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12 changes: 6 additions & 6 deletions exa-ma-d7.1.tex
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\definecolor{CustomBlue}{rgb}{0.25, 0.41, 0.88} % RoyalBlue
\hypersetup{
pdftitle={Benchmarking analysis report},
pdfauthor={[Names of co-authors (partners short names)]},
pdfauthor={[Christophe Prud'homme (UNISTRA), Pierre Alliez (INRIA), Vincent Chabannes (UNISTRA), Rudy Chocat (CEA), Emmanuel Franck (INRIA), Vincent Fraucher (CEA), Floriant Faucher (INRIA), Clément Gauchy (CEA), Christos Georgiadis (INRIA), Luc Giraud (INRIA), Frédéric Hecht (SU), Pierre Jolivet (CNRS), Pierre Ledac (CEA), Gilles Marait (INRIA), Victor Michel-Dansac (INRIA), Frédéric Nataf (SU), Lucas Palazzolo (INRIA), Yannick Privat (UL), Thomas Saigre-Tardif (UNISTRA), Christophe Trophime (CNRS), Pierre Henri Tournier (SU), Céline Van Landeghem (UNISTRA), Raphael Zanella (SU)]},
pdfkeywords={HPC, Exascale, Benchmarking},
bookmarksnumbered,linktocpage,
colorlinks=true,
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\delivResponsible{UNISTRA}

% Deliverable Version, Contractual and Actual Date, Dissemination Level, Type
\delivVersion{v0.0.6}
\delivVersion{v0.2.0}
\ContractualDate{15/10/2024}
\ActualDate{\today}
\delivDissLevel{PU} % PU, PP, RE, CO
\delivType{Report}

% List of Main Authors (usually from the responsible partner)
\delivAuthor{[Names of co-authors (partners short names)]}
\delivAuthor{[Christophe Prud'homme (UNISTRA)]}

% List of Co-Authors (all other co-authors should be listed here)
\delivFPAuthor{[Names of co-authors (partners short names)]}
\delivFPAuthor{[Pierre Alliez (INRIA), Vincent Chabannes (UNISTRA), Rudy Chocat (CEA), Emmanuel Franck (INRIA), Vincent Fraucher (CEA), Floriant Faucher (INRIA), Clément Gauchy (CEA), Christos Georgiadis (INRIA), Luc Giraud (INRIA), Frédéric Hecht (SU), Olivier Jamond (CEA), Pierre Jolivet (CNRS), Pierre Ledac (CEA), Gilles Marait (INRIA), Victor Michel-Dansac (INRIA), Frédéric Nataf (SU), Lucas Palazzolo (INRIA), Yannick Privat (UL), Thomas Saigre-Tardif (UNISTRA), Christophe Trophime (CNRS), Pierre Henri Tournier (SU), Céline Van Landeghem (UNISTRA), Raphael Zanella (SU) ]}

% Provision of Keywords (about 5-10)
\delivKeywords{HPC, Exascale, Benchmarking, Software}
Expand All @@ -144,15 +144,15 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% Change Log
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\istChange{08/10/2024}{v0.2.0}{Prud'homme Christophe (UNISTRA), Thomas Saigre (UNISTRA), Vincent Chabannes(UNISTRA), Céline Van Landeghem (UNISTRA), Victor Dansac(UNISTRA,INRIA),Christos Georgiadis (INRIA), Pierre Alliez(INRIA), Clément Gauchy (CEA), Rudy Rochat(CEA), Florent Faucher (INRIA)}{Initial contributions}
\istChange{11/10/2024}{v0.2.0}{\href{https://github.com/numpex/exa-ma-d7.1/graphs/contributors}{+14 Contributors}}{Initial contributions}
\istChange{30/09/2024}{v0.1.0}{Prud'homme Christophe (UNISTRA)}{setup architecture of D7.1, update profiling tools in toc, updates in methodology chapter, add information store in excel sheet in the report,update benchmark methodology}
\istChange{27/09/2024}{v0.0.6}{Prud'homme Christophe (UNISTRA)}{In the methodology chapter, link the deliverable to the bottlenecks identified in Exa-MA scientific document. Add resilience stats and methdology, benchmark mmg and parmmg indirectly.}
\istChange{26/09/2024}{v0.0.6}{Pierre Jolivet (CNRS)}{Review of the document}
\istChange{16/09/2024}{v0.0.5}{Prud'homme Christophe (UNISTRA)}{ToC: add list of computer science features per software, add list of math features per workpackage, add statistics about Exa-MA software in chapter Software}
\istChange{02/09/2024}{v0.0.4}{Prud'homme Christophe (UNISTRA)}{ToC: add profiling tools in methodology chapter and udated the chapter overall}
\istChange{30/08/2024}{v0.0.3}{Prud'homme Christophe (UNISTRA)}{ToC: setup architecture of D7.1;add benchmarking methodology chapter;add samurai software to be benchmarked}
\istChange{20/08/2024}{v0.0.1}{Prud'homme Christophe (UNISTRA)}{Draft report template}
\istChange{}{}{}{}
%%\istChange{}{}{}{}


