{"items":[{"id":"6986c0ef-fd0d-46e1-9eb2-76d5790f3428","type":"push","org":"zhengqunkoo","repo":"smith-waterman","title":"Expanded documentation for project setup and execution","summary":"Updated the README to provide more explicit instructions on setting up the X10 environment and running the Smith-Waterman implementation. By clarifying the build process and including specific command examples for various test cases, it's now easier to get the project running. This should reduce friction for anyone setting up the repository for the first time.","url":"https://nomit.dev/zhengqunkoo/smith-waterman/status/880b0467a54a9a119c5f091547e86d3e79ea23ceacc8aac7c2466fc666ad34ae","author":"zhengqunkoo","contributors":["zhengqunkoo"],"updated_at":"2019-04-22T05:19:56+00:00"},{"id":"5ed3adab-d2a2-4d71-a1a0-c18c825f9dc5","type":"pull_request","org":"zhengqunkoo","repo":"smith-waterman","title":"Integrated vectorized and striped Smith-Waterman parallel implementations","summary":"This merge introduces high-performance vectorized and striped variations of the Smith-Waterman algorithm for sequence alignment. The update includes significant optimizations, such as replacing cell-based matrix structures with raw memory representations to reduce overhead, alongside improvements to parallel execution patterns. These additions provide researchers with multiple strategies for exploring hardware acceleration and cache-efficient sequence analysis. ![High Variance In Manual Vectorization Performance](https://i.ytimg.com/vi/tIYb95PmtJM/maxresdefault.jpg)","url":"https://nomit.dev/zhengqunkoo/smith-waterman/status/e73c0b8b73be86db0d174ac766592c73e8287a6e57247929f595ce13f5e6eccc","author":"haha001","contributors":["haha001","zhengqunkoo"],"updated_at":"2019-04-20T08:18:25+00:00"},{"id":"fce22615-fc89-442c-9fac-21808cd7afba","type":"push","org":"zhengqunkoo","repo":"smith-waterman","title":"Updated performance benchmark results for parvect","summary":"Updated the expected output and timing benchmarks for parvect across test suites including 'gap', 'men', and 'subst'. These changes reflect adjustments in the algorithm's output alignment and performance metrics. These updates ensure the regression test suite remains synchronized with the latest implementation.","url":"https://nomit.dev/zhengqunkoo/smith-waterman/status/e322b8b827a8af0e3fbfde289bcbbcd58d0f96bca742b847633b67293a18ec61","author":"zhengqunkoo","contributors":["zhengqunkoo"],"updated_at":"2019-04-20T08:16:48+00:00"},{"id":"3a4b0c4a-1202-4978-baa0-afeb8b4a4ef1","type":"push","org":"zhengqunkoo","repo":"smith-waterman","title":"Removed extra benchmark result files to keep the results set consistent and easier to interpret.","summary":"This change deletes duplicate or unnecessary files across several `results/*` benchmark directories, including gap, men, and subst variants in sequential, parallel, and vectorized runs. There’s no code change here, but it does clean up the recorded outputs so future comparisons and analysis are less noisy and less error-prone. The practical effect is a tidier benchmark corpus with fewer confusing extra entries.","url":"https://nomit.dev/zhengqunkoo/smith-waterman/status/080634b5b42710116d75ec8f68874089e3b2302ced5a858f559fdfbf0c407bcd","author":"zhengqunkoo","contributors":["zhengqunkoo"],"updated_at":"2019-04-20T08:15:04+00:00"},{"id":"4aa01e9a-7c28-41c4-b41f-d399a68d6e13","type":"push","org":"zhengqunkoo","repo":"smith-waterman","title":"Reinstated pure Long matrix optimization for the H-matrix to save memory","summary":"This update restores a previous memory optimization that replaces the `Cell` object matrix with a pure `Long` matrix for the H-matrix. By avoiding object allocation for each matrix cell, this significantly reduces the overall memory footprint and avoids object overhead. Ultimately, this change improves runtime performance and cache locality for the Smith-Waterman sequence alignment implementation.","url":"https://nomit.dev/zhengqunkoo/smith-waterman/status/a41fc6c4b202c1db13d0a1d6bfab2cbf2c90973be87dca2819e9ebcf1846b4ec","author":"zhengqunkoo","contributors":["zhengqunkoo"],"updated_at":"2019-04-20T07:30:11+00:00"}],"pagination":{"offset":0,"limit":5,"has_more":true}}