build.rs panics due to _FORTIFY_SOURCE warnings

[cratelyn]

first, thanks for maintaining this crate. it is a very useful piece of software.

i have found that the build.rs panics when i attempt to build this package using clang 17, due to warnings related a missing optimization flag:

the panic looks like:

  thread 'main' panicked at /home/user/.cargo/registry/src/index.crates.io-6f17d22bba15001f/jemalloc-sys-0.5.4+5.3.0-patched/build.rs:351:9:
  command did not execute successfully: cd "/home/user/project/target/debug/build/jemalloc-sys-3acf0278209d6cd4/out/build" && "make" "-j" "24"
  expected success, got: exit status: 2
  stack backtrace:
     0:     0x55d9c7f25c46 - std::backtrace_rs::backtrace::libunwind::trace::hbee8a7973eeb6c93
                                 at /rustc/07dca489ac2d933c78d3c5158e3f43beefeb02ce/library/std/src/../../backtrace/src/backtrace/libunwind.rs:104:5
     1:     0x55d9c7f25c46 - std::backtrace_rs::backtrace::trace_unsynchronized::hc8ac75eea3aa6899
                                 at /rustc/07dca489ac2d933c78d3c5158e3f43beefeb02ce/library/std/src/../../backtrace/src/backtrace/mod.rs:66:5
     2:     0x55d9c7f25c46 - std::sys_common::backtrace::_print_fmt::hc7f3e3b5298b1083
                                 at /rustc/07dca489ac2d933c78d3c5158e3f43beefeb02ce/library/std/src/sys_common/backtrace.rs:68:5
     3:     0x55d9c7f25c46 - <std::sys_common::backtrace::_print::DisplayBacktrace as core::fmt::Display>::fmt::hbb235daedd7c6190
                                 at /rustc/07dca489ac2d933c78d3c5158e3f43beefeb02ce/library/std/src/sys_common/backtrace.rs:44:22
     4:     0x55d9c7f4b570 - core::fmt::rt::Argument::fmt::h76c38a80d925a410
                                 at /rustc/07dca489ac2d933c78d3c5158e3f43beefeb02ce/library/core/src/fmt/rt.rs:142:9
     5:     0x55d9c7f4b570 - core::fmt::write::h3ed6aeaa977c8e45
                                 at /rustc/07dca489ac2d933c78d3c5158e3f43beefeb02ce/library/core/src/fmt/mod.rs:1120:17
     6:     0x55d9c7f2342f - std::io::Write::write_fmt::h78b18af5775fedb5
                                 at /rustc/07dca489ac2d933c78d3c5158e3f43beefeb02ce/library/std/src/io/mod.rs:1810:15
     7:     0x55d9c7f25a24 - std::sys_common::backtrace::_print::h5d645a07e0fcfdbb
                                 at /rustc/07dca489ac2d933c78d3c5158e3f43beefeb02ce/library/std/src/sys_common/backtrace.rs:47:5
     8:     0x55d9c7f25a24 - std::sys_common::backtrace::print::h85035a511aafe7a8
                                 at /rustc/07dca489ac2d933c78d3c5158e3f43beefeb02ce/library/std/src/sys_common/backtrace.rs:34:9
     9:     0x55d9c7f27197 - std::panicking::default_hook::{{closure}}::hcce8cea212785a25
    10:     0x55d9c7f26ef9 - std::panicking::default_hook::hf5fcb0f213fe709a
                                 at /rustc/07dca489ac2d933c78d3c5158e3f43beefeb02ce/library/std/src/panicking.rs:292:9
    11:     0x55d9c7f27628 - std::panicking::rust_panic_with_hook::h095fccf1dc9379ee
                                 at /rustc/07dca489ac2d933c78d3c5158e3f43beefeb02ce/library/std/src/panicking.rs:779:13
    12:     0x55d9c7f27502 - std::panicking::begin_panic_handler::{{closure}}::h032ba12139b353db
                                 at /rustc/07dca489ac2d933c78d3c5158e3f43beefeb02ce/library/std/src/panicking.rs:657:13
