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primitives.h
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27 
28 #pragma once
29 
30 #include <nvbio/basic/types.h>
31 #include <nvbio/basic/console.h>
33 #include <thrust/device_vector.h>
34 #include <cub/cub.cuh>
35 
54 
55 namespace nvbio {
56 namespace cuda {
57 
60 
63 
70 
74 template <typename VectorType>
75 void alloc_temp_storage(VectorType& vec, const uint64 size);
76 
79 template <typename PredicateIterator>
80 bool any(
81  const uint32 n,
82  const PredicateIterator pred);
83 
86 template <typename PredicateIterator>
87 bool all(
88  const uint32 n,
89  const PredicateIterator pred);
90 
93 template <typename Iterator>
94 bool is_sorted(
95  const uint32 n,
96  const Iterator values);
97 
101 template <typename Iterator, typename Headflags>
102 bool is_segment_sorted(
103  const uint32 n,
104  const Iterator values,
105  const Headflags flags);
106 
114 template <typename InputIterator, typename BinaryOp>
115 typename std::iterator_traits<InputIterator>::value_type reduce(
116  const uint32 n,
117  InputIterator d_in,
118  BinaryOp op,
119  thrust::device_vector<uint8>& d_temp_storage);
120 
129 template <typename InputIterator, typename OutputIterator, typename BinaryOp>
130 void inclusive_scan(
131  const uint32 n,
132  InputIterator d_in,
133  OutputIterator d_out,
134  BinaryOp op,
135  thrust::device_vector<uint8>& d_temp_storage);
136 
146 template <typename InputIterator, typename OutputIterator, typename BinaryOp, typename Identity>
147 void exclusive_scan(
148  const uint32 n,
149  InputIterator d_in,
150  OutputIterator d_out,
151  BinaryOp op,
152  Identity identity,
153  thrust::device_vector<uint8>& d_temp_storage);
154 
165 template <typename InputIterator, typename FlagsIterator, typename OutputIterator>
167  const uint32 n,
168  InputIterator d_in,
169  FlagsIterator d_flags,
170  OutputIterator d_out,
171  thrust::device_vector<uint8>& d_temp_storage);
172 
183 template <typename InputIterator, typename OutputIterator, typename Predicate>
185  const uint32 n,
186  InputIterator d_in,
187  OutputIterator d_out,
188  const Predicate pred,
189  thrust::device_vector<uint8>& d_temp_storage);
190 
201 template <typename InputIterator, typename OutputIterator, typename CountIterator>
203  const uint32 n,
204  InputIterator d_in,
205  OutputIterator d_out,
206  CountIterator d_counts,
207  thrust::device_vector<uint8>& d_temp_storage);
208 
221 template <typename KeyIterator, typename ValueIterator, typename OutputKeyIterator, typename OutputValueIterator, typename ReductionOp>
223  const uint32 n,
224  KeyIterator d_keys_in,
225  ValueIterator d_values_in,
226  OutputKeyIterator d_keys_out,
227  OutputValueIterator d_values_out,
228  ReductionOp reduction_op,
229  thrust::device_vector<uint8>& d_temp_storage);
230 
234 
235 } // namespace cuda
236 } // namespace nvbio
237