Global Matching Sphere Optimization - Revision history

Iamkaant at 22:18, 17 April 2026

2026-04-17T22:18:50Z

← Older revision		Revision as of 22:18, 17 April 2026
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	==== Gimel ====		==== Gimel ====
	Juggler is in <code>/mnt/nfs/exa/work/ak87/UCSF/JUGGLER/SCRIPTS/JUGGLER</code>		Juggler is in <code>/mnt/nfs/exa/work/ak87/UCSF/JUGGLER/SCRIPTS/JUGGLER</code>

	Subdock is in <code>/mnt/nfs/exa/work/ak87/PROGRAM/SUBDOCK/SUBDOCK</code>		Subdock is in <code>/mnt/nfs/exa/work/ak87/PROGRAM/SUBDOCK/SUBDOCK</code>

	You can use this file to submit to SLURM queue		You can use this file to submit to SLURM queue

	<syntaxhighlight lang="bash">		<syntaxhighlight lang="bash">
	#! /bin/bash		#! /bin/bash
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	==== Wynton ====		==== Wynton ====

	Juggler is in <code>/wynton/group/bks/work/ak87/UCSF/JUGGLER/SCRIPTS/JUGGLER</code>		Juggler is in <code>/wynton/group/bks/work/ak87/UCSF/JUGGLER/SCRIPTS/JUGGLER</code>

	Subdock is in <code>/wynton/group/bks/work/ak87/UCSF/JUGGLER/SCRIPTS/SUBDOCK</code>		Subdock is in <code>/wynton/group/bks/work/ak87/UCSF/JUGGLER/SCRIPTS/SUBDOCK</code>

	You can use this file to submit to SLURM queue		You can use this file to submit to SLURM queue

	<syntaxhighlight lang="bash">		<syntaxhighlight lang="bash">
	#! /bin/bash		#! /bin/bash

Iamkaant: updated for the new version

2026-04-17T22:16:34Z

updated for the new version

Show changes

Iamkaant at 00:20, 20 July 2023

2023-07-20T00:20:02Z

← Older revision		Revision as of 00:20, 20 July 2023
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	* Gimel (gimel2/gimel5/n-1-XXX ...)		* Gimel (gimel2/gimel5/n-1-XXX ...)

	<code>~~ource~~ /nfs/soft/ian/python3.8.5.sh</code>		<code>source /nfs/soft/ian/python3.8.5.sh</code>

	<code>python /nfs/home/ak87/PROGRAM/juggler/juggler-v0.8.py 2&>1 > juggler.log</code>		<code>python /nfs/home/ak87/PROGRAM/juggler/juggler-v0.8.py 2&>1 > juggler.log</code>
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	* Gimel (gimel2/gimel5/n-1-XXX ...)		* Gimel (gimel2/gimel5/n-1-XXX ...)

	<code>~~ource~~ /nfs/soft/ian/python3.8.5.sh</code>		<code>source /nfs/soft/ian/python3.8.5.sh</code>

	<code>sh /nfs/home/ak87/PROGRAM/juggler/rundockd-v0.8.sh</code>		<code>sh /nfs/home/ak87/PROGRAM/juggler/rundockd-v0.8.sh</code>

Iamkaant at 00:19, 20 July 2023

2023-07-20T00:19:13Z

← Older revision		Revision as of 00:19, 20 July 2023
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	<code>python /wynton/group/bks/soft/juggler/juggler-v0.8.py 2&>1 > juggler.log</code>		<code>python /wynton/group/bks/soft/juggler/juggler-v0.8.py 2&>1 > juggler.log</code>

	* Gimel		* Gimel (gimel2/gimel5/n-1-XXX ...)

	<code>ource /nfs/soft/ian/python3.8.5.sh</code>		<code>ource /nfs/soft/ian/python3.8.5.sh</code>
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	* Wynton		* Wynton

			<code>source /wynton/group/bks/soft/python_envs/python3.8.5.sh</code>

	<code>sh /wynton/group/bks/soft/juggler/rundockd-v0.8.sh</code>		<code>sh /wynton/group/bks/soft/juggler/rundockd-v0.8.sh</code>

	* Gimel		* Gimel (gimel2/gimel5/n-1-XXX ...)

			<code>ource /nfs/soft/ian/python3.8.5.sh</code>

	<code>sh /nfs/home/ak87/PROGRAM/juggler/rundockd-v0.8.sh</code>		<code>sh /nfs/home/ak87/PROGRAM/juggler/rundockd-v0.8.sh</code>

Iamkaant at 00:16, 20 July 2023

2023-07-20T00:16:39Z

← Older revision		Revision as of 00:16, 20 July 2023
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	* Gimel		* Gimel

	<code>~~source~~ /~~wynton/group/bks~~/soft/~~python_envs~~/python3.8.5.sh</code>		<code>ource /nfs/soft/ian/python3.8.5.sh</code>

	<code>python /nfs/home/ak87/PROGRAM/juggler/juggler-v0.8.py 2&>1 > juggler.log</code>		<code>python /nfs/home/ak87/PROGRAM/juggler/juggler-v0.8.py 2&>1 > juggler.log</code>

Iamkaant: updated to describe the new version of Juggler

2023-07-17T16:04:16Z

updated to describe the new version of Juggler

Show changes

Iamkaant at 20:38, 3 May 2023

2023-05-03T20:38:56Z

← Older revision		Revision as of 20:38, 3 May 2023
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	So far, the program is running on Wynton. LMK if you are interested in launching it on Gimel or other clusters.		So far, the program is running on Wynton. LMK if you are interested in launching it on Gimel or other clusters.

