Add bzip2, lz4, and zstd independent compression filter packages #880

mkitti · 2021-12-08T08:36:31Z

This branch splits the compression plugin code into independent subdirectory packages. Consider merging this into #875.

The main purpose of this pull request is to test CI.

licenses/H5Zbzip2_LICENSE.txt

mkitti · 2021-12-11T08:57:41Z

All tests are now passing, including nightly.

musm · 2021-12-11T21:02:14Z

src/filters/H5Zbzip2/Project.toml

@@ -0,0 +1,12 @@
+name = "H5Zbzip2"
+uuid = "094576f2-1e46-4c84-8e32-c46c042eaaa2"
+version = "0.16.0"


The idea will be to sync the version with the main HDF5.jl package version?

I don't have a problem with this, but as you probably already know, these 'independent' packages could also just maintain their own version number that get bumped when we modify the subpackages.

I think the main benefit of the current approach is simplicity in bumping version numbers across all packages. OTOH, if we keep an independent version number I think then that reduces precompilation when we make new releases.
From judging changes in the original blosc file, changes to the filter packages are likely to be infrequent.

Yes. We can only tag the whole repository, so we might as well keep it in sync with the tags.

You can tag a sub-package associated with a subdirectory of a repository via @JuliaRegistrator register subdir=.... Makie e.g., uses this approach.

What I meant is a tag and release from the git perspective.

Let's keep all the subpackages at version 0.1.0 and tag them individually. I think the benefit is we avoid precompilation of the subpackages after new HDF5.jl releases, and most of these filter packages won't be changing frequently. I believe that makes more sense and follows semver, instead of bumping the submodules in instances were HDF5.jl was changed but the subpackages were untouched.

For releases I've been using the registrator bot. It looks like it should be straightforward to accommodate subpackages with the registrator from @thchr comment.

Well we can tell the registrator bot whatever version we want, but the question is how to do you mark these versions in Git? Do you plan on making an individual tag for each sub-package?

Ah, I see your point now, since these are not git submodules...

Thinking about this again, does the git tag version even matter? No.

So, what'll happen is that the git tag version will be synced with the HDF5.jl version as is currently the case.
The git tag version will not agree with the tagged version of the filter subpackages, which will have their own independent versions as specified in their own Project.toml. This is the case since we aren't using git submodules, which is more trouble than it's worth.

To me this makes sense and is desired behavior since we won't have to tag all the filter packages superfluously every time a change is made in the main HDF5.jl module that doesn't modify the filter submodules.

src/filters/H5Zbzip2/src/H5Zbzip2.jl

mkitti · 2021-12-11T21:34:27Z

src/filters/H5Zblosc/src/H5Zblosc.jl

+        # We need to preserve the output of cbuffer_sizes under Julia 1.8 (as of 2021/12/11)
+        # Otherwise their Refs get freed and the buffer becomes corrupted
+        # If this fails, consider copying `in` or wrapping that array.
+        GC.@preserve outbuf_size cbytes blocksize begin


Without this line, H5Zblosc appears to error with Julia 1.8 in development.

cbuffer_sizes calls blosc_cbuffer_sizes which returns a size values via pointers / Refs.

https://github.com/JuliaIO/Blosc.jl/blob/8ab4e3cf60dd45ee598ad879caf99948bd2a2718/src/Blosc.jl#L129-L137

function cbuffer_sizes(buf) s1 = Ref{Csize_t}() s2 = Ref{Csize_t}() s3 = Ref{Csize_t}() ccall((:blosc_cbuffer_sizes,libblosc), Cvoid, (Ptr{UInt8}, Ref{Csize_t}, Ref{Csize_t}, Ref{Csize_t}), buf, s1, s2, s3) return (s1[], s2[], s3[]) end

Somehow it appears that the Refs are getting garbage collected and the value of outbuf_size is corrupted. This does not make sense to me, but this seems to have worked fine until Julia 1.8, so perhaps there is a bug.

This has been resolved in JuliaLang/julia#43408 (pending merge)

Oh okay, so this is unrelated to JuliaIO/Blosc.jl#86 or does the fix also require making the changes according to your comment in JuliaIO/Blosc.jl#86 ?

Looks like the underlying fix has been merged. I propose we remove mitigating patch here as it won't be an issue henceforth.

You can tag a commit as H5Zblosc_v0.1.0 when you make a release. The main convenience of keeping the versions somewhat aligned is making it easy to know what versions are compatible with what other versions.

