Package: guix;
Reported by: Malte Frank Gerdes <malte.f.gerdes <at> gmail.com>
Date: Sat, 27 Jul 2019 17:01:02 UTC
Severity: normal
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(Sat, 27 Jul 2019 17:01:02 GMT) Full text and rfc822 format available.Malte Frank Gerdes <malte.f.gerdes <at> gmail.com>:help-debbugs <at> gnu.org.
(Sat, 27 Jul 2019 17:01:03 GMT) Full text and rfc822 format available.Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):
From: Malte Frank Gerdes <malte.f.gerdes <at> gmail.com> To: submit <at> debbugs.gnu.org Subject: gcc bug prevents go program from starting newer gcc results in race condition Date: Sat, 27 Jul 2019 18:37:41 +0200
Hi,
The precompiled version of Hugo-extended was not able to find some
runtime dependencies:
libstdc++.so.6 => not found
libgcc_s.so.1 => not found
This seems like a version mismatch to me, so i built Hugo with the
following command:
go build --tags extended
Now the error is (<HASH> = ypiv8dj4lkvsnm82s639h18l87frrh5g):
/gnu/store/<HASH>-gcc-6.5.0-lib/lib/libstdc++.so.6: version
`GLIBCXX_3.4.26' not found
The problem seems identical to [1].
I copmiled go-1.4 with gcc:lib from 7, 8 and 9 with no luck (the 9
variant even fails the tests due to a race condition somewhere, i read
that in some other bug report but can't find the ID). Error Message at
the end.
So is there any progress on this? I guess this is necessary to make the
execution of hugo-extended (and maybe other programs?) work.
[1]: https://stackoverflow.com/questions/52663287/glibcxx-3-4-26-not-found
-Malte
##### ../misc/cgo/testsanitizers
--- FAIL: TestShared (0.02s)
--- FAIL: TestShared/tsan_shared (2.04s)
cshared_test.go:71: `/tmp/guix-build-go-1.12.7.drv-0/TestShared821009189/tsan_shared` exited with exit status 66
==================
WARNING: ThreadSanitizer: data race (pid=3613)
Write of size 8 at 0x7ffff6095c20 by thread T1:
#0 pthread_attr_getstacksize <null> (tsan_shared+0x00000041d5b2)
#1 x_cgo_init <null> (libtsan_shared.so+0x0000000968e0)
#2 runtime.rt0_go <null> (libtsan_shared.so+0x00000008cb0e)
Previous write of size 8 at 0x7ffff6095c20 by main thread:
#0 <null> <null> (0x000000000001)
Location is stack of thread T1.
Thread T1 (tid=3619, running) created by main thread at:
#0 pthread_create <null> (tsan_shared+0x00000040dec4)
#1 _cgo_try_pthread_create <null> (libtsan_shared.so+0x0000000967a1)
#2 x_cgo_sys_thread_create <null> (libtsan_shared.so+0x000000096543)
#3 _rt0_amd64_lib <null> (libtsan_shared.so+0x00000008ca16)
SUMMARY: ThreadSanitizer: data race ??:0 pthread_attr_getstacksize
==================
==================
WARNING: ThreadSanitizer: data race (pid=3613)
Read of size 8 at 0x7d080000dfe0 by thread T2:
#0 threadentry <null> (libtsan_shared.so+0x000000096b03)
Previous write of size 8 at 0x7d080000dfe0 by thread T1:
#0 malloc <null> (tsan_shared+0x00000040c2d3)
#1 x_cgo_thread_start <null> (libtsan_shared.so+0x00000009716c)
#2 runtime.asmcgocall <null> (libtsan_shared.so+0x00000008e546)
Location is heap block of size 24 at 0x7d080000dfe0 allocated by thread T1:
#0 malloc <null> (tsan_shared+0x00000040c2d3)
#1 x_cgo_thread_start <null> (libtsan_shared.so+0x00000009716c)
#2 runtime.asmcgocall <null> (libtsan_shared.so+0x00000008e546)
Thread T2 (tid=3621, running) created by thread T1 at:
#0 pthread_create <null> (tsan_shared+0x00000040dec4)
#1 _cgo_try_pthread_create <null> (libtsan_shared.so+0x0000000967a1)
