January 5, 2021, 08:33
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problem with parallel calculations OF8 mpirun
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#1
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Senior Member
Franco
Join Date: Nov 2019
Location: Compiègne, France
Posts: 125
Rep Power: 5
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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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