That is true. OTOH, I think it might not be too difficult to determine if a non-backwards compatible change is made to the filter subpackages. At worst, we could always bump the compatible HDF5 version to the latest one in the filter subpackage every time a change is made to the subpackage or HDF5.jl methods that relate to the filter.

mkitti · 2021-12-11T21:39:48Z

test/external.jl

@@ -50,5 +54,6 @@ close(source_file)

 rm(fn1)
 # rm(fn2)
+@debug "external tests did not delete" fn2


We cannot delete fn2 or run those above tests because some HDF5 handle is still open. Because of the external link, HDF5 is set to use "weak" closing, so closing the file is not sufficient. Ultimately h5close at the end of runtests.jl does close the files and allows for the tempfile to be deleted.

Yep, I have an idea on how to fix this.

Could we split this off from this PR?

Ideally I'd like to squash-merge all the new filter functionality in a single commit/PR.

I removed the debug message

test/runtests.jl

test/swmr.jl

musm · 2021-12-14T21:33:14Z

Any chance you could rebase with master.

musm · 2021-12-14T21:37:08Z

I had this comment here: https://github.com/JuliaIO/HDF5.jl/pull/880/files#r767927849
and also
https://github.com/JuliaIO/HDF5.jl/pull/880/files#r767937926
to remove the mitigating patch as it's now been fixed in Julia. master

Co-authored-by: Mustafa M <mus-m@outlook.com>

mkitti · 2021-12-15T01:47:17Z

These two pull requests should fix the remaining downstream errors.

JuliaIO/MAT.jl#170 (fixes SparseMatrixCSC errors for Julia 1.7)
JuliaIO/JLD.jl#305 (adds H5Zblosc, so set_blosc! exists)

Anything else? You are welcome to make commits directly.

musm · 2021-12-15T05:32:45Z

Anything else? You are welcome to make commits directly.

You'll have to enable "allow commits" in the PR since I don't have access.

mkitti · 2021-12-15T07:44:17Z

Anything else? You are welcome to make commits directly.

You'll have to enable "allow commits" in the PR since I don't have access.

I invited you to the repository. I guess it's trickier since it's coming from an organizational account.

mkitti · 2021-12-15T07:44:26Z

All tests should be passing now.

https://github.com/JuliaIO/HDF5.jl/runs/4530943064?check_suite_focus=true

Project.toml

Co-authored-by: Mustafa M <mus-m@outlook.com>

mkitti · 2021-12-15T21:05:35Z

src/filters/filters.jl

+macro dev_embedded_filters()
+    quote
+        @eval begin
+            using Pkg
+            Pkg.develop(PackageSpec(; path=joinpath(dirname(pathof(HDF5)), "filters", "H5Zblosc")))
+            Pkg.develop(PackageSpec(; path=joinpath(dirname(pathof(HDF5)), "filters", "H5Zbzip2")))
+            Pkg.develop(PackageSpec(; path=joinpath(dirname(pathof(HDF5)), "filters", "H5Zlz4")))
+            Pkg.develop(PackageSpec(; path=joinpath(dirname(pathof(HDF5)), "filters", "H5Zzstd")))
+        end
+    end
+end


Here is the macro which devs the filter packages into the test environment.

musm · 2021-12-15T21:15:04Z

Looks like there may be an aws issue downloading the non ubuntu binaries?

musm · 2021-12-16T05:22:59Z

@mkitti any chance you could review my changes.

musm · 2021-12-16T05:24:07Z

I think we need to in a follow up PR or this PR, either:

(1) deprecate setting :blosc for properties and warn users to load in the external H5Zblosc package to use the blosc filter.

(2) Alternatively, we could add hooks for :zstd, :lz4, :bzip2 like we do for the blosc package
i.e. add the following for the external filters.

    @require H5Zblosc="c8ec2601-a99c-407f-b158-e79c03c2f5f7" @eval begin
        set_blosc!(p::Properties, val::Bool) = val && push!(Filters.FilterPipeline(p), H5Zblosc.BloscFilter())
        set_blosc!(p::Properties, level::Integer) = push!(Filters.FilterPipeline(p), H5Zblosc.BloscFilter(level=level))
    end

@simonbyrne maybe you also have an opinion on which option is more desirable from a ux perspective.

mkitti · 2021-12-16T18:23:44Z

I generally think that we should deprecate the older syntax blosc = 3 or otherwise come up with a way to implement properties in an extensible manner.

