Sysadmin idioms - Revision history

Khtang: /* Cluster 2 */

2019-09-10T00:05:38Z

Cluster 2

← Older revision		Revision as of 00:05, 10 September 2019
Line 8:		Line 8:
	cat /proc/mdstat		cat /proc/mdstat

	add a new CNAME on alpha		add a new CNAME on alpha (''' DO NOT RUN THIS SCRIPT WITHOUT UNDERSTANDING WHAT IT DOES, IT COULD WIPE OUT ALL THE MACHINES CANONICAL NAMES ''')
	sudo /opt/bks/bin/add-host-alias nfs-db3 abacus		sudo /opt/bks/bin/add-host-alias nfs-db3 abacus
	then service named restart		then service named restart

2017-08-17T18:45:21Z

sadf

← Older revision		Revision as of 18:45, 17 August 2017
Line 7:		Line 7:
	See progress of raid rebuild, eg on aleph.		See progress of raid rebuild, eg on aleph.
	cat /proc/mdstat		cat /proc/mdstat

			add a new CNAME on alpha
			sudo /opt/bks/bin/add-host-alias nfs-db3 abacus
			then service named restart

	fire up a vm per sarah/matt		fire up a vm per sarah/matt

2017-08-17T17:35:23Z

asdf

@@ Line 1: / Line 1: @@
 = Cluster 2 =
 See progress of raid rebuild, eg on aleph.
   cat /proc/mdstat
@@ Line 30: / Line 35: @@
   source env.csh
   zincserver.restart-backend.sh
 queue stuck?

2017-08-17T17:33:55Z

asfd

@@ Line 1: / Line 1: @@
-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
 Disc space panic (cluster 0)
   sudo /usr/sbin/repquota /raid1 | sort -nrk3 | head
@@ Line 10: / Line 23: @@
   ~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
@@ Line 16: / Line 30: @@
   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
@@ Line 50: / Line 43: @@
   zincserver.start-backend.sh
   killall -9 gunicorn
 [[Category:Sysadmin]]
 [[Category:Idioms]]

2016-06-10T20:03:33Z

asdf

← Older revision		Revision as of 20:03, 10 June 2016
Line 58:		Line 58:
	update purchasability:		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 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]]

2015-10-01T23:39:22Z

asdf

← Older revision		Revision as of 23:39, 1 October 2015
Line 1:		Line 1:
	~~restart SEA~~		Restart SEA15
	1. login to tau		* login to tau, become www
	2. become www		* source /nfs/soft/www/apps/sea/sea15/env.csh
	3. source /nfs/soft/www/apps/sea/sea15/env.csh		* run run-sea-server.sh
	4. run run-sea-server.sh

	Disc space panic (cluster 0)		Disc space panic (cluster 0)
Line 14:		Line 13:
	qstat -u adler \| grep Eqw \| cut -f 1 -d ' ' \| xargs qmod -cj		qstat -u adler \| grep Eqw \| cut -f 1 -d ' ' \| xargs qmod -cj

	Start ~~server~~		Start/restart ZINC15
	source env.csh		source env.csh
	zincserver.restart-backend.sh		zincserver.restart-backend.sh

	~~see~~ progress of raid rebuild, eg on aleph.		See progress of raid rebuild, eg on aleph.
	cat /proc/mdstat		cat /proc/mdstat
	~~grant~~ access on bet:		Grant access on bet:
	xfs_quota -xc "limit bsoft=1000g bhard=1500g tbalius" /srv/work		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?		queue stuck?

2015-10-01T23:37:28Z

asdf

← Older revision		Revision as of 23:37, 1 October 2015
Line 54:		Line 54:
	find /scratch/adler -mindepth 1 -mtime +3 -exec rm -rvf {} \;		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

2015-10-01T23:30:03Z

asd

← Older revision		Revision as of 23:30, 1 October 2015
Line 13:		Line 13:
	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

			Start server
			source env.csh
			zincserver.restart-backend.sh

	see progress of raid rebuild, eg on aleph.		see progress of raid rebuild, eg on aleph.

2015-07-21T19:17:09Z

asdf

← Older revision		Revision as of 19:17, 21 July 2015
Line 1:		Line 1:
			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)		Disc space panic (cluster 0)

2015-06-22T18:19:14Z

asdf

← Older revision		Revision as of 18:19, 22 June 2015
Line 49:		Line 49:


			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);

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