parallel run in foam extend

CRI_CFD · October 29, 2021, 12:45

Dear foamers,

I have been trying to use foam-extend for parallel meshing and execution of a elasticSolidFoam case...Neither snappy nor the solver are working in parallel when I run:

mpirun -10 64 elasticSolidFOam -parallel
or
mpirun -np 10 snappyHexMesh -parallel

Case is decomposed properly (or this it seems that it is well done) using hierarchical method:

Processor 0: field transfer
Processor 1: field transfer
Processor 2: field transfer
Processor 3: field transfer
Processor 4: field transfer
Processor 5: field transfer
Processor 6: field transfer
Processor 7: field transfer
Processor 8: field transfer
Processor 9: field transfer

End.

Then if I run:

mpirun -np 10 snappyHexMEsh -parallel

I got this error:

......

Removing mesh beyond surface intersections
------------------------------------------

Found point (14.0168 -11.5948 -13.0597) in cell -1 in global region 1 out of 16 regions.
Keeping all cells in region 1 containing point (14.0168 -11.5948 -13.0597)
Selected for keeping : 3282749 cells.
Edge intersection testing:
Number of edges : 11235884
Number of edges to retest : 1111636
Number of intersected edges : 1323711

Shell refinement iteration 0
----------------------------

Marked for refinement due to refinement shells : 0 cells.
Determined cells to refine in = 5.08 s
Selected for internal refinement : 9371 cells (out of 3282749)
[6] Number of cells in new mesh : 50732
[6] Number of faces in new mesh : 180559
[6] Number of points in new mesh: 79946
[8] Number of cells in new mesh : 61503
[8] Number of faces in new mesh : 219215
[8] Number of points in new mesh: 96625
[7] Number of cells in new mesh : 52876
[7] Number of faces in new mesh : 189245
[7] Number of points in new mesh: 84732
[5] Number of cells in new mesh : 58226
[5] Number of faces in new mesh : 204895
[5] Number of points in new mesh: 89917
[2] Number of cells in new mesh : 9937
[2] Number of faces in new mesh : 44155
[2] Number of points in new mesh: 26823
[4] Number of cells in new mesh : 69813
[4] Number of faces in new mesh : 245692
[4] Number of points in new mesh: 107080
[3] Number of cells in new mesh : 60893
[3] Number of faces in new mesh : 218427
[3] Number of points in new mesh: 97886
[1] Number of cells in new mesh : 66549
[1] Number of faces in new mesh : 241097
[1] Number of points in new mesh: 109868
[2] Number of cells in new mesh : 29712
[2] Number of faces in new mesh : 117257
[2] Number of points in new mesh: 60315
[1]
[1]
[1] --> FOAM FATAL ERROR:
[1] Problem. oldPointI:460933 newPointI:-1
[1]
[1] From function fvMeshDistribute::mergeSharedPoints()
[1] in file fvMeshDistribute/fvMeshDistribute.C at line 613.
[1]
FOAM parallel run aborting
[1]
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.

If I create the mesh without parallel run, then decomposePar and then mpirun -np 10 elasticSolidFoam -parallel I get:

Pstream initialized with:
nProcsSimpleSum : 0
commsType : nonBlocking
polling iterations : 0
sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).
allowSystemOperations : Disallowing user-supplied system call operations

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Create time

Create mesh for time = 0

Reading g
Reading field U

Patch x Traction boundary field: U
Patch y Traction boundary field: U
Selecting rheology model linearElastic
Creating constitutive model
Force-displacement for patch mandible will be written to forceDisp.dat
Selecting divSigmaExp calculation method surface

Starting time loop

Time = 1

Predicting U, gradU and snGradU based on V,gradV and snGradV

DICPCG: Solving for Ux, Initial residual = 1, Final residual = 0.0994173, No Iterations 177
DICPCG: Solving for Uy, Initial residual = 1, Final residual = 0.0988017, No Iterations 172
DICPCG: Solving for Uz, Initial residual = 1, Final residual = 0.097128, No Iterations 205
Time 1, Corrector 0, Solving for U using fvMatrix<Type>::solve, res = 1, rel res = 1, aitken = 0.1, inner iters = 0
DICPCG: Solving for Ux, Initial residual = 0.0725996, Final residual = 0.00720234, No Iterations 68
DICPCG: Solving for Uy, Initial residual = 0.101163, Final residual = 0.00998458, No Iterations 51
DICPCG: Solving for Uz, Initial residual = 0.0198838, Final residual = 0.00192552, No Iterations 28
DICPCG: Solving for Ux, Initial residual = 0.0454544, Final residual = 0.00444054, No Iterations 62
.....