	The scripts and example config file are in <code>/wynton/~~home~~/~~irwin~~/~~ak87~~/~~ak87/UCSF/NEOCORTEX/SCRIPTS/RELEASE~~</code>		The scripts and example config file are in <code>/wynton/group/bks/soft/juggler</code>

	=== Preparation ===		=== Preparation ===
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	<code>source /wynton/group/bks/soft/python_envs/python3.8.5.sh</code>		<code>source /wynton/group/bks/soft/python_envs/python3.8.5.sh</code>

	<code>python /wynton/~~home~~/~~irwin~~/~~ak87~~/~~ak87/UCSF/NEOCORTEX/SCRIPTS/RELEASE~~/juggler.py</code>		<code>python /wynton/group/bks/soft/juggler/juggler.py</code>

	You can detach from the screen (Ctrl-A d).		You can detach from the screen (Ctrl-A d).
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	Open a new screen. In the same directory launch a docking daemon		Open a new screen. In the same directory launch a docking daemon

	<code>/wynton/~~home~~/~~irwin~~/~~ak87~~/~~ak87/UCSF/NEOCORTEX/SCRIPTS/RELEASE~~/rundockd-wynton-taskid.sh</code>		<code>/wynton/group/bks/soft/juggler/rundockd-wynton-taskid.sh</code>

	You can run other calculations on Wynton in the meantime, as Juggler will track the task IDs that it launched.		You can run other calculations on Wynton in the meantime, as Juggler will track the task IDs that it launched.
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	You can also track the optimization progress running the following script in your working directory:		You can also track the optimization progress running the following script in your working directory:

	<code>/wynton/~~home~~/~~irwin~~/~~ak87~~/~~ak87/UCSF/NEOCORTEX/SCRIPTS/RELEASE~~/plot_all_metrics.py</code>		<code>/wynton/group/bks/soft/juggler/plot_all_metrics.py</code>

	It produces <code>combined_metrics.png</code>		It produces <code>combined_metrics.png</code>

Iamkaant at 00:02, 2 May 2023

2023-05-02T00:02:35Z

← Older revision		Revision as of 00:02, 2 May 2023
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	The program will stop after 200 generations if convergence is not reached. In case it takes too long you can stop it any time by pressing Ctrl-C. It doesn't mean that you have no results, though. Juggler generates <code>combined_metrics.dat</code> file in the working directory, which contains metrics for all sets explored. It contains the following columns:		The program will stop after 200 generations if convergence is not reached. In case it takes too long you can stop it any time by pressing Ctrl-C. It doesn't mean that you have no results, though. Juggler generates <code>combined_metrics.dat</code> file in the working directory, which contains metrics for all sets explored. It contains the following columns:

	Generations Set# NormLogAUC RMSD Nsph Combined_metrics		Generations Set# NormLogAUC RMSD Nsph Combined_metrics

	You can paste its content into Excel, sort by the highest NormLogAUC and pick a MS set of your liking.		You can paste its content into Excel, sort by the highest NormLogAUC and pick a MS set of your liking.

Iamkaant at 00:01, 2 May 2023

2023-05-02T00:01:45Z

← Older revision		Revision as of 00:01, 2 May 2023
Line 60:		Line 60:

	'''If not converged'''		'''If not converged'''

	The program will stop after 200 generations if convergence is not reached. In case it takes too long you can stop it any time by pressing Ctrl-C. It doesn't mean that you have no results, though. Juggler generates <code>combined_metrics.dat</code> file in the working directory, which contains metrics for all sets explored. It contains the following columns:		The program will stop after 200 generations if convergence is not reached. In case it takes too long you can stop it any time by pressing Ctrl-C. It doesn't mean that you have no results, though. Juggler generates <code>combined_metrics.dat</code> file in the working directory, which contains metrics for all sets explored. It contains the following columns:
	Generations Set# NormLogAUC RMSD Nsph Combined_metrics		Generations Set# NormLogAUC RMSD Nsph Combined_metrics
	You can paste its content into Excel, sort by the highest NormLogAUC and pick a MS set of your liking.		You can paste its content into Excel, sort by the highest NormLogAUC and pick a MS set of your liking.

Iamkaant at 00:01, 2 May 2023

2023-05-02T00:01:25Z

← Older revision		Revision as of 00:01, 2 May 2023
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	[[File:Combined metrics plot from a GA run.png\|thumb\|Combined metrics plot from a GA run]]		[[File:Combined metrics plot from a GA run.png\|thumb\|Combined metrics plot from a GA run]]

	* If not converged*		'''If not converged'''
	The program will stop after 200 generations if convergence is not reached. In case it takes too long you can stop it any time by pressing Ctrl-C. It doesn't mean that you have no results, though. Juggler generates <code>combined_metrics.dat</code> file in the working directory, which contains metrics for all sets explored. It contains the following columns:		The program will stop after 200 generations if convergence is not reached. In case it takes too long you can stop it any time by pressing Ctrl-C. It doesn't mean that you have no results, though. Juggler generates <code>combined_metrics.dat</code> file in the working directory, which contains metrics for all sets explored. It contains the following columns:
	Generations Set# NormLogAUC RMSD Nsph Combined_metrics		Generations Set# NormLogAUC RMSD Nsph Combined_metrics
	You can paste its content into Excel, sort by the highest NormLogAUC and pick a MS set of your liking.		You can paste its content into Excel, sort by the highest NormLogAUC and pick a MS set of your liking.