#2 _cgo_sys_thread_start <null> (libtsan_shared.so+0x000000096a42)
#3 x_cgo_thread_start <null> (libtsan_shared.so+0x0000000971fa)
#4 runtime.asmcgocall <null> (libtsan_shared.so+0x00000008e546)
Thread T1 (tid=3619, running) created by main thread at:
#0 pthread_create <null> (tsan_shared+0x00000040dec4)
#1 _cgo_try_pthread_create <null> (libtsan_shared.so+0x0000000967a1)
#2 x_cgo_sys_thread_create <null> (libtsan_shared.so+0x000000096543)
#3 _rt0_amd64_lib <null> (libtsan_shared.so+0x00000008ca16)
SUMMARY: ThreadSanitizer: data race ??:0 threadentry
==================
==================
WARNING: ThreadSanitizer: data race (pid=3613)
Read of size 8 at 0x7ffff7fcc8b8 by thread T2:
#0 threadentry <null> (libtsan_shared.so+0x000000096b36)
Previous write of size 8 at 0x7ffff7fcc8b8 by thread T1:
#0 x_cgo_init <null> (libtsan_shared.so+0x000000096874)
#1 runtime.rt0_go <null> (libtsan_shared.so+0x00000008cb0e)
Location is global 'setg_gcc' of size 8 at 0x7ffff7fcc8b8 (libtsan_shared.so+0x00000013a8b8)
Thread T2 (tid=3621, running) created by thread T1 at:
#0 pthread_create <null> (tsan_shared+0x00000040dec4)
#1 _cgo_try_pthread_create <null> (libtsan_shared.so+0x0000000967a1)
#2 _cgo_sys_thread_start <null> (libtsan_shared.so+0x000000096a42)
#3 x_cgo_thread_start <null> (libtsan_shared.so+0x0000000971fa)
#4 runtime.asmcgocall <null> (libtsan_shared.so+0x00000008e546)
Thread T1 (tid=3619, running) created by main thread at:
#0 pthread_create <null> (tsan_shared+0x00000040dec4)
#1 _cgo_try_pthread_create <null> (libtsan_shared.so+0x0000000967a1)
#2 x_cgo_sys_thread_create <null> (libtsan_shared.so+0x000000096543)
#3 _rt0_amd64_lib <null> (libtsan_shared.so+0x00000008ca16)
SUMMARY: ThreadSanitizer: data race ??:0 threadentry
==================
==================
WARNING: ThreadSanitizer: data race (pid=3613)
Read of size 8 at 0x7d080000df80 by thread T6:
#0 threadentry <null> (libtsan_shared.so+0x000000096b03)
Previous write of size 8 at 0x7d080000df80 by thread T1:
#0 malloc <null> (tsan_shared+0x00000040c2d3)
#1 x_cgo_thread_start <null> (libtsan_shared.so+0x00000009716c)
#2 runtime.asmcgocall <null> (libtsan_shared.so+0x00000008e507)
Location is heap block of size 24 at 0x7d080000df80 allocated by thread T1:
#0 malloc <null> (tsan_shared+0x00000040c2d3)
#1 x_cgo_thread_start <null> (libtsan_shared.so+0x00000009716c)
#2 runtime.asmcgocall <null> (libtsan_shared.so+0x00000008e507)
Thread T6 (tid=3625, running) created by thread T1 at:
#0 pthread_create <null> (tsan_shared+0x00000040dec4)
#1 _cgo_try_pthread_create <null> (libtsan_shared.so+0x0000000967a1)
#2 _cgo_sys_thread_start <null> (libtsan_shared.so+0x000000096a42)
#3 x_cgo_thread_start <null> (libtsan_shared.so+0x0000000971fa)
#4 runtime.asmcgocall <null> (libtsan_shared.so+0x00000008e507)
Thread T1 (tid=3619, running) created by main thread at:
#0 pthread_create <null> (tsan_shared+0x00000040dec4)
#1 _cgo_try_pthread_create <null> (libtsan_shared.so+0x0000000967a1)
#2 x_cgo_sys_thread_create <null> (libtsan_shared.so+0x000000096543)
#3 _rt0_amd64_lib <null> (libtsan_shared.so+0x00000008ca16)
SUMMARY: ThreadSanitizer: data race ??:0 threadentry
==================
ThreadSanitizer: reported 4 warnings
FAIL
Glenn Morris <rgm <at> gnu.org>
to control <at> debbugs.gnu.org.
(Sat, 27 Jul 2019 17:17:02 GMT) Full text and rfc822 format available.bug-guix <at> gnu.org:bug#36823; Package guix.
