debian/changelog

+spades (3.13.0+dfsg2-2) unstable; urgency=medium
+
+  * Also remove jemalloc from (build-)depends.
+
+ -- Michael R. Crusoe <michael.crusoe@gmail.com>  Thu, 17 Jan 2019 10:12:47 -0800
+
+spades (3.13.0+dfsg2-1) unstable; urgency=medium
+
+  * Restore the bundled jemalloc as Debian's package is too new.
+  * Pull releases from GitHib.
+  * Standards-Version: 4.3.0 (no changes needed)
+  * Install README.md to /usr/share/doc/spades/
+
+ -- Michael R. Crusoe <michael.crusoe@gmail.com>  Thu, 17 Jan 2019 07:54:34 -0800
+
 spades (3.13.0+dfsg-1) unstable; urgency=medium
 
   * New upstream version

debian/control

@@ -15,7 +15,6 @@ Build-Depends: debhelper (>= 11~),
                libboost-dev,
                libbam-dev,
                libbamtools-dev,
-               libjemalloc-dev,
                libhat-trie-dev,
                libhts-dev,
                libnlopt-dev,
@@ -27,7 +26,7 @@ Build-Depends: debhelper (>= 11~),
                bwa,
                libbwa-dev,
                lynx
-Standards-Version: 4.2.1
+Standards-Version: 4.3.0
 Vcs-Browser: https://salsa.debian.org/med-team/spades
 Vcs-Git: https://salsa.debian.org/med-team/spades.git
 Homepage: http://cab.spbu.ru/software/spades/
@@ -42,7 +41,6 @@ Depends: ${shlibs:Depends},
          bwa,
          bamtools,
          samtools,
-         libjemalloc1,
          libnlopt0,
          libhat-trie0,
          libssw0

debian/copyright

@@ -14,8 +14,6 @@ Files-Excluded:
     ext/src/samtools/misc/md5sum-lite
     ext/src/samtools/misc/wgsim
     ext/src/samtools/win32
-    ext/include/jemalloc
-    ext/src/jemalloc
     ext/src/htrie
     ext/src/nlopt
     ext/src/ssw

debian/docs

 *manual.html
+README.md

debian/patches/0114_use_debian_provided_libs.patch

-Description: use Debian-packaged jemalloc library 
- To improve building on non-amd64 archs, it is necessary to not
- use the unpatched libjemalloc copy bundled by upstream. This patch
- makes sure spades links against the packaged copy and no local
- version is built any more.
- The log output of this version will be different from the one of a
- version using the bundled jemalloc as the jemalloc version in Debian
- does not report the 'stats.cactive_max' mallctl stat anymore.
- Hence to avoid a NULL dereference the max rss value is logged.
-Author: Sascha Steinbiss <satta@debian.org>
+Description: use more Debian packaged libraries
+Author: Sascha Steinbiss <satta@debian.org>,
+        Michael R. Crusoe <michael.crusoe@gmail.com>
 --- a/src/cmake/includes.cmake
 +++ b/src/cmake/includes.cmake
 @@ -3,6 +3,8 @@
@@ -19,15 +12,6 @@ Author: Sascha Steinbiss <satta@debian.org>
  include_directories(${SPADES_MAIN_INCLUDE_DIR} ${SPADES_BUILT_INCLUDE_DIR} ${CMAKE_SOURCE_DIR} ${SPADES_MODULES_DIR}) 
  include_directories(SYSTEM "${EXT_DIR}/include")
  include_directories(SYSTEM "${ZLIB_INCLUDE_DIRS}")
---- a/src/cmake/flags.cmake
-+++ b/src/cmake/flags.cmake
-@@ -53,3 +53,5 @@ endif()
- if (SPADES_USE_TCMALLOC)
-   add_compile_options(-fno-omit-frame-pointer)
- endif()
-+
-+add_definitions(-DJEMALLOC_NO_DEMANGLE)
-\ No newline at end of file
 --- a/src/common/assembly_graph/CMakeLists.txt
 +++ b/src/common/assembly_graph/CMakeLists.txt
 @@ -9,4 +9,4 @@ project(assembly_graph CXX)
@@ -58,43 +42,12 @@ Author: Sascha Steinbiss <satta@debian.org>
  
  namespace debruijn_graph {
  
---- a/src/common/utils/logger/logger_impl.cpp
-+++ b/src/common/utils/logger/logger_impl.cpp
-@@ -14,6 +14,7 @@
- 
- #include "utils/logger/logger.hpp"
- #include "utils/perf/memory.hpp"
-+#include "utils/memory_limit.hpp"
- 
- #include "config.hpp"
- 
-@@ -105,15 +106,16 @@ void logger::log(level desired_level, co
-   size_t max_rss;
- 
- #ifdef SPADES_USE_JEMALLOC
--  const size_t *cmem = 0, *cmem_max = 0;
-+  const size_t *cmem = 0;//, *cmem_max = 0;
-   size_t clen = sizeof(cmem);
- 
-   je_mallctl("stats.cactive", &cmem, &clen, NULL, 0);
--  je_mallctl("stats.cactive_max", &cmem_max, &clen, NULL, 0);
-+  //je_mallctl("stats.cactive_max", &cmem_max, &clen, NULL, 0);
-   mem = (*cmem) / 1024;
--  max_rss = (*cmem_max) / 1024;
-+  //max_rss = (*cmem_max) / 1024;
-+  max_rss = utils::get_max_rss();
- #else
--  max_rss = get_max_rss();
-+  max_rss = utils::get_max_rss();
- #endif
- 
-   for (auto it = writers_.begin(); it != writers_.end(); ++it)
 --- a/ext/src/CMakeLists.txt
 +++ b/ext/src/CMakeLists.txt
-@@ -1,16 +1,12 @@
+@@ -1,16 +1,13 @@
  # -*- cmake -*-
  
