Using AstroTime kills the julia jupyter kernel

I can do:

using AstroTime

from the julia console, but if I do it in a jupyter notebook, it crashes the jupyter julia kernel but I have a workaround: this does not happen if I first do:

using Plots

in the notebook, then I can use AstroTime.
but NOT if instead of Plots, I use Polynomials or Optim.

julia 0.6.3 on Linux x64 AstroTime (master), IJulia 1.9.1, jupyter 4.4.0 (anaconda)

Do you get any output from the terminal where you ran jupyter notebook?

Only message appearing in the console is:

[I 18:01:40.648 NotebookApp] KernelRestarter: restarting kernel (1/5), keep random ports
kernel bf2762b3-b282-4830-a89f-0df2a5edf9fe restarted
Starting kernel event loops.

How about if you set c.Session.debug = True in your jupyter_notebook_config.py file (should be in ~/.jupyter/) ? You might need to do jupyter notebook --generate-config first. See: jupyter - How to enable and access debug logging for notebook and IPython kernel - Stack Overflow

Also, if you open a plain Julia console and do:

using IJulia
using AstroTime

does that also crash?

1 Like

Thank you for your help.

               _
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  (_)     | (_) (_)    |  Documentation: https://docs.julialang.org
   _ _   _| |_  __ _   |  Type "?help" for help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 0.6.3 (2018-05-28 20:20 UTC)
 _/ |\__'_|_|_|\__'_|  |  Official http://julialang.org/ release
|__/                   |  x86_64-pc-linux-gnu

julia> using IJulia

julia> using AstroTime

signal (11): Segmentation fault
while loading no file, in expression starting on line 0
unknown function (ip: 0x7f21892d019f)
emit_invoke at /buildworker/worker/package_linux64/build/src/codegen.cpp:3400 [inlined]
emit_expr at /buildworker/worker/package_linux64/build/src/codegen.cpp:4135
emit_assignment at /buildworker/worker/package_linux64/build/src/codegen.cpp:3759 [inlined]
emit_expr at /buildworker/worker/package_linux64/build/src/codegen.cpp:4159
emit_stmtpos at /buildworker/worker/package_linux64/build/src/codegen.cpp:4064 [inlined]
emit_function at /buildworker/worker/package_linux64/build/src/codegen.cpp:6248
jl_compile_linfo at /buildworker/worker/package_linux64/build/src/codegen.cpp:1256
jl_compile_for_dispatch at /buildworker/worker/package_linux64/build/src/gf.c:1668
jl_compile_method_internal at /buildworker/worker/package_linux64/build/src/julia_internal.h:307 [inlined]
jl_call_method_internal at /buildworker/worker/package_linux64/build/src/julia_internal.h:354 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:1926
jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1424 [inlined]
jl_module_run_initializer at /buildworker/worker/package_linux64/build/src/toplevel.c:87
jl_init_restored_modules at /buildworker/worker/package_linux64/build/src/dump.c:2443 [inlined]
_jl_restore_incremental at /buildworker/worker/package_linux64/build/src/dump.c:3318
jl_restore_incremental at /buildworker/worker/package_linux64/build/src/dump.c:3338
_include_from_serialized at ./loading.jl:157
_require_from_serialized at ./loading.jl:200
unknown function (ip: 0x7f216b148ba8)
jl_call_fptr_internal at /buildworker/worker/package_linux64/build/src/julia_internal.h:339 [inlined]
jl_call_method_internal at /buildworker/worker/package_linux64/build/src/julia_internal.h:358 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:1926
_require_search_from_serialized at ./loading.jl:236
unknown function (ip: 0x7f216b14a938)
jl_call_fptr_internal at /buildworker/worker/package_linux64/build/src/julia_internal.h:339 [inlined]
jl_call_method_internal at /buildworker/worker/package_linux64/build/src/julia_internal.h:358 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:1926
_require at ./loading.jl:441
require at ./loading.jl:405
unknown function (ip: 0x7f216b143de2)
jl_call_fptr_internal at /buildworker/worker/package_linux64/build/src/julia_internal.h:339 [inlined]
jl_call_method_internal at /buildworker/worker/package_linux64/build/src/julia_internal.h:358 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:1926
jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1424 [inlined]
eval_import_path_ at /buildworker/worker/package_linux64/build/src/toplevel.c:403
eval_import_path at /buildworker/worker/package_linux64/build/src/toplevel.c:430 [inlined]
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:495
jl_toplevel_eval_in at /buildworker/worker/package_linux64/build/src/builtins.c:496
eval at ./boot.jl:235
unknown function (ip: 0x7f217fa8385f)
jl_call_fptr_internal at /buildworker/worker/package_linux64/build/src/julia_internal.h:339 [inlined]
jl_call_method_internal at /buildworker/worker/package_linux64/build/src/julia_internal.h:358 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:1926
eval_user_input at ./REPL.jl:66
unknown function (ip: 0x7f217fb049cf)
jl_call_fptr_internal at /buildworker/worker/package_linux64/build/src/julia_internal.h:339 [inlined]
jl_call_method_internal at /buildworker/worker/package_linux64/build/src/julia_internal.h:358 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:1926
macro expansion at ./REPL.jl:97 [inlined]
#1 at ./event.jl:73
unknown function (ip: 0x7f216b1372af)
jl_call_fptr_internal at /buildworker/worker/package_linux64/build/src/julia_internal.h:339 [inlined]
jl_call_method_internal at /buildworker/worker/package_linux64/build/src/julia_internal.h:358 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:1926
jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1424 [inlined]
start_task at /buildworker/worker/package_linux64/build/src/task.c:267
unknown function (ip: 0xffffffffffffffff)
Allocations: 11798252 (Pool: 11796158; Big: 2094); GC: 23
Segmentation fault

