User:Frodo: Difference between revisions
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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 | |||
on dock | |||
service httpd start | |||
(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>/...