A weird issue with Julia-1.7.1. on Ubuntu (GibbsSeaWater.jl package)

leon · December 26, 2021, 2:10am

The bleow script runs perfectly fine on my Macbook Pro with Julia-1.7.1, but the same program does not run at all on Ubuntu (20.04) (Julia-1.7.1) and gives me the below error message. Not sure if it is due to Julia itself or the package GibbsSeaWater.jl.

Here is a MAT file with some sample data: test.mat - Google Drive

Here is my code:

using MAT, GibbsSeaWater;

F1 = matopen("test.mat");
SP  = read(F1, "SP");
P   = read(F1, "P");
Lon = read(F1, "Lon");
Lat = read(F1, "Lat");
close(F1);

SA = gsw_sa_from_sp.(SP, P, Lon, Lat); # calculate the Absolute salinity

Here is the error message.

signal (11): Segmentation fault
in expression starting at /home/leon/Desktop/LQ/Julia_models/ESM4/A06_unit_conv_historical.jl:38
gsw_saar at /home/leon/.julia/packages/GibbsSeaWater/vq3GE/deps/usr/lib/libgswteos-10.so (unknown line)
gsw_sa_from_sp at /home/leon/.julia/packages/GibbsSeaWater/vq3GE/deps/usr/lib/libgswteos-10.so (unknown line)
gsw_sa_from_sp at /home/leon/.julia/packages/GibbsSeaWater/vq3GE/src/gen_gswteos10.jl:534 [inlined]
_broadcast_getindex_evalf at ./broadcast.jl:670 [inlined]
_broadcast_getindex at ./broadcast.jl:643 [inlined]
getindex at ./broadcast.jl:597 [inlined]
macro expansion at ./broadcast.jl:961 [inlined]
macro expansion at ./simdloop.jl:77 [inlined]
copyto! at ./broadcast.jl:960 [inlined]
copyto! at ./broadcast.jl:913 [inlined]
copy at ./broadcast.jl:885 [inlined]
materialize at ./broadcast.jl:860
unknown function (ip: 0x7fcb1f0a4a5d)
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2247 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2429
top-level scope at /home/leon/Desktop/LQ/Julia_models/ESM4/A06_unit_conv_historical.jl:41
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:876
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:830
jl_toplevel_eval_in at /buildworker/worker/package_linux64/build/src/toplevel.c:944
eval at ./boot.jl:373 [inlined]
include_string at ./loading.jl:1196
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2247 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2429
_include at ./loading.jl:1253
include at ./Base.jl:418
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2247 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2429
exec_options at ./client.jl:292
_start at ./client.jl:495
jfptr__start_40531.clone_1 at /opt/julia-1.7.1/lib/julia/sys.so (unknown line)
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2247 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2429
jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1788 [inlined]
true_main at /buildworker/worker/package_linux64/build/src/jlapi.c:559
jl_repl_entrypoint at /buildworker/worker/package_linux64/build/src/jlapi.c:701
main at julia (unknown line)
__libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
unknown function (ip: 0x400808)
Allocations: 8021244 (Pool: 8018757; Big: 2487); GC: 7
Segmentation fault (core dumped)

This does not seem to be a performance related issue. It ran on my Mac super fast. On Ubuntu, however, it reported the error message without even trying.

ImreSamu · December 26, 2021, 10:32am

you can test the package with test GibbsSeaWater

my test ( Ubuntu 20.04.3 LTS + Julia 1.7.1 - Linux (x86_64-pc-linux-gnu)

new julia install
old ( julia 1.6) ~/.julia directory has been removed.

test GibbsSeaWater ( GibbsSeaWater v0.1.1 )

(@v1.7) pkg> st
      Status `~/.julia/environments/v1.7/Project.toml`
  [9a22fb26] GibbsSeaWater v0.1.1