--add_subdirectory(jemalloc)
+ add_subdirectory(jemalloc)
 -add_subdirectory(nlopt)
  add_subdirectory(ConsensusCore)
  add_subdirectory(bamtools)

debian/rules

@@ -82,9 +82,11 @@ override_dh_install:
 	install debian/bin/spades debian/$(DEB_SOURCE)/usr/bin/
 	chmod +x debian/$(DEB_SOURCE)/usr/bin/spades
 	rm -f debian/$(DEB_SOURCE)/usr/share/spades/GPLv2.txt
+	rm -f debian/$(DEB_SOURCE)/usr/share/spades/README.md
 	rm -f debian/$(DEB_SOURCE)/usr/share/spades/LICENSE
 	ln -s ../../../share/spades/VERSION debian/$(DEB_SOURCE)/usr/lib/spades/bin/VERSION
 
+
 override_dh_installdocs:
 	dh_installdocs
 	rm -f debian/$(DEB_SOURCE)/usr/share/spades/*.html

debian/watch

 version=4
 
 opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
-  http://cab.spbu.ru/software/spades/ .*/release.*/SPAdes-(\d[\d.]+)@ARCHIVE_EXT@
+  https://github.com/ablab/spades/releases/ .*/download/.*/SPAdes-(\d[\d.]+)@ARCHIVE_EXT@

