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Investigate Memory Actions

Memory actions generally mean:

  • memory access: read, write or execute
  • memory allocation
  • memory deallocation

By far, the most important actions are allocation and deallocation. Because, if not done right, these can get to memory loss and poor memory use.

Memory loss generally happens in the form of memory leaks.

Memory Leaks​

A memory leak occurs when we lose reference to a memory area. That is, a pointer used to point to a memory area. And then it's pointing to a new memory area and the old memory area is lost.

Enter the support/memory-leak/ folder. It stores two files showing memory leaks:

  • one in C++: memory_leak.cpp
  • one in C: memory_leak_malloc

Let's build and run the two executables:

student@os:~/.../lab/support/memory-leak$ make
g++    -c -o memory_leak.o memory_leak.cpp
cc   memory_leak.o  -lstdc++ -o memory_leak
cc    -c -o memory_leak_malloc.o memory_leak_malloc.c
cc   memory_leak_malloc.o  -lstdc++ -o memory_leak_malloc

Running them yields similar output:

student@os:~/.../lab/support/memory-leak$ ./memory_leak
Andrei Popescu is 22 years old and likes Linux
Ioana David is 23 years old and likes macOS
student@os:~/.../lab/support/memory-leak$ ./memory_leak_malloc
Andrei Popescu is 22 years old and likes Linux
Ioana David is 23 years old and likes macOS

We investigate the memory leaks of the two programs by using Valgrind:

student@os:~/.../lab/support/memory-leak$ valgrind ./memory_leak
==22362== Memcheck, a memory error detector
==22362== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al.
==22362== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info
==22362== Command: ./memory_leak
==22362==
Andrei Popescu is 22 years old and likes Linux
Ioana David is 23 years old and likes macOS
==22362==
==22362== HEAP SUMMARY:
==22362==     in use at exit: 72 bytes in 1 blocks
==22362==   total heap usage: 4 allocs, 3 frees, 73,872 bytes allocated
==22362==
==22362== LEAK SUMMARY:
==22362==    definitely lost: 72 bytes in 1 blocks
==22362==    indirectly lost: 0 bytes in 0 blocks
==22362==      possibly lost: 0 bytes in 0 blocks
==22362==    still reachable: 0 bytes in 0 blocks
==22362==         suppressed: 0 bytes in 0 blocks
==22362== Rerun with --leak-check=full to see details of leaked memory
==22362==
==22362== For counts of detected and suppressed errors, rerun with: -v
==22362== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0)

student@os:~/.../lab/support/memory-leak$ valgrind ./memory_leak_malloc
==22369== Memcheck, a memory error detector
==22369== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al.
==22369== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info
==22369== Command: ./memory_leak_malloc
==22369==
Andrei Popescu is 22 years old and likes Linux
Ioana David is 23 years old and likes macOS
==22369==
==22369== HEAP SUMMARY:
==22369==     in use at exit: 148 bytes in 1 blocks
==22369==   total heap usage: 3 allocs, 2 frees, 1,320 bytes allocated
==22369==
==22369== LEAK SUMMARY:
==22369==    definitely lost: 148 bytes in 1 blocks
==22369==    indirectly lost: 0 bytes in 0 blocks
==22369==      possibly lost: 0 bytes in 0 blocks
==22369==    still reachable: 0 bytes in 0 blocks
==22369==         suppressed: 0 bytes in 0 blocks
==22369== Rerun with --leak-check=full to see details of leaked memory
==22369==
==22369== For counts of detected and suppressed errors, rerun with: -v
==22369== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0)

As we are doing allocations that are not freed, this results in memory leaks.

For malloc()-based programs, we can use mtrace() feature and mtrace command to verify proper allocations with malloc() and deallocations with free(). We call mtrace() in the program (in memory_leak_malloc.c) to enable malloc() and free() checking.

