Segmentation fault in tests on 32-bit architectures (i686 and arm)

[ViralBShah]

I just tried running the Sundials tests on Raspberry Pi and they failed with 1.3. Just reporting here for the record.

signal (11): Segmentation fault
in expression starting at /home/pi/.julia/packages/Sundials/MllUG/test/cvode_Roberts_dns.jl:66
_ZL22isExtendedBUILD_VECTORPN4llvm6SDNodeERNS_12SelectionDAGEb at /home/pi/julia-1.3.0/bin/../lib/julia/libLLVM-6.0.so (unknown line)
Allocations: 9997384 (Pool: 9996517; Big: 867); GC: 21
ERROR: Package Sundials errored during testing

julia> versioninfo()
Julia Version 1.3.0
Commit 46ce4d7933 (2019-11-26 06:09 UTC)
Platform Info:
  OS: Linux (arm-linux-gnueabihf)
  CPU: ARMv7 Processor rev 4 (v7l)
  WORD_SIZE: 32
  LIBM: libopenlibm
  LLVM: libLLVM-6.0.1 (ORCJIT, cortex-a53)

[ChrisRackauckas]

For reference, the Sundials build is: https://github.com/JuliaDiffEq/SundialsBuilder/releases/tag/sundials-3.1.1.6 . I assume that segfault means we need to fix that binary builder repo build script.

[ViralBShah]

Is there a minimal example I can try? It could even be Julia itself crashing.

[ChrisRackauckas]

using Sundials
function lorenz(du,u,p,t)
 du[1] = 10.0(u[2]-u[1])
 du[2] = u[1]*(28.0-u[3]) - u[2]
 du[3] = u[1]*u[2] - (8/3)*u[3]
end
u0 = [1.0;0.0;0.0]
tspan = (0.0,100.0)
prob = ODEProblem(lorenz,u0,tspan)
sol = solve(prob,CVODE_Adams())
using Plots; plot(sol,vars=(1,2,3))

is what I'd try.

[ViralBShah]

That example works fine. It's crashing here (which I can verify manually and is what the failing test above showed as well):

https://github.com/JuliaDiffEq/Sundials.jl/blob/90ec5466df22a61129c3d84665bb113cf6aafd81/test/cvode_Roberts_dns.jl#L66

[ViralBShah]

For reference, the Sundials build is: https://github.com/JuliaDiffEq/SundialsBuilder/releases/tag/sundials-3.1.1.6 . I assume that segfault means we need to fix that binary builder repo build script.

Isn't it the Yggdrasil one? https://github.com/JuliaPackaging/Yggdrasil/tree/master/S/Sundials

[ViralBShah]

Off topic, but we should just build KLU as part of the regular SuiteSparse build, and simplify the Sundials build.

[ChrisRackauckas]

This Sundials build was the first BinaryBuilder setup, and it hasn't really been modified since. So anything like Yggdrasil isn't apart of this unless that happened outside of these repos.

No BLAS here, that's an open issue. And getting KLU out of this build would indeed be nice.

[ViralBShah]

I feel like we should get the build upgraded first. KLU would be next. But not sure if any of this would help fix the crash unless it is happening due to some bad combination of things being done in the old way and it is only triggered on arm.

[ChrisRackauckas]

We might as well update to Sundials 5.0 at the same time too. It's an easy enough API change. It mostly just needs someone who wants to make the binaries build

[ViralBShah]

@ChrisRackauckas Should I try this again now? Will it pull Sundials 5 and the new changes? I don't have any use for this myself, but just figured I can close htis out if if it works.

[ChrisRackauckas]

Yes, it should just test it on Sundials 5.

[ViralBShah]

Looks like an error in the same place. Using Julia 1.4 and Sundials 5 through artifacts.

signal (11): Segmentation fault
in expression starting at /home/viral/.julia/packages/Sundials/0yJ3G/test/cvode_Roberts_simplified.jl:14
SUNMatGetID at /home/viral/.julia/artifacts/ee6fe6e3b73ab790eab0ab0d686f5df2933d0498/lib/libsundials_sunmatrixdense.so.3 (unknown line)
Allocations: 19394760 (Pool: 19392171; Big: 2589); GC: 42
ERROR: Package Sundials errored during testing

Stacktrace:
 [1] pkgerror(::String, ::Vararg{String,N} where N) at /buildworker/worker/package_linuxarmv7l/build/usr/share/julia/stdlib/v1.4/Pkg/src/Types.jl:53
 [2] test(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing) at /buildworker/worker/package_linuxarmv7l/build/usr/share/julia/stdlib/v1.4/Pkg/src/Operations.jl:1503
 [3] test(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, kwargs::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}) at /buildworker/worker/package_linuxarmv7l/build/usr/share/julia/stdlib/v1.4/Pkg/src/API.jl:316
 [4] test(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /buildworker/worker/package_linuxarmv7l/build/usr/share/julia/stdlib/v1.4/Pkg/src/API.jl:303
 [5] #test#68 at /buildworker/worker/package_linuxarmv7l/build/usr/share/julia/stdlib/v1.4/Pkg/src/API.jl:297 [inlined]
 [6] test at /buildworker/worker/package_linuxarmv7l/build/usr/share/julia/stdlib/v1.4/Pkg/src/API.jl:297 [inlined]
 [7] #test#67 at /buildworker/worker/package_linuxarmv7l/build/usr/share/julia/stdlib/v1.4/Pkg/src/API.jl:296 [inlined]
 [8] test at /buildworker/worker/package_linuxarmv7l/build/usr/share/julia/stdlib/v1.4/Pkg/src/API.jl:296 [inlined]
 [9] test(::String; kwargs::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}) at /buildworker/worker/package_linuxarmv7l/build/usr/share/julia/stdlib/v1.4/Pkg/src/API.jl:295
 [10] test(::String) at /buildworker/worker/package_linuxarmv7l/build/usr/share/julia/stdlib/v1.4/Pkg/src/API.jl:295
 [11] top-level scope at REPL[2]:1

[ViralBShah]

using Sundials
function lorenz(du,u,p,t)
 du[1] = 10.0(u[2]-u[1])
 du[2] = u[1]*(28.0-u[3]) - u[2]
 du[3] = u[1]*u[2] - (8/3)*u[3]
end
u0 = [1.0;0.0;0.0]
tspan = (0.0,100.0)
prob = ODEProblem(lorenz,u0,tspan)
sol = solve(prob,CVODE_Adams())
using Plots; plot(sol,vars=(1,2,3))

is what I'd try.

This fails now.

julia> sol = solve(prob,CVODE_Adams())

[CVODES WARNING]  CVode
  Internal t = 0 and h = 0 are such that t + h = t on the next step. The solver will continue anyway.

Thread 1 "julia" received signal SIGSEGV, Segmentation fault.
0x59360bac in N_VLinearSum_Serial ()
   from /home/viral/.julia/artifacts/ee6fe6e3b73ab790eab0ab0d686f5df2933d0498/lib/libsundials_nvecserial.so
(gdb) bt
#0  0x59360bac in N_VLinearSum_Serial ()
   from /home/viral/.julia/artifacts/ee6fe6e3b73ab790eab0ab0d686f5df2933d0498/lib/libsundials_nvecserial.so