And this is the GDB backtrace:

$ gdb -p 6668
GNU gdb (GDB) Red Hat Enterprise Linux 7.6.1-110.el7
Copyright (C) 2013 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 "x86_64-redhat-linux-gnu".
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>.
Attaching to process 6668
Reading symbols from /local/scratch/bgodard/sw/julia-0.6.3-linux-x86_64/bin/julia...done.
Reading symbols from /local/scratch/bgodard/sw/julia-0.6.3-linux-x86_64/bin/../lib/libjulia.so.0.6...done.
Loaded symbols for /local/scratch/bgodard/sw/julia-0.6.3-linux-x86_64/bin/../lib/libjulia.so.0.6
Reading symbols from /lib64/libdl.so.2...(no debugging symbols found)...done.
Loaded symbols for /lib64/libdl.so.2
Reading symbols from /lib64/librt.so.1...(no debugging symbols found)...done.
Loaded symbols for /lib64/librt.so.1
Reading symbols from /lib64/libpthread.so.0...(no debugging symbols found)...done.
[New LWP 6673]
[New LWP 6672]
[New LWP 6671]
[New LWP 6669]
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib64/libthread_db.so.1".
Loaded symbols for /lib64/libpthread.so.0
Reading symbols from /lib64/libc.so.6...(no debugging symbols found)...done.
Loaded symbols for /lib64/libc.so.6
Reading symbols from /local/scratch/bgodard/sw/julia-0.6.3-linux-x86_64/bin/../lib/julia/libLLVM-3.9.so...(no debugging symbols found)...done.
Loaded symbols for /local/scratch/bgodard/sw/julia-0.6.3-linux-x86_64/bin/../lib/julia/libLLVM-3.9.so
Reading symbols from /local/scratch/bgodard/sw/julia-0.6.3-linux-x86_64/bin/../lib/julia/libstdc++.so.6...done.
Loaded symbols for /local/scratch/bgodard/sw/julia-0.6.3-linux-x86_64/bin/../lib/julia/libstdc++.so.6
Reading symbols from /lib64/libm.so.6...(no debugging symbols found)...done.
Loaded symbols for /lib64/libm.so.6
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Loaded symbols for /local/scratch/bgodard/sw/julia-0.6.3-linux-x86_64/bin/../lib/julia/libgcc_s.so.1
Reading symbols from /lib64/ld-linux-x86-64.so.2...(no debugging symbols found)...done.
Loaded symbols for /lib64/ld-linux-x86-64.so.2
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Loaded symbols for /local/scratch/bgodard/sw/julia-0.6.3-linux-x86_64/lib/julia/sys.so
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Reading symbols from /local/scratch/bgodard/sw/julia-0.6.3-linux-x86_64/bin/../lib/julia/libccolamd.so...(no debugging symbols found)...done.
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Reading symbols from /local/scratch/bgodard/sw/julia-0.6.3-linux-x86_64/bin/../lib/julia/libsuitesparseconfig.so...(no debugging symbols found)...done.
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Reading symbols from /local/scratch/bgodard/sw/julia-0.6.3-linux-x86_64/bin/../lib/julia/libsuitesparse_wrapper.so...(no debugging symbols found)...done.
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Reading symbols from /local/scratch/bgodard/sw/julia-0.6.3-linux-x86_64/bin/../lib/julia/libumfpack.so...(no debugging symbols found)...done.
Loaded symbols for /local/scratch/bgodard/sw/julia-0.6.3-linux-x86_64/bin/../lib/julia/libumfpack.so
Reading symbols from /local/scratch/bgodard/sw/julia-0.6.3-linux-x86_64/bin/../lib/julia/libspqr.so...(no debugging symbols found)...done.
Loaded symbols for /local/scratch/bgodard/sw/julia-0.6.3-linux-x86_64/bin/../lib/julia/libspqr.so
0x00007f1c8b12fe59 in syscall () from /lib64/libc.so.6
Missing separate debuginfos, use: debuginfo-install glibc-2.17-222.el7.x86_64
(gdb) continue
Continuing.