To use mtrace() we define the MALLOC_TRACE environment variable:

student@os:~/.../lab/support/memory-leak$ MALLOC_TRACE=mem.trace ./memory_leak_malloc
Andrei Popescu is 22 years old and likes Linux
Ioana David is 23 years old and likes macOS

Subsequently, we use the mtrace tool to show information about the leaked data:

student@os:~/.../lab/support/memory-leak$ mtrace ./memory_leak_malloc mem.trace

Memory not freed:
-----------------
           Address     Size     Caller
0x000056506d8be6a0     0x94  at 0x56506c3777ec

The size (0x94) is the same value shown by Valgrind (148).

mtrace provides an outcome similar to Valgrind. Valgrind is however more powerful: it works on different types of memory (not only those allocated with malloc()) and it doesn't require access to the source code (and the compiler phase).

Practice​

  1. Print the size of the Student class and the struct student structure to see if it equates to the leak shown by Valgrind.

  2. Solve the memory leaks in both programs. Validate with Valgrind.

Quiz

Memory Actions (and Leaks) in Existing Programs​

We can use Valgrind to investigate existing programs in the system. This tells us whether they possess memory leaks:

student@os:~/.../lab/support/memory-leak$ valgrind ls
==24669== Memcheck, a memory error detector
==24669== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al.
==24669== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info
==24669== Command: ls
==24669==
Makefile  memory_leak  memory_leak.cpp  memory_leak_malloc  memory_leak_malloc.c  memory_leak_malloc.o  memory_leak.o
==24669==
==24669== HEAP SUMMARY:
==24669==     in use at exit: 21,696 bytes in 14 blocks
==24669==   total heap usage: 51 allocs, 37 frees, 61,331 bytes allocated
==24669==
==24669== LEAK SUMMARY:
==24669==    definitely lost: 0 bytes in 0 blocks
==24669==    indirectly lost: 0 bytes in 0 blocks
==24669==      possibly lost: 0 bytes in 0 blocks
==24669==    still reachable: 21,696 bytes in 14 blocks
==24669==         suppressed: 0 bytes in 0 blocks
==24669== Rerun with --leak-check=full to see details of leaked memory
==24669==
==24669== For counts of detected and suppressed errors, rerun with: -v
==24669== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0)

student@os:~/.../lab/support/memory-leak$ valgrind ps
==24671== Memcheck, a memory error detector
==24671== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al.
==24671== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info
==24671== Command: ps
==24671==
  PID TTY          TIME CMD
24671 pts/22   00:00:00 memcheck-amd64-
26732 pts/22   00:00:01 bash
==24671==
==24671== HEAP SUMMARY:
==24671==     in use at exit: 264,929 bytes in 25 blocks
==24671==   total heap usage: 692 allocs, 667 frees, 334,268 bytes allocated
==24671==
==24671== LEAK SUMMARY:
==24671==    definitely lost: 0 bytes in 0 blocks
==24671==    indirectly lost: 0 bytes in 0 blocks
==24671==      possibly lost: 0 bytes in 0 blocks
==24671==    still reachable: 264,929 bytes in 25 blocks
==24671==         suppressed: 0 bytes in 0 blocks
==24671== Rerun with --leak-check=full to see details of leaked memory
==24671==
==24671== For counts of detected and suppressed errors, rerun with: -v
==24671== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0)

student@os:~/.../lab/support/memory-leak$ valgrind bash -c 'echo "ha"'
==24675== Memcheck, a memory error detector
==24675== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al.
==24675== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info
==24675== Command: bash -c echo\ "ha"
==24675==
ha
==24675==
==24675== HEAP SUMMARY:
==24675==     in use at exit: 43,056 bytes in 672 blocks
==24675==   total heap usage: 774 allocs, 102 frees, 51,405 bytes allocated
==24675==
==24675== LEAK SUMMARY:
==24675==    definitely lost: 12 bytes in 1 blocks
==24675==    indirectly lost: 0 bytes in 0 blocks
==24675==      possibly lost: 0 bytes in 0 blocks
==24675==    still reachable: 43,044 bytes in 671 blocks
==24675==         suppressed: 0 bytes in 0 blocks
==24675== Rerun with --leak-check=full to see details of leaked memory
==24675==
==24675== For counts of detected and suppressed errors, rerun with: -v
==24675== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0)

We can see that ls and ps don't have memory leaks. However, the shell (Bash) shows a memory leak of 12 bytes (on the test system). This may be a false positive or the subject of an actual investigation.

