[Core][MPI] Adding `SpatialSearchResultContainer`/`SpatialSearchResultContainerVector` and `SearchWrapper` (v.3.0) #11719

loumalouomega · 2023-10-25T12:17:34Z

📝 Description

#11416 + addressed comments

This PR introduces a new class named SpatialSearchResultContainer, SpatialSearchResultContainerVector as well as SearchWrapper. The two first classes provides storage and operations related to spatial search results. In addition SearchWrapper class implements an interface for serial/MPI search for different search objects, in current PR adding GeometricalObjectBins and the available trees.

The SpatialSearchResultContainer class stores:

Local pointers of results (in a PointerVectorSet)
Global pointers (empty if not synchronized)
GlobalPointerCommunicator pointer (to synchronize the global pointers)

The class includes functions such as, SynchronizeAll, HasResult, GetResultIndices, AddResult... The interesting part is that integrates a global pointer communicator, so it is possible to calculate anything passing a functor. The most common operations required are already implemented: GetResultShapeFunctions, GetResultIndices and GetResultCoordinates,

The SynchronizeAll method synchronizes the container between partitions. The AddResult method adds a result to the local pointers. There is a push_back which does the same.

The SpatialSearchResultContainerVector class stores a std::vector of SpatialSearchResultContainer pointers. In the SearchWrapper class the index of the vector corresponds with the node id when using nodes and just a counter when simply searching.

Considering general data communicator instead of sub data communicator

TODO: Using coloring utilities instead of manual coloring

🆕 Changelog

The spatial_search_result_container.cpp , spatial_search_result_container.hm spatial_search_result_container_vector.cpp and spatial_search_result_container_vector.h files have been added, representing the implementation and header for the SpatialSearchResultContainer and SpatialSearchResultContainerVector classes.
Expose to python SpatialSearchResultContainer and SpatialSearchResultContainerVector
Adding tests for SpatialSearchResultContainer and SpatialSearchResultContainerVector
Update python interface and redefine tests with new interface
Adding SearchWrapper class, currently just implemented GeometricalObjectBins.
Adding tests for SearchWrapper.
Changes from [Core] Unify SearchUtilities #11710
Changes from [Core][MPI] Adding MinLocAll and MaxLocAll to DataCommunicator #11712
Changes from [Core] Separate PointObject in different file #11725
Changes from [Core] Defining GetBoundingBox in Tree class. Plus adding documentation #11730
Changes from [Core] Defines ObjectType and PointType in GeometricalObjectsBins #11731
Changes from [Core] Adding minor definition for ObjectType for PointObject #11735
Changes from [Core] Adding GetObjectType and define ObjectType in Tree #11737
Changes from [Core] Moving GetObjectType in tree.h #11739
Changes from [Core] Defining bounding box and ObjectType in DynamicBins #11741
Changes from [Core] Defining distance in SearchInRadius in GeometricalObjectBins #11754
Changes from [Core] Add SetRank method to GlobalPointer + documentation #11762
Changes from [Core] Add GetDataCommunicator to GlobalPointerCommunicator #11794
Changes from [Core] Adding SynchronizePointsWithBoundingBox method #11877
Changes from [Core] Missing & in Get method in SpatialSearchResult #12002
Changes from [Core] Fix BB check #12419
Changes from [Core] Refactor search_utilities.h to handle negative tolerance values. Actual fix from 12419 #12430
Update search utilities
Update the SpatialSearchResultContainer adding SpatialSearchCommunicator enum
Update the SpatialSearchResultContainerVector adding SpatialSearchCommunicator enum
Update the SearchWrapper consistently
Update python exposition

RiccardoRossi · 2023-10-25T13:47:40Z

kratos/includes/data_communicator.h


+#ifndef KRATOS_BASE_DATA_COMMUNICATOR_DECLARE_ALLREDUCE_LOC_INTERFACE_FOR_TYPE
+#define KRATOS_BASE_DATA_COMMUNICATOR_DECLARE_ALLREDUCE_LOC_INTERFACE_FOR_TYPE(...)                                                         \
+virtual std::pair<__VA_ARGS__, int> MinLocAll(const __VA_ARGS__& rLocalValue) const { return std::pair<__VA_ARGS__, int>(rLocalValue, 0); } \


just to be sure:

the data_communicator changes being reviewed in a different PR, am i correct?

RiccardoRossi · 2023-10-25T13:51:50Z

kratos/spatial_containers/search_wrapper.cpp

+    const auto& r_local_min = r_local_bb.GetMinPoint();
+
+    // Getting max values
+    r_max[0] = mrDataCommunicator.MaxAll(r_local_max[0]);


unimportant question (just ignore if you feel) but, isn't there a vector version of this? i mean one that considers the vector of components instead of each component separately

I don't know, if I can simplify the code that would be welcomed

RiccardoRossi · 2023-10-25T13:52:47Z

kratos/spatial_containers/search_wrapper.cpp

+    if (mrDataCommunicator.IsDistributed()) {
+        DistributedSearchInRadius(rPoint, Radius, rResults, SyncronizeResults);
+    } else { // Call serial version
+        SerialSearchInRadius(rPoint, Radius, rResults, SyncronizeResults);


why do you pass the "SyncronizeResults" flag to the serial version? in that case it can only be in sync

Let me check if I can simplify code, originally this was supposed to be a derived class and when refactored the code maybe I copy pasted to much

RiccardoRossi

I have the impression that this is really not ready for prime time.