DICPCG: Solving for Uz, Initial residual = 0.000234447, Final residual = 2.34371e-05, No Iterations 42

Time 1, Solving for U, Initial residual = 1, Final residual = 0.000979104, Relative residual = 0.00738358, No outer iterations 48
ExecutionTime = 68.36 s ClockTime = 69 s
Found patch mandible, writing y force and displacement to file
ExecutionTime = 68.41 s ClockTime = 69 s

End

[isma-Super-Server:10376] *** Process received signal ***
[isma-Super-Server:10376] Signal: Segmentation fault (11)
[isma-Super-Server:10376] Signal code: (-6)
[isma-Super-Server:10376] Failing at address: 0x3e800002888
[isma-Super-Server:10377] *** Process received signal ***
[isma-Super-Server:10377] Signal: Segmentation fault (11)
[isma-Super-Server:10377] Signal code: (-6)
[isma-Super-Server:10377] Failing at address: 0x3e800002889
[isma-Super-Server:10378] *** Process received signal ***
[isma-Super-Server:10378] Signal: Segmentation fault (11)
[isma-Super-Server:10378] Signal code: (-6)
[isma-Super-Server:10378] Failing at address: 0x3e80000288a
[isma-Super-Server:10379] *** Process received signal ***
[isma-Super-Server:10379] Signal: Segmentation fault (11)
[isma-Super-Server:10379] Signal code: (-6)
[isma-Super-Server:10379] Failing at address: 0x3e80000288b
[isma-Super-Server:10380] *** Process received signal ***
[isma-Super-Server:10380] Signal: Segmentation fault (11)
[isma-Super-Server:10380] Signal code: (-6)
[isma-Super-Server:10380] Failing at address: 0x3e80000288c
[isma-Super-Server:10381] *** Process received signal ***
[isma-Super-Server:10381] Signal: Segmentation fault (11)
[isma-Super-Server:10381] Signal code: (-6)
[isma-Super-Server:10381] Failing at address: 0x3e80000288d
[isma-Super-Server:10382] *** Process received signal ***
[isma-Super-Server:10382] Signal: Segmentation fault (11)
[isma-Super-Server:10382] Signal code: (-6)
[isma-Super-Server:10382] Failing at address: 0x3e80000288e
[isma-Super-Server:10383] *** Process received signal ***
[isma-Super-Server:10383] Signal: Segmentation fault (11)
[isma-Super-Server:10383] Signal code: (-6)
[isma-Super-Server:10383] Failing at address: 0x3e80000288f
[isma-Super-Server:10384] *** Process received signal ***
[isma-Super-Server:10384] Signal: Segmentation fault (11)
[isma-Super-Server:10384] Signal code: (-6)
[isma-Super-Server:10384] Failing at address: 0x3e800002890
[isma-Super-Server:10375] *** Process received signal ***
[isma-Super-Server:10375] Signal: Segmentation fault (11)
[isma-Super-Server:10375] Signal code: (-6)
[isma-Super-Server:10375] Failing at address: 0x3e800002887
--------------------------------------------------------------------------
mpirun noticed that process rank 4 with PID 10379 on node isma-Super-Server exited on signal 11 (Segmentation fault).

Why these faults? I am a very beginner to foam extend so any help will be really appreciated

CRI_CFD · November 2, 2021, 11:53

BTW I realised that the meshing error also occurs in foam extend 4.1 release, at least in my installation. I am sure I am running the two different releases getting the same error message...

Ideas?

