P4 est enable mpi

README.md

@@ -55,7 +55,7 @@ julia> using p4est_wrapper
   - Latests versions of julia `MPI` use artifacts to locally install a MPI distribution. You should take care with the compatibility (version/vendor/distribution) between the parallel `p4est` and `MPI` libraries. If you want julia `MPI` library to wrap your local MPI library, you must export `JULIA_MPI_BINARY="system"` before installing the package.
   - Parallel `p4est` library can be manually installed in a custom path on your local machine. In order to succesfull describe your custom installation to be discovered by `p4est_wrapper`, you must export `P4EST_ROOT_DIR` environment variable pointing to the installation directory. If this environment variable is not available, and `julia >= 1.3`, `p4est_wrapper` will try to  use [`P4est_jll` artifact](https://github.com/JuliaBinaryWrappers/P4est_jll.jl), but you should take into account that this artifact is not for parallel computations (MPI not enabled). Finally, in other case `p4est_wrapper` will try to find the `p4est` library in the usual linux user library directory (`/usr/lib`).
 
-#### Basic OpenMPIMPI installation in debian based systems
+#### Basic OpenMPI installation in debian based systems
 
 `MPI` can be obtained from the default repositories of your Debian-based OS by means of `apt` tool.
 

deps/build.jl

@@ -1,9 +1,11 @@
 using Libdl
 
+P4EST_ARTIFACT = false
 if VERSION < v"1.3"
     DEFAULT_P4EST_ROOT_DIR = "/usr"
 else
     using P4est_jll
+    P4EST_ARTIFACT = true
     DEFAULT_P4EST_ROOT_DIR = P4est_jll.artifact_dir
 end
 
@@ -15,6 +17,9 @@ P4EST_INCLUDE_DIR  = haskey(ENV,"P4EST_INCLUDE_DIR") ? ENV["P4EST_INCLUDE_DIR"]
 P4EST_LIB_NAME     = haskey(ENV,"P4EST_LIB_NAME") ? ENV["P4EST_LIB_NAME"] : "libp4est"
 P4EST_LIB          = haskey(ENV,"P4EST_LIB") ? ENV["P4EST_LIB"] : ""
 
+DEFAULT_P4EST_ENABLE_MPI = !haskey(ENV,"P4EST_ROOT_DIR") && P4EST_ARTIFACT ? false : true
+P4EST_ENABLE_MPI   = haskey(ENV,"P4EST_ENABLE_MPI") ? Bool(ENV["P4EST_ENABLE_MPI"]) : DEFAULT_P4EST_ENABLE_MPI
+
 
 # Check P4EST_DIR exists
 if isdir(P4EST_DIR)
@@ -68,6 +73,7 @@ P4EST configuration:
   - P4EST_LIB_DIR         = $P4EST_LIB_DIR
   - P4EST_INCLUDE_DIR     = $P4EST_INCLUDE_DIR
   - P4EST_LIB             = $P4EST_LIB
+  - P4EST_ENABLE_MPI      = $P4EST_ENABLE_MPI
 """
 
 if !P4EST_FOUND
@@ -90,4 +96,5 @@ open(deps_jl,"w") do f
   println(f, :(const P4EST_LIB_DIR         = $P4EST_LIB_DIR))
   println(f, :(const P4EST_INCLUDE_DIR     = $P4EST_INCLUDE_DIR))
   println(f, :(const P4EST_LIB             = $P4EST_LIB))
+  println(f, :(const P4EST_ENABLE_MPI      = $P4EST_ENABLE_MPI))
 end

gen/Project.toml

@@ -1,2 +1,7 @@
 [deps]
 Clang = "40e3b903-d033-50b4-a0cc-940c62c95e31"
+
+[compat]
+Clang = "0.10.1"
+julia = "1.0"
+

src/api_fixes.jl

@@ -51,3 +51,25 @@ function p4est_init(log_handler, log_threshold)
     ccall((:p4est_init, p4est_lib), Cvoid, (sc_log_handler_t, Cint), log_handler, log_threshold)
 end
 
