Skip to content

Latest commit

 

History

History
70 lines (60 loc) · 3.37 KB

ChangeLog.md

File metadata and controls

70 lines (60 loc) · 3.37 KB
Raw

ChangeLog.md for MetaHipMer version 2 (aka MHM2 or mhm2)

This is the ChangeLog for MetaHipMer with development at bitbucket

2.1.0 2022-01-24

  • Major updates to GPU offloading in kcount - PR #48
    • Removed bloom filters from CPU & GPU kcount
  • Counting quotient filter in kcount (GPU only) - PR #54
  • Fixed potential deadlock in kcount atomics PR #55, Issue #108
  • Read shuffling based on minimizer kmers, not alignments
  • Improved GPU autodetection and initialization
  • Trimming of read adapters
  • Other PR #40, #42, #44, #45, #46, #49, #51, #53, #55
  • Minor bugfixes Issue #97, #112, #86, #63, #109, #107, #83, #91, #92, #25, #37, #89
  • Fixed mhm2.py script for PBS - Issue #32

2.0.1.2 2021-04-22

  • A very minor bugfix release to facilitate building against UPC++ 2021.3.0

2.0.1 2020-12-17

  • Use minimizer hashes to improve locality of kmers and greatly speed up deBruijn graph traversal - pull request #18
  • Aggregate messages in LocalAssem reducing overall time other optimizations in preparation for GPU acceleration - pull request #17, #16
  • Fixed scaling Issues - #52, #54, #61, #72
  • Fixed cmake/build - Issues #20, #51, #55, #68, #67
  • Fixed paired read usage - Issue #58
  • Fixed minor UI Issues - #53, #33, #50, #46, #45, #80, #78, #77, #79
  • Fixed edge cases of improper lustre striping - Issue #62, #70
  • Added framework for unit tests
  • Added a ability to build a docker image
  • Added better support for paired reads - Issue #65, #64
  • Added better support for unpaired read - Issue #59
  • Better post-assembly sam and depths file - Issue #71
  • Corrected CIGAR alignments in some cases

2.0.0 2020-09-30

  • Updated documentation and added a user guide.
  • Incorporated a 3 tier aggregating store to allow scaling on 1000s of nodes Issue #4
  • Fixed stall on summit with over 200 node - Issue #34
  • Improved reading of multiple input files - Issue #38
  • Greatly improved CI testing, including quality tests - Issue #22
  • Fixed error when writing to a lagging filesystem - Issues #26 #15
  • Various bug fixes - Issues #27 #29 #31 #36 #44
  • Included build support for MacOSX (not tested)
  • Various cosmetic - Issues #38 #40 #42 #47 #43
    • Renamed from MHMXX to MHM2 - Issue #18
    • Reformatted the entire code base

0.1.3 2020-08-20

  • Added support for GPU in alignments with CUDA-enabled detection and build
    • major refactor of adept-sw for better performance and ease of building
  • Fixed fastq reader edge cases in record boundary detection
  • Support in options for 1 contig and 1 scaffolding round
  • Optimal execution environment on Summit with custom spawner
  • Better checkpointing support
  • Various fixes from upcxx-utils including ofstream bugs

0.1.2 2020-07-06

  • Semi-stable alpha release
  • Added skeleton for CI building on cori and hulk development server
  • Fixed re-build issues with upcxx-utils
  • Added warning on build and install when submodule is out of date
  • Various fixes for Summit build including vector support for SSW alignment
  • Added support for more cluster schedulers
  • Added --paired-reads support and modified Fastq class to support two-file libraries
  • Fixed LUSTRE striping on per_thread rank logs

0.1.1 Before 2020-07-01

  • Complete rewrite of MetaHipMer 1.0 using only UPC++