Excessive memory consumption when using malloc()

Excessive memory consumption when using malloc()

[Christian Hoff]

Hello all,

we are facing the a problem with the memory allocator in glibc 2.17 on
RHEL 7.9. Or application allocates about 10 GB of memory (split into
chunks that are each around 512 KB large). This memory is used for some
computations and released afterwards. After a while, the application is
running the same computations again, but this time in different threads.
The first issue we are seeing is that - after the computations are done
- the 10 GB of memory is not released back to the operating system. Only
after calling malloc_trim() manually with GDB, the size of the process
shrinks dramatically from ~10GB to 400 MB. So, at this point, the unused
memory from the computations is finally returned to the OS.

Our wish would be that the memory is returned to the OS without us
having to call malloc_trim(). And I understand that glibc also trims the
heap when there is sufficient free space in top of it (the
M_TRIM_THRESHOLD in mallopt() controls when this should happen). What
could be the reason why this is not working in our case? Could it be
related to heap fragmentation? But assuming that is the reason, why is
malloc_trim() nevertheless able to free this memory?

And then we also have one other problem. The first run of the
computations is always fine: we allocate 10 GB of memory and the
application grows to 10 GB. Afterwards, we release those 10 GB of memory
since the computations are now done and at this point the freed memory
is returned back to the allocator (however, the size of the process
remains 10 GB unless we call malloc_trim()). But if we now re-run the
same computations again a second time (this time using different
threads), a problem occurs. In this case, the size of the application
grows well beyond 10 GB. It can get 20 GB or larger and the process is
eventually killed because the system runs out of memory.

Do you have any idea why this happens? To me it seems like the threads
are assigned to different arenas and therefore the previously freed 10
GB of memory can not be re-used as they are in different arenas. Is that
possible?

A workaround I have found is to set M_MMAP_THRESHOLD to 128 KB - then
the memory for the computations is always allocated using mmap() and
returned back to the system immediately when it is free()'ed. This
solves both of the issues. But I am afraid that this workaround could
degrade the performance of our application. So, we are grateful for any
better solution to this problem.

Kind regards,

    Christian Hoff

Re: Excessive memory consumption when using malloc()

[Konstantin Kharlamov]

On Thu, 2021-11-25 at 18:20 +0100, Christian Hoff via Libc-help wrote:
> Hello all,
> 
> we are facing the a problem with the memory allocator in glibc 2.17 on
> RHEL 7.9. Or application allocates about 10 GB of memory (split into
> chunks that are each around 512 KB large). This memory is used for some
> computations and released afterwards. After a while, the application is
> running the same computations again, but this time in different threads.
> The first issue we are seeing is that - after the computations are done
> - the 10 GB of memory is not released back to the operating system. Only
> after calling malloc_trim() manually with GDB, the size of the process
> shrinks dramatically from ~10GB to 400 MB. So, at this point, the unused
> memory from the computations is finally returned to the OS.
> 
> Our wish would be that the memory is returned to the OS without us
> having to call malloc_trim(). And I understand that glibc also trims the
> heap when there is sufficient free space in top of it (the
> M_TRIM_THRESHOLD in mallopt() controls when this should happen). What
> could be the reason why this is not working in our case? Could it be
> related to heap fragmentation? But assuming that is the reason, why is
> malloc_trim() nevertheless able to free this memory?
> 

I assume the bug you stumbled upon is this one
https://sourceware.org/bugzilla/show_bug.cgi?id=27103

I'm not sure there is anything more to say except that it is a long-standing
glibc bug (it seems to have been known long before I reported it in 2020), and
malloc_trim is the official workaround to it.

For you purposes though you could perhaps try other malloc implementations such
as jemalloc. Try and see if it fixes these problems. Please report back if you
try it, I am curious if that can be used as another workaround.

