Segmentation fault after update in Juno

I have upgraded julia-client package in Atom. There was a prompt to upgrade Atom package in Juno (using Pkg.update). And afterwards Atom Repl gives segmentation fault when doing using Plots and pressing any button. The similar errors appear after writing using with some other modules (e.g. user-defined module that needed pre-compilation).

On the other hand plotting in terminal works fine.

I wouldn’t like to delete my .julia file (I had to do it a month ago). Does anybody know how to proceed?

My Julia is 1.0.5

The error is as follows:

signal (11): Segmentation fault
in expression starting at no file:0
jl_compile_linfo at /buildworker/worker/package_linux64/build/src/codegen.cpp:1191
emit_invoke at /buildworker/worker/package_linux64/build/src/codegen.cpp:3094
emit_expr at /buildworker/worker/package_linux64/build/src/codegen.cpp:3893
emit_ssaval_assign at /buildworker/worker/package_linux64/build/src/codegen.cpp:3615
emit_stmtpos at /buildworker/worker/package_linux64/build/src/codegen.cpp:3801 [inlined]
emit_function at /buildworker/worker/package_linux64/build/src/codegen.cpp:6262
jl_compile_linfo at /buildworker/worker/package_linux64/build/src/codegen.cpp:1159
emit_invoke at /buildworker/worker/package_linux64/build/src/codegen.cpp:3094
emit_expr at /buildworker/worker/package_linux64/build/src/codegen.cpp:3893
emit_ssaval_assign at /buildworker/worker/package_linux64/build/src/codegen.cpp:3615
emit_stmtpos at /buildworker/worker/package_linux64/build/src/codegen.cpp:3801 [inlined]
emit_function at /buildworker/worker/package_linux64/build/src/codegen.cpp:6262
jl_compile_linfo at /buildworker/worker/package_linux64/build/src/codegen.cpp:1159
emit_invoke at /buildworker/worker/package_linux64/build/src/codegen.cpp:3094
emit_expr at /buildworker/worker/package_linux64/build/src/codegen.cpp:3893
emit_ssaval_assign at /buildworker/worker/package_linux64/build/src/codegen.cpp:3615
emit_stmtpos at /buildworker/worker/package_linux64/build/src/codegen.cpp:3801 [inlined]
emit_function at /buildworker/worker/package_linux64/build/src/codegen.cpp:6262
jl_compile_linfo at /buildworker/worker/package_linux64/build/src/codegen.cpp:1159
emit_invoke at /buildworker/worker/package_linux64/build/src/codegen.cpp:3094
emit_expr at /buildworker/worker/package_linux64/build/src/codegen.cpp:3893
emit_ssaval_assign at /buildworker/worker/package_linux64/build/src/codegen.cpp:3615
emit_stmtpos at /buildworker/worker/package_linux64/build/src/codegen.cpp:3801 [inlined]
emit_function at /buildworker/worker/package_linux64/build/src/codegen.cpp:6262
jl_compile_linfo at /buildworker/worker/package_linux64/build/src/codegen.cpp:1159
emit_invoke at /buildworker/worker/package_linux64/build/src/codegen.cpp:3094
emit_expr at /buildworker/worker/package_linux64/build/src/codegen.cpp:3893
emit_ssaval_assign at /buildworker/worker/package_linux64/build/src/codegen.cpp:3615
emit_stmtpos at /buildworker/worker/package_linux64/build/src/codegen.cpp:3801 [inlined]
emit_function at /buildworker/worker/package_linux64/build/src/codegen.cpp:6262
jl_compile_linfo at /buildworker/worker/package_linux64/build/src/codegen.cpp:1159
jl_fptr_trampoline at /buildworker/worker/package_linux64/build/src/gf.c:1774
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2162
wsitem at /home/pgorski/.julia/packages/Atom/XKD0f/src/workspace.jl:22
wsitem at /home/pgorski/.julia/packages/Atom/XKD0f/src/workspace.jl:19
jl_fptr_trampoline at /buildworker/worker/package_linux64/build/src/gf.c:1809
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2162
#235 at /home/pgorski/.julia/packages/Atom/XKD0f/src/workspace.jl:12
_collect at ./generator.jl:47
map at ./array.jl:561 [inlined]
workspace at /home/pgorski/.julia/packages/Atom/XKD0f/src/workspace.jl:12
#232 at /home/pgorski/.julia/packages/Atom/XKD0f/src/workspace.jl:2
jl_fptr_trampoline at /buildworker/worker/package_linux64/build/src/gf.c:1809
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2162
handlemsg at /home/pgorski/.julia/packages/Atom/XKD0f/src/comm.jl:166
unknown function (ip: 0x7f11b0e6b7bc)
jl_fptr_trampoline at /buildworker/worker/package_linux64/build/src/gf.c:1809
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2162
jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1537 [inlined]
jl_f__apply at /buildworker/worker/package_linux64/build/src/builtins.c:556
#19 at ./task.jl:259
unknown function (ip: 0x7f11b0e696f4)
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2162
jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1537 [inlined]
start_task at /buildworker/worker/package_linux64/build/src/task.c:268
unknown function (ip: 0xffffffffffffffff)
Allocations: 58951844 (Pool: 58938262; Big: 13582); GC: 126
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What version of Atom.jl do you have installed?

