radix

.gitconfig

@@ -0,0 +1,3 @@
+[user]
+    name = jerryidk
+    email = [email protected]

include/input_reader/file.hpp

@@ -50,8 +50,10 @@ class FileReader : public InputReader<std::string_view> {
       : FileReader(std::move(input_file), 0, 1) {}
 
   ~FileReader() {
-    PLOG_INFO_IF(offset_ != part_end_)
-        << "Offset mismatch: expected " << part_end_ << "; actual: " << offset_;
+    if(offset_ != part_end_)
+    {
+        PLOG_INFO << "Offset mismatch: expected " << part_end_ << "; actual: " << offset_;
+    }
   }
 
   /// Copy the next line to `output` and advance the offset.
@@ -131,8 +133,11 @@ class FileReader : public InputReader<std::string_view> {
         part_id_(part_id),
         num_parts_(num_parts),
         buffer_(4096) {
-    PLOG_FATAL_IF(part_id >= num_parts)
-        << "part_id(" << part_id << " ) >= num_parts(" << num_parts << ")";
+    if(part_id  >= num_parts)
+    {
+      PLOG_FATAL << "part_id(" << part_id << " ) >= num_parts(" << num_parts << ")";
+    }
+
     // Get the size of the file and calculate the range of this partition.
     // We are doing it here for now because I don't want to mess with the
     // parameter passing.
@@ -158,9 +163,12 @@ class FileReader : public InputReader<std::string_view> {
 
   /// Creats a ifstream and log if fail.
   static std::ifstream open_file(std::string_view filename) {
-    std::ifstream file(filename.data());
-    PLOG_FATAL_IF(file.fail())
-        << "Failed to open file " << filename << ": " << file.rdstate();
+    std::ifstream file(filename.data());        
+
+    if(file.fail())
+    {
+      PLOG_FATAL << "Failed to open file " << filename << ": " << file.rdstate();
+    }
     return file;
   }
 

include/tests/KmerTest.hpp

@@ -17,9 +17,15 @@ class KmerTest {
 
   void count_kmer_radix(Shard *sh, const Configuration &config,
                         std::barrier<VoidFn> *barrier, RadixContext &context);
+
   void count_kmer_radix_custom(Shard *sh, const Configuration &config,
                                std::barrier<VoidFn> *barrier,
                                RadixContext &context);
+
+
+  void count_kmer_radix_jerry(Shard *sh, const Configuration &config,
+                              std::barrier<VoidFn> *barrier,
+                               RadixContext &context, BaseHashTable *ht);
 };
 
 }  // namespace kmercounter

jerry-benchmark.sh

@@ -0,0 +1,44 @@
+#!/bin/bash
+
+# ./build/dramhit --help to see flags
+
+function bench_regular() 
+{
+    sudo ./build/dramhit \
+    --mode 4 \
+    --ht-type 3 \
+    --numa-split 0 \
+    --num-threads 64 \
+    --ht-size 8589934592 \
+    --in-file /opt/dramhit/kmer_dataset/SRR1513870.fastq \
+    --k 6 > jerry_benchmark.log
+}
+
+function bench_radix() 
+{
+    sudo ./build/dramhit \
+    --mode 14 \
+    --ht-type 3 \
+    --numa-split 0 \
+    --num-threads 64 \
+    --ht-size 8589934592 \
+    --in-file /opt/dramhit/kmer_dataset/SRR1513870.fastq \
+    --k 6 --d 8 > jerry_benchmark.log
+}
+
+function bench() {
+    bench_radix
+    bench_regular
+}
+
+function build() {
+    cmake --build build/
+}
+
+if [ "$1" == "build" ]; then
+    build
+elif [ "$1" == "bench" ]; then
+    bench
+else
+    echo "Invalid option"
+fi

src/Application.cpp

@@ -264,7 +264,7 @@ void Application::shard_thread(int tid,
 int Application::spawn_shard_threads() {
   cpu_set_t cpuset;
 
-  PLOG_INFO.printf("kosustartNumber of shards: %u", config.num_threads);
+  PLOG_INFO.printf("Number of shards: %u", config.num_threads);
   this->shards = (Shard *)std::aligned_alloc(
       CACHE_LINE_SIZE, sizeof(Shard) * config.num_threads);
 
@@ -315,14 +315,10 @@ int Application::spawn_shard_threads() {
     exit(-1);
   }
 
-  std::function<void()> on_completion = []() noexcept {
-    // For debugging
-    // PLOG_INFO << "Phase completed.";
-  };
-
   std::function<void()> on_sync_complete = sync_complete;
 
   std::barrier barrier(config.num_threads, on_sync_complete);
+
   uint32_t i = 0;
   for (uint32_t assigned_cpu : this->np->get_assigned_cpu_list()) {
     if (assigned_cpu == 0) continue;
@@ -339,7 +335,6 @@ int Application::spawn_shard_threads() {
     i += 1;
   }
 
-  PLOG_INFO.printf("kos i:%u", i);
   // Pin main application thread to cpu 0 and run our thread routine
   CPU_ZERO(&cpuset);
   CPU_SET(0, &cpuset);
@@ -400,7 +395,8 @@ int Application::process(int argc, char *argv[]) {
         "10: Cache Miss test\n"
         "11: Zipfian non-bqueue test\n"
         "12: RW-ratio test\n"
-        "13: Hashjoin")("base",
+        "13: Hashjoin\n"
+        "14: Fastq insert with Radix Parition")("base",
                         po::value<uint64_t>(&config.kmer_create_data_base)
                             ->default_value(def.kmer_create_data_base),
                         "Number of base K-mers")(