> And then we also have one other problem. The first run of the
> computations is always fine: we allocate 10 GB of memory and the
> application grows to 10 GB. Afterwards, we release those 10 GB of memory
> since the computations are now done and at this point the freed memory
> is returned back to the allocator (however, the size of the process
> remains 10 GB unless we call malloc_trim()). But if we now re-run the
> same computations again a second time (this time using different
> threads), a problem occurs. In this case, the size of the application
> grows well beyond 10 GB. It can get 20 GB or larger and the process is
> eventually killed because the system runs out of memory.
> 
> Do you have any idea why this happens? To me it seems like the threads
> are assigned to different arenas and therefore the previously freed 10
> GB of memory can not be re-used as they are in different arenas. Is that
> possible?
> 
> A workaround I have found is to set M_MMAP_THRESHOLD to 128 KB - then
> the memory for the computations is always allocated using mmap() and
> returned back to the system immediately when it is free()'ed. This
> solves both of the issues. But I am afraid that this workaround could
> degrade the performance of our application. So, we are grateful for any
> better solution to this problem.
> 
> Kind regards,
> 
>     Christian Hoff
> 

Re: Excessive memory consumption when using malloc()

[Konstantin Kharlamov]

On Thu, 2021-11-25 at 20:46 +0300, Konstantin Kharlamov via Libc-help wrote:
> On Thu, 2021-11-25 at 18:20 +0100, Christian Hoff via Libc-help wrote:
> > Hello all,
> > 
> > we are facing the a problem with the memory allocator in glibc 2.17 on
> > RHEL 7.9. Or application allocates about 10 GB of memory (split into
> > chunks that are each around 512 KB large). This memory is used for some
> > computations and released afterwards. After a while, the application is
> > running the same computations again, but this time in different threads.
> > The first issue we are seeing is that - after the computations are done
> > - the 10 GB of memory is not released back to the operating system. Only
> > after calling malloc_trim() manually with GDB, the size of the process
> > shrinks dramatically from ~10GB to 400 MB. So, at this point, the unused
> > memory from the computations is finally returned to the OS.
> > 
> > Our wish would be that the memory is returned to the OS without us
> > having to call malloc_trim(). And I understand that glibc also trims the
> > heap when there is sufficient free space in top of it (the
> > M_TRIM_THRESHOLD in mallopt() controls when this should happen). What
> > could be the reason why this is not working in our case? Could it be
> > related to heap fragmentation? But assuming that is the reason, why is
> > malloc_trim() nevertheless able to free this memory?
> > 
> 
> I assume the bug you stumbled upon is this one
> https://sourceware.org/bugzilla/show_bug.cgi?id=27103
> 
> I'm not sure there is anything more to say except that it is a long-standing
> glibc bug (it seems to have been known long before I reported it in 2020), and
> malloc_trim is the official workaround to it.
> 
> For you purposes though you could perhaps try other malloc implementations such
> as jemalloc. Try and see if it fixes these problems. Please report back if you
> try it, I am curious if that can be used as another workaround.

Hah, FYI, the bug was just closed by Glibc dev with the following, I'm quoting:

> the allocator is under no requirement to
free back the 50MiB to the OS if it believes that the memory will be used again
and that performance is improved by caching it in userspace

So there you go, you 10G of unreleased memory is a Glibc feature, no complaints
;-P

Re: Excessive memory consumption when using malloc()

[Carlos O'Donell]

On 11/25/21 13:12, Konstantin Kharlamov via Libc-help wrote:
> So there you go, you 10G of unreleased memory is a Glibc feature, no complaints
> ;-P

Freeing memory back to the OS is a form of cache invalidation, and cache
invalidation is hard and workload dependent.

In this specific case, particularly with 50MiB, you are within the 64MiB
64-bit process heap size, and the 1024-byte frees do not trigger the
performance expensive consolidation and heap reduction (which requires
a munmap syscall to release the resources).

In the case of 10GiB, and 512KiB allocations, we are talking different
behaviour. I have responded here with my recommendations:
https://sourceware.org/pipermail/libc-help/2021-November/006052.html

-- 
Cheers,
Carlos.

Re: Excessive memory consumption when using malloc()

[Adhemerval Zanella]

On 25/11/2021 15:21, Carlos O'Donell via Libc-help wrote:
> On 11/25/21 13:12, Konstantin Kharlamov via Libc-help wrote:
>> So there you go, you 10G of unreleased memory is a Glibc feature, no complaints
>> ;-P
> 
> Freeing memory back to the OS is a form of cache invalidation, and cache
> invalidation is hard and workload dependent.
> 
> In this specific case, particularly with 50MiB, you are within the 64MiB
> 64-bit process heap size, and the 1024-byte frees do not trigger the
> performance expensive consolidation and heap reduction (which requires
> a munmap syscall to release the resources).
> 
> In the case of 10GiB, and 512KiB allocations, we are talking different
> behaviour. I have responded here with my recommendations:
> https://sourceware.org/pipermail/libc-help/2021-November/006052.html
> 
The BZ#27103 issues seems to be a memory fragmentation due the usage of
sbrk() plus the deallocation done in reverse order, which prevents free()
to coalescence the previous allocation automatically.

