Software:forcebalance - Revision history

Yanxing: Minor update

2024-04-05T06:44:19Z

Minor update

← Older revision		Revision as of 06:44, 5 April 2024
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	http://leeping.github.io/forcebalance/doc/ForceBalance-Manual.pdf		http://leeping.github.io/forcebalance/doc/ForceBalance-Manual.pdf

	=='''~~Customization and parallelization for AMOEBA and AMOEBA+ force fields~~'''==		=='''Configurate which nodes to submit jobs on'''==

	~~1. Backup original FB source files~~		See [https://github.com/leucinw/Software-mod/blob/master/forcebalance-1.7.5/external/nodes.dat Software-mod/forcebalance-1.7.5/external/nodes.dat], which looks like the following
	~~<pre> export condaHOME =~~ /~~home~~/~~liuchw~~/~~anaconda3~~/~~envs~~/~~FB17~~/~~lib~~/~~python3~~.7/~~site~~-~~packages~~/forcebalance ~~(change this accordingly)~~		<pre>#===========================================
	~~cp $condaHOME/binding~~.~~py $condaHOME/binding~~.~~py_back~~		# Any line starts with "#" will be ignored.
	~~cp $condaHOME~~/~~liquid.py $condaHOME~~/~~liquid~~.~~py_back~~		# Only the first two columns matter !!
	~~cp $condaHOME/tinkerio~~.~~py $condaHOME/tinkerio.py_back~~		# Add / remove nodes as needed.
	~~cp $condaHOME/parser.py $condaHOME/parser.py_back~~
	~~cp $condaHOME/data/npt.py $condaHOME/data~~/~~npt~~.~~py_back</pre>~~

	~~2. Download modified files and copy them to the anaconda lib directory~~		# This file is used by submitTinker.py,
	~~<pre> git clone git@github.com:leucinw/Software-mod.git modcode~~		# and must be placed in the same folder.
	~~export modfileHOME=/home/liuchw/modcode/forcebalance-1.7.5~~		# Do not change the filename.
	~~cp $modfileHOME/binding.py $condaHOME/binding~~.py		#===========================================
	~~cp $modfileHOME/liquid~~.~~py $condaHOME/liquid.py~~
	~~cp $modfileHOME/tinkerio~~.~~py $condaHOME/tinkerio.py~~
	~~cp $modfileHOME/parser.py $condaHOME/parser.py~~
	~~cp $modfileHOME/data/npt.py $condaHOME/data/npt.py~~
	~~cp $modfileHOME/minimum_match.py $condaHOME/minimum_match.py~~
	~~cp $modfileHOME/solvation.py $condaHOME/solvation.py~~
	~~</pre>~~

	~~The above customization mostly involves supports for AMOEBA+ keywords and parallelization of the serial jobs in:~~		### GPU nodes mainly use

	*Tinker binding energy calculations (<code>minimize</code> and <code>analyze</code>)		GPU node152 4090 2
	*Tinker post-MD <code>analyze</code> jobs
	*Tinker/Tinker9 <code>dynamic</code> jobs

	~~3. Set environmental variable TINKERPATH, and put the following files in the directory that $TINKERPATH points to~~		GPU node154 4090 2
	~~<div style="background:#eeeeee;border:1px solid #cccccc;padding:5px 10px;">analyze minimize dynamic optimize submitTinker.py nodes.dat</div>~~
	where, `analyze`, `minimize`, `dynamic` and `optimize` are Tinker8 executables; `submitTinker.py` is downloaded from Software-mod in the previous step. This script is responsible for submitting Tinker CPU and GPU ~~jobs on to Ren lab clusters. This script is reading node list from `nodes.dat` file, which looks like the following~~
	~~<div style="background:#eeeeee;border:1px solid #cccccc;padding:5px 10px;">#===========================================~~
	~~<nowiki>#</nowiki> Any line starts with "#" will be ignored.~~