+################################################################
+# Dereference functions
+# Not part of P4est, but really usefull to access data from pointers
+################################################################
+
+PXEST_NAMED_STRUCTS = Union{p4est_quadrant, p4est_tree, p4est_inspect, p4est_connectivity, p4est, p4est_geometry,
+                            p4est_ghost_t, p4est_ghost_exchange, p4est_iter_volume_info, p4est_iter_face_side,
+                            p4est_iter_face_side, p4est_iter_corner_side, p4est_iter_corner_info, p4est_lnodes,
+                            p4est_lnodes_rank, p4est_lnodes_buffer, p4est_search_local_t, p4est_vtk_context, 
+                            p6est_connectivity, p2est_quadrant, p6est_ghost, p8est_quadrant, p8est_tree, sc_array,
+                            p8est_inspect, p8est_connectivity, p8est_connectivity, p8est_geometry, p8est_ghost_t,
+                            p8est_ghost_exchange, p8est_iter_volume_info, p8est_iter_face_side, p8est_iter_face_info,
+                            p8est_iter_edge_side, p8est_iter_edge_info, p8est_iter_corner_side, p8est_iter_corner_info, 
+                            p8est_lnodes, p8est_lnodes_rank, p8est_lnodes_buffer, p8est_search_local_t, p8est_vtk_context}
+
+function Base.getindex(ptr::Ptr{T}) where {T<:PXEST_NAMED_STRUCTS}
+    unsafe_wrap(Array, ptr, 1)[]
+end
+
+function Base.getindex(ptr::Ptr{T}, i) where {T<:PXEST_NAMED_STRUCTS}
+    unsafe_wrap(Array, ptr, i)[i]
+end

src/common_fixes.jl

@@ -1,11 +1,16 @@
 ################################################################
 # Base fixed datatypes
 ################################################################
-const FILE = Cvoid # File descriptor
-const ssize_t = Cssize_t
-const MPI_Comm = MPI.MPI_Comm
-const MPI_File = MPI.MPI_File
+const FILE         = Cvoid # File descriptor
+if P4EST_ENABLE_MPI
+    const MPI_Comm = MPI.MPI_Comm
+else
+    const MPI_Comm = Cint
+end
 const MPI_Datatype = MPI.MPI_Datatype
+const MPI_File     = MPI.MPI_File
+const sc_MPI_Comm  = MPI_Comm
+const ssize_t      = Cssize_t
 
 ################################################################
 # Non-wrapped but required data types

test/example_1.jl

@@ -17,7 +17,7 @@ struct point_t x::Cdouble; y::Cdouble; end
 # Refine callback
 function my_refine( ::Ptr{p4est_t}, which_tree::p4est_topidx_t, quadrant::Ptr{p4est_quadrant_t})
     @assert which_tree == 0
-    q = unsafe_wrap(Array,quadrant,1)[1]
+    q = quadrant[]
     ((q.level == 0) || (q.level < 5 && p4est_quadrant_child_id(quadrant) == 1)) && return Cint(1)
     return Cint(0)
 end
@@ -38,12 +38,14 @@ const search_point_fn_c = @cfunction(search_point_fn, Cint, (Ptr{p4est_t}, p4est
 # Main program
 #############################################################################
 
+mpicomm = p4est_wrapper.P4EST_ENABLE_MPI ? MPI.COMM_WORLD : Cint(0)
+
 # Create a connectivity structure for the unit square.
 unitsquare_connectivity = p4est_connectivity_new_unitsquare() 
 @test unitsquare_connectivity != C_NULL
 
 # Create a new forest
-unitsquare_forest = p4est_new(MPI.COMM_WORLD, unitsquare_connectivity, 0, C_NULL, C_NULL) 
+unitsquare_forest = p4est_new(mpicomm, unitsquare_connectivity, 0, C_NULL, C_NULL) 
 @test unitsquare_forest != C_NULL
 
 # Register callback function to decide for refinement. 
@@ -54,7 +56,7 @@ ptr_to_points_sc_array = sc_array_new_count(sizeof(point_t), 2)
 @test ptr_to_points_sc_array != C_NULL
 
 # Check correct number of elements and its size in sc_array
-points_sc_array = unsafe_wrap(Array, ptr_to_points_sc_array, 1)[1]
+points_sc_array = ptr_to_points_sc_array[]
 @test points_sc_array.elem_count == 2 && points_sc_array.elem_size == sizeof(point_t)
 