For instance with the testcase below:

$ gcc -Wall test.c -o test -DNTIMES=50000 -DCHUNK=1024
$ ./test
memory usage: 1036 Kb
allocate ...done
memory usage: 52812 Kb

If you force the mmap usage:

$ GLIBC_TUNABLES=glibc.malloc.mmap_threshold=0 ./test
memory usage: 1044 Kb
allocate ...done
memory usage: 2052 Kb

As Carlos has put, it is tradeoff since sbrk() is usually faster to expand
the data segments compared to mmap() and subsequent allocations will fill
the fragmented heap (so multiple allocation will avoid further memory
fragmentation).

Just to give you comparative, always using mmap() incurs more page-faults
and way more cpu utilization

$ perf stat ./test
memory usage: 964 Kb
allocate ...done
memory usage: 52796 Kb
memory usage: 52796 Kb
allocate ...done
memory usage: 52796 Kb

 Performance counter stats for './test':

             15.22 msec task-clock                #    0.983 CPUs utilized          
                 0      context-switches          #    0.000 /sec                   
                 0      cpu-migrations            #    0.000 /sec                   
            12,853      page-faults               #  844.546 K/sec                  
        68,518,548      cycles                    #    4.502 GHz                      (73.73%)
           480,717      stalled-cycles-frontend   #    0.70% frontend cycles idle     (73.72%)
             2,333      stalled-cycles-backend    #    0.00% backend cycles idle      (73.72%)
       105,356,108      instructions              #    1.54  insn per cycle         
                                                  #    0.00  stalled cycles per insn  (91.81%)
        23,787,860      branches                  #    1.563 G/sec                  
            58,990      branch-misses             #    0.25% of all branches          (87.01%)

       0.015478114 seconds time elapsed

       0.010348000 seconds user
       0.005174000 seconds sys


$ perf stat env GLIBC_TUNABLES=glibc.malloc.mmap_threshold=0 ./test
memory usage: 956 Kb
allocate ...done
memory usage: 2012 Kb
memory usage: 2012 Kb
allocate ...done
memory usage: 2012 Kb

 Performance counter stats for 'env GLIBC_TUNABLES=glibc.malloc.mmap_threshold=0 ./test':

            156.52 msec task-clock                #    0.998 CPUs utilized          
                 1      context-switches          #    6.389 /sec                   
                 0      cpu-migrations            #    0.000 /sec                   
           100,228      page-faults               #  640.338 K/sec                  
       738,047,682      cycles                    #    4.715 GHz                      (82.11%)
         8,779,463      stalled-cycles-frontend   #    1.19% frontend cycles idle     (82.11%)
            34,195      stalled-cycles-backend    #    0.00% backend cycles idle      (82.97%)
     1,254,219,911      instructions              #    1.70  insn per cycle         
                                                  #    0.01  stalled cycles per insn  (84.68%)
       237,180,662      branches                  #    1.515 G/sec                    (84.67%)
           687,051      branch-misses             #    0.29% of all branches          (83.46%)

       0.156904324 seconds time elapsed

       0.024142000 seconds user
       0.132786000 seconds sys

That's why I think it might not be the best strategy to use the mmap() strategy
as default. What I think we might improve is to maybe add an heuristic to call
malloc_trim once a certain level of fragmentation in the main_arena is found.
The question is which metric and threshold to use.  The trimming does have
a cost, however I think it worth to decrease fragmentation and memory utilization.

---

$ cat test.c
#include <stdlib.h>
#include <fcntl.h>
#include <assert.h>
#include <string.h>
#include <unistd.h>
#include <stdio.h>

static size_t pagesize;

static size_t
read_rss (void)
{
  int fd = open ("/proc/self/statm", O_RDONLY);
  assert (fd != -1);
  char line[256];
  ssize_t r = read (fd, line, sizeof (line));
  assert (r != -1);
  line[r] = '\0';
  size_t rss;
  sscanf (line, "%*u %zu %*u %*u 0 %*u 0\n", &rss);
  close (fd);
  return rss * pagesize;
}

static void *
allocate (void *args)
{
  enum { chunk = CHUNK };
  enum { ntimes = NTIMES * chunk };

  void *chunks[NTIMES];
  for (int i = 0; i < sizeof (chunks) / sizeof (chunks[0]); i++)
    {
      chunks[i] = malloc (chunk);
      memset (chunks[i], 0, chunk);
      assert (chunks[i] != NULL);
    }

