Fix virtual dataset tests #1019
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mkitti
commented
Oct 18, 2022
|
@simonbyrne , how does this look to you? |
simonbyrne
reviewed
Oct 18, 2022
| @@ -62,6 +62,10 @@ end | |||
| include("filters/FilterTestUtils.jl") | |||
| @debug "objects" | |||
| include("objects.jl") | |||
| if VERSION ≥ v"1.6" | |||
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It segfaults otherwise with Julia 1.3. My guess is that Julia 1.3 loads an old JLL which is buggy.
virtual dataset: Error During Test at /home/runner/work/HDF5.jl/HDF5.jl/test/virtual_dataset.jl:32
Test threw exception
Expression: size(d) == (3, 2)
HDF5.API.H5Error: Error getting dataspace
libhdf5 Stacktrace:
[1] H5FO_dest: Object cache/Unable to release object
objects still in open object info set
⋮
Stacktrace:
[1] macro expansion at /home/runner/work/HDF5.jl/HDF5.jl/src/api/error.jl:18 [inlined]
[2] h5d_get_space(::HDF5.Dataset) at /home/runner/work/HDF5.jl/HDF5.jl/src/api/functions.jl:476
[3] dataspace at /home/runner/work/HDF5.jl/HDF5.jl/src/datasets.jl:4 [inlined]
[4] size(::HDF5.Dataset) at /home/runner/work/HDF5.jl/HDF5.jl/src/dataspaces.jl:266
[5] top-level scope at /home/runner/work/HDF5.jl/HDF5.jl/test/virtual_dataset.jl:32
[6] top-level scope at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/Test/src/Test.jl:1107
[7] top-level scope at /home/runner/work/HDF5.jl/HDF5.jl/test/virtual_dataset.jl:4
virtual dataset: Error During Test at /home/runner/work/HDF5.jl/HDF5.jl/test/virtual_dataset.jl:33
Test threw exception
Expression: read(d) == hcat(fill(1.0, 3), fill(2.0, 3))
HDF5.API.H5Error: Error getting dataspace
libhdf5 Stacktrace:
[1] H5FO_dest: Object cache/Unable to release object
objects still in open object info set
⋮
Stacktrace:
[1] macro expansion at /home/runner/work/HDF5.jl/HDF5.jl/src/api/error.jl:18 [inlined]
[2] h5d_get_space(::HDF5.Dataset) at /home/runner/work/HDF5.jl/HDF5.jl/src/api/functions.jl:476
[3] dataspace at /home/runner/work/HDF5.jl/HDF5.jl/src/datasets.jl:4 [inlined]
[4] _size_of_buffer at /home/runner/work/HDF5.jl/HDF5.jl/src/readwrite.jl:324 [inlined]
[5] _generic_read(::HDF5.Dataset, ::HDF5.Datatype, ::Type{Float64}, ::Nothing) at /home/runner/work/HDF5.jl/HDF5.jl/src/readwrite.jl:143
[6] generic_read(::HDF5.Dataset, ::HDF5.Datatype, ::Type{Float64}) at /home/runner/work/HDF5.jl/HDF5.jl/src/readwrite.jl:134
[7] read(::HDF5.Dataset) at /home/runner/work/HDF5.jl/HDF5.jl/src/readwrite.jl:39
[8] top-level scope at /home/runner/work/HDF5.jl/HDF5.jl/test/virtual_dataset.jl:33
[9] top-level scope at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/Test/src/Test.jl:1107
[10] top-level scope at /home/runner/work/HDF5.jl/HDF5.jl/test/virtual_dataset.jl:4
signal (11): Segmentation fault
in expression starting at /home/runner/work/HDF5.jl/HDF5.jl/test/runtests.jl:18
H5AC_cork at /home/runner/.julia/artifacts/997813d46a8a06e6e9871a2a01483f91ce954eca/lib/libhdf5.so (unknown line)
H5D_close at /home/runner/.julia/artifacts/997813d46a8a06e6e9871a2a01483f91ce954eca/lib/libhdf5.so (unknown line)
H5D__virtual_reset_source_dset at /home/runner/.julia/artifacts/997813d46a8a06e6e9871a2a01483f91ce954eca/lib/libhdf5.so (unknown line)
H5D__virtual_reset_layout at /home/runner/.julia/artifacts/997813d46a8a06e6e9871a2a01483f91ce954eca/lib/libhdf5.so (unknown line)
