switch to using c++ compiler instead of g++ to fix cpp-demos on mac os x

.travis.yml

@@ -65,9 +65,12 @@ matrix:
 
     - os: osx
       language: generic
-      osx_image: xcode7.3
+      osx_image: xcode9
       env:
         - TESTATTR="'not linux and not known_failing and not huge'"
+        - CC=cc
+        - CXX=c++
+#        - c++=g++
       before_install:
         - source ci_scripts/install.sh
 

Makefile

@@ -131,7 +131,7 @@ clean: FORCE
 	cd src/oxli && $(MAKE) clean || true
 	cd tests && rm -rf khmertest_* || true
 	rm -f pytests.xml
-	cd third-party/cqf && make clean || true
+	cd third-party/mqf && make clean || true
 	rm -f $(EXTENSION_MODULE)
 	rm -f khmer/*.pyc scripts/*.pyc tests/*.pyc oxli/*.pyc \
 		sandbox/*.pyc khmer/__pycache__/* sandbox/__pycache__/* \

examples/c++-api/Makefile

@@ -1,14 +1,20 @@
 CXXFLAGS=--std=c++11 \
        -I ../../include/ \
 	   -I ../../third-party/smhasher \
-	   -I ../../third-party/cqf \
+	   -I ../../third-party/mqf \
 	   -I ../../third-party/seqan/core/include/ \
 	   -I ../../third-party/rollinghash
 
 TESTS=exact-counting bloom consume
 
+ifneq ($(INCLUDE),)
+	INCLUDE := -I$(INCLUDE)
+endif
+
+all: $(TESTS)
+
 %: %.cc ../../src/oxli/liboxli.a
-	$(CXX) $(CXXFLAGS) $< ../../src/oxli/liboxli.a -o $@
+	$(CXX) -undefined dynamic_lookup -arch x86_64 -lstdc++ -stdlib=libstdc++ -std=c++11 $(CXXFLAGS) $< ../../src/oxli/liboxli.a -o $@
 
 ../../src/oxli/liboxli.a:
 	cd ../../src/oxli && make
@@ -18,7 +24,5 @@ run: all
 	./bloom
 	./consume reads.fastq
 
-all: $(TESTS)
-
 clean:
 	-rm -f exact-counting bloom consume

include/oxli/storage.hh

@@ -44,7 +44,7 @@ Contact: [email protected]
 #include <unordered_map>
 using MuxGuard = std::lock_guard<std::mutex>;
 
-#include "gqf.h"
+#include "gqf.hh"
 
 namespace oxli {
 typedef std::unordered_map<HashIntoType, BoundedCounterType> KmerCountMap;
@@ -410,51 +410,78 @@ public:
  *
  * \brief A Quotient Filter storage
  */
- class QFStorage : public Storage {
+class QFStorage : public Storage
+{
 protected:
-  QF cf;
+    QF mf;
 
