 0.1828, 0.04987, 0 };
Point(20) = { 0.20215, 0.05187, 0 };
Point(21) = { 0.22221, 0.05377, 0 };
Point(22) = { 0.24295, 0.05556, 0 };
Point(23) = { 0.2643, 0.05713, 0 };
Point(24) = { 0.28622, 0.05848, 0 };
Point(25) = { 0.30866, 0.05967, 0 };
Point(26) = { 0.33156, 0.0607, 0 };
Point(27) = { 0.35486, 0.06155, 0 };
Point(28) = { 0.37851, 0.0622, 0 };
Point(29) = { 0.40245, 0.06263, 0 };
Point(30) = { 0.42663, 0.06285, 0 };
Point(31) = { 0.45099, 0.06286, 0 };
Point(32) = { 0.47547, 0.06261, 0 };
Point(33) = { 0.5, 0.06212, 0 };
Point(34) = { 0.52453, 0.06135, 0 };
Point(35) = { 0.54901, 0.0603, 0 };
Point(36) = { 0.57336, 0.05895, 0 };
Point(37) = { 0.59754, 0.05733, 0 };
Point(38) = { 0.62149, 0.05547, 0 };
Point(39) = { 0.64514, 0.05339, 0 };
Point(40) = { 0.66845, 0.05112, 0 };
Point(41) = { 0.69134, 0.04857, 0 };
Point(42) = { 0.71378, 0.04612, 0 };
Point(43) = { 0.7357, 0.04338, 0 };
Point(44) = { 0.75705, 0.04075, 0 };
Point(45) = { 0.77778, 0.03795, 0 };
Point(46) = { 0.79785, 0.03514, 0 };
Point(47) = { 0.8172, 0.03231, 0 };
Point(48) = { 0.83578, 0.02948, 0 };
Point(49) = { 0.85355, 0.0267, 0 };
Point(50) = { 0.87048, 0.02397, 0 };
Point(51) = { 0.88651, 0.02131, 0 };
Point(52) = { 0.9016, 0.01874, 0 };
Point(53) = { 0.91574, 0.01627, 0 };
Point(54) = { 0.92886, 0.01393, 0 };
Point(55) = { 0.94096, 0.0117, 0 };
Point(56) = { 0.952, 0.00964, 0 };
Point(57) = { 0.96194, 0.00775, 0 };
Point(58) = { 0.97077, 0.00606, 0 };
Point(59) = { 0.97847, 0.00455, 0 };
Point(60) = { 0.98502, 0.00326, 0 };
Point(61) = { 0.99039, 0.00218, 0 };
Point(62) = { 0.99459, 0.00132, 0 };
Point(63) = { 0.99759, 0.00069, 0 };
Point(64) = { 0.9994, 0.0003, 0 };
Point(65) = { 1, 0, 0 };
Point(66) = { 0.9994, -0.00001, 0 };
Point(67) = { 0.99759, 0.00009, 0 };
Point(68) = { 0.99459, 0.00026, 0 };
Point(69) = { 0.99039, 0.00048, 0 };
Point(70) = { 0.98502, 0.00071, 0 };
Point(71) = { 0.97847, 0.00094, 0 };
Point(72) = { 0.97077, 0.00113, 0 };
Point(73) = { 0.96194, 0.00125, 0 };
Point(74) = { 0.952, 0.00125, 0 };
Point(75) = { 0.94096, 0.00113, 0 };
Point(76) = { 0.92886, 0.00081, 0 };
Point(77) = { 0.91574, 0.00027, 0 };
Point(78) = { 0.9016, -0.00049, 0 };
Point(79) = { 0.88651, -0.00149, 0 };
Point(80) = { 0.87048, -0.00273, 0 };
Point(81) = { 0.85355, -0.00422, 0 };
Point(82) = { 0.83578, -0.00594, 0 };
Point(83) = { 0.8172, -0.00792, 0 };
Point(84) = { 0.79785, -0.01013, 0 };
Point(85) = { 0.77778, -0.01256, 0 };
Point(86) = { 0.75705, -0.01524, 0 };
Point(87) = { 0.7357, -0.01812, 0 };
Point(88) = { 0.71378, -0.02118, 0 };
Point(89) = { 0.69134, -0.02438, 0 };
Point(90) = { 0.66845, -0.0277, 0 };
Point(91) = { 0.64514, -0.0311, 0 };
Point(92) = { 0.62149, -0.03463, 0 };
Point(93) = { 0.59754, -0.03791, 0 };
Point(94) = { 0.57336, -0.04127, 0 };
Point(95) = { 0.54901, -0.04452, 0 };
Point(96) = { 0.52453, -0.04761, 0 };
Point(97) = { 0.5, -0.05044, 0 };
Point(98) = { 0.47547, -0.05297, 0 };
Point(99) = { 0.45099, -0.05515, 0 };
Point(100) = { 0.42663, -0.05689, 0 };
Point(101) = { 0.40245, -0.05817, 0 };
Point(102) = { 0.37851, -0.05893, 0 };
Point(103) = { 0.35486, -0.05919, 0 };
Point(104) = { 0.33156, -0.059, 0 };
Point(105) = { 0.30866, -0.05843, 0 };
Point(106) = { 0.28622, -0.05753, 0 };
Point(107) = { 0.2643, -0.05638, 0 };
Point(108) = { 0.24295, -0.05498, 0 };
Point(109) = { 0.22221, -0.0534, 0 };
Point(110) = { 0.20215, -0.05167, 0 };