    13:     0x55d9c7f26146 - std::sys_common::backtrace::__rust_end_short_backtrace::h9259bc2ff8fd0f76
                                 at /rustc/07dca489ac2d933c78d3c5158e3f43beefeb02ce/library/std/src/sys_common/backtrace.rs:171:18
    14:     0x55d9c7f27260 - rust_begin_unwind
                                 at /rustc/07dca489ac2d933c78d3c5158e3f43beefeb02ce/library/std/src/panicking.rs:645:5
    15:     0x55d9c7ea27e5 - core::panicking::panic_fmt::h784f20a50eaab275
                                 at /rustc/07dca489ac2d933c78d3c5158e3f43beefeb02ce/library/core/src/panicking.rs:72:14
    16:     0x55d9c7ea9f3a - build_script_build::execute::hbc4736f388b7b82a
    17:     0x55d9c7ea9976 - build_script_build::run::he8ae1f16b0712186
    18:     0x55d9c7ea8cd3 - build_script_build::main::hcfc9252a05fd2a7e
    19:     0x55d9c7eaaeb3 - core::ops::function::FnOnce::call_once::h69b966a051d1c3c4
    20:     0x55d9c7eaa696 - std::sys_common::backtrace::__rust_begin_short_backtrace::ha21bc1e2f23e880e
    21:     0x55d9c7eaa939 - std::rt::lang_start::{{closure}}::h864902cc94152336
    22:     0x55d9c7f1ee91 - core::ops::function::impls::<impl core::ops::function::FnOnce<A> for &F>::call_once::h37600b1e5eea4ecd
                                 at /rustc/07dca489ac2d933c78d3c5158e3f43beefeb02ce/library/core/src/ops/function.rs:284:13
    23:     0x55d9c7f1ee91 - std::panicking::try::do_call::hb4bda49fa13a0c2b
                                 at /rustc/07dca489ac2d933c78d3c5158e3f43beefeb02ce/library/std/src/panicking.rs:552:40
    24:     0x55d9c7f1ee91 - std::panicking::try::h8bbf75149211aaaa
                                 at /rustc/07dca489ac2d933c78d3c5158e3f43beefeb02ce/library/std/src/panicking.rs:516:19
    25:     0x55d9c7f1ee91 - std::panic::catch_unwind::h8c78ec68ebea34cb
                                 at /rustc/07dca489ac2d933c78d3c5158e3f43beefeb02ce/library/std/src/panic.rs:142:14
    26:     0x55d9c7f1ee91 - std::rt::lang_start_internal::{{closure}}::hffdf44a19fd9e220
                                 at /rustc/07dca489ac2d933c78d3c5158e3f43beefeb02ce/library/std/src/rt.rs:148:48
    27:     0x55d9c7f1ee91 - std::panicking::try::do_call::hcb3194972c74716d
                                 at /rustc/07dca489ac2d933c78d3c5158e3f43beefeb02ce/library/std/src/panicking.rs:552:40
    28:     0x55d9c7f1ee91 - std::panicking::try::hcdc6892c5f0dba4c
                                 at /rustc/07dca489ac2d933c78d3c5158e3f43beefeb02ce/library/std/src/panicking.rs:516:19
    29:     0x55d9c7f1ee91 - std::panic::catch_unwind::h4910beb4573f4776
                                 at /rustc/07dca489ac2d933c78d3c5158e3f43beefeb02ce/library/std/src/panic.rs:142:14
    30:     0x55d9c7f1ee91 - std::rt::lang_start_internal::h6939038e2873596b
                                 at /rustc/07dca489ac2d933c78d3c5158e3f43beefeb02ce/library/std/src/rt.rs:148:20
    31:     0x55d9c7eaa917 - std::rt::lang_start::h698ca701eec9f6fd
    32:     0x55d9c7eaa4a5 - main
    33:     0x7faeb41c010e - __libc_start_call_main
    34:     0x7faeb41c01c9 - __libc_start_main@@GLIBC_2.34
    35:     0x55d9c7ea3045 - _start
    36:                0x0 - <unknown>
warning: build failed, waiting for other jobs to finish...

