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problem with parallel calculations OF8 mpirun |
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January 5, 2021, 08:33 |
problem with parallel calculations OF8 mpirun
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Senior Member
Franco
Join Date: Nov 2019
Location: Compiègne, France
Posts: 129
Rep Power: 7 |
hello,
I have recently installed OF8 in a ubuntu machine, and when I tried to run my script that was running correctly in OF7 (in parallel) it gives me an error and snappy stops. i am attaching the snapy.log and also might be usefull information, now I can not implement multi threat process. my compouter has 4 cores with 2 threads, and when I try to use runParallel snappyHexMesh -overwrite with a decomposPartDict with 8 subdomains it gives an error. I reduced to 4 and snappy beings but it stops (see log) Code:
Invalid MIT-MAGIC-COOKIE-1 key/*---------------------------------------------------------------------------*\ ========= | \\ / F ield | OpenFOAM: The Open Source CFD Toolbox \\ / O peration | Website: https://openfoam.org \\ / A nd | Version: 8 \\/ M anipulation | \*---------------------------------------------------------------------------*/ Build : 8-340defec456f Exec : snappyHexMesh -parallel -overwrite Date : Jan 05 2021 Time : 13:07:33 Host : "otaolafr-G551JM" PID : 75533 I/O : uncollated Case : /home/franco/OF_Simulations/OpenFOAM_Simulations/DTS_measurment/SimulationSteadyStateLaminar nProcs : 4 Slaves : 3 ( "otaolafr-G551JM.75534" "otaolafr-G551JM.75535" "otaolafr-G551JM.75536" ) Pstream initialized with: floatTransfer : 0 nProcsSimpleSum : 0 commsType : nonBlocking polling iterations : 0 sigFpe : Enabling floating point exception trapping (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 Read mesh in = 0.38 s Overall mesh bounding box : (-7.55 -7.55 -97.5) (7.55 7.55 97.5) Relative tolerance : 1e-06 Absolute matching distance : 0.000196166 Reading refinement surfaces. Read refinement surfaces in = 11.35 s Reading refinement shells. Read refinement shells in = 0 s Setting refinement level of surface to be consistent with shells. Checked shell refinement in = 19.9 s Reading features. Read edgeMesh model.eMesh points : 181251 edges : 187771 boundingBox : (-5.05 -5.04996 -95) (5.04997 5.05 95) Refinement level according to distance to "model.eMesh" (181251 points, 187771 edges). level 0 for all cells within 0 metre. Read features in = 0.67 s Determining initial surface intersections ----------------------------------------- Edge intersection testing: Number of edges : 1077300 Number of edges to retest : 1077300 Number of intersected edges : 68168 Calculated surface intersections in = 0.49 s Initial mesh : cells:351000 faces:1077300 points:375751 Cells per refinement level: 0 351000 Adding patches for surface regions ---------------------------------- Patch Type Region ----- ---- ------ model: 1 wall inlet 2 wall outlet [3] Selecting decompositionMethod scotch [1] Selecting decompositionMethod scotch 3 wall walls Added patches in = 0.02 s [0] Selecting decompositionMethod scotch Layer thickness specified as final layer and expansion ratio. Refinement phase ---------------- [2] Selecting decompositionMethod scotch Found point (0.00025 0.00025 0.0005) in cell 87765 on processor 0 Feature refinement iteration 0 ------------------------------ Marked for refinement due to explicit features : 0 cells. Determined cells to refine in = 1.33 s Selected for feature refinement : 0 cells (out of 351000) Stopping refining since too few cells selected. Surface refinement iteration 0 ------------------------------ Marked for refinement due to surface intersection : 68896 cells. Marked for refinement due to curvature/regions : 0 cells. Determined cells to refine in = 0.07 s Selected for refinement : 68896 cells (out of 351000) Edge intersection testing: Number of edges : 2684976 Number of edges to retest : 1999848 Number of intersected edges : 345480 Refined mesh in = 2.23 s After refinement surface refinement iteration 0 : cells:833272 faces:2684976 points:1012263 Cells per refinement level: 0 282104 1 551168 Balanced mesh in = 3.63 s After balancing surface refinement iteration 0 : cells:833272 faces:2684976 points:1012263 Cells per refinement level: 0 282104 1 551168 Surface refinement iteration 1 ------------------------------ Marked for refinement due to surface intersection : 516 cells. Marked for refinement due to curvature/regions : 264536 cells. Determined cells to refine in = 7.94 s Selected for refinement : 295444 cells (out of 833272) Edge intersection testing: Number of edges : 9610668 Number of edges to retest : 8630318 Number of intersected edges : 1152285 Refined mesh in = 10.05 s After refinement surface refinement iteration 1 : cells:2901380 faces:9610668 points:3745578 Cells per refinement level: 0 251196 1 533896 2 2116288 Balanced mesh in = 18.87 s After balancing surface refinement iteration 1 : cells:2901380 faces:9610668 points:3745578 Cells per refinement level: 0 251196 1 533896 2 2116288 Surface refinement iteration 2 ------------------------------ Marked for refinement due to surface intersection : 0 cells. Marked for refinement due to curvature/regions : 4153 cells. Determined cells to refine in = 1.81 s Selected for refinement : 4967 cells (out of 2901380) Edge intersection testing: Number of edges : 9718629 Number of edges to retest : 389196 Number of intersected edges : 1152837 Refined mesh in = 7.56 s After refinement surface refinement iteration 2 : cells:2936149 faces:9718629 points:3783135 Cells per refinement level: 0 250382 1 536255 2 2149512 Balanced mesh in = 24.05 s After balancing surface refinement iteration 2 : cells:2936149 faces:9718629 points:3783135 Cells per refinement level: 0 250382 1 536255 2 2149512 Surface refinement iteration 3 ------------------------------ Marked for refinement due to surface intersection : 0 cells. Marked for refinement due to curvature/regions : 5 cells. Determined cells to refine in = 1.99 s Selected for refinement : 5 cells (out of 2936149) Edge intersection testing: Number of edges : 9718731 Number of edges to retest : 411 Number of intersected edges : 1152845 Refined mesh in = 6.92 s After refinement surface refinement iteration 3 : cells:2936184 faces:9718731 points:3783165 Cells per refinement level: 0 250382 1 536250 2 2149552 -------------------------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code. Per user-direction, the job has been aborted. -------------------------------------------------------------------------- -------------------------------------------------------------------------- mpirun noticed that process rank 3 with PID 0 on node otaolafr-G551JM exited on signal 9 (Killed). -------------------------------------------------------------------------- |
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