Sysadmin idioms
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restart SEA
1. login to tau 2. become www 3. source /nfs/soft/www/apps/sea/sea15/env.csh 4. run run-sea-server.sh
Disc space panic (cluster 0)
sudo /usr/sbin/repquota /raid1 | sort -nrk3 | head
Save time as sysadmin C0
~teague/Scripts/sshnodes.py to call ~teague/batch/mount-diva2.sh
Clear errors on jobs
qstat -u adler | grep Eqw | cut -f 1 -d ' ' | xargs qmod -cj
Start server
source env.csh zincserver.restart-backend.sh
see progress of raid rebuild, eg on aleph.
cat /proc/mdstat
grant access on bet:
xfs_quota -xc "limit bsoft=1000g bhard=1500g tbalius" /srv/work
maximum FP FK referenced from substance
select max(ecfp4_fk) from substance;
how many protomers
select count(prot_id) from protomer;
how many substances
select count(sub_id) from substance;
max FP reference in FP master join table:
select max(ecfp4_fk) from fingerprints.ecfp4_data
queue stuck?
Try qmod -c *lamed and qmod -e *@lamed
fire up a vm per sarah/matt
ssh to he as s_xxx sudo virsh vncdisplay phi # Shows the VNC port phi is running on (vnc port 0) sudo vrish edit phi # Open phi's config # search for passwd ( /passwd<ENTER> ) #copy down VNC password #:q! # Exit vim exit # Exit virsh exit # Log out of he vncviewer he:<VNCPORT> (vncviewer he:0) Enter password log in restart: sshd, mysql, iptables, network (if it can't ping)
clean away old scratch files on nodes before your job starts (adler as example user)
find /scratch/adler -mindepth 1 -mtime +3 -exec rm -rvf {} \;
on tau:
cd /nfs/soft/www/apps/zinc15/zinc15-env/lib/python2.7/site-packages/zinc/data/models source /nfs/soft/www/apps/zinc15/zinc15-env/env.csh zincserver.restart-backend.sh zincserver.start-backend.sh killall -9 gunicorn
time wget --user gpcr --password xtal -O - "http://zinc15.docking.org/substances.txt:smiles,zinc_id,purchasability?purchasability:gt=10&mwt:le=350&mwt:gt=50&logp:le=3.5&structure.num_rotatable_bonds:le=7&structure:contains=[C;D1]%3D[CD3]C(%3DO)OC&count=all" | tee 18.txt | cat -n
update purchasability:
update substance set purchasability = substance_best_purchasability(sub_id) where sub_id in (select sub_id from substance where purchasability is null limit 10000);