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Last pushed: a month ago
Short Description
Docker image to run ambertools v16, single thread and OpenMPI
Full Description

Ambertools

Introduction

The docker image is Ubuntu 16.04 LTS with AmberTools v17 compiled with openmpi.
The image is prepared to run as an application. The installation directory is
/usr/local/amber16

It is built from the ansible-role-ambertools

Indigo-DataCloud has produced a tarball of AmberTools16 without the test directories
in order to decrease the size of the image, it is otherwise the same as the official
release: http://www.lip.pt/~david/AmberTools16_indigo-bin.tgz

Build the docker image

docker build -t ambertools .

Or you can pull from the dockerhub

docker pull indigodatacloudapps/ambertools

Run the benchmark

The example below will run the sander benchmark.

$ docker run indigodatacloudapps/ambertools \
/bin/bash -c 'source $AMBERHOME/amber.sh;cd $AMBERHOME/AmberTools/benchmarks/nab;time ./bench_amber gcn4p1'

Or you can instantiate and enter the container

$ docker run -it indigodatacloudapps/ambertools /bin/bash
# source $AMBERHOME/amber.sh
# cd $AMBERHOME/AmberTools/benchmarks/nab
# time ./bench_amber gcn4p1

License

Apache v2

Author Information

Mario David: mariojmdavid@gmail.com

LIP Lisbon: http://www.lip.pt

Indigo DataCloud: https://www.indigo-datacloud.eu/

Acknowledgments

Amber and AmberTools are the work of:
D.A. Case, J.T. Berryman, R.M. Betz, D.S. Cerutti, T.E. Cheatham, III, T.A. Darden, R.E. Duke,
T.J. Giese, H. Gohlke, A.W. Goetz, N. Homeyer, S. Izadi, P. Janowski, J. Kaus, A. Kovalenko,
T.S. Lee, S. LeGrand, P. Li, T. Luchko, R. Luo, B. Madej, K.M. Merz, G. Monard, P. Needham,
H. Nguyen, H.T. Nguyen, I. Omelyan, A. Onufriev, D.R. Roe, A. Roitberg, R. Salomon-Ferrer,
C.L. Simmerling, W. Smith, J. Swails, R.C. Walker, J. Wang, R.M. Wolf, X. Wu, D.M. York and P.A. Kollman (2015),
AMBER 2015, University of California, San Francisco.

http://ambermd.org/

Docker Pull Command
Owner
indigodatacloudapps

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