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Demonstrate cause of nightly stall #881

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@mkitti mkitti commented Dec 11, 2021

The main purpose of this pull request is to identify the issue that was stalling the HDF5.jl tests against Julia nightly.

Suspected cause is JuliaLang/julia#41602

mkitti and others added 27 commits November 1, 2021 02:44
Co-authored-by: Mustafa M <[email protected]>
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mkitti commented Dec 11, 2021

Sat, 11 Dec 2021 20:24:20 GMT
[ Info: libhdf5 v1.12.0
Sat, 11 Dec 2021 20:24:20 GMT
┌ Debug: plain
Sat, 11 Dec 2021 20:24:20 GMT
└ @ Main ~/work/HDF5.jl/HDF5.jl/test/runtests.jl:14
Sat, 11 Dec 2021 20:24:25 GMT
┌ Info: Registering filter
Sat, 11 Dec 2021 20:24:25 GMT
└   F = H5Zblosc.BloscFilter
Sat, 11 Dec 2021 20:25:11 GMT
┌ Debug: compound
Sat, 11 Dec 2021 20:25:11 GMT
└ @ Main ~/work/HDF5.jl/HDF5.jl/test/runtests.jl:16
Sat, 11 Dec 2021 20:25:15 GMT
┌ Debug: custom
Sat, 11 Dec 2021 20:25:15 GMT
└ @ Main ~/work/HDF5.jl/HDF5.jl/test/runtests.jl:18
Sat, 11 Dec 2021 20:25:16 GMT
┌ Debug: reference
Sat, 11 Dec 2021 20:25:16 GMT
└ @ Main ~/work/HDF5.jl/HDF5.jl/test/runtests.jl:20
Sat, 11 Dec 2021 20:25:16 GMT
┌ Debug: dataspace
Sat, 11 Dec 2021 20:25:16 GMT
└ @ Main ~/work/HDF5.jl/HDF5.jl/test/runtests.jl:22
Sat, 11 Dec 2021 20:25:17 GMT
┌ Debug: hyperslab
Sat, 11 Dec 2021 20:25:17 GMT
└ @ Main ~/work/HDF5.jl/HDF5.jl/test/runtests.jl:24
Sat, 11 Dec 2021 20:25:18 GMT
┌ Debug: readremote
Sat, 11 Dec 2021 20:25:18 GMT
└ @ Main ~/work/HDF5.jl/HDF5.jl/test/runtests.jl:26
Sat, 11 Dec 2021 20:25:20 GMT
┌ Debug: extend_test
Sat, 11 Dec 2021 20:25:20 GMT
└ @ Main ~/work/HDF5.jl/HDF5.jl/test/runtests.jl:28
Sat, 11 Dec 2021 20:25:22 GMT
┌ Debug: gc
Sat, 11 Dec 2021 20:25:22 GMT
└ @ Main ~/work/HDF5.jl/HDF5.jl/test/runtests.jl:30
Sat, 11 Dec 2021 20:25:25 GMT
┌ Debug: external
Sat, 11 Dec 2021 20:25:25 GMT
└ @ Main ~/work/HDF5.jl/HDF5.jl/test/runtests.jl:32
Sat, 11 Dec 2021 20:25:26 GMT
┌ Debug: external tests did not delete
Sat, 11 Dec 2021 20:25:26 GMT
│   fn2 = "/tmp/jl_1wzek4"
Sat, 11 Dec 2021 20:25:26 GMT
└ @ Main ~/work/HDF5.jl/HDF5.jl/test/external.jl:57
Sat, 11 Dec 2021 20:25:26 GMT
┌ Debug: swmr
Sat, 11 Dec 2021 20:25:26 GMT
└ @ Main ~/work/HDF5.jl/HDF5.jl/test/runtests.jl:34
Sat, 11 Dec 2021 20:25:42 GMT
┌ Debug: mmap
Sat, 11 Dec 2021 20:25:42 GMT
└ @ Main ~/work/HDF5.jl/HDF5.jl/test/runtests.jl:36
Sat, 11 Dec 2021 20:25:44 GMT
┌ Debug: properties
Sat, 11 Dec 2021 20:25:44 GMT
└ @ Main ~/work/HDF5.jl/HDF5.jl/test/runtests.jl:38
Sat, 11 Dec 2021 20:25:45 GMT
┌ Debug: table
Sat, 11 Dec 2021 20:25:45 GMT
└ @ Main ~/work/HDF5.jl/HDF5.jl/test/runtests.jl:40
Sat, 11 Dec 2021 20:25:45 GMT
┌ Debug: filter
Sat, 11 Dec 2021 20:25:45 GMT
└ @ Main ~/work/HDF5.jl/HDF5.jl/test/runtests.jl:42
Sat, 11 Dec 2021 20:25:48 GMT
┌ Info: Registering filter
Sat, 11 Dec 2021 20:25:48 GMT
└   F = H5Zlz4.Lz4Filter
Sat, 11 Dec 2021 20:25:50 GMT
      From worker 2:	┌ Info: Registering filter
Sat, 11 Dec 2021 20:25:50 GMT
      From worker 2:	└   F = H5Zlz4.Lz4Filter
Sat, 11 Dec 2021 20:43:08 GMT
Error: The operation was canceled.

As seen above with a008acb and debugging enabled, the stall occurs just after loading H5Zlz4. Both the main process as well as worker 2 attempts to load H5Zlz4, and then there are no other messages.

The indicates that the tests do proceed past this line:

using H5Zblosc, H5Zlz4, H5Zbzip2, H5Zzstd

H5Zblosc, H5Zbzip2, H5Zzstd do not appear to have loaded. The stall occurs just initializing H5Zlz4.

@mkitti mkitti reopened this Dec 14, 2021
@musm musm closed this Dec 16, 2021
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2 participants