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November 26, 2013, 15:10 |
How many probes can I have in a simulation ?
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#1 |
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Good afternoon everyone,
I run a flat plate simulation, RANS with rhoCentralFoam, with a 600 probes to compute some boundary layer parameters. It was done in parallel processing, and when I reconstructed the fields...there was no fields. And the probes working were not all, only the first 334 probes defined in the controlDict, that is the folder exists but no sub folders with the starting time and fields. Summarizing, not all the probes worked (and no warnings was given) and I can not view the fields in paraview. And the program runs without any other problem. Thanks in advance.
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January 14, 2014, 07:42 |
Similar problem
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#2 |
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I run other simulation with fewer probes, they did not work at all. Some of them do not have all the time steps.
Does anyone know what is the problem ? I define the probes in the controlDict in the following way (at the bottom of the file): Code:
functions ( probe_number_1 { type probes; functionObjectLibs ("libsampling.so"); region region0; probeLocations ( (-0.0100 0.120001 0) ); fields ( U ); } )
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January 16, 2014, 15:42 |
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#3 |
Retired Super Moderator
Bruno Santos
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Hi guilha,
I got your private message. I suspect that the problem might be simpler than you expect: you might be running out of disk space. To check this, run: Code:
df -h On the other hand, if disk space isn't the problem, then I need some more information:
Best regards, Bruno
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January 17, 2014, 11:59 |
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#4 |
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Thank you Bruno,
If the problem is the lack of memory, should not it give this error http://www.cfd-online.com/Forums/ope...-2-errors.html - my OpenFOAM version is 2.0.1; - debian - I do not know, it might be impossible to know (I am on the university computers) - 3.1 million cells - 900 gb but only 100 gb available - I used 32 nodes and 64 too - I do not know how to use paraView to view the probes, I found a filter with the option of Probe Location but I could not find out anything, but I suppose the problem is not the location - the checkMesh (with the two options) said the Mesh is OK but it gave an error Code:
--> FOAM Serious Error : From function IOobject::readHeader(Istream&) in file db/IOobject/IOobjectReadHeader.C at line 89 Reading "/home/guilha/Desktop/resultados/cavidade_LES_130kx24_smagorinsky_perfil_power_law_v3/0.0144/uniform/time" at line 1 First token could not be read or is not the keyword 'FoamFile' Check header is of the form: /*--------------------------------*- C++ -*----------------------------------*\ | ========= | | | \\ / F ield | OpenFOAM: The Open Source CFD Toolbox | | \\ / O peration | Version: 2.0.1 | | \\ / A nd | Web: www.OpenFOAM.com | | \\/ M anipulation | | \*---------------------------------------------------------------------------*/ FoamFile { version 2.0; format ascii; class dictionary; location "0.0144/uniform"; object time; } // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // End - my controDict file is (I omitted the probes because I have already put an example) Code:
/*--------------------------------*- C++ -*----------------------------------*\ | ========= | | | \\ / F ield | OpenFOAM: The Open Source CFD Toolbox | | \\ / O peration | Version: 2.1.0 | | \\ / A nd | Web: www.OpenFOAM.org | | \\/ M anipulation | | \*---------------------------------------------------------------------------*/ FoamFile { version 2.0; format ascii; class dictionary; location "system"; object controlDict; } // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // application rhoCentralFoam; startFrom latestTime; //startFrom startTime; startTime 0; stopAt endTime; endTime 0.02; deltaT 1.0e-07; writeControl runTime; writeInterval 2.0e-04; // É LES... purgeWrite 0; writeFormat ascii; writePrecision 7; writeCompression off; timeFormat general; timePrecision 6; runTimeModifiable false; adjustTimeStep no; functions ( ); Code:
Mean and max Courant Numbers = 0.04979834 0.1448724 Time = 0.02 diagonal: Solving for rho, Initial residual = 0, Final residual = 0, No Iterations 0 diagonal: Solving for rhoUx, Initial residual = 0, Final residual = 0, No Iterations 0 diagonal: Solving for rhoUy, Initial residual = 0, Final residual = 0, No Iterations 0 diagonal: Solving for rhoUz, Initial residual = 0, Final residual = 0, No Iterations 0 smoothSolver: Solving for Ux, Initial residual = 1.374598e-06, Final residual = 4.865261e-15, No Iterations 3 smoothSolver: Solving for Uy, Initial residual = 3.260119e-06, Final residual = 2.374335e-14, No Iterations 3 smoothSolver: Solving for Uz, Initial residual = 5.533801e-06, Final residual = 4.280753e-15, No Iterations 3 diagonal: Solving for rhoE, Initial residual = 0, Final residual = 0, No Iterations 0 smoothSolver: Solving for e, Initial residual = 5.643462e-06, Final residual = 8.838985e-14, No Iterations 3 ExecutionTime = 54098.04 s ClockTime = 54515 s End Finalising parallel run When I run simulations I can only run 24 hours, then the computer kills the run. When I rerun, from the previous saved time, a new folder is built in the probe's folder. It was on one of those folders that it did not wrote on every probes. For instance if my signal is from 0-0.01 from 0.008 to 0.009, in some probes there is very few results. Edit: I can view the results in paraview.
