Fix TBB allocator used even if HAVE_TBB_MALLOC not available

src/align.cpp

@@ -60,7 +60,7 @@ using std::exception;
 #include <algorithm>
 using std::find_if;
 
-#ifdef HAVE_TBB
+#ifdef HAVE_TBB_MALLOC
 #  include "tbb/tbb_allocator.h"
 #endif
 
@@ -481,7 +481,11 @@ sina::do_align(cseq& c, const cseq& orig, MASTER &m,
     cnsts_type cns(tr);
 
     // create the alignment "mesh" (not quite a matrix)
+#ifdef HAVE_TBB_MALLOC
     using mesh_t = mesh<MASTER, cseq, data_type, tbb::tbb_allocator<data_type>>;
+#else
+    using mesh_t = mesh<MASTER, cseq, data_type>;
+#endif
     logger->debug("Allocating {}MB for alignment matrix", mesh_t::guessMem(m, c)/1024/1024);
     mesh_t A(m, c);
 

src/buffer.h

@@ -29,7 +29,15 @@ for the parts of ARB used as well as that of the covered work.
 #ifndef _BUFFER_H_
 #define _BUFFER_H_
 
+#include <cstddef>
+#include <cstdint>
+#include <new>
+
+#ifdef HAVE_TBB_MALLOC
 #include <tbb/scalable_allocator.h>
+#else
+#include <stdlib.h>
+#endif
 
 namespace sina {
 
@@ -38,10 +46,18 @@ class buffer {
 public:
     using size_type = size_t;
     explicit buffer(size_type size) {
+#ifdef HAVE_TBB_MALLOC
         _start = (T*)scalable_malloc(sizeof(T) * size);
+#else
+        _start = (T*)malloc(sizeof(T) * size);
+#endif
     }
     ~buffer() {
+#ifdef HAVE_TBB_MALLOC
         scalable_free(_start);
+#else
+        free(_start);
+#endif
     }
     inline T& operator[](size_type idx) {
         return _start[idx];
@@ -54,23 +70,35 @@ template<typename T, size_t ALIGN=64>
 class aligned_buffer {
 public:
     using size_type = size_t;
+    using offset_t = uint16_t;
     explicit aligned_buffer(size_type size) {
         size_type alloc = sizeof(T) * size + sizeof(offset_t) + ALIGN - 1;
+#ifdef HAVE_TBB_MALLOC
         void *ptr = scalable_malloc(alloc);
-        if (!ptr) { throw std::bad_alloc(); }
+#else
+        void *ptr = malloc(alloc);
+#endif
+        if (!ptr) {
+            throw std::bad_alloc();
+        }
         size_t res = ((size_t)ptr + sizeof(offset_t) + ALIGN - 1) & ~(ALIGN -1);
         *((offset_t*)res - 1) = (offset_t)((size_t)res - (size_t)ptr);
         _start = (T*)res;
     }
+
     ~aligned_buffer() {
         offset_t offset = *((offset_t*)_start - 1);
+#ifdef HAVE_TBB_MALLOC
         scalable_free((char*)_start - offset);
+#else
+        free((char*)_start - offset);
+#endif
     }
+
     inline T& operator[](size_type idx) {
         return _start[idx];
     }
 private:
-    using offset_t = uint16_t;
     T* _start;
 };
 

src/idset.h

@@ -32,9 +32,6 @@ for the parts of ARB used as well as that of the covered work.
 #include <vector>
 #include <iostream>
 
-#include <tbb/scalable_allocator.h>
-#include <tbb/cache_aligned_allocator.h>
-
 #include "helpers.h"
 
 /** Abstract base class for container of ids
@@ -43,8 +40,6 @@ for the parts of ARB used as well as that of the covered work.
 class idset {
 public:
     using value_type = uint32_t;
-    // using inc_t = std::vector<int16_t, tbb::cache_aligned_allocator<int16_t>>;
-    //using data_t = std::vector<uint8_t, tbb::cache_aligned_allocator<uint8_t>>;
     using inc_t = std::vector<int16_t>;
     using data_t = std::vector<uint8_t>;
 
@@ -96,7 +91,7 @@ class bitmap : public idset {
     }
 
     /* set bit at @id */
-    void set(value_type id) {
+    void set(value_type id) const {
         data[block_index(id)] |= 1 << (block_offset(id));
     }
 
@@ -123,7 +118,6 @@ class bitmap : public idset {
         set(id);
     }
 
-
     int increment(inc_t& t) const override {
         for (value_type i=0; i < data.size(); i++) {
             block_type block = data[i];
@@ -150,7 +144,7 @@ class imap_abs : public idset {
         data_t::const_iterator _it;
     public:
         explicit const_iterator(const data_t::const_iterator& it) : _it(it) {}
-        value_type operator*() {
+        value_type operator*() const {
             return *(value_type*)(&*_it);
         }
         const_iterator& operator++() {

src/kmer_search.cpp

@@ -53,7 +53,6 @@ using std::string;
 namespace fs = boost::filesystem;
 
 #include <tbb/tbb.h>
-#include <tbb/cache_aligned_allocator.h>
 #include <cstdio>
 #include <sys/stat.h>