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October 12, 2012, 11:23 
After 3 iterations the case is kill by system

#1 
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Francesco
Join Date: Jun 2012
Location: Rome, Italy
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Hi at all!
I'm doing a simulation in a combustion chamber with reactingFoam as solutor. The mesh dimension is about 9000000 cells so I have to run my case in parallel. I've decompose the case with the utility decomposePar and I've submitted my job. The job runs, but after the third iteration OF kills my case. The system gives me two files, one is the output (in which it writes the iterations) and the other is the error file (in which it writes the error messages). I post here only the first one because the error file is not understandable: Create time Create mesh for time = 0 Reading g Creating combustion model Selecting combustion model PaSR<psiChemistryCombustionModel> Selecting psiChemistryModel ODEChemistryModel<gasThermoPhysics> Selecting thermodynamics package hsPsiMixtureThermo<reactingMixture<gasThermoPhysic s>> Selecting chemistryReader foamChemistryReader ODEChemistryModel: Number of species = 5 and reactions = 1 Selecting ODE solver SIBS Reading field U Reading/calculating face flux field phi Creating turbulence model. Selecting turbulence model type RASModel Selecting RAS turbulence model kEpsilon kEpsilonCoeffs { Cmu 0.09; C1 1.44; C2 1.92; C3 0.33; sigmak 1; sigmaEps 1.3; Prt 1; } Creating field dpdt Creating field kinetic energy K Courant Number mean: 8.47313e08 max: 0.00822867 PIMPLE: Operating solver in PISO mode Starting time loop Courant Number mean: 8.38923e08 max: 0.0081472 deltaT = 1.17647e07 Time = 1.17647e07 diagonal: Solving for rho, Initial residual = 0, Final residual = 0, No Iterations 0 DILUPBiCG: Solving for O2, Initial residual = 0.403158, Final residual = 0.604033, No Iterations 1001 DILUPBiCG: Solving for H2O, Initial residual = 0, Final residual = 0, No Iterations 0 DILUPBiCG: Solving for CH4, Initial residual = 1, Final residual = 2.77956e09, No Iterations 2 DILUPBiCG: Solving for CO2, Initial residual = 0, Final residual = 0, No Iterations 0 DILUPBiCG: Solving for hs, Initial residual = 1, Final residual = 2.62501e08, No Iterations 2 T gas min/max = 289.99, 290.075 DICPCG: Solving for p, Initial residual = 1, Final residual = 0.0398273, No Iterations 2 diagonal: Solving for rho, Initial residual = 0, Final residual = 0, No Iterations 0 time step continuity errors : sum local = 4.1802e08, global = 1.28528e08, cumulative = 1.28528e08 DICPCG: Solving for p, Initial residual = 0.000255185, Final residual = 5.58144e07, No Iterations 5 diagonal: Solving for rho, Initial residual = 0, Final residual = 0, No Iterations 0 time step continuity errors : sum local = 2.10976e10, global = 3.33482e11, cumulative = 1.28861e08 DILUPBiCG: Solving for epsilon, Initial residual = 1, Final residual = 0.0544124, No Iterations 1001 bounding epsilon, min: 137998 max: 201701 average: 36.6196 DILUPBiCG: Solving for k, Initial residual = 1, Final residual = 9.37466e07, No Iterations 14 bounding k, min: 0.00225299 max: 1 average: 0.0018574 ExecutionTime = 442.31 s ClockTime = 445 s Courant Number mean: 1.62656e06 max: 0.274072 deltaT = 8.51927e08 Time = 2.0284e07 diagonal: Solving for rho, Initial residual = 0, Final residual = 0, No Iterations 0 DILUPBiCG: Solving for O2, Initial residual = 0.999989, Final residual = 0.0161316, No Iterations 1001 DILUPBiCG: Solving for H2O, Initial residual = 0.914623, Final residual = 0.0295428, No Iterations 1001 DILUPBiCG: Solving for CH4, Initial residual = 1, Final residual = 3.56746e07, No Iterations 13 DILUPBiCG: Solving for CO2, Initial residual = 0.929003, Final residual = 0.605438, No Iterations 1001 DILUPBiCG: Solving for hs, Initial residual = 1, Final residual = 3.58028e07, No Iterations 13 T gas min/max = 289.724, 295.613 DICPCG: Solving for p, Initial residual = 0.00303426, Final residual = 0.000263235, No Iterations 1 diagonal: Solving for rho, Initial residual = 0, Final residual = 0, No Iterations 0 time step continuity errors : sum local = 1.00107e07, global = 5.77487e08, cumulative = 7.06349e08 DICPCG: Solving for p, Initial residual = 0.000283424, Final residual = 2.9303e07, No Iterations 4 diagonal: Solving for rho, Initial residual = 0, Final residual = 0, No Iterations 0 time step continuity errors : sum local = 3.11907e10, global = 9.62024e12, cumulative = 7.06252e08 DILUPBiCG: Solving for epsilon, Initial residual = 1, Final residual = 1.76135e07, No Iterations 13 DILUPBiCG: Solving for k, Initial residual = 1, Final residual = 1219.46, No Iterations 1001 bounding k, min: 1.21469e+13 max: 4.22607e+14 average: 9.00783e+08 ExecutionTime = 1074.09 s ClockTime = 1078 s Courant Number mean: 1.69728e06 max: 0.411373 deltaT = 4.13382e08 Time = 2.44178e07 diagonal: Solving for rho, Initial residual = 0, Final residual = 0, No Iterations 0 DILUPBiCG: Solving for O2, Initial residual = 0.999999, Final residual = 1.94716e06, No Iterations 1001 DILUPBiCG: Solving for H2O, Initial residual = 1, Final residual = 8.35736e07, No Iterations 44 DILUPBiCG: Solving for CH4, Initial residual = 1, Final residual = 9.30056e07, No Iterations 45 DILUPBiCG: Solving for CO2, Initial residual = 1, Final residual = 6.7396e07, No Iterations 44 DILUPBiCG: Solving for hs, Initial residual = 1, Final residual = 9.9648e07, No Iterations 46 T gas min/max = 289.606, 300.728 DICPCG: Solving for p, Initial residual = 0.0133159, Final residual = 9.70516e06, No Iterations 1 diagonal: Solving for rho, Initial residual = 0, Final residual = 0, No Iterations 0 time step continuity errors : sum local = 7.10937e09, global = 1.8755e09, cumulative = 7.25007e08 DICPCG: Solving for p, Initial residual = 0.000272168, Final residual = 6.89739e07, No Iterations 2 diagonal: Solving for rho, Initial residual = 0, Final residual = 0, No Iterations 0 time step continuity errors : sum local = 1.068e09, global = 3.76896e10, cumulative = 7.21238e08 DILUPBiCG: Solving for epsilon, Initial residual = 1, Final residual = 7.16581e07, No Iterations 140 bounding epsilon, min: 1608.29 max: 2506.99 average: 33.376 255 additional processes aborted (not shown) PS: Read file <react.err> for stderr output of this job. Someone knows why OF kills the job? thank you very much for the hints! 