\begin{document}
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22 changes: 11 additions & 11 deletions gitHeadLocal.gin
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\usepackage[%
shash={b26bd7c},
lhash={b26bd7c5389f87390796c7310db5829e332eb9b6},
shash={33226e4},
lhash={33226e4c3c8eb1f0f7aafc37af995d5e65515962},
authname={Christophe Prud'homme},
authemail={christophe.prudhomme@cemosis.fr},
authsdate={2024-09-27},
authidate={2024-09-27 13:21:07 +0200},
authudate={1727436067},
authsdate={2024-10-11},
authidate={2024-10-11 09:05:41 +0200},
authudate={1728630341},
commname={Christophe Prud'homme},
commemail={christophe.prudhomme@cemosis.fr},
commsdate={2024-09-27},
commidate={2024-09-27 13:21:07 +0200},
commudate={1727436067},
refnames={ (HEAD -> main, tag: v0.1.0, origin/main, origin/HEAD)},
firsttagdescribe={v0.1.0},
reltag={v0.1.0-0-gb26bd7c}
commsdate={2024-10-11},
commidate={2024-10-11 09:05:41 +0200},
commudate={1728630341},
refnames={ (HEAD -> main, tag: v0.2.0, origin/main, origin/HEAD)},
firsttagdescribe={v0.2.0},
reltag={v0.2.0-0-g33226e4}
]{gitexinfo}
95 changes: 95 additions & 0 deletions references.bib
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@@ -1,5 +1,100 @@


@phdthesis{daver2016,
type = {phd},
title = {Reduced basis method applied to large non-linear multi-physics problems : application to high field magnets design},
url = {http://www.theses.fr/2016STRAD019},
author = {Daversin - Catty, Cécile},
year = {2016},
note = {tex.note+duplicate-1: 2016STRAD019},
}

@phdthesis{Hild2020,
type = {phd},
title = {Control and optimization of high magnetic fields},
url = {http://www.theses.fr/2020STRAD031},
author = {Hild, Romain},
year = {2020},
note = {tex.note+duplicate-1: 2020STRAD031},
}

@article{wang_fluid_2016,
title = {Fluid and structure coupling analysis of the interaction between aqueous humor and iris},
volume = {15},
issn = {1475-925X},
url = {http://biomedical-engineering-online.biomedcentral.com/articles/10.1186/s12938-016-0261-3},
doi = {10.1186/s12938-016-0261-3},
language = {en},
number = {S2},
urldate = {2024-10-14},
journal = {BioMedical Engineering OnLine},
author = {Wang, Wenjia and Qian, Xiuqing and Song, Hongfang and Zhang, Mindi and Liu, Zhicheng},
month = dec,
year = {2016},
pages = {133},
}

@book{ansorge_programming_2022,
edition = {1},
title = {Programming in {Parallel} with {CUDA}: {A} {Practical} {Guide}},
copyright = {https://www.cambridge.org/core/terms},
isbn = {978-1-108-85527-3 978-1-108-47953-0},
shorttitle = {Programming in {Parallel} with {CUDA}},
url = {https://www.cambridge.org/core/product/identifier/9781108855273/type/book},
abstract = {CUDA is now the dominant language used for programming GPUs, one of the most exciting hardware developments of recent decades. With CUDA, you can use a desktop PC for work that would have previously required a large cluster of PCs or access to a HPC facility. As a result, CUDA is increasingly important in scientific and technical computing across the whole STEM community, from medical physics and financial modelling to big data applications and beyond. This unique book on CUDA draws on the author's passion for and long experience of developing and using computers to acquire and analyse scientific data. The result is an innovative text featuring a much richer set of examples than found in any other comparable book on GPU computing. Much attention has been paid to the C++ coding style, which is compact, elegant and efficient. A code base of examples and supporting material is available online, which readers can build on for their own projects.},
language = {en},
urldate = {2024-10-11},
publisher = {Cambridge University Press},
author = {Ansorge, Richard},
month = may,
year = {2022},
doi = {10.1017/9781108855273},
}

@article{noauthor_cuda_nodate,
title = {{CUDA} {GRAPHS} in {GROMACS}},
language = {en},
}

@article{schoonover_mpi_nodate,
title = {{MPI}+ {Programming} with {HIP} and {OpenMP}},
language = {en},
author = {Schoonover, Dr Joe},
}

@article{edvalson_readthedocs-breathe_nodate,
title = {{ReadTheDocs}-{Breathe} {Documentation}},
language = {en},
author = {Edvalson, Thomas},
}

@article{maia_rocm_nodate,
title = {{ROCm}™ {Library} {Support} \& {Profiling} {Tools}},
language = {en},
author = {Maia, Julio and Chalmers, Noel and Bauman, Paul T and Curtis, Nicholas and Malaya, Nicholas and McDougall, Damon and van Oostrum, Rene},
}

@article{malavally_amd_nodate,
title = {{AMD} {HIP} {Programming} {Guide}},
language = {en},
author = {Malavally, Roopa},
}

@article{noauthor_use_nodate,
title = {Use {ROCm}™ on {Radeon}™ {GPUs} {Documentation}},
language = {en},
}

