GNU bug report logs - #31925
'guix substitutes' sometimes hangs on glibc 2.27

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Package: guix; Severity: serious; Reported by: ludo@HIDDEN (Ludovic Courtès); dated Thu, 21 Jun 2018 11:46:01 UTC; Maintainer for guix is bug-guix@HIDDEN.
Severity set to 'serious' from 'normal' Request was from ludo@HIDDEN (Ludovic Courtès) to control <at> debbugs.gnu.org. Full text available.

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From: Ricardo Wurmus <rekado@HIDDEN>
To: Ludovic =?utf-8?Q?Court=C3=A8s?= <ludo@HIDDEN>
Subject: Re: bug#31925: 'guix substitutes' sometimes hangs on glibc 2.27
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Hi Ludo,

> When downloading a number of substitutes, =E2=80=98guix substitute=E2=80=
=99 sometimes
> hangs for me since the switch to glibc 2.27.  Anyone else experiencing
> this?  It=E2=80=99s relatively frequent for me.

It has never happened to me.

--=20
Ricardo





Information forwarded to bug-guix@HIDDEN:
bug#31925; Package guix. Full text available.

Message received at submit <at> debbugs.gnu.org:


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From: ludo@HIDDEN (Ludovic =?utf-8?Q?Court=C3=A8s?=)
To: bug-guix@HIDDEN
Subject: 'guix substitutes' sometimes hangs on glibc 2.27
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Hello Guix!

When downloading a number of substitutes, =E2=80=98guix substitute=E2=80=99=
 sometimes
hangs for me since the switch to glibc 2.27.  Anyone else experiencing
this?  It=E2=80=99s relatively frequent for me.

The backtrace shows this:

--8<---------------cut here---------------start------------->8---
(gdb) bt
#0  0x00007fbb34bf794d in __GI___pthread_timedjoin_ex (threadid=3D140441961=
314048, thread_return=3Dthread_return@entry=3D0x0, abstime=3Dabstime@entry=
=3D0x0, block=3Dblock@entry=3Dtrue)
    at pthread_join_common.c:89
#1  0x00007fbb34bf773c in __pthread_join (threadid=3D<optimized out>, threa=
d_return=3Dthread_return@entry=3D0x0) at pthread_join.c:24
#2  0x00007fbb350d7548 in stop_finalization_thread () at finalizers.c:265
#3  0x00007fbb350d7759 in scm_i_finalizer_pre_fork () at finalizers.c:290
#4  0x00007fbb3514f256 in scm_fork () at posix.c:1222
#5  0x00007fbb351477fd in vm_regular_engine (thread=3D0x7fbb313739d0, vp=3D=
0x1569f30, registers=3D0x52de, resume=3D884963661) at vm-engine.c:784
#6  0x00007fbb3514ae5a in scm_call_n (proc=3D<error reading variable: ERROR=
: Cannot access memory at address 0x355c2030>0x7fbb355c2030, argv=3Dargv@en=
try=3D0x7fff856ae7f8, nargs=3Dnargs@entry=3D1)
    at vm.c:1257
#7  0x00007fbb350ceff7 in scm_primitive_eval (exp=3Dexp@entry=3D<error read=
ing variable: ERROR: Cannot access memory at address 0x31738cf8>0x164fb00) =
at eval.c:662
#8  0x00007fbb350cf053 in scm_eval (exp=3D<error reading variable: ERROR: C=
annot access memory at address 0x31738cf8>0x164fb00,=20
    module_or_state=3Dmodule_or_state@entry=3D<error reading variable: ERRO=
R: Cannot access memory at address 0x354750d8>0x162b140) at eval.c:696
#9  0x00007fbb3511a0b0 in scm_shell (argc=3D10, argv=3D0x15f0390) at script=
.c:454
#10 0x00007fbb350e5add in invoke_main_func (body_data=3D0x7fff856aed10) at =
init.c:340
#11 0x00007fbb350c82da in c_body (d=3D0x7fff856aec50) at continuations.c:422
#12 0x00007fbb351477fd in vm_regular_engine (thread=3D0x7fbb313739d0, vp=3D=
0x1569f30, registers=3D0x52de, resume=3D884963661) at vm-engine.c:784
#13 0x00007fbb3514ae5a in scm_call_n (proc=3Dproc@entry=3D#<smob catch-clos=
ure 1564200>, argv=3Dargv@entry=3D0x0, nargs=3Dnargs@entry=3D0) at vm.c:1257
#14 0x00007fbb350cdef9 in scm_call_0 (proc=3Dproc@entry=3D#<smob catch-clos=
ure 1564200>) at eval.c:481
#15 0x00007fbb3513a026 in catch (tag=3Dtag@entry=3D#t, thunk=3D#<smob catch=
-closure 1564200>, handler=3D<error reading variable: ERROR: Cannot access =
memory at address 0x0>0x15641e0,=20
    pre_unwind_handler=3D<error reading variable: ERROR: Cannot access memo=
ry at address 0x0>0x15641c0) at throw.c:137
#16 0x00007fbb3513a365 in scm_catch_with_pre_unwind_handler (key=3Dkey@entr=
y=3D#t, thunk=3D<optimized out>, handler=3D<optimized out>, pre_unwind_hand=
ler=3D<optimized out>) at throw.c:254
#17 0x00007fbb3513a51f in scm_c_catch (tag=3Dtag@entry=3D#t, body=3Dbody@en=
try=3D0x7fbb350c82d0 <c_body>, body_data=3Dbody_data@entry=3D0x7fff856aec50=
, handler=3Dhandler@entry=3D0x7fbb350c8560 <c_handler>,=20
    handler_data=3Dhandler_data@entry=3D0x7fff856aec50, pre_unwind_handler=
=3Dpre_unwind_handler@entry=3D0x7fbb350c83c0 <pre_unwind_handler>, pre_unwi=