ext/include/jemalloc/internal/atomic.h

+/******************************************************************************/
+#ifdef JEMALLOC_H_TYPES
+
+#endif /* JEMALLOC_H_TYPES */
+/******************************************************************************/
+#ifdef JEMALLOC_H_STRUCTS
+
+#endif /* JEMALLOC_H_STRUCTS */
+/******************************************************************************/
+#ifdef JEMALLOC_H_EXTERNS
+
+#define	atomic_read_uint64(p)	atomic_add_uint64(p, 0)
+#define	atomic_read_uint32(p)	atomic_add_uint32(p, 0)
+#define	atomic_read_z(p)	atomic_add_z(p, 0)
+#define	atomic_read_u(p)	atomic_add_u(p, 0)
+
+#endif /* JEMALLOC_H_EXTERNS */
+/******************************************************************************/
+#ifdef JEMALLOC_H_INLINES
+
+#ifndef JEMALLOC_ENABLE_INLINE
+uint64_t	atomic_add_uint64(uint64_t *p, uint64_t x);
+uint64_t	atomic_sub_uint64(uint64_t *p, uint64_t x);
+uint32_t	atomic_add_uint32(uint32_t *p, uint32_t x);
+uint32_t	atomic_sub_uint32(uint32_t *p, uint32_t x);
+size_t	atomic_add_z(size_t *p, size_t x);
+size_t	atomic_sub_z(size_t *p, size_t x);
+unsigned	atomic_add_u(unsigned *p, unsigned x);
+unsigned	atomic_sub_u(unsigned *p, unsigned x);
+#endif
+
+#if (defined(JEMALLOC_ENABLE_INLINE) || defined(JEMALLOC_ATOMIC_C_))
+/******************************************************************************/
+/* 64-bit operations. */
+#if (LG_SIZEOF_PTR == 3 || LG_SIZEOF_INT == 3)
+#  ifdef __GCC_HAVE_SYNC_COMPARE_AND_SWAP_8
+JEMALLOC_INLINE uint64_t
+atomic_add_uint64(uint64_t *p, uint64_t x)
+{
+
+	return (__sync_add_and_fetch(p, x));
+}
+
+JEMALLOC_INLINE uint64_t
+atomic_sub_uint64(uint64_t *p, uint64_t x)
+{
+
+	return (__sync_sub_and_fetch(p, x));
+}
+#elif (defined(_MSC_VER))
+JEMALLOC_INLINE uint64_t
+atomic_add_uint64(uint64_t *p, uint64_t x)
+{
+
+	return (InterlockedExchangeAdd64(p, x));
+}
+
+JEMALLOC_INLINE uint64_t
+atomic_sub_uint64(uint64_t *p, uint64_t x)
+{
+
+	return (InterlockedExchangeAdd64(p, -((int64_t)x)));
+}
+#elif (defined(JEMALLOC_OSATOMIC))
+JEMALLOC_INLINE uint64_t
+atomic_add_uint64(uint64_t *p, uint64_t x)
+{
+
+	return (OSAtomicAdd64((int64_t)x, (int64_t *)p));
+}
+
+JEMALLOC_INLINE uint64_t
+atomic_sub_uint64(uint64_t *p, uint64_t x)
+{
+
+	return (OSAtomicAdd64(-((int64_t)x), (int64_t *)p));
+}
+#  elif (defined(__amd64__) || defined(__x86_64__))
+JEMALLOC_INLINE uint64_t
+atomic_add_uint64(uint64_t *p, uint64_t x)
+{
+
+	asm volatile (
+	    "lock; xaddq %0, %1;"
+	    : "+r" (x), "=m" (*p) /* Outputs. */
+	    : "m" (*p) /* Inputs. */
+	    );
+
+	return (x);
+}
+
+JEMALLOC_INLINE uint64_t
+atomic_sub_uint64(uint64_t *p, uint64_t x)
+{
+
+	x = (uint64_t)(-(int64_t)x);
+	asm volatile (
+	    "lock; xaddq %0, %1;"
+	    : "+r" (x), "=m" (*p) /* Outputs. */
+	    : "m" (*p) /* Inputs. */
+	    );
+
+	return (x);
+}
+#  elif (defined(JEMALLOC_ATOMIC9))
+JEMALLOC_INLINE uint64_t
+atomic_add_uint64(uint64_t *p, uint64_t x)
+{
+
+	/*
+	 * atomic_fetchadd_64() doesn't exist, but we only ever use this
+	 * function on LP64 systems, so atomic_fetchadd_long() will do.
+	 */
+	assert(sizeof(uint64_t) == sizeof(unsigned long));
+
+	return (atomic_fetchadd_long(p, (unsigned long)x) + x);
+}
+
+JEMALLOC_INLINE uint64_t
+atomic_sub_uint64(uint64_t *p, uint64_t x)
+{
+
+	assert(sizeof(uint64_t) == sizeof(unsigned long));
+
+	return (atomic_fetchadd_long(p, (unsigned long)(-(long)x)) - x);
+}
+#  elif (defined(JE_FORCE_SYNC_COMPARE_AND_SWAP_8))
+JEMALLOC_INLINE uint64_t
+atomic_add_uint64(uint64_t *p, uint64_t x)
+{
+
+	return (__sync_add_and_fetch(p, x));
+}
+
+JEMALLOC_INLINE uint64_t
+atomic_sub_uint64(uint64_t *p, uint64_t x)
+{
+
+	return (__sync_sub_and_fetch(p, x));
+}
+#  else
+#    error "Missing implementation for 64-bit atomic operations"
+#  endif
+#endif
+
+/******************************************************************************/
+/* 32-bit operations. */
+#ifdef __GCC_HAVE_SYNC_COMPARE_AND_SWAP_4
+JEMALLOC_INLINE uint32_t
+atomic_add_uint32(uint32_t *p, uint32_t x)
+{
+
+	return (__sync_add_and_fetch(p, x));
+}
+
+JEMALLOC_INLINE uint32_t
+atomic_sub_uint32(uint32_t *p, uint32_t x)
+{
+
+	return (__sync_sub_and_fetch(p, x));
+}
+#elif (defined(_MSC_VER))
+JEMALLOC_INLINE uint32_t
+atomic_add_uint32(uint32_t *p, uint32_t x)
+{
+
+	return (InterlockedExchangeAdd(p, x));
+}
+
+JEMALLOC_INLINE uint32_t
+atomic_sub_uint32(uint32_t *p, uint32_t x)
+{
+
+	return (InterlockedExchangeAdd(p, -((int32_t)x)));
+}
+#elif (defined(JEMALLOC_OSATOMIC))
+JEMALLOC_INLINE uint32_t
+atomic_add_uint32(uint32_t *p, uint32_t x)
+{
+
+	return (OSAtomicAdd32((int32_t)x, (int32_t *)p));
+}
+
+JEMALLOC_INLINE uint32_t
+atomic_sub_uint32(uint32_t *p, uint32_t x)
+{
+
+	return (OSAtomicAdd32(-((int32_t)x), (int32_t *)p));
+}
+#elif (defined(__i386__) || defined(__amd64__) || defined(__x86_64__))
+JEMALLOC_INLINE uint32_t
+atomic_add_uint32(uint32_t *p, uint32_t x)
+{
+
+	asm volatile (
+	    "lock; xaddl %0, %1;"
+	    : "+r" (x), "=m" (*p) /* Outputs. */
+	    : "m" (*p) /* Inputs. */
+	    );
+
+	return (x);
+}
+
+JEMALLOC_INLINE uint32_t
+atomic_sub_uint32(uint32_t *p, uint32_t x)
+{
+
+	x = (uint32_t)(-(int32_t)x);
+	asm volatile (
+	    "lock; xaddl %0, %1;"
+	    : "+r" (x), "=m" (*p) /* Outputs. */
+	    : "m" (*p) /* Inputs. */
+	    );
+
+	return (x);
+}
+#elif (defined(JEMALLOC_ATOMIC9))
+JEMALLOC_INLINE uint32_t
+atomic_add_uint32(uint32_t *p, uint32_t x)
+{
+
+	return (atomic_fetchadd_32(p, x) + x);
+}
+
+JEMALLOC_INLINE uint32_t
+atomic_sub_uint32(uint32_t *p, uint32_t x)
+{
+
+	return (atomic_fetchadd_32(p, (uint32_t)(-(int32_t)x)) - x);
+}
+#elif (defined(JE_FORCE_SYNC_COMPARE_AND_SWAP_4))
+JEMALLOC_INLINE uint32_t
+atomic_add_uint32(uint32_t *p, uint32_t x)
+{
+
+	return (__sync_add_and_fetch(p, x));
+}
+
+JEMALLOC_INLINE uint32_t
+atomic_sub_uint32(uint32_t *p, uint32_t x)
+{
+
+	return (__sync_sub_and_fetch(p, x));
+}
+#else
+#  error "Missing implementation for 32-bit atomic operations"
+#endif
+
+/******************************************************************************/
+/* size_t operations. */
+JEMALLOC_INLINE size_t
+atomic_add_z(size_t *p, size_t x)
+{
+
+#if (LG_SIZEOF_PTR == 3)
+	return ((size_t)atomic_add_uint64((uint64_t *)p, (uint64_t)x));
+#elif (LG_SIZEOF_PTR == 2)
+	return ((size_t)atomic_add_uint32((uint32_t *)p, (uint32_t)x));
+#endif
+}
+
+JEMALLOC_INLINE size_t
+atomic_sub_z(size_t *p, size_t x)
+{
+
+#if (LG_SIZEOF_PTR == 3)
+	return ((size_t)atomic_add_uint64((uint64_t *)p,
+	    (uint64_t)-((int64_t)x)));
+#elif (LG_SIZEOF_PTR == 2)
+	return ((size_t)atomic_add_uint32((uint32_t *)p,
+	    (uint32_t)-((int32_t)x)));
+#endif
+}
+
+/******************************************************************************/
+/* unsigned operations. */
+JEMALLOC_INLINE unsigned
+atomic_add_u(unsigned *p, unsigned x)
+{
+
+#if (LG_SIZEOF_INT == 3)
+	return ((unsigned)atomic_add_uint64((uint64_t *)p, (uint64_t)x));
+#elif (LG_SIZEOF_INT == 2)
+	return ((unsigned)atomic_add_uint32((uint32_t *)p, (uint32_t)x));
+#endif
+}
+
+JEMALLOC_INLINE unsigned
+atomic_sub_u(unsigned *p, unsigned x)
+{
+
+#if (LG_SIZEOF_INT == 3)
+	return ((unsigned)atomic_add_uint64((uint64_t *)p,
+	    (uint64_t)-((int64_t)x)));
+#elif (LG_SIZEOF_INT == 2)
+	return ((unsigned)atomic_add_uint32((uint32_t *)p,
+	    (uint32_t)-((int32_t)x)));
+#endif
+}
+/******************************************************************************/
+#endif
+
+#endif /* JEMALLOC_H_INLINES */
+/******************************************************************************/

