glibc undefined symbol: fcntl64 when using zig cc as a drop-in compiler

[creationix]

I'm trying to build a small test application with libuv embedded. I want to use zig cc because the caching system makes it much faster. The following command works for clang and gcc, but not zig cc.

zig cc -o main main.c libuv/src/fs-poll.c libuv/src/idna.c libuv/src/inet.c libuv/src/random.c libuv/src/strscpy.c libuv/src/threadpool.c libuv/src/timer.c libuv/src/uv-common.c libuv/src/uv-data-getter-setters.c libuv/src/version.c libuv/src/unix/async.c libuv/src/unix/core.c libuv/src/unix/dl.c libuv/src/unix/fs.c libuv/src/unix/getaddrinfo.c libuv/src/unix/getnameinfo.c libuv/src/unix/loop-watcher.c libuv/src/unix/loop.c libuv/src/unix/pipe.c libuv/src/unix/poll.c libuv/src/unix/process.c libuv/src/unix/random-devurandom.c libuv/src/unix/signal.c libuv/src/unix/stream.c libuv/src/unix/tcp.c libuv/src/unix/thread.c libuv/src/unix/tty.c libuv/src/unix/udp.c libuv/src/unix/proctitle.c libuv/src/unix/linux-core.c libuv/src/unix/linux-inotify.c libuv/src/unix/linux-syscalls.c libuv/src/unix/procfs-exepath.c libuv/src/unix/random-getrandom.c libuv/src/unix/random-sysctl-linux.c -pthread -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -D_POSIX_C_SOURCE=200112 -Os -ldl -lrt  -Ilibuv/include -Ilibuv/src
Compile C Objects [36/36] random-sysctl-linux.c...lld: error: undefined symbol: fcntl64
>>> referenced by core.c
>>>               zig-cache/o/a98yrC-16nzaiLvm0YSsj7Kr64jgWlKyw30Ca_aTuY8lBx8HcWfjUWLmNzWOQ59K/core.o:(uv__nonblock_fcntl)
>>> referenced by core.c
>>>               zig-cache/o/a98yrC-16nzaiLvm0YSsj7Kr64jgWlKyw30Ca_aTuY8lBx8HcWfjUWLmNzWOQ59K/core.o:(uv__nonblock_fcntl)
>>> referenced by core.c
>>>               zig-cache/o/a98yrC-16nzaiLvm0YSsj7Kr64jgWlKyw30Ca_aTuY8lBx8HcWfjUWLmNzWOQ59K/core.o:(uv__cloexec_fcntl)
>>> referenced by core.c
>>>               zig-cache/o/a98yrC-16nzaiLvm0YSsj7Kr64jgWlKyw30Ca_aTuY8lBx8HcWfjUWLmNzWOQ59K/core.o:(uv__cloexec_fcntl)
>>> referenced by pipe.c
>>>               zig-cache/o/Gp2nxP14BgUu9fMnuMMJ4gryoTCPAocIoqmgTAVdptPg5_FP1QjIdJRHfMpqm3ls/pipe.o:(uv_pipe_open)
>>> referenced by process.c
>>>               zig-cache/o/Z2n-GR8LD-1fXu4uIs37LmdvcK0K1mfCZ4iNwE1idOtrGfUhw6eXoJ8i5oMbsgSg/process.o:(uv__process_child_init)
>>> did you mean: fcntl64
>>> defined in: /home/tim/.cache/zig/stage1/h/pVSItZEIxIXx_ZQQwt9SLNNbPH8xxZp1plbirUK6SOmyZ4FTf2EOP08onozfGP03/libc.so.6.0.0

Is there something special I need to pass in for this to build?

[creationix]

In particular, I'm confused by lld: error: undefined symbol: fcntl64 and then did you mean: fcntl64

[andrewrk]

Hmm that is indeed confusing. I think the next step towards troubleshooting this would be to hop into one of the LLVM chat rooms and ask LLD developers if they know why this could happen.

