From 8fe4088bf76d1f72847fe43e388e08f414f8ce83 Mon Sep 17 00:00:00 2001 From: Rossen Apostolov Date: Tue, 17 Jun 2014 14:01:03 +0200 Subject: [PATCH] Small changes in appendix A of the manual. Final fixes #552. Change-Id: I8e7939ae70eb14d2e1fc0a25b50774d472889bd1 --- manual/install.tex | 34 ++++++++-------------------------- 1 file changed, 8 insertions(+), 26 deletions(-) diff --git a/manual/install.tex b/manual/install.tex index 24bcf9c79e..0f9e2fe76a 100644 --- a/manual/install.tex +++ b/manual/install.tex @@ -388,34 +388,16 @@ processes. To run {\gromacs} in parallel over multiple nodes in a cluster of a supercomputer, you need to configure and compile {\gromacs} with an external MPI library. All supercomputers are shipped with MPI libraries optimized for that particular platform, and if you are using a cluster of workstations -there are several good free MPI implementations; -Open MPI is usually a good choice. Once you have an MPI library -installed it's trivial to compile {\gromacs} with MPI support: Just pass -the option {\tt -DGMX_MPI=on} to {\tt cmake} and (re-)compile. Please see -{\wwwpage} for more detailed instructions. -Note that in addition to MPI parallelization, {\gromacs} supports -thread-parallelization through \normindex{OpenMP}. MPI and OpenMP parallelization -can be combined, which results in, so called, hybrid parallelization. -See {\wwwpage} for details on use and performance of the parallelization -schemes. - -For communications over multiple nodes connected by a network, -there is a program usually called {\tt mpirun} with which you can start -the parallel processes. A typical command line could look like: -{\tt mpirun -np 10 mdrun_mpi -s topol -v} - -With the implementation of threading available by default in {\gromacs} version 4.5, -if you have a single machine with multiple processors you don't have to -use the {\tt mpirun} command, or compile with MPI. Instead, you can -allow {\gromacs} to determine the number of threads automatically, or use the {\tt mdrun} option {\tt -nt}: -{\tt mdrun -nt 8 -s topol.tpr} +there are several good free MPI implementations; OpenMPI is usually a good choice. +Note that MPI and threaded-MPI support are mutually incompatible. -Check your local manuals (or online manual) for exact details -of your MPI implementation. - -If you are interested in programming MPI yourself, you can find -manuals and reference literature on the internet. +In addition to MPI parallelization, {\gromacs} supports also +thread-parallelization through \normindex{OpenMP}. MPI and OpenMP parallelization +can be combined, which results in, so called, hybrid parallelization. It can offer +better performance and scaling in some cases. +See {\wwwpage} for details on the use and performance of the different +parallelization schemes. \section{Running {\gromacs} on \normindex{GPUs}} As of version 4.6, {\gromacs} has native GPU support through CUDA. -- 2.22.0