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Se Urso Vires Foge Tocando Gaita Para Hamburgo Last edited by guilha; January 17, 2014 at 12:12. Reason: Forget to say |
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January 18, 2014, 11:54 |
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#5 | ||||||
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Bruno Santos
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Hi Guilha,
Quote:
OK, that would be roughly 3 GiB of RAM for running the case. 900GB of RAM? That's one powerful machine or cluster! 32 and 64 sub-domains... that equates to roughly 96000 and 48000 cells per processor. This could imply that so many divisions could lead to problems with cyclic patches, if there are any present; I say this because cyclic patches use to be a headache to use in parallel running, because the entry "preservePatches" had to be used for making sure the patches were not divided between processors. I can't remember when this was fixed, but I suspect that 2.0.1 did not have this fixed yet. Quote:
Quote:
But have a look at the contents of the file "0.0144/uniform/time", to check if it's empty or not. So much for the evidence of the crime Quote:
Nonetheless, everything seems fine with the settings in "controlDict". By the way, I strongly suggest that you use the following settings, if you're trying to save disk space: Code:
writeFormat binary; writeCompression on; Quote:
To check the OpenFOAM version, check the beginning of the output. Actually, we already have gotten the confirmation of the version number, from the error message that checkMesh gave you. Quote:
As for 24h, there are some job schedulers in clusters that allow requesting for more runtime than the default. Best regards, Bruno
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January 23, 2014, 10:42 |
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#6 |
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Thank you Bruno for your reply,
When I said that the available memory is 900 gb, it is 900 gb to storage data, the RAM is 32 gb. And the memory RAM that this case needs is about 8 gb. When I used the decomposePar, I used the preservePatch however it gave me random errors again on the first iterations the ones from the printstack thread. The checkMesh output is: Code:
/*---------------------------------------------------------------------------*\ | ========= | | | \\ / F ield | OpenFOAM: The Open Source CFD Toolbox | | \\ / O peration | Version: 2.0.1 | | \\ / A nd | Web: www.OpenFOAM.com | | \\/ M anipulation | | \*---------------------------------------------------------------------------*/ Build : 2.0.1-51f1de99a4bc Exec : checkMesh -allGeometry -allTopology Date : Jan 23 2014 Time : 13:31:00 Host : bandido PID : 27213 Case : /home/guilha/Desktop/resultados/cavidade_LES_130kx24_smagorinsky_perfil_power_law_v3 nProcs : 1 sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE). fileModificationChecking : Monitoring run-time modified files using timeStampMaster allowSystemOperations : Disallowing user-supplied system call operations // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // Create time Create polyMesh for time = 0 Time = 0 Mesh stats points: 3245325 faces: 9431000 internal faces: 9128872 cells: 3093312 boundary patches: 6 point zones: 0 face zones: 0 cell zones: 0 Overall number of cells of each type: hexahedra: 3093312 prisms: 0 wedges: 0 pyramids: 0 tet wedges: 0 tetrahedra: 0 polyhedra: 0 Checking topology... Boundary definition OK. Cell to face addressing OK. Point usage OK. Upper triangular ordering OK. Face vertices OK. Topological cell zip-up check OK. Face-face connectivity OK. Number of regions: 1 (OK). Checking patch topology for multiply connected surfaces ... Patch Faces Points Surface topology Bounding box entrada 5280 5525 ok (non-closed singly connected) (-0.05 0.12 -0.06) (-0.05 0.22 0.06) topo 11424 11925 ok (non-closed singly connected) (-0.05 0.22 -0.06) (0.25 0.22 0.06) saida 5280 5525 ok (non-closed singly connected) (0.25 0.12 -0.06) (0.25 0.22 0.06) parede 22368 23325 ok (non-closed singly connected) (-0.05 0 -0.06) (0.25 0.12 0.06) tras 128888 129813 ok (non-closed singly connected) (-0.05 0 -0.06) (0.25 0.22 -0.06) frente 128888 129813 ok (non-closed singly connected) (-0.05 0 0.06) (0.25 0.22 0.06) Checking geometry... Overall domain bounding box (-0.05 0 -0.06) (0.25 0.22 0.06) Mesh (non-empty, non-wedge) directions (1 1 1) Mesh (non-empty) directions (1 1 1) Boundary openness (3.435074e-15 6.089719e-15 2.451804e-14) OK. Max cell openness = 2.149904e-16 OK. Max aspect ratio = 12.2 OK. Minumum face area = 1.70765e-07. Maximum face area = 5.854043e-06. Face area magnitudes OK. Min volume = 8.53825e-10. Max volume = 2.927022e-09. Total volume = 0.00432. Cell volumes OK. Mesh non-orthogonality Max: 0 average: 0 Non-orthogonality check OK. Face pyramids OK. Max