6

For the last week or so I've been investigating a problem in an application where the memory usage accumulates over time. I narrowed it down to a line that copies a

std::vector< std::vector< std::vector< std::map< uint, map< uint, std::bitset< N> > > > > >

in a worker thread (I realize this is a ridiculous way to organize memory). On a regular basis, the worker thread is destroyed, recreated, and that memory structure copied by the thread when it starts. The original data that gets copied is passed to the worker thread by reference from the main thread.

Using malloc_stat and malloc_info, I can see that when the worker thread is destroyed, the arena/heap it was using retains the memory used for that structure in its free list of fastbins. This make sense, since there are many individual allocations less than 64 bytes.

The problem is, when the worker thread is recreated, it creates a new arena/heap instead of reusing the previous one, such that the fastbins from previous arenas/heaps are never reused. Eventually the system runs out of memory before reusing a previous heap/arena to reuse the fastbins they're holding onto.

Somewhat by accident, I discovered that calling malloc_trim(0) in my main thread, after joining the worker thread, causes the fastbins in the thread arenas/heaps to be released. This behavior is undocumented as far as I can see. Does anyone have an explanation?

Here is some test code I'm using to see this behavior:

// includes
#include <stdio.h>
#include <algorithm>
#include <vector>
#include <iostream>
#include <stdexcept>
#include <stdio.h>
#include <string>
#include <mcheck.h>
#include <malloc.h>
#include <map>
#include <bitset>
#include <boost/thread.hpp>
#include <boost/shared_ptr.hpp>

// Number of bits per bitset.
const int sizeOfBitsets = 40;

// Executes a system command. Used to get output of "free -m".
std::string ExecuteSystemCommand(const char* cmd) {
    char buffer[128];
    std::string result = "";
    FILE* pipe = popen(cmd, "r");
    if (!pipe) throw std::runtime_error("popen() failed!");
    try {
        while (!feof(pipe)) {
            if (fgets(buffer, 128, pipe) != NULL)
                result += buffer;
        }
    } catch (...) {
        pclose(pipe);
        throw;
    }
    pclose(pipe);
    return result;
}

// Prints output of "free -m" and output of malloc_stat().
void PrintMemoryStats()
{
    try
    {
        char *buf;
        size_t size;
        FILE *fp;

        std::string myCommand("free -m");
        std::string result = ExecuteSystemCommand(myCommand.c_str());
        printf("Free memory is \n%s\n", result.c_str());

        malloc_stats();

        fp = open_memstream(&buf, &size);
        malloc_info(0, fp);
        fclose(fp);
        printf("# Memory Allocation Stats\n%s\n#> ", buf);
        free(buf);

    }
    catch(...)
    {
        printf("Unable to print memory stats.\n");
        throw;
    }
}

void MakeCopies(std::vector<std::vector<std::map<uint, std::map<uint, std::bitset<sizeOfBitsets> > > > >& data)
{
    try
    {
        // Create copies.
        std::vector<std::vector<std::map<uint, std::map<uint, std::bitset<sizeOfBitsets> > > > > dataCopyA(data);
        std::vector<std::vector<std::map<uint, std::map<uint, std::bitset<sizeOfBitsets> > > > > dataCopyB(data);
        std::vector<std::vector<std::map<uint, std::map<uint, std::bitset<sizeOfBitsets> > > > > dataCopyC(data);

        // Print memory info.
        printf("Memory after creating data copies:\n");
        PrintMemoryStats();
    }
    catch(...)
    {
        printf("Unable to make copies.");
        throw;
    }
}

int main(int argc, char** argv)
{
    try
    {
          // When uncommented, disables the use of fastbins.
//        mallopt(M_MXFAST, 0);

        // Print memory info.
        printf("Memory to start is:\n");
        PrintMemoryStats();

