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| -rw-r--r-- | issues/slow-correlations.gmi | 14 | ||||
| -rw-r--r-- | topics/bnw/GN2-BNW-data-transfer.gmi | 33 |
2 files changed, 47 insertions, 0 deletions
diff --git a/issues/slow-correlations.gmi b/issues/slow-correlations.gmi index 30cd980..955800c 100644 --- a/issues/slow-correlations.gmi +++ b/issues/slow-correlations.gmi @@ -91,3 +91,17 @@ Something cool that Alex pointed is an interesting "manual" testing 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 + +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 +complains. Correlation is slower than it was ever before; and search +is broken. For a simple search of 10,000 phenotypes, it takes a lot of +time to compute. + +According to Rob, GN1 does not rely on a cache. Instead it is +computing from a materialized view of the database that is +intentionally designed for a fast web service.
\ No newline at end of file diff --git a/topics/bnw/GN2-BNW-data-transfer.gmi b/topics/bnw/GN2-BNW-data-transfer.gmi index 427d608..e4ef6d0 100644 --- a/topics/bnw/GN2-BNW-data-transfer.gmi +++ b/topics/bnw/GN2-BNW-data-transfer.gmi @@ -26,3 +26,36 @@ but is not accepted by the latest version of BNW. ## Notes Found the PHP file on Xeon. Sent to Jesse for comment. Made a backup on rabbit. + +### Run bnw test instance + +``` + # Launch php-fpm + guix environment --ad-hoc php -- php-fpm --fpm-config php-fpm.conf + + # Launch nginx + guix environment -L guix-past/modules -L guix-bioinformatics bnw --ad-hoc nginx -- nginx -p tmp/var/run/nginx - +c nginx.conf + + # To see the BNW website + # From your local machine: + ssh -L 8888:localhost:8888 -N penguin2 + # and then it should be visible in your webbrowser at localhost:8888 + # I believe any local changes should be reflected immediately. + # I believe any local changes should be reflected immediately. + + # stopping nginx + kill $(pgrep nginx -u jessez | head -n1) + + # stopping php-fpm + kill $(pgrep php-fpm -u jessez | head -n1) +``` + +When you have that running I can switch over the BNW website to yours, +so you can test run with GN. Do run BNW from GN you can: + +1. Search for 'shh' in http://genenetwork.org/ +2. checkbox the 3 results +3. hit the BNW button + + |