skewness = 2.927997e-06 OK. Face tets OK. Min/max edge length = 0.000409836 0.005 OK. All angles in faces OK. Face flatness (1 = flat, 0 = butterfly) : average = 1 min = 1 All face flatness OK. Cell determinant (wellposedness) : minimum: 0.03420856 average: 0.588144 Cell determinant check OK. Concave cell check OK. Mesh OK. --> FOAM Serious Error : From function IOobject::readHeader(Istream&) in file db/IOobject/IOobjectReadHeader.C at line 89 Reading "/home/guilha/Desktop/resultados/cavidade_LES_130kx24_smagorinsky_perfil_power_law_v3/0.0144/uniform/time" at line 1 First token could not be read or is not the keyword 'FoamFile' Check header is of the form: /*--------------------------------*- C++ -*----------------------------------*\ | ========= | | | \\ / F ield | OpenFOAM: The Open Source CFD Toolbox | | \\ / O peration | Version: 2.0.1 | | \\ / A nd | Web: www.OpenFOAM.com | | \\/ M anipulation | | \*---------------------------------------------------------------------------*/ FoamFile { version 2.0; format ascii; class dictionary; location "0.0144/uniform"; object time; } // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // End The probes, I could not do csv file because there is too many probes but they are definitely in the domain. And I say it again that it only did not save some iterations from one time file. Off-topic 1 I had this output in the checkMesh (other case, RANS k-omega) Code:
/*---------------------------------------------------------------------------*\ | ========= | | | \\ / F ield | OpenFOAM: The Open Source CFD Toolbox | | \\ / O peration | Version: 2.0.1 | | \\ / A nd | Web: www.OpenFOAM.com | | \\/ M anipulation | | \*---------------------------------------------------------------------------*/ Build : 2.0.1-51f1de99a4bc Exec : checkMesh -allGeometry -allTopology Date : Jan 23 2014 Time : 14:21:31 Host : bandido PID : 27432 Case : /home/guilha/Desktop/resultados/cavidade_RANS_32k_pontos_k_omega_SST nProcs : 1 sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE). fileModificationChecking : Monitoring run-time modified files using timeStampMaster allowSystemOperations : Disallowing user-supplied system call operations // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // Create time Create polyMesh for time = 0 Time = 0 Mesh stats points: 63210 internal points: 0 edges: 157095 internal edges: 30679 internal edges using one boundary point: 0 internal edges using two boundary points: 30679 faces: 125027 internal faces: 61819 cells: 31141 boundary patches: 6 point zones: 0 face zones: 0 cell zones: 0 Overall number of cells of each type: hexahedra: 31141 prisms: 0 wedges: 0 pyramids: 0 tet wedges: 0 tetrahedra: 0 polyhedra: 0 Checking topology... Boundary definition OK. Cell to face addressing OK. Point usage OK. Upper triangular ordering OK. Face vertices OK. Topological cell zip-up check OK. Face-face connectivity OK. <<Writing 6 cells with with two non-boundary faces to set twoInternalFacesCells Number of regions: 1 (OK). Checking patch topology for multiply connected surfaces ... Patch Faces Points Surface topology Bounding box entrada 114 230 ok (non-closed singly connected) (-0.05 0.12 -0.06) (-0.05 0.22 0.06) topo 216 434 ok (non-closed singly connected) (-0.05 0.22 -0.06) (0.25 0.22 0.06) saida 114 230 ok (non-closed singly connected) (0.25 0.12 -0.06) (0.25 0.22 0.06) parede_longitudinal 167 338 ok (non-closed singly connected) (-0.05 0.12 -0.06) (0.25 0.12 0.06) parede_sem_funcao_de_parede315 632 ok (non-closed singly connected) (0 0 -0.06) (0.05 0.12 0.06) trasEfrente 62282 63210 ok (non-closed singly connected) (-0.05 0 -0.06) (0.25 0.22 0.06) Checking geometry... Overall domain bounding box (-0.05 0 -0.06) (0.25 0.22 0.06) Mesh (non-empty, non-wedge) directions (1 1 0) Mesh (non-empty) directions (1 1 0) All edges aligned with or perpendicular to non-empty directions. Boundary openness (-5.6637258e-17 -4.5615823e-16 -3.0267009e-15) OK. Max cell openness = 2.2156954e-16 OK. Max aspect ratio = 361.70727 OK. Minumum face area = 4.4305555e-09. Maximum face area = 0.00027692309. Face area magnitudes OK. Min volume = 5.3166666e-10. Max volume = 2.6373629e-07. Total volume = 0.00432. Cell volumes OK. Mesh non-orthogonality Max: 0.12530119 average: 0.0010267398 Non-orthogonality check OK. Face pyramids OK. Max skewness = 0.00093247095 OK. Face tets OK. Min/max edge length = 6.38e-06 0.12 OK. All angles in faces OK. Face flatness (1 = flat, 0 = butterfly) : average = 1 min = 1 All face flatness OK. Cell determinant (wellposedness) : minimum: 0.000120951 average: 3.5305081 ***Cells with small determinant found, number of cells: 5 <<Writing 5 under-determined cells to set underdeterminedCells Concave cell check OK. Failed 1 mesh checks. End Off-topic 2 when I use paraview to view the colour plots I have always the average on the cells, I do not have the option to select the color by interpolation. Is this why I can not plot the streamlines nor isosurface and contour plots ?
