X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?p=unres.git;a=blobdiff_plain;f=doc%2F3.2.1%2Flatex%2Finstallman.tex;fp=doc%2F3.2.1%2Flatex%2Finstallman.tex;h=714438dac8999e5514a60d788257868e8b1c3675;hp=0000000000000000000000000000000000000000;hb=b75425747e3e2b448ca5e0ef8367712e1f339124;hpb=ce0fdb6f6e62a69055ec0f737c339851ee4b43b4 diff --git a/doc/3.2.1/latex/installman.tex b/doc/3.2.1/latex/installman.tex new file mode 100644 index 0000000..714438d --- /dev/null +++ b/doc/3.2.1/latex/installman.tex @@ -0,0 +1,313 @@ +\documentclass[12pt]{article} +%\usepackage{latex2html} +\usepackage{enumerate} +\usepackage{longtable} +\usepackage{hyperref} +\usepackage{amsmath} +\usepackage{color} +\parindent=0pt +\parskip=12pt +\textheight=24cm +\textwidth=18cm +\topmargin=-2.5cm +\oddsidemargin=-0.5cm +\setcounter{secnumdepth}{5} +\setcounter{tocdepth}{5} +\begin{document} +\sloppy + +\title{UNRES.3.2.1 -- INSTALLATION GUIDE} + +\author{Dawid Jagie{\l}a, Adam Liwo\\ Laboratory of Molecular Modeling\\ Faculty of Chemistry\\ University of Gdansk\\ Wita Stwosza 63\\ 80-308 Gdansk, Poland} + +\maketitle + +\newpage + +\tableofcontents + +\newpage + +\section{Putting the package on your system} +\label{section:put} + +The distribution is contained in the unrespack-v.3.2.1.tar.gz file. To put the package +on your system, copy the archive to your UNRES directory (you might want to create +an environmental variable, \$UNRESROOT or so, to define the location of UNRES on +your system) and say: + +\begin{verbatim} +gzip -cd unrespack-v.3.2.1.tar.gz | tar xf - +\end{verbatim} + +This will produce the directory structure shown in Figure \ref{fig:distr}. + +\begin{figure} +{\small +\begin{verbatim} +$UNRESROOT + | + |---------doc (documentation) + | + |---------PARAM (force field parameters) + | + |---------source + | | + | |-----unres (UNRES source codes; various versions) + | | | + | | |---src_MIN (only energy evaluation and minimization) + | | |---src_CSA (all functions except MD, includes CSA) + | | |---src_MD (all functions except CSA, includes MD, single chains) + | | |---src_MD-M (all functions except CSA, includes MD, oligomeric proteins) + | |-----wham (weighted analysis method source codes) + | | | + | | |---src (single chains) + | | |---src-M (oligomeric proteins) + | | + | |-----cluster (cluster analysis source coded) + | | | + | | |---clust-unres + | | | | + | | | |----src (input data from UNRES) + | | | + | | |---clust-wham (input data from WHAM) + | | | + | | |----src (for single-chain proteins) + | | |----src-M (for oligomeric proteins) + | | + | |-----xdrfpdb (file format conversion source codes) + | | + | |---src (single chains) + | |---src-M (oligomers) + | + |----------bin (C-shell script, batch scripts, and pre-compiled binaries) + | | + | |-----unres + | | | + | | |---CSA + | | |---MD + | | + | |-----wham + | |-----cluster + | |-----xdrfpdb + | + |--------examples + | + |-----unres + |-----wham + |-----cluster +\end{verbatim} +} +\caption{Directory structure of the unres-3.2.1 package} +\label{fig:distr} +\end{figure} + +\section{Installation options} +\label{sect:general} + +The most convenient way to install the package is using Cmake, as described +in section 2. If your system does not run the required version of Cmake or +installation does not work, do step-by-step compilation of the components +of the package, as described in section 3. + +\subsection{Requirements} + +\begin{description} +\item{--} C compiler +\item{--} Fortran compiler (must understant the Fortran 77 instructions) +\item{--} MPI (for CSA and MREMD) +\end{description} + +\section{Installation using Cmake} +\label{section:Cmake} + +\subsection{Requirements} + +\begin{description} +\item{--} CMake 2.8.0 or later +\item{--} C compiler +\item{--} Fortran compiler +\item{--} MPI (for CSA and MREMD) +\end{description} + +\subsection{Basic installation} + +These instructions give a very basic overview of how to configure, compile and +install UNRESPACK on most systems. If you are using unique install locations +and/or libraries that are not automatically detected please consult the 'Advanced' +section. + +\begin{enumerate} + +\item +Create a 'build' directory in the package source directory. + +\begin{verbatim} + mkdir build + cd build +\end{verbatim} + +\item +Configure the build system + +\begin{verbatim} + cmake .. +\end{verbatim} + +\item +Compile + +\begin{verbatim} + make +\end{verbatim} + +\item +Install + +\begin{verbatim} + sudo make install +\end{verbatim} + +\noindent or + +\begin{verbatim} + make install +\end{verbatim} + +\end{enumerate} + +\subsection{Advanced installation} + +The build system (CMake) provides mechanisms for specifying non-standard +build parameters. + +\begin{enumerate} + +\item +\underline{Compilers \& installation} + +\begin{verbatim} + -DCMAKE_Fortran_COMPILER=xxx equal to name of Fortran Compiler you wish to use + (ifort, gfortran) + + -DCMAKE_INSTALL_PREFIX=xxx specify the binaries installation prefix + (default UNRESPACK_source_dir/bin) +\end{verbatim} + +\item +\underline{Force fields} + +\begin{verbatim} + -DUNRES_MD_FF=xxx compiles the MD versions with given force field. + Options are: GAB, E0LL2Y. Default: GAB + + -DUNRES_CSA_FF=xxx compiles the CSA versions with given force field + Options are: CASP3, ALPHA, BETA, ALPHABETA, CASP5, 3P, 4P. Default: 4P. +\end{verbatim} + +Please read the online documentation on force fields available at + http://unres.eu/unres\#SECTION00090000000000000000 + + +\item +\underline{MPI} + +MPI implementation on your system should be automatically detected ("MPI Found" +message after runing cmake). If not you have two options: + +\begin{enumerate} + +\item +Try setting the path to you MPI wrapper implementation + +\begin{verbatim} + -DMPI_Fortran_COMPILER=xxx MPI wrapper +\end{verbatim} + +\item +If option 1 fails or your MPI implementation does not come with a compiler wrapper + try setting both the MPI include and library paths manually. This will circumvent + autodetection entirely. + +\begin{verbatim} + -DMPI_Fortran_INCLUDE_PATH=xxx + -DMPI_Fortran_LIBRARY="xxx" +\end{verbatim} + +\end{enumerate} +\end{enumerate} + +\section{Step-by-step installation} +\label{sect:stepbystep} + +For this installation, you will need to visit each source directory (see doc/UNRESPACK.txt +for directory structure). Specific installation instructions are in the documentation of +of the particular components of the package (UNRES, WHAM, CLUSTER, XDRFPDB). Only general +instructions are given here. + +\begin{enumerate} + +\item +Go to the respective source directory. + +\item +Determine if any of the Makefiles present there matches your needs. The Makefiles for +Intel Fortran and Gnu Fortran are present everywhere and are guaranteed to work (provided +that your compiler/MPI installation is correct). Use this Makefile as the working Makefile + +If your system uses a different compiler, copy the most matching Makefile to your working +Makefile (e.g., to Makefile\_CRAY if you'll be working with Cray Fortran). + +\item +Make a symbolic link of the working Makefile to Makefile, e.g., + +\begin{verbatim} +ln -s Makefile_gfortran Makefile +\end{verbatim} + +Before that, you'll need to remove the existing symbolic link (in the distribution, it +points to Makefile\_ifort). + +\item +Edit the Makefile to define MPI location, libraries, and the binaries directory +and executalble names, if you want to use different location/names from those in the +distribution Makefiles. The present locations are the subdirectories of the bin +directory and executable names include package component, compiler, MPI information, +and force field, e.g. unres\_csa\_gfort\_MPICH\_4P.exe stands for the CSA component, +compiled with GNU Fortran in a parallel mode (using MPICH) to run calculations with +the 4P force field. + +\item +For the components of XDRFPDB and in the directory cluster/unres/src, say + +\begin{verbatim} +make +\end{verbatim} + +In other directories say + +\begin{verbatim} +make +\end{verbatim} + +to create the respective executable. + +The compiler flags are specified for the 4P (also covers the 3P, and CASP5 ff), +GAB (also covers E0G), and E0LL2Y force fields for all components; the CASP3 force field +is also specified for the CSA and MINIM component. +\end{enumerate} + +\section{TECHNICAL SUPPORT CONTACT INFORMATION} +\label{sect:support} + + Dawid Jagie{\l}a\\ + Faculty of Chemistry, University of Gdansk\\ + ul. Wita Stwosza 63, 80-308 Gdansk Poland.\\ + fax: +48 58 523 5012\\ + e-mail: \href{mailto:lightnir@gmail.com}{lightnir@gmail.com}\\ + +\small{ + Prepared by Dawid Jagie{\l}a and Adam Liwo, 4/12/2014\\ +} + +\end{document}