Note that the still reachable section of the output refers to memory that wasn't freed, but still has pointers referring to it. A true memory leak occurs when no pointers refer any memory area.

Practice​

  1. Investigate 2-3 other executables in the system using Valgrind.

  2. Use ltrace to list malloc() and free() calls made by the investigated system executables.

Note that, as explained in the Software Stack lab, on some systems, ltrace does not accurately show the output, due to now binding. Fear not, you can always check the library calls with a more verbose and harder to parse ltrace command:

student@os:~$ ltrace -x "*"

Quiz

jemalloc​

jemalloc is a featureful allocator that is intended to replace the standard allocator in the standard C library (libc). jemalloc provides replacements for the general malloc() and free() functions, and also provides a custom API targeted for performance tuning.

As documented, there are multiple ways to use jemalloc, the easiest of which is to use the LD_PRELOAD environment variable and preload the library and hook into malloc() and free() function calls.

First install jemalloc on our system. On your typical Ubuntu / Debian-based system, use apt:

student@os:~/.../data/lab/content$ sudo apt -y install libjemalloc-dev

Note that this installs the distribution package, not the latest one (that may provide more features).

With this in place, we can use jemalloc against our pre-built executables or system executables (such as ls, ps). We can test it against the executable files from support/memory-leak/:

student@os:~/.../lab/support/memory-leak$ LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libjemalloc.so ./memory_leak_malloc
Andrei Popescu is 22 years old and likes Linux
Ioana David is 23 years old and likes macOS

jemalloc can use the MALLOC_CONF environment variable for a diverse set of configurations. For example, by using stats_print:true we print out information regarding the use of the library functions:

student@os:~/.../lab/support/memory-leak$ LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libjemalloc.so MALLOC_CONF="stats_print:true" ./memory_leak_malloc
Andrei Popescu is 22 years old and likes Linux
Ioana David is 23 years old and likes macOS
___ Begin jemalloc statistics ___
Version: 3.6.0-11
Assertions disabled
Run-time option settings:
  opt.abort: false
  opt.lg_chunk: 22
  opt.dss: "secondary"
  opt.narenas: 32
  opt.lg_dirty_mult: 3
  opt.stats_print: true
  opt.junk: false
  opt.quarantine: 0
  opt.redzone: false
[...]
dirty pages: 26:0 active:dirty, 0 sweeps, 0 madvises, 0 purged
            allocated      nmalloc      ndalloc    nrequests
small:          72672          114            0            3
large:          32768            1            0            1
total:         105440          115            0            4
active:        106496
mapped:       4194304
[...]

jemalloc doesn't work against system executables using preloading, likely because of security options disabling the use of the library:

student@os:~/.../lab/support/memory-leak$ LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libjemalloc.so MALLOC_CONF="stats_print:true" /bin/ls
Makefile  memory_leak  memory_leak.cpp  memory_leak_malloc  memory_leak_malloc.c  memory_leak_malloc.o  memory_leak.o

student@os:~/.../lab/support/memory-leak$ LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libjemalloc.so MALLOC_CONF="stats_print:true" /bin/ps
  PID TTY          TIME CMD
 1581 pts/22   00:00:00 ps
26732 pts/22   00:00:01 bash

malloc in Musl​

Each libc (or memory allocator such as jemalloc) uses their own implementation of malloc(), free() and other functions. Musl libc is a lightweight standard C library that provides compatible features with the more heavyweights GNU libc.

Take a look through implementation of malloc() and free() in Musl libc. See all three implementations for malloc():

  • the one in lite_malloc.c
  • the one in mallocng/malloc.c
  • the one in oldmalloc/malloc

See also the implementation of free(). And the implementation of calloc().