 public:
-  QFStorage(int size) {
-    // size is the power of two to specify the number of slots in
-    // the filter (2**size). Third argument sets the number of bits used
-    // in the key (current value of size+8 is copied from the CQF example)
-    // Final argument is the number of bits allocated for the value, which
-    // we do not use.
-    qf_init(&cf, (1ULL << size), size+8, 0);
-  }
-
-  ~QFStorage() { qf_destroy(&cf); }
-
-  BoundedCounterType test_and_set_bits(HashIntoType khash) {
-    BoundedCounterType x = get_count(khash);
-    add(khash);
-    return !x;
-  }
-
-  //
-  bool add(HashIntoType khash) {
-      bool is_new = get_count(khash) == 0;
-      qf_insert(&cf, khash % cf.range, 0, 1);
-      return is_new;
-  }
-
-  // get the count for the given k-mer hash.
-  const BoundedCounterType get_count(HashIntoType khash) const {
-    return qf_count_key_value(&cf, khash % cf.range, 0);
-  }
-
-  // Accessors for protected/private table info members
-  // xnslots is larger than nslots. It includes some extra slots to deal
-  // with some details of how the counting is implemented
-  std::vector<uint64_t> get_tablesizes() const { return {cf.xnslots}; }
-  const size_t n_tables() const { return 1; }
-  const uint64_t n_unique_kmers() const { return cf.ndistinct_elts; }
-  const uint64_t n_occupied() const { return cf.noccupied_slots; }
-  void save(std::string outfilename, WordLength ksize);
-  void load(std::string infilename, WordLength &ksize);
-
-  Byte **get_raw_tables() { return nullptr; }
+    QFStorage(int size)
+    {
+        // size is the power of two to specify the number of slots in
+        // the filter (2**size). Third argument sets the number of bits used
+        // in the key (current value of size+8 is copied from the CQF example)
+        // Final argument is the number of bits allocated for the value, which
+        // we do not use.
+        _supports_bigcount = true;
+        qf_init(&mf, (1ULL << size), size+8, 0,2,true,"",2038074761);
+
+
+
+    }
+
+    ~QFStorage()
+    {
+        qf_destroy(&mf);
+    }
+
+    BoundedCounterType test_and_set_bits(HashIntoType khash)
+    {
+        BoundedCounterType x = get_count(khash);
+        add(khash);
+        return !x;
+    }
+
+    //
+    bool add(HashIntoType khash)
+    {
+        bool is_new = get_count(khash) == 0;
+        qf_insert(&mf, khash % mf.metadata->range, 1,false,false);
+        return is_new;
+    }
+
+    // get the count for the given k-mer hash.
+    const BoundedCounterType get_count(HashIntoType khash) const
+    {
+        return qf_count_key(&mf, khash % mf.metadata->range);
+    }
+
+    // Accessors for protected/private table info members
+    // xnslots is larger than nslots. It includes some extra slots to deal
+    // with some details of how the counting is implemented
+    std::vector<uint64_t> get_tablesizes() const
+    {
+        return {mf.metadata->xnslots};
+    }
+    const size_t n_tables() const
+    {
+        return 1;
+    }
+    const uint64_t n_unique_kmers() const
+    {
+        return mf.metadata->ndistinct_elts;
+    }
+    const uint64_t n_occupied() const
+    {
+        return mf.metadata->noccupied_slots;
+    }
+    void save(std::string outfilename, WordLength ksize);
+    void load(std::string infilename, WordLength &ksize);
+
+    Byte **get_raw_tables()
+    {
+        return nullptr;
+    }
 };
 
 

setup.cfg

@@ -6,7 +6,7 @@ undef = NO_UNIQUE_RC
 # docker/Dockerfile
 # libraries = z,bz2
 ## if using system libraries
-include-dirs = include:third-party/zlib:third-party/bzip2:third-party/seqan/core/include:third-party/smhasher:third-party/cqf:third-party/rollinghash
+include-dirs = include:third-party/zlib:third-party/bzip2:third-party/seqan/core/include:third-party/smhasher:third-party/rollinghash:third-party/mqf
 # include-dirs = lib
 ## if using system libraries (broken)
 

setup.py

@@ -187,7 +187,7 @@ def build_dir():
     # force 64bit only builds
     EXTRA_COMPILE_ARGS.extend(['-arch', 'x86_64', '-mmacosx-version-min=10.7',
                                '-stdlib=libc++'])
-    EXTRA_LINK_ARGS.append('-mmacosx-version-min=10.7')
+    EXTRA_LINK_ARGS.extend(['-mmacosx-version-min=10.7', '-lstdc++'])
 
 if check_for_openmp():
     EXTRA_COMPILE_ARGS.extend(['-fopenmp'])
@@ -330,10 +330,10 @@ def run(self):
         if sys.platform == 'darwin' and 'gcov' in self.libraries:
             self.libraries.remove('gcov')
 
-        cqfcmd = ['bash', '-c', 'cd third-party/cqf && make']
-        spawn(cmd=cqfcmd, dry_run=self.dry_run)
+        mqfcmd = ['bash', '-c', 'cd third-party/mqf && make']
+        spawn(cmd=mqfcmd, dry_run=self.dry_run)
         for ext in self.extensions:
-            ext.extra_objects.append(path_join("third-party", "cqf", "gqf.o"))
+            ext.extra_objects.append(path_join("third-party", "mqf", "gqf.o"))
 
         if "z" not in self.libraries:
             zcmd = ['bash', '-c', 'cd ' + ZLIBDIR + ' && ( test Makefile -nt'

src/oxli/Makefile

@@ -69,8 +69,9 @@ PREFIX=/usr/local
 
 INCLUDES= -I ../../include/ -I ../../third-party/seqan/core/include/ \
 	      -I ../../third-party/smhasher/ \
-				-I ../../third-party/cqf/ \
-				-I ../../third-party/rollinghash
+				-I ../../third-party/mqf/ \
+				-I ../../third-party/rollinghash \
+
 
 ifeq ($(USE_SYSTEM_ZLIB), false)
 INCLUDES += -I ../../third-party/zlib/
@@ -102,6 +103,8 @@ CFLAGS   += -Wshadow -Wcast-align -Wstrict-prototypes
 CFLAGS   += $(INCLUDES) $(CPPFLAGS)
 
