indigodatacloudapps/ambertools-oneclient repository overview

⁠Ambertools

⁠Introduction

The docker image is Ubuntu 16.04 LTS with AmberTools v17 compiled with openmpi and with no mpi. The image is prepared to run as an application.

It is built from the ansible-role-ambertools

It depends/installs as well the oneclient in order to use oneprovider

Indigo-DataCloud has produced a tarball of AmberTools15 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-oneclient .

Or you can pull from the dockerhub

docker pull indigodatacloudapps/ambertools-oneclient

⁠Run the benchmark

The example below will run the sander benchmark.

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

⁠License

Apache v2

⁠Author Information

Mario David: [email protected]⁠

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/⁠