Program received signal SIGSEGV, Segmentation fault.
0x00007f1c896991a0 in llvm::Value::getName() const () from /local/scratch/bgodard/sw/julia-0.6.3-linux-x86_64/bin/../lib/julia/libLLVM-3.9.so
(gdb) bt
#0  0x00007f1c896991a0 in llvm::Value::getName() const () from /local/scratch/bgodard/sw/julia-0.6.3-linux-x86_64/bin/../lib/julia/libLLVM-3.9.so
#1  0x00007f1c8bb0599e in jl_compile_linfo (pli=pli@entry=0x7ffd4108b6a8, src=<optimized out>, src@entry=0x0, world=21867, params=0x7f1c8bdfd700 <jl_default_cgparams>)
    at /buildworker/worker/package_linux64/build/src/codegen.cpp:1292
#2  0x00007f1c8baf7217 in emit_invoke (ctx=0x7ffd4108be50, ex=0x7f1c6389a5b0) at /buildworker/worker/package_linux64/build/src/codegen.cpp:3400
#3  emit_expr (expr=expr@entry=0x7f1c6389a5b0, ctx=ctx@entry=0x7ffd4108be50) at /buildworker/worker/package_linux64/build/src/codegen.cpp:4135
#4  0x00007f1c8baf7e12 in emit_assignment (ctx=0x7ffd4108be50, r=0x7f1c6389a5b0, l=<optimized out>) at /buildworker/worker/package_linux64/build/src/codegen.cpp:3759
#5  emit_expr (expr=expr@entry=0x7f1c6389a590, ctx=ctx@entry=0x7ffd4108be50) at /buildworker/worker/package_linux64/build/src/codegen.cpp:4159
#6  0x00007f1c8bb022c3 in emit_stmtpos (ctx=0x7ffd4108be50, expr=0x7f1c6389a590) at /buildworker/worker/package_linux64/build/src/codegen.cpp:4064
#7  emit_function (lam=lam@entry=0x7f1c67211e90, src=<optimized out>, world=world@entry=21867, declarations=<optimized out>, params=params@entry=0x7f1c8bdfd700 <jl_default_cgparams>)
    at /buildworker/worker/package_linux64/build/src/codegen.cpp:6248
#8  0x00007f1c8bb05658 in jl_compile_linfo (pli=pli@entry=0x7ffd4108c4d8, src=<optimized out>, world=world@entry=21867, params=0x7f1c8bdfd700 <jl_default_cgparams>)
    at /buildworker/worker/package_linux64/build/src/codegen.cpp:1256
#9  0x00007f1c8ba6a52d in jl_compile_for_dispatch (pli=pli@entry=0x7ffd4108c550, world=world@entry=21867) at /buildworker/worker/package_linux64/build/src/gf.c:1668
#10 0x00007f1c8ba6c190 in jl_compile_method_internal (meth=<optimized out>, fptr=<synthetic pointer>) at /buildworker/worker/package_linux64/build/src/julia_internal.h:307
#11 jl_call_method_internal (nargs=1, args=0x7ffd4108c5c8, meth=<optimized out>) at /buildworker/worker/package_linux64/build/src/julia_internal.h:354
#12 jl_apply_generic (args=args@entry=0x7ffd4108c5c8, nargs=nargs@entry=1) at /buildworker/worker/package_linux64/build/src/gf.c:1926
#13 0x00007f1c8ba963a5 in jl_apply (nargs=1, args=0x7ffd4108c5c8) at /buildworker/worker/package_linux64/build/src/julia.h:1424
#14 jl_module_run_initializer (m=m@entry=0x7f1c67d21d50) at /buildworker/worker/package_linux64/build/src/toplevel.c:87