@article{edvalson_readthedocs-breathe_nodate-1,
title = {{ReadTheDocs}-{Breathe} {Documentation}},
language = {en},
author = {Edvalson, Thomas},
}

@article{noauthor_cuda_nodate-1,
title = {{CUDA} {C}++ {Programming} {Guide}},
}

@article{parks_recycling_2006,
title = {Recycling {Krylov} {Subspaces} for {Sequences} of {Linear} {Systems}},
volume = {28},
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1 change: 1 addition & 0 deletions software/composyx/WP3/WP3.tex
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Expand Up @@ -130,6 +130,7 @@ \subsection{12-Month Roadmap}
\rowcolor{numpexlightergray} B11 - Reproducibility and Replicability of Computation & Guix-HPC \\
\rowcolor{white} B6 - Data Management & not applicable \\
\rowcolor{numpexlightergray} B7 - Exascale Algorithms & Tune CPU and GPU features - Possibly add numerical resiliency eventhough we still believe that the resilincy should be addressed in an hollistic fashion as advocated in~\cite{agullo_resiliency_2022}. \\

\end{tabular}
}
}
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44 changes: 17 additions & 27 deletions software/composyx/composyx.tex
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Expand Up @@ -45,6 +45,7 @@ \subsection{Software summary}
\begin{figure}
\centering
\includegraphics[width=0.8\textwidth]{graphics/composyx/composyx-solverstack.png}
%\includegraphics[width=0.8\textwidth]{graphics/composyx/composyx-solverstack.pdf}
\caption{Composyx dependencies}
\label{fig:composyx}
\end{figure}
Expand Down Expand Up @@ -77,31 +78,15 @@ \subsection{Programming and Computational Environment}
GPU\\
MPI\\
Multithread\\
\end{tabular} & Parallel computing methods and frameworks utilized by the software.\\
\rowcolor{white}Data Formats & \begin{tabular}{l}
None\\
\end{tabular} & Data formats that the software can handle or produce.\\
\rowcolor{numpexlightergray}Resilience & \begin{tabular}{l}
None\\
\end{tabular} & Fault tolerance and recovery mechanisms employed by the software.\\
\rowcolor{white}DevOps & \begin{tabular}{l}
Continuous Integration\\
\end{tabular} & Outlines the development and operational practices including continuous integration, containerization, and testing methodologies. \\
\rowcolor{numpexlightergray}Packaging & \begin{tabular}{l}
GUIX-HPC\\
\end{tabular} & Software packaging and distribution.\\
\rowcolor{white}Testing & \begin{tabular}{l}
Verification\\
\end{tabular} & Testing methodologies employed to ensure software quality and correctness.\\
\rowcolor{numpexlightergray}Containerization & \begin{tabular}{l}
Singularity\\
\end{tabular} & Container technologies used to package and deploy the software.\\
\rowcolor{white}Interfaces & \begin{tabular}{l}
MUMPS\\
PaStiX\\
Scotch\\
qr\_mumps\\
\end{tabular} & List of software Composyx has interfaces with.\\
\end{tabular} & Multithreading OpenMP and Posix, hybrid CPU-GPU with StarPU.\\
%\rowcolor{white}Data Formats & \begin{tabular}{l} None\\ \end{tabular} & Data formats that the software can handle or produce.\\
%\rowcolor{numpexlightergray}Resilience & \begin{tabular}{l} None\\ \end{tabular} & \\
\rowcolor{white}DevOps & \begin{tabular}{l} Continuous Integration\\ \end{tabular} & Outlines the development and operational practices including continuous integration, containerization, and testing methodologies. \\
%
\rowcolor{numpexlightergray}Packaging & \begin{tabular}{l} GUIX-HPC\\ \end{tabular} & Software packaging and distribution.\\
\rowcolor{white}Testing & \begin{tabular}{l} Verification\\ \end{tabular} & Testing methodologies employed to ensure software quality and correctness.\\
\rowcolor{numpexlightergray}Containerization & \begin{tabular}{l} Singularity\\ \end{tabular} & Container technologies used to package and deploy the software.\\
\rowcolor{white}Interfaces & \begin{tabular}{l} MUMPS\\ PaStiX\\ Scotch\\ qr\_mumps\\ \end{tabular} & List of software Composyx has interfaces with.\\
\bottomrule
\end{tabular}
}}
Expand Down Expand Up @@ -134,10 +119,15 @@ \subsection{Acknowledgements}
\label{sec::Composyx:acknowledgements}

The software has been developed with the support of the following funding agencies and institutions:
\begin{itemize}
\item Inria,
\item H2020 Center of Excellence EoCoE-2 and 3,
\item H2020 PRACE-6IP,
\item DGA through the Hi-Box project,
\item Software development was performed using the PlaFRIM experimental testbed, supported by Inria, CNRS (LABRI and IMB), Université de Bordeaux, Bordeaux INP and Conseil R\'egional d’Aquitaine (see https://www.plafrim.fr) as well as on national GENCI platform.
\end{itemize}




Acknowledgements not available.


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