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main.tex
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% -*- mode: latex; mode: visual-line; fill-column: 9999; coding: utf-8 -*-
%
% For submission to 'Concurrency and Computation: Practice and Experience'
% http://www.cc-pe.net/journalinfo/index.html
%
% ACM classifiers https://www.acm.org/publications/computing-classification-system/1998
% D.1.3 Concurrent Programming (parallel)
% J.2 PHYSICAL SCIENCES AND ENGINEERING
%
\documentclass[LATO1COL]{WileyNJD-v2}
\usepackage[numbers,super,sort&compress]{NJDnatbib}
%%%%%%%%%%%%%%%%%%%%%%%
%% Wiley bibliography styles
%%%%%%%%%%%%%%%%%%%%%%%
% included with AMA option
%%\bibliographystyle{WileyNJD-AMA}
%
% use home-grown BST file with author-year capabilities, implementing
% subset of AMA as in https://wol-prod-cdn.literatumonline.com/pb-assets/assets/15320634/amaguide-1509470359000.pdf
% and derived from WileyNJD-AMA
\bibliographystyle{WileyNJD-CCPE}
\makeatletter
\renewcommand{\@biblabel}[1]{\quad#1.}
\makeatother
% fix doi (not sure how to properly enable it in my bst)
\usepackage{hyperref}
\renewcommand{\doi}[1]{doi: \href{https://doi.org/#1}{#1}}
%------------------------------------------------------------
\input{preamble.tex}
\input{commands.tex}
%------------------------------------------------------------
\articletype{Research Article}%
\received{\color{red}Added at production}
\revised{\color{red}Added at production}
\accepted{\color{red}Added at production}
\raggedbottom
%%%%%%%%%%%%%%%%%%%%%%%
\begin{document}
\title{Parallel Performance of Molecular Dynamics Trajectory Analysis}
%% Group authors per affiliation:
\author[1]{Mahzad Khoshlessan}
\author[2]{Ioannis Paraskevakos}
\author[3]{Geoffrey C. Fox}
\author[2]{Shantenu Jha}
\author[1,4]{Oliver Beckstein*}
\authormark{KHOSHLESSAN \textsc{et al}}
\address[1]{\orgdiv{Department of Physics}, \orgname{Arizona State University},
\orgaddress{Tempe, AZ 85281}, \country{USA}}
\address[2]{\orgdiv{Department of Electrical \& Computer Engineering},
\orgname{Rutgers University}, \orgaddress{Piscataway, NJ 08854}, \country{USA}}
\address[3]{\orgdiv{Digital Science Center}, \orgname{Indiana University},
\orgaddress{Bloomington, IN 47405}, \country{USA}}
\address[4]{\orgdiv{Center for Biological Physics}, \orgname{Arizona State University},
\orgaddress{Tempe, AZ 85281}, \country{USA}}
\corres{*Oliver Beckstein, \orgdiv{Department of Physics}, \orgname{Arizona State University},
\orgaddress{Tempe, AZ 85281}, \country{USA}. \email{[email protected]}}
\input{abstract.tex}
\keywords{Python, MPI, HPC, MDAnalysis, MPI I/O, HDF5, Straggler, Molecular Dynamics, Big Data, Trajectory Analysis}
\maketitle
\input{introduction.tex}
\input{background.tex}
\input{applications.tex}
\input{system.tex}
\input{methods.tex}
\input{experiments.tex}
\input{clusters.tex}
\input{guideline.tex}
\input{conclusion.tex}
\section*{Acknowledgements}
\label{acknowledgements}
% The \ack command is supposed to generate the Acknowledgements section but it doesn't.
\ack
We are grateful to Sarp Oral for insightful comments on this manuscript.
This work was supported by the National Science Foundation under grant numbers ACI-1443054 and ACI-1440677.
This work used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation grant number ACI-1548562.
\emph{SDSC Comet} at the San Diego Supercomputer Center, \emph{LSU SuperMic} at Louisiana State University, and \emph{PSC Bridges} at the Pittsburgh Supercomputing Center were used under allocations TG-MCB090174 and TG-MCB130177.
\bibliography{main}
\clearpage
\appendix
\input{additional_data.tex}
\input{shiftload.tex}
\input{chainreader.tex}
\end{document}