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.
 
disk trouble?
 
echo 1 > /proc/sys/vm/drop_caches
 
 
mount -o remount /mnt/nfs/scratch/A
 
 
= 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 =  

Revision as of 17:36, 17 August 2017

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

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>/...