 # Obtain reference to first point_t 

test/example_2.jl

@@ -14,7 +14,7 @@ end
 # Refine callback
 function my_refine( ::Ptr{p4est_t}, which_tree::p4est_topidx_t, quadrant::Ptr{p4est_quadrant_t})
     @assert which_tree == 0
-    q = unsafe_wrap(Array,quadrant,1)[1]
+    q = quadrant[]
     ((q.level == 0) || (q.level < 2 && p4est_quadrant_child_id(quadrant) == 1)) && return Cint(1)
     return Cint(0)
 end
@@ -26,12 +26,14 @@ const my_refine_c = @cfunction(my_refine, Cint, (Ptr{p4est_t}, p4est_topidx_t, P
 # Main program
 #############################################################################
 
+mpicomm = p4est_wrapper.P4EST_ENABLE_MPI ? MPI.COMM_WORLD : Cint(0)
+
 # Create a connectivity structure for the unit square.
 unitsquare_connectivity = p4est_connectivity_new_unitsquare() 
 @assert Bool(p4est_connectivity_is_valid(unitsquare_connectivity))
 
 # Create a new forest
-unitsquare_forest = p4est_new(MPI.COMM_WORLD, unitsquare_connectivity, sizeof(p4est_quadrant_t), C_NULL, C_NULL) 
+unitsquare_forest = p4est_new(mpicomm, unitsquare_connectivity, sizeof(p4est_quadrant_t), C_NULL, C_NULL) 
 @test unitsquare_forest != C_NULL
 
 # Register callback function to decide for refinement. 
@@ -42,23 +44,20 @@ p4est_partition(unitsquare_forest, 0, C_NULL);
 
 # Build the ghost layer. 
 ptr_to_p4est_ghost = p4est_ghost_new(unitsquare_forest, p4est_wrapper.P4EST_CONNECT_FULL)
-p4est_ghost = unsafe_wrap(Array,ptr_to_p4est_ghost,1)[1]
+p4est_ghost = ptr_to_p4est_ghost[]
 
 # Obtain ghost quadrants
 ##p4est_quadrant_t * ptr_ghost_quadrants = (p4est_quadrant_t *) p4est_ghost->ghosts.array;
 ptr_ghost_quadrants = Ptr{p4est_quadrant_t}(p4est_ghost.ghosts.array)
 proc_offsets = unsafe_wrap(Array, p4est_ghost.proc_offsets, p4est_ghost.mpisize+1)
-ghost_quadrants = unsafe_wrap(Array, ptr_ghost_quadrants, p4est_ghost.ghosts.elem_count)
 
-let mpirank = MPI.Comm_rank(MPI.COMM_WORLD)
-    for i=1:p4est_ghost.mpisize
-        for j=proc_offsets[i]:proc_offsets[i+1]-1
-            quadrant = ghost_quadrants[j+1]
-            piggy3 = quadrant.p.piggy3
-            @test Bool(p4est_quadrant_is_valid(ptr_ghost_quadrants+(sizeof(p4est_quadrant_t)*j)))
-            p4est_quadrant_print(p4est_wrapper.SC_LP_INFO, ptr_ghost_quadrants+(sizeof(p4est_quadrant_t)*j))
-            print("(rank, local_num, which_tree) ($(mpirank),$(piggy3.local_num),$(piggy3.which_tree)) \n")
-        end
+for i=1:p4est_ghost.mpisize
+    for j=proc_offsets[i]:proc_offsets[i+1]-1
+        quadrant = ptr_ghost_quadrants[j+1]
+        piggy3 = quadrant.p.piggy3
+        @test Bool(p4est_quadrant_is_valid(ptr_ghost_quadrants+(sizeof(p4est_quadrant_t)*j)))
+        p4est_quadrant_print(p4est_wrapper.SC_LP_INFO, ptr_ghost_quadrants+(sizeof(p4est_quadrant_t)*j))
+        print("(i, j, local_num, which_tree) ($(i),$(j),$(piggy3.local_num),$(piggy3.which_tree)) \n")
     end
 end
 

