enhancements to matset to_silo (#677)

* enhancements to matset to_silo

* fix missing hdf5 guard, use diff to check to_silo results

* fix from joe for unibuffer case

CHANGELOG.md

@@ -27,6 +27,9 @@ and this project aspires to adhere to [Semantic Versioning](https://semver.org/s
 - Added `truncate` option to `conduit::relay::io::blueprint::write_mesh`, this is used by `save_mesh`.
 - Improve capture and reporting of I/O errors in `conduit::relay::[mpi::]io::blueprint::{save_mesh|write_mesh}`. Now in the MPI case, If any rank fails to open or write to a file all ranks will throw an exception.
 
+#### Blueprint
+- Added `conduit::blueprint::mesh::matset::to_silo()` which converts a valid blueprint matset to a node that contains arrays that follow Silo's sparse mix slot volume fraction representation.
+
 
 ## [0.6.0] - Released 2020-11-02
 

src/libs/blueprint/CMakeLists.txt

@@ -22,7 +22,6 @@ set(blueprint_headers
     conduit_blueprint_mesh_examples.hpp
     conduit_blueprint_mesh_examples_julia.hpp
     conduit_blueprint_mesh_examples_venn.hpp
-    conduit_blueprint_util_mesh.hpp
     conduit_blueprint_mcarray.hpp
     conduit_blueprint_mcarray_examples.hpp
     conduit_blueprint_o2mrelation.hpp
@@ -48,10 +47,10 @@ set(blueprint_c_headers
 set(blueprint_sources
     conduit_blueprint.cpp
     conduit_blueprint_mesh.cpp
+    conduit_blueprint_mesh_matset_xforms.cpp
     conduit_blueprint_mesh_examples.cpp
     conduit_blueprint_mesh_examples_julia.cpp
     conduit_blueprint_mesh_examples_venn.cpp
-    conduit_blueprint_util_mesh.cpp
     conduit_blueprint_mcarray.cpp
     conduit_blueprint_mcarray_examples.cpp
     conduit_blueprint_o2mrelation.cpp

src/libs/blueprint/conduit_blueprint.hpp

@@ -23,8 +23,6 @@
 #include "conduit_blueprint_mesh_examples_julia.hpp"
 #include "conduit_blueprint_mesh_examples_venn.hpp"
 
-#include "conduit_blueprint_util_mesh.hpp"
-
 #include "conduit_blueprint_o2mrelation.hpp"
 #include "conduit_blueprint_o2mrelation_examples.hpp"
 #include "conduit_blueprint_o2mrelation_iterator.hpp"

src/libs/blueprint/conduit_blueprint_mesh.hpp

@@ -407,6 +407,17 @@ namespace matset
     //-------------------------------------------------------------------------
     bool CONDUIT_BLUEPRINT_API is_material_dominant(const conduit::Node &n);
 
+    //-------------------------------------------------------------------------
+    // Converts a blueprint matset to the silo style sparse mixed slot 
+    // representation.
+    //
+    // For details about the silo format, see documentation for 
+    // 'DBPutMaterial' at:
+    // https://wci.llnl.gov/content/assets/docs/simulation/computer-codes/silo/LLNL-SM-654357.pdf
+    void CONDUIT_BLUEPRINT_API to_silo(const conduit::Node &n,
+                                       conduit::Node &dest,
+                                       const float64 epsilon = CONDUIT_EPSILON);
+
     //-------------------------------------------------------------------------
     // blueprint::mesh::matset::index protocol interface
     //-------------------------------------------------------------------------

src/libs/blueprint/conduit_blueprint_mesh_examples_venn.cpp

@@ -356,10 +356,10 @@ void venn_sparse_by_element_matset(Node &res)
     // Build the rest of the single-buffer matset
     res["matsets/matset/topology"] = "topo";
     // This is the "key" that tells what material each volume fraction refers to
-    res["matsets/matset/material_map/cir_a"] = 1;
-    res["matsets/matset/material_map/cir_b"] = 2;
-    res["matsets/matset/material_map/cir_c"] = 3;
-    res["matsets/matset/material_map/bg"] = 0;
+    res["matsets/matset/material_map/circle_a"] = 1;
+    res["matsets/matset/material_map/circle_b"] = 2;
+    res["matsets/matset/material_map/circle_c"] = 3;
+    res["matsets/matset/material_map/background"] = 0;
 