and i see warnings (promoted to errors) that look like this:

  /nix/store/yp441ann6ch705yk708h61ywxn7ayhj3-glibc-2.39-52-dev/include/features.h:414:4: warning: _FORTIFY_SOURCE requires compiling with optimization (-O) [-W#warnings]
    414 | #  warning _FORTIFY_SOURCE requires compiling with optimization (-O)                                                                                                                                          
        |    ^                                                                                              
  1 warning generated.
  In file included from src/pac.c:1:
  In file included from include/jemalloc/internal/jemalloc_preamble.h:5:
  In file included from include/jemalloc/internal/jemalloc_internal_decls.h:4:
  In file included from /nix/store/yp441ann6ch705yk708h61ywxn7ayhj3-glibc-2.39-52-dev/include/math.h:27:
  In file included from /nix/store/yp441ann6ch705yk708h61ywxn7ayhj3-glibc-2.39-52-dev/include/bits/libc-header-start.h:33:
  /nix/store/yp441ann6ch705yk708h61ywxn7ayhj3-glibc-2.39-52-dev/include/features.h:414:4: warning: _FORTIFY_SOURCE requires compiling with optimization (-O) [-W#warnings]
    414 | #  warning _FORTIFY_SOURCE requires compiling with optimization (-O)
        |    ^                                                                                                                                                                                                          
  1 warning generated.                                                                                                                                                                                                  
  In file included from src/peak_event.c:1:
  In file included from include/jemalloc/internal/jemalloc_preamble.h:5:
  In file included from include/jemalloc/internal/jemalloc_internal_decls.h:4:                
  In file included from /nix/store/yp441ann6ch705yk708h61ywxn7ayhj3-glibc-2.39-52-dev/include/math.h:27:                                                                                                                
  In file included from /nix/store/yp441ann6ch705yk708h61ywxn7ayhj3-glibc-2.39-52-dev/include/bits/libc-header-start.h:33:
  /nix/store/yp441ann6ch705yk708h61ywxn7ayhj3-glibc-2.39-52-dev/include/features.h:414:4: warning: _FORTIFY_SOURCE requires compiling with optimization (-O) [-W#warnings]
    414 | #  warning _FORTIFY_SOURCE requires compiling with optimization (-O)        
        |    ^                                                                                                                                                                                                          
  In file included from src/prof_data.c:1:                                                                                                                                                                              
  In file included from include/jemalloc/internal/jemalloc_preamble.h:5:                                                                                                                                                
  In file included from include/jemalloc/internal/jemalloc_internal_decls.h:4:
  In file included from /nix/store/yp441ann6ch705yk708h61ywxn7ayhj3-glibc-2.39-52-dev/include/math.h:27:                                                                                                                
  In file included from /nix/store/yp441ann6ch705yk708h61ywxn7ayhj3-glibc-2.39-52-dev/include/bits/libc-header-start.h:33:
  /nix/store/yp441ann6ch705yk708h61ywxn7ayhj3-glibc-2.39-52-dev/include/features.h:414:4: warning: _FORTIFY_SOURCE requires compiling with optimization (-O) [-W#warnings]
    414 | #  warning _FORTIFY_SOURCE requires compiling with optimization (-O)
        |    ^                                                                     

these are observed with the following clang/llvm toolchain:

[nix-shell:~/linkerd/linkerd2-proxy]$ clang --version
clang version 17.0.6
Target: x86_64-unknown-linux-gnu
Thread model: posix
InstalledDir: /nix/store/95iw6rgr5fbmywa8cbpzqgyakfkjh0ka-clang-17.0.6/bin

however, i do not see this panic if i revert to an older version of clang,

[nix-shell:~/linkerd/linkerd2-proxy]$ clang --version
clang version 14.0.6
Target: x86_64-unknown-linux-gnu
Thread model: posix
InstalledDir: /nix/store/fx89cvsnz3wrx1ljsng8d54n6x4kq3cq-clang-14.0.6/bin

[BusyJay]

and i see warnings (promoted to errors)

We don't enable warnings_into_errors flag, and according to https://docs.rs/cc/latest/cc/struct.Build.html#method.warnings_into_errors, it's disabled by default.

Can you compile github.com/jemalloc/jemalloc successfully?

[cratelyn]

interesting, thank you @BusyJay. i'll close this issue, pardon the trouble! it sounds like the -W flag is coming from elsewhere.

[cratelyn]

and i see warnings (promoted to errors)

We don't enable warnings_into_errors flag, and according to https://docs.rs/cc/latest/cc/struct.Build.html#method.warnings_into_errors, it's disabled by default.

Can you compile github.com/jemalloc/jemalloc successfully?

https://github.com/tikv/jemallocator/blob/main/jemalloc-sys/configure/configure#L3811-L3819

it looks like -Wall is set by the configure script within this repo?

this leads me to see these CFLAGS in my build output:

CFLAGS="-O0 -ffunction-sections -fdata-sections -fPIC -gdwarf-4 -fno-omit-frame-pointer -m64 --target=x86_64-unknown-linux-gnu -Wall"          

jemalloc builds successfully if i pin myself to an older LLVM/clang version. that will work for me in the short term, i provide these extra notes in case they're of use to someone else someday. 🙂

[dpc]

I came here to report the same issue.