ext/include/jemalloc/internal/base.h

+/******************************************************************************/
+#ifdef JEMALLOC_H_TYPES
+
+#endif /* JEMALLOC_H_TYPES */
+/******************************************************************************/
+#ifdef JEMALLOC_H_STRUCTS
+
+#endif /* JEMALLOC_H_STRUCTS */
+/******************************************************************************/
+#ifdef JEMALLOC_H_EXTERNS
+
+void	*base_alloc(size_t size);
+void	*base_calloc(size_t number, size_t size);
+extent_node_t *base_node_alloc(void);
+void	base_node_dealloc(extent_node_t *node);
+bool	base_boot(void);
+void	base_prefork(void);
+void	base_postfork_parent(void);
+void	base_postfork_child(void);
+
+#endif /* JEMALLOC_H_EXTERNS */
+/******************************************************************************/
+#ifdef JEMALLOC_H_INLINES
+
+#endif /* JEMALLOC_H_INLINES */
+/******************************************************************************/

ext/include/jemalloc/internal/bitmap.h

+/******************************************************************************/
+#ifdef JEMALLOC_H_TYPES
+
+/* Maximum bitmap bit count is 2^LG_BITMAP_MAXBITS. */
+#define	LG_BITMAP_MAXBITS	LG_RUN_MAXREGS
+
+typedef struct bitmap_level_s bitmap_level_t;
+typedef struct bitmap_info_s bitmap_info_t;
+typedef unsigned long bitmap_t;
+#define	LG_SIZEOF_BITMAP	LG_SIZEOF_LONG
+
+/* Number of bits per group. */
+#define	LG_BITMAP_GROUP_NBITS		(LG_SIZEOF_BITMAP + 3)
+#define	BITMAP_GROUP_NBITS		(ZU(1) << LG_BITMAP_GROUP_NBITS)
+#define	BITMAP_GROUP_NBITS_MASK		(BITMAP_GROUP_NBITS-1)
+
+/* Maximum number of levels possible. */
+#define	BITMAP_MAX_LEVELS						\
+    (LG_BITMAP_MAXBITS / LG_SIZEOF_BITMAP)				\
+    + !!(LG_BITMAP_MAXBITS % LG_SIZEOF_BITMAP)
+
+#endif /* JEMALLOC_H_TYPES */
+/******************************************************************************/
+#ifdef JEMALLOC_H_STRUCTS
+
+struct bitmap_level_s {
+	/* Offset of this level's groups within the array of groups. */
+	size_t group_offset;
+};
+
+struct bitmap_info_s {
+	/* Logical number of bits in bitmap (stored at bottom level). */
+	size_t nbits;
+
+	/* Number of levels necessary for nbits. */
+	unsigned nlevels;
+
+	/*
+	 * Only the first (nlevels+1) elements are used, and levels are ordered
+	 * bottom to top (e.g. the bottom level is stored in levels[0]).
+	 */
+	bitmap_level_t levels[BITMAP_MAX_LEVELS+1];
+};
+
+#endif /* JEMALLOC_H_STRUCTS */
+/******************************************************************************/
+#ifdef JEMALLOC_H_EXTERNS
+
+void	bitmap_info_init(bitmap_info_t *binfo, size_t nbits);
+size_t	bitmap_info_ngroups(const bitmap_info_t *binfo);
+size_t	bitmap_size(size_t nbits);
+void	bitmap_init(bitmap_t *bitmap, const bitmap_info_t *binfo);
+
+#endif /* JEMALLOC_H_EXTERNS */
+/******************************************************************************/
+#ifdef JEMALLOC_H_INLINES
+
+#ifndef JEMALLOC_ENABLE_INLINE
+bool	bitmap_full(bitmap_t *bitmap, const bitmap_info_t *binfo);
+bool	bitmap_get(bitmap_t *bitmap, const bitmap_info_t *binfo, size_t bit);
+void	bitmap_set(bitmap_t *bitmap, const bitmap_info_t *binfo, size_t bit);
+size_t	bitmap_sfu(bitmap_t *bitmap, const bitmap_info_t *binfo);
+void	bitmap_unset(bitmap_t *bitmap, const bitmap_info_t *binfo, size_t bit);
+#endif
+
+#if (defined(JEMALLOC_ENABLE_INLINE) || defined(JEMALLOC_BITMAP_C_))
+JEMALLOC_INLINE bool
+bitmap_full(bitmap_t *bitmap, const bitmap_info_t *binfo)
+{
+	unsigned rgoff = binfo->levels[binfo->nlevels].group_offset - 1;
+	bitmap_t rg = bitmap[rgoff];
+	/* The bitmap is full iff the root group is 0. */
+	return (rg == 0);
+}
+
+JEMALLOC_INLINE bool
+bitmap_get(bitmap_t *bitmap, const bitmap_info_t *binfo, size_t bit)
+{
+	size_t goff;
+	bitmap_t g;
+
+	assert(bit < binfo->nbits);
+	goff = bit >> LG_BITMAP_GROUP_NBITS;
+	g = bitmap[goff];
+	return (!(g & (1LU << (bit & BITMAP_GROUP_NBITS_MASK))));
+}
+
+JEMALLOC_INLINE void
+bitmap_set(bitmap_t *bitmap, const bitmap_info_t *binfo, size_t bit)
+{
+	size_t goff;
+	bitmap_t *gp;
+	bitmap_t g;
+
+	assert(bit < binfo->nbits);
+	assert(bitmap_get(bitmap, binfo, bit) == false);
+	goff = bit >> LG_BITMAP_GROUP_NBITS;
+	gp = &bitmap[goff];
+	g = *gp;
+	assert(g & (1LU << (bit & BITMAP_GROUP_NBITS_MASK)));
