NetCDF_jll v400.702.402+0 and later broken on Windows

[visr]

Describe the bug

A new NetCDF_jll release was made a few days ago. It appears that this doesn't communicate well with the HDF5 dependency.

This was introduced in JuliaPackaging/Yggdrasil#4481, cc @felixcremer. I don't see anything wrong in the build file, but the main difference is that it is linked to HDF5_jll v1.12.1+0 instead of the older v1.12.0+1.

Shall we yank the build? We would lose a functioning Apple M1 build however.

Side note: this is not directly related to NCDatasets. @Alexander-Barth do you prefer that I create these issues in Yggdrasil? I thought here might be better for visibility for users.

To Reproduce

Here is an example using only NetCDF_jll, to keep it as simple as possible.

julia> using NetCDF_jll
julia> unsafe_string(ccall((:nc_inq_libvers, libnetcdf), Cstring, ()))
"4.7.4 of Feb 22 2022 14:00:01 \$"
julia> NC_CLASSIC_MODEL = 0x0100
julia> NC_NETCDF4 = 0x1000
julia> # it can create a classic netcdf (no HDF5 needed)
julia> ccall((:nc_create, libnetcdf), Cint, (Cstring, Cint, Ptr{Cint}), "test.nc3", NC_CLASSIC_MODEL, Ref(Cint(0)))
julia> # but gives a segfault on netcdf4
julia> ccall((:nc_create, libnetcdf), Cint, (Cstring, Cint, Ptr{Cint}), "test.nc4", NC_NETCDF4, Ref(Cint(0)))

Expected behavior

Create an empty ""test.nc4" file.

Environment

Julia Version 1.7.2
Commit bf53498635 (2022-02-06 15:21 UTC)
Platform Info:
  OS: Windows (x86_64-w64-mingw32)
  CPU: Intel(R) Core(TM) i7-6700HQ CPU @ 2.60GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-12.0.1 (ORCJIT, skylake)
Environment:
  JULIA_EDITOR = code
  JULIA_NUM_THREADS = 3

Full output

Please submit a bug report with steps to reproduce this fault, and any error messages that follow (in their entirety). Thanks.
Exception: EXCEPTION_ACCESS_VIOLATION at 0x2374cb3 -- .text at C:\Users\visser_mn\.julia\artifacts\2b6e2ce84250e36811c3019c1ad253c1739c888f\bin\libnetcdf-18.dll (unknown line)
in expression starting at REPL[13]:1
.text at C:\Users\visser_mn\.julia\artifacts\2b6e2ce84250e36811c3019c1ad253c1739c888f\bin\libnetcdf-18.dll (unknown line)
NC4_create at C:\Users\visser_mn\.julia\artifacts\2b6e2ce84250e36811c3019c1ad253c1739c888f\bin\libnetcdf-18.dll (unknown line)
NC_create at C:\Users\visser_mn\.julia\artifacts\2b6e2ce84250e36811c3019c1ad253c1739c888f\bin\libnetcdf-18.dll (unknown line)
nc__create at C:\Users\visser_mn\.julia\artifacts\2b6e2ce84250e36811c3019c1ad253c1739c888f\bin\libnetcdf-18.dll (unknown line)
nc_create at C:\Users\visser_mn\.julia\artifacts\2b6e2ce84250e36811c3019c1ad253c1739c888f\bin\libnetcdf-18.dll (unknown line)
top-level scope at .\REPL[13]:1
jl_toplevel_eval_flex at /cygdrive/c/buildbot/worker/package_win64/build/src\toplevel.c:876
jl_toplevel_eval_flex at /cygdrive/c/buildbot/worker/package_win64/build/src\toplevel.c:830
jl_toplevel_eval_flex at /cygdrive/c/buildbot/worker/package_win64/build/src\toplevel.c:830
jl_toplevel_eval at /cygdrive/c/buildbot/worker/package_win64/build/src\toplevel.c:894 [inlined]
jl_toplevel_eval_in at /cygdrive/c/buildbot/worker/package_win64/build/src\toplevel.c:944
eval at .\boot.jl:373 [inlined]
eval_user_input at C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.7\REPL\src\REPL.jl:150
repl_backend_loop at C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.7\REPL\src\REPL.jl:246
start_repl_backend at C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.7\REPL\src\REPL.jl:231
#run_repl#47 at C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.7\REPL\src\REPL.jl:364
run_repl at C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.7\REPL\src\REPL.jl:351
#930 at .\client.jl:394
jfptr_YY.930_36349.clone_1 at C:\Users\visser_mn\.julia\juliaup\julia-1.7.2+0~x64\lib\julia\sys.dll (unknown line)
jl_apply at /cygdrive/c/buildbot/worker/package_win64/build/src\julia.h:1788 [inlined]
jl_f__call_latest at /cygdrive/c/buildbot/worker/package_win64/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_21275.clone_1 at C:\Users\visser_mn\.julia\juliaup\julia-1.7.2+0~x64\lib\julia\sys.dll (unknown line)
jl_apply at /cygdrive/c/buildbot/worker/package_win64/build/src\julia.h:1788 [inlined]
true_main at /cygdrive/c/buildbot/worker/package_win64/build/src\jlapi.c:559
jl_repl_entrypoint at /cygdrive/c/buildbot/worker/package_win64/build/src\jlapi.c:701
mainCRTStartup at /cygdrive/c/buildbot/worker/package_win64/build/cli\loader_exe.c:42
BaseThreadInitThunk at C:\WINDOWS\System32\KERNEL32.DLL (unknown line)
RtlUserThreadStart at C:\WINDOWS\SYSTEM32\ntdll.dll (unknown line)
Allocations: 9681000 (Pool: 9675485; Big: 5515); GC: 13

Workaround

add NetCDF_jll@400.702.400

or

[compat]
NetCDF_jll = "=400.702.400"

[Alexander-Barth]

Thanks a lot for letting me know!
Can somebody on Windows test if HDF5 with HDF5_jll v1.12.1+0 can run its test suite without failure?

[visr]

Yes, I just checked, HDF5.jl, doesn't have an issue with that HDF5_jll, so it seems both libs work individually, but not together, on Windows.

[Alexander-Barth]

Thanks @visr for the update! Filled also a bug report here:
JuliaPackaging/Yggdrasil#4511

[Alexander-Barth]

Shall we yank the build? We would lose a functioning Apple M1 build however.

As there are many more Windows users than Apple M1 users, I would indeed be in favour to yank the build of NetCDF_jll.

[Alexander-Barth]

This issue is not resolved but mitigated by declaring NCDatasets incompatible with v400.702.402+0 in NCDatasets 0.12.