Point(111) = { 0.1828, -0.04977, 0 };
Point(112) = { 0.16422, -0.04775, 0 };
Point(113) = { 0.14645, -0.04561, 0 };
Point(114) = { 0.12952, -0.04333, 0 };
Point(115) = { 0.11349, -0.04094, 0 };
Point(116) = { 0.0984, -0.03844, 0 };
Point(117) = { 0.08427, -0.03584, 0 };
Point(118) = { 0.07114, -0.03315, 0 };
Point(119) = { 0.05904, -0.03042, 0 };
Point(120) = { 0.04801, -0.02761, 0 };
Point(121) = { 0.03806, -0.02472, 0 };
Point(122) = { 0.02923, -0.0218, 0 };
Point(123) = { 0.02153, -0.0188, 0 };
Point(124) = { 0.01498, -0.0158, 0 };
Point(125) = { 0.00961, -0.01273, 0 };
Point(126) = { 0.00541, -0.00957, 0 };
Point(127) = { 0.00241, -0.00658, 0 };
Point(128) = { 0.0006, -0.00317, 0 };
//Airfoil
Spline(1) = {1:128, 1};
//Circle Points
Point(130) = {0.5, 0.00183, 0};
Point(131) = {100.5, 0.00183, 0};
Point(132) = {0.5, -99.99817, 0};
Point(133) = {-99.5, 0.00183, 0};
Point(134) = {0.5, 100.00183, 0};
//farfield circle
Circle(1001) = {131, 130, 132};
Circle(1002) = {132, 130, 133};
Circle(1003) = {133, 130, 134};
Circle(1004) = {131, 130, 134};
//Surface
Line Loop(1) = {1003, -1004, 1001, 1002}; //Circle
Line Loop(2) = {1, 2}; //airfoil
Plane Surface(1) = {1,2};
//Boundaries
Physical Line("farfield") = {1002, 1001, 1004, 1003};
Physical Line("airfoil") = {1};
//Mesh lengths
Mesh.CharacteristicLengthMax = 0.001;
Mesh.CharacteristicLengthMax = 40;
Characteristic Length {1:128} = 0.01;
Ive attached the .su2, .cfg, and second error (as it was too many characters) file. Any help or suggestions would be greatly appreciated. Chris |
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July 31, 2017, 07:47
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#2 |
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Super Moderator
Tim Albring
Join Date: Sep 2015
Posts: 195
Rep Power: 10 |
Hi Chris
try to add also a physical volume that represents the fluid domain, that should solve the problem. Tim |
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August 6, 2017, 20:31
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#3 | |
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New Member
Chris McInally
Join Date: Jun 2017
Location: Scotland
Posts: 7
Rep Power: 8 |
Quote:
I'm able to run SU2 with the mesh made with lines instead of splines, however this leads to inaccurate results due to the sharp changes in geometry caused by straight lines instead of curves. |
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August 7, 2017, 05:13
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#4 |
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New Member
Alberto Pizarro
Join Date: Feb 2016
Posts: 18
Rep Power: 10 |
Hi,
In "Line Loop(2) = {1, 2};" what is line 2?. Maybe you have to change it to "Line Loop(2) = {1};" I tried your script in Gmsh and it doesn't seem a good mesh. Use and lower length to the elements and a Frontal algorithm to increase de quality. For example you can add: Mesh.Algorithm = 6; // FrontalYou have add de fluid marker as Physical Surface too. And try to run SU2 without mpirun to have more errors information. Regards. |
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August 7, 2017, 08:41
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#5 | |
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New Member
Chris McInally
Join Date: Jun 2017
Location: Scotland
Posts: 7
Rep Power: 8 |