test/example_3.jl

@@ -32,9 +32,9 @@ function init_fn_callback_2d(forest_ptr::Ptr{p4est_t},
                             quadrant_ptr::Ptr{p4est_quadrant_t})
     @assert which_tree == 0
     # Extract a reference to the first (and uniquely allowed) tree
-    forest = unsafe_wrap(Array, forest_ptr, 1)[1]
-    tree = unsafe_wrap(Array, p4est_tree_array_index(forest.trees, 0), 1)[1]
-    quadrant = unsafe_wrap(Array, quadrant_ptr, 1)[1]
+    forest = forest_ptr[]
+    tree = p4est_tree_array_index(forest.trees, 0)[]
+    quadrant = quadrant_ptr[]
     q = p4est_quadrant_array_index(tree.quadrants, current_quadrant_index)
     @assert p4est_quadrant_compare(q,quadrant_ptr) == 0
     user_data  = unsafe_wrap(Array, Ptr{Cint}(forest.user_pointer), current_quadrant_index+1)[current_quadrant_index+1]
@@ -49,8 +49,8 @@ function refine_callback_2d(::Ptr{p4est_t},
                             which_tree::p4est_topidx_t, 
                             quadrant_ptr::Ptr{p4est_quadrant_t})
     @assert which_tree == 0
-    quadrant = unsafe_wrap(Array, quadrant_ptr, 1)[1]
-    return Cint(unsafe_wrap(Array, Ptr{Cint}(quadrant.p.user_data),1)[1] == refine_flag)
+    quadrant = quadrant_ptr[]
+    return Cint(unsafe_wrap(Array, Ptr{Cint}(quadrant.p.user_data),1)[] == refine_flag)
 end
 
 const refine_callback_2d_c = @cfunction(refine_callback_2d, Cint, (Ptr{p4est_t}, p4est_topidx_t, Ptr{p4est_quadrant_t}))
@@ -69,7 +69,7 @@ function refine_replace_callback_2d(forest_ptr::Ptr{p4est_t},
     @assert num_incoming == p4est_wrapper.P4EST_CHILDREN
     incoming = unsafe_wrap(Array, incoming_ptr, p4est_wrapper.P4EST_CHILDREN)
     for quadrant_index = 1:p4est_wrapper.P4EST_CHILDREN
-        quadrant = unsafe_wrap(Array, incoming[quadrant_index], 1)[1]
+        quadrant = incoming[quadrant_index][]
         if (num_calls % 2 == 0)
             unsafe_store!(Ptr{Cint}(quadrant.p.user_data), nothing_flag, 1)
         else
@@ -89,8 +89,8 @@ function coarsen_callback_2d(forest_ptr::Ptr{p4est_t},
     coarsen = Cint(1)
     quadrants = unsafe_wrap(Array, quadrants_ptr, p4est_wrapper.P4EST_CHILDREN)
     for quadrant_index = 1:p4est_wrapper.P4EST_CHILDREN
-        quadrant = unsafe_wrap(Array, quadrants[quadrant_index], 1)[1]
-        coarsen = Cint(unsafe_wrap(Array, Ptr{Cint}(quadrant.p.user_data), 1)[1] ==  coarsen_flag)
+        quadrant = quadrants[quadrant_index][]
+        coarsen = Cint(unsafe_wrap(Array, Ptr{Cint}(quadrant.p.user_data), 1)[] ==  coarsen_flag)
         if (!Bool(coarsen)) return coarsen end
     end
     return coarsen
@@ -101,8 +101,8 @@ const coarsen_callback_2d_c = @cfunction(coarsen_callback_2d, Cint, (Ptr{p4est_t
 ## Refine those cells with even identifier    (0,2,4,6,8,...)
 ## Leave untouched cells with odd identifier  (1,3,5,7,9,...)
 function allocate_and_set_refinement_and_coarsening_flags(forest_ptr::Ptr{p4est_t})
-    forest = unsafe_wrap(Array, forest_ptr, 1)[1]
-    tree = unsafe_wrap(Array, p4est_tree_array_index(forest.trees, 0), 1)[1]
+    forest = forest_ptr[]
+    tree = p4est_tree_array_index(forest.trees, 0)[]
     refinement_and_coarsening_flags = Ptr{Cint}(Libc.malloc(sizeof(Cint)*tree.quadrants.elem_count))
     for i = 1:tree.quadrants.elem_count
         if (i%2 == 0)
@@ -129,11 +129,12 @@ end
 # Main program
 #############################################################################
 