	~~<nowiki>~~#~~</nowiki> Only the first two columns matter !!~~		#CPU nodes nthreads

	~~<nowiki>#</nowiki> This file is used by submitTinker.py~~		CPU node145 32

	~~<nowiki>#</nowiki>===========================================~~		CPU node146 32

	~~<nowiki>###</nowiki> GPU nodes mainly use~~		CPU node152 64

	~~GPU node152 4090 2~~		CPU node153 64
			</pre>
	~~GPU node154 4090 2~~

	~~<nowiki>#</nowiki>~~CPU ~~nodes nthreads~~

	~~CPU node145 32~~

	~~CPU node146 32~~

	~~CPU node152 64~~

	~~CPU node153~~ 64
	</~~div>4. Set the .forcebalance.bashrc, please change accordingly~~
	~~#!/usr/bin/bash~~
	~~source ~/.bashrc~~
	~~conda activate FB17~~

	~~export TINKERPATH=/home/liuchw/bin/TinkerGPU2022~~
	~~export PATH=$PATH:$TINKERPATH~~

	~~VAL=`nvidia-smi &~~> ~~/dev/null; echo $?`~~
	~~# check existence~~
	~~if [ $VALi!= 0 ]; then~~
	~~echo -e " \e[101mCUDA utility not installed on `hostname`\e[0m"~~
	~~else~~
	~~export tk9home=/home/liuchw/Softwares/tinkers/Tinker9/2403/build~~
	~~export DYNAMIC="$tk9home/dynamic9"~~
	~~export ANALYZE="$tk9home/analyze9"~~
	~~export BAR="$tk9home/bar9"~~
	~~export MINIMIZE="$tk9home/minimize9"~~
	~~export TESTGRAD="$tk9home/testgrad9"~~
	fi

	~~# used by ForceBalance.py via~~
	~~# os.environ["JOBPOOL"]~~
	~~# os.environ["FBBASHRC"]~~
	~~export JOBPOOL=/home/liuchw/bin/JobPool~~
	~~export FBBASHRC=/home/liuchw/.forcebalanceOrganic~~
	where there is another directory `JOBPOOL` needs to be set. In that directory, there are `subCPU.py` and `subGPU.py` which are keeping submitting the `*.sh` files appear in that directory. Please see `/home/liuchw/bin/JobPool` for detail. FBBASHRC is the absolute file path of the above bashrc file.

Yanxing: Updated tutorial according to new installer script.

2024-04-05T06:36:29Z

Updated tutorial according to new installer script.

← Older revision		Revision as of 06:36, 5 April 2024
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	<span style="font-size:medium">Here, a brief tutorial on how to install, set up, parallelize and run FB is provided below.   </span>		<span style="font-size:medium">Here, a brief tutorial on how to install, set up, parallelize and run FB is provided below.   </span>

	''See "/home/~~liuchw~~/FB-demo" for local files.''		''See "/home/yw24267/FB-demo" for local files.''

	== <span style="font-size:large">'''ForceBalance Installation'''</span> ==		== <span style="font-size:large">'''ForceBalance Installation'''</span> ==

	ForceBalance ~~can be installed in different ways~~. ~~Here I recommend installing FB through conda software manager (either Anaconda or Miniconda)~~. ~~For how to install conda~~, ~~please go to the anaconda download page ([~~https://~~www.anaconda~~.com/~~products~~/~~individual https://www~~.~~anaconda~~.~~com/products/individual])~~.		To make ForceBalance work better on Ren lab cluster, a great amount of modifications have been made based on version 1.7.5, which is recorded at https://github.com/leucinw/Software-mod. To install ForceBalance 1.7.5 along with all the modifications, run the following first.

