Taming the ‘stat’ storm with a loader cache

Ludovic Courtès — 2021-08-02

It was one of these days where some of us on IRC were rehashing that old problem—that application startup in Guix causes a “stat storm”—and lamenting the lack of a solution when suddenly, Ricardo proposes what, in hindsight, looks like an obvious solution: “maybe we could use a per-application ld cache?”. A moment where collective thinking exceeds the sum of our individual thoughts. The result is one of the many features that made it in the core-updates branch, slated to be merged in the coming weeks, one that reduces application startup time.

ELF files and their dependencies

Before going into detail, let’s look at what those “stat storms” look like and where they come from. Loading an ELF executable involves loading the shared libraries (the .so files, for “shared objects”) it depends on, recursively. This is the job of the loader (or dynamic linker), ld.so, which is part of the GNU C Library (glibc) package. What shared libraries an executable like that of Emacs depends on? The ldd command answers that question:

$ ldd $(type -P .emacs-27.2-real)
        linux-vdso.so.1 (0x00007fff565bb000)
        libtiff.so.5 => /gnu/store/l1wwr5c34593gqxvp34qbwdkaf7xhdbd-libtiff-4.2.0/lib/libtiff.so.5 (0x00007fd5aa2b1000)
        libjpeg.so.62 => /gnu/store/5khkwz9g6vza1n4z8xlmdrwhazz7m8wp-libjpeg-turbo-2.0.5/lib/libjpeg.so.62 (0x00007fd5aa219000)
        libpng16.so.16 => /gnu/store/3x2kak8abb6z2klch72kfff2qxzv00pj-libpng-1.6.37/lib/libpng16.so.16 (0x00007fd5aa1e4000)
        libz.so.1 => /gnu/store/rykm237xkmq7rl1p0nwass01p090p88x-zlib-1.2.11/lib/libz.so.1 (0x00007fd5aa1c2000)
        libgif.so.7 => /gnu/store/bpw826hypzlnl4gr6d0v8m63dd0k8waw-giflib-5.2.1/lib/libgif.so.7 (0x00007fd5aa1b8000)
        libXpm.so.4 => /gnu/store/jgdsl6whyimkz4hxsp2vrl77338kpl0i-libxpm-3.5.13/lib/libXpm.so.4 (0x00007fd5aa1a4000)
[…]
$ ldd $(type -P .emacs-27.2-real) | wc -l
89

(If you’re wondering why we’re looking at .emacs-27.2-real rather than emacs-27.2, it’s because in Guix the latter is a tiny shell wrapper around the former.)

To load a graphical program like Emacs, the loader needs to load more than 80 shared libraries! Each is in its own /gnu/store sub-directory in Guix, one directory per package.

But how does ld.so know where to find these libraries in the first place? In Guix, during the link phase that produces an ELF file (executable or shared library), we tell the linker to populate the RUNPATH entry of the ELF file with the list of directories where its dependencies may be found. This is done by passing -rpath options to the linker, which Guix’s “linker wrapper” takes care of. The RUNPATH is the run-time library search path: it’s a colon-separated list of directories where ld.so will look for shared libraries when it loads an ELF file. We can look at the RUNPATH of our Emacs executable like this:

$ objdump -x $(type -P .emacs-27.2-real) | grep RUNPATH
  RUNPATH              /gnu/store/fa6wj5bxkj5ll1d7292a70knmyl7a0cr-glibc-2.31/lib:/gnu/store/01b4w3m6mp55y531kyi1g8shh722kwqm-gcc-7.5.0-lib/lib:/gnu/store/l1wwr5c34593gqxvp34qbwdkaf7xhdbd-libtiff-4.2.0/lib:/gnu/store/5khkwz9g6vza1n4z8xlmdrwhazz7m8wp-libjpeg-turbo-2.0.5/lib:[…]

This RUNPATH has 39 entries, which roughly corresponds to the number of direct dependencies of the executable—dependencies are listed as NEEDED entries in the ELF file:

$ objdump -x $(type -P .emacs-27.2-real) | grep NEED | head
  NEEDED               libtiff.so.5
  NEEDED               libjpeg.so.62
  NEEDED               libpng16.so.16
  NEEDED               libz.so.1
  NEEDED               libgif.so.7
  NEEDED               libXpm.so.4
  NEEDED               libgtk-3.so.0
  NEEDED               libgdk-3.so.0
  NEEDED               libpangocairo-1.0.so.0
  NEEDED               libpango-1.0.so.0
$ objdump -x $(type -P .emacs-27.2-real) | grep NEED | wc -l
52

(Some of these .so files live in the same directory, which is why there are more NEEDED entries than directories in the RUNPATH.)

A system such as Debian that follows the file system hierarchy standard (FHS), where all libraries are in /lib or /usr/lib, does not have to bother with RUNPATH: all .so files are known to be found in one of these two “standard” locations. Anyway, let’s get back to our initial topic: the “stat storm”.