October 13, 2012, 03:53 

#2  
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Bruno Santos
Join Date: Mar 2009
Location: Lisbon, Portugal
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Greetings Bombolati,
Uhm... Have you looked at the numbers? Quote:
As for the reason for the crash... plenty of possibilities, of which these are some of the many reasons why this might have happened:
From your description, I would guess that you didn't prepare properly for scaling things up to the 256 subdomains. You should have started with a small example case that reflected your setup, because that way you would have found out about this problem sooner, because divisions by zero or infinite are very common for people that have just started using OpenFOAM Best regards, Bruno
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October 17, 2012, 04:58 

#4 
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Francesco
Join Date: Jun 2012
Location: Rome, Italy
Posts: 23
Rep Power: 6 
I've tried to change the initial conditions but it occurs the same error. To check mesh I run the checkMesh utility ad I find a strange situation:
if I run this utility from a pc that has OF v.2.1.1 it gives me ok; if I run the same utility on the v.2.1.0 it gives me an error on the last check: Create time Create polyMesh for time = 0 Time = 0 Mesh stats points: 1527113 faces: 17663239 internal faces: 17406505 cells: 8766526 boundary patches: 20 point zones: 0 face zones: 4 cell zones: 1 Overall number of cells of each type: hexahedra: 0 prisms: 0 wedges: 0 pyramids: 3640 tet wedges: 0 tetrahedra: 8762886 polyhedra: 0 Checking topology... Boundary definition OK. Cell to face addressing OK. Point usage OK. Upper triangular ordering OK. Face vertices OK. Number of regions: 1 (OK). Checking patch topology for multiply connected surfaces ... Patch Faces Points Surface topology CameraFSup 40844 20654 ok (nonclosed singly connected) IngAria 12544 6427 ok (nonclosed singly connected) CombIng2 1684 891 ok (nonclosed singly connected) CombIng1 1682 890 ok (nonclosed singly connected) CameraFL 10446 5408 ok (nonclosed singly connected) MixerFint 7254 3817 ok (nonclosed singly connected) MixerFext 11222 5788 ok (nonclosed singly connected) IniettoreAriaFint 12196 6261 ok (nonclosed singly connected) TestaPiano 1959 1040 ok (nonclosed singly connected) IniettoreAriaFext 36654 18584 ok (nonclosed singly connected) Bordo 12707 6474 ok (nonclosed singly connected) CameraFinf 16196 8269 ok (nonclosed singly connected) CameraFL2_sh 9308 4792 ok (nonclosed singly connected) CamerFL2 9308 4792 ok (nonclosed singly connected) CameraFL1_sh 19082 9725 ok (nonclosed singly connected) CamerFL1 19082 9725 ok (nonclosed singly connected) MixerFL_sh 1820 1908 ok (nonclosed singly connected) MixFL 1820 1908 ok (nonclosed singly connected) IniettoreAriaFL_sh 15463 7907 ok (nonclosed singly connected) IniettorAriaFL 15463 7907 ok (nonclosed singly connected) Checking geometry... Overall domain bounding box (3.2684804e19 2.1706595e17 7.1054274e18) (0.098 0.098 0.057) Mesh (nonempty, nonwedge) directions (1 1 1) Mesh (nonempty) directions (1 1 1) Boundary openness (1.5454146e17 3.0346545e15 8.5450276e17) OK. Max cell openness = 3.1859414e16 OK. Max aspect ratio = 8.8739399 OK. Minumum face area = 2.1118586e09. Maximum face area = 1.3930115e06. Face area magnitudes OK. Min volume = 5.4359761e14. Max volume = 4.4160393e10. Total volume = 0.00023160389. Cell volumes OK. Mesh nonorthogonality Max: 67.249804 average: 19.728405 Nonorthogonality check OK. Face pyramids OK. Max skewness = 0.95427342 OK. **Error in coupled point location: 45583 faces have their 0th vertex not opposite their coupled equivalent. Average mismatch 0.038782438. <<Writing 45583 faces with incorrectly matched 0th vertex to set coupledFaces Failed 1 mesh checks. End unfortunately, the version on the parallel platform is the 2.1.0. What could I do? Thank you 

October 20, 2012, 16:30 

#5 
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Bruno Santos
Join Date: Mar 2009
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Greetings Francesco,
Mmm... this is indeed strange. Try doing the complete check on both versions: Code:
checkMesh allTopology allGeometry
Bruno
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October 23, 2012, 03:53 