Quote:
I'm not concerned with the mesh quality at the moment, as I've written a script that takes the output from su2 and uses it to improve the mesh in the next iterations (more detail along shock waves, high gradients etc) The addition of the physical surface seems to not make a difference either, still same error. Does the physical surface need to be used in the SU2 cfg file? I've not seen this in any documentation? using su2 without mpi gets the same errors as posted above |
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August 7, 2017, 12:16
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#6 | |
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New Member
Alberto Pizarro
Join Date: Feb 2016
Posts: 18
Rep Power: 10 |
Quote:
The quality mesh is not very important, but it shouldn't have degenerated elements. It is not necesary to use the surface of the flow field at the config file. Could show me your config file? Regards |
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August 7, 2017, 12:37
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#7 | |
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New Member
Chris McInally
Join Date: Jun 2017
Location: Scotland
Posts: 7
Rep Power: 8 |
Quote:
% % Physical governing equations (EULER, NAVIER_STOKES, % WAVE_EQUATION, HEAT_EQUATION, FEM_ELASTICITY, % POISSON_EQUATION) PHYSICAL_PROBLEM= EULER % % Specify turbulent model (NONE, SA, SA_NEG, SST) KIND_TURB_MODEL= NONE % % Mathematical problem (DIRECT, CONTINUOUS_ADJOINT) MATH_PROBLEM= DIRECT % % Restart solution (NO, YES) RESTART_SOL= NO % % Minimize the required output memory LOW_MEMORY_OUTPUT= NO % -------------------- COMPRESSIBLE FREE-STREAM DEFINITION --------------------% % % Mach number (non-dimensional, based on the free-stream values) MACH_NUMBER= 1.1 % % Angle of attack (degrees, only for compressible flows) AOA= 0 % % Free-stream temperature (288.15 K by default) FREESTREAM_TEMPERATURE= 255.556 FREESTREAM_PRESSURE= 108987.77275 % % Reynolds number (non-dimensional, based on the free-stream values) REYNOLDS_NUMBER= 6.5E6 % % Reynolds length (1 m by default) REYNOLDS_LENGTH= 1.0 % ---------------------- REFERENCE VALUE DEFINITION ---------------------------% % % Reference origin for moment computation REF_ORIGIN_MOMENT_X = 0.25 REF_ORIGIN_MOMENT_Y = 0.00 REF_ORIGIN_MOMENT_Z = 0.00 % % Reference length for pitching, rolling, and yawing non-dimensional moment REF_LENGTH_MOMENT= 1.0 % % Reference area for force coefficients (0 implies automatic calculation) REF_AREA= 0 % % Flow non-dimensionalization (DIMENSIONAL, FREESTREAM_PRESS_EQ_ONE, % FREESTREAM_VEL_EQ_MACH, FREESTREAM_VEL_EQ_ONE) REF_DIMENSIONALIZATION= FREESTREAM_PRESS_EQ_ONE % -------------------- BOUNDARY CONDITION DEFINITION --------------------------% % % Navier-Stokes wall boundary marker(s) (NONE = no marker) MARKER_EULER= ( airfoil, 0.0 ) % % Farfield boundary marker(s) (NONE = no marker) MARKER_FAR= ( farfield ) % % Marker(s) of the surface to be plotted or designed MARKER_PLOTTING= ( airfoil ) % % Marker(s) of the surface where the functional (Cd, Cl, etc.) will be evaluated MARKER_MONITORING= ( airfoil ) % ------------- COMMON PARAMETERS DEFINING THE NUMERICAL METHOD ---------------% % % Numerical method for spatial gradients (GREEN_GAUSS, WEIGHTED_LEAST_SQUARES) NUM_METHOD_GRAD= WEIGHTED_LEAST_SQUARES % % Courant-Friedrichs-Lewy