 LDFLAGS  ?=
+LDFLAGS  += -lstdc++
+
 ifneq ($(USE_SYSTEM_ZLIB), false)
 LDFLAGS  += -lz
 endif
@@ -164,6 +167,8 @@ SONAME       = liboxli.$(SHARED_EXT).$(LIB_VERSION)
 SONAME_FLAGS = -install_name $(PREFIX)/lib/$(SONAME) \
 	       -compatibility_version $(LIB_VERSION) \
 	       -current_version $(LIB_VERSION)
+LDFLAGS  +=  -stdlib=libstdc++ -std=c++11 -arch x86_64
+CXXFLAGS  +=  -stdlib=libstdc++ -std=c++11
 else
 SHARED_EXT   = so
 SONAME       = liboxli.$(SHARED_EXT).$(LIB_VERSION)
@@ -221,10 +226,10 @@ BZIP2_OBJS_BASE= \
 BZIP2_OBJS=$(addprefix $(BZIP2_DIR)/, $(BZIP2_OBJS_BASE))
 
 # Counting bloom filter
-CQF_DIR=../../third-party/cqf
-CQF_OBJS_BASE= gqf.o
+MQF_DIR=../../third-party/mqf
+MQF_OBJS_BASE= gqf.o
 
-CQF_OBJS=$(addprefix $(CQF_DIR)/, $(CQF_OBJS_BASE))
+MQF_OBJS=$(addprefix $(MQF_DIR)/, $(MQF_OBJS_BASE))
 
 #### oxli proper below here ####
 
@@ -259,9 +264,9 @@ PRECOMILE_OBJS += $(BZIP2_OBJS)
 PRECLEAN_TARGS += libbz2clean
 endif
 
-LIBOXLI_OBJS  += $(CQF_OBJS)
-PRECOMILE_OBJS += $(CQF_OBJS)
-PRECLEAN_TARGS += libcqfclean
+LIBOXLI_OBJS  += $(MQF_OBJS)
+PRECOMILE_OBJS += $(MQF_OBJS)
+PRECLEAN_TARGS += libmqfclean
 
 HEADERS= \
 	hashtable.hh \
@@ -290,8 +295,8 @@ zlibclean:
 	(cd $(ZLIB_DIR) && make distclean)
 libbz2clean:
 	(cd $(BZIP2_DIR) && make -f Makefile-libbz2_so clean)
-libcqfclean:
-	(cd $(CQF_DIR) && make clean)
+libmqfclean:
+	(cd $(MQF_DIR) && make clean)
 
 clean: $(PRECLEAN_TARGS)
 	rm -f *.o *.a *.$(SHARED_EXT)* oxli.pc $(TEST_PROGS)
@@ -315,8 +320,8 @@ $(ZLIB_OBJS):
 $(BZIP2_OBJS):
 	(cd $(BZIP2_DIR) && make -f Makefile-libbz2_so $(BZIP2_OBJS_BASE))
 
-$(CQF_OBJS):
-	(cd $(CQF_DIR) && make)
+$(MQF_OBJS):
+	(cd $(MQF_DIR) && make)
 
 # MurMur3
 murmur3.o: ../../third-party/smhasher/MurmurHash3.cc
@@ -326,7 +331,7 @@ murmur3.o: ../../third-party/smhasher/MurmurHash3.cc
 	$(CXX) $(CXXFLAGS) $(LDFLAGS) -c -o $@ $<
 
 $(LIBOXLISO): $(LIBOXLI_OBJS)
-	$(CXX) $(CXXFLAGS) $(LDFLAGS) $(SONAME_FLAGS) -shared -o $@ $^
+	clang++ $(CXXFLAGS) $(LDFLAGS) $(SONAME_FLAGS) -shared -o $@ $^
 	ln -sf $(SONAME) liboxli.$(SHARED_EXT)
 
 liboxli.a: $(LIBOXLI_OBJS)

src/oxli/storage.cc

@@ -923,34 +923,14 @@ void QFStorage::save(std::string outfilename, WordLength ksize)
     unsigned char version = SAVED_FORMAT_VERSION;
     unsigned char ht_type = SAVED_QFCOUNT;
 
+
     outfile.write(SAVED_SIGNATURE, 4);
     outfile.write((const char *) &version, 1);
     outfile.write((const char *) &ht_type, 1);
     outfile.write((const char *) &ksize, sizeof(ksize));
 
