My distro (Antergos; x86_64 Linux 4.12.13-1-ARCH) recently updated to LLVM 5 and my julia installation (https://aur.archlinux.org/packages/julia-mkl/) stopped working since it was searching for LLVM 4 libs. I removed the package and installed the julia version from the arch repo (Arch Linux - julia 2:1.7.3-3 (x86_64)).
After this switch I encountered a strange segfault which I could not reproduce on another system. I tried recompiling all the packages and the system image, but it didn’t help.
The error looks like this:
signal (11): Segmentation fault
while loading /run/media/user/Windows/Users/sebastian/Documents/Physics/Projects/Nuclear_surface_vibrations/classical/src/plot_poincare.jl, in expression starting on line 86
unknown function (ip: 0x7f55a08de761)
unknown function (ip: 0x7f55a08e05d4)
_ZN4llvm12RegAllocBase16postOptimizationEv at /usr/bin/../lib/libLLVM-3.9.so (unknown line)
unknown function (ip: 0x7f55a0a2f1d7)
_ZN4llvm19MachineFunctionPass13runOnFunctionERNS_8FunctionE at /usr/bin/../lib/libLLVM-3.9.so (unknown line)
_ZN4llvm13FPPassManager13runOnFunctionERNS_8FunctionE at /usr/bin/../lib/libLLVM-3.9.so (unknown line)
_ZN4llvm13FPPassManager11runOnModuleERNS_6ModuleE at /usr/bin/../lib/libLLVM-3.9.so (unknown line)
_ZN4llvm6legacy15PassManagerImpl3runERNS_6ModuleE at /usr/bin/../lib/libLLVM-3.9.so (unknown line)
unknown function (ip: 0x7f55a3b5799d)
unknown function (ip: 0x7f55a3b5d34f)
unknown function (ip: 0x7f55a3b5de27)
unknown function (ip: 0x7f55a3b109b1)
unknown function (ip: 0x7f55a3b4dc07)
jl_apply_generic at /usr/bin/../lib/libjulia.so.0.6 (unknown line)
#nlsolve at ./<missing>:0
#call#17 at /home/user/.julia/v0.6/DiffEqCallbacks/src/manifold.jl:40
unknown function (ip: 0x7f5565c7a21d)
jl_apply_generic at /usr/bin/../lib/libjulia.so.0.6 (unknown line)
ManifoldProjection at /home/user/.julia/v0.6/DiffEqCallbacks/src/manifold.jl:87
apply_discrete_callback! at /home/user/.julia/v0.6/OrdinaryDiffEq/src/callbacks.jl:183 [inlined]
handle_callbacks! at /home/user/.julia/v0.6/OrdinaryDiffEq/src/integrators/integrator_utils.jl:308
loopfooter! at /home/user/.julia/v0.6/OrdinaryDiffEq/src/integrators/integrator_utils.jl:271
solve! at /home/user/.julia/v0.6/OrdinaryDiffEq/src/solve.jl:323
unknown function (ip: 0x7f5565c65002)
jl_apply_generic at /usr/bin/../lib/libjulia.so.0.6 (unknown line)
#solve#1832 at /home/user/.julia/v0.6/OrdinaryDiffEq/src/solve.jl:7
unknown function (ip: 0x7f558b2b9166)
jl_apply_generic at /usr/bin/../lib/libjulia.so.0.6 (unknown line)
jl_invoke at /usr/bin/../lib/libjulia.so.0.6 (unknown line)
#solve at ./<missing>:0
#poincareSection!#1 at /run/media/user/Windows/Users/sebastian/Documents/Physics/Projects/Nuclear_surface_vibrations/classical/src/poincare.jl:21
unknown function (ip: 0x7f558b2b7b73)
jl_apply_generic at /usr/bin/../lib/libjulia.so.0.6 (unknown line)
#poincareSection! at ./<missing>:0
unknown function (ip: 0x7f558b2b680c)
jl_apply_generic at /usr/bin/../lib/libjulia.so.0.6 (unknown line)
#createMap#7 at /run/media/user/Windows/Users/sebastian/Documents/Physics/Projects/Nuclear_surface_vibrations/classical/src/poincare.jl:96
unknown function (ip: 0x7f558b276ea9)
jl_apply_generic at /usr/bin/../lib/libjulia.so.0.6 (unknown line)
createMap at /run/media/user/Windows/Users/sebastian/Documents/Physics/Projects/Nuclear_surface_vibrations/classical/src/poincare.jl:85
unknown function (ip: 0x7f558b2768d3)
jl_apply_generic at /usr/bin/../lib/libjulia.so.0.6 (unknown line)
unknown function (ip: 0x7f55a3ac051f)
unknown function (ip: 0x7f55a3abf64e)
unknown function (ip: 0x7f55a3ac0453)
unknown function (ip: 0x7f55a3ad8585)
unknown function (ip: 0x7f55a3ab4ec6)
jl_load at /usr/bin/../lib/libjulia.so.0.6 (unknown line)
include_from_node1 at ./loading.jl:569
unknown function (ip: 0x7f559c3c87fb)
jl_apply_generic at /usr/bin/../lib/libjulia.so.0.6 (unknown line)
include at ./sysimg.jl:14
unknown function (ip: 0x7f559c26c38b)
jl_apply_generic at /usr/bin/../lib/libjulia.so.0.6 (unknown line)
process_options at ./client.jl:305
_start at ./client.jl:371
unknown function (ip: 0x7f559c3d4318)
jl_apply_generic at /usr/bin/../lib/libjulia.so.0.6 (unknown line)
unknown function (ip: 0x558ed4e5dc4b)
unknown function (ip: 0x558ed4e5d652)
__libc_start_main at /usr/bin/../lib/libc.so.6 (unknown line)
unknown function (ip: 0x558ed4e5d709)
Allocations: 46266621 (Pool: 46254919; Big: 11702); GC: 91
[1] 23041 segmentation fault (core dumped) julia plot_poincare.jl
Here is a gist with 3 files
- segfault.ipynb is with the output from my machine, and the kernel crashes
- segfault.txt is with what happens if I download the above as .jl and run it
- segfault_remote.ipynb is with the output from a remote server where everything is working as expected
https://gist.github.com/SebastianM-C/16343e6869b303b609e51bef090f208b
Would reinstalling julia (again) help? If so how should I properly do this?