0.12.6

I have also noticed (while running using) in terminal following message:

Expr(:block, #= Symbol("/home/pgorski/.julia/packages/Plots/12uaJ/src/backends.jl"):360 =#, Expr(:import, Expr(:., :ORCA)))
** incremental compilation may be broken for this module **

I can repro the issue on Julia 1.0.x, but not on Julia 1.3. Can you upgrade the version of Julia you use?

Well, in general yes.
But
I had 1.0.3 and I had many problems with Plots, so I upgraded to 1.0.5 (which is LTS) so as I will not have to upgrade for a long time. And after my upgrade to 1.0.5 I still had to remove folder .julia and reinstall everything. So I would like to try other solution if it exists.

Fair enough. Do you remember which version of Atom.jl you had before you had those segfaults?

I don’t know whether I can find it anywhere. I checked I upgraded Julia to 1.0.5 on Feb 3. Looking at the releases dates of Atom.jl it should be 0.11.3 by then.

I upgraded Atom to 0.12.7, but still the same error.

Yeah, I can see the segfaults on Julia 1.0.x, but not with newer Julia versions. I’d recommend upgrading until we can figure out what’s going wrong.

OK, thank you.

If it helps: I observe the same error with Julia 1.1.0 and Atom 0.12.7

Hi @pfitzseb @pjgorski and maybe @mike_k :slight_smile:

Ok so specifically re: Issue: signal (11): Segmentation fault in expression starting at no file:0 at /buildworker/worker/package_linux64/build/src/codegen.cpp :1191
when using julia> versioninfo() >> When using Atom IDE w Juno w Julia Version 1.0.5 ** w OS: Linux (x86_64-pc-linux-gnu)

It was my goof because I moved my Julia code and Atom IDE to my new AMD Threadripper Machine and I needed to install various additional Ubuntu libraries ;

IOW Summarizing below

signal (11): Segmentation fault - yada yada - codegen.cpp means that one’s cmake is missing

ergo Solution was :

sudo apt-get install cmake

- or-

use Synaptic to search for and install cmake

More generally (Julia developers) you may want to read over this

https://github.com/JuliaLang/julia/blob/master/doc/build/ build.md#required-build-tools-and-external-libraries

-AND This-

From (OLD) file: JuliaProQuickStartGuideLinux.pdf

Required Julia libraries

Section : 2.1.3 Prerequisites for Installation on Ubuntu 16.04

When installing JuliaPro on Ubuntu 16.04, a particular set of system libraries

need to be installed by a user with appropriate Administrator or sudo privileges.

On Debian-based distributions (e.g. Ubuntu ), you can easily install them with apt-get :

sudo apt-get install build-essential libatomic1 python gfortran perl wget m4 cmake pkg-config 

-OR THIS-

Likely the fastest easier way to go is here >> https://juliacomputing.com/products/juliapro.html and download and Install per >>

Quick-start Guide

Current stable release ( v1.4.1-1 )

Operating system

windows

mac**

linux

linux (GPG)

AND Release with long-term support ( v1.0.5-2 )

As usual “Your mileage may differ” :slightly_smiling_face: , but
I HTH
-Marc

1 Like