0003348: MPI Segmentation fault: address not mapped to object at address 0x5745368 - OpenFOAM Issue Tracking

ID	Project	Category	View Status	Date Submitted	Last Update

0003348	OpenFOAM	Bug	public	2019-09-13 19:09	2019-09-13 19:59

Reporter	shan_lyu	Assigned To	henry
Priority	urgent	Severity	crash	Reproducibility	always
Status	closed	Resolution	no change required
Platform	GNU/Linux	OS	Other	OS Version	(please specify)
Product Version	dev

Summary	0003348: MPI Segmentation fault: address not mapped to object at address 0x5745368
Description	I was trying to run an OpenFoam code on the cluster, the solver is customer defined and it was compiled successfully on the cluster. Currently, I am using OpenFoam version - v/1812. I always got this error when I am using the customer defined solver. I have no problem with the default solver, for example, interFoam, twoLiquidMixingFoam, etc.
Steps To Reproduce	1. Compile the solver (miscible solver), which I have attached to the report. 2. run the code in v1812.
Additional Information	module --force purge module load nixpkgs/16.09 module load gcc/7.3.0 module load openmpi/3.1.2 module load openfoam/v1812 decomposePar srun miscible -parallel This is my submit document to the cluster to establish a job.
Tags	No tags attached.

shan_lyu 2019-09-13 19:09 reporter	slurm-19283863.out (28,297 bytes) /---------------------------------------------------------------------------\ \| ========= \| \| \| \\ / F ield \| OpenFOAM: The Open Source CFD Toolbox \| \| \\ / O peration \| Version: v1812 \| \| \\ / A nd \| Web: www.OpenFOAM.com \| \| \\/ M anipulation \| \| \---------------------------------------------------------------------------/ Build : v1812 OPENFOAM=1812 Arch : "LSB;label=32;scalar=64" Exec : decomposePar Date : Sep 13 2019 Time : 01:21:42 Host : gra226 PID : 9797 I/O : uncollated Case : /home/shlv0/projects/def-staghavi/shlv0/miscibletest1At001WT010V020R00 nProcs : 1 trapFpe: Floating point exception trapping enabled (FOAM_SIGFPE). fileModificationChecking : Monitoring run-time modified files using timeStampMaster (fileModificationSkew 10) allowSystemOperations : Allowing user-supplied system call operations // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // Create time Decomposing mesh region0 Create mesh Calculating distribution of cells Selecting decompositionMethod simple [64] Finished decomposition in 2.14 s Calculating original mesh data Distributing cells to processors Distributing faces to processors Distributing points to processors Constructing processor meshes Processor 0 Number of cells = 39900 Number of faces shared with processor 1 = 1400 Number of processor patches = 1 Number of processor faces = 1400 Number of boundary faces = 4184 Processor 1 Number of cells = 39900 Number of faces shared with processor 0 = 1400 Number of faces shared with processor 2 = 1402 Number of processor patches = 2 Number of processor faces = 2802 Number of boundary faces = 2866 Processor 2 Number of cells = 39900 Number of faces shared with processor 1 = 1402 Number of faces shared with processor 3 = 1376 Number of processor patches = 2 Number of processor faces = 2778 Number of boundary faces = 2858 Processor 3 Number of cells = 39900 Number of faces shared with processor 2 = 1376 Number of faces shared with processor 4 = 1396 Number of processor patches = 2 Number of processor faces = 2772 Number of boundary faces = 2824 Processor 4 Number of cells = 39900 Number of faces shared with processor 3 = 1396 Number of faces shared with processor 5 = 1406 Number of processor patches = 2 Number of processor faces = 2802 Number of boundary faces = 2866 Processor 5 Number of cells = 39900 Number of faces shared with processor 4 = 1406 Number of faces shared with processor 6 = 1386 Number of processor patches = 2 Number of processor faces = 2792 Number of boundary faces = 2860 Processor 6 Number of cells = 39900 Number of faces shared with processor 5 = 1386 Number of faces shared with processor 7 = 1392 Number of processor patches = 2 Number of processor faces = 2778 Number of boundary faces = 2822 Processor 7 Number of cells = 39900 Number of faces shared with processor 6 = 1392 Number of faces shared with processor 8 = 1408 Number of processor patches = 2 Number of processor faces = 2800 Number of boundary faces = 2864 Processor 8 Number of cells = 39900 Number of faces shared with processor 7 = 1408 Number of faces shared with processor 9 = 1392 Number of processor patches = 2 Number of processor faces = 2800 Number of boundary faces = 2864 Processor 9 Number of cells = 39900 Number of faces shared with processor 8 = 1392 Number of faces shared with processor 10 = 1386 Number of processor patches = 2 Number of processor faces = 2778 Number of boundary faces = 2822 Processor 10 Number of cells = 39900 Number of faces shared with processor 9 = 1386 Number of faces shared with processor 11 = 1406 Number of processor patches = 2 Number of processor faces = 2792 Number of boundary faces = 2860 Processor 11 Number of cells = 39900 Number of faces shared with processor 10 = 1406 Number of faces shared with processor 12 = 1396 Number of processor patches = 2 Number of processor faces = 2802 Number of boundary faces = 2866 Processor 12 Number of cells = 39900 Number of faces shared with processor 11 = 1396 Number of faces shared with processor 13 = 1376 Number of processor patches = 2 Number of processor faces = 2772 Number of boundary faces = 2824 Processor 13 Number of cells = 39900 Number of faces shared with processor 12 = 1376 Number of faces shared with processor 14 = 1402 Number of processor patches = 2 Number of processor faces = 2778 Number of boundary faces = 2858 Processor 14 Number of cells = 39900 Number of faces shared with processor 13 = 1402 Number of faces shared with processor 15 = 1400 Number of processor patches = 2 Number of processor faces = 2802 Number of boundary faces = 2866 Processor 15 Number of cells = 39900 Number of faces shared with processor 14 = 1400 Number of faces shared with processor 16 = 1344 Number of processor patches = 2 Number of processor faces = 2744 Number of boundary faces = 2840 Processor 16 Number of cells = 39900 Number of faces shared with processor 15 = 1344 Number of faces shared with processor 17 = 1400 Number of processor patches = 2 Number of processor faces = 2744 Number of boundary faces = 2840 Processor 17 Number of cells = 39900 Number of faces shared with processor 16 = 1400 Number of faces shared with processor 18 = 1402 Number of processor patches = 2 Number of processor faces = 2802 Number of boundary faces = 2866 Processor 18 Number of cells = 39900 Number of faces shared with processor 17 = 1402 Number of faces shared with processor 19 = 1376 Number of processor patches = 2 Number of processor faces = 2778 Number of boundary faces = 2858 Processor 19 Number of cells = 39900 Number of faces shared with processor 18 = 1376 Number of faces shared with processor 20 = 1396 Number of processor patches = 2 Number of processor faces = 2772 Number of boundary faces = 2824 Processor 20 Number of cells = 39900 Number of faces shared with processor 19 = 1396 Number of faces shared with processor 21 = 1406 Number of processor patches = 2 Number of processor faces = 2802 Number of boundary faces = 2866 Processor 21 Number of cells = 39900 Number of faces shared with processor 20 = 1406 Number of faces shared with processor 22 = 1386 Number of processor patches = 2 Number of processor faces = 2792 Number of boundary faces = 2860 Processor 22 Number of cells = 39900 Number of faces shared with processor 21 = 1386 Number of faces shared with processor 23 = 1392 Number of processor patches = 2 Number of processor faces = 2778 Number of boundary faces = 2822 Processor 23 Number of cells = 39900 Number of faces shared with processor 22 = 1392 Number of faces shared with processor 24 = 1408 Number of processor patches = 2 Number of processor faces = 2800 Number of boundary faces = 2864 Processor 24 Number of cells = 39900 Number of faces shared with processor 23 = 1408 Number of faces shared with processor 25 = 1392 Number of processor patches = 2 Number of processor faces = 2800 Number of boundary faces = 2864 Processor 25 Number of cells = 39900 Number of faces shared with processor 24 = 1392 Number of faces shared with processor 26 = 1386 Number of processor patches = 2 Number of processor faces = 2778 Number of boundary faces = 2822 Processor 26 Number of cells = 39900 Number of faces shared with processor 25 = 1386 Number of faces shared with processor 27 = 1406 Number of processor patches = 2 Number of processor faces = 2792 Number of boundary faces = 2860 Processor 27 Number of cells = 39900 Number of faces shared with processor 26 = 1406 Number of faces shared with processor 28 = 1396 Number of processor patches = 2 Number of processor faces = 2802 Number of boundary faces = 2866 Processor 28 Number of cells = 39900 Number of faces shared with processor 27 = 1396 Number of faces shared with processor 29 = 1376 Number of processor patches = 2 Number of processor faces = 2772 Number of boundary faces = 2824 Processor 29 Number of cells = 39900 Number of faces shared with processor 28 = 1376 Number of faces shared with processor 30 = 1402 Number of processor patches = 2 Number of processor faces = 2778 Number of boundary faces = 2858 Processor 30 Number of cells = 39900 Number of faces shared with processor 29 = 1402 Number of faces shared with processor 31 = 1400 Number of processor patches = 2 Number of processor faces = 2802 Number of boundary faces = 2866 Processor 31 Number of cells = 39900 Number of faces shared with processor 30 = 1400 Number of faces shared with processor 32 = 1344 Number of processor patches = 2 Number of processor faces = 2744 Number of boundary faces = 2840 Processor 32 Number of cells = 39900 Number of faces shared with processor 31 = 1344 Number of faces shared with processor 33 = 1400 Number of processor patches = 2 Number of processor faces = 2744 Number of boundary faces = 2840 Processor 33 Number of cells = 39900 Number of faces shared with processor 32 = 1400 Number of faces shared with processor 34 = 1402 Number of processor patches = 2 Number of processor faces = 2802 Number of boundary faces = 2866 Processor 34 Number of cells = 39900 Number of faces shared with processor 33 = 1402 Number of faces shared with processor 35 = 1376 Number of processor patches = 2 Number of processor faces = 2778 Number of boundary faces = 2858 Processor 