#6 
New Member
Francesco
Join Date: Jun 2012
Location: Rome, Italy
Posts: 23
Rep Power: 6 
Ok, I've done the checkMesh that you hint me and for the 2.1.0 version this is the result:
Create time Create polyMesh for time = 0 Time = 0 Mesh stats points: 1527113 faces: 17663239 internal faces: 17406505 cells: 8766526 boundary patches: 20 point zones: 0 face zones: 4 cell zones: 1 Overall number of cells of each type: hexahedra: 0 prisms: 0 wedges: 0 pyramids: 3640 tet wedges: 0 tetrahedra: 8762886 polyhedra: 0 Checking topology... Boundary definition OK. Cell to face addressing OK. Point usage OK. Upper triangular ordering OK. Face vertices OK. Topological cell zipup check OK. Faceface connectivity OK. <<Writing 576 cells with with two nonboundary faces to set twoInternalFacesCells Number of regions: 1 (OK). Checking patch topology for multiply connected surfaces ... Patch Faces Points Surface topology Bounding box CameraFSup 40844 20654 ok (nonclosed singly connected) (1.83691e18 1.98697e17 0.057) (0.098 0.098 0.057) IngAria 12544 6427 ok (nonclosed singly connected) (1.40097e18 5.63649e18 7.10543e18) (0.018 0.018 7.10543e18) CombIng2 1684 891 ok (nonclosed singly connected) (0.00621508 0.00142632 0.025) (0.00736313 0.00419796 0.028) CombIng1 1682 890 ok (nonclosed singly connected) (0.00142632 0.00621508 0.025) (0.00419796 0.00736313 0.028) CameraFL 10446 5408 ok (nonclosed singly connected) (1.54106e17 1.42109e17 0.027) (0.098 0.098 0.057) MixerFint 7254 3817 ok (nonclosed singly connected) (2.90746e19 1.87531e18 0.023) (0.0075 0.0075 0.03) MixerFext 11222 5788 ok (nonclosed singly connected) (1.23214e18 4.4964e18 0.023) (0.018 0.018 0.03) IniettoreAriaFint 12196 6261 ok (nonclosed singly connected) (2.90746e19 2.26208e18 7.10543e18) (0.006 0.006 0.023) TestaPiano 1959 1040 ok (nonclosed singly connected) (1.83691e19 1.46982e18 0.03) (0.0075 0.0075 0.03) IniettoreAriaFext 36654 18584 ok (nonclosed singly connected) (1.23214e18 4.4964e18 7.10543e18) (0.018 0.018 0.023) Bordo 12707 6474 ok (nonclosed singly connected) (2.53981e18 4.39687e18 0.027) (0.024 0.024 0.03) CameraFinf 16196 8269 ok (nonclosed singly connected) (3.12488e18 2.17066e17 0.027) (0.098 0.098 0.027) CameraFL2_sh 9308 4792 ok (nonclosed singly connected) (0.024 2.17066e17 0.027) (0.098 8.94476e19 0.057) CamerFL2 9308 4792 ok (nonclosed singly connected) (1.19323e18 0.024 0.027) (2.28941e17 0.098 0.057) CameraFL1_sh 19082 9725 ok (nonclosed singly connected) (1.83691e19 1.83691e19 0.03) (7.14048e18 0.024 0.057) CamerFL1 19082 9725 ok (nonclosed singly connected) (1.83691e19 6.04122e18 0.03) (0.024 1.83691e18 0.057) MixerFL_sh 1820 1908 ok (nonclosed singly connected) (0.0075 4.4964e18 0.023) (0.018 4.01533e19 0.03) MixFL 1820 1908 ok (nonclosed singly connected) (3.04229e19 0.0075 0.023) (4.26287e18 0.018 0.03) IniettoreAriaFL_sh 15463 7907 ok (nonclosed singly connected) (0.006 5.63649e18 7.10543e18) (0.018 9.35895e19 0.023) IniettorAriaFL 15463 7907 ok (nonclosed singly connected) (3.26848e19 0.006 7.10543e18) (3.08186e18 0.018 0.023) Checking geometry... Overall domain bounding box (3.26848e19 2.17066e17 7.10543e18) (0.098 0.098 0.057) Mesh (nonempty, nonwedge) directions (1 1 1) Mesh (nonempty) directions (1 1 1) Boundary openness (1.54541e17 3.03465e15 8.54503e17) OK. Max cell openness = 3.18594e16 OK. Max aspect ratio = 8.87394 OK. Minumum face area = 2.11186e09. Maximum face area = 1.39301e06. Face area magnitudes OK. Min volume = 5.43598e14. Max volume = 4.41604e10. Total volume = 0.000231604. Cell volumes OK. Mesh nonorthogonality Max: 67.2498 average: 19.7284 Nonorthogonality check OK. Face pyramids OK. Max skewness = 0.954273 OK. **Error in coupled point location: 45583 faces have their 0th vertex not opposite their coupled equivalent. Average mismatch 0.0387824. <<Writing 45583 faces with incorrectly matched 0th vertex to set coupledFaces ***Error in face tets: 91346 faces with low quality or negative volume decomposition tets. <<Writing 91346 faces with low quality or negative volume decomposition tets to set lowQualityTetFaces Min/max edge length = 5.29271e05 0.00201282 OK. All angles in faces OK. Face flatness (1 = flat, 0 = butterfly) : average = 1 min = 1 All face flatness OK. Cell determinant (wellposedness) : minimum: 