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At startup, when using a database plugin, display the latency to access the DB
author Alain Mazy <am@osimis.io>
date Mon, 15 Jan 2024 18:25:08 +0100
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In Orthanc 1.11.3, we have introduced a Housekeeper thread that 
tries to give back unused memory back to the system.  This is implemented 
by calling malloc_trim every 30s (note: on 1.11.3 and 1.12.0, the interval
was 100ms which caused high idle CPU load).


Here is how we validated the effect of this new feature:
-------------------------------------------------------

We compared the behaviour of 2 osimis/orthanc Docker images from the mainline
on Feb 1st 2023.  One image without the call to malloc_trim and the other with
this call.


1st test: unconstrained Docker containers
.........................................

5 large studies are uploaded to each instance of Orthanc (around 1GB in total).
A script triggers anonymization of these studies as quick as possible.
We compare the memory used by the containers after 2 minutes of execution 
(using `docker stats`):
- without malloc_trim:                   1500 MB
- with malloc_trim:                       410 MB


2nd test: memory constrained Docker containers
..............................................

Each Orthanc container is limited to 400MB (through the docker-compose configuration
`mem_limit: 400m`)
5 large studies are uploaded to each instance of Orthanc (around 1GB in total).
Each study is anonymized manually, one by one and then, we repeat the operation.
We compare the memory used by the containers after each anonymization 
(using `docker stats`):
            
# study            without malloc_trim         with_malloc_trim
0                       ~   50 MB                     ~   50 MB
1                       ~  140 MB                     ~  140 MB
2                       ~  390 MB                     ~  340 MB
3                       ~  398 MB                     ~  345 MB
4                  out-of-memory crash                ~  345 MB
5..20                                                 ~  380 MB (stable)


3rd test: memory constrained Docker containers
..............................................

In this last test, we lowered the memory allocation to 300MB and have been able to
run the first test script for at least 7 minutes (we did not try longer !).  The 
consumed memory is most of the time around 99% but it seems that the memory constrain
is handled correctly.  Note that, in this configuration, 128 MB are used by the Dicom
Cache.

The same test without malloc_trim could never run for more than 35 seconds.


4th test: performance impact of malloc_trim and available memory
................................................................

In this test, we have measured the time required to anonymize a 2000 instances study
with various configurations.  It appears that malloc_trim or the total amount
of memory available in the system has no significant impact on performance.

- No malloc trim, 300 MB in the system:       ~ 38s
- No malloc trim, 1500 MB in the system:      ~ 38s
- With malloc trim, 300 MB in the system:     ~ 38s
- With malloc trim, 1500 MB in the system:    ~ 38s


Conclusion: 
----------

The use of malloc_trim reduces the overall memory consumption of Orthanc
and avoids some of the out-of-memory situations.

However, it does not guarantee that Orthanc will never reach a
out-of-memory error, especially on very constrained systems.  

Depending on the allocation pattern, the Orthanc memory can get
very fragmented and increase regularly since malloc_trim only releases memory
at the end of each of malloc arena.  However, note that, even long before the 
introduction of malloc_trim, we have observed Orthanc instances running for years
without ever reaching out-of-memory errors and Orthanc is usually considered as
very stable.

Moreover, before each release, Orthanc integration tests are run against Valgrind
and no memory leaks have been identified.


malloc_trim documentation
-------------------------

from (https://stackoverflow.com/questions/40513716/malloc-trim0-releases-fastbins-of-thread-arenas)

    If possible, gives memory back to the system (via negative
    arguments to sbrk) if there is unused memory at the `high' end of
    the malloc pool. You can call this after freeing large blocks of
    memory to potentially reduce the system-level memory requirements
    of a program. However, it cannot guarantee to reduce memory. Under
    some allocation patterns, some large free blocks of memory will be
    locked between two used chunks, so they cannot be given back to
    the system.

    The `pad' argument to malloc_trim represents the amount of free
    trailing space to leave untrimmed. If this argument is zero,
    only the minimum amount of memory to maintain internal data
    structures will be left (one page or less). Non-zero arguments
    can be supplied to maintain enough trailing space to service
    future expected allocations without having to re-obtain memory
    from the system.

    Malloc_trim returns 1 if it actually released any memory, else 0.
    On systems that do not support "negative sbrks", it will always
    return 0.


glibc internals
---------------

Lots of useful info here: https://man7.org/linux/man-pages/man3/mallopt.3.html

summary:
- malloc uses sbrk() or mmap() to allocate memory.  mmap() is used to allocate 
  large memory chunks, larger than M_MMAP_THRESHOLD.
- about mmap(): On the other hand, there are some disadvantages to
              the use of mmap(2): deallocated space is not placed on the
              free list for reuse by later allocations; memory may be
              wasted because mmap(2) allocations must be page-aligned;
              and the kernel must perform the expensive task of zeroing
              out memory allocated via mmap(2).  Balancing these factors
              leads to a default setting of 128*1024 for the
              M_MMAP_THRESHOLD parameter.
- free() employs sbrk() to release memory back to the system and M_TRIM_THRESHOLD
  specifies the minimum size that is released.  So, even without
  malloc_trim, Orthanc is able to give back memory to the system.
- free() never gives back block allocated by mmap() to the system, only malloc_trim() does !

UPDATE on June 2023:
-------------------

Given this discussion: https://discourse.orthanc-server.org/t/onchange-callbacks-and-cpu-loads/3534,
changed the interval from 100ms to 30s.
We also added a metrics to monitor the duration: orthanc_memory_trimming_duration_ms

Good reference article:
https://www.algolia.com/blog/engineering/when-allocators-are-hoarding-your-precious-memory/