     // All the volume fractions go here ("one big buffer")
     res["matsets/matset/volume_fractions"].set(DataType::float64(vfcount));

src/libs/blueprint/conduit_blueprint_util_mesh.cpp → src/libs/blueprint/conduit_blueprint_mesh_matset_xforms.cpp

@@ -4,7 +4,7 @@
 
 //-----------------------------------------------------------------------------
 ///
-/// file: conduit_blueprint_util_mesh.cpp
+/// file: conduit_blueprint_mesh_matset_xforms.cpp
 ///
 //-----------------------------------------------------------------------------
 
@@ -22,7 +22,6 @@
 #include "conduit_blueprint_mesh.hpp"
 #include "conduit_blueprint_o2mrelation.hpp"
 #include "conduit_blueprint_o2mrelation_iterator.hpp"
-#include "conduit_blueprint_util_mesh.hpp"
 
 // FIXME(JRC): The helper functions below are hackily copied over from
 // 'conduit_blueprint_mesh.cpp'; these helpers should ultimately be abstracted
@@ -118,19 +117,13 @@ namespace blueprint
 {
 
 //-----------------------------------------------------------------------------
-// -- begin conduit::blueprint::util --
-//-----------------------------------------------------------------------------
-namespace util
-{
-
-//-----------------------------------------------------------------------------
-// -- begin conduit::blueprint::util::mesh --
+// -- begin conduit::blueprint::mesh --
 //-----------------------------------------------------------------------------
 namespace mesh
 {
 
 //-----------------------------------------------------------------------------
-// -- begin conduit::blueprint::util::mesh::matset --
+// -- begin conduit::blueprint::mesh::matset --
 //-----------------------------------------------------------------------------
 namespace matset
 {
@@ -154,7 +147,7 @@ to_silo(const conduit::Node &n,
     Node matset_mat_map;
     if(mset_is_unibuffer)
     {
-        matset_mat_map.set_external(n["volume_fractions/material_map"]);
+        matset_mat_map.set_external(n["material_map"]);
     }
     else // if(!mset_is_unibuffer)
     {
@@ -187,12 +180,12 @@ to_silo(const conduit::Node &n,
     }
     else // if(!mset_is_matdom)
     {
-        // may need to do a bit of sculping here; embed the base array into
+        // may need to do a bit of sculpting here; embed the base array into
         // something w/ "values" child, as below
         Node mat_vfs;
         if(mset_is_unibuffer)
         {
-            mat_vfs["values"].set_external(n["volume_fractions/values"]);
+            mat_vfs.set_external(n);
         }
         else
         {
@@ -253,8 +246,8 @@ to_silo(const conduit::Node &n,
                     (void*)mat_mids.element_ptr(mat_ind_index));
                 const index_t mat_id = temp.to_index_t();
 
-                // if this elem has a non-zero (or non-trival) volume fraction for this
-                // materal, add it do the map
+                // if this elem has a non-zero (or non-trivial) volume fraction for this
+                // material, add it do the map
                 if(mat_vf > epsilon)
                 {
                     elem_mat_maps[elem_index][mat_id] = mat_vf;
@@ -312,8 +305,8 @@ to_silo(const conduit::Node &n,
                 }
                 const index_t mat_elem = mset_is_matdom ? temp.to_index_t() : mat_index;
 
-                // if this elem has a non-zero (or non-trival) volume fraction for this
-                // materal, add it do the map
+                // if this elem has a non-zero (or non-trivial) volume fraction for this
+                // material, add it do the map
                 if(mat_vf > epsilon)
                 {
                     elem_mat_maps[mat_elem][mat_id] = mat_vf;
@@ -333,6 +326,9 @@ to_silo(const conduit::Node &n,
 
     dest.reset();
     dest["topology"].set(n["topology"]);
+    // in some cases, this method will sort the material names
+    // so always include the material map
+    dest["material_map"].set(matset_mat_map);
     dest["matlist"].set(DataType(int_dtype.id(), mset_num_elems));
     dest["mix_next"].set(DataType(int_dtype.id(), mset_num_slots));
     dest["mix_mat"].set(DataType(int_dtype.id(), mset_num_slots));
@@ -388,7 +384,7 @@ to_silo(const conduit::Node &n,
 //-----------------------------------------------------------------------------
 }
 //-----------------------------------------------------------------------------
-// -- end conduit::blueprint::util::mesh::matset --
+// -- end conduit::blueprint::mesh::matset --
 //-----------------------------------------------------------------------------
 
