Merge branch 'master' of github.com:gridap/GridapDistributed.jl into …

…p4est-migration
gridap · Jan 17, 2023 · 506c8b8 · 506c8b8
2 parents ae1cc6f + aa345f3
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diff --git a/NEWS.md b/NEWS.md
@@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Added
 - Added `DistributedCellDof`, a distributed wrapper for `Gridap.CellDof`. This new wrapper acts on `DistributedCellField` in the same way `Gridap.CellDof` acts on `CellField`. Added `get_fe_dof_basis` function, which extracts a `DistributedCellDof` from a `DistributedFESpace`. Since PR [#97](https://github.com/gridap/GridapDistributed.jl/pull/97).
 - Added `gather_free_and_dirichlet_values!` and `gather_free_values!` wrapper functions. Since PR [#97](https://github.com/gridap/GridapDistributed.jl/pull/97).
+- Added compatibility with MPI v0.20 and PartitionedArrays v0.2.13
 
 ## [0.2.6] - 2022-06-07
 

diff --git a/Project.toml b/Project.toml
@@ -1,6 +1,6 @@
 name = "GridapDistributed"
 uuid = "f9701e48-63b3-45aa-9a63-9bc6c271f355"
-authors = ["S. Badia <santiago.badia@monash.edu>", "A. F. Martin <alberto.martin@monash.edu>", "F. Verdugo <fverdugo@cimne.upc.edu>"]
+authors = ["S. Badia <santiago.badia@monash.edu>", "A. F. Martin <alberto.f.martin@anu.edu.au>", "F. Verdugo <fverdugo@cimne.upc.edu>"]
 version = "0.2.6"
 
 [deps]
@@ -15,8 +15,9 @@ WriteVTK = "64499a7a-5c06-52f2-abe2-ccb03c286192"
 
 [compat]
 FillArrays = "0.8.4, 0.9, 0.10, 0.11, 0.12"
-MPI = "0.16, 0.17, 0.18, 0.19"
-PartitionedArrays = "0.2.10"
+Gridap = "0.17.11"
+MPI = "0.16, 0.17, 0.18, 0.19, 0.20"
+PartitionedArrays = "0.2.13"
 SparseMatricesCSR = "0.6.6"
 WriteVTK = "1.12.0"
 julia = "1.3"

diff --git a/README.md b/README.md
@@ -38,14 +38,14 @@ with the appropriate number of MPI tasks, `-n 4` in this particular example.
 
 ## Simple example (MPI-parallel execution mode)
 
-The following Julia code snippet solves a 2D Poisson problem in parallel on the unit square. The example follows the MPI-parallel execution mode (note the `mpi` argument to the `prun` function call) and thus it must be executed on 4 MPI tasks (note the mesh is partitioned into 4 parts) using the instructions [below](https://github.com/gridap/GridapDistributed.jl#mpi-parallel-julia-script-execution-instructions). If a user wants to use the sequential execution mode, one just replaces `mpi` by `sequential` in the call to `prun`. `GridapDistributed.jl` sequential execution mode scripts are executed as any other julia sequential script.
+The following Julia code snippet solves a 2D Poisson problem in parallel on the unit square. The example follows the MPI-parallel execution mode (note the `MPIBackend()` argument to the `with_backend` function call) and thus it must be executed on 4 MPI tasks (note the mesh is partitioned into 4 parts) using the instructions [below](https://github.com/gridap/GridapDistributed.jl#mpi-parallel-julia-script-execution-instructions). If a user wants to use the sequential execution mode, one just replaces `MPIBackend()` by `SequentialBackend()` in the call to `with_backend`. `GridapDistributed.jl` sequential execution mode scripts are executed as any other julia sequential script.
 
 ```julia
 using Gridap
 using GridapDistributed
 using PartitionedArrays
 partition = (2,2)
-prun(mpi,partition) do parts
+with_backend(MPIBackend(),partition) do parts
   domain = (0,1,0,1)
   mesh_partition = (4,4)
   model = CartesianDiscreteModel(parts,domain,mesh_partition)
@@ -64,7 +64,7 @@ prun(mpi,partition) do parts
   writevtk(Ω,"results",cellfields=["uh"=>uh,"grad_uh"=>∇(uh)])
 end
 ```
-The domain is discretized using the parallel Cartesian-like mesh generator built-in in `GridapDistributed`. The only minimal difference with respect to the sequential `Gridap` script is a call to the `prun` function of [`PartitionedArrays.jl`](https://github.com/fverdugo/PartitionedArrays.jl) right at the beginning of the program. With this function, the programer sets up the `PartitionedArrays.jl` communication backend (i.e., MPI in the example), specifies the number of parts and their layout (i.e., 2x2 partition in the example), and provides a function (using Julia do-block syntax for function arguments in the example) to be run on each part. The function body is equivalent to a sequential `Gridap` script, except for the `CartesianDiscreteModel` call, which in `GridapDistributed` also requires the `parts` argument passed back by the `prun` function.
+The domain is discretized using the parallel Cartesian-like mesh generator built-in in `GridapDistributed`. The only minimal difference with respect to the sequential `Gridap` script is a call to the `with_backend` function of [`PartitionedArrays.jl`](https://github.com/fverdugo/PartitionedArrays.jl) right at the beginning of the program. With this function, the programer sets up the `PartitionedArrays.jl` communication backend (i.e., MPI in the example), specifies the number of parts and their layout (i.e., 2x2 partition in the example), and provides a function (using Julia do-block syntax for function arguments in the example) to be run on each part. The function body is equivalent to a sequential `Gridap` script, except for the `CartesianDiscreteModel` call, which in `GridapDistributed` also requires the `parts` argument passed back by the `with_backend` function.
 
