Merge pull request #73 from KIwabuchi/feature/dnnd_new_api

New (advanced) API, obsolete old API

examples/CMakeLists.txt

@@ -37,28 +37,16 @@ function(add_saltatlas_dnnd_example_feature_type example_name type_name)
             PRIVATE "SALTATLAS_DNND_EXAMPLE_FEATURE_ELEMENT_TYPE=${type_name}")
 endfunction()
 
-if (SALTATLAS_USE_METALL)
-    add_saltatlas_example(dnnd_example)
-    add_saltatlas_example(dnnd_custom_point_example)
-    add_saltatlas_example(dnnd_string_example)
-    add_saltatlas_example(dnnd_pm_const_example)
-    add_saltatlas_example(dnnd_pm_optimize_example)
-    add_saltatlas_example(dnnd_pm_query_example)
-    add_saltatlas_example(dnnd_simple_example)
-    add_saltatlas_example(dnnd_simple_custom_distance_example)
-    add_saltatlas_example(dnnd_simple_custom_point_example)
-
-    add_saltatlas_dnnd_example_feature_type(dnnd_pm_const_example float)
-    add_saltatlas_dnnd_example_feature_type(dnnd_pm_optimize_example float)
-    add_saltatlas_dnnd_example_feature_type(dnnd_pm_query_example float)
+add_saltatlas_example(dnnd_simple_example)
+add_saltatlas_example(dnnd_simple_custom_distance_example)
+add_saltatlas_example(dnnd_simple_custom_point_example)
 
-    add_saltatlas_dnnd_example_feature_type(dnnd_pm_const_example uint8_t)
-    add_saltatlas_dnnd_example_feature_type(dnnd_pm_optimize_example uint8_t)
-    add_saltatlas_dnnd_example_feature_type(dnnd_pm_query_example uint8_t)
+add_saltatlas_dnnd_example_feature_type(dnnd_bench float)
+add_saltatlas_dnnd_example_feature_type(dnnd_bench uint8_t)
+add_saltatlas_dnnd_example_feature_type(dnnd_bench double)
 
-    add_saltatlas_dnnd_example_feature_type(dnnd_pm_const_example double)
-    add_saltatlas_dnnd_example_feature_type(dnnd_pm_optimize_example double)
-    add_saltatlas_dnnd_example_feature_type(dnnd_pm_query_example double)
+if (SALTATLAS_USE_METALL)
+    add_saltatlas_example(dnnd_advanced_example)
 endif ()
 
 add_subdirectory(datasets)

examples/dnnd_advanced_example.cpp

@@ -0,0 +1,115 @@
+// Copyright 2024 Lawrence Livermore National Security, LLC and other
+// saltatlas Project Developers. See the top-level COPYRIGHT file for details.
+//
+// SPDX-License-Identifier: MIT
+
+/// \brief A simple example of using DNND's simple with a custom distance
+/// function. It is recommended to see the examples/dnnd_simple_example.cpp
+/// beforehand. Usage:
+///     cd build
+///     mpirun -n 2 ./example/dnnd_simple_custom_distance_example
+
+#include <iostream>
+#include <vector>
+
+#include <ygm/comm.hpp>
+
+#include <saltatlas/dnnd/dnnd_advanced.hpp>
+
+// Point ID type
+using id_t   = uint32_t;
+using dist_t = double;
+
+// Point Type
+using point_type = saltatlas::feature_vector<float>;
+
+// Custom distance function
+// The distance function should have the signature as follows:
+// distance_type(const point_type& a, const point_type& b);
+dist_t custom_distance(const point_type& p1, const point_type& p2) {
+  // A simple (squared) L2 distance example
+  dist_t dist = 0.0;
+  for (size_t i = 0; i < p1.size(); ++i) {
+    dist += (p1[i] - p2[i]) * (p1[i] - p2[i]);
+  }
+  return dist;
+}
+
+int main(int argc, char** argv) {
+  ygm::comm comm(&argc, &argv);
+
+  {
+    saltatlas::dnnd<id_t, point_type, dist_t> g(comm);
+    std::vector<std::filesystem::path>        paths{
+        "../examples/datasets/point_5-4.txt"};
+    g.load_points(paths.begin(), paths.end(), "wsv");
+
+    // ----- NNG build and NN search APIs ----- //
+    int        k  = 4;
+    const auto id = g.build(custom_distance, k);
+
+    bool make_graph_undirected = true;
+    g.optimize(id, custom_distance, make_graph_undirected);
+
+    // Run queries
+    std::vector<point_type> queries;
+    if (comm.rank() == 0) {
+      queries.push_back(point_type{61.58, 29.68, 20.43, 99.22, 21.81});
+    }
+    int        num_to_search = 4;
+    const auto results       = g.query(id, custom_distance, queries.begin(),
+                                       queries.end(), num_to_search);
+
+    if (comm.rank() == 0) {
+      std::cout << "Neighbours (id, distance):";
+      for (const auto& [nn_id, nn_dist] : results[0]) {
+        std::cout << " " << nn_id << " (" << nn_dist << ")";
+      }
+      std::cout << std::endl;
+    }
+  }
+
+  std::filesystem::path datastorepath = "/tmp/dnnd-knng";
+  std::error_code       ec;
+  std::filesystem::remove_all(datastorepath, ec);
+  comm.cf_barrier();
+  {
+    saltatlas::dnnd<id_t, point_type, dist_t> g(saltatlas::create_only,
+                                                datastorepath, comm);
+    std::vector<std::filesystem::path>        paths{
+        "../examples/datasets/point_5-4.txt"};
+    g.load_points(paths.begin(), paths.end(), "wsv");
+    const auto id = g.build(custom_distance, 2);
+    comm.cout0() << "Created" << std::endl;
+  }
+
+  {
+    saltatlas::dnnd<id_t, point_type, dist_t> g(saltatlas::open_only,
+                                                datastorepath, comm);
+    if (g.contains_local(0)) g.get_local_point(0);
+    comm.cf_barrier();
+    g.update(0, custom_distance, 4);
+    comm.cout0() << "Updated" << std::endl;
+
+    g.build(custom_distance, 4);
+  }
+
+  {
+    saltatlas::dnnd<id_t, point_type, dist_t> g(saltatlas::open_read_only,
+                                                datastorepath, comm);
+    std::vector<point_type> queries;
+    if (comm.rank() == 0) {
+      queries.push_back(point_type{61.58, 29.68, 20.43, 99.22, 21.81});
+    }
+    comm.cout0() << "Query 1" << std::endl;
+    g.query(0, custom_distance, queries.begin(), queries.end(), 4);
+
+
+    comm.cout0() << "Query 2" << std::endl;
+    std::vector<std::size_t> ids{0, 1};
+    g.query(ids.begin(), ids.end(), custom_distance, queries.begin(),
+            queries.end(), 4);
+  }
+
+  return 0;
+}