	~~After you have conda installed, FB can be easily installed through the following commands:~~		<pre>git clone https://github.com/leucinw/Software-mod.git
	<pre> ~~conda create~~ --~~name FB17~~		cd Software-mod/forcebalance-1.7.5
	~~conda activate FB17~~		</pre>
	~~conda install~~ forcebalance=1.7.5</pre>

	~~Note that in~~ the ~~above we installed~~ forcebalance ~~version~~ 1.7.5. ~~If you need new features beyond this version, just remove "=~~1.7.5~~" in~~ the ~~above~~ installation. ~~Now~~ ForceBalance is installed. ~~You should be able to run (but not efficiently)~~ FB ~~jobs with~~ the ~~following settings~~.		The installer requires conda. For how to install conda, please go to the anaconda download page ([https://www.anaconda.com/products/individual https://www.anaconda.com/products/individual]). Then, open `installer.sh` and modify the variables at the beginning of the script to fit your case. You may also want to read [https://github.com/leucinw/Software-mod/blob/master/forcebalance-1.7.5/README.md Software-mod/forcebalance-1.7.5/README.md] for details before you continue. Then, simply running the following will complete the whole installation and patching for you.

			<pre>bash installer.sh</pre>

			If you need the original ForceBalance, it can be installed with conda directly.

			<pre>conda create --name FB forcebalance -c conda-forge</pre>

			Note that this will install the latest version without any modification for Ren lab cluster. See the official documentation for more installation methods.

	=='''<span style="font-size:large">ForceBalance input files</span>'''==		=='''<span style="font-size:large">ForceBalance input files</span>'''==

	<font size="3">In the following I will use amoeba water as an example. All the files are located in Renlab cluster at</font>		<font size="3">In the following I will use amoeba water as an example. All the files are located in Renlab cluster at</font>
	<div style="background:#eeeeee;border:1px solid #cccccc;padding:5px 10px;"><code>/home/~~liuchw~~/FB-demo~~/015_amoeba_tinker~~</code></div>		<div style="background:#eeeeee;border:1px solid #cccccc;padding:5px 10px;"><code>/home/yw24267/FB-demo</code></div>
	<font size="3">A  typical job of ForceBalance folder looks like: </font>		<font size="3">A  typical job of ForceBalance folder looks like: </font>
	<div style="background:#eeeeee;border:1px solid #cccccc;padding:5px 10px;"><code>├── example.in<br /> ├── forcefield<br /> │   └── water.prm<br /> └── targets<br />     ├── DimerMin<br />     ├── Interactions_CCSDT<br />     ├── Interactions_MP2<br/>     ├── Liquid<br />     ├── Monomer_Moments<br />     ├── Monomer_Vibration<br />     ├── cluster-02<br />     ├── cluster-03</code></div>		<div style="background:#eeeeee;border:1px solid #cccccc;padding:5px 10px;"><code>├── example.in<br /> ├── forcefield<br /> │   └── water.prm<br /> └── targets<br />     ├── DimerMin<br />     ├── Interactions_CCSDT<br />     ├── Interactions_MP2<br/>     ├── Liquid<br />     ├── Monomer_Moments<br />     ├── Monomer_Vibration<br />     ├── cluster-02<br />     ├── cluster-03</code></div>
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	<font size="3">A QM target folder (showing below) typically contains xyz files, interactions.key and interactions.txt, which defines the QM reference and how you calculate the interaction energy for AMOEBA. </font>		<font size="3">A QM target folder (showing below) typically contains xyz files, interactions.key and interactions.txt, which defines the QM reference and how you calculate the interaction energy for AMOEBA. </font>
	<div style="background:#eeeeee;border:1px solid #cccccc;padding:5px 10px;"><code>Interactions_CCSDT/<br /> ├── 01-Prism.xyz<br /> ├── 02-Cage.xyz<br /> ├── 03-Bag.xyz<br /> ├── 04-Cyclic-Chair.xyz<br /> ├── 05-Book-1.xyz<br /> ├── 06-Book-2.xyz<br /> ├── 07-Cyclic-Boat-1.xyz<br /> ├── 08-Cyclic-Boat-2.xyz<br /> ├── interactions.key<br /> ├── interactions.txt<br /> ├── monomer_exp.xyz<br /> ├── monomer_mp2.xyz<br /> ├── monomer_opt.xyz</code></div>		<div style="background:#eeeeee;border:1px solid #cccccc;padding:5px 10px;"><code>Interactions_CCSDT/<br /> ├── 01-Prism.xyz<br /> ├── 02-Cage.xyz<br /> ├── 03-Bag.xyz<br /> ├── 04-Cyclic-Chair.xyz<br /> ├── 05-Book-1.xyz<br /> ├── 06-Book-2.xyz<br /> ├── 07-Cyclic-Boat-1.xyz<br /> ├── 08-Cyclic-Boat-2.xyz<br /> ├── interactions.key<br /> ├── interactions.txt<br /> ├── monomer_exp.xyz<br /> ├── monomer_mp2.xyz<br /> ├── monomer_opt.xyz</code></div>
	<span style="font-size:small;">After setting up the above files, you should be able to run ForceBalance using the ~~simple command~~:</span>		<span style="font-size:small;">After setting up the above files, if you installed the modified version through the procedures stated above, you should be able to run ForceBalance using the following. Just make sure the tinkerpath in example.in is properly set! Note: The name of the bashrc file may vary depending what you set in the installer.sh file.</span>
	<div style="background:#eeeeee;border:1px solid #cccccc;padding:5px 10px;"><code><span style="font-size:medium">ForceBalance example.in</span></code></div>		<div style="background:#eeeeee;border:1px solid #cccccc;padding:5px 10px;"><code><span style="font-size:medium">source ~/.bashrc.FB17<br />ForceBalance example.in</span></code></div>
	If ForceBalance jobs crash, check the error message and modify your setting.  More information about settings in the example.in, please refer to ForceBalance manual file<span style="display: none"> </span>		If ForceBalance jobs crash, check the error message and modify your setting.  More information about settings in the example.in, please refer to ForceBalance manual file<span style="display: none"> </span>

