Difference between revisions of "User:Frodo"

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This is the Frodo user page.
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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.
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* Curator: [[Idioms]] [[ZINC15:videos]]
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move dbraw disks
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/opt/bks/src/cluster/puppet/modules/bks-nfs_mounts/
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chcon system_u:object_r:nfs_t:s0 ex3/dbraw/zinc/?? ex3/dbraw/zinc ex3/dbraw ex3
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ln -sf /nfs/ex3/dbraw/zinc/80 .
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puppet module build .
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how to monitor on mem
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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;"'
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= things to explore =
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* kekule.js
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= idioms =
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Build covalent library as jji
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qsub -t 1-1 ~/bin/example_covalent_wrapper.sh `readlink -f ..`
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Build non-cov library as jji
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http://zinc15.docking.org/genes/EGFR/activities/subsets/100nM/having/substance/subsets/fda/
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Build non-cov library as xyz
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Run sea kraken as xyz
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qsub -t 1-N ~/bin/sea-wrapper.csh `readlink -f ..`
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Set up for cov dock
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$DOCKBASE/docking/setup/setup_db2.csh /nfs/work/jji/docking/lib2/ahl/one/gz_files
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$DOCKBASE/docking/submit/submit.csh
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cd /opt/bks/src/cluster/puppet/modules/bks-packages/manifests
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vi init.pp and add package
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puppet parser validate init.pp
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cd ..
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vi Modulefile (up number)
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puppet module build .
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puppet module install -f pkg/bks-packages-0.0.26.tar.gz
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Then on client machine (or just wait 30 mins, assuming puppet agent is running)
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puppet agent -t
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(in the zinc15-env)
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python -m zinc.management shell (Open a ZINC15 shell)
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python -m zinc.management server (Start a single-core test server)
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zincserver.start-backend.sh (start the multicore backend as the current user)
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zincserver.stop-backend.sh (stop the multicore backend as the current user)
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Config/logs/pid file, etc. is all in /nfs/soft/www/apps/zinc15/run/<HOSTNAME>/...
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[[Category:Lab members]]
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[[Category:jji]]

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>/...