You needn't spend too much time browsing the implementation of these functions, just having a broad understanding of how they work.

App Investigation: Deluge​

Deluge is a Bittorrent client written in Python.

We want to locate places that allocate memory in Deluge (in Python). This generally means locating instantiation of classes.

Let's clone the source code:

student@os:~/.../data/lab/support$ git clone https://github.com/deluge-torrent/deluge
Cloning into 'deluge'...
[...]

student@os:~/.../data/lab/support$ cd deluge/

student@os:~/.../lab/support/deluge$ ls
AUTHORS       deluge      docs             gen_web_gettext.py  MANIFEST.in       msgfmt.py  pyproject.toml  requirements-dev.txt    requirements.txt  setup.py  version.py
CHANGELOG.md  DEPENDS.md  generate_pot.py  LICENSE             minify_web_js.py  packaging  README.md       requirements-tests.txt  setup.cfg         tox.ini

And enter the deluge/core/ subdirectory:

student@os:~/.../lab/support/deluge$ cd deluge/core/

student@os:~/.../deluge/deluge/core$ ls
alertmanager.py  core.py          daemon.py        filtermanager.py  pluginmanager.py       rpcserver.py       torrent.py
authmanager.py   daemon_entry.py  eventmanager.py  __init__.py       preferencesmanager.py  torrentmanager.py

Most files in the subdirectory have a class defined. We can search for instantiations of that class using grep:

student@os:~/.../deluge/deluge/core$ grep -rn 'Torrent('
torrentmanager.py:644:        torrent = Torrent(handle, options, state, filename, magne

student@os:~/.../deluge/deluge/core$ grep -rn 'TorrentManager('
core.py:139:        self.torrentmanager = TorrentManager()
torrentmanager.py:135:class TorrentManager(component.Component):

This gives us an overview of when memory is allocated in Deluge / Python.

Practice​

  1. Investigate the lines shown to contain instantiations of classes. Explore the source code and understand their placements in the source code.

  2. Find out other classes and search for their instantiation in the source code.

App Investigation: Servo​

Servo is a browser engine written in Rust that provides reusable components to implement web standards.

We do not clone the repository, since it's very large.

We find information about allocator used, by accessing the components/allocator/ in its source code. In Cargo.toml we see that it requires jemalloc for non-Windows implementations and the standard Windows API (called heapapi) for Windows:

[...]
[lib]
path = "lib.rs"

[target.'cfg(not(windows))'.dependencies]
jemalloc-sys = { version = "0.3.2" }

[target.'cfg(windows)'.dependencies]
winapi = { version = "0.3", features = ["heapapi"] }
ust: https://github.com/servo/servo

In lib.rs, in GlobalAlloc:alloc() we see it is using the mallocx custom function from jemalloc(). See the initialization of ffi.

See the use of the allocator in the Cargo.toml file in the net component. Search for the alloc string.

Practice​

  1. Look for uses of the allocator in other components of Servo.

Investigation: Alocator in the D Programming Language​

Phobos is the standard library that comes with the D programming language compiler.

Let's clone the source code:

student@os:~/.../std/experimental/allocator$ git clone https://github.com/dlang/phobos
[...]

student@os:~/.../data/lab/support$ cd phobos/

student@os:~/.../lab/support/phobos$ ls
azure-pipelines.yml  changelog  CODEOWNERS  CONTRIBUTING.md  dub.sdl  etc  index.dd  LICENSE_1_0.txt  posix.mak  project.ddoc  README.md  std  test  unittest.d  win32.mak  win64.mak

And enter std/experimental/allocator/ to browse information about the allocator:

student@os:~/.../lab/support/phobos$ cd std/experimental/allocator/

student@os:~/.../std/experimental/allocator$ ls
building_blocks  common.d  gc_allocator.d  mallocator.d  mmap_allocator.d  package.d  showcase.d  typed.d

We then do a search of the allocate( string to find instances of allocation calls:

student@os:~/.../std/experimental/allocator$ grep -r 'allocate('
[...]