#15 0x00007f1c8ba910fb in jl_init_restored_modules (init_order=0x7f1c64a68d90) at /buildworker/worker/package_linux64/build/src/dump.c:2443
#16 _jl_restore_incremental (f=f@entry=0x7ffd4108c920) at /buildworker/worker/package_linux64/build/src/dump.c:3318
#17 0x00007f1c8ba9326d in jl_restore_incremental (fname=0x7f1c676fe3b8 "/home/bgodard/.julia/lib/v0.6/AstroTime.ji") at /buildworker/worker/package_linux64/build/src/dump.c:3338
#18 0x00007f1c7ff6f61d in julia__include_from_serialized_23375 () at loading.jl:157
#19 0x00007f1c6b50adf2 in julia__require_from_serialized_62650 () at loading.jl:200
#20 0x00007f1c6b50b9e9 in jlcall__require_from_serialized_62649 ()
#21 0x00007f1c8ba6bd9a in jl_call_fptr_internal (fptr=<optimized out>, fptr=<optimized out>, nargs=<optimized out>, args=<optimized out>, meth=<optimized out>)
    at /buildworker/worker/package_linux64/build/src/julia_internal.h:339
#22 jl_call_method_internal (nargs=5, args=0x7ffd4108cf10, meth=<optimized out>) at /buildworker/worker/package_linux64/build/src/julia_internal.h:358
#23 jl_apply_generic (args=0x7ffd4108cf10, nargs=5) at /buildworker/worker/package_linux64/build/src/gf.c:1926
#24 0x00007f1c6b50d34b in julia__require_search_from_serialized_62653 () at loading.jl:236
#25 0x00007f1c6b50d779 in jlcall__require_search_from_serialized_62652 ()
#26 0x00007f1c8ba6bd9a in jl_call_fptr_internal (fptr=<optimized out>, fptr=<optimized out>, nargs=<optimized out>, args=<optimized out>, meth=<optimized out>)
    at /buildworker/worker/package_linux64/build/src/julia_internal.h:339
#27 jl_call_method_internal (nargs=5, args=0x7ffd4108d510, meth=<optimized out>) at /buildworker/worker/package_linux64/build/src/julia_internal.h:358
#28 jl_apply_generic (args=0x7ffd4108d510, nargs=5) at /buildworker/worker/package_linux64/build/src/gf.c:1926
#29 0x00007f1c6b50bed2 in julia__require_62632 () at loading.jl:441
#30 0x00007f1c6b506b49 in julia_require_62631 () at loading.jl:405
#31 0x00007f1c6b506c33 in jlcall_require_62630 ()
#32 0x00007f1c8ba6bd9a in jl_call_fptr_internal (fptr=<optimized out>, fptr=<optimized out>, nargs=<optimized out>, args=<optimized out>, meth=<optimized out>)
    at /buildworker/worker/package_linux64/build/src/julia_internal.h:339
#33 jl_call_method_internal (nargs=2, args=0x7ffd4108d770, meth=<optimized out>) at /buildworker/worker/package_linux64/build/src/julia_internal.h:358
#34 jl_apply_generic (args=args@entry=0x7ffd4108d770, nargs=nargs@entry=2) at /buildworker/worker/package_linux64/build/src/gf.c:1926
#35 0x00007f1c8ba95c03 in jl_apply (nargs=2, args=0x7ffd4108d770) at /buildworker/worker/package_linux64/build/src/julia.h:1424