        // Sizes of original data.
        int sizeOfDataA = 2048;
        int sizeOfDataB = 4;
        int sizeOfDataC = 128;
        int sizeOfDataD = 20;
        std::vector<std::vector<std::map<uint, std::map<uint, std::bitset<sizeOfBitsets> > > > > testData;

        // Populate data.
        testData.resize(sizeOfDataA);
        for(int a = 0; a < sizeOfDataA; ++a)
        {
            testData.at(a).resize(sizeOfDataB);
            for(int b = 0; b < sizeOfDataB; ++b)
            {
                for(int c = 0; c < sizeOfDataC; ++c)
                {
                    std::map<uint, std::bitset<sizeOfBitsets> > dataMap;
                    testData.at(a).at(b).insert(std::pair<uint, std::map<uint, std::bitset<sizeOfBitsets> > >(c, dataMap));
                    for(int d = 0; d < sizeOfDataD; ++d)
                    {
                        std::bitset<sizeOfBitsets> testBitset;
                        testData.at(a).at(b).at(c).insert(std::pair<uint, std::bitset<sizeOfBitsets> >(d, testBitset));
                    }
                }
            }
        }

        // Print memory info.
        printf("Memory to after creating original data is:\n");
        PrintMemoryStats();

        // Start thread to make copies and wait to join.
        {
            boost::shared_ptr<boost::thread> makeCopiesThread = boost::shared_ptr<boost::thread>(new boost::thread(&MakeCopies, boost::ref(testData)));
            makeCopiesThread->join();
        }

        // Print memory info.
        printf("Memory to after joining thread is:\n");
        PrintMemoryStats();

        malloc_trim(0);

        // Print memory info.
        printf("Memory to after malloc_trim(0) is:\n");
        PrintMemoryStats();

        return 0;

    }
    catch(...)
    {
        // Log warning.
        printf("Unable to run application.");

        // Return failure.
        return 1;
    }

    // Return success.
    return 0;
}

The interesting output from before and after the malloc trim call is (look for "LOOK HERE!"):

#> Memory to after joining thread is:
Free memory is
              total        used        free      shared  buff/cache   available
Mem:         257676        7361      246396          25        3918      249757
Swap:          1023           0        1023

Arena 0:
system bytes     = 1443450880
in use bytes     = 1443316976
Arena 1:
system bytes     =   35000320
in use bytes     =       6608
Total (incl. mmap):
system bytes     = 1478451200
in use bytes     = 1443323584
max mmap regions =          0
max mmap bytes   =          0
# Memory Allocation Stats
<malloc version="1">
<heap nr="0">
<sizes>
<size from="241" to="241" total="241" count="1"/>
<size from="529" to="529" total="529" count="1"/>
</sizes>
<total type="fast" count="0" size="0"/>
<total type="rest" count="2" size="770"/>
<system type="current" size="1443450880"/>
<system type="max" size="1443459072"/>
<aspace type="total" size="1443450880"/>
<aspace type="mprotect" size="1443450880"/>
</heap>
<heap nr="1">
<sizes>
<size from="33" to="48" total="48" count="1"/>
<size from="49" to="64" total="4026531712" count="62914558"/> <-- LOOK HERE!
<size from="65" to="80" total="160" count="2"/>
<size from="81" to="96" total="301989888" count="3145728"/> <-- LOOK HERE!
<size from="33" to="33" total="231" count="7"/>
<size from="49" to="49" total="1274" count="26"/>
<unsorted from="0" to="49377" total="1431600" count="6144"/>
</sizes>
<total type="fast" count="66060289" size="4328521808"/>
<total type="rest" count="6177" size="1433105"/>
<system type="current" size="4329967616"/>
<system type="max" size="4329967616"/>
<aspace type="total" size="35000320"/>
<aspace type="mprotect" size="35000320"/>
</heap>
<total type="fast" count="66060289" size="4328521808"/>
<total type="rest" count="6179" size="1433875"/>
<total type="mmap" count="0" size="0"/>
<system type="current" size="5773418496"/>
<system type="max" size="5773426688"/>
<aspace type="total" size="1478451200"/>
<aspace type="mprotect" size="1478451200"/>
</malloc>

