Sysadmin idioms: Difference between revisions

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Restart SEA15
= Cluster 2 =
* login to tau, become www
See progress of raid rebuild, eg on aleph.
* source /nfs/soft/www/apps/sea/sea15/env.csh
cat /proc/mdstat
* run run-sea-server.sh


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)
= Cluster 0 =
Disc space panic (cluster 0)
Disc space panic (cluster 0)
  sudo /usr/sbin/repquota /raid1 | sort -nrk3 | head
  sudo /usr/sbin/repquota /raid1 | sort -nrk3 | head
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  ~teague/Scripts/sshnodes.py to call ~teague/batch/mount-diva2.sh  
  ~teague/Scripts/sshnodes.py to call ~teague/batch/mount-diva2.sh  


= So obvious as to no longer be worth of being documented =
Clear errors on jobs
Clear errors on jobs
  qstat -u adler | grep Eqw | cut -f 1 -d ' ' | xargs qmod -cj
  qstat -u adler | grep Eqw | cut -f 1 -d ' ' | xargs qmod -cj
Line 16: Line 30:
  source env.csh
  source env.csh
  zincserver.restart-backend.sh
  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?
queue stuck?
  Try qmod -c *lamed and qmod -e *@lamed
  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)
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 {} \;
  find /scratch/adler -mindepth 1 -mtime +3 -exec rm -rvf {} \;


Restart ZINC15
 
on tau:
 
  cd /nfs/soft/www/apps/zinc15/zinc15-env/lib/python2.7/site-packages/zinc/data/models
  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
  source /nfs/soft/www/apps/zinc15/zinc15-env/env.csh
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  zincserver.start-backend.sh
  zincserver.start-backend.sh
  killall -9 gunicorn
  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


[[Category:Sysadmin]]
[[Category:Sysadmin]]
[[Category:Idioms]]
[[Category:Idioms]]

Revision as of 17:33, 17 August 2017

Cluster 2

See progress of raid rebuild, eg on aleph.

cat /proc/mdstat

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)

Cluster 0

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 

So obvious as to no longer be worth of being documented

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

queue stuck?

Try qmod -c *lamed and qmod -e *@lamed

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 {} \;

Restart ZINC15

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