#36 eval_import_path_ (args=0x7f1c69563f10, retrying=retrying@entry=0) at /buildworker/worker/package_linux64/build/src/toplevel.c:403
#37 0x00007f1c8ba969ab in eval_import_path (args=<optimized out>) at /buildworker/worker/package_linux64/build/src/toplevel.c:430
#38 jl_toplevel_eval_flex (e=e@entry=0x7f1c6956d910, expanded=expanded@entry=0, fast=1) at /buildworker/worker/package_linux64/build/src/toplevel.c:495
#39 0x00007f1c8ba966d4 in jl_toplevel_eval (v=v@entry=0x7f1c6956d910) at /buildworker/worker/package_linux64/build/src/toplevel.c:600
#40 0x00007f1c8ba79f18 in jl_toplevel_eval_in (m=0x7f1c7b404010, ex=0x7f1c6956d910) at /buildworker/worker/package_linux64/build/src/builtins.c:496
#41 0x00007f1c7fe4c84a in julia_eval_18218 () at boot.jl:235
#42 0x00007f1c7fe4c860 in jlcall_eval_18217 () from /local/scratch/bgodard/sw/julia-0.6.3-linux-x86_64/lib/julia/sys.so
#43 0x00007f1c8ba6bd9a in jl_call_fptr_internal (fptr=<optimized out>, fptr=<optimized out>, nargs=<optimized out>, args=<optimized out>, meth=<optimized out>)
    at /buildworker/worker/package_linux64/build/src/julia_internal.h:339
#44 jl_call_method_internal (nargs=3, args=0x7ffd4108dc48, meth=<optimized out>) at /buildworker/worker/package_linux64/build/src/julia_internal.h:358
#45 jl_apply_generic (args=0x7ffd4108dc48, nargs=3) at /buildworker/worker/package_linux64/build/src/gf.c:1926
---Type <return> to continue, or q <return> to quit---
#46 0x00007f1c7fecd7b3 in julia_eval_user_input_20534 () at REPL.jl:66
#47 0x00007f1c7fecd9d0 in jlcall_eval_user_input_20533 () from /local/scratch/bgodard/sw/julia-0.6.3-linux-x86_64/lib/julia/sys.so
#48 0x00007f1c8ba6bd9a in jl_call_fptr_internal (fptr=<optimized out>, fptr=<optimized out>, nargs=<optimized out>, args=<optimized out>, meth=<optimized out>)
    at /buildworker/worker/package_linux64/build/src/julia_internal.h:339
#49 jl_call_method_internal (nargs=3, args=0x7ffd4108dde8, meth=<optimized out>) at /buildworker/worker/package_linux64/build/src/julia_internal.h:358
#50 jl_apply_generic (args=0x7ffd4108dde8, nargs=3) at /buildworker/worker/package_linux64/build/src/gf.c:1926
#51 0x00007f1c6b500036 in ?? ()
#52 0x00007ffd4108dd90 in ?? ()
#53 0x0000000000000042 in ?? ()
#54 0x0000000000000000 in ?? ()
(gdb) 

Using the debug option in Jupyter, I cannot see any relevant information in the console.

I can reproduce the problem on v0.6.4 on macOS but not on v0.7.0-rc2 with the epoch2 branch of AstroTime. Since the release of 0.7/1.0 is imminent and I intend to finish [WIP] Rewrite the whole thing based on a high-accuracy epoch type by helgee · Pull Request #43 · JuliaAstro/AstroTime.jl · GitHub soon we should not invest too much energy in this.