Commit 5359112d authored by Pilar Cossio's avatar Pilar Cossio
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Manual & readme consitency

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......@@ -186,10 +186,11 @@ of the BioEM theory. Therefore, it is encouraged to read refs.~\cite{CossioHumme
\section{Installation}
\subsection{Prerequisite programs and libraries}
Before installation, there are several programs and libraries that should be preinstalled on the compute node. In the following,
we give a brief explanation of the mandatory, and optional prerequisite programs. {\bf PC: The following needs checking::}
Before installation, there are several programs and libraries that should be preinstalled on the compute node.
First check that the compiler is a modern C++ compiler which is OpenMP compliant.
In the following, we give a brief explanation of the mandatory, and optional prerequisite programs. %{\bf PC: The following needs checking::}
\subsubsection{Mandatory preinstalled libraries/programs}
\subsubsection{Mandatory preinstalled libraries}
\begin{itemize}
......@@ -202,8 +203,8 @@ such as linear algebra, pseudorandom number generation, multithreading,
image processing, and unit testing. In particular, this library is used to access and organize input-data in the BioEM code.
BOOST can be downloaded from www.boost.org.
\item {\it OpenMP:} is a programming interface that supports shared memory parallel programming.
It is normally, included in the standard GNU or Intel c++ compliers, so no downloading should be necessary. For more information see http://openmp.org/.
%\item {\it OpenMP:} is a programming interface that supports shared memory parallel programming.
%It is normally, included in the standard GNU or Intel c++ compliers, so no downloading should be necessary. For more information see http://openmp.org/.
\end{itemize}
......@@ -325,7 +326,7 @@ standard host compiler is incompatible with CUDA)\\
\parbox{12cm}{
{\texttt{mkdir build \&\& cd build}}}}
\item[--] Run CMake with the desired options and the {\it CMakeLists.txt} file {\bf PC: Not working for me in the Bio cluster where the build is in-source??}
\item[--] Run CMake with the desired options and the {\it CMakeLists.txt} file {\bf PC: This is not working for me, I'm getting in-source builds?}
\fbox{%
\parbox{12cm}{
......@@ -353,39 +354,25 @@ For a simple test, run the BioEM executable
\vspace{0.5cm}
If the code runs successfully, the output on the terminal screen should be as that shown in Table \ref{tableBioEM}.
\vspace{0.5cm}
\begin{table}[h]
\begin{center}
\begin{tabular}{l}
\fbox{%
\parbox{12cm}{
{\texttt{
Command line inputs:\\
--Modelfile arg (Mandatory) Name of model file\\
--Particlesfile arg if BioEM (Mandatory) Name of particle-image file\\
--Inputfile arg if BioEM (Mandatory) Name of input parameter file\\
--PrintBestCalMap arg (Optional) Only print best calculated map. NO BioEM (!)\\
--ReadOrientation arg (Optional) Read file name containing orientations\\
--ReadPDB (Optional) If reading model file in PDB format\\
--ReadMRC (Optional) If reading particle file in MRC format\\
--ReadMultipleMRC (Optional) If reading Multiple MRCs\\
--DumpMaps (Optional) Dump maps after they were read from particle-image file\\
--LoadMapDump (Optional) Read Maps from dump option\\
--OutputFile arg (Optional) For changing the outputfile name\\
If the code runs successfully, the output on the terminal screen should be as that shown in Listing \ref{tableBioEM}.
\begin{lstlisting}[frame=single,basicstyle={\ttfamily\small},label={tableBioEM},caption={BioEM commandline input options.}\\ ]
Command line inputs:
--Modelfile arg (Mandatory) Name of model file
--Particlesfile arg if BioEM (Mandatory) Name of particle-image file
--Inputfile arg if BioEM (Mandatory) Name of input parameter file
--PrintBestCalMap arg (Optional) Only print best calculated map. NO BioEM (!)
--ReadOrientation arg (Optional) Read file name containing orientations
--ReadPDB (Optional) If reading model file in PDB format
--ReadMRC (Optional) If reading particle file in MRC format
--ReadMultipleMRC (Optional) If reading Multiple MRCs
--DumpMaps (Optional) Dump maps after they were read from
particle-image file
--LoadMapDump (Optional) Read Maps from dump option
--OutputFile arg (Optional) For changing the outputfile name
--help (Optional) Produce help message
}}}
}
\end{tabular}
\end{center}
\caption{BioEM commandline input options.}
\label{tableBioEM}
\end{table}
\end{lstlisting}
......@@ -394,7 +381,7 @@ Command line inputs:\\
\chapter{BioEM Input}
In this chapter, we describe the BioEM input commands and keywords. BioEM has two
main sources of input: from the commandline and from the input-parameter file. In the first section, we describe each commandline item from Table \ref{tableBioEM}.
main sources of input: from the commandline and from the input-parameter file. In the first section, we describe each commandline item from Listing \ref{tableBioEM}.
In the second section, we describe the keywords that should be specified in the input-parameter file. Lastly, we describe the specific formats of the model, particle-image,
and input-paramter files that are used in the BioEM software.
......@@ -403,7 +390,7 @@ and input-paramter files that are used in the BioEM software.
The BioEM software requires a model, a set of experimental images and a input-parameter file.
The names of these files are passed to the \texttt{bioEM} executable via the commandline, as well as their format specifications.
We now give a detailed description of the commandline input items shown in Table \ref{tableBioEM}.
We now give a detailed description of the commandline input items shown in Listing \ref{tableBioEM}.
\subsection{Model file}
\label{modfile}
......
......@@ -46,7 +46,7 @@ Details for the inputfiles and formats are provided in chapters 1 and 2 of the B
### Output
* Main output file with, default name "Output_Probabilities", provides the posterior probability for each image, as well as the paramters that give a maximum value of the posterior:
* Main output file with, default name "Output_Probabilities", provides the posterior probability for each image, as well as the parameters that give a maximum value of the posterior:
RefMap #(number Particle Map) Probability #(log(P))
......@@ -117,4 +117,4 @@ threads etc. These are passed via environment variables. See chapter 3 of the Bi
### License
The BioEM program is a free software, under the terms of the GNU General Public License as published by the Free Software Foundation, version 3 of the License.
This program is distributed in the hope that it will be useful, but without any warranty. See License.txt for more details.
\ No newline at end of file
This program is distributed in the hope that it will be useful, but without any warranty. See License.txt for more details.
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