chapter 5 and 7

[book_gpu.git] / BookGPU / Chapters / chapter15 / ch15.tex

diff --git a/BookGPU/Chapters/chapter15/ch15.tex b/BookGPU/Chapters/chapter15/ch15.tex
index 1eca6ecc065f99e36b13709fdf11ffa9b64dd59b..5dae9b22fdb97d2982d3e8f1eff38ec0cb84548d 100644 (file)
--- a/BookGPU/Chapters/chapter15/ch15.tex
+++ b/BookGPU/Chapters/chapter15/ch15.tex
@@ -7,8 +7,7 @@ The Queen's University of Belfast}
 
 \newcommand{\fixme}[1]{{\bf #1}}
 
 
 \newcommand{\fixme}[1]{{\bf #1}}
 

-\chapter{Numerical validation and performance optimization on GPUs of
-an application in atomic physics} 
+\chapter[Numerical validation and performance optimization on GPUs in atomic physics]{Numerical validation and performance optimization on GPUs of an application in atomic physics} 

 \label{chapter15}
 
 \section{Introduction}\label{ch15:intro}
 \label{chapter15}
 
 \section{Introduction}\label{ch15:intro}


@@ -22,11 +21,11 @@ GPUs, applications should be coarse-grained and have a high arithmetic
 intensity 
 ($i.e.$ the ratio of arithmetic operations to memory operations). 
 Another important aspect of GPU programming is that floating-point
 intensity 
 ($i.e.$ the ratio of arithmetic operations to memory operations). 
 Another important aspect of GPU programming is that floating-point

-operations are preferably performed in single precision, if the
+operations are preferably performed in single precision\index{precision!single precision}, if the

  validity of results is not impacted by that format.   
 The GPU compute power for floating-point operations is indeed greater in
  validity of results is not impacted by that format.   
 The GPU compute power for floating-point operations is indeed greater in

-single precision than in double precision.  
-The peak performance ratio between single precision and double
+single precision\index{precision!single precision} than in double precision\index{precision!double precision}.  
+The peak performance ratio between single precision\index{precision!single precision} and double

 precision varies for example for NVIDIA GPUs from $12$ for the first Tesla
 GPUs (C1060), 
 to $2$ for the Fermi GPUs (C2050 and C2070)  
 precision varies for example for NVIDIA GPUs from $12$ for the first Tesla
 GPUs (C1060), 
 to $2$ for the Fermi GPUs (C2050 and C2070)  


@@ -34,7 +33,7 @@ and to $3$ for the latest Kepler architecture (K20/K20X).
 As far as AMD GPUs are concerned, the latest AMD GPU (Tahiti HD 7970)
 presents a ratio of $4$.  
 Moreover, GPU internal memory accesses and CPU-GPU data transfers are
 As far as AMD GPUs are concerned, the latest AMD GPU (Tahiti HD 7970)
 presents a ratio of $4$.  
 Moreover, GPU internal memory accesses and CPU-GPU data transfers are

-faster in single precision than in double precision,  
+faster in single precision\index{precision!single precision} than in double precision\index{precision!double precision},  

 because of the different format lengths. 
 
 This chapter describes the deployment on GPUs of PROP, a program of the
 because of the different format lengths. 
 
 This chapter describes the deployment on GPUs of PROP, a program of the


@@ -66,7 +65,7 @@ For matrix products the GPU performance gain over CPU increases indeed
 with the matrix size, since the 
 CPU-GPU transfer overhead becomes less significant and since CPUs are
 still more efficient for fine computation grains. 
 with the matrix size, since the 
 CPU-GPU transfer overhead becomes less significant and since CPUs are
 still more efficient for fine computation grains. 

-Then, using HMPP\footnote{
+Then, using HMPP\index{HMPP}\footnote{

 HMPP or {\em CAPS compiler}, see: \url{www.caps-entreprise.com/hmpp.html}},
 a commercial 
 hybrid and parallel compiler, CAPS 
 HMPP or {\em CAPS compiler}, see: \url{www.caps-entreprise.com/hmpp.html}},
 a commercial 
 hybrid and parallel compiler, CAPS 


@@ -79,8 +78,8 @@ significant acceleration.
 The work described in this chapter, which is based on a study presented in \cite{PF_PDSEC2011}, aims at 
  improving PROP performance on 
 GPUs by exploring two directions. First, because the original version of PROP is written
 The work described in this chapter, which is based on a study presented in \cite{PF_PDSEC2011}, aims at 
  improving PROP performance on 
 GPUs by exploring two directions. First, because the original version of PROP is written

-in double precision, 
-we study the numerical stability of PROP in single precision. 
+in double precision\index{precision!double precision}, 
+we study the numerical stability of PROP in single precision\index{precision!single precision}. 

