Seg fault when building from git

Seg fault when building from git

[John Darrington]

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Trying to build guix from the git repository:

make[2]: Entering directory `/Scratch/john/guix-dev'
/bin/mkdir -p `dirname "guix/scripts/build.go"` ;                       \
        LC_ALL=C                                                        \
        ./pre-inst-env                                  \
        /usr/bin/guild compile -L "." -L "/home/john/guix"      \
          -Wformat -Wunbound-variable -Warity-mismatch                  \
          --target="i686-pc-linux-gnu"                                          \
          -o "guix/scripts/build.go" "/home/john/guix/guix/scripts/build.scm"
/bin/bash: line 6: 26023 Segmentation fault      LC_ALL=C ./pre-inst-env /usr/bin/guild compile -L "." -L "/home/john/guix" -Wformat -Wunbound-variable -Warity-mismatch --target="i686-pc-linux-gnu" -o "guix/scripts/build.go" "/home/john/guix/guix/scripts/build.scm"
make[2]: *** [guix/scripts/build.go] Error 139


Any ideas what to do about this?

J'

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Re: Seg fault when building from git

[Ludovic Courtès]

John Darrington <john@darrington.wattle.id.au> skribis:

> Trying to build guix from the git repository:
>
> make[2]: Entering directory `/Scratch/john/guix-dev'
> /bin/mkdir -p `dirname "guix/scripts/build.go"` ;                       \
>         LC_ALL=C                                                        \
>         ./pre-inst-env                                  \
>         /usr/bin/guild compile -L "." -L "/home/john/guix"      \
>           -Wformat -Wunbound-variable -Warity-mismatch                  \
>           --target="i686-pc-linux-gnu"                                          \
>           -o "guix/scripts/build.go" "/home/john/guix/guix/scripts/build.scm"
> /bin/bash: line 6: 26023 Segmentation fault      LC_ALL=C ./pre-inst-env /usr/bin/guild compile -L "." -L "/home/john/guix" -Wformat -Wunbound-variable -Warity-mismatch --target="i686-pc-linux-gnu" -o "guix/scripts/build.go" "/home/john/guix/guix/scripts/build.scm"
> make[2]: *** [guix/scripts/build.go] Error 139

Could you do:

  ulimit -c unlimited
  rm -f guix/scripts/build.go
  make guix/scripts/build.go

and then, assuming it segfaulted again:

  gdb $(which guile) core
  (gdb) bt full

What does ‘guile --version’ say?

Thanks,
Ludo’.

Re: Seg fault when building from git

[John Darrington]

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On Sat, Nov 23, 2013 at 04:27:34PM +0100, Ludovic Court??s wrote:
     
     Could you do:
     
       ulimit -c unlimited
       rm -f guix/scripts/build.go
       make guix/scripts/build.go
     
     and then, assuming it segfaulted again:
     
       gdb $(which guile) core
       (gdb) bt full

Backtrace is attached.
     
     What does ???guile --version??? say?

guile (GNU Guile) 2.0.5-deb+1-3
     

Also,  the problem appears to be related to lack of space in /tmp

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john@jocasta:/Scratch/john/guix-dev$ ulimit -c unlimited
john@jocasta:/Scratch/john/guix-dev$ rm -rf guix/scripts/build.go 
john@jocasta:/Scratch/john/guix-dev$ make !$
make guix/scripts/build.go
/bin/mkdir -p `dirname "guix/scripts/build.go"` ;                       \
        LC_ALL=C                                                        \
        ./pre-inst-env                                  \
        /usr/bin/guild compile -L "." -L "/home/john/guix"      \
          -Wformat -Wunbound-variable -Warity-mismatch                  \
          --target="i686-pc-linux-gnu"                                          \
          -o "guix/scripts/build.go" "/home/john/guix/guix/scripts/build.scm"
;;; note: source file /Scratch/john/guix-dev/srfi/srfi-37.scm
;;;       newer than compiled /usr/lib/guile/2.0/ccache/srfi/srfi-37.go
;;; found fresh local cache at /home/john/.cache/guile/ccache/2.0-LE-4-2.0/Scratch/john/guix-dev/srfi/srfi-37.scm.go
/bin/bash: line 6: 32675 Segmentation fault      (core dumped) LC_ALL=C ./pre-inst-env /usr/bin/guild compile -L "." -L "/home/john/guix" -Wformat -Wunbound-variable -Warity-mismatch --target="i686-pc-linux-gnu" -o "guix/scripts/build.go" "/home/john/guix/guix/scripts/build.scm"
make: *** [guix/scripts/build.go] Error 139
john@jocasta:/Scratch/john/guix-dev$ ls core 
core
john@jocasta:/Scratch/john/guix-dev$ gdb $(which guile) core
GNU gdb (GDB) 7.4.1-debian
Copyright (C) 2012 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
and "show warranty" for details.
This GDB was configured as "i486-linux-gnu".
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>...
Reading symbols from /usr/bin/guile...(no debugging symbols found)...done.
[New LWP 32675]

