add buffer partition

mars-research · Feb 23, 2024 · 96f8045 · 96f8045
1 parent c06c5cd
commit 96f8045
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Showing 8 changed files with 870 additions and 575 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -3,7 +3,7 @@ project(dramhit VERSION 0.1.0)
 
 # Declare options
 option(SANITIZE "Enable ASAN." OFF)
-option(SANITIZE_TESTING "Enable ASAN for tests." ON)
+option(SANITIZE_TESTING "Enable ASAN for tests." OFF)
 option(BUILD_APP "Build the main application, dramhit." ON)
 option(BUILD_TESTING "Build tests." OFF)
 option(BUILD_EXAMPLE "Build examples." OFF)
@@ -13,10 +13,10 @@ option(VTUNE "Use VTUNE to do performance monitering." OFF)
 option(AGGR "Use aggregation hashtable (histogram)" ON)
 option(BQUEUE "Enable bqueue tests" OFF)
 option(XORWOW "Xorwow" OFF)
-option(BQ_ZIPFIAN "Enable global zipfian distribution generation" ON)
+option(BQ_ZIPFIAN "Enable global zipfian distribution generation" OFF)
 option(BQ_ZIPFIAN_LOCAL "Enable local zipfian distribution generation" OFF)
 option(CALC_STATS "Enable hashtable statistics" ON)
-option(ZIPF_FAST "Enable faster zipfian distribution generation" ON)
+option(ZIPF_FAST "Enable faster zipfian distribution generation" OFF)
 option(LATENCY_COLLECTION "Enable latency data collection" OFF)
 option(BQ_KMER_TEST "Bqueue kmer test" OFF)
 

diff --git a/include/Application.hpp b/include/Application.hpp
@@ -19,7 +19,7 @@ class Application {
   std::vector<std::thread> threads;
   Shard *shards;
   MsrHandler *msr_ctrl;
-  RadixContext radixContext;
+  RadixContext *radixContext;
 
  public:
   std::vector<numa_node> nodes;

diff --git a/include/input_reader/fastq.hpp b/include/input_reader/fastq.hpp
@@ -111,6 +111,7 @@ class FastqReader : public FileReader {
   }
 };
 
+
 /// Reads KMers from a Fastq file.
 template <size_t K>
 class FastqKMerReader : public InputReaderU64 {

diff --git a/include/tests/KmerTest.hpp b/include/tests/KmerTest.hpp
@@ -16,16 +16,21 @@ class KmerTest {
   void count_kmer(Shard *sh, const Configuration &config, BaseHashTable *ht,
                   std::barrier<VoidFn> *barrier);
 
-  void count_kmer_radix(Shard *sh, const Configuration &config,
-                        std::barrier<VoidFn> *barrier, RadixContext &context);
+//   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_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);
+//   void count_kmer_radix_partition(Shard *sh, const Configuration &config,
+//                               std::barrier<VoidFn> *barrier,
+//                                RadixContext &context, BaseHashTable *ht);
+
+
+    void count_kmer_radix_partition_global(Shard* sh, const Configuration& config,
+                            std::barrier<VoidFn>* barrier,
+                            RadixContext* context, BaseHashTable* ht);
 };
 
 }  // namespace kmercounter
-Original file line number
+Diff line change
@@ Expand Up / @@ -111,6 +111,7 @@ class FastqReader : public FileReader { @@
       }
     };
     /// Reads KMers from a Fastq file.
     template <size_t K>
     class FastqKMerReader : public InputReaderU64 {
@@ Expand Down @@