35 Number of cells = 39900 Number of faces shared with processor 34 = 1376 Number of faces shared with processor 36 = 1396 Number of processor patches = 2 Number of processor faces = 2772 Number of boundary faces = 2824 Processor 36 Number of cells = 39900 Number of faces shared with processor 35 = 1396 Number of faces shared with processor 37 = 1406 Number of processor patches = 2 Number of processor faces = 2802 Number of boundary faces = 2866 Processor 37 Number of cells = 39900 Number of faces shared with processor 36 = 1406 Number of faces shared with processor 38 = 1386 Number of processor patches = 2 Number of processor faces = 2792 Number of boundary faces = 2860 Processor 38 Number of cells = 39900 Number of faces shared with processor 37 = 1386 Number of faces shared with processor 39 = 1392 Number of processor patches = 2 Number of processor faces = 2778 Number of boundary faces = 2822 Processor 39 Number of cells = 39900 Number of faces shared with processor 38 = 1392 Number of faces shared with processor 40 = 1408 Number of processor patches = 2 Number of processor faces = 2800 Number of boundary faces = 2864 Processor 40 Number of cells = 39900 Number of faces shared with processor 39 = 1408 Number of faces shared with processor 41 = 1392 Number of processor patches = 2 Number of processor faces = 2800 Number of boundary faces = 2864 Processor 41 Number of cells = 39900 Number of faces shared with processor 40 = 1392 Number of faces shared with processor 42 = 1386 Number of processor patches = 2 Number of processor faces = 2778 Number of boundary faces = 2822 Processor 42 Number of cells = 39900 Number of faces shared with processor 41 = 1386 Number of faces shared with processor 43 = 1406 Number of processor patches = 2 Number of processor faces = 2792 Number of boundary faces = 2860 Processor 43 Number of cells = 39900 Number of faces shared with processor 42 = 1406 Number of faces shared with processor 44 = 1396 Number of processor patches = 2 Number of processor faces = 2802 Number of boundary faces = 2866 Processor 44 Number of cells = 39900 Number of faces shared with processor 43 = 1396 Number of faces shared with processor 45 = 1376 Number of processor patches = 2 Number of processor faces = 2772 Number of boundary faces = 2824 Processor 45 Number of cells = 39900 Number of faces shared with processor 44 = 1376 Number of faces shared with processor 46 = 1402 Number of processor patches = 2 Number of processor faces = 2778 Number of boundary faces = 2858 Processor 46 Number of cells = 39900 Number of faces shared with processor 45 = 1402 Number of faces shared with processor 47 = 1400 Number of processor patches = 2 Number of processor faces = 2802 Number of boundary faces = 2866 Processor 47 Number of cells = 39900 Number of faces shared with processor 46 = 1400 Number of faces shared with processor 48 = 1344 Number of processor patches = 2 Number of processor faces = 2744 Number of boundary faces = 2840 Processor 48 Number of cells = 39900 Number of faces shared with processor 47 = 1344 Number of faces shared with processor 49 = 1400 Number of processor patches = 2 Number of processor faces = 2744 Number of boundary faces = 2840 Processor 49 Number of cells = 39900 Number of faces shared with processor 48 = 1400 Number of faces shared with processor 50 = 1402 Number of processor patches = 2 Number of processor faces = 2802 Number of boundary faces = 2866 Processor 50 Number of cells = 39900 Number of faces shared with processor 49 = 1402 Number of faces shared with processor 51 = 1376 Number of processor patches = 2 Number of processor faces = 2778 Number of boundary faces = 2858 Processor 51 Number of cells = 39900 Number of faces shared with processor 50 = 1376 Number of faces shared with processor 52 = 1396 Number of processor patches = 2 Number of processor faces = 2772 Number of boundary faces = 2824 Processor 52 Number of cells = 39900 Number of faces shared with processor 51 = 1396 Number of faces shared with processor 53 = 1406 Number of processor patches = 2 Number of processor faces = 2802 Number of boundary faces = 2866 Processor 53 Number of cells = 39900 Number of faces shared with processor 52 = 1406 Number of faces shared with processor 54 = 1386 Number of processor patches = 2 Number of processor faces = 2792 Number of boundary faces = 2860 Processor 54 Number of cells = 39900 Number of faces shared with processor 53 = 1386 Number of faces shared with processor 55 = 1392 Number of processor patches = 2 Number of processor faces = 2778 Number of boundary faces = 2822 Processor 55 Number of cells = 39900 Number of faces shared with processor 54 = 1392 Number of faces shared with processor 56 = 1408 Number of processor patches = 2 Number of processor faces = 2800 Number of boundary faces = 2864 Processor 56 Number of cells = 39900 Number of faces shared with processor 55 = 1408 Number of faces shared with processor 57 = 1392 Number of processor patches = 2 Number of processor faces = 2800 Number of boundary faces = 2864 Processor 57 Number of cells = 39900 Number of faces shared with processor 56 = 1392 Number of faces shared with processor 58 = 1386 Number of processor patches = 2 Number of processor faces = 2778 Number of boundary