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| author | Pjotr Prins | 2025-11-27 08:02:24 +0100 |
|---|---|---|
| committer | Pjotr Prins | 2025-11-29 13:02:49 +0100 |
| commit | 2016c6465085a7e02b92db6db1d22456d4e4ad5f (patch) | |
| tree | d36f4e7179edcafb81c2eed7d9fd9a821b40482f | |
| parent | 0773ded8f7beede31d6e111be4f4a16a7282b37a (diff) | |
| download | gn-ai-2016c6465085a7e02b92db6db1d22456d4e4ad5f.tar.gz | |
Speed up gemma
| -rw-r--r-- | issues/genetics/speeding-up-gemma.gmi | 8 |
1 files changed, 5 insertions, 3 deletions
diff --git a/issues/genetics/speeding-up-gemma.gmi b/issues/genetics/speeding-up-gemma.gmi index eb99b99a..a6a959b0 100644 --- a/issues/genetics/speeding-up-gemma.gmi +++ b/issues/genetics/speeding-up-gemma.gmi @@ -24,9 +24,10 @@ There is no such thing as a free lunch. So, let's dive in. * - [X] convert genotypes to lmdb * - [ ] replace GEMMA ReadGenotypes * - [ ] replace reading genotypes in AnalyzeBimbam -* [ ] Use lmdb for SNPs? -* [ ] Optimize openblas for target architecture -* [ ] Try a faster malloc library for GEMMA +* [ ] Use lmdb for SNPs +* [X] Optimize openblas for target architecture +* [ ] Perhaps try a faster malloc library for GEMMA +* [ ] Fix sqrt(NaN) when running big file example with -debug * [ ] Other improvements... # Analysis @@ -396,6 +397,7 @@ Compare that with guile: (result-collector result-channel 2))))) ``` +The Boost fiber is a relatively mature library now, with about 8+ years of development and real-world usage. Interestingly Boost.fibers has work stealing built in. We can look at that later: => https://www.boost.org/doc/libs/1_66_0/libs/fiber/doc/html/fiber/worker.html |