Major reworks to internals.

Project.toml

@@ -1,6 +1,6 @@
 name = "Exodus"
 uuid = "f57ae99e-f805-4780-bdca-96e224be1e5a"
-version = "0.14.4"
+version = "0.15.0"
 authors = ["cmhamel <cmhamel32@gmail.com>"]
 
 [deps]

lib/IncludeMe.jl

@@ -1,11 +1,9 @@
 include("LibExodus.jl")
 # TODO make below constants not hardcoded. Read from LibExodus.
-const cpu_word_size = Int32(sizeof(Float64)) # TODO make parametric so we can have float models
-const IO_word_size = Int32(8)                # This was what we did before
+const cpu_word_size  = Int32(sizeof(Float64)) # TODO make parametric so we can have float models
+const IO_word_size   = Int32(8)               # This was what we did before
 const version_number = LibExodus.EX_API_VERS
 import .LibExodus:
-    ex_entity_type,
-    ex_inquiry,
     EX_ABORT,
     EX_API_VERS_NODOT,
     EX_BULK_INT64_API,
@@ -27,4 +25,4 @@ import .LibExodus:
     EX_WRITE,
     EX_VERBOSE,
     MAX_LINE_LENGTH,
-    MAX_STR_LENGTH
+    MAX_STR_LENGTH

lib/LibExodus.jl

@@ -5,6 +5,11 @@ export Exodus_jll
 
 using CEnum: CEnum, @cenum
 
+to_c_type(t::Type) = t
+to_c_type_pairs(va_list) = map(enumerate(to_c_type.(va_list))) do (ind, type)
+    :(va_list[$ind]::$type)
+end
+
 function interface(nvtxs, start, adjacency, vwgts, ewgts, x, y, z, outassignname, outfilename, assignment, architecture, ndims_tot, mesh_dims, goal, global_method, local_method, rqi_flag, vmax, ndims, eigtol, seed)
     @ccall libexodus.interface(nvtxs::Cint, start::Ptr{Cint}, adjacency::Ptr{Cint}, vwgts::Ptr{Cint}, ewgts::Ptr{Cfloat}, x::Ptr{Cfloat}, y::Ptr{Cfloat}, z::Ptr{Cfloat}, outassignname::Cstring, outfilename::Cstring, assignment::Ptr{Cint}, architecture::Cint, ndims_tot::Cint, mesh_dims::Ptr{Cint}, goal::Ptr{Cdouble}, global_method::Cint, local_method::Cint, rqi_flag::Cint, vmax::Cint, ndims::Cint, eigtol::Cdouble, seed::Clong)::Cint
 end
@@ -2258,8 +2263,6 @@ const CHACO_VERSION_MINOR = 0
 
 const CHACO_VERSION_PATCH = 0
 
-# const EX_MAX_NAME = NC_MAX_NAME
-
 const EXODUS_VERSION = "9.04"
 
 const EXODUS_VERSION_MAJOR = 9

lib/generator.toml

@@ -46,17 +46,9 @@ epilogue_file_path = ""
 
 # node with an id in the `output_ignorelist` will be ignored in the printing passes.
 # this is very useful for custom editing.
-# output_ignorelist = [
-#     "CINDEX_EXPORTS",
-#     "CINDEX_VERSION",
-#     "CINDEX_VERSION_STRING",
-#     "CINDEX_LINKAGE",
-#     "CINDEX_DEPRECATED",
-#     "LLVM_CLANG_C_STRICT_PROTOTYPES_BEGIN",
-#     "LLVM_CLANG_C_STRICT_PROTOTYPES_END",
-#     "LLVM_CLANG_C_EXTERN_C_BEGIN",
-#     "LLVM_CLANG_C_EXTERN_C_END"
-# ]
+output_ignorelist = [
+    "EX_MAX_NAME"
+]
 
 # Julia's `@enum` do not allow duplicated values, so by default, C enums are translated to
 # CEnum.jl's `@cenum`.
@@ -176,7 +168,7 @@ opaque_as_mutable_struct = true
 use_ccall_macro = true
 