(@v1.7) pkg> test GibbsSeaWater
     Testing GibbsSeaWater
      Status `/tmp/jl_Ow8oLP/Project.toml`
  [b99e7846] BinaryProvider v0.5.10
  [34da2185] Compat v3.41.0
  [9a22fb26] GibbsSeaWater v0.1.1
  [8f399da3] Libdl `@stdlib/Libdl`
  [8dfed614] Test `@stdlib/Test`
      Status `/tmp/jl_Ow8oLP/Manifest.toml`
  [b99e7846] BinaryProvider v0.5.10
  [34da2185] Compat v3.41.0
  [9a22fb26] GibbsSeaWater v0.1.1
  [0dad84c5] ArgTools `@stdlib/ArgTools`
  [56f22d72] Artifacts `@stdlib/Artifacts`
  [2a0f44e3] Base64 `@stdlib/Base64`
  [ade2ca70] Dates `@stdlib/Dates`
  [8bb1440f] DelimitedFiles `@stdlib/DelimitedFiles`
  [8ba89e20] Distributed `@stdlib/Distributed`
  [f43a241f] Downloads `@stdlib/Downloads`
  [b77e0a4c] InteractiveUtils `@stdlib/InteractiveUtils`
  [b27032c2] LibCURL `@stdlib/LibCURL`
  [76f85450] LibGit2 `@stdlib/LibGit2`
  [8f399da3] Libdl `@stdlib/Libdl`
  [37e2e46d] LinearAlgebra `@stdlib/LinearAlgebra`
  [56ddb016] Logging `@stdlib/Logging`
  [d6f4376e] Markdown `@stdlib/Markdown`
  [a63ad114] Mmap `@stdlib/Mmap`
  [ca575930] NetworkOptions `@stdlib/NetworkOptions`
  [44cfe95a] Pkg `@stdlib/Pkg`
  [de0858da] Printf `@stdlib/Printf`
  [3fa0cd96] REPL `@stdlib/REPL`
  [9a3f8284] Random `@stdlib/Random`
  [ea8e919c] SHA `@stdlib/SHA`
  [9e88b42a] Serialization `@stdlib/Serialization`
  [1a1011a3] SharedArrays `@stdlib/SharedArrays`
  [6462fe0b] Sockets `@stdlib/Sockets`
  [2f01184e] SparseArrays `@stdlib/SparseArrays`
  [10745b16] Statistics `@stdlib/Statistics`
  [fa267f1f] TOML `@stdlib/TOML`
  [a4e569a6] Tar `@stdlib/Tar`
  [8dfed614] Test `@stdlib/Test`
  [cf7118a7] UUIDs `@stdlib/UUIDs`
  [4ec0a83e] Unicode `@stdlib/Unicode`
  [e66e0078] CompilerSupportLibraries_jll `@stdlib/CompilerSupportLibraries_jll`
  [deac9b47] LibCURL_jll `@stdlib/LibCURL_jll`
  [29816b5a] LibSSH2_jll `@stdlib/LibSSH2_jll`
  [c8ffd9c3] MbedTLS_jll `@stdlib/MbedTLS_jll`
  [14a3606d] MozillaCACerts_jll `@stdlib/MozillaCACerts_jll`
  [4536629a] OpenBLAS_jll `@stdlib/OpenBLAS_jll`
  [83775a58] Zlib_jll `@stdlib/Zlib_jll`
  [8e850b90] libblastrampoline_jll `@stdlib/libblastrampoline_jll`
  [8e850ede] nghttp2_jll `@stdlib/nghttp2_jll`
  [3f19e933] p7zip_jll `@stdlib/p7zip_jll`
     Testing Running tests...
Test Summary:              | Pass  Total
Practical Salinity, PSS-78 |    3      3
Test Summary:                                                      | Pass  Total
Absolute Salinity, Preformed Salinity and Conservative Temperature |    3      3
Test Summary:                                                                    | Pass  Total
Other conversions between Temperatures, Salinities, Entropy, Pressure and Height |   18     18
Test Summary:                         | Pass  Total
Specific Volume, Density and Enthalpy |   38     38
     Testing GibbsSeaWater tests passed

leon · December 26, 2021, 1:52pm

Thanks! I got a “pass” for my test. Unfortunately, the error persists.

