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.
 +
 +
= after a vmware1 failure =
 +
ssh root@vmware1.bkslab.org
 +
(based on C0,  twice)
 +
 +
vim-cmd vmsvc/getallvms
 +
vim-cmd vmsvc/power.on 1792
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on dock
 +
service httpd start
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(root on dock)
 +
 
= idioms =  
 
= idioms =  
 
Build covalent library as jji
 
Build covalent library as jji

Revision as of 02:31, 17 June 2016

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

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>/...