H5O__layout_reset at /home/runner/.julia/artifacts/997813d46a8a06e6e9871a2a01483f91ce954eca/lib/libhdf5.so (unknown line)
H5O_msg_reset at /home/runner/.julia/artifacts/997813d46a8a06e6e9871a2a01483f91ce954eca/lib/libhdf5.so (unknown line)
H5D_close at /home/runner/.julia/artifacts/997813d46a8a06e6e9871a2a01483f91ce954eca/lib/libhdf5.so (unknown line)
H5VL__native_dataset_close at /home/runner/.julia/artifacts/997813d46a8a06e6e9871a2a01483f91ce954eca/lib/libhdf5.so (unknown line)
H5VL_dataset_close at /home/runner/.julia/artifacts/997813d46a8a06e6e9871a2a01483f91ce954eca/lib/libhdf5.so (unknown line)
H5D__close_cb at /home/runner/.julia/artifacts/997813d46a8a06e6e9871a2a01483f91ce954eca/lib/libhdf5.so (unknown line)
H5I__clear_type_cb at /home/runner/.julia/artifacts/997813d46a8a06e6e9871a2a01483f91ce954eca/lib/libhdf5.so (unknown line)
H5SL_try_free_safe at /home/runner/.julia/artifacts/997813d46a8a06e6e9871a2a01483f91ce954eca/lib/libhdf5.so (unknown line)
H5I_clear_type at /home/runner/.julia/artifacts/997813d46a8a06e6e9871a2a01483f91ce954eca/lib/libhdf5.so (unknown line)
H5D_top_term_package at /home/runner/.julia/artifacts/997813d46a8a06e6e9871a2a01483f91ce954eca/lib/libhdf5.so (unknown line)
H5_term_library.part.0 at /home/runner/.julia/artifacts/997813d46a8a06e6e9871a2a01483f91ce954eca/lib/libhdf5.so (unknown line)
H5close at /home/runner/.julia/artifacts/997813d46a8a06e6e9871a2a01483f91ce954eca/lib/libhdf5.so (unknown line)
h5_close at /home/runner/work/HDF5.jl/HDF5.jl/src/api/functions.jl:20
unknown function (ip: 0x7f2e33f1333c)
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2141 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2305
jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1631 [inlined]
do_call at /buildworker/worker/package_linux64/build/src/interpreter.c:328
eval_value at /buildworker/worker/package_linux64/build/src/interpreter.c:417
eval_stmt_value at /buildworker/worker/package_linux64/build/src/interpreter.c:368 [inlined]
eval_body at /buildworker/worker/package_linux64/build/src/interpreter.c:778
eval_body at /buildworker/worker/package_linux64/build/src/interpreter.c:705
eval_body at /buildworker/worker/package_linux64/build/src/interpreter.c:705
jl_interpret_toplevel_thunk_callback at /buildworker/worker/package_linux64/build/src/interpreter.c:888
unknown function (ip: 0xfffffffffffffffe)
unknown function (ip: 0x7f2e38fbdc0f)
unknown function (ip: 0x390)
jl_interpret_toplevel_thunk at /buildworker/worker/package_linux64/build/src/interpreter.c:897
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:814
jl_parse_eval_all at /buildworker/worker/package_linux64/build/src/ast.c:873
jl_load at /buildworker/worker/package_linux64/build/src/toplevel.c:878
include at ./boot.jl:328 [inlined]
include_relative at ./loading.jl:1105
include at ./Base.jl:31
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2135 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2305
include at ./client.jl:424
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2135 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2305
jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1631 [inlined]
do_call at /buildworker/worker/package_linux64/build/src/interpreter.c:328
eval_value at /buildworker/worker/package_linux64/build/src/interpreter.c:417
eval_stmt_value at /buildworker/worker/package_linux64/build/src/interpreter.c:368 [inlined]