Liuchw at 16:12, 3 April 2024

2024-04-03T16:12:10Z

← Older revision		Revision as of 16:12, 3 April 2024
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	cp $modfileHOME/tinkerio.py $condaHOME/tinkerio.py		cp $modfileHOME/tinkerio.py $condaHOME/tinkerio.py
	cp $modfileHOME/parser.py $condaHOME/parser.py		cp $modfileHOME/parser.py $condaHOME/parser.py
	cp $modfileHOME/data/npt.py $condaHOME/data/npt.py</pre>		cp $modfileHOME/data/npt.py $condaHOME/data/npt.py
			cp $modfileHOME/minimum_match.py $condaHOME/minimum_match.py
			cp $modfileHOME/solvation.py $condaHOME/solvation.py
			</pre>

	The above customization mostly involves supports for AMOEBA+ keywords and parallelization of the serial jobs in:		The above customization mostly involves supports for AMOEBA+ keywords and parallelization of the serial jobs in:

Liuchw at 14:52, 3 April 2024

2024-04-03T14:52:49Z

← Older revision		Revision as of 14:52, 3 April 2024
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	VAL=`nvidia-smi &> /dev/null; echo $?`		VAL=`nvidia-smi &> /dev/null; echo $?`
	# check existence		# check existence
	if [ $~~VAL~~ != 0 ]; then		if [ $VALi!= 0 ]; then
	echo -e " \e[101mCUDA utility not installed on `hostname`\e[0m"		echo -e " \e[101mCUDA utility not installed on `hostname`\e[0m"
	else		else
Line 117:		Line 117:
	fi		fi

			# used by ForceBalance.py via
	export JOBPOOL=/home/liuchw/bin/JobPool		# os.environ["JOBPOOL"]
	where there is another directory `JOBPOOL` needs to be set. In that directory, there are `subCPU.py` and `subGPU.py` which are keeping submitting the `*.sh` files appear in that directory. Please see `/home/liuchw/bin/JobPool` for detail.		# os.environ["FBBASHRC"]
			export JOBPOOL=/home/liuchw/bin/JobPool
			export FBBASHRC=/home/liuchw/.forcebalanceOrganic
			where there is another directory `JOBPOOL` needs to be set. In that directory, there are `subCPU.py` and `subGPU.py` which are keeping submitting the `*.sh` files appear in that directory. Please see `/home/liuchw/bin/JobPool` for detail. FBBASHRC is the absolute file path of the above bashrc file.

