Sea16 restart - Revision history

Khtang at 17:34, 11 October 2019

2019-10-11T17:34:14Z

← Older revision		Revision as of 17:34, 11 October 2019
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	</pre>		</pre>

	[[Category:Curator]]		[[Category:Curator]][[Category:SEA]]

Matthew O'Meara at 18:10, 14 January 2019

2019-01-14T18:10:09Z

← Older revision		Revision as of 18:10, 14 January 2019
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	export PATH=/nfs/soft/www/apps/sea/conda_sea16/anaconda2/envs/sea16/bin:$PATH		export PATH=/nfs/soft/www/apps/sea/conda_sea16/anaconda2/envs/sea16/bin:$PATH
	export PATH=/nfs/home/momeara/opt/bin:$PATH		export PATH=/nfs/home/momeara/opt/bin:$PATH
			# In particular this needs the path to 'svgo' to optimize images of compounds to be sent to client

	source activate sea16		source activate sea16
	sh SEAserver/scripts/stop-sea-server.sh production		sh SEAserver/scripts/stop-sea-server.sh production

Matthew O'Meara at 14:08, 5 September 2017

2017-09-05T14:08:16Z

← Older revision		Revision as of 14:08, 5 September 2017
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	export PATH=/nfs/home/momeara/opt/bin:$PATH		export PATH=/nfs/home/momeara/opt/bin:$PATH
	source activate sea16		source activate sea16
	sh SEAserver/scripts/stop-sea-server.sh		sh SEAserver/scripts/stop-sea-server.sh production
	sh SEAserver/scripts/run-sea-server.sh		sh SEAserver/scripts/run-sea-server.sh production

Enkhjargal at 21:07, 9 August 2017

2017-08-09T21:07:14Z

← Older revision		Revision as of 21:07, 9 August 2017
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	ssh s_enkhee@gimel		ssh s_enkhee@gimel
			su - www
	cd /nfs/soft/www/apps/sea/conda_sea16/anaconda2/envs/sea16/src/seaware-academic/		cd /nfs/soft/www/apps/sea/conda_sea16/anaconda2/envs/sea16/src/seaware-academic/
	export PATH=/nfs/soft/www/apps/sea/conda_sea16/anaconda2/envs/sea16/bin:$PATH		export PATH=/nfs/soft/www/apps/sea/conda_sea16/anaconda2/envs/sea16/bin:$PATH
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	git pull		git pull
	git submodule update --init --recursive		git submodule update --init --recursive
			kill all sea-server related processes e.g. from htop
	make clean		make clean
	delete sea related libraries (fitcore, fpcore, libcore, seacore, seashell, seaserver) from your site-packages folder under the conda env		delete sea related libraries (fitcore, fpcore, libcore, seacore, seashell, seaserver) from your site-packages folder under the conda env
	rm -rf /nfs/soft/www/apps/sea/conda_sea16/anaconda2/envs/sea16/lib/python2.7/site-packages/seaserver		rm -rf /nfs/soft/www/apps/sea/conda_sea16/anaconda2/envs/sea16/lib/python2.7/site-packages/seaserver
	make all		make all
	~~kill all sea-server related processes e.g. from htop~~		make SEAserver-start-production
	make SEAserver-start-production ~~cd SEAserver~~

	# run the test:		# run the test:

Enkhjargal at 17:45, 6 July 2017

2017-07-06T17:45:58Z

← Older revision		Revision as of 17:45, 6 July 2017
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	export PATH=/nfs/home/momeara/opt/bin:$PATH		export PATH=/nfs/home/momeara/opt/bin:$PATH
	source activate sea16		source activate sea16
	~~cd SEAsever~~		sh SEAserver/scripts/stop-sea-server.sh
	sh scripts/stop-sea-server.sh		sh SEAserver/scripts/run-sea-server.sh
	sh scripts/run-sea-server.sh

Frodo: sdfg

2017-06-09T17:59:52Z

sdfg

← Older revision		Revision as of 17:59, 9 June 2017
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	make all		make all
	kill all sea-server related processes e.g. from htop		kill all sea-server related processes e.g. from htop
	cd SEAserver		make SEAserver-start-production cd SEAserver
	~~sh scripts/run~~-~~sea~~-~~server.sh~~