nd_handler_data=3D0x1564b60) at throw.c:377
#18 0x00007fbb350c88c0 in scm_i_with_continuation_barrier (body=3Dbody@entr=
y=3D0x7fbb350c82d0 <c_body>, body_data=3Dbody_data@entry=3D0x7fff856aec50, =
handler=3Dhandler@entry=3D0x7fbb350c8560 <c_handler>,=20
    handler_data=3Dhandler_data@entry=3D0x7fff856aec50, pre_unwind_handler=
=3Dpre_unwind_handler@entry=3D0x7fbb350c83c0 <pre_unwind_handler>, pre_unwi=
nd_handler_data=3D0x1564b60) at continuations.c:360
#19 0x00007fbb350c8955 in scm_c_with_continuation_barrier (func=3D<optimize=
d out>, data=3D<optimized out>) at continuations.c:456
#20 0x00007fbb35138c3c in with_guile (base=3Dbase@entry=3D0x7fff856aecb8, d=
ata=3Ddata@entry=3D0x7fff856aece0) at threads.c:661
#21 0x00007fbb34e2afb8 in GC_call_with_stack_base (fn=3Dfn@entry=3D0x7fbb35=
138bf0 <with_guile>, arg=3Darg@entry=3D0x7fff856aece0) at misc.c:1949
#22 0x00007fbb35138fd8 in scm_i_with_guile (dynamic_state=3D<optimized out>=
, data=3Ddata@entry=3D0x7fff856aece0, func=3Dfunc@entry=3D0x7fbb350e5ac0 <i=
nvoke_main_func>) at threads.c:704
#23 scm_with_guile (func=3Dfunc@entry=3D0x7fbb350e5ac0 <invoke_main_func>, =
data=3Ddata@entry=3D0x7fff856aed10) at threads.c:710
#24 0x00007fbb350e5c72 in scm_boot_guile (argc=3Dargc@entry=3D7, argv=3Darg=
v@entry=3D0x7fff856aee68, main_func=3Dmain_func@entry=3D0x400ce0 <inner_mai=
n>, closure=3Dclosure@entry=3D0x0) at init.c:323
#25 0x0000000000400b80 in main (argc=3D7, argv=3D0x7fff856aee68) at guile.c=
:101
(gdb) info threads
  Id   Target Id         Frame=20
* 1    Thread 0x7fbb355cab80 (LWP 21207) "guix substitute" 0x00007fbb34bf79=
4d in __GI___pthread_timedjoin_ex (threadid=3D140441961314048, thread_retur=
n=3Dthread_return@entry=3D0x0,=20
    abstime=3Dabstime@entry=3D0x0, block=3Dblock@entry=3Dtrue) at pthread_j=
oin_common.c:89
  2    Thread 0x7fbb3342c700 (LWP 21208) ".guix-real" 0x00007fbb34bfc552 in=
 futex_wait_cancelable (private=3D<optimized out>, expected=3D0, futex_word=
=3D0x7fbb3504f6ec <mark_cv+44>)
    at ../sysdeps/unix/sysv/linux/futex-internal.h:88
  3    Thread 0x7fbb32c2b700 (LWP 21209) ".guix-real" 0x00007fbb34bfc552 in=
 futex_wait_cancelable (private=3D<optimized out>, expected=3D0, futex_word=
=3D0x7fbb3504f6ec <mark_cv+44>)
    at ../sysdeps/unix/sysv/linux/futex-internal.h:88
  4    Thread 0x7fbb3242a700 (LWP 21210) ".guix-real" 0x00007fbb34bfc552 in=
 futex_wait_cancelable (private=3D<optimized out>, expected=3D0, futex_word=
=3D0x7fbb3504f6ec <mark_cv+44>)
    at ../sysdeps/unix/sysv/linux/futex-internal.h:88
  5    Thread 0x7fbb2eb78700 (LWP 21212) ".guix-real" 0x00007fbb34bffaac in=
 __libc_read (fd=3D9, buf=3Dbuf@entry=3D0x7fbb2eb77540, nbytes=3Dnbytes@ent=
ry=3D1) at ../sysdeps/unix/sysv/linux/read.c:27
  6    Thread 0x7fbb31373700 (LWP 21214) "guix substitute" 0x00007fbb34bffa=
ac in __libc_read (fd=3D5, buf=3Dbuf@entry=3D0x7fbb31372a30, nbytes=3Dnbyte=
s@entry=3D1) at ../sysdeps/unix/sysv/linux/read.c:27
--8<---------------cut here---------------end--------------->8---