  for (int i = (sizeof (chunks) / sizeof (chunks[0])) - 1; i >= 0; i--)
    free (chunks[i]);

  return NULL;
}

int main (int argc, char *argv[])
{
  pagesize = sysconf (_SC_PAGESIZE);
  assert (pagesize != -1);
  {
    printf ("memory usage: %zu Kb\n", read_rss () / 1024);
    printf ("allocate ...");
    allocate (NULL);
    printf ("done\n");
    printf ("memory usage: %zu Kb\n", read_rss () / 1024);
  }

  return 0;
} 

Re: Excessive memory consumption when using malloc()

[Christian Hoff]

Hello Adhemerval,

On 11/25/21 9:56 PM, Adhemerval Zanella wrote:
> What I think we might improve is to maybe add an heuristic to call
> malloc_trim once a certain level of fragmentation in the main_arena is found.
> The question is which metric and threshold to use.  The trimming does have
> a cost, however I think it worth to decrease fragmentation and memory utilization.

Yes, I think this is a very good idea. It is difficult for us to tell
our customers that our application consumes so much memory even while it
is not running any computations. Of course, we can call malloc_trim() as
a workaround, but even this is difficult as this is a Java application,
so calling system functions is not so straightforward. Any glibc
improvements in this area would be highly welcome.


Best regards,

    Christian

Re: Excessive memory consumption when using malloc()

[Patrick McGehearty]

I wonder if a useful heuristic would be for under some
circumstances for the malloc library to call malloc_trim()
every so often, based on passage of time in addition to
the current calls to malloc_trim() based on user calls to free().

If free memory is cached but unused for a 'substantial'
time while the program is doing 'other' things, it gets
freed for other use by the OS. Setting the default to
a time is large enough to avoid excess syscall overhead
while being below typical human perception would be right
for most contexts.

This option could be under tunable control (at least
until we understand better heuristics) with two
variables:
1) A variable that says yes/no we will call malloc_trim()
based on time. (Initial default: NO)
2) A variable that specifies the time frequency.
(Initial default: 1/10 second or reasonable approximation)

This approach avoids the need to have malloc_trim()
or calls to other malloc internals appear in user
applications.

I have not made any investigation of implementation
details. If anyone wants to take this idea and run
with it, they are welcome to do so.

- Patrick McGehearty


On 11/26/2021 12:10 PM, Christian Hoff via Libc-help wrote:
> Hello Adhemerval,
>
> On 11/25/21 9:56 PM, Adhemerval Zanella wrote:
>> What I think we might improve is to maybe add an heuristic to call
>> malloc_trim once a certain level of fragmentation in the main_arena 
>> is found.
>> The question is which metric and threshold to use.  The trimming does 
>> have
>> a cost, however I think it worth to decrease fragmentation and memory 
>> utilization.
>
> Yes, I think this is a very good idea. It is difficult for us to tell
> our customers that our application consumes so much memory even while it
> is not running any computations. Of course, we can call malloc_trim() as
> a workaround, but even this is difficult as this is a Java application,
> so calling system functions is not so straightforward. Any glibc
> improvements in this area would be highly welcome.
>
>
> Best regards,
>
>    Christian
>

Re: Excessive memory consumption when using malloc()

[Carlos O'Donell]

On 11/25/21 12:20, Christian Hoff via Libc-help wrote:
> Hello all,
>
> we are facing the a problem with the memory allocator in glibc 2.17 on
> RHEL 7.9. Or application allocates about 10 GB of memory (split into
> chunks that are each around 512 KB large). This memory is used for some
> computations and released afterwards. After a while, the application is
> running the same computations again, but this time in different threads.
> The first issue we are seeing is that - after the computations are done
> - the 10 GB of memory is not released back to the operating system. Only
> after calling malloc_trim() manually with GDB, the size of the process
> shrinks dramatically from ~10GB to 400 MB. So, at this point, the unused
> memory from the computations is finally returned to the OS.

How many cpus does the system have?

How many threads do you create?

Is this 10GiB of RSS or VSS?

For very large systems glibc malloc will create up to 8 arenas per CPU.

Each arena starts with a default 64MiB VMA reservation.

On a 128 core system this appears as a ~65GiB VSS reservation.
 
