Sysadmin idioms

Restart SEA15

• login to tau, become www
• source /nfs/soft/www/apps/sea/sea15/env.csh
• 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/restart ZINC15

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

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);

update magdalena on work

quota -us mkorcz
xfs_quota -xc "limit bsoft=4000g bhard=4000g mkorcz" /srv/work
quota -us mkorcz