Walking search paths

As you can guess, when we run Emacs, the loader first needs to locate and load the 80+ shared libraries it depends on. That’s where things get pretty inefficient: the loader will search each .so file Emacs depends on in one of the 39 directories listed in its RUNPATH. Likewise, when it finally finds libgtk-3.so, it’ll look for its dependencies in each of the directories in its RUNPATH. We can see that at play by tracing system calls with the strace command:

$ strace -c emacs --version
GNU Emacs 27.2
Copyright (C) 2021 Free Software Foundation, Inc.
GNU Emacs comes with ABSOLUTELY NO WARRANTY.
You may redistribute copies of GNU Emacs
under the terms of the GNU General Public License.
For more information about these matters, see the file named COPYING.
% time     seconds  usecs/call     calls    errors syscall
------ ----------- ----------- --------- --------- ----------------
 55.46    0.006629           3      1851      1742 openat
 16.06    0.001919           4       422           mmap
 11.46    0.001370           2       501       477 stat
  4.79    0.000573           4       122           mprotect
  3.84    0.000459           4       111           read
  2.45    0.000293           2       109           fstat
  2.34    0.000280           2       111           close
[…]
------ ----------- ----------- --------- --------- ----------------
100.00    0.011952           3      3325      2227 total

For this simple emacs --version command, the loader and emacs probed for more than 2,200 files, with the openat and stat system calls, and most of these probes were unsuccessful (counted as “errors” here, meaning that the call returned an error). The fraction of “erroneous” system calls is no less than 67% (2,227 over 3,325). We can see the desperate search of .so files by looking at individual calls:

$ strace -e openat,stat emacs --version
[…]
openat(AT_FDCWD, "/gnu/store/fa6wj5bxkj5ll1d7292a70knmyl7a0cr-glibc-2.31/lib/libpng16.so.16", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/gnu/store/01b4w3m6mp55y531kyi1g8shh722kwqm-gcc-7.5.0-lib/lib/libpng16.so.16", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/gnu/store/l1wwr5c34593gqxvp34qbwdkaf7xhdbd-libtiff-4.2.0/lib/libpng16.so.16", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/gnu/store/5khkwz9g6vza1n4z8xlmdrwhazz7m8wp-libjpeg-turbo-2.0.5/lib/libpng16.so.16", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/gnu/store/3x2kak8abb6z2klch72kfff2qxzv00pj-libpng-1.6.37/lib/tls/haswell/x86_64/libpng16.so.16", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/gnu/store/3x2kak8abb6z2klch72kfff2qxzv00pj-libpng-1.6.37/lib/tls/haswell/x86_64", 0x7ffe428a1c70) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/gnu/store/3x2kak8abb6z2klch72kfff2qxzv00pj-libpng-1.6.37/lib/tls/haswell/libpng16.so.16", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/gnu/store/3x2kak8abb6z2klch72kfff2qxzv00pj-libpng-1.6.37/lib/tls/haswell", 0x7ffe428a1c70) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/gnu/store/3x2kak8abb6z2klch72kfff2qxzv00pj-libpng-1.6.37/lib/tls/x86_64/libpng16.so.16", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/gnu/store/3x2kak8abb6z2klch72kfff2qxzv00pj-libpng-1.6.37/lib/tls/x86_64", 0x7ffe428a1c70) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/gnu/store/3x2kak8abb6z2klch72kfff2qxzv00pj-libpng-1.6.37/lib/tls/libpng16.so.16", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/gnu/store/3x2kak8abb6z2klch72kfff2qxzv00pj-libpng-1.6.37/lib/tls", 0x7ffe428a1c70) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/gnu/store/3x2kak8abb6z2klch72kfff2qxzv00pj-libpng-1.6.37/lib/haswell/x86_64/libpng16.so.16", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/gnu/store/3x2kak8abb6z2klch72kfff2qxzv00pj-libpng-1.6.37/lib/haswell/x86_64", 0x7ffe428a1c70) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/gnu/store/3x2kak8abb6z2klch72kfff2qxzv00pj-libpng-1.6.37/lib/haswell/libpng16.so.16", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/gnu/store/3x2kak8abb6z2klch72kfff2qxzv00pj-libpng-1.6.37/lib/haswell", 0x7ffe428a1c70) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/gnu/store/3x2kak8abb6z2klch72kfff2qxzv00pj-libpng-1.6.37/lib/x86_64/libpng16.so.16", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/gnu/store/3x2kak8abb6z2klch72kfff2qxzv00pj-libpng-1.6.37/lib/x86_64", 0x7ffe428a1c70) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/gnu/store/3x2kak8abb6z2klch72kfff2qxzv00pj-libpng-1.6.37/lib/libpng16.so.16", O_RDONLY|O_CLOEXEC) = 3
[…]

Above is the sequence where we see ld.so look for libpng16.so.16, searching in locations where we know it’s not going to find it. A bit ridiculous. How does this affect performance? The impact is small in the most favorable case—on a hot cache, with fast solid state device (SSD) storage. But it likely has a visible effect in other cases—on a cold cache, with a slower spinning hard disk drive (HDD), on a network file system (NFS).