 # if true, variadic functions are wrapped with `@ccall` macro. Otherwise variadic functions are ignored.
-wrap_variadic_function = false
+wrap_variadic_function = true
 
 # Generate getproperty/setproperty! methods for the types in the following list.
 # Warning: the generated methods will only work on the architecture that they
@@ -213,4 +205,7 @@ ignore_header_guards = true
 ignore_header_guards_with_suffixes = []
 
 # if true, ignore those pure definition macros in the C code
-ignore_pure_definition = true
+ignore_pure_definition = true
+
+[codegen.typemap]
+"Ptr{Cvoid}" = "Ptr{Cfloat}"

lib/make.jl

@@ -1,7 +1,22 @@
 using Clang.Generators
-# using Clang.LibClang.Clang_unified_jll
 using Exodus_jll
 
+function patch!(ctx)
+    Clang.Generators.walk!(ctx.dag) do node
+        if node isa Clang.Generators.FunctionDecl
+            for arg in node.args
+                if arg.type == :(Ptr{Cvoid})
+                    arg.type = :(Ptr{Cfloat})
+                end
+            end
+
+            if node.rettype == :(Ptr{Cvoid})
+                node.rettype = :(Ptr{Cfloat})
+            end
+        end
+    end
+end
+
 cd(@__DIR__)
 
 include_dir = normpath(Exodus_jll.artifact_dir, "include")

src/Blocks.jl

@@ -6,32 +6,29 @@ TODO fix this to not use void_int... use a proper type
 function read_block_id_map(exo::ExodusDatabase{M, I, B, F}, block_id) where {M, I, B, F}
   _, num_elem, _, _, _, _ = read_block_parameters(exo, block_id)
   block_id_map = Vector{get_map_int_type(exo)}(undef, num_elem)
-  error_code = @ccall libexodus.ex_get_block_id_map(
-    get_file_id(exo)::Cint, EX_ELEM_BLOCK::ex_entity_type, block_id::ex_entity_id, block_id_map::Ptr{B}
-  )::Cint
-  exodus_error_check(exo, error_code, "Exodus.read_element_block_id_map -> libexodus.ex_get_block_id_map")
+  error_code = LibExodus.ex_get_block_id_map(get_file_id(exo), EX_ELEM_BLOCK, block_id, block_id_map)
+  exodus_error_check(exo, error_code, "Exodus.read_element_block_id_map -> LibExodus.ex_get_block_id_map")
   return block_id_map
 end
 