CRI_CFD · November 4, 2021, 11:59

It is worth to mention that using cfMesh (foam extend 4.1 Ubuntu 20.04) in parallel is failing as well:

Create time

Setting root cube size and refinement parameters
Root box (-32.8483 -62.2672 -70.6166) (90.0317 60.6128 52.2634)
Requested cell size corresponds to octree level 11
Requested boundary cell size corresponds to octree level 12
Refining boundary
Refining boundary boxes to the given size
Number of leaves per processor 1
Distributing leaves to processors
Finished distributing leaves to processors
Distributing load between processors
Finished distributing load between processors
Distributing load between processors
Finished distributing load between processors
Distributing load between processors
Finished distributing load between processors
Distributing load between processors
Finished distributing load between processors
Distributing load between processors
Finished distributing load between processors
Distributing load between processors
Finished distributing load between processors
Distributing load between processors
Finished distributing load between processors
Distributing load between processors
Finished distributing load between processors
Distributing load between processors
Finished distributing load between processors
Distributing load between processors
[isma-Super-Server:108623] *** An error occurred in MPI_Bsend
[isma-Super-Server:108623] *** reported by process [2400190465,4]
[isma-Super-Server:108623] *** on communicator MPI_COMM_WORLD
[isma-Super-Server:108623] *** MPI_ERR_BUFFER: invalid buffer pointer
[isma-Super-Server:108623] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
[isma-Super-Server:108623] *** and potentially your MPI job)

Any help will be really appreciated

CRI_CFD · December 10, 2021, 13:54

Same settings are working properly with OF9:

mpirun -np x snappyHexMesh -parallel

I was considering to jump between releases using alias but mesh files generated with snappy in OF9 are slightly different compared to foam extend ones (for example, version is not included within the text files, so foam extend is sending an error)

Does anyone know what is wrong with MPI implementation of foam-extend? Am I the only one experiencing this issue?

Thanks and sorry for bothering

Yann Scott · December 13, 2023, 06:14

Same erro using foam-extend-4.1. Any updates on how to parallel run cases using this OF version?

MiladBagheri · March 28, 2024, 08:36

This is an old thread but in case anyone is looking for a solution, increase the number of cells in blockMeshDict and if it still did not work change your decomposition method to parMetis, if it still did not work try different decompostion method or divisions.