+	g ^= 1LU << (bit & BITMAP_GROUP_NBITS_MASK);
+	*gp = g;
+	assert(bitmap_get(bitmap, binfo, bit));
+	/* Propagate group state transitions up the tree. */
+	if (g == 0) {
+		unsigned i;
+		for (i = 1; i < binfo->nlevels; i++) {
+			bit = goff;
+			goff = bit >> LG_BITMAP_GROUP_NBITS;
+			gp = &bitmap[binfo->levels[i].group_offset + goff];
+			g = *gp;
+			assert(g & (1LU << (bit & BITMAP_GROUP_NBITS_MASK)));
+			g ^= 1LU << (bit & BITMAP_GROUP_NBITS_MASK);
+			*gp = g;
+			if (g != 0)
+				break;
+		}
+	}
+}
+
+/* sfu: set first unset. */
+JEMALLOC_INLINE size_t
+bitmap_sfu(bitmap_t *bitmap, const bitmap_info_t *binfo)
+{
+	size_t bit;
+	bitmap_t g;
+	unsigned i;
+
+	assert(bitmap_full(bitmap, binfo) == false);
+
+	i = binfo->nlevels - 1;
+	g = bitmap[binfo->levels[i].group_offset];
+	bit = ffsl(g) - 1;
+	while (i > 0) {
+		i--;
+		g = bitmap[binfo->levels[i].group_offset + bit];
+		bit = (bit << LG_BITMAP_GROUP_NBITS) + (ffsl(g) - 1);
+	}
+
+	bitmap_set(bitmap, binfo, bit);
+	return (bit);
+}
+
+JEMALLOC_INLINE void
+bitmap_unset(bitmap_t *bitmap, const bitmap_info_t *binfo, size_t bit)
+{
+	size_t goff;
+	bitmap_t *gp;
+	bitmap_t g;
+	bool propagate;
+
+	assert(bit < binfo->nbits);
+	assert(bitmap_get(bitmap, binfo, bit));
+	goff = bit >> LG_BITMAP_GROUP_NBITS;
+	gp = &bitmap[goff];
+	g = *gp;
+	propagate = (g == 0);
+	assert((g & (1LU << (bit & BITMAP_GROUP_NBITS_MASK))) == 0);
+	g ^= 1LU << (bit & BITMAP_GROUP_NBITS_MASK);
+	*gp = g;
+	assert(bitmap_get(bitmap, binfo, bit) == false);
+	/* Propagate group state transitions up the tree. */
+	if (propagate) {
+		unsigned i;
+		for (i = 1; i < binfo->nlevels; i++) {
+			bit = goff;
+			goff = bit >> LG_BITMAP_GROUP_NBITS;
+			gp = &bitmap[binfo->levels[i].group_offset + goff];
+			g = *gp;
+			propagate = (g == 0);
+			assert((g & (1LU << (bit & BITMAP_GROUP_NBITS_MASK)))
+			    == 0);
+			g ^= 1LU << (bit & BITMAP_GROUP_NBITS_MASK);
+			*gp = g;
+			if (propagate == false)
+				break;
+		}
+	}
+}
+
+#endif
+
+#endif /* JEMALLOC_H_INLINES */
+/******************************************************************************/

ext/include/jemalloc/internal/chunk.h

+/******************************************************************************/
+#ifdef JEMALLOC_H_TYPES
+
+/*
+ * Size and alignment of memory chunks that are allocated by the OS's virtual
+ * memory system.
+ */
+#define	LG_CHUNK_DEFAULT	22
+
+/* Return the chunk address for allocation address a. */
+#define	CHUNK_ADDR2BASE(a)						\
+	((void *)((uintptr_t)(a) & ~chunksize_mask))
+
+/* Return the chunk offset of address a. */
+#define	CHUNK_ADDR2OFFSET(a)						\
+	((size_t)((uintptr_t)(a) & chunksize_mask))
+
+/* Return the smallest chunk multiple that is >= s. */
+#define	CHUNK_CEILING(s)						\
+	(((s) + chunksize_mask) & ~chunksize_mask)
+
+#endif /* JEMALLOC_H_TYPES */
+/******************************************************************************/
+#ifdef JEMALLOC_H_STRUCTS
+
+#endif /* JEMALLOC_H_STRUCTS */
+/******************************************************************************/
+#ifdef JEMALLOC_H_EXTERNS
+
+extern size_t		opt_lg_chunk;
+extern const char	*opt_dss;
+
+/* Protects stats_chunks; currently not used for any other purpose. */
+extern malloc_mutex_t	chunks_mtx;
+/* Chunk statistics. */
+extern chunk_stats_t	stats_chunks;
+
+extern rtree_t		*chunks_rtree;
+
+extern size_t		chunksize;
+extern size_t		chunksize_mask; /* (chunksize - 1). */
+extern size_t		chunk_npages;
+extern size_t		map_bias; /* Number of arena chunk header pages. */
+extern size_t		arena_maxclass; /* Max size class for arenas. */
+
+void	*chunk_alloc(size_t size, size_t alignment, bool base, bool *zero,
+    dss_prec_t dss_prec);
+void	chunk_unmap(void *chunk, size_t size);
+void	chunk_dealloc(void *chunk, size_t size, bool unmap);
+bool	chunk_boot(void);
+void	chunk_prefork(void);
+void	chunk_postfork_parent(void);
+void	chunk_postfork_child(void);
+
+#endif /* JEMALLOC_H_EXTERNS */
+/******************************************************************************/
+#ifdef JEMALLOC_H_INLINES
+
+#endif /* JEMALLOC_H_INLINES */
+/******************************************************************************/
+
+#include "jemalloc/internal/chunk_dss.h"
+#include "jemalloc/internal/chunk_mmap.h"