eval_body at /buildworker/worker/package_linux64/build/src/interpreter.c:778
jl_interpret_toplevel_thunk_callback at /buildworker/worker/package_linux64/build/src/interpreter.c:888
unknown function (ip: 0xfffffffffffffffe)
unknown function (ip: 0x7f2e48297a8f)
unknown function (ip: 0xffffffffffffffff)
jl_interpret_toplevel_thunk at /buildworker/worker/package_linux64/build/src/interpreter.c:897
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:814
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:764
jl_toplevel_eval_in at /buildworker/worker/package_linux64/build/src/toplevel.c:843
eval at ./boot.jl:330
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2135 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2305
exec_options at ./client.jl:263
_start at ./client.jl:460
jfptr__start_2084.clone_1 at /opt/hostedtoolcache/julia/1.3.1/x64/lib/julia/sys.so (unknown line)
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2135 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2305
jl_apply at /buildworker/worker/package_linux64/build/ui/../src/julia.h:1631 [inlined]
true_main at /buildworker/worker/package_linux64/build/ui/repl.c:96
main at /buildworker/worker/package_linux64/build/ui/repl.c:217
__libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
_start at /opt/hostedtoolcache/julia/1.3.1/x64/bin/julia (unknown line)
Allocations: 130050426 (Pool: 130024572; Big: 25854); GC: 166
ERROR: LoadError: Package HDF5 errored during testing
Stacktrace:
[1] pkgerror(::String, ::Vararg{String,N} where N) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/Pkg/src/Types.jl:[113](https://github.com/JuliaIO/HDF5.jl/actions/runs/3269882844/jobs/5377897344#step:5:116)
[2] #test#[131](https://github.com/JuliaIO/HDF5.jl/actions/runs/3269882844/jobs/5377897344#step:5:134)(::Bool, ::Nothing, ::Cmd, ::Cmd, ::typeof(Pkg.Operations.test), ::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/Pkg/src/Operations.jl:[137](https://github.com/JuliaIO/HDF5.jl/actions/runs/3269882844/jobs/5377897344#step:5:140)2
[3] #test at ./none:0 [inlined]
[4] #test#62(::Bool, ::Nothing, ::Cmd, ::Cmd, ::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}, ::typeof(Pkg.API.test), ::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/Pkg/src/API.jl:253
[5] (::Pkg.API.var"#kw##test")(::NamedTuple{(:coverage,),Tuple{Bool}}, ::typeof(Pkg.API.test), ::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at ./none:0
[6] #test#58 at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/Pkg/src/API.jl:233 [inlined]
[7] (::Pkg.API.var"#kw##test")(::NamedTuple{(:coverage,),Tuple{Bool}}, ::typeof(Pkg.API.test)) at ./none:0
[8] top-level scope at /home/runner/work/_actions/julia-actions/julia-runtest/latest/test_harness.jl:15
[9] include at ./boot.jl:328 [inlined]
[10] include_relative(::Module, ::String) at ./loading.jl:1105
[11] include(::Module, ::String) at ./Base.jl:31
[12] include(::String) at ./client.jl:424
[13] top-level scope at none:1
in expression starting at /home/runner/work/_actions/julia-actions/julia-runtest/latest/test_harness.jl:7
simonbyrne
approved these changes
Oct 18, 2022
|
@musm want to merge this one and do another release? |
|
It only modifies the tests, so I don't think a release is required. |
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See #1018 for explanation.
Create a testset.
Restrict testing to greater than Julia 1.3 due to JLL issues.