> Our wish would be that the memory is returned to the OS without us
> having to call malloc_trim(). And I understand that glibc also trims the
> heap when there is sufficient free space in top of it (the
> M_TRIM_THRESHOLD in mallopt() controls when this should happen). What
> could be the reason why this is not working in our case? Could it be
> related to heap fragmentation? But assuming that is the reason, why is
> malloc_trim() nevertheless able to free this memory?

The normal trimming strategy is to trim from the top of the heap down.

Chunks at the top of the heap are coalesced and eventually when the chunk is big enough
the heap is freed down.

This coalescing and freeing is prevented it there are in-use chunks in the heap.

Consider this scenario:
- Make many large allocations that have a short lifetime.
- Make one small allocation that has a very long lifetime.
- Free all the large allocations.

The heap cannot be freed downwards because of the small long liftetime allocation.

The call to malloc_trim() walks the heap chunks and frees page-sized chunks or
larger without the requirement that they come from the top of the heap.

In glibc's allocator, mixing lifetimes for allocations will cause heap growth.

I have an important question to ask now:

Do you use aligned allocations?

We have right now an outstanding defect where aligned allocations create small
residual free chunks, and when free'd back and allocated again as an aligned
chunk, we are forced to split chunks again, which can lead to ratcheting effects
with certain aligned allocations.

We had a prototype patch for this in Fedora in 2019:
https://lists.fedoraproject.org/archives/list/glibc@lists.fedoraproject.org/thread/2PCHP5UWONIOAEUG34YBAQQYD7JL5JJ4/
 
> And then we also have one other problem. The first run of the
> computations is always fine: we allocate 10 GB of memory and the
> application grows to 10 GB. Afterwards, we release those 10 GB of memory
> since the computations are now done and at this point the freed memory
> is returned back to the allocator (however, the size of the process
> remains 10 GB unless we call malloc_trim()). But if we now re-run the
> same computations again a second time (this time using different
> threads), a problem occurs. In this case, the size of the application
> grows well beyond 10 GB. It can get 20 GB or larger and the process is
> eventually killed because the system runs out of memory.

You need to determine what is going on under the hood here.

You may want to just use malloc_info() to get a routine dump of the heap state.

This will give us a starting point to see what is growing.

We have a malloc allocation tracer that you can use to capture a workload and
share a snapshot of the workload with upstream:
https://pagure.io/glibc-malloc-trace-utils

Sharing the workload might be hard because this is a full API trace and it gets
difficult to share.

> Do you have any idea why this happens? To me it seems like the threads
> are assigned to different arenas and therefore the previously freed 10
> GB of memory can not be re-used as they are in different arenas. Is that
> possible?

I don't know why this happens.

Threads once bound to an arena are normally never move unless an allocation fails.
 
> A workaround I have found is to set M_MMAP_THRESHOLD to 128 KB - then
> the memory for the computations is always allocated using mmap() and
> returned back to the system immediately when it is free()'ed. This
> solves both of the issues. But I am afraid that this workaround could
> degrade the performance of our application. So, we are grateful for any
> better solution to this problem.

It will degrade performance because you must do a syscall all the time. You can try
raising the value.

-- 
Cheers,
Carlos.

Re: Excessive memory consumption when using malloc()

[Christian Hoff]

[-- Attachment #1: Type: text/plain, Size: 6249 bytes --]

Hello Carlos,

many thanks for your support.

On 11/25/21 7:20 PM, Carlos O'Donell wrote:

> How many cpus does the system have?
We have 8 CPUs.
> How many threads do you create?
Our computations are running in 2 threads. However, the lifetime of both
threads is limited to the duration of the computation. Both threads exit
after the calculations are complete. The next round of computations will
be performed by 2 other, newly started threads.
> Is this 10GiB of RSS or VSS?

It is 10 GiB of RSS memory. Meaning that the calculations each time
allocate 10 GiB of memory, which is then used and so it becomes resident
RSS memory. After the calculations are done, we free() this memory
again. At this point, the memory is returned to the glibc allocator