@loumalouomega can we have a call to speak about this ?

kratos/python/add_search_strategies_to_python.cpp

kratos/spatial_containers/search_wrapper.cpp

kratos/spatial_containers/search_wrapper.h

kratos/spatial_containers/spatial_search_result_container.cpp

loumalouomega · 2023-11-08T14:55:23Z

After all PR are merged, this is ready for final review

loumalouomega · 2023-11-09T11:05:05Z

@pooyan-dadvand @RiccardoRossi I removed the shared_ptr

@pooyan

leaving the review to @pooyan

loumalouomega · 2023-11-16T14:38:52Z

@RiccardoRossi you mentioned a random pooyan instead of @pooyan-dadvand

roigcarlo · 2023-11-29T10:20:48Z

kratos/spatial_containers/search_wrapper.cpp

+    const int rank = GetRank();
+
+    // If we are using GeometricalObjectBins we can use the optimized search
+    if constexpr (IsGeometricalObjectBins) {


Wouldn't be easier for this to just have a specialized version? They don't share any code

Yes, they share part of the code, I am not using that constexpr all the time

i see

auto rank = getRank() if constexpr(x) { do_something() } else { do_another_thing() }

What is being shared?

Edit: I mean specialization for <> generic and <GeometricalBins> only.

But in that case I would need to put the constexpr ina different place...

I think it would be cleaner if you specialize the method for GeomtricalObjectBin:

template<SpatialSearchCommunication TSpatialSearchCommunication> void SearchWrapper<GeomtricalObjectBin, TSpatialSearchCommunication>::LocalSearchInRadius(

kratos/spatial_containers/search_wrapper.h

roigcarlo

Aside for the fact that I still find the search_wrapper odd, I see no other problem.

@RiccardoRossi for me this is ok to merge...

…osal-v3

… doc/document-search-mpi

…-mpi [Doc] Document search mpi

…osal-v3

loumalouomega · 2024-10-08T08:55:04Z

@pooyan-dadvand we need to revisit this

…osal-v3

loumalouomega · 2024-11-20T10:33:58Z

@pooyan-dadvand We must check this eventually

loumalouomega · 2024-12-04T13:35:34Z

@pooyan-dadvand We must check this eventually

Just reminder

loumalouomega added Enhancement Kratos Core Testing Parallel-MPI Distributed memory parallelism for HPC / clusters Feature labels Oct 25, 2023

loumalouomega requested review from roigcarlo and pooyan-dadvand October 25, 2023 12:17

loumalouomega requested review from a team as code owners October 25, 2023 12:17

RiccardoRossi reviewed Oct 26, 2023

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RiccardoRossi reviewed Nov 7, 2023

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loumalouomega mentioned this pull request Nov 8, 2023

[Core] Unify SearchUtilities #11710

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loumalouomega requested a review from RiccardoRossi November 8, 2023 14:55

loumalouomega enabled auto-merge November 20, 2023 14:10

loumalouomega mentioned this pull request Nov 27, 2023

[Core] Optimize allocation and MPI management in #11719 #11857

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loumalouomega added 6 commits June 20, 2024 08:52

Merge branch 'master' into doc/document-search-mpi

403d792

Delete duplicated doc

89aa204

[Core] Adding documentation for MPI classes

37d9391

Merge branch 'master' into core/mpi/spatial-search-container-new-prop…

e393e73

…osal-v3

Merge branch 'core/mpi/spatial-search-container-new-proposal-v3' into…

3c29117

… doc/document-search-mpi

Merge pull request #12480 from KratosMultiphysics/doc/document-search…

f78191c

…-mpi [Doc] Document search mpi

loumalouomega temporarily deployed to github-pages June 25, 2024 15:53 — with GitHub Actions Inactive

Minor doc update

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loumalouomega temporarily deployed to github-pages June 26, 2024 11:28 — with GitHub Actions Inactive

loumalouomega added 4 commits July 17, 2024 14:18

Merge branch 'master' into core/mpi/spatial-search-container-new-prop…

8fc59ae

…osal-v3

Update the includes

b8badaf

Deactivate hetereogeneous tests

854466e

Merge branch 'master' into core/mpi/spatial-search-container-new-prop…

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…osal-v3

loumalouomega temporarily deployed to github-pages July 17, 2024 14:02 — with GitHub Actions Inactive

loumalouomega added 3 commits July 18, 2024 11:59

Cleanup subdatacommunicators in SearchWrapper destructor

f5984de

Redundant

d45c5f2

Reactivate hetereogeneous tests

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loumalouomega temporarily deployed to github-pages July 18, 2024 10:03 — with GitHub Actions Inactive

Simplify code with data communicator implementation

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Merge branch 'master' into core/mpi/spatial-search-container-new-prop…

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Merge branch 'master' into core/mpi/spatial-search-container-new-prop…

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[Docs] Workshops #12718

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[Core][MPI] Adding `SpatialSearchResultContainer`/`SpatialSearchResultContainerVector` and `SearchWrapper` (v.3.0) #11719

[Core][MPI] Adding `SpatialSearchResultContainer`/`SpatialSearchResultContainerVector` and `SearchWrapper` (v.3.0) #11719

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[Core][MPI] Adding SpatialSearchResultContainer/SpatialSearchResultContainerVector and SearchWrapper (v.3.0) #11719

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[Core][MPI] Adding SpatialSearchResultContainer/SpatialSearchResultContainerVector and SearchWrapper (v.3.0) #11719

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[Core][MPI] Adding `SpatialSearchResultContainer`/`SpatialSearchResultContainerVector` and `SearchWrapper` (v.3.0) #11719

[Core][MPI] Adding `SpatialSearchResultContainer`/`SpatialSearchResultContainerVector` and `SearchWrapper` (v.3.0) #11719

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