[andrewrk]

One work around would be to try musl libc instead of glibc: -target native-native-musl

[squeek502]

This is the same problem I was running into here https://github.com/luvit/luvi/issues/231#issuecomment-604227535:

Now I'm running into a problem with mismatched glibc versions (zig cc is compiling against a newer one than my system glibc; specifically it's trying to use fnctl64 which my glibc doesn't have). Zig has the ability to target specific glibc versions (e.g. -target native-native-gnu.2.23) but I'm not sure it affects zig cc.

and https://github.com/luvit/luvi/issues/231#issuecomment-608640080.

Targeting musl should work unless you need dynamic loading (https://github.com/luvit/luvi/issues/231#issuecomment-606512367).

[creationix]

@squeek502 yep, you're right that I missed your comment in the luvi repo. This is the exact same issue! I guess it's something in libuv that's causing the problem since I don't have luajit at all in this project.

I tried -target native-native-musl and I get the same error though. Let me push my code and see if I'm doing it right...

[creationix]

https://github.com/creationix/polluv/blob/9ccc3c952ffb18b09148f22e8346acc9667b1097/Makefile#L2-L29

[marler8997]

Just a thought, maybe fcntl64 is versioned? I was recently working with libefivar and they version their symbols using -Wl,--version-script=FILE, not sure exactly how versioning symbols works but could be a potential explanation for this error.

[daurnimator]

As in #6036, could you try using a newer glibc version as part of your target?

[aniljava]

Using c library triggers this errors, either as built.zig or in build-exe

/ws/projects/zig/sqlite :: # zig build
Build Dependencies... lld: error: /usr/lib/libsqlite3.so: undefined reference to fcntl64

/ws/projects/zig/sqlite :: # ldd --version
ldd (Ubuntu GLIBC 2.31-0ubuntu9) 2.31

exe.linkSystemLibrary("c");

/ws/projects/zig/sqlite :: # zig build-exe src/main.zig  -lsqlite3 -lc
Build Dependencies... lld: error: /usr/lib/libsqlite3.so: undefined reference to fcntl64

main.zig

const std = @import("std");
const sqlite = @cImport(@cInclude("sqlite3.h"));

pub fn main() anyerror!void {
    var db: ?*sqlite.sqlite3 = undefined;

}

addition to init-exe generated build.zig

const exe = b.addExecutable("sqlite", "src/main.zig");

exe.linkSystemLibrary("c");
exe.linkSystemLibrary("sqlite3");

[zhaozg]

cross build libuv for linux on macos, failed with

[100%] Linking C executable luvi
ld.lld: error: undefined symbol: fcntl64
>>> referenced by amalgamation.c
>>>               CMakeFiles/luvi.dir/custom/sqlitext/amalgamation.c.o:(aSyscall)
>>> referenced by core.c
>>>               core.c.o:(uv__nonblock_fcntl) in archive luv.dir/deps/libuv/libuv_a.a
>>> referenced by core.c
>>>               core.c.o:(uv__nonblock_fcntl) in archive luv.dir/deps/libuv/libuv_a.a
>>> referenced 5 more times
>>> did you mean: fcntl64@GLIBC_2.28
>>> defined in: /Users/zhaozg/.cache/zig/o/2723a939ae2a5ffa91d29e2389d18ffc/libc.so.6
error: LLDReportedFailure
make[6]: *** [luvi] Error 1
make[5]: *** [CMakeFiles/luvi.dir/all] Error 2
make[4]: *** [all] Error 2
make[3]: *** [luvi-prefix/src/luvi-stamp/luvi-build] Error 2
make[2]: *** [CMakeFiles/luvi.dir/all] Error 2
make[1]: *** [all] Error 2
make: *** [luvi] Error 2

[zhaozg]

After read how-to-force-linkage-to-older-libc-fcntl-instead-of-fcntl64, I found an alternative way to build libuv with zig cc.

make a fcntl.map file

GLIBC_2.2.5 {
   fcntl;
};

And update luv/deps/libuv/src/unix/internal.h, and add a line asm (".symver fcntl64, fcntl@GLIBC_2.2.5"); before #endif /* UV_UNIX_INTERNAL_H_ */

use CC="zig cc -target x86_64-linux-gnu.2.17 -Wl,--version-script,path_of_fcntl.map" ~or "CC="zig cc -target aarch64-linux-gnu.2.17 -Wl,--version-script,path_of_fcntl.map"`~ to build libuv.