Enter the per-package loader cache

The idea that Ricardo submitted, using a loader cache, makes a lot of sense: we know from the start that libpng.so may only be found in /gnu/store/…-libpng-1.6.37, no need to look elsewhere. In fact, it’s not new: glibc has had such a cache “forever”; it’s the /etc/ld.so.cache file you can see on FHS distros and which is typically created by running ldconfig when a package has been installed. Roughly, the cache maps library SONAMEs, such as libpng16.so.16, to their file name on disk, say /usr/lib/libpng16.so.16.

The problem is that this cache is inherently system-wide: it assumes that there is only one libpng16.so on the system; any binary that depends on libpng16.so will load it from its one and only location. This models perfectly matches the FHS, but it’s at odds with the flexibility offered by Guix, where several variants or versions of the library can coexist on the system, used by different applications. That’s the reason why Guix and other non-FHS distros such as NixOS or GoboLinux typically turn off that feature altogether… and pay the cost of those stat storms.

The insight we gained on that Tuesday evening IRC conversation is that we could adapt glibc’s loader cache to our setting: instead of a system-wide cache, we’d have a per-application loader cache. As one of the last package build phases, we’d run ldconfig to create etc/ld.so.cache within that package’s /gnu/store sub-directory. We then need to modify the loader so it would look for ${ORIGIN}/../etc/ld.so.cache instead of /etc/ld.so.cache, where ${ORIGIN} is the location of the ELF file being loaded. A discussion of these changes is in the issue tracker; you can see the glibc patch and the new make-dynamic-linker-cache build phase. In short, the make-dynamic-linker-cache phase computes the set of direct and indirect dependencies of an ELF file using the file-needed/recursive procedure and derives from that the library search path, creates a temporary ld.so.conf file containing this search path for use by ldconfig, and finally runs ldconfig to actually build the cache.

How does this play out in practice? Let’s try an emacs build that uses this new loader cache:

$ strace -c /gnu/store/ijgcbf790z4x2mkjx2ha893hhmqrj29j-emacs-27.2/bin/emacs --version
GNU Emacs 27.2
Copyright (C) 2021 Free Software Foundation, Inc.
GNU Emacs comes with ABSOLUTELY NO WARRANTY.
You may redistribute copies of GNU Emacs
under the terms of the GNU General Public License.
For more information about these matters, see the file named COPYING.
% time     seconds  usecs/call     calls    errors syscall
------ ----------- ----------- --------- --------- ----------------
 28.68    0.002909          26       110        13 openat
 25.13    0.002549          26        96           read
 20.41    0.002070           4       418           mmap
  9.34    0.000947          10        90           pread64
  6.60    0.000669           5       123           mprotect
  4.12    0.000418           3       107         1 newfstatat
  2.19    0.000222           2        99           close
[…]
------ ----------- ----------- --------- --------- ----------------
100.00    0.010144           8      1128        24 total

Compared to what we have above, the total number of system calls has been divided by 3, and the fraction of erroneous system calls goes from 67% to 0.2%. Quite a difference! We count on you, dear users, to let us know how this impacts load time for you.

Flexibility without stat storms

With GNU Stow in the 1990s, and then Nix, Guix, and other distros, the benefits of flexible file layouts rather than the rigid Unix-inherited FHS have been demonstrated—nowadays I see it as an antidote to opaque and bloated application bundles à la Docker. Luckily, few of our system tools have FHS assumptions baked in, probably in large part thanks to GNU’s insistence on a rigorous installation directory categorization in the early days rather than hard-coded directory names. The loader cache is one of the few exceptions. Adapting it to a non-FHS context is fruitful for Guix and for the other distros and packaging tools in a similar situation; perhaps it could become an option in glibc proper?

This is not the end of stat storms, though. Interpreters and language run-time systems rely on search paths—GUILE_LOAD_PATH for Guile, PYTHONPATH for Python, OCAMLPATH for OCaml, etc.—and are equally prone to stormy application startups. Unlike ELF, they do not have a mechanism akin to RUNPATH, let alone a run-time search path cache. We have yet to find ways to address these.

About GNU Guix

GNU Guix is a transactional package manager and an advanced distribution of the GNU system that respects user freedom. Guix can be used on top of any system running the Hurd or the Linux kernel, or it can be used as a standalone operating system distribution for i686, x86_64, ARMv7, AArch64 and POWER9 machines.

In addition to standard package management features, Guix supports transactional upgrades and roll-backs, unprivileged package management, per-user profiles, and garbage collection. When used as a standalone GNU/Linux distribution, Guix offers a declarative, stateless approach to operating system configuration management. Guix is highly customizable and hackable through Guile programming interfaces and extensions to the Scheme language.