warning: Can't read pathname for load map: Input/output error.
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/i386-linux-gnu/i686/cmov/libthread_db.so.1".
Core was generated by `/usr/bin/guile -e (@@ (guild) main) -s /usr/bin/guild compile -L . -L /home/joh'.
Program terminated with signal 11, Segmentation fault.
#0  0x408701e5 in scm_init_gnutls () from /usr/lib/i386-linux-gnu/libguile-gnutls-v-1.so
(gdb) bt full
#0  0x408701e5 in scm_init_gnutls () from /usr/lib/i386-linux-gnu/libguile-gnutls-v-1.so
No symbol table info available.
#1  0x4012aee2 in scm_dynamic_call () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#2  0x40093949 in ?? () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#3  0x40093980 in scm_load_extension () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#4  0x401282ce in ?? () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#5  0x40129afa in ?? () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#6  0x4008f887 in scm_primitive_eval () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#7  0x400b61f3 in scm_primitive_load () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#8  0x400b66cc in scm_primitive_load_path () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#9  0x401282dc in ?? () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#10 0x40129afa in ?? () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#11 0x4008f21c in scm_call_3 () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#12 0x400bac4a in scm_module_variable () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#13 0x400baafc in scm_module_variable () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#14 0x401282ce in ?? () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#15 0x40129afa in ?? () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#16 0x4008f887 in scm_primitive_eval () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#17 0x400b61f3 in scm_primitive_load () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#18 0x400b66cc in scm_primitive_load_path () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#19 0x401282dc in ?? () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#20 0x40129afa in ?? () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#21 0x4008f887 in scm_primitive_eval () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#22 0x400b61f3 in scm_primitive_load () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#23 0x400b66cc in scm_primitive_load_path () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#24 0x401282dc in ?? () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#25 0x40129afa in ?? () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#26 0x4008f887 in scm_primitive_eval () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#27 0x400b61f3 in scm_primitive_load () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#28 0x400b66cc in scm_primitive_load_path () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#29 0x401282dc in ?? () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#30 0x40129afa in ?? () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#31 0x4008f887 in scm_primitive_eval () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#32 0x400b61f3 in scm_primitive_load () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#33 0x400b66cc in scm_primitive_load_path () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#34 0x401282dc in ?? () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#35 0x40129afa in ?? () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#36 0x4008f887 in scm_primitive_eval () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#37 0x400b61f3 in scm_primitive_load () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#38 0x400b66cc in scm_primitive_load_path () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#39 0x401282dc in ?? () from /usr/lib/libguile-2.0.so.22
---Type <return> to continue, or q <return> to quit--- 
No symbol table info available.
#40 0x40129afa in ?? () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#41 0x4008f887 in scm_primitive_eval () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#42 0x400b61f3 in scm_primitive_load () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#43 0x400b66cc in scm_primitive_load_path () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#44 0x401282dc in ?? () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#45 0x40129afa in ?? () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#46 0x4008f887 in scm_primitive_eval () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#47 0x400b61f3 in scm_primitive_load () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#48 0x400b66cc in scm_primitive_load_path () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#49 0x401282dc in ?? () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#50 0x40129afa in ?? () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#51 0x4008f887 in scm_primitive_eval () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#52 0x4008f900 in scm_eval () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#53 0x400e6ae3 in scm_shell () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#54 0x400afcdc in ?? () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#55 0x400849b0 in ?? () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#56 0x4010ff58 in ?? () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#57 0x401284bf in ?? () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#58 0x40129afa in ?? () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#59 0x4008f284 in scm_call_4 () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#60 0x401103ea in scm_catch_with_pre_unwind_handler () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#61 0x401105dc in scm_c_catch () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#62 0x400852a3 in ?? () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#63 0x40085386 in scm_c_with_continuation_barrier () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#64 0x4010d7c0 in ?? () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#65 0x4038ea2e in GC_call_with_stack_base () from /usr/lib/libgc.so.1
No symbol table info available.
#66 0x4010d98f in scm_with_guile () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#67 0x400afe65 in scm_boot_guile () from /usr/lib/libguile-2.0.so.22
No symbol table info available.
#68 0x080487b5 in ?? ()
No symbol table info available.
#69 0x4022ce46 in __libc_start_main (main=0x8048780, argc=17, ubp_av=0xbfcae7f4, init=0x80488a0, fini=0x8048890, rtld_fini=0x4000e590, 
    stack_end=0xbfcae7ec) at libc-start.c:228
        result = <optimized out>
        unwind_buf = {cancel_jmp_buf = {{jmp_buf = {1077366772, 0, 0, -1077221432, -1950746100, 1542147571}, mask_was_saved = 0}}, 
          priv = {pad = {0x0, 0x0, 0x11, 0x80487bc}, data = {prev = 0x0, cleanup = 0x0, canceltype = 17}}}
        not_first_call = <optimized out>
#70 0x080487dd in ?? ()
No symbol table info available.
(gdb) quit

