https://github.com/biocore/unifrac-binaries - Add unweighted_unnormalized method and AMD GPU support

What's Changed

• Add unweighted_unnormalized method by @sfiligoi in https://github.com/biocore/unifrac-binaries/pull/55
• Add dense pair support by @sfiligoi in https://github.com/biocore/unifrac-binaries/pull/57
• Add support for OpenMP Target GPU offload by @sfiligoi in https://github.com/biocore/unifrac-binaries/pull/49
• Refactor build system, CPU and GPU code now uses separate compilers by @sfiligoi in https://github.com/biocore/unifrac-binaries/pull/61, https://github.com/biocore/unifrac-binaries/pull/62, https://github.com/biocore/unifrac-binaries/pull/63, https://github.com/biocore/unifrac-binaries/pull/65,
• Added support for AMD GPU by @sfiligoi in https://github.com/biocore/unifrac-binaries/pull/66
• Additional performance optimization by @sfiligoi in https://github.com/biocore/unifrac-binaries/pull/67 , https://github.com/biocore/unifrac-binaries/pull/68
• Add proper support for ARM MacOS builds by @sfiligoi https://github.com/biocore/unifrac-binaries/pull/58, https://github.com/biocore/unifrac-binaries/pull/59
• Add support for SLES OS by @sfiligoi in https://github.com/biocore/unifrac-binaries/pull/69
• Properly handle empty table in _inmem version by @sfiligoi in https://github.com/biocore/unifrac-binaries/pull/54
• Filter elements with zero sample size in fathpd by @sfiligoi in https://github.com/biocore/unifrac-binaries/pull/53

Full Changelog: https://github.com/biocore/unifrac-binaries/compare/v1.4...v1.5

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Published by sfiligoi about 1 year ago

https://github.com/biocore/unifrac-binaries - Improve subsampling support

What's Changed

• Add support for subsampling without replacement by @sfiligoi in https://github.com/biocore/unifrac-binaries/pull/43
• Make subsampling with replacement multi-threaded by @sfiligoi in https://github.com/biocore/unifrac-binaries/pull/44
• Clean up the build process by @emollier in https://github.com/biocore/unifrac-binaries/pull/45 and by @mr-c in https://github.com/biocore/unifrac-binaries/pull/46

Full Changelog: https://github.com/biocore/unifrac-binaries/compare/v1.3.2...v1.4

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Published by sfiligoi almost 3 years ago

https://github.com/biocore/unifrac-binaries - Auto-detect CPU capabilities at runtime in Linux

What's Changed

• Tune the build procedure, use AVX2 for performance build by @sfiligoi in https://github.com/biocore/unifrac-binaries/pull/41
• Auto-detect CPU capabilities at runtime in Linux by @sfiligoi in https://github.com/biocore/unifrac-binaries/pull/42

Full Changelog: https://github.com/biocore/unifrac-binaries/compare/v1.3.1...v1.3.2

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Published by sfiligoi about 3 years ago

https://github.com/biocore/unifrac-binaries - Fix memory leak and improve build procedure

What's Changed

• Fix memory leak by @sfiligoi in https://github.com/biocore/unifrac-binaries/pull/39
• Add option to disable AVX optimization by @sfiligoi in https://github.com/biocore/unifrac-binaries/pull/37 and https://github.com/biocore/unifrac-binaries/pull/40
• Add oneoffmatrixinmemv2 by @sfiligoi in https://github.com/biocore/unifrac-binaries/pull/38

Full Changelog: https://github.com/biocore/unifrac-binaries/compare/v1.3...v1.3.1

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Published by sfiligoi about 3 years ago

https://github.com/biocore/unifrac-binaries - Add support for PERMANOVA, subsampling and the multi mode

What's Changed

• Allow to set random seed by @sfiligoi in https://github.com/biocore/unifrac-binaries/pull/31
• Add support for permanova by @sfiligoi in https://github.com/biocore/unifrac-binaries/pull/32
• Add support for subsampling with replacement by @sfiligoi in https://github.com/biocore/unifrac-binaries/pull/33
• Add multi mode by @sfiligoi in https://github.com/biocore/unifrac-binaries/pull/36

Full Changelog: https://github.com/biocore/unifrac-binaries/compare/v1.2.1...v1.3

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Published by sfiligoi about 3 years ago

https://github.com/biocore/unifrac-binaries - Better GPU detection and PCoA-only output