 ## Using parallel solvers
 
@@ -89,7 +89,7 @@ using GridapPETSc
 using GridapDistributed
 using PartitionedArrays
 n = 6
-prun(mpi,n) do parts
+with_backend(MPIBackend(),n) do parts
   options = "-ksp_type cg -pc_type gamg -ksp_monitor"
   GridapPETSc.with(args=split(options)) do
     model = GmshDiscreteModel(parts,"demo.msh")

diff --git a/test/StokesOpenBoundaryTests.jl b/test/StokesOpenBoundaryTests.jl
@@ -22,7 +22,7 @@ function main(parts)
   g(t) = x -> (∇⋅u(t))(x)
   h(t) = x -> ∇(u(t))(x)⋅VectorValue(0.0,1.0) - p(t)(x)*VectorValue(0.0,1.0)
 
-  parts = get_part_ids(sequential,(2,2))
+  parts = get_part_ids(SequentialBackend(),(2,2))
   domain = (0,1,0,1)
   partition = (4,4)
   model = CartesianDiscreteModel(parts,domain,partition)

diff --git a/test/SurfaceCouplingTests.jl b/test/SurfaceCouplingTests.jl
@@ -21,7 +21,7 @@ g(x) = tr(∇u(x))
 function main(parts)
 
   # Mesh
-  parts = get_part_ids(sequential,(2,2))
+  parts = get_part_ids(SequentialBackend(),(2,2))
   cells = (10,10)
   domain = (0,1,0,1)
   model = CartesianDiscreteModel(parts,domain,cells)

diff --git a/test/TestApp/compile/compile.jl b/test/TestApp/compile/compile.jl
@@ -10,7 +10,7 @@ module sysimagegenerator
 
    include("../../mpi/runtests_np4_body.jl")
 
-   prun(all_tests,mpi,(1,1))
+   with_backend(all_tests,MPIBackend(),(1,1))
 
    MPI.Finalize()
 

diff --git a/test/mpi/runtests_np4.jl b/test/mpi/runtests_np4.jl
@@ -13,9 +13,9 @@ end
 include("runtests_np4_body.jl")
 
 if MPI.Comm_size(MPI.COMM_WORLD) == 4
-  prun(all_tests,mpi,(2,2))
+  with_backend(all_tests,MPIBackend(),(2,2))
 elseif MPI.Comm_size(MPI.COMM_WORLD) == 1
-  prun(all_tests,mpi,(1,1))
+  with_backend(all_tests,MPIBackend(),(1,1))
 else
   MPI.Abort(MPI.COMM_WORLD,0)
 end

