User:Frodo

This is the Frodo user page. Frodo is one of the identities John Irwin uses for maintaining the wiki and ZINC.

• Curator: Idioms ZINC15:videos

move dbraw disks

/opt/bks/src/cluster/puppet/modules/bks-nfs_mounts/
chcon system_u:object_r:nfs_t:s0 ex3/dbraw/zinc/?? ex3/dbraw/zinc ex3/dbraw ex3
ln -sf /nfs/ex3/dbraw/zinc/80 .
puppet module build .

how to monitor on mem

watch 'df /var/lib/pgsql ; tail  /var/lib/pgsql/9.2/data/pg_log/postgresql-Tue.log ; psql -c "select now() - pg_last_xact_replay_timestamp() AS replication_delay;"'

things to explore

• kekule.js

idioms

Build covalent library as jji

qsub -t 1-1 ~/bin/example_covalent_wrapper.sh `readlink -f ..`

Build non-cov library as jji

http://zinc15.docking.org/genes/EGFR/activities/subsets/100nM/having/substance/subsets/fda/

Build non-cov library as xyz

Run sea kraken as xyz

qsub -t 1-N ~/bin/sea-wrapper.csh `readlink -f ..`

Set up for cov dock

$DOCKBASE/docking/setup/setup_db2.csh /nfs/work/jji/docking/lib2/ahl/one/gz_files
$DOCKBASE/docking/submit/submit.csh

cd /opt/bks/src/cluster/puppet/modules/bks-packages/manifests
vi init.pp and add package
puppet parser validate init.pp
cd ..
vi Modulefile (up number)
puppet module build . 
puppet module install -f pkg/bks-packages-0.0.26.tar.gz

Then on client machine (or just wait 30 mins, assuming puppet agent is running)

puppet agent -t

(in the zinc15-env)

python -m zinc.management shell (Open a ZINC15 shell)
python -m zinc.management server (Start a single-core test server)

zincserver.start-backend.sh (start the multicore backend as the current user)
zincserver.stop-backend.sh (stop the multicore backend as the current user)

Config/logs/pid file, etc. is all in /nfs/soft/www/apps/zinc15/run/<HOSTNAME>/...