Software:tinkergpu - Revision history

Pren: /* Compile Tinker9 */

2024-10-11T16:35:00Z

Compile Tinker9

← Older revision		Revision as of 16:35, 11 October 2024
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	</syntaxhighlight>This is to say, after downloading Tinker9, make a build directory in tinker9 home directory. Then running the above should do everything.		</syntaxhighlight>This is to say, after downloading Tinker9, make a build directory in tinker9 home directory. Then running the above should do everything.
			==2024 Tinker compiling==
			To build tinker9 on Rocky 9.3 Linux cuda 11.8, gcc 11.4, cmake 3.28
			<syntaxhighlight lang="bash">
			git clone https://github.com/TinkerTools/tinker9 tinker9_R93
			cd tinker9_R93 && mkdir build
			cd build
			cp /home/pren/tinker9/run.sh.r9 .
			./run.sh.r9
			in run.sh.r9:
			#!/bin/bash

			# build on bme-sugar
			# Chengwen Liu
			rm -fr .sh src Make cmake-* tinker9
			export CUDAHOME=/usr/local/cuda-11.8
			export CUDACXX=$CUDAHOME/bin/nvcc
			export FC=gfortran compute_capability=70 gpu_lang=cuda cmake ..
			export cuda_dir=$CUDAHOME
			export CMAKEHOME=/home/pren/Software/cmake-3.28.0/bin
			$CMAKEHOME/cmake ..
			make -j 6
			</syntaxhighlight>

	== Example ==		== Example ==

Pren at 18:00, 19 September 2023

2023-09-19T18:00:31Z

← Older revision		Revision as of 18:00, 19 September 2023
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			[[Category:labsoftware]]
	==Tinker9 GPU Molecular Dynamics==		==Tinker9 GPU Molecular Dynamics==

Pren: /* Run Script */

2023-02-04T17:34:16Z

Run Script

← Older revision		Revision as of 17:34, 4 February 2023
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	nohup tinker9 dynamic your.xyz -k your.key 1000 2.0 2.0 4 298.15 1.0 >your.log 2>&1 &		nohup tinker9 dynamic your.xyz -k your.key 1000 2.0 2.0 4 298.15 1.0 >your.log 2>&1 &

	To use Tinker 9 on RTX4090 or A6000, node15x & node 16x		To use Tinker 9 on RTX4090 or A6000, node15x & node 16x, or 30x0/20x0 with older Xeon processors (eg node 10x, node4x):
	#!/bin/bash		#!/bin/bash
	export TINKER9=/home/pren/tinker9/tinker9_xeon/build/		export TINKER9=/home/pren/tinker9/tinker9_xeon/build/

Pren: /* Run Script */

2023-02-04T17:30:47Z

Run Script

← Older revision		Revision as of 17:30, 4 February 2023
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	To use Tinker 9 on RTX4090 or A6000, node15x & node 16x		To use Tinker 9 on RTX4090 or A6000, node15x & node 16x
	#!/bin/bash		#!/bin/bash
	export TINKER9=/home/pren/tinker9/~~tinker9_4090~~/build/		export TINKER9=/home/pren/tinker9/tinker9_xeon/build/
	export CUDA_DEVICE_ORDER=PCI_BUS_ID		export CUDA_DEVICE_ORDER=PCI_BUS_ID
	export CUDA_VISIBLE_DEVICES=0 # device number if there are multiple GPU cards		export CUDA_VISIBLE_DEVICES=0 # device number if there are multiple GPU cards
	$TINKER9/tinker9 dynamic bench7.xyz -k bench7.key 5000 2.0 400.0 4 298.15 1.0 N > out &		$TINKER9/tinker9 dynamic bench7.xyz -k bench7.key 5000 2.0 400.0 4 298.15 1.0 N > out &

	~~To use Tinker9~~ on xeon ~~processor~~ (tacc node, see lscpu~~) use the CW 2205 built, or below latest build (Jan 2023~~)		The above also tested on RTX 30x0 with older xeon processors (tacc node, see "lscpu")