 Second, we deploy  the whole
 computation code of PROP on
 GPUs to avoid the overhead generated by
 Second, we deploy  the whole
 computation code of PROP on
 GPUs to avoid the overhead generated by


@@ -276,21 +275,21 @@ $\Re^{O}$.
 the output $R$-matrix becomes  the input $R$-matrix 
 for the next evaluation.  
 
 the output $R$-matrix becomes  the input $R$-matrix 
 for the next evaluation.  
 

-%% \begin{algorithm}
-%% \caption{\label{prop-algo}PROP algorithm}
-%% \begin{algorithmic}
-%% \FOR{all scattering energies}
-%%  \FOR{all sectors}
-%%  \STATE Read amplitude arrays
-%%  \STATE Read correction data
-%% \STATE Construct local $R$-matrices
-%% \STATE From $\Re^{I}$ and local $R$-matrices, compute $\Re^{O}$
-%% \STATE $\Re^{O}$ becomes $\Re^{I}$ for the next sector 
-%%  \ENDFOR
-%%  \STATE Compute physical $R$-Matrix 
-%% \ENDFOR
-%% \end{algorithmic}
-%% \end{algorithm}
+\begin{algorithm}
+\caption{\label{prop-algo}PROP algorithm}
+\begin{algorithmic}
+\FOR{all scattering energies}
+ \FOR{all sectors}
+ \STATE Read amplitude arrays
+ \STATE Read correction data
+\STATE Construct local $R$-matrices
+\STATE From $\Re^{I}$ and local $R$-matrices, compute $\Re^{O}$
+\STATE $\Re^{O}$ becomes $\Re^{I}$ for the next sector 
+ \ENDFOR
+ \STATE Compute physical $R$-Matrix 
+\ENDFOR
+\end{algorithmic}
+\end{algorithm}

 
 
 On the first sector, there is no input $R$-matrix yet. To bootstrap
 
 
 On the first sector, there is no input $R$-matrix yet. To bootstrap


@@ -310,7 +309,7 @@ depending on the computation performed:
 
 
 The serial version of PROP is implemented in Fortran~90 and uses
 
 
 The serial version of PROP is implemented in Fortran~90 and uses

-for linear algebra operations BLAS and LAPACK routines
+for linear algebra operations BLAS\index{BLAS} and LAPACK\index{LAPACK} routines

 which are fully optimized for x86 architecture.
 This 
 program 
 which are fully optimized for x86 architecture.
 This 
 program 


@@ -359,20 +358,20 @@ copies fall from 22 to 5, matrix multiplications from 4 to~1 and calls
 to a linear equation solver from 2 to 1. 
 
 To implement this version, CAPS 
 to a linear equation solver from 2 to 1. 
 
 To implement this version, CAPS 

-used HMPP, a 
+used HMPP\index{HMPP}, a 

 commercial hybrid and parallel compiler, 
 commercial hybrid and parallel compiler, 

-based on compiler directives like the new OpenACC standard\footnote{See: \url{www.openacc-standard.org}}.  
+based on compiler directives like the new OpenACC\index{OpenACC} standard\footnote{See: \url{www.openacc-standard.org}}.  

 If the matrices are large enough (the limit sizes are experimental parameters), 
 they are multiplied on the GPU, otherwise on the CPU. 
 CAPS 
 If the matrices are large enough (the limit sizes are experimental parameters), 
 they are multiplied on the GPU, otherwise on the CPU. 
 CAPS 

- used the MKL BLAS implementation on an Intel Xeon
+ used the MKL BLAS\index{BLAS} implementation on an Intel Xeon

 x5560 quad core CPU (2.8 GHz) 
 x5560 quad core CPU (2.8 GHz) 

-and the CUBLAS library (CUDA 2.2) on one Tesla C1060 GPU. 
+and the CUBLAS\index{CUBLAS} library (CUDA 2.2) on one Tesla C1060 GPU. 