0 average: 1.5153 ***Cells with small determinant found, number of cells: 1888 <<Writing 1888 underdetermined cells to set underdeterminedCells Concave cell check OK. Failed 3 mesh checks. End And for the 2.1.1 version: Create time Create polyMesh for time = 0 Time = 0 Mesh stats points: 1527113 faces: 17663239 internal faces: 17406505 cells: 8766526 boundary patches: 20 point zones: 0 face zones: 4 cell zones: 1 Overall number of cells of each type: hexahedra: 0 prisms: 0 wedges: 0 pyramids: 3640 tet wedges: 0 tetrahedra: 8762886 polyhedra: 0 Checking topology... Boundary definition OK. Cell to face addressing OK. Point usage OK. Upper triangular ordering OK. Face vertices OK. Topological cell zipup check OK. Faceface connectivity OK. <<Writing 576 cells with with two nonboundary faces to set twoInternalFacesCells Number of regions: 1 (OK). Checking patch topology for multiply connected surfaces ... Patch Faces Points Surface topology Bounding box CameraFSup 40844 20654 ok (nonclosed singly connected) (1.83691e18 1.98697e17 0.057) (0.098 0.098 0.057) IngAria 12544 6427 ok (nonclosed singly connected) (1.40097e18 5.63649e18 7.10543e18) (0.018 0.018 7.10543e18) CombIng2 1684 891 ok (nonclosed singly connected) (0.00621508 0.00142632 0.025) (0.00736313 0.00419796 0.028) CombIng1 1682 890 ok (nonclosed singly connected) (0.00142632 0.00621508 0.025) (0.00419796 0.00736313 0.028) CameraFL 10446 5408 ok (nonclosed singly connected) (1.54106e17 1.42109e17 0.027) (0.098 0.098 0.057) MixerFint 7254 3817 ok (nonclosed singly connected) (2.90746e19 1.87531e18 0.023) (0.0075 0.0075 0.03) MixerFext 11222 5788 ok (nonclosed singly connected) (1.23214e18 4.4964e18 0.023) (0.018 0.018 0.03) IniettoreAriaFint 12196 6261 ok (nonclosed singly connected) (2.90746e19 2.26208e18 7.10543e18) (0.006 0.006 0.023) TestaPiano 1959 1040 ok (nonclosed singly connected) (1.83691e19 1.46982e18 0.03) (0.0075 0.0075 0.03) IniettoreAriaFext 36654 18584 ok (nonclosed singly connected) (1.23214e18 4.4964e18 7.10543e18) (0.018 0.018 0.023) Bordo 12707 6474 ok (nonclosed singly connected) (2.53981e18 4.39687e18 0.027) (0.024 0.024 0.03) CameraFinf 16196 8269 ok (nonclosed singly connected) (3.12488e18 2.17066e17 0.027) (0.098 0.098 0.027) CameraFL2_sh 9308 4792 ok (nonclosed singly connected) (0.024 2.17066e17 0.027) (0.098 8.94476e19 0.057) CamerFL2 9308 4792 ok (nonclosed singly connected) (1.19323e18 0.024 0.027) (2.28941e17 0.098 0.057) CameraFL1_sh 19082 9725 ok (nonclosed singly connected) (1.83691e19 1.83691e19 0.03) (7.14048e18 0.024 0.057) CamerFL1 19082 9725 ok (nonclosed singly connected) (1.83691e19 6.04122e18 0.03) (0.024 1.83691e18 0.057) MixerFL_sh 1820 1908 ok (nonclosed singly connected) (0.0075 4.4964e18 0.023) (0.018 4.01533e19 0.03) MixFL 1820 1908 ok (nonclosed singly connected) (3.04229e19 0.0075 0.023) (4.26287e18 0.018 0.03) IniettoreAriaFL_sh 15463 7907 ok (nonclosed singly connected) (0.006 5.63649e18 7.10543e18) (0.018 9.35895e19 0.023) IniettorAriaFL 15463 7907 ok (nonclosed singly connected) (3.26848e19 0.006 7.10543e18) (3.08186e18 0.018 0.023) Checking geometry... Overall domain bounding box (3.26848e19 2.17066e17 7.10543e18) (0.098 0.098 0.057) Mesh (nonempty, nonwedge) directions (1 1 1) Mesh (nonempty) directions (1 1 1) Boundary openness (1.54541e17 3.03465e15 8.54503e17) OK. Max cell openness = 3.18594e16 OK. Max aspect ratio = 8.87394 OK. Minumum face area = 2.11186e09. Maximum face area = 1.39301e06. Face area magnitudes OK. Min volume = 5.43598e14. Max volume = 4.41604e10. Total volume = 0.000231604. Cell volumes OK. Mesh nonorthogonality Max: 67.2498 average: 19.7284 Nonorthogonality check OK. Face pyramids OK. Max skewness = 0.954273 OK. Coupled point location match (average 3.46652e20) OK. Face tets OK. Min/max edge length = 5.29271e05 0.00201282 OK. All angles in faces OK. Face flatness (1 = flat, 0 = butterfly) : average = 1 min = 1 All face flatness OK. Cell determinant (wellposedness) : minimum: 0 average: 1.5153 ***Cells with small determinant found, number of cells: 1888 <<Writing 1888 underdetermined cells to set underdeterminedCells Concave cell check OK. Failed 1 mesh checks. End What could I do for my mesh? Could be this the cause of my problems with iterations? thak you 