Rather than this

HDF5.jl/src/properties.jl

Lines 438 to 452 in 00dcb13

    
           function class_setproperty!(::Type{DatasetCreateProperties}, p::Properties, name::Symbol, val) 
        
               name === :alloc_time  ? set_alloc_time!(p, val) : 
        
               name === :chunk       ? set_chunk!(p, val) : 
        
               name === :external    ? API.h5p_set_external(p, val...) : 
        
               name === :filters     ? set_filters!(p, val) : 
        
               name === :layout      ? set_layout!(p, val) : 
        
               # set-only for convenience 
        
               name === :blosc       ? set_blosc!(p, val) : 
        
               name === :deflate     ? set_deflate!(p, val) : 
        
               name === :fletcher32  ? set_fletcher32!(p, val) : 
        
               name === :shuffle     ? set_shuffle!(p, val) : 
        
               # deprecated 
        
               name === :compress    ? (depwarn("`compress=$val` keyword option is deprecated, use `deflate=$val` instead",:class_setproperty!); set_deflate!(p, val)) : 
        
               class_setproperty!(superclass(DatasetCreateProperties), p, name, val) 
        
           end

an extensible system would work as follows

# Defined in HDF5.jl
function class_setproperty!(::Type{DatasetCreateProperties}, p::Properties, name::Symbol, val)
   class_setproperty!(::Type{DatasetCreateProperties}, p, Val(name), val)
end

# Defined in H5Zblosc.jl
import HDF5: class_setproperty!
class_setproperty!(::Type{DatasetCreateProperties}, p::Properties, Val{:blosc}, val) = set_blosc!(p, val)

That said, I think the filters interface is much better and is already extensible. Filters should have an order to them in a pipeline. Thus, I would lean towards deprecating the properties interface for filters.

mkitti · 2021-12-16T18:29:37Z

test/runtests.jl

+filter_path = joinpath(dirname(pathof(HDF5)), "filters")
+Pkg.develop(PackageSpec(path=joinpath(filter_path, "H5Zblosc")))
+Pkg.develop(PackageSpec(path=joinpath(filter_path, "H5Zbzip2")))
+Pkg.develop(PackageSpec(path=joinpath(filter_path, "H5Zlz4")))
+Pkg.develop(PackageSpec(path=joinpath(filter_path, "H5Zzstd")))


I did like the idea of having this in some kind of callable closure. I anticipate downstream projects may want to do something similar via CI. Perhaps though it could it its own file under test/?

mkitti · 2021-12-16T22:03:23Z

Overall the changes look fine to me. We just need to register the packages for some of the tests to work. 👍

mkitti · 2021-12-16T22:05:54Z

It will probably be easier to iterate and test this once the subpackages are registered. I suggest registering the subpackages well before we register HDF5 0.16 itself. Then at least we can dev everything in the normal fashion.

musm · 2021-12-16T23:02:07Z

Sure, is dev'ing not working in some cases for you ? I've just manually kept calling

Pkg.develop(PackageSpec(path=joinpath(filter_path, "H5Zblosc")))

when need be...

In any case, we'll have to register the subpackages first. I think I'll merge this PR now and we then need to iterate on the new filters interface. I do agree that the second approach is much more flexible, so we'd have to appropriately deprecate existing calls.

musm · 2021-12-17T04:16:36Z

Thank you very much @mkitti for your effort and patience with these PRs! I'm really excited for these changes in the upcoming v0.16 release. Also sorry to drag out some of the licensing issues.

musm · 2021-12-19T17:55:00Z

I've submitted registration for all the subpackages, they will take a day or two since they are blocked until a manual merge is done, as they depend on v0.16 which is yet released.

mkitti · 2021-12-19T18:54:18Z

We could ask for manual merge if needed. Perhaps it might be good to reach out so others know what we are doing.