ext/include/jemalloc/internal/chunk_dss.h

+/******************************************************************************/
+#ifdef JEMALLOC_H_TYPES
+
+typedef enum {
+	dss_prec_disabled  = 0,
+	dss_prec_primary   = 1,
+	dss_prec_secondary = 2,
+
+	dss_prec_limit     = 3
+} dss_prec_t ;
+#define	DSS_PREC_DEFAULT	dss_prec_secondary
+#define	DSS_DEFAULT		"secondary"
+
+#endif /* JEMALLOC_H_TYPES */
+/******************************************************************************/
+#ifdef JEMALLOC_H_STRUCTS
+
+extern const char *dss_prec_names[];
+
+#endif /* JEMALLOC_H_STRUCTS */
+/******************************************************************************/
+#ifdef JEMALLOC_H_EXTERNS
+
+dss_prec_t	chunk_dss_prec_get(void);
+bool	chunk_dss_prec_set(dss_prec_t dss_prec);
+void	*chunk_alloc_dss(size_t size, size_t alignment, bool *zero);
+bool	chunk_in_dss(void *chunk);
+bool	chunk_dss_boot(void);
+void	chunk_dss_prefork(void);
+void	chunk_dss_postfork_parent(void);
+void	chunk_dss_postfork_child(void);
+
+#endif /* JEMALLOC_H_EXTERNS */
+/******************************************************************************/
+#ifdef JEMALLOC_H_INLINES
+
+#endif /* JEMALLOC_H_INLINES */
+/******************************************************************************/

ext/include/jemalloc/internal/chunk_mmap.h

+/******************************************************************************/
+#ifdef JEMALLOC_H_TYPES
+
+#endif /* JEMALLOC_H_TYPES */
+/******************************************************************************/
+#ifdef JEMALLOC_H_STRUCTS
+
+#endif /* JEMALLOC_H_STRUCTS */
+/******************************************************************************/
+#ifdef JEMALLOC_H_EXTERNS
+
+bool	pages_purge(void *addr, size_t length);
+
+void	*chunk_alloc_mmap(size_t size, size_t alignment, bool *zero);
+bool	chunk_dealloc_mmap(void *chunk, size_t size);
+
+#endif /* JEMALLOC_H_EXTERNS */
+/******************************************************************************/
+#ifdef JEMALLOC_H_INLINES
+
+#endif /* JEMALLOC_H_INLINES */
+/******************************************************************************/

ext/include/jemalloc/internal/ckh.h

+/******************************************************************************/
+#ifdef JEMALLOC_H_TYPES
+
+typedef struct ckh_s ckh_t;
+typedef struct ckhc_s ckhc_t;
+
+/* Typedefs to allow easy function pointer passing. */
+typedef void ckh_hash_t (const void *, unsigned, size_t *, size_t *);
+typedef bool ckh_keycomp_t (const void *, const void *);
+
+/* Maintain counters used to get an idea of performance. */
+/* #define	CKH_COUNT */
+/* Print counter values in ckh_delete() (requires CKH_COUNT). */
+/* #define	CKH_VERBOSE */
+
+/*
+ * There are 2^LG_CKH_BUCKET_CELLS cells in each hash table bucket.  Try to fit
+ * one bucket per L1 cache line.
+ */
+#define LG_CKH_BUCKET_CELLS (LG_CACHELINE - LG_SIZEOF_PTR - 1)
+
+#endif /* JEMALLOC_H_TYPES */
+/******************************************************************************/
+#ifdef JEMALLOC_H_STRUCTS
+
+/* Hash table cell. */
+struct ckhc_s {
+	const void	*key;
+	const void	*data;
+};
+
+struct ckh_s {
+#ifdef CKH_COUNT
+	/* Counters used to get an idea of performance. */
+	uint64_t	ngrows;
+	uint64_t	nshrinks;
+	uint64_t	nshrinkfails;
+	uint64_t	ninserts;
+	uint64_t	nrelocs;
+#endif
+
+	/* Used for pseudo-random number generation. */
+#define	CKH_A		1103515241
+#define	CKH_C		12347
+	uint32_t	prng_state;
+
+	/* Total number of items. */
+	size_t		count;
+
+	/*
+	 * Minimum and current number of hash table buckets.  There are
+	 * 2^LG_CKH_BUCKET_CELLS cells per bucket.
+	 */
+	unsigned	lg_minbuckets;
+	unsigned	lg_curbuckets;
+
+	/* Hash and comparison functions. */
+	ckh_hash_t	*hash;
+	ckh_keycomp_t	*keycomp;
+
+	/* Hash table with 2^lg_curbuckets buckets. */
+	ckhc_t		*tab;
+};
+
+#endif /* JEMALLOC_H_STRUCTS */
+/******************************************************************************/
+#ifdef JEMALLOC_H_EXTERNS
+
+bool	ckh_new(ckh_t *ckh, size_t minitems, ckh_hash_t *hash,
+    ckh_keycomp_t *keycomp);
+void	ckh_delete(ckh_t *ckh);
+size_t	ckh_count(ckh_t *ckh);
+bool	ckh_iter(ckh_t *ckh, size_t *tabind, void **key, void **data);
+bool	ckh_insert(ckh_t *ckh, const void *key, const void *data);
+bool	ckh_remove(ckh_t *ckh, const void *searchkey, void **key,
+    void **data);
+bool	ckh_search(ckh_t *ckh, const void *seachkey, void **key, void **data);
+void	ckh_string_hash(const void *key, unsigned minbits, size_t *hash1,
+    size_t *hash2);
+bool	ckh_string_keycomp(const void *k1, const void *k2);
+void	ckh_pointer_hash(const void *key, unsigned minbits, size_t *hash1,
+    size_t *hash2);
+bool	ckh_pointer_keycomp(const void *k1, const void *k2);
+
+#endif /* JEMALLOC_H_EXTERNS */
+/******************************************************************************/
+#ifdef JEMALLOC_H_INLINES
+
+#endif /* JEMALLOC_H_INLINES */
+/******************************************************************************/

