1. Richard Mills
  2. pflotran-dev

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Peter Lichtner  committed 13ee7e1

Added url references to QG.

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File docs/user_manual/installation.tex

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 of the PETSc build process; once PETSc is built, building PFLOTRAN is  
 straightforward.
 
-Besides MPI and PETSc, libraries commonly installed are
-
+Besides \href{http://www.mcs.anl.gov/petsc/}{PETSc}, third party libraries commonly installed are
 \begin{itemize}
-\item HDF5, required for parallel I/O and reading HDF5-formatted input files
-\item ParMetis and Metis, graph partitioning libraries required for 
+\item MPI, message passing interface [\href{http://www.open-mpi.org/}{OpenMPI} or \href{http://www.mpich.org/}{MPICH}, note for parallel IO MPICH is required (see Section~\S\ref{parallelio})]
+\item \href{http://www.hdfgroup.org/HDF5/}{HDF5}, required for parallel I/O and reading HDF5-formatted input files
+\item \href{http://glaros.dtc.umn.edu/gkhome/views/metis}{Metis} and \href{http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview}{ParMetis}, graph partitioning libraries required for 
       unstructured grids
-\item Hypre, which provides a variety of preconditioners and multilevel 
+\item \href{http://acts.nersc.gov/hypre/}{Hypre}, which provides a variety of preconditioners and multilevel 
       solves
 \end{itemize}
 
+PETSc can be used to download, compile and install all of these third party libraries during compilation of PETSc as explained below, so that the user does not have to do this themselves individually for each library.
+
 \subsection{Compilers}
 
 The installation of PFLOTRAN on MacOSX requires compiler versions 4.7 or later for gfortran and gcc to be compatible with Fortran 2003. 
 See the PFLOTRAN \verb|makefile| for additional options.
 
 \subsection{Parallel I/O using Sarat Sreepathi's PARALLELIO\_LIB with PFLOTRAN}
+\label{parallelio}
 
 The parallel I/O library enables a scalable general purpose parallel I/O capability for HPC by taking advantage of existing parallel I/O libraries, such as HDF5 which are being widely used by scientific applications, and modifying these algorithms to better scale to larger number of processors. The library has been tested with MPICH-3.0.2.
 

File docs/user_manual/intro.tex

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 \section{Introduction}
 
-PFLOTRAN solves a system of generally nonlinear partial differential equations describing multiphase, multicomponent and multiscale reactive flow and transport in porous materials. The code is designed to run on massively parallel computing architectures as well as workstations and laptops (Hammond et al., 2011). Parallelization is achieved through domain decomposition using the PETSc (Port\-a\-ble Extensible Toolkit for Scientific Computation) libraries for the parallelization framework  (Balay et al., 1997).
+PFLOTRAN solves a system of generally nonlinear partial differential equations describing multiphase, multicomponent and multiscale reactive flow and transport in porous materials. The code is designed to run on massively parallel computing architectures as well as workstations and laptops (e.g. Hammond et al., 2011). Parallelization is achieved through domain decomposition using the PETSc (Port\-a\-ble Extensible Toolkit for Scientific Computation) libraries for the parallelization framework (Balay et al., 1997).
 
-Additional instructions can be found on the PFLOTRAN wiki home page: \linebreak \verb|https://bitbucket.org/pflotran/pflotran-dev/wiki/Home|.
-Questions regarding the PFLOTRAN installation, and bug reports may be directed to: \linebreak {\tt pflotran-dev at googlegroups dot com}.
-For questions regarding running PFLOTRAN contact: {\tt pflotran-users at googlegroups dot com}.
+Additional instructions can be found on the PFLOTRAN \href{https://bitbucket.org/pflotran/pflotran-dev/wiki/Home}{wiki home page}.
+Questions regarding the PFLOTRAN installation, and bug reports may be directed to: \linebreak {\footnotesize\tt pflotran-dev at googlegroups dot com}.
+For questions regarding running PFLOTRAN contact: {\footnotesize\tt pflotran-users at googlegroups dot com}.