User:Frodo

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

disk trouble?

echo 1 > /proc/sys/vm/drop_caches

after a vmware1 failure

ssh root@vmware1.bkslab.org
(based on C0,  twice)

vim-cmd vmsvc/getallvms

vim-cmd vmsvc/power.on 1792

on dock

service httpd start
(root on dock)

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>/...