	# run the test:		# run the test:

Frodo: JJI small changes Jun 8 to make it work

2017-06-08T21:15:57Z

JJI small changes Jun 8 to make it work

← Older revision		Revision as of 21:15, 8 June 2017
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	git submodule update --init --recursive		git submodule update --init --recursive
	make clean		make clean
	delete sea related libraries (fitcore, fpcore, libcore, seacore, seashell, seaserver) from your site-packages folder under the conda env (rm -rf /nfs/soft/www/apps/sea/conda_sea16/anaconda2/envs/sea16/lib/python2.7/site-packages/seaserver)		delete sea related libraries (fitcore, fpcore, libcore, seacore, seashell, seaserver) from your site-packages folder under the conda env
			rm -rf /nfs/soft/www/apps/sea/conda_sea16/anaconda2/envs/sea16/lib/python2.7/site-packages/seaserver
	make all		make all
	kill all sea-server related processes e.g. from htop		kill all sea-server related processes e.g. from htop
	~~make~~ SEAserver-~~start~~		cd SEAserver
			sh scripts/run-sea-server.sh

	# run the test:		# run the test:

Enkhjargal at 18:51, 30 May 2017

2017-05-30T18:51:28Z

← Older revision		Revision as of 18:51, 30 May 2017
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	#		# Redis config

	As for the Redis warnings, these are not new, but probably something worth taking care of (https://redis.io/topics/admin):		As for the Redis warnings, these are not new, but probably something worth taking care of (https://redis.io/topics/admin):

Enkhjargal at 18:51, 30 May 2017

2017-05-30T18:51:08Z

← Older revision	Revision as of 18:51, 30 May 2017
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		#
		As for the Redis warnings, these are not new, but probably something worth taking care of (https://redis.io/topics/admin):

		add 'vm.overcommit_memory = 1' to /etc/sysctl.conf

		From here: The Linux kernel will always overcommit memory, and never check if enough memory is available. This increases the risk of out-of-memory situations, but also improves memory-intensive workloads.

		run echo never > /sys/kernel/mm/transparent_hugepage/enabled
		add 'echo never > /sys/kernel/mm/transparent_hugepage/enabled' to /etc/rc.local

		From here: Latency induced by transparent huge pages

		Unfortunately when a Linux kernel has transparent huge pages enabled, Redis incurs to a big latency penalty after the fork call is used in order to persist on disk. Huge pages are the cause of the following issue:

		Fork is called, two processes with shared huge pages are created.
		In a busy instance, a few event loops runs will cause commands to target a few thousand of pages, causing the copy on write of almost the whole process memory.
		This will result in big latency and big memory usage.

		Make sure to disable transparent huge pages using the following command:

		echo never > /sys/kernel/mm/transparent_hugepage/enabled

Enkhjargal at 18:43, 30 May 2017

2017-05-30T18:43:56Z

← Older revision		Revision as of 18:43, 30 May 2017
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	# restart conda_sea16 server		# restart conda_sea16 server

	~~ssh s_enkhee$n~~-~~1-110~~		screen -r sea16 on gimel
	cd /nfs/soft/www/apps/sea/conda_sea16/anaconda2/envs/sea16/src/seaware-academic/		cd /nfs/soft/www/apps/sea/conda_sea16/anaconda2/envs/sea16/src/seaware-academic/
	export PATH=/nfs/soft/www/apps/sea/conda_sea16/anaconda2/envs/sea16/bin:$PATH		export PATH=/nfs/soft/www/apps/sea/conda_sea16/anaconda2/envs/sea16/bin:$PATH
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	source activate sea16		source activate sea16
	cd SEAsever		cd SEAsever
			sh scripts/stop-sea-server.sh
	sh scripts/run-sea-server.sh		sh scripts/run-sea-server.sh

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	git submodule update --init --recursive		git submodule update --init --recursive
	make clean		make clean
	delete sea related libraries from your site-packages folder under the conda env (rm -rf /nfs/soft/www/apps/sea/conda_sea16/anaconda2/envs/sea16/lib/python2.7/site-packages/seaserver)		delete sea related libraries (fitcore, fpcore, libcore, seacore, seashell, seaserver) from your site-packages folder under the conda env (rm -rf /nfs/soft/www/apps/sea/conda_sea16/anaconda2/envs/sea16/lib/python2.7/site-packages/seaserver)
	make all		make all
	kill all sea-server related processes e.g. from htop		kill all sea-server related processes e.g. from htop
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	# run the test ~~to check~~:		# run the test:
	-> export SEA_APP_ROOT=$CONDA_PREFIX/var/seaserver		-> export SEA_APP_ROOT=$CONDA_PREFIX/var/seaserver
	-> export SEA_RUN_FOLDER=$SEA_APP_ROOT/run		-> export SEA_RUN_FOLDER=$SEA_APP_ROOT/run