ZINC22:Singularity - Revision history

Btingle: /* how to build the singularity image */

2021-02-09T21:40:32Z

how to build the singularity image

← Older revision		Revision as of 21:40, 9 February 2021
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	singularity run build3d.simg		singularity run build3d.simg

	You may also want to use a working directory that isn't in the default singularity bindings (i.e default root directories like /tmp, /dev/shm), for example a /scratch directory~~, you would do the following:~~		You may also want to use a working directory that isn't in the default singularity bindings (i.e default root directories like /tmp, /dev/shm), for example a /scratch directory.

	...		...

Btingle: /* how to build the singularity image */

2021-02-09T21:37:45Z

how to build the singularity image

← Older revision		Revision as of 21:37, 9 February 2021
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	singularity run build3d.simg		singularity run build3d.simg

	SHRTCACHE specifies the base working directory for the script where temporary files will be saved. Without ~~adding~~ any additional entries to SINGULARITY_BINDPATH, the two sane choices for SHRTCACHE are /tmp or /dev/shm (the default).		SHRTCACHE specifies the base working directory for the script where temporary files will be saved. Without any additional entries to SINGULARITY_BINDPATH, the two sane choices for SHRTCACHE are /tmp or /dev/shm (the default).

	[[Category:ZINC22]]		[[Category:ZINC22]]
	[[Category:DOCK 3.8]]		[[Category:DOCK 3.8]]

Btingle: /* how to build the singularity image */

2021-02-09T21:36:13Z

how to build the singularity image

← Older revision		Revision as of 21:36, 9 February 2021
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	singularity run build3d.simg		singularity run build3d.simg

	SHRTCACHE specifies the base working directory for the script.		SHRTCACHE specifies the base working directory for the script where temporary files will be saved. Without adding any additional entries to SINGULARITY_BINDPATH, the two sane choices for SHRTCACHE are /tmp or /dev/shm (the default).

	[[Category:ZINC22]]		[[Category:ZINC22]]
	[[Category:DOCK 3.8]]		[[Category:DOCK 3.8]]

Btingle: /* how to build the singularity image */

2021-02-09T21:33:51Z

how to build the singularity image

← Older revision		Revision as of 21:33, 9 February 2021
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	export SINGULARITY_BINDPATH=$INPUT,$OUTPUT,$LOGGING,$(dirname $OE_LICENSE),$(dirname $CHEMAXON_LICENSE_URL)		export SINGULARITY_BINDPATH=$INPUT,$OUTPUT,$LOGGING,$(dirname $OE_LICENSE),$(dirname $CHEMAXON_LICENSE_URL)
	singularity run build3d.simg		singularity run build3d.simg

			You may also want to use a working directory that isn't in the default singularity bindings (i.e default root directories like /tmp, /dev/shm), for example a /scratch directory, you would do the following:

			...
			export SHRTCACHE=/scratch
			export SINGULARITY_BINDPATH=$SINGULARITY_BINDPATH,$SHRTCACHE
			singularity run build3d.simg

			SHRTCACHE specifies the base working directory for the script.

	[[Category:ZINC22]]		[[Category:ZINC22]]
	[[Category:DOCK 3.8]]		[[Category:DOCK 3.8]]

Btingle: /* how to use the singularity image */

2021-02-08T22:02:35Z

how to use the singularity image

← Older revision		Revision as of 22:02, 8 February 2021
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	export LOGGING= ((((wherever logs should go))))		export LOGGING= ((((wherever logs should go))))
	export SGE_TASK_ID=((((whatever you want, the script will evaluate the SGE_TASK_ID'th entry in $(find -type f $INPUT \| sort) ))))		export SGE_TASK_ID=((((whatever you want, the script will evaluate the SGE_TASK_ID'th entry in $(find -type f $INPUT \| sort) ))))
	export SGE_JOB_ID=~~test~~		export SGE_JOB_ID=((((again, whatever you want. Just a label for the job))))