Here is a MAT file with some sample data: test.mat - Google Drive

Here is my code:

using MAT, GibbsSeaWater;

F1 = matopen("test.mat");
SP  = read(F1, "SP");
P   = read(F1, "P");
Lon = read(F1, "Lon");
Lat = read(F1, "Lat");
close(F1);

SA = gsw_sa_from_sp.(SP, P, Lon, Lat); # calculate the Absolute salinity

woclass · December 26, 2021, 3:41pm

Simplified test code:

using GibbsSeaWater

# julia> i=79; (SP[i], P[i], Lon[i], Lat[i])
# (34.05199699401855, 10.0, 377.5, -62.5)

# gsw_sa_from_sp(34.0, 10.0, 377.5, -62.5)
gsw_saar(10.0, 377.5, -62.5)

https://github.com/TEOS-10/GSW-C/blob/13ab33cea0e9059d3b3f3dfef78e9591c94af9f8/gsw_saar.c#L33-L42

Is 377.5 a legal longitude?

julia> Lon[61:82]
22-element Vector{Float64}:
 359.5
 360.5
 361.5
 362.5
 363.5
 364.5
 365.5
 366.5
 367.5
 368.5
 369.5
 370.5
 371.5
 372.5
 373.5
 374.5
 375.5
 376.5
 377.5
 378.5
 379.5
  20.5

~~Next you can compile GSW-C in debug mode, then call gsw_saar with the same arguments and debug with gdb to find out which line is wrong.~~

https://github.com/TEOS-10/GSW-C/blob/13ab33cea0e9059d3b3f3dfef78e9591c94af9f8/gsw_saar.c#L69-L70

Breakpoint 6, gsw_saar (p=10, lon=377.5, lat=-62.5) at gsw_saar.c:69
69              indx0   = floor(0 + (nx-1)*(lon-longs_ref[0])/(longs_ref[nx-1]-
70                          longs_ref[0]));
(gdb) p nx
$13 = 91
(gdb) p lon
$14 = 377.5
(gdb) p longs_ref[0]
$15 = 0
(gdb) p longs_ref[nx - 1]
$16 = 360

When lon > 360, indx0 > (nx-1), which then causes the array (longs_ref[indx0]) to go out of bounds.

I can reproduce the error in WSL (Ubuntu 20.04.3 LTS).

julia> SA = gsw_sa_from_sp.(SP, P, Lon, Lat);

signal (11): Segmentation fault
in expression starting at REPL[10]:1
gsw_saar at /home/woclass/.julia/packages/GibbsSeaWater/vq3GE/deps/usr/lib/libgswteos-10.so (unknown line)
gsw_sa_from_sp at /home/woclass/.julia/packages/GibbsSeaWater/vq3GE/deps/usr/lib/libgswteos-10.so (unknown line)
gsw_sa_from_sp at /home/woclass/.julia/packages/GibbsSeaWater/vq3GE/src/gen_gswteos10.jl:534 [inlined]

On Windows, everything works fine.

win REPL

julia> SA
201-element Vector{Float64}:
 33.978850980733235
 34.112732625974715
 34.20779818246909
 34.26127607610699
 34.29615007324156
 34.29711167161423
 34.28884564139484
 34.318206662266995
 34.32395340273992
 34.33207869075504
 34.345693213139945
 34.36708801832739
 34.374648814324125
  ⋮
 33.96205590976534
 33.957670222578585
 33.948449301367084
 33.937740328020595
 33.93005643268858
 33.92895873943964
 33.93384238282935
 33.93726330942629
 33.93330105293442
 33.92392157797163
 33.91456389969976
 33.908278813955846

(@v1.7) pkg> st
      Status `C:\Users\woclass\.julia\environments\v1.7\Project.toml`
  [6e4b80f9] BenchmarkTools v1.2.2
  [31a5f54b] Debugger v0.6.8
  [9a22fb26] GibbsSeaWater v0.1.1
  [23992714] MAT v0.10.2

julia> versioninfo()
Julia Version 1.7.1
Commit ac5cc99908 (2021-12-22 19:35 UTC)
Platform Info:
  OS: Windows (x86_64-w64-mingw32)
  CPU: Intel(R) Core(TM) i5-9400F CPU @ 2.90GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-12.0.1 (ORCJIT, skylake)

ImreSamu · December 26, 2021, 3:47pm

Ouch …
I can replicate the error - with your code … ( Ubuntu20.04 X86-64 + Julia 1.7.1 )

IMHO: You have to create an issue in the project repo:

https://github.com/TEOS-10/GibbsSeaWater.jl

Crash log - Segmentation fault (core dumped)