 On the large data set (see Table~\ref{data-sets}), CAPS 
  obtained a speedup of 1.15 for the GPU 
 version over the CPU one (with multi-threaded MKL calls on the four
 CPU cores). This limited gain in performance is mainly
 On the large data set (see Table~\ref{data-sets}), CAPS 
  obtained a speedup of 1.15 for the GPU 
 version over the CPU one (with multi-threaded MKL calls on the four
 CPU cores). This limited gain in performance is mainly

-due to the use of double precision computation 
+due to the use of double precision\index{precision!double precision} computation 

 and to the small or medium sizes of most matrices.
 For these matrices, the computation gain on  
 the GPU is indeed
 and to the small or medium sizes of most matrices.
 For these matrices, the computation gain on  
 the GPU is indeed


@@ -386,14 +385,14 @@ code to the GPU and therefore avoiding
 the 
 intermediate data transfers between
 the host (CPU) and the GPU. We will also study the
 the 
 intermediate data transfers between
 the host (CPU) and the GPU. We will also study the

-stability of PROP in single precision because 
-single precision computation is faster on the GPU  
+stability of PROP in single precision\index{precision!single precision} because 
+single precision\index{precision!single precision} computation is faster on the GPU  

 and CPU-GPU data transfers are twice as fast as those performed in
 and CPU-GPU data transfers are twice as fast as those performed in

-double precision. 
+double precision\index{precision!double precision}. 

 
 
 
 
 
 

-\section{Numerical validation of PROP in single precision}
+\section{Numerical validation\index{numerical validation} of PROP in single precision\index{precision!single precision}}

 \label{single-precision}
 
 \begin{comment}
 \label{single-precision}
 
 \begin{comment}


@@ -419,13 +418,13 @@ double precision.
   \hline
 \end{tabular}
 \end{center}
   \hline
 \end{tabular}
 \end{center}

-\caption{\label{sp-distrib}Error distribution for medium case in single precision}
+\caption{\label{sp-distrib}Error distribution for medium case in single precision\index{precision!single precision}}

 \end{table}
 \end{comment}
 
 
 Floating-point input data, computation and output data of PROP are 
 \end{table}
 \end{comment}
 
 
 Floating-point input data, computation and output data of PROP are 

-originally in double precision format.
+originally in double precision\index{precision!double precision} format.

 PROP produces a standard $R$-matrix H-file \cite{FARM_2DRMP}
  and a collection of Rmat00X files (where X
 ranges from 0 to the number of scattering energies - 1)
 PROP produces a standard $R$-matrix H-file \cite{FARM_2DRMP}
  and a collection of Rmat00X files (where X
 ranges from 0 to the number of scattering energies - 1)


@@ -435,21 +434,21 @@ The  H-file  and the Rmat00X files are binary input files of the FARM program \c
 (last program of the 2DRMP suite).
 Their text equivalent are the  prop.out 
 and the prop00X.out files. 
 (last program of the 2DRMP suite).
 Their text equivalent are the  prop.out 
 and the prop00X.out files. 

-To study the validity of PROP results in  single precision,
+To study the validity of PROP results in  single precision\index{precision!single precision},

 first,
 reference results are 
 first,
 reference results are 

- generated by running the serial version of PROP in double precision.
+ generated by running the serial version of PROP in double precision\index{precision!double precision}.

 Data used in the most costly computation parts are read from input files in
 Data used in the most costly computation parts are read from input files in

-double precision format and then 
-cast to single precision format.
-PROP results  (input of FARM) are computed in single precision and  written
-into files in double precision. 
+double precision\index{precision!double precision} format and then 
+cast to single precision\index{precision!single precision} format.
+PROP results  (input of FARM) are computed in single precision\index{precision!single precision} and  written
+into files in double precision\index{precision!double precision}. 

