LibGit2.set_ssl_cert_locations segfaults on a cluster

[andreasnoack]

I got the #15128 error on a cluster when running Pkg.init() and when trying to point set_ssl_cert_locations to the certificates I get segfaults.

julia> LibGit2.set_ssl_cert_locations("/etc/ssl/certs/Go_Daddy_Root_Certificate_Authority_G2.pem")
ERROR: ReadOnlyMemoryError()

julia> LibGit2.set_ssl_cert_locations("/etc/ssl/certs/Staat_der_Nederlanden_Root_CA.pem")

signal (11): Segmentation fault
while loading no file, in expression starting on line 0
unknown function (ip: 0x2ba68c5a7fff)
Allocations: 1671531 (Pool: 1670594; Big: 937); GC: 0
Segmentation fault

This is on

julia> versioninfo()
Julia Version 0.5.0-rc0+146
Commit 37e6397* (2016-08-03 00:47 UTC)
Platform Info:
  System: Linux (x86_64-suse-linux)
  CPU: Intel(R) Xeon(R) CPU E5-2695 v2 @ 2.40GHz
  WORD_SIZE: 64
  BLAS: libmkl_rt
  LAPACK: libmkl_rt
  LIBM: libimf
  LLVM: libLLVM-3.7.1 (ORCJIT, ivybridge)

[Keno]

I cannot reproduce this. Are there additional instruction required? Alternatively, can you post the contents of the two pem files?

[andreasnoack]

They were randomly chosen. Just pointing to the directory "/etc/ssl/certs/" was sufficient to segfault with

julia> LibGit2.set_ssl_cert_locations("/etc/ssl/certs")

Breakpoint 1, 0x00002aacbbbe7240 in git_libgit2_opts ()
   from /scratch1/scratchdirs/noack/julia/usr/bin/../lib/libgit2.so
(gdb) s
Single stepping until exit from function git_libgit2_opts,
which has no line number information.
0x00002aacbbbe71a4 in git_reflog_drop ()
   from /scratch1/scratchdirs/noack/julia/usr/bin/../lib/libgit2.so
(gdb)
Single stepping until exit from function git_reflog_drop,
which has no line number information.

Program received signal SIGSEGV, Segmentation fault.
0x0000000000000000 in ?? ()
(gdb)

[andreasnoack]

Removing the cache didn't help but updating Julia did.

[andreasnoack]

Wrong issue

[wildart]

it would be helpful if you rebuild libgit2 with debug info. Just change -DCMAKE_BUILD_TYPE=Release in deps/libgit2.mk:10 to -DCMAKE_BUILD_TYPE=Debug and run make -C deps distclean-libgit2 && make -C deps install-libgit2

[andreasnoack]

I'll try that.

[andreasnoack]

Is this useful?

julia> LibGit2.set_ssl_cert_locations("/etc/ssl/certs")

Program received signal SIGILL, Illegal instruction.
0x00002aacbbbec6b8 in git_reflog_entry_committer (entry=0x7fffffff4c48)
    at /scratch1/scratchdirs/noack/julia/deps/srccache/libgit2-211e117a0590583a720c53172406f34186c543b
---Type <return> to continue, or q <return> to quit---
d/src/reflog.c:177
177             return entry->committer;
(gdb) bt
#0  0x00002aacbbbec6b8 in git_reflog_entry_committer (entry=0x7fffffff4c48)
    at /scratch1/scratchdirs/noack/julia/deps/srccache/libgit2-211e117a0590583a720c53172406f34186c543b
d/src/reflog.c:177
#1  0x00002aaab0b216eb in julia_set_ssl_cert_locations_22823 (cert_loc=...) at libgit2/libgit2.jl:525
#2  0x00002aaab0b2173c in jlcall_set_ssl_cert_locations_22823 ()
   from /scratch1/scratchdirs/noack/julia/usr/lib/julia/sys-debug.so
#3  0x00002aaaaad1463d in jl_call_method_internal ()
   from /scratch1/scratchdirs/noack/julia/usr/bin/../lib/libjulia-debug.so.0.6
#4  0x00002aaaaad1d7be in jl_apply_generic ()
   from /scratch1/scratchdirs/noack/julia/usr/bin/../lib/libjulia-debug.so.0.6
#5  0x00002aaaaad3be13 in do_call ()
   from /scratch1/scratchdirs/noack/julia/usr/bin/../lib/libjulia-debug.so.0.6
#6  0x00002aaaaad3cbac in eval ()
   from /scratch1/scratchdirs/noack/julia/usr/bin/../lib/libjulia-debug.so.0.6

[Keno]

That backtrace makes no sense. Does this machine have perf counters? Can you run this in RR?

[andreasnoack]

I tried to build RR but the build fails because the linux/seccomp.h cannot be found.

[Keno]

Old kernel?

[andreasnoack]

Yes slightly (but recent enough that it ought to have it I think)

Linux nid00237 3.0.101-0.35.1_1.0502.8640-cray_ari_c #1 SMP Wed Feb 18 05:13:50 UTC 2015 x86_64 x86_64
 x86_64 GNU/Linux