[cig-commits] [commit] QA: User manual: ADIOS + PML + author list updated. (8b5d44e)

Fri Jan 24 08:36:00 PST 2014

Repository : ssh://geoshell/specfem3d

On branch  : QA
Link       : https://github.com/geodynamics/specfem3d/compare/8e7fca259d3e520c105549cfacfb92b6c83f8971...6a53e191f97b6aefb97401beae9901e58f2e8088

>---------------------------------------------------------------

commit 8b5d44e659a02e9b846968db198a35165ba72a70
Author: Matthieu Lefebvre <ml15 at princeton.edu>
Date:   Fri Jan 24 11:17:06 2014 -0500

    User manual: ADIOS + PML + author list updated.


>---------------------------------------------------------------

8b5d44e659a02e9b846968db198a35165ba72a70
 doc/USER_MANUAL/bibliography.bib               |  12 +++++++++
 doc/USER_MANUAL/manual_SPECFEM3D_Cartesian.pdf | Bin 12632570 -> 12634307 bytes
 doc/USER_MANUAL/manual_SPECFEM3D_Cartesian.tex |  35 +++++++++++++++++++++----
 3 files changed, 42 insertions(+), 5 deletions(-)

diff --git a/doc/USER_MANUAL/bibliography.bib b/doc/USER_MANUAL/bibliography.bib
index e3a80aa..588e9e0 100644
--- a/doc/USER_MANUAL/bibliography.bib
+++ b/doc/USER_MANUAL/bibliography.bib
@@ -9208,6 +9208,18 @@
   pages = {41-58}
 }
 
+ at ARTICLE{Liu2013,
+  author = {Liu, Qing and Logan, Jeremy and Tian, Yuan and Abbasi, Hasan and Podhorszki, Norbert and Choi, Jong Youl and Klasky, Scott and Tchoua, Roselyne and Lofstead, Jay and Oldfield, Ron and Parashar, Manish and Samatova, Nagiza and Schwan, Karsten and Shoshani, Arie and Wolf, Matthew and Wu, Kesheng and Yu, Weikuan},
+  doi = {10.1002/cpe.3125},
+  issn = {15320626},
+  journal = {Concurrency and Computation: Practice and Experience},
+  month = aug,
+  pages = {n/a--n/a},
+  title = {{Hello ADIOS: the challenges and lessons of developing leadership class I/O frameworks}},
+  url = {http://doi.wiley.com/10.1002/cpe.3125},
+  year = {2013}
+}
+
 @ARTICLE{LiuLi05,
   author = {Liu, J. and Li, B.},
   title = {A unified viscous-spring artificial boundary for {3-D} static and
diff --git a/doc/USER_MANUAL/manual_SPECFEM3D_Cartesian.pdf b/doc/USER_MANUAL/manual_SPECFEM3D_Cartesian.pdf
index 257c073..a16950d 100644
Binary files a/doc/USER_MANUAL/manual_SPECFEM3D_Cartesian.pdf and b/doc/USER_MANUAL/manual_SPECFEM3D_Cartesian.pdf differ
diff --git a/doc/USER_MANUAL/manual_SPECFEM3D_Cartesian.tex b/doc/USER_MANUAL/manual_SPECFEM3D_Cartesian.tex
index f8cc62e..5ff3e7b 100644
--- a/doc/USER_MANUAL/manual_SPECFEM3D_Cartesian.tex
+++ b/doc/USER_MANUAL/manual_SPECFEM3D_Cartesian.tex
@@ -1,3 +1,4 @@
+% !TEX encoding = IsoLatin
 %% LyX 2.0.2 created this file.  For more info, see http://www.lyx.org/.
 %% Do not edit unless you really know what you are doing.
 \documentclass[oneside,english]{book}
@@ -132,10 +133,10 @@ Since then it has been developed and maintained by a development team:
 in alphabetical order, Jean-Paul (Pablo) Ampuero, Piero Basini, Céline
 Blitz, Ebru Bozda\u{g}, Emanuele Casarotti, Joseph Charles, Min Chen,
 Percy Galvez, Dominik Göddeke, Vala Hjörleifsdóttir, Sue Kientz, Dimitri
-Komatitsch, Jesús Labarta, Nicolas Le Goff, Pieyre Le Loher, Qinya
-Liu, Yang Luo, Alessia Maggi, Federica Magnoni, Roland Martin, René
-Matzen, Dennis McRitchie, Matthias Meschede, Peter Messmer, David
-Michéa, Surendra Nadh Somala, Tarje Nissen-Meyer, Daniel Peter, Max
+Komatitsch, Jesús Labarta, Nicolas Le Goff, Pieyre Le Loher, Matthieu
+Lefebvre, Qinya Liu, Yang Luo, Alessia Maggi, Federica Magnoni, Roland
+Martin, René Matzen, Dennis McRitchie, Matthias Meschede, Peter Messmer, 
+David Michéa, Surendra Nadh Somala, Tarje Nissen-Meyer, Daniel Peter, Max
 Rietmann, Elliott Sales de Andrade, Brian Savage, Bernhard Schuberth,
 Anne Sieminski, Leif Strand, Carl Tape, Jeroen Tromp, Jean-Pierre
 Vilotte, Zhinan Xie, Hejun Zhu.\\
@@ -614,6 +615,21 @@ Packages such as \texttt{doxywizard} can be used to visualize the
 subroutine calling tree of the source code. \texttt{Doxywizard} is
 a GUI front-end for configuring and running \texttt{doxygen}.
 