This was referenced Dec 8, 2021

Add bzip2, lz4, and zstd filters from HDF5Plugins.jl #875

Closed

Installing HDF5.jl on ARM M1 #870

Closed

M1 Monterey: libblosc not defined JuliaIO/Blosc.jl#85

Closed

musm reviewed Dec 10, 2021

View reviewed changes

licenses/H5Zbzip2_LICENSE.txt Outdated Show resolved Hide resolved

musm reviewed Dec 11, 2021

View reviewed changes

src/filters/H5Zbzip2/src/H5Zbzip2.jl Show resolved Hide resolved

mkitti commented Dec 11, 2021

View reviewed changes

test/runtests.jl Outdated Show resolved Hide resolved

mkitti commented Dec 11, 2021

View reviewed changes

test/swmr.jl Outdated Show resolved Hide resolved

mkitti mentioned this pull request Dec 11, 2021

GC.@preserve the results of cbuffer_sizes JuliaIO/Blosc.jl#86

Closed

mkitti marked this pull request as ready for review December 13, 2021 19:56

mkitti and others added 15 commits December 14, 2021 19:06

Add bzip2, lz4, and zstd filters from HDF5Plugins.jl

d7bcada

Create Filters interface def, add tests

3561115

Filters return 0 rather than rethrowing error

b7b7f24

Move blosc.jl to H5Zblosc.jl

a5100e5

Optimize method inference, init, precompile

424de91

Register filters as when dep packages are loaded

cbfb653

Fix tests for lazy loaded filters

58f8a7c

Move plugin licenses to licenses folder

55bb1c5

Add HHMI copyright to LICENSE.txt

9a8f3e9

Remove generic register_filter method

b215ded

Apply suggestions from code review for license notices

26dbde0

Co-authored-by: Mustafa M <mus-m@outlook.com>

Implement generic register_filter on filter type

0e011dd

Update test/filter.jl

b253de1

Co-authored-by: Mustafa M <mus-m@outlook.com>

Define filters API on the type alone

84085b4

H5Zblosc, H5Zbzip2, H5Zlz4, H5Zzstd as subdir pkgs

d6d7fd4

Start H5Z* pkgs at 0.1.0

e344882

mkitti force-pushed the janelia/h5z_subdir_packages branch from f796447 to e344882 Compare December 15, 2021 00:08

musm reviewed Dec 15, 2021

View reviewed changes

Project.toml Outdated Show resolved Hide resolved

mkitti and others added 4 commits December 15, 2021 14:08

Update Project.toml

e23d739

Co-authored-by: Mustafa M <mus-m@outlook.com>

Update Project.toml

ed1b342

Add filters as test targets

55afa4f

Update Project.toml

393711b

mkitti commented Dec 15, 2021

View reviewed changes

musm added 2 commits December 15, 2021 21:45

Cosmetic changes and instantiate filters packages directly in test file

b2e16d3

Update docs remove external exports

82fba8e

musm changed the title ~~Independent compression filter packages~~ Add bzip2, lz4, and zstd independent compression filter packages Dec 16, 2021

mkitti commented Dec 16, 2021

View reviewed changes

musm merged commit 4639336 into JuliaIO:master Dec 17, 2021

musm mentioned this pull request Dec 17, 2021

HDF5Plugins.jl: lz4, zstd, and bzip2 filter support #874

Closed

musm deleted the janelia/h5z_subdir_packages branch December 19, 2021 17:54

musm mentioned this pull request Jan 21, 2022

add exported function set_blosc_property #484

Closed

Add bzip2, lz4, and zstd independent compression filter packages #880

Add bzip2, lz4, and zstd independent compression filter packages #880

Conversation

mkitti commented Dec 8, 2021

mkitti commented Dec 11, 2021

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

musm Dec 13, 2021 • edited Loading

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

mkitti Dec 11, 2021 • edited Loading

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

musm Dec 15, 2021 • edited Loading

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

musm commented Dec 14, 2021

musm commented Dec 14, 2021

mkitti commented Dec 15, 2021 • edited Loading

musm commented Dec 15, 2021

mkitti commented Dec 15, 2021

mkitti commented Dec 15, 2021 • edited Loading

Choose a reason for hiding this comment

musm commented Dec 15, 2021

musm commented Dec 16, 2021

musm commented Dec 16, 2021

mkitti commented Dec 16, 2021

Choose a reason for hiding this comment

mkitti commented Dec 16, 2021 • edited Loading

mkitti commented Dec 16, 2021

musm commented Dec 16, 2021

musm commented Dec 17, 2021

musm commented Dec 19, 2021

mkitti commented Dec 19, 2021 • edited Loading

musm Dec 13, 2021 •

edited

Loading

mkitti Dec 11, 2021 •

edited

Loading

musm Dec 15, 2021 •

edited

Loading

mkitti commented Dec 15, 2021 •

edited

Loading

mkitti commented Dec 15, 2021 •

edited

Loading

mkitti commented Dec 16, 2021 •

edited

Loading

mkitti commented Dec 19, 2021 •

edited

Loading