 """
 $(TYPEDSIGNATURES)
 """
 function read_block_parameters(exo::ExodusDatabase{M, I, B, F}, block_id::Integer) where {M, I, B, F}
-  num_elem       = Ref{B}(0)
-  num_nodes      = Ref{B}(0)
-  num_edges      = Ref{B}(0)
-  num_faces      = Ref{B}(0)
-  num_attributes = Ref{B}(0)
-
-  element_type = Vector{UInt8}(undef, MAX_STR_LENGTH)
-
-  error_code = @ccall libexodus.ex_get_block(
-    get_file_id(exo)::Cint, EX_ELEM_BLOCK::ex_entity_type, block_id::ex_entity_id,
-    element_type::Ptr{UInt8}, 
-    num_elem::Ptr{B}, num_nodes::Ptr{B}, num_edges::Ptr{B},
-    num_faces::Ptr{B}, num_attributes::Ptr{B}
-  )::Cint
-  exodus_error_check(exo, error_code, "Exodus.read_element_block_parameters -> libexodus.ex_get_block")
+  num_elem       = Base.RefValue{B}(0)
+  num_nodes      = Base.RefValue{B}(0)
+  num_edges      = Base.RefValue{B}(0)
+  num_faces      = Base.RefValue{B}(0)
+  num_attributes = Base.RefValue{B}(0)
+  element_type   = Vector{Cchar}(undef, MAX_STR_LENGTH)
+
+  error_code = LibExodus.ex_get_block(
+    get_file_id(exo), EX_ELEM_BLOCK, block_id,
+    pointer(element_type),
+    num_elem, num_nodes, num_edges,
+    num_faces, num_attributes
+  )
+  exodus_error_check(exo, error_code, "Exodus.read_element_block_parameters -> LibExodus.ex_get_block")
   element_type_out = unsafe_string(pointer(element_type))
   return element_type_out, num_elem[], num_nodes[], num_edges[], num_faces[], num_attributes[]
 end
@@ -41,11 +38,11 @@ $(TYPEDSIGNATURES)
 """
 function read_block_connectivity(exo::ExodusDatabase{M, I, B, F}, block_id::Integer, conn_length::Integer) where {M, I, B, F}
   conn = Vector{B}(undef, conn_length)
-  error_code = @ccall libexodus.ex_get_conn(
-    get_file_id(exo)::Cint, EX_ELEM_BLOCK::ex_entity_type, block_id::ex_entity_id,
-    conn::Ptr{B}, C_NULL::Ptr{Cvoid}, C_NULL::Ptr{Cvoid}
-  )::Cint
-  exodus_error_check(exo, error_code, "Exodus.read_element_block_connectivity -> libexodus.ex_get_conn")
+  error_code = LibExodus.ex_get_conn(
+    get_file_id(exo), EX_ELEM_BLOCK, block_id,
+    conn, C_NULL, C_NULL
+  )
+  exodus_error_check(exo, error_code, "Exodus.read_element_block_connectivity -> LibExodus.ex_get_conn")
   return conn
 end
 
@@ -60,11 +57,11 @@ function write_block_connectivity(exo::ExodusDatabase, block_id::Integer, conn::
   # TODO currently not using face or edges, should probably be there own methods maybe?
   conn_face = C_NULL  # Not using these currently
   conn_edge = C_NULL  # Not using these currently
-  error_code = @ccall libexodus.ex_put_conn(
-    get_file_id(exo)::Cint, EX_ELEM_BLOCK::ex_entity_type, block_id::ex_entity_id,
-    conn::Ptr{void_int}, conn_face::Ptr{void_int}, conn_edge::Ptr{void_int} 
-  )::Cint
-  exodus_error_check(exo, error_code, "Exodus_write_block_connectivity -> libexodus.ex_put_conn")
+  error_code = LibExodus.ex_put_conn(
+    get_file_id(exo), EX_ELEM_BLOCK, block_id,
+    conn, conn_face, conn_edge
+  )
+  exodus_error_check(exo, error_code, "Exodus_write_block_connectivity -> LibExodus.ex_put_conn")
 end
 
 """
@@ -76,24 +73,22 @@ function read_partial_block_connectivity(exo::ExodusDatabase, block_id::I, start
   conn = Vector{get_bulk_int_type(exo)}(undef, num_nodes * num_ent)
   conn_face = Vector{get_bulk_int_type(exo)}(undef, num_nodes * num_ent)  # Not using these currently
   conn_edge = Vector{get_bulk_int_type(exo)}(undef, num_nodes * num_ent)  # Not using these currently
-  error_code = @ccall libexodus.ex_get_partial_conn(
-    get_file_id(exo)::Cint, EX_ELEM_BLOCK::ex_entity_type, block_id::ex_entity_id,
-    start_num::Clonglong, num_ent::Clonglong,
-    conn::Ptr{void_int}, conn_face::Ptr{void_int}, conn_edge::Ptr{void_int}
-  )::Cint
-  exodus_error_check(exo, error_code, "Exodus.read_partial_element_block_connectivity -> libexodus.ex_get_partial_conn")
+  error_code = LibExodus.ex_get_partial_conn(
+    get_file_id(exo), EX_ELEM_BLOCK, block_id,
+    start_num, num_ent,
+    conn, conn_face, conn_edge
+  )
+  exodus_error_check(exo, error_code, "Exodus.read_partial_element_block_connectivity -> LibExodus.ex_get_partial_conn")
   return conn
 end
 