faces = 2822 Processor 58 Number of cells = 39900 Number of faces shared with processor 57 = 1386 Number of faces shared with processor 59 = 1406 Number of processor patches = 2 Number of processor faces = 2792 Number of boundary faces = 2860 Processor 59 Number of cells = 39900 Number of faces shared with processor 58 = 1406 Number of faces shared with processor 60 = 1396 Number of processor patches = 2 Number of processor faces = 2802 Number of boundary faces = 2866 Processor 60 Number of cells = 39900 Number of faces shared with processor 59 = 1396 Number of faces shared with processor 61 = 1376 Number of processor patches = 2 Number of processor faces = 2772 Number of boundary faces = 2824 Processor 61 Number of cells = 39900 Number of faces shared with processor 60 = 1376 Number of faces shared with processor 62 = 1402 Number of processor patches = 2 Number of processor faces = 2778 Number of boundary faces = 2858 Processor 62 Number of cells = 39900 Number of faces shared with processor 61 = 1402 Number of faces shared with processor 63 = 1400 Number of processor patches = 2 Number of processor faces = 2802 Number of boundary faces = 2866 Processor 63 Number of cells = 39900 Number of faces shared with processor 62 = 1400 Number of processor patches = 1 Number of processor faces = 1400 Number of boundary faces = 4184 Number of processor faces = 87728 Max number of cells = 39900 (0% above average 39900) Max number of processor patches = 2 (1.5873016% above average 1.96875) Max number of faces between processors = 2802 (2.2068211% above average 2741.5) Time = 0 Processor 0: field transfer Processor 1: field transfer Processor 2: field transfer Processor 3: field transfer Processor 4: field transfer Processor 5: field transfer Processor 6: field transfer Processor 7: field transfer Processor 8: field transfer Processor 9: field transfer Processor 10: field transfer Processor 11: field transfer Processor 12: field transfer Processor 13: field transfer Processor 14: field transfer Processor 15: field transfer Processor 16: field transfer Processor 17: field transfer Processor 18: field transfer Processor 19: field transfer Processor 20: field transfer Processor 21: field transfer Processor 22: field transfer Processor 23: field transfer Processor 24: field transfer Processor 25: field transfer Processor 26: field transfer Processor 27: field transfer Processor 28: field transfer Processor 29: field transfer Processor 30: field transfer Processor 31: field transfer Processor 32: field transfer Processor 33: field transfer Processor 34: field transfer Processor 35: field transfer Processor 36: field transfer Processor 37: field transfer Processor 38: field transfer Processor 39: field transfer Processor 40: field transfer Processor 41: field transfer Processor 42: field transfer Processor 43: field transfer Processor 44: field transfer Processor 45: field transfer Processor 46: field transfer Processor 47: field transfer Processor 48: field transfer Processor 49: field transfer Processor 50: field transfer Processor 51: field transfer Processor 52: field transfer Processor 53: field transfer Processor 54: field transfer Processor 55: field transfer Processor 56: field transfer Processor 57: field transfer Processor 58: field transfer Processor 59: field transfer Processor 60: field transfer Processor 61: field transfer Processor 62: field transfer Processor 63: field transfer End /---------------------------------------------------------------------------\ \| ========= \| \| \| \\ / F ield \| OpenFOAM: The Open Source CFD Toolbox \| \| \\ / O peration \| Version: v1812 \| \| \\ / A nd \| Web: www.OpenFOAM.com \| \| \\/ M anipulation \| \| \---------------------------------------------------------------------------/ Build : v1812 OPENFOAM=1812 Arch : "LSB;label=32;scalar=64" Exec : /home/shlv0/OpenFOAM/shlv0-v1812/platforms/linux64GccDPInt32Opt/bin/miscible -parallel Date : Sep 13 2019 Time : 01:22:22 Host : gra226 PID : 10647 I/O : uncollated Case : /home/shlv0/projects/def-staghavi/shlv0/miscibletest1At001WT010V020R00 nProcs : 64 Hosts : ( (gra226 32) (gra227 32) ) Pstream initialized with: floatTransfer : 0 nProcsSimpleSum : 0 commsType : nonBlocking polling iterations : 0 trapFpe: Floating point exception trapping enabled (FOAM_SIGFPE). fileModificationChecking : Monitoring run-time modified files using timeStampMaster (fileModificationSkew 10) allowSystemOperations : Allowing user-supplied system call operations // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // Create time Create mesh for time = 0 PIMPLE: Operating solver in PISO mode Reading field p_rgh Reading field U Reading/calculating face flux field phi Reading transportProperties Selecting incompressible transport model Newtonian Selecting incompressible transport model HerschelBulkley Selecting turbulence model type laminar Selecting laminar stress model Stokes Reading g Reading hRef Calculating field g.h Reading field psi No MRF models present No finite volume options present DICPCG: Solving for pcorr, Initial residual = 1, Final residual = 25.344471, No Iterations 1000 time step continuity errors : sum local = 1.2672235e-05, global = -5e-07, cumulative = -5e-07 Courant Number mean: 0.000437197 max: 