The finalization thread is itself stuck reading from its pipe:

--8<---------------cut here---------------start------------->8---
(gdb) thread 6
[Switching to thread 6 (Thread 0x7fbb31373700 (LWP 21214))]
#0  0x00007fbb34bffaac in __libc_read (fd=3D5, buf=3Dbuf@entry=3D0x7fbb3137=
2a30, nbytes=3Dnbytes@entry=3D1) at ../sysdeps/unix/sysv/linux/read.c:27
27      in ../sysdeps/unix/sysv/linux/read.c
(gdb) bt
#0  0x00007fbb34bffaac in __libc_read (fd=3D5, buf=3Dbuf@entry=3D0x7fbb3137=
2a30, nbytes=3Dnbytes@entry=3D1) at ../sysdeps/unix/sysv/linux/read.c:27
#1  0x00007fbb350d74d7 in read_finalization_pipe_data (data=3D0x7fbb31372a3=
0) at finalizers.c:199
#2  0x00007fbb34e30b63 in GC_do_blocking_inner (data=3D0x7fbb313729f0 "\300=
t\r5\273\177", context=3D<optimized out>) at pthread_support.c:1353
#3  0x00007fbb34e25389 in GC_with_callee_saves_pushed (fn=3D0x7fbb34e30b20 =
<GC_do_blocking_inner>, arg=3Darg@entry=3D0x7fbb313729f0 "\300t\r5\273\177"=
) at mach_dep.c:322
#4  0x00007fbb34e2afec in GC_do_blocking (fn=3Dfn@entry=3D0x7fbb350d74c0 <r=
ead_finalization_pipe_data>, client_data=3Dclient_data@entry=3D0x7fbb31372a=
30) at misc.c:2061
#5  0x00007fbb3513902a in scm_without_guile (func=3D0x7fbb350d74c0 <read_fi=
nalization_pipe_data>, data=3D0x7fbb31372a30) at threads.c:722
#6  0x00007fbb350d7887 in finalization_thread_proc (unused=3D<optimized out=
>) at finalizers.c:212
#7  0x00007fbb350c82da in c_body (d=3D0x7fbb31372e50) at continuations.c:422
#8  0x00007fbb351477fd in vm_regular_engine (thread=3D0x5, vp=3D0x172aea0, =
registers=3D0x1, resume=3D884996780) at vm-engine.c:784
#9  0x00007fbb3514ae5a in scm_call_n (proc=3Dproc@entry=3D#<smob catch-clos=
ure 1c1ff60>, argv=3Dargv@entry=3D0x0, nargs=3Dnargs@entry=3D0) at vm.c:1257
#10 0x00007fbb350cdef9 in scm_call_0 (proc=3Dproc@entry=3D#<smob catch-clos=
ure 1c1ff60>) at eval.c:481
#11 0x00007fbb3513a026 in catch (tag=3Dtag@entry=3D#t, thunk=3D#<smob catch=
-closure 1c1ff60>, handler=3D<error reading variable: ERROR: Cannot access =
memory at address 0x0>0x1c1ff40,=20
    pre_unwind_handler=3D<error reading variable: ERROR: Cannot access memo=
ry at address 0x0>0x1c1ff00) at throw.c:137
#12 0x00007fbb3513a365 in scm_catch_with_pre_unwind_handler (key=3Dkey@entr=
y=3D#t, thunk=3D<optimized out>, handler=3D<optimized out>, pre_unwind_hand=
ler=3D<optimized out>) at throw.c:254
#13 0x00007fbb3513a51f in scm_c_catch (tag=3Dtag@entry=3D#t, body=3Dbody@en=
try=3D0x7fbb350c82d0 <c_body>, body_data=3Dbody_data@entry=3D0x7fbb31372e50=
, handler=3Dhandler@entry=3D0x7fbb350c8560 <c_handler>,=20
    handler_data=3Dhandler_data@entry=3D0x7fbb31372e50, pre_unwind_handler=
=3Dpre_unwind_handler@entry=3D0x7fbb350c83c0 <pre_unwind_handler>, pre_unwi=
nd_handler_data=3D0x1564b60) at throw.c:377
#14 0x00007fbb350c88c0 in scm_i_with_continuation_barrier (body=3Dbody@entr=
y=3D0x7fbb350c82d0 <c_body>, body_data=3Dbody_data@entry=3D0x7fbb31372e50, =
handler=3Dhandler@entry=3D0x7fbb350c8560 <c_handler>,=20
    handler_data=3Dhandler_data@entry=3D0x7fbb31372e50, pre_unwind_handler=
=3Dpre_unwind_handler@entry=3D0x7fbb350c83c0 <pre_unwind_handler>, pre_unwi=
nd_handler_data=3D0x1564b60) at continuations.c:360
#15 0x00007fbb350c8955 in scm_c_with_continuation_barrier (func=3D<optimize=
d out>, data=3D<optimized out>) at continuations.c:456
#16 0x00007fbb35138c3c in with_guile (base=3Dbase@entry=3D0x7fbb31372eb8, d=
ata=3Ddata@entry=3D0x7fbb31372ee0) at threads.c:661
#17 0x00007fbb34e2afb8 in GC_call_with_stack_base (fn=3Dfn@entry=3D0x7fbb35=
138bf0 <with_guile>, arg=3Darg@entry=3D0x7fbb31372ee0) at misc.c:1949
#18 0x00007fbb35138fd8 in scm_i_with_guile (dynamic_state=3D<optimized out>=
, data=3D<optimized out>, func=3D<optimized out>) at threads.c:704
#19 scm_with_guile (func=3D<optimized out>, data=3D<optimized out>) at thre=
ads.c:710
#20 0x00007fbb34bf6567 in start_thread (arg=3D0x7fbb31373700) at pthread_cr=
eate.c:463
#21 0x00007fbb3351eeaf in clone () at ../sysdeps/unix/sysv/linux/x86_64/clo=
ne.S:95
--8<---------------cut here---------------end--------------->8---

The =E2=80=98primitive-fork=E2=80=99 call itself presumably comes from
=E2=80=98decompressed-port=E2=80=99, used in (guix scripts substitute).

Ludo=E2=80=99.




Acknowledgement sent to ludo@HIDDEN (Ludovic Courtès):
New bug report received and forwarded. Copy sent to bug-guix@HIDDEN. Full text available.
Report forwarded to bug-guix@HIDDEN:
bug#31925; Package guix. Full text available.
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Copyright (C) 1999 Darren O. Benham, 1997 nCipher Corporation Ltd, 1994-97 Ian Jackson.