add perf_bc_reverse_complement.cpp

perf/CMakeLists.txt

@@ -29,6 +29,7 @@ endforeach()
 
 set(BOOST_COMPUTE_BENCHMARKS
   bc_random_sequence
+  bc_reverse_complement
 )
 
 foreach(BENCHMARK ${BOOST_COMPUTE_BENCHMARKS})

perf/perf_bc_reverse_complement.cpp

+//----------------------------------------------------------------------------//
+//  Copyright (c) 2018 Armin Sobhani <arminms@gmail.com>
+//
+//  Distributed under the Boost Software License Version 1.0.
+//  (See accompanying file LICENSE_1_0.txt or copy at
+//  http://www.boost.org/LICENSE_1_0.txt)
+//
+//----------------------------------------------------------------------------//
+
+#include <iostream>
+#include <iomanip>
+#include <numeric>
+#include <vector>
+#include <random>
+
+#include <boost/compute/system.hpp>
+#include <boost/compute/command_queue.hpp>
+#include <boost/compute/container/vector.hpp>
+#include <boost/compute/algorithm/transform.hpp>
+#include <boost/compute/random.hpp>
+// #include <boost/compute/algorithm/sort.hpp>
+
+// #include <boost/compute/random/default_random_engine.hpp>
+// #include <boost/compute/random/uniform_int_distribution.hpp>
+
+#include <boost/bioseq/type_traits.hpp>
+#include <boost/bioseq/sequence.hpp>
+
+#include "perf.hpp"
+#include "rss.hpp"
+
+namespace bsq = boost::bioseq;
+namespace bc  = boost::compute;
+
+typedef bsq::sequence_host<char, std::allocator, std::vector> seq;
+
+int main(int argc, char *argv[])
+{
+    perf_parse_args(argc, argv);
+    std::cout << "size: " << PERF_N << std::endl;
+
+    // char acgt[] = "ACGT";
+    // std::random_device rd;
+    // std::uniform_int_distribution<int> dist(0, 3);
+    // seq rs;
+    // rs.reserve(PERF_N);
+
+    // // create vector of random sequence
+    // std::generate_n(
+    //     std::back_inserter(rs)
+    // ,   PERF_N
+    // ,   [&] () { return acgt[dist(rd)]; } );
+
+    // std::cout << rs[0] << rs[1] << rs[2] << rs[3] << std::endl;
+
+    for (auto const& platform : bc::system::platforms())
+    {
+        std::cout << ">>>>>>>>>> " << platform.name() << " <<<<<<<<<<\n:" << std::endl;
+        for (auto const& device : platform.devices())
+        {
+            std::cout << "device: " << device.name() << std::endl;
+            bc::context context(device);
+            bc::command_queue queue(context, device);
+
+            boost::compute::default_random_engine rng(queue);
+            bc::uniform_int_distribution<int> dist(0, 3);
+
+            BOOST_COMPUTE_FUNCTION(char, acgt, (char b),
+            {
+                char acgt[] = "ACGT";
+                return acgt[b];
+            });
+
+            bc::vector<char> rs(PERF_N, context);
+            dist.generate(
+                rs.begin()
+            ,   rs.end()
+            ,   rng
+            ,   queue);
+            queue.finish();
+            bc::transform(
+                rs.begin()
+            ,   rs.end()
+            ,   rs.begin()
+            ,   acgt
+            ,   queue);
+            queue.finish();
+
+            boost::compute::copy(
+                rs.begin()
+            ,   rs.begin() + 10
+            ,   std::ostream_iterator<char>(std::cout)
+            ,   queue );
+            std::cout << std::endl;
+
+            // bc::vector<char> cs(PERF_N, context);
+            // bc::copy(rs.begin(), rs.end(), cs.begin(), queue);
+
+            BOOST_COMPUTE_FUNCTION(char, complement, (char b),
+            {
+                char cmplmnt[] =
+                    "--------------------------------"
+                    " !-#$%&-()*+,-./0123456789:;<=>?"
+                    "@TVGHEFCHIJMLKNOPQYSAUBWXRZ[-]^_"
+                    "`tvghefcdijmlknopqysaubwxrz{|}~";
+                return cmplmnt[b];
+            });
+
+            // BOOST_COMPUTE_CLOSURE(char, complement, (char b), (cmplmnt),
+            // {
+            //     return cmplmnt[b];
+            // });
+
+            perf_timer t;
+            for (size_t trial = 0; trial < PERF_TRIALS; ++trial)
+            {
+                t.start();
+                // bc::sort(rs.begin(), rs.end(), queue);
+                bc::transform(
+                    rs.begin()
+                ,   rs.end()
+                ,   rs.begin()
+                ,   complement
+                ,   queue);
+                queue.finish();
+                t.stop();
+            }
+
+            seq cs;
+            cs.reserve(PERF_N);
+            bc::copy(rs.begin(), rs.end(), std::back_inserter(cs), queue);
+
+            std::cout << cs(0, 10) << std::endl;
+            std::cout << "time: "
+                    << std::fixed << std::setprecision(2)
+                    << t.min_time() / 1e6 << " ms"
+                    << std::endl;
+            std::cout << "rate: "
+                    << perf_rate<char>(PERF_N, t.min_time()) << " MB/s"
+                    << std::endl;
+            std::cout << "mrss: "
+                    << bytes2size(get_peak_rss())
+                    << std::endl
+                    << ':'
+                    << std::endl;
+        }
+    }
+
+    return 0;
+}
\ No newline at end of file