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Re: Seg fault when building from git

[Ludovic Courtès]

John Darrington <john@darrington.wattle.id.au> skribis:

> guile (GNU Guile) 2.0.5-deb+1-3

OK.  (It should work, but that’s very old.)

> Also,  the problem appears to be related to lack of space in /tmp

Not sure.

> Program terminated with signal 11, Segmentation fault.
> #0  0x408701e5 in scm_init_gnutls () from /usr/lib/i386-linux-gnu/libguile-gnutls-v-1.so
> (gdb) bt full
> #0  0x408701e5 in scm_init_gnutls () from /usr/lib/i386-linux-gnu/libguile-gnutls-v-1.so
> No symbol table info available.
> #1  0x4012aee2 in scm_dynamic_call () from /usr/lib/libguile-2.0.so.22
> No symbol table info available.
> #2  0x40093949 in ?? () from /usr/lib/libguile-2.0.so.22
> No symbol table info available.
> #3  0x40093980 in scm_load_extension () from /usr/lib/libguile-2.0.so.22
> No symbol table info available.

What does ‘ldd /usr/lib/i386-linux-gnu/libguile-gnutls-v-1.so’ report?

It may be that it’s linked against libguile.so from Guile 1.8, which
would obviously break the whole thing.

Thanks,
Ludo’.

Re: Seg fault when building from git

[John Darrington]

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On Sat, Nov 23, 2013 at 06:31:22PM +0100, Ludovic Court??s wrote:
     
     
     > Program terminated with signal 11, Segmentation fault.
     > #0  0x408701e5 in scm_init_gnutls () from /usr/lib/i386-linux-gnu/libguile-gnutls-v-1.so
     > (gdb) bt full
     > #0  0x408701e5 in scm_init_gnutls () from /usr/lib/i386-linux-gnu/libguile-gnutls-v-1.so
     > No symbol table info available.
     > #1  0x4012aee2 in scm_dynamic_call () from /usr/lib/libguile-2.0.so.22
     > No symbol table info available.
     > #2  0x40093949 in ?? () from /usr/lib/libguile-2.0.so.22
     > No symbol table info available.
     > #3  0x40093980 in scm_load_extension () from /usr/lib/libguile-2.0.so.22
     > No symbol table info available.
     
     What does ???ldd /usr/lib/i386-linux-gnu/libguile-gnutls-v-1.so??? report?
     
$ ldd /usr/lib/i386-linux-gnu/libguile-gnutls-v-1.so
        linux-gate.so.1 =>  (0xb77c9000)
        libgnutls.so.26 => /usr/lib/i386-linux-gnu/libgnutls.so.26 (0xb76bc000)
        libguile.so.17 => /usr/lib/libguile.so.17 (0xb75c0000)
        libgmp.so.10 => /usr/lib/i386-linux-gnu/libgmp.so.10 (0xb7545000)
        libcrypt.so.1 => /lib/i386-linux-gnu/i686/cmov/libcrypt.so.1 (0xb7513000)
        libm.so.6 => /lib/i386-linux-gnu/i686/cmov/libm.so.6 (0xb74ed000)
        libltdl.so.7 => /usr/lib/i386-linux-gnu/libltdl.so.7 (0xb74e3000)
        libp11-kit.so.0 => /usr/lib/i386-linux-gnu/libp11-kit.so.0 (0xb74d1000)
        libc.so.6 => /lib/i386-linux-gnu/i686/cmov/libc.so.6 (0xb736d000)
        libtasn1.so.3 => /usr/lib/i386-linux-gnu/libtasn1.so.3 (0xb735b000)
        libgcrypt.so.11 => /lib/i386-linux-gnu/libgcrypt.so.11 (0xb72d6000)
        libz.so.1 => /lib/i386-linux-gnu/libz.so.1 (0xb72bd000)
        libpthread.so.0 => /lib/i386-linux-gnu/i686/cmov/libpthread.so.0 (0xb72a4000)
        /lib/ld-linux.so.2 (0xb77ca000)
        libdl.so.2 => /lib/i386-linux-gnu/i686/cmov/libdl.so.2 (0xb729f000)
        libgpg-error.so.0 => /lib/i386-linux-gnu/libgpg-error.so.0 (0xb729b000)