> This coalescing and freeing is prevented it there are in-use chunks in the heap.
>
> Consider this scenario:
> - Make many large allocations that have a short lifetime.
> - Make one small allocation that has a very long lifetime.
> - Free all the large allocations.
>
> The heap cannot be freed downwards because of the small long liftetime allocation.
>
> The call to malloc_trim() walks the heap chunks and frees page-sized chunks or
> larger without the requirement that they come from the top of the heap.
>
> In glibc's allocator, mixing lifetimes for allocations will cause heap growth.
I think that is exactly what is happening in our case. Thanks for the
explanation!
> I have an important question to ask now:
>
> Do you use aligned allocations?
>
> We have right now an outstanding defect where aligned allocations create small
> residual free chunks, and when free'd back and allocated again as an aligned
> chunk, we are forced to split chunks again, which can lead to ratcheting effects
> with certain aligned allocations.
>
> We had a prototype patch for this in Fedora in 2019:
> https://lists.fedoraproject.org/archives/list/glibc@lists.fedoraproject.org/thread/2PCHP5UWONIOAEUG34YBAQQYD7JL5JJ4/
>
No, the 512 KiB allocations for the computation are not aligned. We just
request it using malloc(). But the application is a Java application
that is running some native C++ code. And I don't know if Java allocates
some aligned memory. But the vast majority of allocations are ~512 KiB
and these are not aligned.
>> And then we also have one other problem. The first run of the
>> computations is always fine: we allocate 10 GB of memory and the
>> application grows to 10 GB. Afterwards, we release those 10 GB of memory
>> since the computations are now done and at this point the freed memory
>> is returned back to the allocator (however, the size of the process
>> remains 10 GB unless we call malloc_trim()). But if we now re-run the
>> same computations again a second time (this time using different
>> threads), a problem occurs. In this case, the size of the application
>> grows well beyond 10 GB. It can get 20 GB or larger and the process is
>> eventually killed because the system runs out of memory.
> You need to determine what is going on under the hood here.
>
> You may want to just use malloc_info() to get a routine dump of the heap state.
>
> This will give us a starting point to see what is growing.

To make it easier to run multiple rounds of calculations, I have now
modified the code a bit so that only ~5 GiB of memory is allocated every
time when we perform the computations. The 5 GiB are still allocated in
chunks of about 512 KiB. After the calculations, all this memory is
free()'ed again.

After running the calculations for the first time, we see that the
application consumes about 5 GiB of RSS memory. But our problem is that
if we run the computations again for a second and third time, the memory
usage increases even beyond 5 GiB, even though we release all memory
that the calculation consumes after each iteration. After running the
same workload 12 times, our processing workstation runs out of memory
and gets very slow. In detail, the memory consumption after each round
of calculations is captured in the table below.

After Iteration   Memory Consumption
1             5.13 GiB
2             8.9 GiB
3             10.48 GiB
4             14.48 GiB
5             18.11 GiB
6             16.03 GiB
......           ..............
12            21.79 GiB

As you can see, the RSS memory usage of our application increases
continuously, especially during the first few rounds of calculations.
Our expectation would be that the RSS memory usage remains at 5 GiB as
the computations only allocate about 5 GiB of memory each time. After
running the computations 12 times, glibc allocator caches have grown to
over 20 GiB. All this memory can only be reclaimed by calling malloc_trim().

I have also attached the traces from malloc_info() after each iteration
of the computations. The first trace ("after_run_no_1.txt") was captured
after running the computations once and shows a relatively low memory
usage of 5 GiB. But in the subsequent traces, memory consumption
increases. Our application has 64 arenas (which is eight times eight CPUs).

As I mentioned, the lifetime of the 2 computation threads is limited to
the computation itself. The threads will be restarted with each run of
the computations. Once the computation starts, the threads are assigned
to an arena. Could it be that these two threads are always assigned to
different arenas on each run of the computations and could that explain
that the glibc allocator caches are growing from run to run?

> We have a malloc allocation tracer that you can use to capture a workload and
> share a snapshot of the workload with upstream:
> https://pagure.io/glibc-malloc-trace-utils
>
> Sharing the workload might be hard because this is a full API trace and it gets
> difficult to share.

For now, I haven't done that yet (as it would be difficult to share,
just as you said). I hope that the malloc_info() traces already give a
picture of what is happening. But if we need them, I will be happy to
capture these traces.