0.0059347956 Starting time loop Courant Number mean: 0.000437197 max: 0.0059347956 Interface Courant Number mean: 0 max: 0 deltaT = 0.00012004802 Time = 0.000120048 PIMPLE: iteration 1 MULES: Solving for alpha.fuel Phase-1 volume fraction = 0.2500003 Min(alpha.fuel) = 0 Max(alpha.fuel) = 1.005505 MULES: Solving for alpha.fuel Phase-1 volume fraction = 0.2500006 Min(alpha.fuel) = 0 Max(alpha.fuel) = 1.0109668 DICPCG: Solving for p_rgh, Initial residual = 1, Final residual = 10.365283, No Iterations 1000 time step continuity errors : sum local = 6.2523992e-06, global = -6.0024326e-07, cumulative = -1.1002433e-06 DICPCG: Solving for p_rgh, Initial residual = 0.93905088, Final residual = 0.12914103, No Iterations 1000 time step continuity errors : sum local = 7.6854567e-06, global = -6.0024983e-07, cumulative = -1.7004931e-06 DICPCG: Solving for p_rgh, Initial residual = 0.32625506, Final residual = 0.16968887, No Iterations 1000 time step continuity errors : sum local = 1.6829705e-05, global = -6.0024248e-07, cumulative = -2.3007356e-06 GAMG: Solving for psi, Initial residual = 2.2435911e-05, Final residual = 1.7535956e-11, No Iterations 1 ExecutionTime = 29.15 s ClockTime = 29 s Courant Number mean: 0.00054057118 max: 0.20831896 Interface Courant Number mean: 4.6242104e-09 max: 0.014234502 deltaT = 0.00014412691 Time = 0.000264175 PIMPLE: iteration 1 MULES: Solving for alpha.fuel Phase-1 volume fraction = 0.25000096 Min(alpha.fuel) = -2.9819125e-44 Max(alpha.fuel) = 1.0150146 MULES: Solving for alpha.fuel Phase-1 volume fraction = 0.25000132 Min(alpha.fuel) = -3.1759654e-44 Max(alpha.fuel) = 1.0296758 DICPCG: Solving for p_rgh, Initial residual = 0.94566463, Final residual = 0.046916049, No Iterations 44 time step continuity errors : sum local = 0.0042702612, global = -7.2037202e-07, cumulative = -3.0211076e-06 DICPCG: Solving for p_rgh, Initial residual = 0.89058899, Final residual = 0.03811291, No Iterations 547 time step continuity errors : sum local = 0.000288125, global = -7.2069388e-07, cumulative = -3.7418015e-06 DICPCG: Solving for p_rgh, Initial residual = 0.77799522, Final residual = 0.69454683, No Iterations 1000 time step continuity errors : sum local = 0.00070811648, global = -7.3154202e-07, cumulative = -4.4733435e-06 GAMG: Solving for psi, Initial residual = 0.00094309055, Final residual = 1.3124494e-09, No Iterations 1 ExecutionTime = 33.16 s ClockTime = 33 s Courant Number mean: 0.0024299555 max: 0.21686309 Interface Courant Number mean: 1.7688447e-07 max: 0.063634035 deltaT = 0.00017285238 Time = 0.000437027 PIMPLE: iteration 1 MULES: Solving for alpha.fuel Phase-1 volume fraction = 0.25000175 Min(alpha.fuel) = -1.3316063e-37 Max(alpha.fuel) = 1.1424325 MULES: Solving for alpha.fuel Phase-1 volume fraction = 0.25000219 Min(alpha.fuel) = -1.0652851e-36 Max(alpha.fuel) = 1.2633697 DICPCG: Solving for p_rgh, Initial residual = 0.27114881, Final residual = 0.013526434, No Iterations 706 time step continuity errors : sum local = 0.000502811, global = 2.3539761e-06, cumulative = -2.1193674e-06 DICPCG: Solving for p_rgh, Initial residual = 0.04199656, Final residual = 0.013944877, No Iterations 1000 time step continuity errors : sum local = 0.00030086102, global = 1.1446458e-06, cumulative = -9.7472154e-07 DICPCG: Solving for p_rgh, Initial residual = 0.082748938, Final residual = 0.034255578, No Iterations 1000 time step continuity errors : sum local = 0.0002388273, global = -1.8185892e-06, cumulative = -2.7933107e-06 GAMG: Solving for psi, Initial residual = 0.00018608395, Final residual = 4.556215e-09, No Iterations 1 ExecutionTime = 39.68 s ClockTime = 39 s Courant Number mean: 0.012965766 max: 0.21630953 Interface Courant Number mean: 9.8152358e-05 max: 0.19876746 deltaT = 0.00020742286 Time = 0.00064445 PIMPLE: iteration 1 MULES: Solving for alpha.fuel Phase-1 volume fraction = 0.2500027 Min(alpha.fuel) = -6.0840609e-23 Max(alpha.fuel) = 1.2726318 MULES: Solving for alpha.fuel Phase-1 volume fraction = 0.25000322 Min(alpha.fuel) = -5.2887608e-22 Max(alpha.fuel) = 1.3092826 DICPCG: Solving for p_rgh, Initial residual = 0.79766488, Final residual = 0.084426127, No Iterations 1000 time step continuity errors : sum local = 0.0037316194, global = 4.5569623e-05, cumulative = 4.2776313e-05 DICPCG: Solving for p_rgh, Initial residual = 0.043963922, Final residual = 0.0064157594, No Iterations 1000 time step continuity errors : sum local = 0.000796627, global = 3.8635e-05, cumulative = 8.1411313e-05 DICPCG: Solving for p_rgh, Initial residual = 0.017692524, Final residual = 0.015190359, No Iterations 1000 time step continuity errors : sum local = 0.0018675616, global = 5.8280427e-05, cumulative = 0.00013969174 GAMG: Solving for psi, Initial residual = 0.00092727174, Final residual = 5.7774905e-08, No Iterations 1 ExecutionTime = 46.47 s ClockTime = 46 s Courant Number mean: 0.11624918 max: 0.68301387 Interface Courant Number mean: 0.00031575416 max: 0.39435085 deltaT = 0.0002278797 Time = 0.00087233 PIMPLE: iteration 1 MULES: Solving for alpha.fuel Phase-1 volume fraction = 0.25000379 Min(alpha.fuel) = -3.1657338e-20 Max(alpha.fuel) = 1.3693173 MULES: Solving for alpha.fuel Phase-1 volume fraction = 0.25000436 Min(alpha.fuel) = -4.0402131e-18 Max(alpha.fuel) = 1.504377 