October 23, 2012, 15:08 

#7  
Super Moderator
Bruno Santos
Join Date: Mar 2009
Location: Lisbon, Portugal
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Hi Francesco,
From what I can discern, these two are common on both checks: Quote:
Currently I'm not aware of any tools for OpenFOAM that can properly help you fix the mesh. You could try modifyMesh for manipulating the mesh, but I'm not aware of any tutorial that shows how it's used. The other hypothesis would be to use setSet + subsetMesh to removed the damaged cells (described here http://openfoamwiki.net/index.php/SetSet#Usage_example), but that's not a very good idea either. Like I wrote in the previous mesh: either you redo the mesh again, with better options; or you can try polyDualMesh. Last but not least, if you must recover this damaged mesh and the data therein, then you could also try the official OpenFOAM support: http://www.openfoam.com/support/software.php  or any other company that provides support for it, as indicated in the main page of the openfoamwiki.net: http://openfoamwiki.net/index.php/Ma...cial_Companies Good luck! Bruno
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October 26, 2012, 04:34 

#8 
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Francesco
Join Date: Jun 2012
Location: Rome, Italy
Posts: 23
Rep Power: 6 
Hi Bruno and at all foamers!
In this days I had time to think the best way to solve my problem. I think to open my mesh in fluent only to do a reorder domain and a reorder zones. After I should export the mesh in ASCII mode. The questions are: 1) could I have some hopes to solve the problem in this way? 2) If I do the previous steps to my mesh, the conversion gives me a file that has just 100 MB dimension when the starting file size is almost 800MB, why? The proof that something is wrong is that this converted file is unreadable by the foam3DmeshToFoam utility that gives me an error about the kind of file that it is reading. Thank you very much for every ideas! 

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