Pren: /* Run Script */

2023-02-04T17:19:15Z

Run Script

← Older revision		Revision as of 17:19, 4 February 2023
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	export CUDA_VISIBLE_DEVICES=0 # device number if there are multiple GPU cards		export CUDA_VISIBLE_DEVICES=0 # device number if there are multiple GPU cards
	$TINKER9/tinker9 dynamic bench7.xyz -k bench7.key 5000 2.0 400.0 4 298.15 1.0 N > out &		$TINKER9/tinker9 dynamic bench7.xyz -k bench7.key 5000 2.0 400.0 4 298.15 1.0 N > out &

			To use Tinker9 on xeon processor (tacc node, see lscpu) use the CW 2205 built, or below latest build (Jan 2023)

Pren at 20:34, 27 January 2023

2023-01-27T20:34:20Z

← Older revision		Revision as of 20:34, 27 January 2023
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	nohup tinker9 dynamic your.xyz -k your.key 1000 2.0 2.0 4 298.15 1.0 >your.log 2>&1 &		nohup tinker9 dynamic your.xyz -k your.key 1000 2.0 2.0 4 298.15 1.0 >your.log 2>&1 &

	To use Tinker 9 on RTX4090, node15x & node 16x		To use Tinker 9 on RTX4090 or A6000, node15x & node 16x
	#!/bin/bash		#!/bin/bash
	export TINKER9=/home/pren/tinker9/tinker9_4090/build/		export TINKER9=/home/pren/tinker9/tinker9_4090/build/

Pren: /* Run Script */

2023-01-27T20:29:58Z

Run Script

← Older revision		Revision as of 20:29, 27 January 2023
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	# option 2 to run dynamic		# option 2 to run dynamic
	nohup tinker9 dynamic your.xyz -k your.key 1000 2.0 2.0 4 298.15 1.0 >your.log 2>&1 &		nohup tinker9 dynamic your.xyz -k your.key 1000 2.0 2.0 4 298.15 1.0 >your.log 2>&1 &

			To use Tinker 9 on RTX4090, node15x & node 16x
			#!/bin/bash
			export TINKER9=/home/pren/tinker9/tinker9_4090/build/
			export CUDA_DEVICE_ORDER=PCI_BUS_ID
			export CUDA_VISIBLE_DEVICES=0 # device number if there are multiple GPU cards
			$TINKER9/tinker9 dynamic bench7.xyz -k bench7.key 5000 2.0 400.0 4 298.15 1.0 N > out &

Pren: /* Compile Tinker9 */

2023-01-12T22:55:00Z

Compile Tinker9

← Older revision		Revision as of 22:55, 12 January 2023
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	== Compile Tinker9 ==		== Compile Tinker9 ==
	Please read Tinker9 Github site for how to setup the environmental variables and compile Tinker9 code (https://github.com/TinkerTools/tinker9). Successful builds on various hardware and cuda version can also be found at https://github.com/TinkerTools/tinker9/discussions/121.		Please read Tinker9 Github site for how to setup the environmental variables and compile Tinker9 code (https://github.com/TinkerTools/tinker9). Successful builds on various hardware and cuda version can also be found at https://github.com/TinkerTools/tinker9/discussions/121.

			Note that Tinker9 required "matching" canonical Tinker 8, which should be automated by CMAKE script now.https://github.com/TinkerTools/tinker9/blob/master/README.md



	As of May 23, 2022, Ren lab clusters equiped with GPU cards all have cuda version 11 with compatitable cuda driver. Here is a script file to compile tinker9 <syntaxhighlight lang="bash">		As of May 23, 2022, Ren lab clusters equiped with GPU cards all have cuda version 11 with compatitable cuda driver. Here is a script file to compile tinker9 <syntaxhighlight lang="bash">

Liuchw: /* Compile Tinker9 */

2022-05-23T21:45:51Z

Compile Tinker9

← Older revision		Revision as of 21:45, 23 May 2022
Line 15:		Line 15:
	Please read Tinker9 Github site for how to setup the environmental variables and compile Tinker9 code (https://github.com/TinkerTools/tinker9). Successful builds on various hardware and cuda version can also be found at https://github.com/TinkerTools/tinker9/discussions/121.		Please read Tinker9 Github site for how to setup the environmental variables and compile Tinker9 code (https://github.com/TinkerTools/tinker9). Successful builds on various hardware and cuda version can also be found at https://github.com/TinkerTools/tinker9/discussions/121.