#> Memory to after malloc_trim(0) is:
Free memory is
              total        used        free      shared  buff/cache   available
Mem:         257676        3269      250488          25        3918      253850
Swap:          1023           0        1023

Arena 0:
system bytes     = 1443319808
in use bytes     = 1443316976
Arena 1:
system bytes     =   35000320
in use bytes     =       6608
Total (incl. mmap):
system bytes     = 1478320128
in use bytes     = 1443323584
max mmap regions =          0
max mmap bytes   =          0
# Memory Allocation Stats
<malloc version="1">
<heap nr="0">
<sizes>
<size from="209" to="209" total="209" count="1"/>
<size from="529" to="529" total="529" count="1"/>
<unsorted from="0" to="49377" total="1431600" count="6144"/>
</sizes>
<total type="fast" count="0" size="0"/>
<total type="rest" count="6146" size="1432338"/>
<system type="current" size="1443459072"/>
<system type="max" size="1443459072"/>
<aspace type="total" size="1443459072"/>
<aspace type="mprotect" size="1443459072"/>
</heap>
<heap nr="1"> <---------------------------------------- LOOK HERE!
<sizes> <-- HERE!
<unsorted from="0" to="67108801" total="4296392384" count="6208"/>
</sizes>
<total type="fast" count="0" size="0"/>
<total type="rest" count="6208" size="4296392384"/>
<system type="current" size="4329967616"/>
<system type="max" size="4329967616"/>
<aspace type="total" size="35000320"/>
<aspace type="mprotect" size="35000320"/>
</heap>
<total type="fast" count="0" size="0"/>
<total type="rest" count="12354" size="4297824722"/>
<total type="mmap" count="0" size="0"/>
<system type="current" size="5773426688"/>
<system type="max" size="5773426688"/>
<aspace type="total" size="1478459392"/>
<aspace type="mprotect" size="1478459392"/>
</malloc>

#>

There is little to no documentation on the output of malloc_info, so I wasn't sure if those outputs I pointed out were really fast bins. To verify that they are indeed fastbins, I uncomment the code line

mallopt(M_MXFAST, 0);

to disable the use of fastbins and the memory usage for heap 1 after joining the thread, before calling malloc_trim(0), looks like it does in with fastbins enabled, after calling malloc_trim(0). Most importantly, disabling the use of fastbins returns the memory to the system immediately after the thread is joined. Calling malloc_trim(0), after joining the thread with fastbins enabled, also returns memory to the system.

The documentation for malloc_trim(0) states that it can only free memory from the top of the main arena heap, so what is going on here? I'm running on CentOS 7 with glibc version 2.17.

osgx
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user1777820
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1 Answers1

6

malloc_trim(0) states that it can only free memory from the top of the main arena heap, so what is going on here?

It can be called "outdated" or "incorrect" documentation. Glibc have no documentation of malloc_trim function; and Linux uses man pages from man-pages project. The man page of malloc_trim http://man7.org/linux/man-pages/man3/malloc_trim.3.html was written in 2012 by maintainer of man-pages as new. Probably he used some comments from glibc malloc/malloc.c source code http://code.metager.de/source/xref/gnu/glibc/malloc/malloc.c#675

676  malloc_trim(size_t pad);
677
678  If possible, gives memory back to the system (via negative
679  arguments to sbrk) if there is unused memory at the `high' end of
680  the malloc pool. You can call this after freeing large blocks of
681  memory to potentially reduce the system-level memory requirements
682  of a program. However, it cannot guarantee to reduce memory. Under
683  some allocation patterns, some large free blocks of memory will be
684  locked between two used chunks, so they cannot be given back to
685  the system.
686
687  The `pad' argument to malloc_trim represents the amount of free
688  trailing space to leave untrimmed. If this argument is zero,
689  only the minimum amount of memory to maintain internal data
690  structures will be left (one page or less). Non-zero arguments
691  can be supplied to maintain enough trailing space to service
692  future expected allocations without having to re-obtain memory
693  from the system.
694
695  Malloc_trim returns 1 if it actually released any memory, else 0.
696  On systems that do not support "negative sbrks", it will always
697  return 0.

