Apply patch for jemalloc-5. Thank you Faidon Liambotis!

spades (3.13.0+dfsg-2~0jemalloc5) experimental; urgency=medium

  * Apply patch for jemalloc-5. Thank you Faidon Liambotis!

 -- Michael R. Crusoe <michael.crusoe@gmail.com>  Wed, 09 Jan 2019 23:52:01 -0800

spades (3.13.0+dfsg-1) unstable; urgency=medium

  * New upstream version

Author: Faidon Liambotis <paravoid@debian.org>

Description: Add jemalloc 3.6.0+ compatibility

--- a/src/common/adt/kmer_vector.hpp

+++ b/src/common/adt/kmer_vector.hpp

@@ -26,18 +26,12 @@ private:

     ElTy *realloc() {

 #ifdef SPADES_USE_JEMALLOC

-        // First, try to expand in-place

-        if (storage_ && sizeof(ElTy) * capacity_ * el_sz_ > 4096 &&

-            je_rallocm((void **) &storage_, NULL, sizeof(ElTy) * capacity_ * el_sz_, 0, ALLOCM_NO_MOVE) ==

-            ALLOCM_SUCCESS)

-            return storage_;

-

-        // Failed, do usual malloc / memcpy / free cycle

-        ElTy *res = (ElTy *) je_malloc(sizeof(ElTy) * capacity_ * el_sz_);

-        if (storage_)

-            std::memcpy(res, storage_, size_ * sizeof(ElTy) * el_sz_);

-        je_free(storage_);

-        storage_ = res;

+        // could simply be je_realloc(), if the realloc name wasn't redefined here

+        if (storage_) {

+            storage_ = (ElTy *) je_rallocx(storage_, sizeof(ElTy) * capacity_ * el_sz_, 0);

+        } else {

+            storage_ = (ElTy *) je_malloc(sizeof(ElTy) * capacity_ * el_sz_);

+        }

 #else

         // No JEMalloc, no cookies

         ElTy *res = new ElTy[capacity_ * el_sz_];

--- a/src/common/utils/logger/logger_impl.cpp

+++ b/src/common/utils/logger/logger_impl.cpp

@@ -106,17 +106,13 @@ void logger::log(level desired_level, const char* file, size_t line_num, const c

   size_t max_rss;

 #ifdef SPADES_USE_JEMALLOC

-  const size_t *cmem = 0;//, *cmem_max = 0;

+  size_t cmem = 0;

   size_t clen = sizeof(cmem);

-  je_mallctl("stats.cactive", &cmem, &clen, NULL, 0);

-  //je_mallctl("stats.cactive_max", &cmem_max, &clen, NULL, 0);

-  mem = (*cmem) / 1024;

-  //max_rss = (*cmem_max) / 1024;

-  max_rss = utils::get_max_rss();

-#else

-  max_rss = utils::get_max_rss();

+  je_mallctl("stats.active", (void *)&cmem, &clen, NULL, 0);

+  mem = cmem / 1024;

 #endif

+  max_rss = utils::get_max_rss();

   for (auto it = writers_.begin(); it != writers_.end(); ++it)

     (*it)->write_msg(time, mem, max_rss, desired_level, file, line_num, source, msg);

--- a/src/common/utils/memory_limit.cpp

+++ b/src/common/utils/memory_limit.cpp

@@ -83,11 +83,11 @@ size_t get_max_rss() {

 size_t get_used_memory() {

 #ifdef SPADES_USE_JEMALLOC

-    const size_t *cmem = 0;

+    size_t cmem;

     size_t clen = sizeof(cmem);

-    je_mallctl("stats.cactive", &cmem, &clen, NULL, 0);

-    return *cmem;

+    je_mallctl("stats.active", &cmem, &clen, NULL, 0);

+    return cmem;

 #else

     return get_max_rss();

 #endif

-- 

2.20.1

fix-bool-cast

spelling

gcc7.patch

jemalloc-5-compatibility-fixes.patch