-    /* just a hack to handle __uint128_t value. Don't know a better to handle it
-     * right now */
-    uint64_t tmp_range;
-    tmp_range = cf.range;
-
-    outfile.write((const char *) &cf.nslots, sizeof(cf.nslots));
-    outfile.write((const char *) &cf.xnslots, sizeof(cf.xnslots));
-    outfile.write((const char *) &cf.key_bits, sizeof(cf.key_bits));
-    outfile.write((const char *) &cf.value_bits, sizeof(cf.value_bits));
-    outfile.write((const char *) &cf.key_remainder_bits, sizeof(cf.key_remainder_bits));
-    outfile.write((const char *) &cf.bits_per_slot, sizeof(cf.bits_per_slot));
-    outfile.write((const char *) &tmp_range, sizeof(tmp_range));
-    outfile.write((const char *) &cf.nblocks, sizeof(cf.nblocks));
-    outfile.write((const char *) &cf.nelts, sizeof(cf.nelts));
-    outfile.write((const char *) &cf.ndistinct_elts, sizeof(cf.ndistinct_elts));
-    outfile.write((const char *) &cf.noccupied_slots, sizeof(cf.noccupied_slots));
-
-    #if BITS_PER_SLOT == 8 || BITS_PER_SLOT == 16 || BITS_PER_SLOT == 32 || BITS_PER_SLOT == 64
-        outfile.write((const char *) cf.blocks, sizeof(qfblock) * cf.nblocks);
-    #else
-        outfile.write((const char *) cf.blocks,
-                      (sizeof(qfblock) + SLOTS_PER_BLOCK * cf.bits_per_slot / 8) * cf.nblocks);
-    #endif
+    outfile.write((const char *)mf.metadata,sizeof(qfmetadata));
+    outfile.write((const char *)mf.blocks,mf.metadata->size);
     outfile.close();
 }
 
@@ -1011,34 +991,22 @@ void QFStorage::load(std::string infilename, WordLength &ksize)
     infile.read((char *) &save_ksize, sizeof(save_ksize));
     ksize = save_ksize;
 
-    infile.read((char *) &cf.nslots, sizeof(cf.nslots));
-    infile.read((char *) &cf.xnslots, sizeof(cf.xnslots));
-    infile.read((char *) &cf.key_bits, sizeof(cf.key_bits));
-    infile.read((char *) &cf.value_bits, sizeof(cf.value_bits));
-    infile.read((char *) &cf.key_remainder_bits, sizeof(cf.key_remainder_bits));
-    infile.read((char *) &cf.bits_per_slot, sizeof(cf.bits_per_slot));
-    infile.read((char *) &tmp_range, sizeof(tmp_range));
-
-    infile.read((char *) &cf.nblocks, sizeof(cf.nblocks));
-    infile.read((char *) &cf.nelts, sizeof(cf.nelts));
-    infile.read((char *) &cf.ndistinct_elts, sizeof(cf.ndistinct_elts));
-    infile.read((char *) &cf.noccupied_slots, sizeof(cf.noccupied_slots));
-    /* just a hack to handle __uint128_t value. Don't know a better to handle it
-     * right now */
-    cf.range = tmp_range;
-    // deallocate previously allocated blocks
-    free(cf.blocks);
-    /* allocate the space for the actual qf blocks */
-    #if BITS_PER_SLOT == 8 || BITS_PER_SLOT == 16 || BITS_PER_SLOT == 32 || BITS_PER_SLOT == 64
-        cf.blocks = (qfblock *)calloc(cf.nblocks, sizeof(qfblock));
-    #else
-        cf.blocks = (qfblock *)calloc(cf.nblocks, sizeof(qfblock) + SLOTS_PER_BLOCK * cf.bits_per_slot / 8);
-    #endif
-    #if BITS_PER_SLOT == 8 || BITS_PER_SLOT == 16 || BITS_PER_SLOT == 32 || BITS_PER_SLOT == 64
-        infile.read((char *) cf.blocks, sizeof(qfblock) * cf.nblocks);
-    #else
-        infile.read((char *) cf.blocks,
-                    (sizeof(qfblock) + SLOTS_PER_BLOCK * cf.bits_per_slot / 8) * cf.nblocks);
-    #endif
+    mf.mem = (qfmem *)calloc(sizeof(qfmem), 1);
+    mf.metadata = (qfmetadata *)calloc(sizeof(qfmetadata), 1);
+    infile.read((char*)mf.metadata,sizeof(qfmetadata));
+    mf.blocks = (qfblock *)calloc(mf.metadata->size, 1);
+    infile.read((char*)mf.blocks, mf.metadata->size);
+
+    mf.metadata->num_locks =
+        10;//should be changed to something realistic like function qf_deserialize
+    mf.mem->metadata_lock = 0;
+    /* initialize all the locks to 0 */
+    mf.mem->locks = (volatile int *)calloc(mf.metadata->num_locks,
+                                           sizeof(volatile int));
+
+
+
+
+
     infile.close();
 }