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January 26, 2014, 09:14 |
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#7 | ||||||
Retired Super Moderator
Bruno Santos
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Hi guilha,
Quote:
Quote:
I'm starting to feel that you should try and upgrade to the latest OpenFOAM version, because I think this is a bug that has been fixed a long time ago. Quote:
What does the file "0.0144/uniform/time" contain? Again I suspect this is another bug that has already been fixed. Quote:
The problem is only when you continued the simulation? Then I suspect that it's a bug that has already been fixed in the latest versions. Keep in mind that you are using 2.0.1 and the latest is 2.2.2. Quote:
Quote:
And which file extension? ".OpenFOAM", ".foam" or ".VTK"? Best regards, Bruno
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January 26, 2014, 14:07 |
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#8 |
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Hello Bruno, thanks for your replies.
I think the same about the OpenFOAM versions, but that does not depend on me. Does newer versions accept the same files ? About the off-topics, the 1st it is the same mesh (blocks and boundaries) of another case I ran (RANS k-epsilon, but I put the first cell farther the k-omega) so it seems strange to me that it is badly built. The second, I execute the command foamToEnsight then I simply open ParaView with ./paraview, the file extension is .case
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January 26, 2014, 14:42 |
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#9 | |||
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Bruno Santos
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Hi guilha,
Quote:
You can at least try building/using OpenFOAM 2.0.x - http://www.openfoam.org/download/git.php but replace 2.2.x for 2.0.x - which has several bug fixes in the 2.0 series and should be directly compatible with 2.0.1. The other possibility is to talk to your supervisor and/or cluster administrator and up the time constraint for your runs to 48h or 72h. It's LES, therefore 24h is waaay too little time to solve anything. Quote:
In other words, what was the change you made in "blockMeshDict"? Quote:
If you are using 3.10.1 or 3.12.0, run: Code:
touch case.foam paraview Best regards, Bruno
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January 26, 2014, 14:58 |
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#10 |
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The meshes only have one difference that is on the walls.
My first point of the block which contains the wall in one case is closer to the wall than the other. Something like this: ....................................... ______________________ \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ ....................................... ______________________ \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ This is to respect the y+. The paraview version I have is the 3.14.1 64 bit.
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January 26, 2014, 15:15 |
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#11 | |
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Quote:
Even better! Follow the steps I mentioned and you should get a much better user interface. |
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January 27, 2014, 12:15 |
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#12 |
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Sorry, of course it was not only one point, what I meant was that I only changed one thing which was the position of the points just next to the wall. I did not know I had my mesh with a bad topology, I only realised it now
However, I found out that increasing the distance it does not give any problem in the determinants.
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September 15, 2016, 06:36 |
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#13 |
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hello ,
i am facing similar problem i have check the storage space. its fine the problem i dectected is 0 directory missing in processor folder. and while decomposing . i have seen a message stating First token could not be read or is not the keyword 'FoamFile' thanks in advance manikanth |
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September 17, 2016, 08:26 |
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#14 |
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Bruno Santos
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Quick answer: If that error message is given while running decomposePar, then we need more details. What is the complete message that decomposePar gives you?
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