If x86_64-linux-gnu version below 2.17, maybe need more glibc api map, and I have not test that.

aarch64-linux-gnu not pass, because has no fcntl@GLIBC_2.2.5

[harryhaaren]

I've just bumped into this issue too, when compiling a native C project that extensively uses linker scripts for both visibility and versioning of symbols. A quick web search brings me to this issue, root cause was the undefined symbol: fcntl64, and suggests did you mean fcntl64@GLIB_2.28 (from the Zig musl build cache for this architecture).

[nektro]

can confirm this works if you add -target native-native-gnu.2.28 since fcntl64 was removed in glibc 2.29+

the main.c I used can be found here https://nikhilm.github.io/uvbook/basics.html#hello-world

$ zig version
0.8.0-dev.2591+4b69bd61e

$ uname -a
Linux Meghans-PBP 5.7.0-2-pinebookpro-arm64 #1 SMP PREEMPT Sat Apr 24 11:16:25 UTC 2021 aarch64 GNU/Linux

$ zigmod fetch
fetch: libuv: git: https://github.com/libuv/libuv

$ zig build -Dtarget=native-native-gnu.2.28

$ ./zig-out/bin/zig-libuv 
Now quitting.

edit: zig.mod: https://clbin.com/ITDC2 build.zig: https://zigbin.io/0a334f

[motiejus]

I have the same problem building sqlite3 amalgamation (3.36.0) for glibc 2.27 or older:

~/sqlite-amalgamation-3360000 $ zig cc --target=x86_64-linux-gnu.2.24 shell.c sqlite3.c -lpthread -ldl -lm -o sqlite.2.24
ld.lld: error: undefined symbol: fcntl64
>>> referenced by sqlite3.c
>>>               /home/motiejus/.cache/zig/o/b0eefed440b6d330af020a2a209205de/sqlite3.o:(aSyscall)
>>> did you mean: fcntl64@GLIBC_2.28
>>> defined in: /home/motiejus/.cache/zig/o/d7adab72898642dac7322f4d250dbd1a/libc.so.6

I cannot use older glibc version, because some production hosts run 2.24; I also cannot use the musl target, because some applications expose NSS symbols, thus must be linked against glibc (vaguely mentioned in https://eng.uber.com/hadoop-container-blog/).

Suggestion by @zhaozg (above) works! But ... is there a way to pass the asm line in a cflag directive instead of patching the source? In our case, sqlite is a dependency of a dependency, so even creating a patch is non-trivial to begin with, let alone maintain it during upgrades.

[motiejus]

Following @zhaozg 's suggestion I found a slightly different approach that does not require changing the source files:

fcntl.h

#ifdef __ASSEMBLER__
.symver fcntl64, fcntl@GLIBC_2.2.5
#else
__asm__(".symver fcntl64, fcntl@GLIBC_2.2.5");
#endif

fcntl.map

GLIBC_2.2.5 {
   fcntl;
};

Compile command:

zig cc --target=x86_64-linux-gnu.2.24 shell.c sqlite3.c -lpthread -ldl -lm -Wl,--version-script,fcntl.map -include fcntl.h -o sqlite.2.24

[motiejus]

I created https://github.com/ziglang/zig/issues/9485, which captures the problem with a very small C file.

[ratfactor]

Also ran into this compiling https://github.com/vrischmann/zig-sqlite with the included SQLite 3.35.5 amalgam.

