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problem with parallel calculations OF8 mpirun

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Old   January 5, 2021, 08:33
Default problem with parallel calculations OF8 mpirun
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Franco
Join Date: Nov 2019
Location: Compiègne, France
Posts: 125
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otaolafr is on a distinguished road
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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