ext/include/jemalloc/internal/ctl.h

+/******************************************************************************/
+#ifdef JEMALLOC_H_TYPES
+
+typedef struct ctl_node_s ctl_node_t;
+typedef struct ctl_named_node_s ctl_named_node_t;
+typedef struct ctl_indexed_node_s ctl_indexed_node_t;
+typedef struct ctl_arena_stats_s ctl_arena_stats_t;
+typedef struct ctl_stats_s ctl_stats_t;
+
+#endif /* JEMALLOC_H_TYPES */
+/******************************************************************************/
+#ifdef JEMALLOC_H_STRUCTS
+
+struct ctl_node_s {
+	bool			named;
+};
+
+struct ctl_named_node_s {
+	struct ctl_node_s	node;
+	const char		*name;
+	/* If (nchildren == 0), this is a terminal node. */
+	unsigned		nchildren;
+	const			ctl_node_t *children;
+	int			(*ctl)(const size_t *, size_t, void *, size_t *,
+	    void *, size_t);
+};
+
+struct ctl_indexed_node_s {
+	struct ctl_node_s	node;
+	const ctl_named_node_t	*(*index)(const size_t *, size_t, size_t);
+};
+
+struct ctl_arena_stats_s {
+	bool			initialized;
+	unsigned		nthreads;
+	const char		*dss;
+	size_t			pactive;
+	size_t			pdirty;
+	arena_stats_t		astats;
+
+	/* Aggregate stats for small size classes, based on bin stats. */
+	size_t			allocated_small;
+	uint64_t		nmalloc_small;
+	uint64_t		ndalloc_small;
+	uint64_t		nrequests_small;
+
+	malloc_bin_stats_t	bstats[NBINS];
+	malloc_large_stats_t	*lstats;	/* nlclasses elements. */
+};
+
+struct ctl_stats_s {
+	size_t			allocated;
+	size_t			active;
+	size_t			mapped;
+	struct {
+		size_t		current;	/* stats_chunks.curchunks */
+		uint64_t	total;		/* stats_chunks.nchunks */
+		size_t		high;		/* stats_chunks.highchunks */
+	} chunks;
+	struct {
+		size_t		allocated;	/* huge_allocated */
+		uint64_t	nmalloc;	/* huge_nmalloc */
+		uint64_t	ndalloc;	/* huge_ndalloc */
+	} huge;
+	unsigned		narenas;
+	ctl_arena_stats_t	*arenas;	/* (narenas + 1) elements. */
+};
+
+#endif /* JEMALLOC_H_STRUCTS */
+/******************************************************************************/
+#ifdef JEMALLOC_H_EXTERNS
+
+int	ctl_byname(const char *name, void *oldp, size_t *oldlenp, void *newp,
+    size_t newlen);
+int	ctl_nametomib(const char *name, size_t *mibp, size_t *miblenp);
+
+int	ctl_bymib(const size_t *mib, size_t miblen, void *oldp, size_t *oldlenp,
+    void *newp, size_t newlen);
+bool	ctl_boot(void);
+void	ctl_prefork(void);
+void	ctl_postfork_parent(void);
+void	ctl_postfork_child(void);
+
+#define	xmallctl(name, oldp, oldlenp, newp, newlen) do {		\
+	if (je_mallctl(name, oldp, oldlenp, newp, newlen)		\
+	    != 0) {							\
+		malloc_printf(						\
+		    "<jemalloc>: Failure in xmallctl(\"%s\", ...)\n",	\
+		    name);						\
+		abort();						\
+	}								\
+} while (0)
+
+#define	xmallctlnametomib(name, mibp, miblenp) do {			\
+	if (je_mallctlnametomib(name, mibp, miblenp) != 0) {		\
+		malloc_printf("<jemalloc>: Failure in "			\
+		    "xmallctlnametomib(\"%s\", ...)\n", name);		\
+		abort();						\
+	}								\
+} while (0)
+
+#define	xmallctlbymib(mib, miblen, oldp, oldlenp, newp, newlen) do {	\
+	if (je_mallctlbymib(mib, miblen, oldp, oldlenp, newp,		\
+	    newlen) != 0) {						\
+		malloc_write(						\
+		    "<jemalloc>: Failure in xmallctlbymib()\n");	\
+		abort();						\
+	}								\
+} while (0)
+
+#endif /* JEMALLOC_H_EXTERNS */
+/******************************************************************************/
+#ifdef JEMALLOC_H_INLINES
+
+#endif /* JEMALLOC_H_INLINES */
+/******************************************************************************/
+