--- a/Cargo.toml
+++ b/Cargo.toml
@@ -160,6 +160,7
[profile.dev.package]
 ring = { opt-level = 3 }
+tikv-jemalloc-sys = { opt-level = 3 }

fixes it.

I was not aware it is caused by -Wall. I was actually going to ask for build.rs to automatically compile with -O2 or something.

Anyway, this is definitely a problem, possibly in newer versions of LLVM, and it affects all our downstream users, and explaining to them they should add that line to their Cargo.toml is not a great workaround. And rocksdb without jemalloc suffers from terrible memory fragmentation, so we greatly appreciate tikv-jemallocator and would love to keep using it.

[cratelyn]

i'll reopen this on behalf of @dpc, since this is affecting others as well.

[dpc]

Huh...

I found some time to do more investigation, and it seems the actual failure was:

 fedi-fedimint-pkgs-group-ci-deps>   /nix/store/wmq01pqz681xdgq2n0hl5w7bbdr738g1-clang-wrapper-16.0.6/bin/clang -std=gnu11 -Werror=unknown-warning-option -Wall -Wextra -Wshorten-64-to-32 -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -Wno-missing-field-initializers -pipe -g3 -fvisibility=hidden -Wimplicit-fallthrough -O3 -funroll-loops -O0 -ffunction-sections -fdata-sections -fPIC -gdwarf-4 -fno-omit-frame-pointer -m64 --target=x86_64-unknown-linux-gnu -Wall -c -O0 -ffunction-sections -fdata-sections -fPIC -gdwarf-4 -fno-omit-frame-pointer -m64 --target=x86_64-unknown-linux-gnu -Wall -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/psset.sym.o src/psset.c


...


fedi-fedimint-pkgs-group-ci-deps>   src/malloc_io.c:107:9: error: incompatible pointer to integer conversion returning 'char *' from a function with result type 'int' [-Wint-conversion]
fedi-fedimint-pkgs-group-ci-deps>           return strerror_r(err, buf, buflen);
fedi-fedimint-pkgs-group-ci-deps>                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
fedi-fedimint-pkgs-group-ci-deps>   1 warning generated.
fedi-fedimint-pkgs-group-ci-deps>   1 warning and 1 error generated.
fedi-fedimint-pkgs-group-ci-deps>   1 warning generated.
fedi-fedimint-pkgs-group-ci-deps>   make: *** [Makefile:480: src/malloc_io.sym.o] Error 1
fedi-fedimint-pkgs-group-ci-deps>   make: *** Waiting for unfinished jobs....

clang 16, on Linux, the _FORTIFY_SOURCE warning seems like a red hearing-ish?

I verified again that forcing opt-level = 3 makes the problem go away.

[BusyJay]

Can someone provide full build logs? Especially the file in target/debug/build/tikv-jemalloc-sys-*/{output,stderr,out/build/config.log}.

[dpc]

@BusyJay https://privatebin.net/?ad34988dfa9659f7#JDDeeshFA65rDgVUNxWMAQnwe3h27HRzrHW8MTrQBGbw

[BusyJay]

I can't reproduce it on an alpine image that has clang 19. I notice that all provided logs in the issue are related to nix. However, I have never used nix before. I suspects there is some misconfiguration during compilation.

strerror_r should return an int when it's XSI-compliant, but GNU-specific version will return a char*. From the configure logs, jemalloc detects that strerror_r is not GNU-specific:

checking whether strerror_r returns char with gnu source is compilable... no

however, the function somehow returns char* in the end, which leads to the error. This can happen only when different headers are used between detection and compilation.

[dpc]

It isn't impossible it is a NixOS issue. It seems it doesn't happen with clang14 provided by NixOS, but it does with clang16 (would need to confirm it again). It's unlikely the c toolchain got switched during building of a single cargo crate, but it could be something internally that goes wrong / confuses autoconf?

[BusyJay]

It's unlikely the c toolchain got switched during building of a single cargo crate

I don't mean header is switched. configure only checks strerror_r from string.h, it's possible when compiling malloc_io.c, a different version of strerror_r from different header is used.

[jr1221]

I have the same problem on NixOS with gcc 14.2.1. Downgrading to gcc13 fixed the issue for me. Very peculiar, and most definitely related to Nix.

[dpc]

I guess it makes sense to report to nixpkgs then: NixOS/nixpkgs#370494