DICPCG: Solving for p_rgh, Initial residual = 0.048965251, Final residual = 0.014332423, No Iterations 1000 time step continuity errors : sum local = 0.0081902435, global = 0.00019912581, cumulative = 0.00033881755 DICPCG: Solving for p_rgh, Initial residual = 0.022201215, Final residual = 0.041090847, No Iterations 1000 time step continuity errors : sum local = 0.020023392, global = 0.00024238538, cumulative = 0.00058120293 DICPCG: Solving for p_rgh, Initial residual = 0.066178286, Final residual = 0.019774317, No Iterations 1000 time step continuity errors : sum local = 0.0072475025, global = 0.00024098558, cumulative = 0.00082218851 [19] #0 Foam::error::printStack(Foam::Ostream&)#0 [gra226:10666:0:12077] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x5745368) [20] #0 Foam::error::printStack(Foam::Ostream&) addr2line failed [20] #1 Foam::sigFpe::sigHandler(int) addr2line failed [20] #2 ?#0 [gra226:10667:0:12079] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x461da28) slurm-19283863.out (28,297 bytes) alphaSuSp.H (44 bytes) zeroField Su; zeroField Sp; zeroField divU; alphaSuSp.H (44 bytes) correctPhi.H (166 bytes) CorrectPhi ( U, phi, p_rgh, surfaceScalarField("rAUf", fvc::interpolate(rAU())), geometricZeroField(), pimple ); #include "continuityErrs.H" correctPhi.H (166 bytes) createFields.H (2,694 bytes) #include "createRDeltaT.H" Info<< "Reading field p_rgh\n" << endl; volScalarField p_rgh ( IOobject ( "p_rgh", runTime.timeName(), mesh, IOobject::MUST_READ, IOobject::AUTO_WRITE ), mesh ); Info<< "Reading field U\n" << endl; volVectorField U ( IOobject ( "U", runTime.timeName(), mesh, IOobject::MUST_READ, IOobject::AUTO_WRITE ), mesh ); #include "createPhi.H" Info<< "Reading transportProperties\n" << endl; immiscibleIncompressibleTwoPhaseMixture mixture(U, phi); volScalarField& alpha1(mixture.alpha1()); volScalarField& alpha2(mixture.alpha2()); const dimensionedScalar& rho1 = mixture.rho1(); const dimensionedScalar& rho2 = mixture.rho2(); // Need to store rho for ddt(rho, U) volScalarField rho ( IOobject ( "rho", runTime.timeName(), mesh, IOobject::READ_IF_PRESENT ), alpha1rho1 + alpha2rho2 ); rho.oldTime(); //The gamma variable //dimensionedScalar gamma //( // transportProperties.lookup("gamma") //); // Mass flux surfaceScalarField rhoPhi ( IOobject ( "rhoPhi", runTime.timeName(), mesh, IOobject::NO_READ, IOobject::NO_WRITE ), fvc::interpolate(rho)phi ); // Construct incompressible turbulence model autoPtr<incompressible::turbulenceModel> turbulence ( incompressible::turbulenceModel::New(U, phi, mixture) ); #include "readGravitationalAcceleration.H" #include "readhRef.H" #include "gh.H" volScalarField p ( IOobject ( "p", runTime.timeName(), mesh, IOobject::NO_READ, IOobject::AUTO_WRITE ), p_rgh + rhogh ); label pRefCell = 0; scalar pRefValue = 0.0; setRefCell ( p, p_rgh, pimple.dict(), pRefCell, pRefValue ); if (p_rgh.needReference()) { p += dimensionedScalar ( "p", p.dimensions(), pRefValue - getRefCellValue(p, pRefCell) ); p_rgh = p - rhogh; } mesh.setFluxRequired(p_rgh.name()); mesh.setFluxRequired(alpha1.name()); // MULES compressed flux is registered in case scalarTransport FO needs it. surfaceScalarField alphaPhiUn ( IOobject ( "alphaPhiUn", runTime.timeName(), mesh, IOobject::NO_READ, IOobject::NO_WRITE ), mesh, dimensionedScalar(phi.dimensions(), Zero) ); Info<< "Reading field psi\n" << endl; volScalarField psi ( IOobject ( "psi", runTime.timeName(), mesh, IOobject::MUST_READ, IOobject::AUTO_WRITE ), mesh ); #include "createMRF.H" #include "createFvOptions.H" createFields.H (2,694 bytes) initCorrectPhi.H (584 bytes) tmp<volScalarField> rAU; if (correctPhi) { rAU = new volScalarField ( IOobject ( "rAU", runTime.timeName(), mesh, IOobject::READ_IF_PRESENT, IOobject::AUTO_WRITE ), mesh, dimensionedScalar("rAU", dimTime/dimDensity, 1) ); #include "correctPhi.H" } else { CorrectPhi ( U, phi, p_rgh, dimensionedScalar("rAUf", dimTime/rho.dimensions(), 1), geometricZeroField(), pimple ); #include "continuityErrs.H" } initCorrectPhi.H (584 bytes) miscible.C (5,167 bytes) /---------------------------------------------------------------------------\ ========= \| \\ / F ield \| OpenFOAM: The Open Source CFD Toolbox \\ / O peration \| \\ / A nd \| Copyright (C) 2011-2017 OpenFOAM Foundation \\/ M anipulation \| ------------------------------------------------------------------------------- License This file is part of OpenFOAM. OpenFOAM is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. OpenFOAM 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 General Public License for more details. You should have received a copy of the GNU General Public License along with OpenFOAM. If not, see <http://www.gnu.org/licenses/>. Application miscible Group grpMultiphaseSolvers Description Solver for 2 incompressible, isothermal miscible fluids using a VOF (volume of fluid) phase-fraction based interface capturing approach, with optional mesh motion and mesh topology changes including adaptive re-meshing. A dummy variable to see mixing. \---------------------------------------------------------------------------/ #include "fvCFD.H" #include "dynamicFvMesh.H" #include "CMULES.H" #include "EulerDdtScheme.H" #include "localEulerDdtScheme.H" #include "CrankNicolsonDdtScheme.H" #include "subCycle.H" #include "immiscibleIncompressibleTwoPhaseMixture.H" #include "turbulentTransportModel.H" #include "pimpleControl.H" #include "fvOptions.H" #include "CorrectPhi.H" #include "fvcSmooth.H" // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // int main(int argc, char argv[]) { #include "postProcess.H" #include "addCheckCaseOptions.H" #include "setRootCase.H" #include "createTime.H" #include "createDynamicFvMesh.H" #include "initContinuityErrs.H" #include "createDyMControls.H" #include "createFields.H" #include "createAlphaFluxes.H" #include "initCorrectPhi.H" #include "createUfIfPresent.H" turbulence->validate(); if (!LTS) { #include "CourantNo.H" #include "setInitialDeltaT.H" } // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // Info<< "\nStarting time loop\n" << endl; while (runTime.run()) { #include "readDyMControls.H" if (LTS) { #include "setRDeltaT.H" } else { #include "CourantNo.H" #include "alphaCourantNo.H" #include "setDeltaT.H" } runTime++; Info<< "Time = " << runTime.timeName() << nl << endl; // --- Pressure-velocity PIMPLE corrector loop while (pimple.loop()) { if (pimple.firstIter() \|\| moveMeshOuterCorrectors) { mesh.update(); if (mesh.changing()) { // Do not apply previous time-step mesh compression flux // if the mesh topology changed if (mesh.topoChanging()) { talphaPhi1Corr0.clear(); } gh = (g & mesh.C()) - ghRef; ghf = (g & mesh.Cf()) - ghRef; MRF.update(); if (correctPhi) { // Calculate absolute flux // from the mapped surface velocity phi = mesh.Sf() & Uf(); #include "correctPhi.H" // Make the flux relative to the mesh motion fvc::makeRelative(phi, U); mixture.correct(); } if (checkMeshCourantNo) { #include "meshCourantNo.H" } } } #include "alphaControls.H" #include "alphaEqnSubCycle.H" mixture.correct(); if (pimple.frozenFlow()) { continue; } #include "UEqn.H" // --- Pressure corrector loop while (pimple.correct()) { #include "pEqn.H" } if (pimple.turbCorr()) { turbulence->correct(); } } fvScalarMatrix psiEqn ( fvm::ddt(psi) + fvm::div(phi, psi) //- fvm::laplacian(gamma, psi)//diffusion is not important, since Pe is infinity and convection is dominant ); psiEqn.relax(); psiEqn.solve(); runTime.write(); runTime.printExecutionTime(Info); } Info<< "End\n" << endl; return 0; } // ************************************************************************* // miscible.C (5,167 bytes) pEqn.H (2,001 bytes) { if (correctPhi) { rAU.ref() = 1.0/UEqn.A(); } else { rAU = 1.0/UEqn.A(); } surfaceScalarField rAUf("rAUf", fvc::interpolate(rAU())); volVectorField HbyA(constrainHbyA(rAU()UEqn.H(), U, p_rgh)); surfaceScalarField phiHbyA ( "phiHbyA", fvc::flux(HbyA) + MRF.zeroFilter(fvc::interpolate(rhorAU())fvc::ddtCorr(U, phi, Uf)) ); MRF.makeRelative(phiHbyA); if (p_rgh.needReference()) { fvc::makeRelative(phiHbyA, U); adjustPhi(phiHbyA, U, p_rgh); fvc::makeAbsolute(phiHbyA, U); } surfaceScalarField phig ( ( mixture.surfaceTensionForce() - ghffvc::snGrad(rho) )rAUfmesh.magSf() ); phiHbyA += phig; // Update the pressure BCs to ensure flux consistency constrainPressure(p_rgh, U, phiHbyA, rAUf, MRF); while (pimple.correctNonOrthogonal()) { fvScalarMatrix p_rghEqn ( fvm::laplacian(rAUf, p_rgh) == fvc::div(phiHbyA) ); p_rghEqn.setReference(pRefCell, getRefCellValue(p_rgh, pRefCell)); p_rghEqn.solve(mesh.solver(p_rgh.select(pimple.finalInnerIter()))); if (pimple.finalNonOrthogonalIter()) { phi = phiHbyA - p_rghEqn.flux(); p_rgh.relax(); U = HbyA + rAU()fvc::reconstruct((phig - p_rghEqn.flux())/rAUf); U.correctBoundaryConditions(); fvOptions.correct(U); } } #include "continuityErrs.H" // Correct Uf if the mesh is moving fvc::correctUf(Uf, U, phi); // Make the fluxes relative to the mesh motion fvc::makeRelative(phi, U); p == p_rgh + rhogh; if (p_rgh.needReference()) { p += dimensionedScalar ( "p", p.dimensions(), pRefValue - getRefCellValue(p, pRefCell) ); p_rgh = p - rhogh; } if (!correctPhi) { rAU.clear(); } } pEqn.H (2,001 bytes) rhofs.H (76 bytes) const dimensionedScalar& rho1f(rho1); const dimensionedScalar& rho2f(rho2); rhofs.H (76 bytes) setInitialrDeltaT.H (557 bytes) scalar maxDeltaT ( pimple.dict().lookupOrDefault<scalar>("maxDeltaT", GREAT) ); volScalarField rDeltaT ( IOobject ( "rDeltaT", runTime.timeName(), mesh, IOobject::NO_READ, IOobject::AUTO_WRITE ), mesh, 1/dimensionedScalar("maxDeltaT", dimTime, maxDeltaT), zeroGradientFvPatchScalarField::typeName ); volScalarField rSubDeltaT ( IOobject ( "rSubDeltaT", runTime.timeName(), mesh ), mesh, 1/dimensionedScalar("maxDeltaT", dimTime, maxDeltaT) ); setInitialrDeltaT.H (557 bytes) setrDeltaT.H (3,501 bytes) { const dictionary& pimpleDict = pimple.dict(); scalar maxCo ( pimpleDict.lookupOrDefault<scalar>("maxCo", 0.9) ); scalar maxAlphaCo ( pimpleDict.lookupOrDefault<scalar>("maxAlphaCo", 0.2) ); scalar rDeltaTSmoothingCoeff ( pimpleDict.lookupOrDefault<scalar>("rDeltaTSmoothingCoeff", 0.1) ); label nAlphaSpreadIter ( pimpleDict.lookupOrDefault<label>("nAlphaSpreadIter", 1) ); scalar alphaSpreadDiff ( pimpleDict.lookupOrDefault<scalar>("alphaSpreadDiff", 0.2) ); scalar alphaSpreadMax ( pimpleDict.lookupOrDefault<scalar>("alphaSpreadMax", 0.99) ); scalar alphaSpreadMin ( pimpleDict.lookupOrDefault<scalar>("alphaSpreadMin", 0.01) ); label nAlphaSweepIter ( pimpleDict.lookupOrDefault<label>("nAlphaSweepIter", 