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Re: Seg fault when building from git

[Ludovic Courtès]

John Darrington <john@darrington.wattle.id.au> skribis:

> On Sat, Nov 23, 2013 at 06:31:22PM +0100, Ludovic Court??s wrote:
>      
>      
>      > Program terminated with signal 11, Segmentation fault.
>      > #0  0x408701e5 in scm_init_gnutls () from /usr/lib/i386-linux-gnu/libguile-gnutls-v-1.so
>      > (gdb) bt full
>      > #0  0x408701e5 in scm_init_gnutls () from /usr/lib/i386-linux-gnu/libguile-gnutls-v-1.so
>      > No symbol table info available.
>      > #1  0x4012aee2 in scm_dynamic_call () from /usr/lib/libguile-2.0.so.22
>      > No symbol table info available.
>      > #2  0x40093949 in ?? () from /usr/lib/libguile-2.0.so.22
>      > No symbol table info available.
>      > #3  0x40093980 in scm_load_extension () from /usr/lib/libguile-2.0.so.22
>      > No symbol table info available.
>      
>      What does ???ldd /usr/lib/i386-linux-gnu/libguile-gnutls-v-1.so??? report?
>      
> $ ldd /usr/lib/i386-linux-gnu/libguile-gnutls-v-1.so
>         linux-gate.so.1 =>  (0xb77c9000)
>         libgnutls.so.26 => /usr/lib/i386-linux-gnu/libgnutls.so.26 (0xb76bc000)
>         libguile.so.17 => /usr/lib/libguile.so.17 (0xb75c0000)

So indeed, that’s the problem: the guile-gnutls package is linked
against Guile 1.8.

What could work for you is:

  sudo apt-get remove guile-gnutls
  guix package -i guile -i gnutls

HTH,
Ludo’.

Re: Seg fault when building from git

[John Darrington]

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On Sat, Nov 23, 2013 at 10:48:29PM +0100, Ludovic Courtès wrote:
     John Darrington <john@darrington.wattle.id.au> skribis:
     
     > On Sat, Nov 23, 2013 at 06:31:22PM +0100, Ludovic Court??s wrote:
     >      
     >      
     >      > Program terminated with signal 11, Segmentation fault.
     >      > #0  0x408701e5 in scm_init_gnutls () from /usr/lib/i386-linux-gnu/libguile-gnutls-v-1.so
     >      > (gdb) bt full
     >      > #0  0x408701e5 in scm_init_gnutls () from /usr/lib/i386-linux-gnu/libguile-gnutls-v-1.so
     >      > No symbol table info available.
     >      > #1  0x4012aee2 in scm_dynamic_call () from /usr/lib/libguile-2.0.so.22
     >      > No symbol table info available.
     >      > #2  0x40093949 in ?? () from /usr/lib/libguile-2.0.so.22
     >      > No symbol table info available.
     >      > #3  0x40093980 in scm_load_extension () from /usr/lib/libguile-2.0.so.22
     >      > No symbol table info available.
     >      
     >      What does ???ldd /usr/lib/i386-linux-gnu/libguile-gnutls-v-1.so??? report?
     >      
     > $ ldd /usr/lib/i386-linux-gnu/libguile-gnutls-v-1.so
     >         linux-gate.so.1 =>  (0xb77c9000)
     >         libgnutls.so.26 => /usr/lib/i386-linux-gnu/libgnutls.so.26 (0xb76bc000)
     >         libguile.so.17 => /usr/lib/libguile.so.17 (0xb75c0000)
     
     So indeed, that’s the problem: the guile-gnutls package is linked
     against Guile 1.8.
     
     What could work for you is:
     
       sudo apt-get remove guile-gnutls
       guix package -i guile -i gnutls
     

It is odd then that:

1. Since this is a bog standard debian stable system, nobody has noticed before;
2. The problem seems to manifest itself only when /tmp starts to get low on space.

J'

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Re: Seg fault when building from git

[Ludovic Courtès]

John Darrington <john@darrington.wattle.id.au> skribis:

> On Sat, Nov 23, 2013 at 10:48:29PM +0100, Ludovic Courtès wrote:

[...]

>      So indeed, that’s the problem: the guile-gnutls package is linked
>      against Guile 1.8.

[...]

> It is odd then that:
>
> 1. Since this is a bog standard debian stable system, nobody has noticed before;

Perhaps nobody who uses Guix installed guile-gnutls from Debian, or
added it to the $GUILE_LOAD_PATH.  Fortunately this is easily worked
around by uninstalling that Debian package.

(Remember Guix does not require the GnuTLS Guile bindings; it can use
them for ‘guix download’, but that’s optional.)

> 2. The problem seems to manifest itself only when /tmp starts to get low on space.

There can’t be any connection between the two, AFAICS.

HTH,
Ludo’.