Actual implementation in glibc is __malloc_trim and it has code for iterating over arenas:

http://code.metager.de/source/xref/gnu/glibc/malloc/malloc.c#4552

4552 int
4553 __malloc_trim (size_t s)

4560  mstate ar_ptr = &main_arena;
4561  do
4562    {
4563      (void) mutex_lock (&ar_ptr->mutex);
4564      result |= mtrim (ar_ptr, s);
4565      (void) mutex_unlock (&ar_ptr->mutex);
4566
4567      ar_ptr = ar_ptr->next;
4568    }
4569  while (ar_ptr != &main_arena);

Every arena is trimmed using mtrim() (mTRIm()) function, which calls malloc_consolidate() to convert all free segments from fastbins (they are not coalesced at free as they are fast) to normal free chunks (which are coalesced with adjacent chunks)

4498  /* Ensure initialization/consolidation */
4499  malloc_consolidate (av);

4111  malloc_consolidate is a specialized version of free() that tears
4112  down chunks held in fastbins. 

1581   Fastbins
1591    Chunks in fastbins keep their inuse bit set, so they cannot
1592    be consolidated with other free chunks. malloc_consolidate
1593    releases all chunks in fastbins and consolidates them with
1594    other free chunks.

The problem is, when the worker thread is recreated, it creates a new arena/heap instead of reusing the previous one, such that the fastbins from previous arenas/heaps are never reused.

This is strange. By design, maximum number of arenas is limited in glibc malloc by cpu_core_count * 8 (for 64-bit platform); cpu_core_count * 2 (for 32-bit platform) or by environment variable MALLOC_ARENA_MAX / mallopt parameter M_ARENA_MAX.

You can limit count of arenas for your application; call malloc_trim() periodically or call to malloc() with "large" size (it will call malloc_consolidate) and then free() for it from your threads just before destroying:

3319 _int_malloc (mstate av, size_t bytes)
3368  if ((unsigned long) (nb) <= (unsigned long) (get_max_fast ()))
 // fastbin allocation path
3405  if (in_smallbin_range (nb))
 // smallbin path; malloc_consolidate may be called
3437     If this is a large request, consolidate fastbins before continuing.
3438     While it might look excessive to kill all fastbins before
3439     even seeing if there is space available, this avoids
3440     fragmentation problems normally associated with fastbins.
3441     Also, in practice, programs tend to have runs of either small or
3442     large requests, but less often mixtures, so consolidation is not
3443     invoked all that often in most programs. And the programs that
3444     it is called frequently in otherwise tend to fragment.
3445   */
3446
3447  else
3448    {
3449      idx = largebin_index (nb);
3450      if (have_fastchunks (av))
3451        malloc_consolidate (av);
3452    }

PS: there is comment in man page of malloc_trim https://github.com/mkerrisk/man-pages/commit/a15b0e60b297e29c825b7417582a33e6ca26bf65: 

+.SH NOTES
+This function only releases memory in the main arena.
+.\" malloc/malloc.c::mTRIm():
+.\" return result | (av == &main_arena ? sYSTRIm (pad, av) : 0);

Yes, there is check for main_arena, but it is at very end of malloc_trim implementation mTRIm() and it is just for calling sbrk() with negative offset. Since 2007 (glibc 2.9 and newer) there is another method to return memory back to the OS: madvise(MADV_DONTNEED) which is used in all arenas (and is not documented by author of glibc patch or author of man page). Consolidate is called for every arena. There is also code for trimming (munmapping) top chunk of mmap-ed heaps (heap_trim/shrink_heap called from slow path free()), but it is not called from malloc_trim.

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