Promote trustworthiness_score to public header, add missing include…

…s, update dependencies (#3968) * Updates dask/distributed versions to match cuDF (rapidsai/cudf#8458) * Updates to Thrust v1.12.0 to align with cuDF and cuGraph * Don't include the src and src_prims directories in `cuml::cuml++` target's public include paths * Add missing `<cstddef>` and `<cstdint>` include directives * Promote `trustworthiness_score` to public `cuml/metrics/metrics.hpp` header and update Cython * Compile Cython with `-std=c++17` * Remove `-Wstrict-prototypes` Cython warning * Fixes linker error in debug builds * Fixes #3885 Authors: - Paul Taylor (https://github.com/trxcllnt) Approvers: - Dante Gama Dessavre (https://github.com/dantegd) - AJ Schmidt (https://github.com/ajschmidt8) URL: #3968
rapidsai · Jun 16, 2021 · afdeda9 · afdeda9
1 parent dc82e88
commit afdeda9
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Showing 17 changed files with 91 additions and 84 deletions.
diff --git a/conda/environments/cuml_dev_cuda11.0.yml b/conda/environments/cuml_dev_cuda11.0.yml
@@ -23,6 +23,10 @@ dependencies:
 - umap-learn
 - scikit-learn=0.23.1
 - treelite=1.3.0
+- statsmodels
+- seaborn
+- hdbscan
+- nltk
 - pip
 - pip:
     - sphinx_markdown_tables

diff --git a/conda/environments/cuml_dev_cuda11.2.yml b/conda/environments/cuml_dev_cuda11.2.yml
@@ -23,6 +23,10 @@ dependencies:
 - umap-learn
 - scikit-learn=0.23.1
 - treelite=1.3.0
+- statsmodels
+- seaborn
+- hdbscan
+- nltk
 - pip
 - pip:
     - sphinx_markdown_tables

diff --git a/conda/recipes/cuml/meta.yaml b/conda/recipes/cuml/meta.yaml
@@ -27,7 +27,7 @@ requirements:
     - python x.x
     - setuptools
     - cython>=0.29,<0.30
-    - cmake>=3.14
+    - cmake>=3.20.1
     - treelite=1.3.0
     - cudf {{ minor_version }}
     - libcuml={{ version }}
@@ -46,8 +46,8 @@ requirements:
     - nccl>=2.9.9
     - ucx-py 0.21
     - ucx-proc=*=gpu
-    - dask>=2.12.0
-    - distributed>=2.12.0
+    - dask>=2021.6.0
+    - distributed>=2021.6.0
     - joblib >=0.11
     - {{ pin_compatible('cudatoolkit', max_pin='x.x') }}
 

diff --git a/cpp/CMakeLists.txt b/cpp/CMakeLists.txt
@@ -206,6 +206,17 @@ endif()
 ##############################################################################
 # - build libcuml++ shared library -------------------------------------------
 
+if(BUILD_CUML_C_LIBRARY OR BUILD_CUML_CPP_LIBRARY)
+  file(WRITE "${CMAKE_CURRENT_BINARY_DIR}/fatbin.ld"
+[=[
+SECTIONS
+{
+.nvFatBinSegment : { *(.nvFatBinSegment) }
+.nv_fatbin : { *(.nv_fatbin) }
+}
+]=])
+endif()
+
 if(BUILD_CUML_CPP_LIBRARY)
 
   # single GPU components
@@ -309,11 +320,11 @@ if(BUILD_CUML_CPP_LIBRARY)
   target_include_directories(${CUML_CPP_TARGET}
     PUBLIC
       $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
-      $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/src>
-      $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/src_prims>
       $<BUILD_INTERFACE:$<$<BOOL:${ENABLE_CUMLPRIMS_MG}>:${cumlprims_mg_INCLUDE_DIRS}>>
       $<$<BOOL:Treelite_ADDED>:${Treelite_SOURCE_DIR}/include>
     PRIVATE
+      $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/src>
+      $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/src_prims>
       $<$<OR:$<BOOL:BUILD_CUML_STD_COMMS>,$<BOOL:BUILD_CUML_MPI_COMMS>>:${NCCL_INCLUDE_DIRS}>
       $<$<BOOL:BUILD_CUML_MPI_COMMS>:${MPI_CXX_INCLUDE_PATH}>
     INTERFACE
@@ -347,6 +358,8 @@ if(BUILD_CUML_CPP_LIBRARY)
   target_link_options(${CUML_CPP_TARGET} PRIVATE "-Wl,--exclude-libs,libdmlc.a")
   # same as above, but for protobuf library
   target_link_options(${CUML_CPP_TARGET} PRIVATE "-Wl,--exclude-libs,libprotobuf.a")
+  # ensure CUDA symbols aren't relocated to the middle of the debug build binaries
+  target_link_options(${CUML_CPP_TARGET} PRIVATE "${CMAKE_CURRENT_BINARY_DIR}/fatbin.ld")
 
 endif(BUILD_CUML_CPP_LIBRARY)
 