October 29, 2021, 12:45	parallel run in foam extend	#1
CRI_CFD Member Richardpluff Join Date: May 2014 Posts: 95 Rep Power: 11	Dear foamers, I have been trying to use foam-extend for parallel meshing and execution of a elasticSolidFoam case...Neither snappy nor the solver are working in parallel when I run: mpirun -10 64 elasticSolidFOam -parallel or mpirun -np 10 snappyHexMesh -parallel Case is decomposed properly (or this it seems that it is well done) using hierarchical method: Processor 0: field transfer Processor 1: field transfer Processor 2: field transfer Processor 3: field transfer Processor 4: field transfer Processor 5: field transfer Processor 6: field transfer Processor 7: field transfer Processor 8: field transfer Processor 9: field transfer End. Then if I run: mpirun -np 10 snappyHexMEsh -parallel I got this error: ...... Removing mesh beyond surface intersections ------------------------------------------ Found point (14.0168 -11.5948 -13.0597) in cell -1 in global region 1 out of 16 regions. Keeping all cells in region 1 containing point (14.0168 -11.5948 -13.0597) Selected for keeping : 3282749 cells. Edge intersection testing: Number of edges : 11235884 Number of edges to retest : 1111636 Number of intersected edges : 1323711 Shell refinement iteration 0 ---------------------------- Marked for refinement due to refinement shells : 0 cells. Determined cells to refine in = 5.08 s Selected for internal refinement : 9371 cells (out of 3282749) [6] Number of cells in new mesh : 50732 [6] Number of faces in new mesh : 180559 [6] Number of points in new mesh: 79946 [8] Number of cells in new mesh : 61503 [8] Number of faces in new mesh : 219215 [8] Number of points in new mesh: 96625 [7] Number of cells in new mesh : 52876 [7] Number of faces in new mesh : 189245 [7] Number of points in new mesh: 84732 [5] Number of cells in new mesh : 58226 [5] Number of faces in new mesh : 204895 [5] Number of points in new mesh: 89917 [2] Number of cells in new mesh : 9937 [2] Number of faces in new mesh : 44155 [2] Number of points in new mesh: 26823 [4] Number of cells in new mesh : 69813 [4] Number of faces in new mesh : 245692 [4] Number of points in new mesh: 107080 [3] Number of cells in new mesh : 60893 [3] Number of faces in new mesh : 218427 [3] Number of points in new mesh: 97886 [1] Number of cells in new mesh : 66549 [1] Number of faces in new mesh : 241097 [1] Number of points in new mesh: 109868 [2] Number of cells in new mesh : 29712 [2] Number of faces in new mesh : 117257 [2] Number of points in new mesh: 60315 [1] [1] [1] --> FOAM FATAL ERROR: [1] Problem. oldPointI:460933 newPointI:-1 [1] [1] From function fvMeshDistribute::mergeSharedPoints() [1] in file fvMeshDistribute/fvMeshDistribute.C at line 613. [1] FOAM parallel run aborting [1] -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. If I create the mesh without parallel run, then decomposePar and then mpirun -np 10 elasticSolidFoam -parallel I get: Pstream initialized with: nProcsSimpleSum : 0 commsType : nonBlocking polling iterations : 0 sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE). allowSystemOperations : Disallowing user-supplied system call operations // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // Create time Create mesh for time = 0 Reading g Reading field U Patch x Traction boundary field: U Patch y Traction boundary field: U Selecting rheology model linearElastic Creating constitutive model Force-displacement for patch mandible will be written to forceDisp.dat Selecting divSigmaExp calculation method surface Starting time loop Time = 1 Predicting U, gradU and snGradU based on V,gradV and snGradV DICPCG: Solving for Ux, Initial residual = 1, Final residual = 0.0994173, No Iterations 177 DICPCG: Solving for Uy, Initial residual = 1, Final residual = 0.0988017, No Iterations 172 DICPCG: Solving for Uz, Initial residual = 1, Final residual = 0.097128, No Iterations 205 Time 1, Corrector 0, Solving for U using fvMatrix<Type>::solve, res = 1, rel res = 1, aitken = 0.1, inner iters = 0 DICPCG: Solving for Ux, Initial residual = 0.0725996, Final residual = 0.00720234, No Iterations 68 DICPCG: Solving for Uy, Initial residual = 0.101163, Final residual = 0.00998458, No Iterations 51 DICPCG: Solving for Uz, Initial residual = 0.0198838, Final residual = 0.00192552, No Iterations 28 DICPCG: Solving for Ux, Initial residual = 0.0454544, Final residual = 0.00444054, No Iterations 62 ..... DICPCG: Solving for Uz, Initial residual = 0.000234447, Final residual = 2.34371e-05, No Iterations 42 Time 1, Solving for U, Initial residual = 1, Final residual = 0.000979104, Relative residual = 0.00738358, No outer iterations 48 ExecutionTime = 68.36 s ClockTime = 69 s Found patch mandible, writing y force and displacement to file ExecutionTime = 68.41 s ClockTime = 69 s End [isma-Super-Server:10376] * Process received signal * [isma-Super-Server:10376] Signal: Segmentation fault (11) [isma-Super-Server:10376] Signal code: (-6) [isma-Super-Server:10376] Failing at address: 0x3e800002888 [isma-Super-Server:10377] * Process received signal * [isma-Super-Server:10377] Signal: Segmentation fault (11) [isma-Super-Server:10377] Signal code: (-6) [isma-Super-Server:10377] Failing at address: 0x3e800002889 [isma-Super-Server:10378] * Process received signal * [isma-Super-Server:10378] Signal: Segmentation fault (11) [isma-Super-Server:10378] Signal code: (-6) [isma-Super-Server:10378] Failing at address: 0x3e80000288a [isma-Super-Server:10379] * Process received signal * [isma-Super-Server:10379] Signal: Segmentation fault (11) [isma-Super-Server:10379] Signal code: (-6) [isma-Super-Server:10379] Failing at address: 0x3e80000288b [isma-Super-Server:10380] * Process received signal * [isma-Super-Server:10380] Signal: Segmentation fault (11) [isma-Super-Server:10380] Signal code: (-6) [isma-Super-Server:10380] Failing at address: 0x3e80000288c [isma-Super-Server:10381] * Process received signal * [isma-Super-Server:10381] Signal: Segmentation fault (11) [isma-Super-Server:10381] Signal code: (-6) [isma-Super-Server:10381] Failing at address: 0x3e80000288d [isma-Super-Server:10382] * Process received signal * [isma-Super-Server:10382] Signal: Segmentation fault (11) [isma-Super-Server:10382] Signal code: (-6) [isma-Super-Server:10382] Failing at address: 0x3e80000288e [isma-Super-Server:10383] * Process received signal * [isma-Super-Server:10383] Signal: Segmentation fault (11) [isma-Super-Server:10383] Signal code: (-6) [isma-Super-Server:10383] Failing at address: 0x3e80000288f [isma-Super-Server:10384] * Process received signal * [isma-Super-Server:10384] Signal: Segmentation fault (11) [isma-Super-Server:10384] Signal code: (-6) [isma-Super-Server:10384] Failing at address: 0x3e800002890 [isma-Super-Server:10375] * Process received signal * [isma-Super-Server:10375] Signal: Segmentation fault (11) [isma-Super-Server:10375] Signal code: (-6) [isma-Super-Server:10375] Failing at address: 0x3e800002887 -------------------------------------------------------------------------- mpirun noticed that process rank 4 with PID 10379 on node isma-Super-Server exited on signal 11 (Segmentation fault). Why these faults? I am a very beginner to foam extend so any help will be really appreciated