Liuchw: /* ForceBalance Installation */

2024-04-02T16:52:27Z

ForceBalance Installation

Show changes

Admin at 20:30, 16 November 2023

2023-11-16T20:30:11Z

← Older revision		Revision as of 20:30, 16 November 2023
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	<span style="font-size:medium">Here, a brief tutorial on how to install, set up, parallelize and run FB is provided below.   </span>		<span style="font-size:medium">Here, a brief tutorial on how to install, set up, parallelize and run FB is provided below.   </span>

	See "/home/liuchw/FB-demo" for local files.		''See "/home/liuchw/FB-demo" for local files.''

	== <span style="font-size:large">'''ForceBalance Installation'''</span> ==		== <span style="font-size:large">'''ForceBalance Installation'''</span> ==

Admin at 20:30, 16 November 2023

2023-11-16T20:30:00Z

← Older revision		Revision as of 20:30, 16 November 2023
Line 10:		Line 10:

	<span style="font-size:medium">Here, a brief tutorial on how to install, set up, parallelize and run FB is provided below.   </span>		<span style="font-size:medium">Here, a brief tutorial on how to install, set up, parallelize and run FB is provided below.   </span>

			See "/home/liuchw/FB-demo" for local files.

	== <span style="font-size:large">'''ForceBalance Installation'''</span> ==		== <span style="font-size:large">'''ForceBalance Installation'''</span> ==

Admin: /* test */

2023-11-16T20:29:21Z

test

← Older revision		Revision as of 20:29, 16 November 2023
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	[http://leeping.github.io/forcebalance/doc/ForceBalance-Manual.pdf http://leeping.github.io/forcebalance/doc/ForceBalance-Manual.pdf]		[http://leeping.github.io/forcebalance/doc/ForceBalance-Manual.pdf http://leeping.github.io/forcebalance/doc/ForceBalance-Manual.pdf]

	~~==test==~~
	=='''Customization and parallelization for AMOEBA(+)'''==		=='''Customization and parallelization for AMOEBA(+)'''==

Admin: /* Background */

2023-11-16T20:29:08Z

Background

← Older revision		Revision as of 20:29, 16 November 2023
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	= <span style="font-size:large">'''Background'''</span> =		== <span style="font-size:large">'''Background'''</span> ==

	<span style="font-size:medium">ForceBalance is an automatic force field parametrization tool developed by Lee-Ping Wang et al. It allows one to use both quantum chemical data and experimental observables of the liquid phase. It has been applied to parameterize a bunch of water models and organic molecules. The following examples are some of them.</span>		<span style="font-size:medium">ForceBalance is an automatic force field parametrization tool developed by Lee-Ping Wang et al. It allows one to use both quantum chemical data and experimental observables of the liquid phase. It has been applied to parameterize a bunch of water models and organic molecules. The following examples are some of them.</span>

Admin at 20:28, 16 November 2023

2023-11-16T20:28:34Z

← Older revision		Revision as of 20:28, 16 November 2023
Line 46:		Line 46:
	[http://leeping.github.io/forcebalance/doc/ForceBalance-Manual.pdf http://leeping.github.io/forcebalance/doc/ForceBalance-Manual.pdf]		[http://leeping.github.io/forcebalance/doc/ForceBalance-Manual.pdf http://leeping.github.io/forcebalance/doc/ForceBalance-Manual.pdf]

			==test==
	=='''Customization and parallelization for AMOEBA(+)'''==		=='''Customization and parallelization for AMOEBA(+)'''==