5) ); scalar rDeltaTDampingCoeff ( pimpleDict.lookupOrDefault<scalar>("rDeltaTDampingCoeff", 1.0) ); scalar maxDeltaT ( pimpleDict.lookupOrDefault<scalar>("maxDeltaT", GREAT) ); volScalarField rDeltaT0("rDeltaT0", rDeltaT); // Set the reciprocal time-step from the local Courant number rDeltaT.dimensionedInternalField() = max ( 1/dimensionedScalar("maxDeltaT", dimTime, maxDeltaT), fvc::surfaceSum(mag(rhoPhi))().dimensionedInternalField() /((2maxCo)mesh.V()rho.dimensionedInternalField()) ); if (maxAlphaCo < maxCo) { // Further limit the reciprocal time-step // in the vicinity of the interface volScalarField alpha1Bar(fvc::average(alpha1)); rDeltaT.dimensionedInternalField() = max ( rDeltaT.dimensionedInternalField(), pos(alpha1Bar.dimensionedInternalField() - alphaSpreadMin) pos(alphaSpreadMax - alpha1Bar.dimensionedInternalField()) fvc::surfaceSum(mag(phi))().dimensionedInternalField() /((2maxAlphaCo)mesh.V()) ); } // Update tho boundary values of the reciprocal time-step rDeltaT.correctBoundaryConditions(); Info<< "Flow time scale min/max = " << gMin(1/rDeltaT.internalField()) << ", " << gMax(1/rDeltaT.internalField()) << endl; if (rDeltaTSmoothingCoeff < 1.0) { fvc::smooth(rDeltaT, rDeltaTSmoothingCoeff); } if (nAlphaSpreadIter > 0) { fvc::spread ( rDeltaT, alpha1, nAlphaSpreadIter, alphaSpreadDiff, alphaSpreadMax, alphaSpreadMin ); } if (nAlphaSweepIter > 0) { fvc::sweep(rDeltaT, alpha1, nAlphaSweepIter, alphaSpreadDiff); } Info<< "Smoothed flow time scale min/max = " << gMin(1/rDeltaT.internalField()) << ", " << gMax(1/rDeltaT.internalField()) << endl; // Limit rate of change of time scale // - reduce as much as required // - only increase at a fraction of old time scale if ( rDeltaTDampingCoeff < 1.0 && runTime.timeIndex() > runTime.startTimeIndex() + 1 ) { rDeltaT = max ( rDeltaT, (scalar(1.0) - rDeltaTDampingCoeff)rDeltaT0 ); Info<< "Damped flow time scale min/max = " << gMin(1/rDeltaT.internalField()) << ", " << gMax(1/rDeltaT.internalField()) << endl; } #include "alphaControls.H" rSubDeltaT = rDeltaTnAlphaSubCycles; } setrDeltaT.H (3,501 bytes) UEqn.H (654 bytes) MRF.correctBoundaryVelocity(U); fvVectorMatrix UEqn ( fvm::ddt(rho, U) + fvm::div(rhoPhi, U) + MRF.DDt(rho, U) + turbulence->divDevRhoReff(rho, U) == fvOptions(rho, U) ); UEqn.relax(); fvOptions.constrain(UEqn); if (pimple.momentumPredictor()) { solve ( UEqn == fvc::reconstruct ( ( mixture.surfaceTensionForce() - ghffvc::snGrad(rho) - fvc::snGrad(p_rgh) ) mesh.magSf() ) ); fvOptions.correct(U); } UEqn.H (654 bytes) files (47 bytes) miscible.C EXE = $(FOAM_USER_APPBIN)/miscible files (47 bytes) options (880 bytes) EXE_INC = \ -I$(FOAM_SOLVERS)/multiphase/VoF \ -I$(LIB_SRC)/transportModels/twoPhaseMixture/lnInclude \ -I$(LIB_SRC)/transportModels \ -I$(LIB_SRC)/transportModels/incompressible/lnInclude \ -I$(LIB_SRC)/transportModels/interfaceProperties/lnInclude \ -I$(LIB_SRC)/TurbulenceModels/turbulenceModels/lnInclude \ -I$(LIB_SRC)/TurbulenceModels/incompressible/lnInclude \ -I$(LIB_SRC)/transportModels/immiscibleIncompressibleTwoPhaseMixture/lnInclude \ -I$(LIB_SRC)/finiteVolume/lnInclude \ -I$(LIB_SRC)/dynamicFvMesh/lnInclude \ -I$(LIB_SRC)/meshTools/lnInclude \ -I$(LIB_SRC)/sampling/lnInclude EXE_LIBS = \ -limmiscibleIncompressibleTwoPhaseMixture \ -lturbulenceModels \ -lincompressibleTurbulenceModels \ -lfiniteVolume \ -ldynamicFvMesh \ -lfvOptions \ -lmeshTools \ -lsampling \ -lwaveModels options (880 bytes)

henry 2019-09-13 19:59 manager ~0010741	v1812 is a fork of OpenFOAM and not an official release by the OpenFOAM Foundation. The OpenFOAM Foundation is the independent distributor of OpenFOAM The OpenFOAM Foundation is the organisaton which holds the copyright of the OpenFOAM software and documentation, whose purpose is to manage and distribute OpenFOAM as free, open source software for the benefit of its users. It is a registered company, limited by guarantee based in England. As such, it has no share capital or shareholders, but has individual members committed to free, open source software, who run the organisation on a voluntary basis. It has no employees and any annual profit is retained within the organisation and cannot be distributed to members. Please upgrade to an official release before reporting issues here: https://openfoam.org/version/7/ https://openfoam.org/version/dev/

Date Modified	Username	Field	Change
2019-09-13 19:09	shan_lyu	New Issue
2019-09-13 19:09	shan_lyu	File Added: slurm-19283863.out
2019-09-13 19:09	shan_lyu	File Added: alphaSuSp.H
2019-09-13 19:09	shan_lyu	File Added: correctPhi.H
2019-09-13 19:09	shan_lyu	File Added: createFields.H
2019-09-13 19:09	shan_lyu	File Added: initCorrectPhi.H
2019-09-13 19:09	shan_lyu	File Added: miscible.C
2019-09-13 19:09	shan_lyu	File Added: pEqn.H
2019-09-13 19:09	shan_lyu	File Added: rhofs.H
2019-09-13 19:09	shan_lyu	File Added: setInitialrDeltaT.H
2019-09-13 19:09	shan_lyu	File Added: setrDeltaT.H
2019-09-13 19:09	shan_lyu	File Added: UEqn.H
2019-09-13 19:09	shan_lyu	File Added: files
2019-09-13 19:09	shan_lyu	File Added: options
2019-09-13 19:59	henry	Assigned To	=> henry
2019-09-13 19:59	henry	Status	new => closed
2019-09-13 19:59	henry	Resolution	open => no change required
2019-09-13 19:59	henry	Note Added: 0010741