	As of May 23, 2022, Ren lab clusters equiped with GPU cards all have cuda version 11 with compatitable cuda driver. ~~An example~~ compile ~~script can be found at:~~ <syntaxhighlight lang="bash">		As of May 23, 2022, Ren lab clusters equiped with GPU cards all have cuda version 11 with compatitable cuda driver. Here is a script file to compile tinker9 <syntaxhighlight lang="bash">
	/home/liuchw/~~Softwares~~/~~tinkers~~/~~Tinker9~~/~~2205~~/~~build_cuda11~~/~~compile_cuda11~~.2		#!/bin/bash
	</syntaxhighlight>This is to say, after downloading Tinker9, make a ~~folder called "build_cuda11". From that folder,~~ .~~/compile_cuda11.2 will~~ do everything.
			# build on bme-sugar
			# Chengwen Liu

			rm -fr .sh src Make cmake-* tinker9

			export CUDAHOME=/usr/local/cuda-11.2
			export CUDACXX=$CUDAHOME/bin/nvcc
			export FC=/usr/bin/gfortran
			export CXX=/usr/bin/g++
			export ACC=/home/liuchw/shared/nvidia/hpc_sdk/Linux_x86_64/21.1/compilers/bin/nvc++
			export opt=release
			export host=0
			export prec=m
			export compute_capability=60,70,75,80
			export cuda_dir=$CUDAHOME
			export CMAKEHOME=/home/liuchw/shared/cmake3.21/bin/

			$CMAKEHOME/cmake ..

			make -j


			</syntaxhighlight>This is to say, after downloading Tinker9, make a build directory in tinker9 home directory. Then running the above should do everything.

	== Example ==		== Example ==

	Example setup, xyz and key files for protein simulations:~~ ~~[https://github.com/TinkerTools/tinker9/blob/master/example/ https://github.com/TinkerTools/tinker9/blob/master/example/]		Example setup, xyz and key files for protein simulations: [https://github.com/TinkerTools/tinker9/blob/master/example/ https://github.com/TinkerTools/tinker9/blob/master/example/]

	Recommend to use RESPA integrator with 2fs time step and write out less frequent (e.g. every 2 ps). On RTX3070, you should be able to achieve ~40ns/day for DHFR.		Recommend to use RESPA integrator with 2fs time step and write out less frequent (e.g. every 2 ps). On RTX3070, you should be able to achieve ~40ns/day for DHFR.

Liuchw: /* Run Script */

2022-05-23T21:40:11Z

Run Script

← Older revision		Revision as of 21:40, 23 May 2022
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	#!/bin/bash		#!/bin/bash

			# set the GPU device
			export CUDA_DEVICE_ORDER=PCI_BUS_ID
			export CUDA_VISIBLE_DEVICES=0 # set to 1,2, etc to specify the one you want

			# add tinker9 executables to PATH
	export TINKER9=/home/liuchw/Softwares/tinkers/Tinker9/2205/build_cuda11		export TINKER9=/home/liuchw/Softwares/tinkers/Tinker9/2205/build_cuda11
	export PATH=$PATH:$TINKER9		export PATH=$PATH:$TINKER9

	# option 1		# option 1 to run dynamic
	nohup dynamic9 your.xyz -k your.key 1000 2.0 2.0 4 298.15 1.0 >your.log 2>&1 &		nohup dynamic9 your.xyz -k your.key 1000 2.0 2.0 4 298.15 1.0 >your.log 2>&1 &

	# option 2		# option 2 to run dynamic
	nohup tinker9 dynamic your.xyz -k your.key 1000 2.0 2.0 4 298.15 1.0 >your.log 2>&1 &		nohup tinker9 dynamic your.xyz -k your.key 1000 2.0 2.0 4 298.15 1.0 >your.log 2>&1 &