Difference between revisions of "User:Frodo"

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This is the Frodo user page.  Frodo is one of the identities John Irwin uses for maintaining the wiki and ZINC.
 
This is the Frodo user page.  Frodo is one of the identities John Irwin uses for maintaining the wiki and ZINC.
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* Curator: [[Idioms]] [[ZINC15:videos]]
  
 
move dbraw disks
 
move dbraw disks

Latest revision as of 17:42, 3 May 2021

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

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>/...