@@ -382,6 +395,9 @@ if(BUILD_CUML_C_LIBRARY)
       FAISS::FAISS
   )
 
+  # ensure CUDA symbols aren't relocated to the middle of the debug build binaries
+  target_link_options(${CUML_C_TARGET} PRIVATE "${CMAKE_CURRENT_BINARY_DIR}/fatbin.ld")
+
 endif()
 
 ##############################################################################

diff --git a/cpp/cmake/thirdparty/get_thrust.cmake b/cpp/cmake/thirdparty/get_thrust.cmake
@@ -26,4 +26,4 @@ function(find_and_configure_thrust VERSION)
 
 endfunction()
 
-find_and_configure_thrust(1.10.0)
+find_and_configure_thrust(1.12.0)
diff --git a/cpp/include/cuml/manifold/umap.hpp b/cpp/include/cuml/manifold/umap.hpp
@@ -16,6 +16,9 @@
 
 #pragma once
 
+#include <cstddef>
+#include <cstdint>
+
 namespace raft {
 class handle_t;
 }

diff --git a/cpp/include/cuml/metrics/metrics.hpp b/cpp/include/cuml/metrics/metrics.hpp
@@ -18,6 +18,8 @@
 
 #include <raft/linalg/distance_type.h>
 
+#include <cstdint>
+
 namespace raft {
 class handle_t;
 }
@@ -337,5 +339,24 @@ void pairwiseDistance_sparse(const raft::handle_t &handle, float *x, float *y,
                              raft::distance::DistanceType metric,
                              float metric_arg);
 
+/**
+ * @brief Compute the trustworthiness score
+ *
+ * @param h Raft handle
+ * @param X Data in original dimension
+ * @param X_embedded Data in target dimension (embedding)
+ * @param n Number of samples
+ * @param m Number of features in high/original dimension
+ * @param d Number of features in low/embedded dimension
+ * @param n_neighbors Number of neighbors considered by trustworthiness score
+ * @param batchSize Batch size
+ * @tparam distance_type: Distance type to consider
+ * @return Trustworthiness score
+ */
+template <typename math_t, raft::distance::DistanceType distance_type>
+double trustworthiness_score(const raft::handle_t &h, const math_t *X,
+                             math_t *X_embedded, int n, int m, int d,
+                             int n_neighbors, int batchSize = 512);
+
 }  // namespace Metrics
 }  // namespace ML
diff --git a/cpp/src/metrics/trustworthiness.cu b/cpp/src/metrics/trustworthiness.cu
@@ -15,6 +15,9 @@
  */
 
 #include <metrics/trustworthiness_score.cuh>
+
+#include <cuml/metrics/metrics.hpp>
+
 #include <raft/distance/distance.cuh>
 #include <raft/handle.hpp>
 
@@ -23,14 +26,15 @@ namespace Metrics {
 
 /**
  * @brief Compute the trustworthiness score
- * @param h: Raft handle
- * @param X[in]: Data in original dimension
- * @param X_embedded[in]: Data in target dimension (embedding)
- * @param n[in]: Number of samples
- * @param m[in]: Number of features in high/original dimension
- * @param d[in]: Number of features in low/embedded dimension
- * @param n_neighbors[in]: Number of neighbors considered by 
- *   trustworthiness score
+ *
+ * @param h Raft handle
+ * @param X Data in original dimension
+ * @param X_embedded Data in target dimension (embedding)
+ * @param n Number of samples
+ * @param m Number of features in high/original dimension
+ * @param d Number of features in low/embedded dimension
+ * @param n_neighbors Number of neighbors considered by trustworthiness score
+ * @param batchSize Batch size
  * @tparam distance_type: Distance type to consider
  * @return Trustworthiness score
  */

diff --git a/cpp/src/metrics/trustworthiness.cuh b/cpp/src/metrics/trustworthiness.cuh
diff --git a/cpp/src/metrics/trustworthiness_c.h b/cpp/src/metrics/trustworthiness_c.h
diff --git a/cpp/src/svm/workingset.cuh b/cpp/src/svm/workingset.cuh
@@ -343,8 +343,8 @@ class WorkingSet {
       // Determine temporary device storage requirements for cub
       size_t cub_bytes2 = 0;
       cub::DeviceRadixSort::SortPairs(
-        NULL, cub_bytes, f_idx.data(), f_idx_sorted.data(), f_sorted.data(),
-        f_sorted.data(), n_train, 0, 8 * sizeof(int), stream);
+        NULL, cub_bytes, f_sorted.data(), f_sorted.data(), f_idx.data(),
+        f_idx_sorted.data(), n_train, 0, 8 * sizeof(math_t), stream);
       cub::DeviceSelect::If(NULL, cub_bytes2, f_idx.data(), f_idx.data(),
                             d_num_selected, n_train, dummy_select_op, stream);
       cub_bytes = max(cub_bytes, cub_bytes2);

diff --git a/cpp/src/tsa/auto_arima.cuh b/cpp/src/tsa/auto_arima.cuh
@@ -49,7 +49,8 @@ void cumulative_sum_helper(
   std::shared_ptr<raft::mr::device::allocator> allocator, cudaStream_t stream) {
   // Determine temporary storage size
   size_t temp_storage_bytes = 0;
-  cub::DeviceScan::InclusiveSum(NULL, temp_storage_bytes, mask, cumul,
+  cub::DeviceScan::InclusiveSum(NULL, temp_storage_bytes,
+                                reinterpret_cast<const char*>(mask), cumul,
                                 mask_size, stream);
 