Both target suggestions above worked for me:

zig build run -Dtarget=native-native-musl

and

zig build -Dtarget=native-native-gnu.2.28

The error (might help someone else searching for this issue):

ld.lld: error: undefined symbol: fcntl64
>>> referenced by sqlite3.c
>>>               /home/dave/sync/proj/zig/shoebox6/zig-cache/o/4089122d496bd76a6e71a1ea3f7f7ee6/sqlite3.o:(aSyscall)
>>> did you mean: fcntl64@GLIBC_2.28
>>> defined in: /home/dave/.cache/zig/o/7fec61c5e150add8cc9a2bc712cfb30a/libc.so.6
error: LLDReportedFailure

[bradclawsie]

I stumbled upon this issue while trying to use the sqlite library. To add to the stopgap solutions provided above, here are some snippets for build.zig:

let's say there is a library state.zig written with sqlite support...to build:

const state_lib = b.addStaticLibrary("state", "lib/state.zig");
state_lib.setBuildMode(mode);
deps.addAllTo(state_lib);
state_lib.setTarget(std.build.Target{ .glibc_version = std.build.Target.SemVer{ .major = 2, .minor = 28 } });
state_lib.install();
var state_pkg = std.build.Pkg{ .name = state_lib.name, .path = std.build.FileSource{ .path = state_lib.root_src.?.path }, .dependencies = state_lib.packages.items };

and for tests:

var state_tests = b.addTest("lib/state.zig");
state_tests.setBuildMode(mode);
deps.addAllTo(state_tests);
state_tests.setTarget(std.build.Target{ .glibc_version = std.build.Target.SemVer{ .major = 2, .minor = 28 } });
state_tests.addPackage(state_pkg);

maybe these snippets help someone until a more automatic solution arrives...

[andrewrk]

Closing as a duplicate of #9485 since that one has a minimal reproduction test case.

[motiejus]

Note to followers of this issue: fcntl64 and a few more functions got resolved in #15101. Try compiling your stuff now. :)

[chee-z1]

I had the same problem using raylib.

"C:\Program Files\zig\zig.exe" run C:/Users/userName/IdeaProjects/new_/main.zig
error: lld-link: undefined symbol: InitWindow
    note: referenced by C:\Users\userName\IdeaProjects\new_\main.zig:18
    note:               C:\Users\userName\AppData\Local\zig\o\f59599752f0cead73359b7fdc6eb46c9\main.exe.obj:(main.main)
error: lld-link: undefined symbol: SetTargetFPS
    note: referenced by C:\Users\userName\IdeaProjects\new_\main.zig:19
    note:               C:\Users\userName\AppData\Local\zig\o\f59599752f0cead73359b7fdc6eb46c9\main.exe.obj:(main.main)
error: lld-link: undefined symbol: CloseWindow
    note: referenced by C:\Users\userName\IdeaProjects\new_\main.zig:20
    note:               C:\Users\userName\AppData\Local\zig\o\f59599752f0cead73359b7fdc6eb46c9\main.exe.obj:(main.main)
error: lld-link: undefined symbol: WindowShouldClose
    note: referenced by C:\Users\userName\IdeaProjects\new_\main.zig:21
    note:               C:\Users\userName\AppData\Local\zig\o\f59599752f0cead73359b7fdc6eb46c9\main.exe.obj:(main.main)
error: lld-link: undefined symbol: BeginDrawing
    note: referenced by C:\Users\userName\IdeaProjects\new_\main.zig:22
    note:               C:\Users\userName\AppData\Local\zig\o\f59599752f0cead73359b7fdc6eb46c9\main.exe.obj:(main.main)
error: lld-link: undefined symbol: ClearBackground
    note: referenced by C:\Users\userName\IdeaProjects\new_\main.zig:24
    note:               C:\Users\userName\AppData\Local\zig\o\f59599752f0cead73359b7fdc6eb46c9\main.exe.obj:(main.main)
error: lld-link: undefined symbol: DrawText
    note: referenced by C:\Users\userName\IdeaProjects\new_\main.zig:25
    note:               C:\Users\userName\AppData\Local\zig\o\f59599752f0cead73359b7fdc6eb46c9\main.exe.obj:(main.main)
error: lld-link: undefined symbol: EndDrawing
    note: referenced by C:\Users\userName\IdeaProjects\new_\main.zig:23
    note:               C:\Users\userName\AppData\Local\zig\o\f59599752f0cead73359b7fdc6eb46c9\main.exe.obj:(main.main)