(Sun, 04 Jul 2021 20:43:01 GMT) Full text and rfc822 format available.Message #10 received at 36823 <at> debbugs.gnu.org (full text, mbox):
From: Sarah Morgensen <iskarian <at> mgsn.dev> To: Malte Frank Gerdes <malte.f.gerdes <at> gmail.com> Cc: 36823 <at> debbugs.gnu.org Subject: Re: bug#36823: gcc bug prevents go program from starting newer gcc results in race condition Date: Sun, 04 Jul 2021 13:41:54 -0700
[Message part 1 (text/plain, inline)]
Hello, Thanks for the report. Malte Frank Gerdes <malte.f.gerdes <at> gmail.com> writes: > Hi, > > The precompiled version of Hugo-extended was not able to find some > runtime dependencies: > libstdc++.so.6 => not found > libgcc_s.so.1 => not found In case you haven't discovered this in the past two years (oops), this is because Guix does not typically work with pre-compiled software that relies on system libraries being in /lib, since there is no system-wide /lib. > This seems like a version mismatch to me, so i built Hugo with the > following command: > go build --tags extended > > Now the error is (<HASH> = ypiv8dj4lkvsnm82s639h18l87frrh5g): > /gnu/store/<HASH>-gcc-6.5.0-lib/lib/libstdc++.so.6: version > `GLIBCXX_3.4.26' not found If I build hugo with gcc-toolchain <at> 7 in my user profile, it works fine. However.... I can still repro this issue with gcc-toolchain <at> 8+: $ go build --tags extended $ ./hugo --help ./hugo: /gnu/store/01b4w3m6mp55y531kyi1g8shh722kwqm-gcc-7.5.0-lib/lib/libstdc++.so.6: version `GLIBCXX_3.4.26' not found (required by ./hugo) ./hugo: /gnu/store/01b4w3m6mp55y531kyi1g8shh722kwqm-gcc-7.5.0-lib/lib/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by ./hugo) This is because gcc 7's libraries are shadowing the newer gcc's libraries: $ readelf -d hugo | grep RUNPATH 0x000000000000001d (RUNPATH) Library runpath: [/gnu/store/01b4w3m6mp55y531kyi1g8shh722kwqm-gcc-7.5.0-lib/lib:/gnu/store/fa6wj5bxkj5ll1d7292a70knmyl7a0cr-glibc-2.31/lib:/gnu/store/3h7xd0d47a286b6r9qhz4ybi5iaxkfwi-gcc-11.1.0-lib/lib:/home/sarah/.guix-profile/lib:/gnu/store/3h7xd0d47a286b6r9qhz4ybi5iaxkfwi-gcc-11.1.0-lib/lib/gcc/x86_64-unknown-linux-gnu/11.1.0/../../..] If I use patchelf to remove the gcc 7 library dir from RUNPATH, hugo works fine. This is because Go is patched to unconditionally add a runpath to gcc 7's libraries but erroneously does not explicitly set CXX. (See also <https://issues.guix.gnu.org/39400>.) The following patch should explicitly set CXX for Go, so that it always uses the "system" version:
[go-explicitly-set-CXX.patch (text/x-patch, inline)]
diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm
index 0318918a37..a27f57aa30 100644
--- a/gnu/packages/golang.scm
+++ b/gnu/packages/golang.scm
@@ -395,6 +395,7 @@ in the style of communicating sequential processes (@dfn{CSP}).")
;; FIXME: Some of the .a files are not bit-reproducible.
(let* ((output (assoc-ref outputs "out")))
(setenv "CC" (which "gcc"))
+ (setenv "CXX" (which "g++"))
(setenv "GOOS" "linux")
(setenv "GOROOT" (dirname (getcwd)))
(setenv "GOROOT_FINAL" output)
@@ -577,6 +578,7 @@ in the style of communicating sequential processes (@dfn{CSP}).")
(loader (string-append (assoc-ref inputs "libc")
,(glibc-dynamic-linker))))
(setenv "CC" (which "gcc"))
+ (setenv "CXX" (which "g++"))
(setenv "GO_LDSO" loader)
(setenv "GOOS" "linux")
(setenv "GOROOT" (dirname (getcwd)))
[Message part 3 (text/plain, inline)]
Hope that helps, Sarah
bug-guix <at> gnu.org:bug#36823; Package guix.