ext/include/jemalloc/internal/extent.h

+/******************************************************************************/
+#ifdef JEMALLOC_H_TYPES
+
+typedef struct extent_node_s extent_node_t;
+
+#endif /* JEMALLOC_H_TYPES */
+/******************************************************************************/
+#ifdef JEMALLOC_H_STRUCTS
+
+/* Tree of extents. */
+struct extent_node_s {
+	/* Linkage for the size/address-ordered tree. */
+	rb_node(extent_node_t)	link_szad;
+
+	/* Linkage for the address-ordered tree. */
+	rb_node(extent_node_t)	link_ad;
+
+	/* Profile counters, used for huge objects. */
+	prof_ctx_t		*prof_ctx;
+
+	/* Pointer to the extent that this tree node is responsible for. */
+	void			*addr;
+
+	/* Total region size. */
+	size_t			size;
+
+	/* True if zero-filled; used by chunk recycling code. */
+	bool			zeroed;
+};
+typedef rb_tree(extent_node_t) extent_tree_t;
+
+#endif /* JEMALLOC_H_STRUCTS */
+/******************************************************************************/
+#ifdef JEMALLOC_H_EXTERNS
+
+rb_proto(, extent_tree_szad_, extent_tree_t, extent_node_t)
+
+rb_proto(, extent_tree_ad_, extent_tree_t, extent_node_t)
+
+#endif /* JEMALLOC_H_EXTERNS */
+/******************************************************************************/
+#ifdef JEMALLOC_H_INLINES
+
+#endif /* JEMALLOC_H_INLINES */
+/******************************************************************************/
+

ext/include/jemalloc/internal/hash.h

+/******************************************************************************/
+#ifdef JEMALLOC_H_TYPES
+
+#endif /* JEMALLOC_H_TYPES */
+/******************************************************************************/
+#ifdef JEMALLOC_H_STRUCTS
+
+#endif /* JEMALLOC_H_STRUCTS */
+/******************************************************************************/
+#ifdef JEMALLOC_H_EXTERNS
+
+#endif /* JEMALLOC_H_EXTERNS */
+/******************************************************************************/
+#ifdef JEMALLOC_H_INLINES
+
+#ifndef JEMALLOC_ENABLE_INLINE
+uint64_t	hash(const void *key, size_t len, uint64_t seed);
+#endif
+
+#if (defined(JEMALLOC_ENABLE_INLINE) || defined(JEMALLOC_HASH_C_))
+/*
+ * The following hash function is based on MurmurHash64A(), placed into the
+ * public domain by Austin Appleby.  See http://murmurhash.googlepages.com/ for
+ * details.
+ */
+JEMALLOC_INLINE uint64_t
+hash(const void *key, size_t len, uint64_t seed)
+{
+	const uint64_t m = UINT64_C(0xc6a4a7935bd1e995);
+	const int r = 47;
+	uint64_t h = seed ^ (len * m);
+	const uint64_t *data = (const uint64_t *)key;
+	const uint64_t *end = data + (len/8);
+	const unsigned char *data2;
+
+	assert(((uintptr_t)key & 0x7) == 0);
+
+	while(data != end) {
+		uint64_t k = *data++;
+
+		k *= m;
+		k ^= k >> r;
+		k *= m;
+
+		h ^= k;
+		h *= m;
+	}
+
+	data2 = (const unsigned char *)data;
+	switch(len & 7) {
+	case 7: h ^= ((uint64_t)(data2[6])) << 48;
+	case 6: h ^= ((uint64_t)(data2[5])) << 40;
+	case 5: h ^= ((uint64_t)(data2[4])) << 32;
+	case 4: h ^= ((uint64_t)(data2[3])) << 24;
+	case 3: h ^= ((uint64_t)(data2[2])) << 16;
+	case 2: h ^= ((uint64_t)(data2[1])) << 8;
+	case 1: h ^= ((uint64_t)(data2[0]));
+		h *= m;
+	}
+
+	h ^= h >> r;
+	h *= m;
+	h ^= h >> r;
+
+	return (h);
+}
+#endif
+
+#endif /* JEMALLOC_H_INLINES */
+/******************************************************************************/

ext/include/jemalloc/internal/huge.h

+/******************************************************************************/
+#ifdef JEMALLOC_H_TYPES
+
+#endif /* JEMALLOC_H_TYPES */
+/******************************************************************************/
+#ifdef JEMALLOC_H_STRUCTS
+
+#endif /* JEMALLOC_H_STRUCTS */
+/******************************************************************************/
+#ifdef JEMALLOC_H_EXTERNS
+
+/* Huge allocation statistics. */
+extern uint64_t		huge_nmalloc;
+extern uint64_t		huge_ndalloc;
+extern size_t		huge_allocated;
+
+/* Protects chunk-related data structures. */
+extern malloc_mutex_t	huge_mtx;
+
+void	*huge_malloc(size_t size, bool zero);
+void	*huge_palloc(size_t size, size_t alignment, bool zero);
+void	*huge_ralloc_no_move(void *ptr, size_t oldsize, size_t size,
+    size_t extra);
+void	*huge_ralloc(void *ptr, size_t oldsize, size_t size, size_t extra,
+    size_t alignment, bool zero, bool try_tcache_dalloc);
+void	huge_dalloc(void *ptr, bool unmap);
+size_t	huge_salloc(const void *ptr);
+prof_ctx_t	*huge_prof_ctx_get(const void *ptr);
+void	huge_prof_ctx_set(const void *ptr, prof_ctx_t *ctx);
+bool	huge_boot(void);
+void	huge_prefork(void);
+void	huge_postfork_parent(void);
+void	huge_postfork_child(void);
+
+#endif /* JEMALLOC_H_EXTERNS */
+/******************************************************************************/
+#ifdef JEMALLOC_H_INLINES
+
+#endif /* JEMALLOC_H_INLINES */
+/******************************************************************************/