Best regards,

    Christian


[-- Attachment #2: after_run_no_1.txt --]
[-- Type: text/plain, Size: 31593 bytes --]

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[-- Attachment #3: after_run_no_2.txt --]
[-- Type: text/plain, Size: 35291 bytes --]

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[-- Attachment #4: after_run_no_3.txt --]
[-- Type: text/plain, Size: 35254 bytes --]

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[-- Attachment #5: after_run_no_4.txt --]
[-- Type: text/plain, Size: 35423 bytes --]

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[-- Attachment #6: after_run_no_5.txt --]
[-- Type: text/plain, Size: 36878 bytes --]

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[-- Attachment #7: after_run_no_6.txt --]
[-- Type: text/plain, Size: 36506 bytes --]

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[-- Attachment #8: after_run_no_12.txt --]
[-- Type: text/plain, Size: 37517 bytes --]

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Re: Excessive memory consumption when using malloc()

[Christian Hoff]

Hello all,

meanwhile, I spent quite some time analyzing the reports generated by
malloc_info() at various stages of my program. I also ran a few
additional experiments. By now, I am quite confident that I have found
the root cause of the problem.

As you might remember, my application spawns two threads that execute
the memory-intensive computations. The lifetime of these threads is
limited to the computations, so when the computations end, both
computation threads will be terminated. As soon as the computations are
resumed, the two threads are started again.

The issue why memory consumption increases so much over time must be
that the computation threads are randomly assigned to different arenas.
But then, memory can seemingly not be moved between arenas. This is also
what I found in some tcmalloc documentation
(http://goog-perftools.sourceforge.net/doc/tcmalloc.html):

 > ptmalloc2 also reduces lock contention by using per-thread arenas but
there is a big problem with ptmalloc2's use of per-thread arenas.
 > In ptmalloc2 memory can never move from one arena to another. This
can lead to huge amounts of wasted space. For example, in one
 > Google application, the first phase would allocate approximately
300MB of memory for its data structures. When the first phase finished,
 > a second phase would be started in the same address space. If this
second phase was assigned a different arena than the one used by the
 > first phase, this phase would not reuse any of the memory left after
the first phase and would add another 300MB to the address space.
 > Similar memory blowup problems were also noticed in other applications.

That seems to describe exactly the issue I am experiencing. I tried to
change the number of arenas (via M_ARENA_MAX in mallopt()) and found out
that the memory usage of my application varies greatly depending on the
number of arenas. Memory usage remains below 10 GB if I execute the
calculations repeatedly with just one arena, but increases as soon as I
configure my application to use 2 or more arenas. When using 5 arenas,
the memory usage gets so high that my processing workstation eventually
runs out of memory.

In the reports generated by malloc_info(), I can see that the size of 1
or 2 arenas increases between each runs of the computations. Because of
heap fragmentation, spare memory in the unused arenas is not returned
back to the OS and the memory footprint of the application grows.

Of course, calling malloc_trim() internally (as is currently being
discussed here on this mailing list) would solve this problem, but even
more promising to me seems how tcmalloc handles large allocations (>256
KB). In tcmalloc, large allocations are done in the backend and there is
only one backend per application. This makes sure that big memory chunks
can be reused around thread boundaries. This avoids the memory blowup
problems in my application. I guess using tcmalloc is the better choice
for me - even if glibc malloc would call malloc_trim() internally, then
I guess the repeated calls to malloc_trim() would slow my application
down. With tcmalloc, my application should perform better. Even though
tcmalloc also suffers from the problem that it cannot compact a
fragmented heap, it doesn't hurt so much as there is only one "arena"
where large memory chunks are allocated - and that is the backend. This
one arena never gets so large that my workstation runs out of memory.