(@v1.7) pkg> ^C

julia> using MAT, GibbsSeaWater;

julia> F1 = matopen("test.mat");

julia> SP  = read(F1, "SP");

julia> P   = read(F1, "P");

julia> Lon = read(F1, "Lon");

julia> Lat = read(F1, "Lat");

julia> close(F1);

julia> SA = gsw_sa_from_sp.(SP, P, Lon, Lat); # calculate the Absolute salinity

signal (11): Segmentation fault
in expression starting at REPL[11]:1
gsw_saar at /home/pella/.julia/packages/GibbsSeaWater/vq3GE/deps/usr/lib/libgswteos-10.so (unknown line)
gsw_sa_from_sp at /home/pella/.julia/packages/GibbsSeaWater/vq3GE/deps/usr/lib/libgswteos-10.so (unknown line)
gsw_sa_from_sp at /home/pella/.julia/packages/GibbsSeaWater/vq3GE/src/gen_gswteos10.jl:534 [inlined]
_broadcast_getindex_evalf at ./broadcast.jl:670 [inlined]
_broadcast_getindex at ./broadcast.jl:643 [inlined]
getindex at ./broadcast.jl:597 [inlined]
macro expansion at ./broadcast.jl:961 [inlined]
macro expansion at ./simdloop.jl:77 [inlined]
copyto! at ./broadcast.jl:960 [inlined]
copyto! at ./broadcast.jl:913 [inlined]
copy at ./broadcast.jl:885 [inlined]
materialize at ./broadcast.jl:860
unknown function (ip: 0x7f00ff86444d)
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2247 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2429
jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1788 [inlined]
do_call at /buildworker/worker/package_linux64/build/src/interpreter.c:126
eval_value at /buildworker/worker/package_linux64/build/src/interpreter.c:215
eval_stmt_value at /buildworker/worker/package_linux64/build/src/interpreter.c:166 [inlined]
eval_body at /buildworker/worker/package_linux64/build/src/interpreter.c:587
jl_interpret_toplevel_thunk at /buildworker/worker/package_linux64/build/src/interpreter.c:731
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:885
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:830
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:830
jl_toplevel_eval_in at /buildworker/worker/package_linux64/build/src/toplevel.c:944
eval at ./boot.jl:373 [inlined]
eval_user_input at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.7/REPL/src/REPL.jl:150
repl_backend_loop at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.7/REPL/src/REPL.jl:244
start_repl_backend at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.7/REPL/src/REPL.jl:229
#run_repl#47 at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.7/REPL/src/REPL.jl:362
run_repl at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.7/REPL/src/REPL.jl:349
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2247 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2429
#930 at ./client.jl:394
jfptr_YY.930_40362.clone_1 at /usr/local/julia/lib/julia/sys.so (unknown line)
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2247 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2429
jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1788 [inlined]
jl_f__call_latest at /buildworker/worker/package_linux64/build/src/builtins.c:757
#invokelatest#2 at ./essentials.jl:716 [inlined]
invokelatest at ./essentials.jl:714 [inlined]
run_main_repl at ./client.jl:379
exec_options at ./client.jl:309
_start at ./client.jl:495
jfptr__start_40531.clone_1 at /usr/local/julia/lib/julia/sys.so (unknown line)
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2247 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2429
jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1788 [inlined]
true_main at /buildworker/worker/package_linux64/build/src/jlapi.c:559
jl_repl_entrypoint at /buildworker/worker/package_linux64/build/src/jlapi.c:701
main at julia (unknown line)
__libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
unknown function (ip: 0x400808)
Allocations: 19134489 (Pool: 19123101; Big: 11388); GC: 25
Segmentation fault (core dumped)

ImreSamu · December 26, 2021, 3:50pm

I have tested the master version - same result
(@v1.7) pkg> add https://github.com/TEOS-10/GibbsSeaWater.jl#master

→ Segmentation fault (core dumped)

leon · December 26, 2021, 5:33pm

@woclass – Thank you so much. This indeed fixes the issue!

@ImreSamu – Yes, I’ll open up an issue there. It is common for my community to use a 20-380 degree system. That way, all the major oceans are in one piece.

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A weird issue with Julia-1.7.1. on Ubuntu (GibbsSeaWater.jl package)

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