diff --git a/test/sequential/CellDataTests.jl b/test/sequential/CellDataTests.jl
@@ -1,5 +1,5 @@
 module CellDataTestsSeq
 using PartitionedArrays
 include("../CellDataTests.jl")
-prun(CellDataTests.main,sequential,(2,2))
+with_backend(CellDataTests.main,SequentialBackend(),(2,2))
 end # module
diff --git a/test/sequential/DivConformingTests.jl b/test/sequential/DivConformingTests.jl
@@ -1,5 +1,5 @@
 module DivConformingTestsSeq
 using PartitionedArrays
 include("../DivConformingTests.jl")
-prun(DivConformingTests.main,sequential,2)
+with_backend(DivConformingTests.main,SequentialBackend(),2)
 end # module
diff --git a/test/sequential/FESpacesTests.jl b/test/sequential/FESpacesTests.jl
@@ -1,5 +1,5 @@
 module FESpacesTestsSeq
 using PartitionedArrays
 include("../FESpacesTests.jl")
-prun(FESpacesTests.main,sequential,(2,2))
+with_backend(FESpacesTests.main,SequentialBackend(),(2,2))
 end # module
diff --git a/test/sequential/GeometryTests.jl b/test/sequential/GeometryTests.jl
@@ -1,6 +1,6 @@
 module GeometryTestsSeq
 using PartitionedArrays
 include("../GeometryTests.jl")
-prun(GeometryTests.main,sequential,(2,2))
-prun(GeometryTests.main,sequential,(2,2,2))
+with_backend(GeometryTests.main,SequentialBackend(),(2,2))
+with_backend(GeometryTests.main,SequentialBackend(),(2,2,2))
 end
diff --git a/test/sequential/HeatEquationTests.jl b/test/sequential/HeatEquationTests.jl
@@ -1,5 +1,5 @@
 module HeatEquationTestsSeq
 using PartitionedArrays
 include("../HeatEquationTests.jl")
-prun(HeatEquationTests.main,sequential,(2,2))
+with_backend(HeatEquationTests.main,SequentialBackend(),(2,2))
 end # module
diff --git a/test/sequential/MultiFieldTests.jl b/test/sequential/MultiFieldTests.jl
@@ -1,5 +1,5 @@
 module MultiFieldTestsSeq
 using PartitionedArrays
 include("../MultiFieldTests.jl")
-prun(MultiFieldTests.main,sequential,(2,2))
+with_backend(MultiFieldTests.main,SequentialBackend(),(2,2))
 end # module
diff --git a/test/sequential/PLaplacianTests.jl b/test/sequential/PLaplacianTests.jl
@@ -1,5 +1,5 @@
 module PLaplacianTestsSeq
 using PartitionedArrays
 include("../PLaplacianTests.jl")
-prun(PLaplacianTests.main,sequential,(2,2))
+with_backend(PLaplacianTests.main,SequentialBackend(),(2,2))
 end # module
diff --git a/test/sequential/PeriodicBCsTests.jl b/test/sequential/PeriodicBCsTests.jl
@@ -12,17 +12,17 @@ reffe = ReferenceFE(lagrangian,Float64,1)
 ndofss = [25,20,20,16]
 for np in nps
   for (ndofs, isperiodic) in zip(ndofss,isperiodics)
-    parts = get_part_ids(sequential,np)
+    parts = get_part_ids(SequentialBackend(),np)
     model = CartesianDiscreteModel(parts,domain,cells;isperiodic=isperiodic)
     V = FESpace(model,reffe)
     @test ndofs == num_free_dofs(V)
   end
 end
 
 include("../PeriodicBCsTests.jl")
-prun(PeriodicBCsTests.main,sequential,(2,2))
-prun(PeriodicBCsTests.main,sequential,(2,1))
-prun(PeriodicBCsTests.main,sequential,(1,1))
-prun(PeriodicBCsTests.main,sequential,(1,2))
-prun(PeriodicBCsTests.main,sequential,(2,3))
+with_backend(PeriodicBCsTests.main,SequentialBackend(),(2,2))
+with_backend(PeriodicBCsTests.main,SequentialBackend(),(2,1))
+with_backend(PeriodicBCsTests.main,SequentialBackend(),(1,1))
+with_backend(PeriodicBCsTests.main,SequentialBackend(),(1,2))
+with_backend(PeriodicBCsTests.main,SequentialBackend(),(2,3))
 end # module
diff --git a/test/sequential/PoissonTests.jl b/test/sequential/PoissonTests.jl
@@ -1,5 +1,5 @@
 module PoissonTestsSeq
 using PartitionedArrays
 include("../PoissonTests.jl")
-prun(PoissonTests.main,sequential,(2,2))
+with_backend(PoissonTests.main,SequentialBackend(),(2,2))
 end # module
diff --git a/test/sequential/StokesOpenBoundaryTests.jl b/test/sequential/StokesOpenBoundaryTests.jl
@@ -1,5 +1,5 @@
 module StokesOpenBoundaryTestsSeq
 using PartitionedArrays
 include("../StokesOpenBoundaryTests.jl")
-prun(StokesOpenBoundaryTests.main,sequential,(2,2))
+with_backend(StokesOpenBoundaryTests.main,SequentialBackend(),(2,2))
 end # module
diff --git a/test/sequential/SurfaceCouplingTests.jl b/test/sequential/SurfaceCouplingTests.jl
@@ -1,6 +1,6 @@
 module SurfaceCouplingTestsSeq
 using PartitionedArrays
 include("../SurfaceCouplingTests.jl")
-prun(SurfaceCouplingTests.main,sequential,(2,2))
+with_backend(SurfaceCouplingTests.main,SequentialBackend(),(2,2))
 end # module
 
diff --git a/test/sequential/TransientDistributedCellFieldTests.jl b/test/sequential/TransientDistributedCellFieldTests.jl
@@ -1,5 +1,5 @@
 module TransientDistributedCellFieldTestsSeq
 using PartitionedArrays
 include("../TransientDistributedCellFieldTests.jl")
-prun(TransientDistributedCellFieldTests.main,sequential,(2,2))
+with_backend(TransientDistributedCellFieldTests.main,SequentialBackend(),(2,2))
 end # module
diff --git a/test/sequential/TransientMultiFieldDistributedCellFieldTests.jl b/test/sequential/TransientMultiFieldDistributedCellFieldTests.jl
@@ -1,5 +1,5 @@
 module TransientMultiFieldDistributedCellFieldTestsSeq
 using PartitionedArrays
 include("../TransientMultiFieldDistributedCellFieldTests.jl")
-prun(TransientMultiFieldDistributedCellFieldTests.main,sequential,(2,2))
+with_backend(TransientMultiFieldDistributedCellFieldTests.main,SequentialBackend(),(2,2))
 end # module