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Diffstat (limited to 'issues')
| -rw-r--r-- | issues/slow-correlations.gmi | 70 |
1 files changed, 51 insertions, 19 deletions
diff --git a/issues/slow-correlations.gmi b/issues/slow-correlations.gmi index 169eb95..092c340 100644 --- a/issues/slow-correlations.gmi +++ b/issues/slow-correlations.gmi @@ -1,29 +1,46 @@ + # Slow Correlations and UI crashes -Correlations for huge data set(like the exo dataset) is very slow; and the UI crashes. +Correlation in gn2 has regressed when compared gn1 + +Issue experienced by users include + +* Correlation being slow + +* Browser crush and timeout for huge datasets like (exo dataset) + + ## Tags * type: bug * priority: critical -* assigned: bonfacekilz, alex +* assigned: alexm, bonfacekilz * keywords: correlations, ui, crash * status: in progress ## Tasks -* [ ] Caching slow queries -* [ ] Server side pagination +[x] separation of concerns +split between correlation code and code to database part +for easier debug + +[x] optimize db queries + +[x] Cache for huge datasets in text files + +[x] Cache for traits metadata + +[x] refactor data structures used + +[x] limit number of results rendered to user + +[] implement parralel computation for correlation -## Background +[] Server side pagination -First, what we've done: -- Optimised a bunch of SQL. -- https://mariadb.com/kb/en/query-cache/ -- General code clean-up in some places. -- Futile experiments with code parallelisation. -- Add a "test compute" button. More on this later. +### Background on the issue As Rob has pointed out before, gn2 is much much slower than gn1. Before, we mistakenly thought that it was because that it only @@ -97,9 +114,11 @@ mechanism which he can feel free to try out: Separate the actual "computation" and the "pre-fetching" in code. And see what takes time. -# Notes -#### Mon 18 Oct 2021 12:42:17 PM EAT + +# Updates + +### Mon 18 Oct 2021 12:42:17 PM EAT Atm GN2 is un-usable for Rob for basic tours and show-and-tells, and it is a persistent problem that is getting worse the more he @@ -112,11 +131,24 @@ computing from a materialized view of the database that is intentionally designed for a fast web service. -## Update -implementation of caching for huge datasets done.Moreover -this has also been implemented for metadata hence speeding -up the correlation immensely. -Code for correlation has also undergone refactoring to optimise -the datastrcutures used
\ No newline at end of file +# Notes + +### Tue, 12 April 2022 + +Most of the above issue have been addressed + +correlation speed has greatly improved no complain't +on the issue as of 12/04/2022 + +for example the dataset below no longer crashes for this datashe computa + +=> http://gn2.genenetwork.org/show_trait?trait_id=ENSG00000244734&dataset=GTEXv8_Wbl_tpm_0220 + +Also, wrt to parralel computation +implementation in python leads +to memory error for forked processes and +is best implemented in a different +language if the issue arises + |