	export SINGULARITY_BINDPATH=$LICENSE_DIR,$OUTPUT,$INPUT		export SINGULARITY_BINDPATH=$LICENSE_DIR,$OUTPUT,$INPUT

Btingle: /* how to build the singularity image */

2021-02-08T22:01:11Z

how to build the singularity image

← Older revision		Revision as of 22:01, 8 February 2021
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	export JOB_ID		export JOB_ID
	export SGE_TASK_ID		export SGE_TASK_ID
	export		export SINGULARITY_BINDPATH=$INPUT,$OUTPUT,$LOGGING,$(dirname $OE_LICENSE),$(dirname $CHEMAXON_LICENSE_URL)
	singularity run build3d.simg		singularity run build3d.simg

	[[Category:ZINC22]]		[[Category:ZINC22]]
	[[Category:DOCK 3.8]]		[[Category:DOCK 3.8]]

Btingle: /* how to build the singularity image */

2021-02-08T22:00:09Z

how to build the singularity image

← Older revision		Revision as of 22:00, 8 February 2021
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	export OUTPUT		export OUTPUT
	export LOGGING		export LOGGING
	export ~~LICENSE_DIR~~		export OE_LICENSE
			export CHEMAXON_LICENSE_URL
	export JOB_ID		export JOB_ID
	export SGE_TASK_ID		export SGE_TASK_ID

Btingle: /* how to build the singularity image */

2021-02-08T21:59:41Z

how to build the singularity image

← Older revision		Revision as of 21:59, 8 February 2021
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	== how to build the singularity image ==		== how to build the singularity image ==

	~~Ben~~, ~~we should write how~~ you ~~did it here~~.		BKS uses centos7 for our operating system, which can cause issues when building with singularity, particularly if you are building on ubuntu. See https://singularity.lbl.gov/building-centos-image for more details.

			The gist is, our singularity image needs to be built on a centos machine.

	~~Ben Wong wrote a page on [[Singularity]].~~		To build our image, simply pull the necessary files from dockerhub (link not yet here), chdir to the directory you just cloned and run the following command:

			singularity build build3d.simg Singularity3D

			The resulting build3d.simg can be used to run 3d building jobs with singularity.

			export INPUT
			export OUTPUT
			export LOGGING
			export LICENSE_DIR
			export JOB_ID
			export SGE_TASK_ID
			export
			singularity run build3d.simg

	[[Category:ZINC22]]		[[Category:ZINC22]]
	[[Category:DOCK 3.8]]		[[Category:DOCK 3.8]]

Frodo: asdf

2021-02-08T21:50:28Z

asdf

← Older revision		Revision as of 21:50, 8 February 2021
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	Ben, we should write how you did it here.		Ben, we should write how you did it here.


			Ben Wong wrote a page on [[Singularity]].


	[[Category:ZINC22]]		[[Category:ZINC22]]
	[[Category:~~DOCK3~~.8]]		[[Category:DOCK 3.8]]

Frodo: asdf

2021-02-08T21:49:06Z

asdf

New page

Info on using ZINC-22 3D building in singularity.

== how to use the singularity image ==
ok, the image is @ /nfs/home/xyz/soft/build3d.img
so, to run it, do the following:
LICENSE_DIR= ((((whatever you want it to be))))
export OE_LICENSE=$LICENSE_DIR/oe-license.txt (((((or whatever it is called)))))
export CHEMAXON_LICENSE_URL=$LICENSE_DIR/jchem-license.cxl

export OUTPUT= ((((some directory on the nfs where output is going))))
export INPUT= ((((some directory on nfs where input resides))))
export LOGGING= ((((wherever logs should go))))
export SGE_TASK_ID=((((whatever you want, the script will evaluate the SGE_TASK_ID'th entry in $(find -type f $INPUT | sort) ))))
export SGE_JOB_ID=test

export SINGULARITY_BINDPATH=$LICENSE_DIR,$OUTPUT,$INPUT

singularity run build3d.img

== how to build the singularity image ==

Ben, we should write how you did it here.

[[Category:ZINC22]]
[[Category:DOCK3.8]]