-sc_init(MPI.COMM_WORLD, Cint(true), Cint(true), C_NULL, p4est_wrapper.SC_LP_DEFAULT)
+mpicomm = p4est_wrapper.P4EST_ENABLE_MPI ? MPI.COMM_WORLD : Cint(0)
+sc_init(mpicomm, Cint(true), Cint(true), C_NULL, p4est_wrapper.SC_LP_DEFAULT)
 p4est_init(C_NULL, p4est_wrapper.SC_LP_DEFAULT)
 
 unitsquare_connectivity = p4est_connectivity_new_unitsquare()
-unitsquare_forest = p4est_new(MPI.COMM_WORLD, unitsquare_connectivity, 0, C_NULL, C_NULL)
+unitsquare_forest = p4est_new(mpicomm, unitsquare_connectivity, 0, C_NULL, C_NULL)
 
 for i=1:7
     perform_single_mesh_adaptation_step(unitsquare_forest,i)

test/test_p4est_bindings.jl

@@ -11,6 +11,8 @@ end
 # Definition of data structures and function callbacks
 #############################################################################
 
+mpicomm = p4est_wrapper.P4EST_ENABLE_MPI ? MPI.COMM_WORLD : Cint(0)
+
 # Dummy callback
 dummy_callback( ::Ptr{p4est_t}, which_tree::p4est_topidx_t, quadrant::Ptr{p4est_quadrant_t}) = Cint(0)
 
@@ -44,7 +46,7 @@ for test_conn in [p4est_connectivity_new_periodic(),
 end
 
 # Create a new forest
-unitsquare_forest = p4est_new(MPI.COMM_WORLD, unitsquare_connectivity, 0, C_NULL, C_NULL) 
+unitsquare_forest = p4est_new(mpicomm, unitsquare_connectivity, 0, C_NULL, C_NULL) 
 @test unitsquare_forest != C_NULL
 
 # Create/Destroy geometry

test/test_p8est_bindings.jl

@@ -10,6 +10,7 @@ end
 #############################################################################
 # Definition of data structures and function callbacks
 #############################################################################
+mpicomm = p4est_wrapper.P4EST_ENABLE_MPI ? MPI.COMM_WORLD : Cint(0)
 
 # Dummy callback
 dummy_callback( ::Ptr{p8est_t}, which_tree::p4est_topidx_t, quadrant::Ptr{p8est_quadrant_t}) = Cint(0)
@@ -43,7 +44,7 @@ for test_conn in [p8est_connectivity_new_periodic(),
 end
 
 # Create a new forest
-unitcube_forest = p8est_new(MPI.COMM_WORLD, unitcube_connectivity, 0, C_NULL, C_NULL) 
+unitcube_forest = p8est_new(mpicomm, unitcube_connectivity, 0, C_NULL, C_NULL) 
 @test unitcube_forest != C_NULL
 
 # Create/Destroy geometry

test/test_sc_bindings.jl

@@ -10,9 +10,11 @@ if !MPI.Initialized()
     MPI.Init()
 end
 
+mpicomm = p4est_wrapper.P4EST_ENABLE_MPI ? MPI.COMM_WORLD : Cint(0)
+
 # SC library initialization
-sc_init(MPI.COMM_WORLD, Cint(true), Cint(true), C_NULL, p4est_wrapper.SC_LP_DEFAULT)
-@test sc_is_root() ==  (MPI.Comm_rank(MPI.COMM_WORLD) == 0 ? 1 : 0)
+sc_init(mpicomm, Cint(true), Cint(true), C_NULL, p4est_wrapper.SC_LP_DEFAULT)
+@test typeof(sc_is_root()) == Cint
 
 # SC package related API
 id = sc_package_register(C_NULL, p4est_wrapper.SC_LP_INFO, "p4est", "A forest of octrees")