condition of the finest grid CFL_NUMBER= 0.75 % % Max Delta time %MAX_DELTA_TIME= 1E10 % % Adaptive CFL number (NO, YES) CFL_ADAPT= YES % % Parameters of the adaptive CFL number (factor down, factor up, CFL min value, % CFL max value ) CFL_ADAPT_PARAM= ( 1.5, 0.5, 0.05, 1 ) % % Number of total iterations EXT_ITER= 99999 % ----------------------- SLOPE LIMITER DEFINITION ----------------------------% % % Reference element length for computing the slope and sharp edges limiters. REF_ELEM_LENGTH= 0.01 % % Coefficient for the limiter LIMITER_COEFF= 0.1 % % Freeze the value of the limiter after a number of iterations LIMITER_ITER= 10000 % ------------------------ LINEAR SOLVER DEFINITION ---------------------------% % % Linear solver or smoother for implicit formulations (BCGSTAB, MULTIGRID, FGMRES, SMOOTHER_JACOBI, % SMOOTHER_ILU0, SMOOTHER_LUSGS, % SMOOTHER_LINELET) LINEAR_SOLVER= FGMRES % % Preconditioner of the Krylov linear solver (ILU0, LU_SGS, LINELET, JACOBI) LINEAR_SOLVER_PREC= LU_SGS % % Minimum error of the linear solver for implicit formulations LINEAR_SOLVER_ERROR= 1E-6 % % Max number of iterations of the linear solver for the implicit formulation LINEAR_SOLVER_ITER= 5 % -------------------------- MULTIGRID PARAMETERS -----------------------------% % % Multi-Grid Levels (0 = no multi-grid) MGLEVEL= 3 % % Multi-grid cycle (V_CYCLE, W_CYCLE, FULLMG_CYCLE) MGCYCLE= W_CYCLE % % Multigrid pre-smoothing level MG_PRE_SMOOTH= ( 1, 2, 3, 3 ) % % Multigrid post-smoothing level MG_POST_SMOOTH= ( 0, 0, 0, 0) % % Jacobi implicit smoothing of the correction MG_CORRECTION_SMOOTH= ( 0, 0, 0, 0) % % Damping factor for the residual restriction MG_DAMP_RESTRICTION= 1 % % Damping factor for the correction prolongation MG_DAMP_PROLONGATION= 1 % -------------------- FLOW NUMERICAL METHOD DEFINITION -----------------------% % % Convective numerical method (JST, LAX-FRIEDRICH, CUSP, ROE, AUSM, HLLC, % TURKEL_PREC, MSW) CONV_NUM_METHOD_FLOW= JST % % Spatial numerical order integration (1ST_ORDER, 2ND_ORDER, 2ND_ORDER_LIMITER) SPATIAL_ORDER_FLOW= 2ND_ORDER_LIMITER % % Slope limiter (VENKATAKRISHNAN, MINMOD) SLOPE_LIMITER_FLOW= VENKATAKRISHNAN % % 1st, 2nd and 4th order artificial dissipation coefficients AD_COEFF_FLOW= ( 0.15, 0.5, 0.02 ) % % Time discretization (RUNGE-KUTTA_EXPLICIT, EULER_IMPLICIT, EULER_EXPLICIT) TIME_DISCRE_FLOW= RUNGE-KUTTA_EXPLICIT % -------------------- TURBULENT NUMERICAL METHOD DEFINITION ------------------% % % Convective numerical method (SCALAR_UPWIND) CONV_NUM_METHOD_TURB= SCALAR_UPWIND % % Spatial numerical order integration (1ST_ORDER, 2ND_ORDER, 2ND_ORDER_LIMITER) SPATIAL_ORDER_TURB= 2ND_ORDER % % Slope limiter (VENKATAKRISHNAN, MINMOD) SLOPE_LIMITER_TURB= VENKATAKRISHNAN % % Time discretization (EULER_IMPLICIT) TIME_DISCRE_TURB= EULER_IMPLICIT % % Reduction factor of the CFL coefficient in the turbulence problem CFL_REDUCTION_TURB= 1.0 % --------------------------- CONVERGENCE PARAMETERS --------------------------% % % Convergence criteria (CAUCHY, RESIDUAL) % CONV_CRITERIA= RESIDUAL % % Residual reduction (order of magnitude with respect to the initial value) RESIDUAL_REDUCTION= 10 % % Min value of the residual (log10 of the residual) RESIDUAL_MINVAL= -8 % % Start convergence criteria at iteration number STARTCONV_ITER= 10 % % Number of elements to apply the criteria CAUCHY_ELEMS= 100 % % Epsilon to control the series convergence CAUCHY_EPS= 1E-6 % % Function to apply the criteria (LIFT, DRAG, NEARFIELD_PRESS, SENS_GEOMETRY, % SENS_MACH, DELTA_LIFT, DELTA_DRAG) CAUCHY_FUNC_FLOW= DRAG % ------------------------- INPUT/OUTPUT INFORMATION --------------------------% % % Mesh input file MESH_FILENAME= RAE2822_mesh_G0.su2 % % Mesh input file format (SU2, CGNS, NETCDF_ASCII) MESH_FORMAT= SU2 % % Mesh output file MESH_OUT_FILENAME= mesh_out.su2 % % Restart flow input file SOLUTION_FLOW_FILENAME= solution_flow.dat % % Restart adjoint input file SOLUTION_ADJ_FILENAME= solution_adj.dat % % Output file format (PARAVIEW, TECPLOT, STL) OUTPUT_FORMAT= PARAVIEW % % Output file convergence history (w/o extension) CONV_FILENAME= history % % Output file restart flow RESTART_FLOW_FILENAME= solution_flow.dat % % Output file restart adjoint RESTART_ADJ_FILENAME= restart_adj.dat % % Output file flow (w/o extension) variables VOLUME_FLOW_FILENAME= flow % % Output file adjoint (w/o extension) variables VOLUME_ADJ_FILENAME= adjoint % % Output objective function gradient (using continuous adjoint) GRAD_OBJFUNC_FILENAME= of_grad.dat % % Output file surface flow coefficient (w/o extension) SURFACE_FLOW_FILENAME= surface_flow % % Output file surface adjoint coefficient (w/o extension) SURFACE_ADJ_FILENAME= surface_adjoint % % Writing solution file frequency WRT_SOL_FREQ= 250 % % Writing convergence history frequency WRT_CON_FREQ= 1 |
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August 7, 2017, 12:56
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#8 | |
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New Member
Alberto Pizarro
Join Date: Feb 2016
Posts: 18
Rep Power: 10 |
Quote:
"MARKER_EULER= ( airfoil, 0.0 )" At Euler problems, the walls don't need heatflux, change it to MARKER_EULER= ( airfoil). I hope it works then. 
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August 7, 2017, 13:21
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#9 | |
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New Member
Chris McInally
Join Date: Jun 2017
Location: Scotland
Posts: 7
Rep Power: 8 |
Quote:
*** Error in `SU2_CFD': corrupted size vs. prev_size: 0x00000000015edb90 *** As I've mentioned further up I only get this problem when I use splines in gmsh, when I use straight lines SU2 runs no problems. However the straight lines aren't great for curved shapes and cause the flow to behave differently, where theres a sudden change. Have you ever been able to use splines from gmsh in an su2 problem? |
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August 8, 2017, 04:13
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#10 | |
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New Member
Alberto Pizarro
Join Date: Feb 2016
Posts: 18
Rep Power: 10 |
Quote:
The error "corrupted size vs. prev_size" seems to be a python error. Are you sure that you are only running SU2_CFD in serie? |
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August 9, 2017, 12:19
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#11 | |
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New Member
Chris McInally
Join Date: Jun 2017
Location: Scotland
Posts: 7
Rep Power: 8 |
Quote:
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| Tags |
| gmsh, rae2822, rans, su2 error |
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