+\section{Using the ADIOS library for I/O}
+Regular POSIX I/O can be problematic when dealing with large simulations one large
+clusters (typically more than $10,000$ processes). SPECFEM3D use the ADIOS library~\cite{Liu2013}
+to deal transparently take advantage of advanced paralllel file system features. To enable
+ADIOS, the following steps should be done:
+\begin{enumerate}
+\item Install ADIOS (available from \url{https://www.olcf.ornl.gov/center-projects/adios/}). 
+Make sure that your environment variables reference it. 
+\item You may want to change ADIOS related values in the \texttt{constants.h.in} file.
+The default values probably suit most cases.
+\item Configure using the \texttt{--with-adios} flag.
+\end{enumerate}
+ADIOS is currently only usable for meshfem3D generated mesh (i.e. not for meshes generated
+with CUBTI). Additional control parameters are discussed in section~\ref{cha:Main-Parameter}.
+
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 
@@ -1494,7 +1510,7 @@ model using Olsen's empirical relation (see \citet{OlDaBr03}).
 in Olsen's empirical relation (see \citet{OlDaBr03}).
 \item [{\texttt{PML\_CONDITIONS}}] Set to \texttt{.true.} to turn on C-PML
 boundary conditions for a regional simulation. Both fluids and elastic
-solids are supported.
+solids are supported. Note that xmeshfem3d generated meshes do not support C-PML yet.
 \item [{\texttt{PML\_INSTEAD\_OF\_FREE\_SURFACE}}] Set to \texttt{.true.}
 to turn on C-PML boundary conditions on the top surface instead of
 the usual free surface.
@@ -1617,6 +1633,15 @@ Any other source-time function may then be obtained by convolution.
 information about the source time function in the file \texttt{OUTPUT\_FILES/plot\_source\_time\_function.txt}.
 This feature is only relevant for the solver.
 \item [{\texttt{GPU\_MODE}}] Turn this flag on to use GPUs.
+
+\item [\texttt{ADIOS\_ENABLED}] Turn this flag on to enable ADIOS. If set to \texttt{.false.}, subsequent ADIOS 
+parameters will not be considered.
+\item [\texttt{ADIOS\_FOR\_DATABASES}] Turn this flag on to use ADIOS for xmeshfem3D output and 
+xgenerate\_database input.
+\item [\texttt{ADIOS\_FOR\_MESH}]  Turn this flag on to use ADIOS for generated databases.
+\item [\texttt{ADIOS\_FOR\_FORWARD\_ARRAYS}] Turn this flag on to read and write forward arrays using ADIOS.
+\item [\texttt{ADIOS\_FOR\_KERNELS}] Turn this flag on to produce ADIOS kernels that can later be visualized with the ADIOS version of combine\_vol\_data.
+ 
 \end{description}
 If you use PML, the mesh elements that belong to the PML layers can
 be acoustic or elastic, but not viscoelastic nor poroelastic. Then,