 
@@ -397,13 +393,6 @@ to_silo(const conduit::Node &n,
 // -- end conduit::blueprint::util::mesh --
 //-----------------------------------------------------------------------------
 
-
-}
-//-----------------------------------------------------------------------------
-// -- end conduit::blueprint::util --
-//-----------------------------------------------------------------------------
-
-
 }
 //-----------------------------------------------------------------------------
 // -- end conduit::blueprint --

src/libs/relay/conduit_relay_io_blueprint.cpp

@@ -1452,7 +1452,10 @@ void read_mesh(const std::string &root_file_path,
 
     // assume hdf5, but check for json file
     std::string root_protocol = "hdf5";
-    char buff[5] = {0,0,0,0,0};
+    // we will read the first 5 bytes, but
+    // make sure our buff is null termed, unless you
+    // want a random chance at sadness.
+    char buff[6] = {0,0,0,0,0,0};
 
     // heuristic, if json, we expect to see "{" in the first 5 chars of the file.
     std::ifstream ifs;

src/tests/blueprint/CMakeLists.txt

@@ -19,7 +19,7 @@ set(BLUEPRINT_TESTS t_blueprint_smoke
                     t_blueprint_mesh_relay
                     t_blueprint_mesh_generate
                     t_blueprint_mesh_examples
-                    t_blueprint_util_mesh)
+                    t_blueprint_mesh_matset_xforms)
 
 ################################
 # Add our Main Unit Tests

src/tests/blueprint/t_blueprint_mesh_examples.cpp

@@ -467,20 +467,40 @@ TEST(conduit_blueprint_mesh_examples, check_gen_index_state_prop)
     EXPECT_TRUE(idx.has_path("state/time"));
 }
 
+
+
 //-----------------------------------------------------------------------------
 void venn_test_small_yaml(const std::string &venn_type)
 {
     // provide small example save to yaml for folks to look at
-    const int nx = 25, ny = 25;
+    const int nx = 4, ny = 4;
     const double radius = 0.25;
 
     Node res, info, n_idx;
     blueprint::mesh::examples::venn(venn_type, nx, ny, radius, res);
-    blueprint::mesh::examples::venn(venn_type, nx, ny, radius, res);
+
     EXPECT_TRUE(blueprint::mesh::verify(res, info));
     blueprint::mesh::generate_index(res,"",1,n_idx);
     EXPECT_TRUE(blueprint::verify("mesh/index",n_idx,info));
-    res.save("venn_small_example_" + venn_type + ".yaml");
+
+    std::string ofbase= "venn_small_example_" + venn_type;
+
+    // save yaml and hdf5 versions
+    relay::io::blueprint::save_mesh(res,
+                                    ofbase + ".yaml",
+                                    "yaml");
+
+    Node io_protos;
+    relay::io::about(io_protos["io"]);
+    bool hdf5_enabled =io_protos["io/protocols/hdf5"].as_string() == "enabled";
+
+    if(hdf5_enabled)
+    {
+        relay::io::blueprint::save_mesh(res,
+                                        ofbase+ ".blueprint_root",
+                                        "hdf5");
+    }
+
 }
 
 //-----------------------------------------------------------------------------
@@ -499,7 +519,24 @@ void venn_test(const std::string &venn_type)
 
     std::string ofbase = "venn_example_" + venn_type;
     std::cout << "[Saving " << ofbase << "]" << std::endl;
-    relay::io_blueprint::save(res, ofbase + ".blueprint_root");
+
+    std::string ofile_root= "venn_small_example_" + venn_type;
+
+    // save yaml and hdf5 versions
+    relay::io::blueprint::save_mesh(res,
+                                    ofbase + ".yaml",
+                                    "yaml");
+
+    Node io_protos;
+    relay::io::about(io_protos["io"]);
+    bool hdf5_enabled =io_protos["io/protocols/hdf5"].as_string() == "enabled";
+
+    if(hdf5_enabled)
+    {
+        relay::io::blueprint::save_mesh(res,
+                                        ofbase+ ".blueprint_root",
+                                        "hdf5");
+    }
 
     {
         std::cout << "[Verifying field area is correct]" << std::endl;