We see that there are definitions of the function (as expected) as part of ...allocator files: mallocator.d, gc_allocator.d, mmap_allocator.d. Browse the functions and look for implementations of the allocate() function.

Practice​

  1. Do a similar search and then source code browsing for the deallocate() function.

App Investigation: Git​

Git is among the most used source code management system, powering development infrastructures such as GitHub, GitLab and Bitbucket.

Let's clone the repository. Note that it is about 200MB large:

student@os:~/.../data/lab/support$ git clone https://github.com/git/git
[...]

student@os:~/.../data/lab/support$ cd git/

We look of uses of malloc():

student@os:~/.../lab/support/git$ grep -r 'malloc(' .

We see there are multiple calls to the xmalloc() function, which is likely a wrapper for malloc(). We search for the definition of xmalloc():

student@os:~/.../lab/support/git$ grep -rn 'xmalloc(' . | grep -v ';'
./commit.c:188:                 graft = xmalloc(st_add(sizeof(*graft),
./add-interactive.c:157:        list->sorted.items = xmalloc(st_mult(sizeof(*list->sorted.items),
./Documentation/RelNotes/2.24.0.txt:91: * xmalloc() used to have a mechanism to ditch memory and address
./Documentation/RelNotes/2.24.0.txt:210:   xmalloc() wrapper, as the rest of the system, for consistency.
./Documentation/RelNotes/2.34.0.txt:230: * mmap() imitation used to call xmalloc() that dies upon malloc()
./Documentation/RelNotes/2.33.1.txt:44: * mmap() imitation used to call xmalloc() that dies upon malloc()
./diffcore-delta.c:56:  new_spanhash = xmalloc(st_add(sizeof(*orig),
./diffcore-delta.c:135: hash = xmalloc(st_add(sizeof(*hash),
./kwset.c:41:/* adapter for `xmalloc()`, which takes `size_t`, not `long` */
./builtin/fast-import.c:461:    b = xmalloc(sizeof(struct object_entry_pool)
./hashmap.h:311: * your structure was allocated with xmalloc(), you can just free(3) it,
./xdiff/xdiff.h:122:#define xdl_malloc(x) xmalloc(x)
./wrapper.c:45:static void *do_xmalloc(size_t size, int gentle)
./wrapper.c:70:void *xmalloc(size_t size)
./contrib/credential/wincred/git-credential-wincred.c:26:static void *xmalloc(size_t size)
Binary file ./.git/objects/pack/pack-c587b9f11a82bc4d49848d74132e60ea4dbeb177.pack matches
./git-compat-util.h:1046:# define xalloca(size)      (xmalloc(size))
./git-compat-util.h:1086:#define ALLOC_ARRAY(x, alloc) (x) = xmalloc(st_mult(sizeof(*(x)), (alloc)))
./read-cache.c:3768:    ieot = xmalloc(sizeof(struct index_entry_offset_table)

Line ./wrapper.c:70 is the one with the definition of the xmalloc() function. It makes a call of the do_xmalloc() function, that makes extra checks. Also, if the XMALLOC_POISON macro is defined, all the allocated data is overwritten with a "poison" value (0xA5). This is useful for early detection of memory-related issues, although, evidently, it adds overhead.

We can look for parts of the source code with the largest number of uses of xmalloc():

student@os:~/.../lab/support/git$ grep -rc 'xmalloc(' . | grep -v ':0' | sort -n -t ':' -k 20
[...]
./compat/mingw.c:6
./submodule-config.c:6
./merge-recursive.c:7

We can look into the merge-recursive.c file for uses of the xmalloc() function.

Practice​

  1. Do the same actions as above for the mmap() and xmmap() function calls.

    Note that these are not memory allocation calls, since a valid fd file argument is passed. These are file mapping calls, that we will talk more as part of the I/O chapter.