What's Changed

• Use OpenACC to detect GPU presence by @sfiligoi in https://github.com/biocore/unifrac-binaries/pull/25
• Add support for hdf5_nodist by @sfiligoi in https://github.com/biocore/unifrac-binaries/pull/27
• Bug fix: Enforce int64, to avoid overflow by @sfiligoi in https://github.com/biocore/unifrac-binaries/pull/28

Full Changelog: https://github.com/biocore/unifrac-binaries/compare/v1.2...v1.2.1

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Published by sfiligoi over 3 years ago

https://github.com/biocore/unifrac-binaries - Change default precision and deprecate -n

What's Changed

• Fix static hdf5 linking by @sfiligoi in https://github.com/biocore/unifrac-binaries/pull/15
• Reprecate -n and add --n-substeps by @sfiligoi in https://github.com/biocore/unifrac-binaries/pull/18
• Rename some of the variables to clarify semantics. No change in behavior by @sfiligoi in https://github.com/biocore/unifrac-binaries/pull/19
• Change default method precision to fp32, and add explicit _fp64 equivalent by @sfiligoi in https://github.com/biocore/unifrac-binaries/pull/20
• add citation by @wasade in https://github.com/biocore/unifrac-binaries/pull/16
• Request build on linux-gpu-cuda and cleanup code by @sfiligoi in https://github.com/biocore/unifrac-binaries/pull/22
• Reduce disk usage of the GPU compiler by @sfiligoi in https://github.com/biocore/unifrac-binaries/pull/23

Full Changelog: https://github.com/biocore/unifrac-binaries/compare/v1.1.3...v1.2

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Published by sfiligoi over 3 years ago

https://github.com/biocore/unifrac-binaries - Bug fix and speed improvements

A buffer overflow bug was fixed.

Moreover, the Unweighted Unifrac has been significantly sped up and there has been additional CPU speedups across the board, too.

What's Changed

• Add precomputed sums for Unweighted + bug fix by @sfiligoi in https://github.com/biocore/unifrac-binaries/pull/13
• Add tiling to speed CPU code by @sfiligoi in https://github.com/biocore/unifrac-binaries/pull/14

Full Changelog: https://github.com/biocore/unifrac-binaries/compare/v1.1.2...v1.1.3

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Published by sfiligoi over 3 years ago

https://github.com/biocore/unifrac-binaries - CPU optimizations

CPU optimizations yielding 1.5x speedup across the board on CPUs, no change to GPU performance.

What's Changed

• Add CPPFLAGS to R compile by @sfiligoi in https://github.com/biocore/unifrac-binaries/pull/7
• Add support for UNIFRACTIMINGINFO env variable by @sfiligoi in https://github.com/biocore/unifrac-binaries/pull/8
• Vectorize Weighted unifrac for CPUs by @sfiligoi in https://github.com/biocore/unifrac-binaries/pull/9
• Add larger unifrac tests by @sfiligoi in https://github.com/biocore/unifrac-binaries/pull/10
• Use plain mkstemp() if O_NOATIME is not available by @jmarshall in https://github.com/biocore/unifrac-binaries/pull/6
• More aggressive vectorization of Weighted by @sfiligoi in https://github.com/biocore/unifrac-binaries/pull/11
• Add zero checking to Unweighted for CPU code by @sfiligoi in https://github.com/biocore/unifrac-binaries/pull/12

New Contributors

• @jmarshall made their first contribution in https://github.com/biocore/unifrac-binaries/pull/6

Full Changelog: https://github.com/biocore/unifrac-binaries/compare/v1.1.1...v1.1.2

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Published by wasade over 3 years ago

https://github.com/biocore/unifrac-binaries - Address performance regression

The switch from 0.20.3 -> 1.0.0 introduced a 10% performance regression on CPUs by compiling for general targets. This minor release addresses the build change.

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Published by wasade about 4 years ago

https://github.com/biocore/unifrac-binaries - Expose in-memory API options

With this release, we introduce the ability to call the API using in-memory objects instead of requiring on-disk representations. We also parallelize a few components of the BIOM constructor.

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Published by wasade about 4 years ago

https://github.com/biocore/unifrac-binaries - Standalone UniFrac binaries package

Since the UniFrac binaries do not depend on python, this new package provides a simplified packaging solution for them. (unlike the original unifrac package where they originally lived)

Imported from unifrac 0.20.3.

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Published by sfiligoi over 4 years ago