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November 2, 2021, 11:53		#2
CRI_CFD Member Richardpluff Join Date: May 2014 Posts: 95 Rep Power: 11	BTW I realised that the meshing error also occurs in foam extend 4.1 release, at least in my installation. I am sure I am running the two different releases getting the same error message... Ideas?

November 4, 2021, 11:59		#3
CRI_CFD Member Richardpluff Join Date: May 2014 Posts: 95 Rep Power: 11	It is worth to mention that using cfMesh (foam extend 4.1 Ubuntu 20.04) in parallel is failing as well: Create time Setting root cube size and refinement parameters Root box (-32.8483 -62.2672 -70.6166) (90.0317 60.6128 52.2634) Requested cell size corresponds to octree level 11 Requested boundary cell size corresponds to octree level 12 Refining boundary Refining boundary boxes to the given size Number of leaves per processor 1 Distributing leaves to processors Finished distributing leaves to processors Distributing load between processors Finished distributing load between processors Distributing load between processors Finished distributing load between processors Distributing load between processors Finished distributing load between processors Distributing load between processors Finished distributing load between processors Distributing load between processors Finished distributing load between processors Distributing load between processors Finished distributing load between processors Distributing load between processors Finished distributing load between processors Distributing load between processors Finished distributing load between processors Distributing load between processors Finished distributing load between processors Distributing load between processors [isma-Super-Server:108623] * An error occurred in MPI_Bsend [isma-Super-Server:108623] * reported by process [2400190465,4] [isma-Super-Server:108623] * on communicator MPI_COMM_WORLD [isma-Super-Server:108623] * MPI_ERR_BUFFER: invalid buffer pointer [isma-Super-Server:108623] * MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, [isma-Super-Server:108623] * and potentially your MPI job) Any help will be really appreciated

December 10, 2021, 13:54		#4
CRI_CFD Member Richardpluff Join Date: May 2014 Posts: 95 Rep Power: 11	Same settings are working properly with OF9: mpirun -np x snappyHexMesh -parallel I was considering to jump between releases using alias but mesh files generated with snappy in OF9 are slightly different compared to foam extend ones (for example, version is not included within the text files, so foam extend is sending an error) Does anyone know what is wrong with MPI implementation of foam-extend? Am I the only one experiencing this issue? Thanks and sorry for bothering

December 13, 2023, 06:14		#5
Yann Scott New Member Yann Scott Join Date: Oct 2019 Posts: 5 Rep Power: 6	Same erro using foam-extend-4.1. Any updates on how to parallel run cases using this OF version?

March 28, 2024, 08:36		#6
MiladBagheri New Member Milad Bagheri Join Date: May 2019 Posts: 4 Rep Power: 6	This is an old thread but in case anyone is looking for a solution, increase the number of cells in blockMeshDict and if it still did not work change your decomposition method to parMetis, if it still did not work try different decompostion method or divisions.