Best regards,

    Christian

On 11/26/21 6:58 PM, Christian Hoff via Libc-help wrote:
> Hello Carlos,
>
> many thanks for your support.
>
> On 11/25/21 7:20 PM, Carlos O'Donell wrote:
>
>> How many cpus does the system have?
> We have 8 CPUs.
>> How many threads do you create?
> Our computations are running in 2 threads. However, the lifetime of both
> threads is limited to the duration of the computation. Both threads exit
> after the calculations are complete. The next round of computations will
> be performed by 2 other, newly started threads.
>> Is this 10GiB of RSS or VSS?
>
> It is 10 GiB of RSS memory. Meaning that the calculations each time
> allocate 10 GiB of memory, which is then used and so it becomes resident
> RSS memory. After the calculations are done, we free() this memory
> again. At this point, the memory is returned to the glibc allocator
>
>> This coalescing and freeing is prevented it there are in-use chunks
>> in the heap.
>>
>> Consider this scenario:
>> - Make many large allocations that have a short lifetime.
>> - Make one small allocation that has a very long lifetime.
>> - Free all the large allocations.
>>
>> The heap cannot be freed downwards because of the small long
>> liftetime allocation.
>>
>> The call to malloc_trim() walks the heap chunks and frees page-sized
>> chunks or
>> larger without the requirement that they come from the top of the heap.
>>
>> In glibc's allocator, mixing lifetimes for allocations will cause
>> heap growth.
> I think that is exactly what is happening in our case. Thanks for the
> explanation!
>> I have an important question to ask now:
>>
>> Do you use aligned allocations?
>>
>> We have right now an outstanding defect where aligned allocations
>> create small
>> residual free chunks, and when free'd back and allocated again as an
>> aligned
>> chunk, we are forced to split chunks again, which can lead to
>> ratcheting effects
>> with certain aligned allocations.
>>
>> We had a prototype patch for this in Fedora in 2019:
>> https://lists.fedoraproject.org/archives/list/glibc@lists.fedoraproject.org/thread/2PCHP5UWONIOAEUG34YBAQQYD7JL5JJ4/
>>
>>
> No, the 512 KiB allocations for the computation are not aligned. We just
> request it using malloc(). But the application is a Java application
> that is running some native C++ code. And I don't know if Java allocates
> some aligned memory. But the vast majority of allocations are ~512 KiB
> and these are not aligned.
>>> And then we also have one other problem. The first run of the
>>> computations is always fine: we allocate 10 GB of memory and the
>>> application grows to 10 GB. Afterwards, we release those 10 GB of
>>> memory
>>> since the computations are now done and at this point the freed memory
>>> is returned back to the allocator (however, the size of the process
>>> remains 10 GB unless we call malloc_trim()). But if we now re-run the
>>> same computations again a second time (this time using different
>>> threads), a problem occurs. In this case, the size of the application
>>> grows well beyond 10 GB. It can get 20 GB or larger and the process is
>>> eventually killed because the system runs out of memory.
>> You need to determine what is going on under the hood here.
>>
>> You may want to just use malloc_info() to get a routine dump of the
>> heap state.
>>
>> This will give us a starting point to see what is growing.
>
> To make it easier to run multiple rounds of calculations, I have now
> modified the code a bit so that only ~5 GiB of memory is allocated every
> time when we perform the computations. The 5 GiB are still allocated in
> chunks of about 512 KiB. After the calculations, all this memory is
> free()'ed again.
>
> After running the calculations for the first time, we see that the
> application consumes about 5 GiB of RSS memory. But our problem is that
> if we run the computations again for a second and third time, the memory
> usage increases even beyond 5 GiB, even though we release all memory
> that the calculation consumes after each iteration. After running the
> same workload 12 times, our processing workstation runs out of memory
> and gets very slow. In detail, the memory consumption after each round
> of calculations is captured in the table below.
>
> After Iteration   Memory Consumption
> 1             5.13 GiB
> 2             8.9 GiB
> 3             10.48 GiB
> 4             14.48 GiB
> 5             18.11 GiB
> 6             16.03 GiB
> ......           ..............
> 12            21.79 GiB
>
> As you can see, the RSS memory usage of our application increases
> continuously, especially during the first few rounds of calculations.
> Our expectation would be that the RSS memory usage remains at 5 GiB as
> the computations only allocate about 5 GiB of memory each time. After
> running the computations 12 times, glibc allocator caches have grown to
> over 20 GiB. All this memory can only be reclaimed by calling
> malloc_trim().
>
> I have also attached the traces from malloc_info() after each iteration
> of the computations. The first trace ("after_run_no_1.txt") was captured
> after running the computations once and shows a relatively low memory
> usage of 5 GiB. But in the subsequent traces, memory consumption
> increases. Our application has 64 arenas (which is eight times eight
> CPUs).
>
> As I mentioned, the lifetime of the 2 computation threads is limited to
> the computation itself. The threads will be restarted with each run of
> the computations. Once the computation starts, the threads are assigned
> to an arena. Could it be that these two threads are always assigned to
> different arenas on each run of the computations and could that explain
> that the glibc allocator caches are growing from run to run?
>
>> We have a malloc allocation tracer that you can use to capture a
>> workload and
>> share a snapshot of the workload with upstream:
>> https://pagure.io/glibc-malloc-trace-utils
>>
>> Sharing the workload might be hard because this is a full API trace
>> and it gets
>> difficult to share.
>
> For now, I haven't done that yet (as it would be difficult to share,
> just as you said). I hope that the malloc_info() traces already give a
> picture of what is happening. But if we need them, I will be happy to
> capture these traces.
>
>
> Best regards,
>
>    Christian
>