   // Allocate temporary storage
@@ -58,7 +59,8 @@ void cumulative_sum_helper(
   void* d_temp_storage = (void*)temp_storage.data();
 
   // Execute the scan
-  cub::DeviceScan::InclusiveSum(d_temp_storage, temp_storage_bytes, mask, cumul,
+  cub::DeviceScan::InclusiveSum(d_temp_storage, temp_storage_bytes,
+                                reinterpret_cast<const char*>(mask), cumul,
                                 mask_size, stream);
 }
 

diff --git a/cpp/test/sg/trustworthiness_test.cu b/cpp/test/sg/trustworthiness_test.cu
@@ -14,9 +14,12 @@
  * limitations under the License.
  */
 
+#include <cuml/metrics/metrics.hpp>
+
+#include <raft/handle.hpp>
+
 #include <gtest/gtest.h>
 #include <raft/cudart_utils.h>
-#include <metrics/trustworthiness.cuh>
 #include <raft/cuda_utils.cuh>
 #include <vector>
 

diff --git a/cpp/test/sg/tsne_test.cu b/cpp/test/sg/tsne_test.cu
@@ -15,6 +15,8 @@
  */
 
 #include <cuml/manifold/tsne.h>
+#include <cuml/metrics/metrics.hpp>
+
 #include <datasets/boston.h>
 #include <datasets/breast_cancer.h>
 #include <datasets/diabetes.h>
@@ -26,7 +28,6 @@
 #include <cuml/common/device_buffer.hpp>
 #include <cuml/common/logger.hpp>
 #include <iostream>
-#include <metrics/trustworthiness.cuh>
 #include <raft/mr/device/allocator.hpp>
 #include <tsne/distances.cuh>
 #include <vector>
@@ -174,4 +175,4 @@ TEST_P(TSNETestF, Result) {
   assert_score(knn_score_fft, "knn_fft\n", trustworthiness_threshold);
 }
 
-INSTANTIATE_TEST_CASE_P(TSNETests, TSNETestF, ::testing::ValuesIn(inputs));
+INSTANTIATE_TEST_CASE_P(TSNETests, TSNETestF, ::testing::ValuesIn(inputs));
diff --git a/cpp/test/sg/umap_parametrizable_test.cu b/cpp/test/sg/umap_parametrizable_test.cu
@@ -14,6 +14,8 @@
  * limitations under the License.
  */
 
+#include <cuml/metrics/metrics.hpp>
+
 #include <gtest/gtest.h>
 #include <iostream>
 #include <vector>
@@ -27,7 +29,6 @@
 #include <cuml/manifold/umap.hpp>
 #include <cuml/neighbors/knn.hpp>
 #include <linalg/reduce_rows_by_key.cuh>
-#include <metrics/trustworthiness.cuh>
 #include <raft/cuda_utils.cuh>
 #include <raft/distance/distance.cuh>
 #include <raft/handle.hpp>

diff --git a/python/cuml/metrics/trustworthiness.pyx b/python/cuml/metrics/trustworthiness.pyx
@@ -33,7 +33,7 @@ cdef extern from "raft/linalg/distance_type.h" namespace "raft::distance":
     ctypedef int DistanceType
     ctypedef DistanceType euclidean "(raft::distance::DistanceType)5"
 
-cdef extern from "metrics/trustworthiness_c.h" namespace "ML::Metrics":
+cdef extern from "cuml/metrics/metrics.hpp" namespace "ML::Metrics":
 
     cdef double trustworthiness_score[T, DistanceType](const handle_t& h,
                                                        T* X,

diff --git a/python/setup.py b/python/setup.py
@@ -190,7 +190,7 @@ def finalize_options(self):
                       ],
                       libraries=libs,
                       language='c++',
-                      extra_compile_args=['-std=c++14'])
+                      extra_compile_args=['-std=c++17'])
         ]
 
         self.distribution.ext_modules = extensions
@@ -207,6 +207,14 @@ class cuml_build_ext(cython_build_ext, object):
 
     boolean_options = ["singlegpu"] + cython_build_ext.boolean_options
 
+    def build_extensions(self):
+        try:
+            # Silence the '-Wstrict-prototypes' warning
+            self.compiler.compiler_so.remove("-Wstrict-prototypes")
+        except Exception:
+            pass
+        cython_build_ext.build_extensions(self)
+
     def initialize_options(self):
 
         self.singlegpu = None