(Tue, 06 Jul 2021 13:17:01 GMT) Full text and rfc822 format available.Message #13 received at 36823 <at> debbugs.gnu.org (full text, mbox):
From: Malte Frank Gerdes <malte.f.gerdes <at> gmail.com> To: Sarah Morgensen <iskarian <at> mgsn.dev> Cc: 36823 <at> debbugs.gnu.org Subject: Re: bug#36823: gcc bug prevents go program from starting newer gcc results in race condition Date: Tue, 06 Jul 2021 15:14:30 +0200
Thanks for your answer :-)
I don't use hugo anymore but at least i now know what the problem was,
but i really appreciate that you took the time to reproduce this. Does
it make sense to keep this ticket open, because as you found out there
still /is/ a bug?
(also just rediscovering the subject line: what the heck did i mean with
that?!)
Malte
Sarah Morgensen <iskarian <at> mgsn.dev> writes:
> Hello,
>
> Thanks for the report.
>
> Malte Frank Gerdes <malte.f.gerdes <at> gmail.com> writes:
>
>> Hi,
>>
>> The precompiled version of Hugo-extended was not able to find some
>> runtime dependencies:
>> libstdc++.so.6 => not found
>> libgcc_s.so.1 => not found
>
> In case you haven't discovered this in the past two years (oops), this
> is because Guix does not typically work with pre-compiled software that
> relies on system libraries being in /lib, since there is no system-wide
> /lib.
>
>> This seems like a version mismatch to me, so i built Hugo with the
>> following command:
>> go build --tags extended
>>
>> Now the error is (<HASH> = ypiv8dj4lkvsnm82s639h18l87frrh5g):
>> /gnu/store/<HASH>-gcc-6.5.0-lib/lib/libstdc++.so.6: version
>> `GLIBCXX_3.4.26' not found
>
> If I build hugo with gcc-toolchain <at> 7 in my user profile, it works fine.
> However.... I can still repro this issue with gcc-toolchain <at> 8+:
>
> $ go build --tags extended
> $ ./hugo --help
> ./hugo: /gnu/store/01b4w3m6mp55y531kyi1g8shh722kwqm-gcc-7.5.0-lib/lib/libstdc++.so.6: version `GLIBCXX_3.4.26' not found (required by ./hugo)
> ./hugo: /gnu/store/01b4w3m6mp55y531kyi1g8shh722kwqm-gcc-7.5.0-lib/lib/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by ./hugo)
>
> This is because gcc 7's libraries are shadowing the newer gcc's
> libraries:
>
> $ readelf -d hugo | grep RUNPATH
> 0x000000000000001d (RUNPATH) Library runpath:
> [/gnu/store/01b4w3m6mp55y531kyi1g8shh722kwqm-gcc-7.5.0-lib/lib:/gnu/store/fa6wj5bxkj5ll1d7292a70knmyl7a0cr-glibc-2.31/lib:/gnu/store/3h7xd0d47a286b6r9qhz4ybi5iaxkfwi-gcc-11.1.0-lib/lib:/home/sarah/.guix-profile/lib:/gnu/store/3h7xd0d47a286b6r9qhz4ybi5iaxkfwi-gcc-11.1.0-lib/lib/gcc/x86_64-unknown-linux-gnu/11.1.0/../../..]
>
> If I use patchelf to remove the gcc 7 library dir from RUNPATH, hugo
> works fine. This is because Go is patched to unconditionally add a
> runpath to gcc 7's libraries but erroneously does not explicitly set
> CXX. (See also <https://issues.guix.gnu.org/39400>.)
>
> The following patch should explicitly set CXX for Go, so that it always
> uses the "system" version:
>
> diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm
> index 0318918a37..a27f57aa30 100644
> --- a/gnu/packages/golang.scm
> +++ b/gnu/packages/golang.scm
> @@ -395,6 +395,7 @@ in the style of communicating sequential processes (@dfn{CSP}).")
> ;; FIXME: Some of the .a files are not bit-reproducible.
> (let* ((output (assoc-ref outputs "out")))
> (setenv "CC" (which "gcc"))
> + (setenv "CXX" (which "g++"))
> (setenv "GOOS" "linux")
> (setenv "GOROOT" (dirname (getcwd)))
> (setenv "GOROOT_FINAL" output)
> @@ -577,6 +578,7 @@ in the style of communicating sequential processes (@dfn{CSP}).")
> (loader (string-append (assoc-ref inputs "libc")
> ,(glibc-dynamic-linker))))
> (setenv "CC" (which "gcc"))
> + (setenv "CXX" (which "g++"))
> (setenv "GO_LDSO" loader)
> (setenv "GOOS" "linux")
> (setenv "GOROOT" (dirname (getcwd)))
>
>
> Hope that helps,
> Sarah
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