 """
 $(TYPEDSIGNATURES)
 """
 function read_element_type(exo::ExodusDatabase, block_id::I) where I <: Integer
-  element_type = Vector{UInt8}(undef, MAX_STR_LENGTH)
-  error_code = @ccall libexodus.ex_get_elem_type(
-    get_file_id(exo)::Cint, block_id::ex_entity_id, element_type::Ptr{UInt8}
-  )::Cint
-  exodus_error_check(exo, error_code, "Exodus.read_element_type -> libexodus.ex_get_elem_type")
+  element_type = Vector{Cchar}(undef, MAX_STR_LENGTH)
+  error_code = LibExodus.ex_get_elem_type(get_file_id(exo), block_id, pointer(element_type))
+  exodus_error_check(exo, error_code, "Exodus.read_element_type -> LibExodus.ex_get_elem_type")
   return unsafe_string(pointer(element_type))
 end
 
@@ -144,13 +139,13 @@ WARNING:
 currently does not support edges, faces and attributes
 """
 function write_block(exo::ExodusDatabase, block::Block)
-  error_code = @ccall libexodus.ex_put_block(
-    get_file_id(exo)::Cint, EX_ELEM_BLOCK::ex_entity_type, block.id::ex_entity_id,
-    block.elem_type::Ptr{UInt8},
-    block.num_elem::Clonglong, block.num_nodes_per_elem::Clonglong,
-    0::Clonglong, 0::Clonglong, 0::Clonglong
-  )::Cint
-  exodus_error_check(exo, error_code, "Exodus.write_element_block -> libexodus.ex_put_block")
+  error_code = LibExodus.ex_put_block(
+    get_file_id(exo), EX_ELEM_BLOCK, block.id,
+    block.elem_type,
+    block.num_elem, block.num_nodes_per_elem,
+    0, 0, 0
+  )
+  exodus_error_check(exo, error_code, "Exodus.write_element_block -> LibExodus.ex_put_block")
   write_block_connectivity(exo, block.id, block.conn)
 end
 
@@ -160,13 +155,13 @@ $(TYPEDSIGNATURES)
 function write_block(exo::ExodusDatabase, block_id::Integer, elem_type::String, conn::Matrix{I}) where I <: Integer
   num_nodes_per_elem, num_elem = size(conn)
   elem_type = uppercase(elem_type)
-  error_code = @ccall libexodus.ex_put_block(
-    get_file_id(exo)::Cint, EX_ELEM_BLOCK::ex_entity_type, block_id::ex_entity_id,
-    elem_type::Ptr{UInt8},
-    num_elem::Clonglong, num_nodes_per_elem::Clonglong,
-    0::Clonglong, 0::Clonglong, 0::Clonglong
-  )::Cint
-  exodus_error_check(exo, error_code, "Exodus.write_element_block -> libexodus.ex_put_block")
+  error_code = LibExodus.ex_put_block(
+    get_file_id(exo), EX_ELEM_BLOCK, block_id,
+    elem_type,
+    num_elem, num_nodes_per_elem,
+    0, 0, 0
+  )
+  exodus_error_check(exo, error_code, "Exodus.write_element_block -> LibExodus.ex_put_block")
   write_block_connectivity(exo, block_id, conn)
 end
 
@@ -178,18 +173,3 @@ function write_blocks(exo::ExodusDatabase, blocks::Vector{<:Block})
     write_block(exo, block)
   end
 end
-
-# # some tools below
-# """
-# TODO reduce allocations and check for type instabilities
-# """
-# function collect_block_connectivities(exo::ExodusDatabase, block_ids::Vector{<:Integer})
-#   blocks = Block.((exo,), block_ids)
-#   conns = [block.conn for block in blocks]
-#   return mapreduce(permutedims, vcat, conns)' |> collect
-# end
-
-# """
-# """
-# collect_block_connectivities(exo::ExodusDatabase) = 
-# collect_block_connectivities(exo, read_ids(exo, Block))