 
 \subsection{Medium case study}
 \begin{figure}[h]
 \begin{center}
 \includegraphics*[width=0.9\linewidth]{Chapters/chapter15/figures/error.pdf} 
 
 \subsection{Medium case study}
 \begin{figure}[h]
 \begin{center}
 \includegraphics*[width=0.9\linewidth]{Chapters/chapter15/figures/error.pdf} 

-\caption{\label{fig:sp-distrib} Error distribution for medium case in single precision}
+\caption{\label{fig:sp-distrib} Error distribution for medium case in single precision\index{precision!single precision}}

 \end{center}
 \end{figure}
 
 \end{center}
 \end{figure}
 


@@ -476,11 +475,11 @@ in the same prop00X.out file.
   Relative errors of approximately 5\% impact values the order of
   magnitude of which is at most 1.E2. 
   For instance, the value 164 produced by the reference version of
   Relative errors of approximately 5\% impact values the order of
   magnitude of which is at most 1.E2. 
   For instance, the value 164 produced by the reference version of

-  PROP becomes 172 in the single precision version.
+  PROP becomes 172 in the single precision\index{precision!single precision} version.

 
 \end{itemize}
 
 
 \end{itemize}
 

-To study the impact of the single precision version of PROP on the
+To study the impact of the single precision\index{precision!single precision} version of PROP on the

 FARM program, the cross-section
 results files corresponding to 
 transitions 
 FARM program, the cross-section
 results files corresponding to 
 transitions 


@@ -504,25 +503,25 @@ values are impacted by low errors. For instance, the maximum value
  {1s2p} &  0.08 & {1s4s} &  0.20  \\ \hline
  {1s3s} &  0.17 &2p4d & 1.60  \\ \hline
 \end{tabular}
  {1s2p} &  0.08 & {1s4s} &  0.20  \\ \hline
  {1s3s} &  0.17 &2p4d & 1.60  \\ \hline
 \end{tabular}

-\caption{\label{sp-farm}Impact  on FARM  of the single precision version of PROP}
+\caption{\label{sp-farm}Impact  on FARM  of the single precision\index{precision!single precision} version of PROP}

 \end{center}
 \end{table}
 
 To examine in more detail the impact of PROP on FARM, 
 cross sections above the ionization threshold (1 Ryd)
 are compared in single and
 \end{center}
 \end{table}
 
 To examine in more detail the impact of PROP on FARM, 
 cross sections above the ionization threshold (1 Ryd)
 are compared in single and

-double precision  for 
+double precision\index{precision!double precision}  for 

 transitions amongst the 1s, \dots 4s, 2p, \dots 4p, 3d, 4d target states.  
 This comparison is carried out by generating 45 plots.  In all the
 transitions amongst the 1s, \dots 4s, 2p, \dots 4p, 3d, 4d target states.  
 This comparison is carried out by generating 45 plots.  In all the

- plots, results in single and double precision match except for few
+ plots, results in single and double precision\index{precision!double precision} match except for few

  scattering energies which are very close to pseudo-state thresholds. 
 For example Fig.~\ref{1s2p} and \ref{1s4d} present the scattering energies corresponding to the
  scattering energies which are very close to pseudo-state thresholds. 
 For example Fig.~\ref{1s2p} and \ref{1s4d} present the scattering energies corresponding to the

-{1s2p} and {1s4d} cross-sections computed in single and double precision.   For some cross-sections, 
+{1s2p} and {1s4d} cross-sections computed in single and double precision\index{precision!double precision}.   For some cross-sections, 

 increasing a threshold parameter from 1.E-4 to 1.E-3 in the FARM
 program
 results in energies close to threshold being avoided
  and therefore
 increasing a threshold parameter from 1.E-4 to 1.E-3 in the FARM
 program
 results in energies close to threshold being avoided
  and therefore

-the cross-sections in double and single precision match more
+the cross-sections in double and single precision\index{precision!single precision} match more

 accurately. 
 This is the case for instance for cross-section 1s2p (see Fig.~\ref{1s2p3}). 
 However for other cross-sections (such as 1s4d) some problematic energies remain even if the 
 accurately. 
 This is the case for instance for cross-section 1s2p (see Fig.~\ref{1s2p3}). 
 However for other cross-sections (such as 1s4d) some problematic energies remain even if the 


@@ -559,12 +558,12 @@ threshold parameter would be required for such cross-sections.
 \end{figure}
 
 As a conclusion, the medium case study shows that the execution of
 \end{figure}
 
 As a conclusion, the medium case study shows that the execution of

-PROP in single precision leads to a few inexact scattering energies to
+PROP in single precision\index{precision!single precision} leads to a few inexact scattering energies to

 be computed by the FARM program for some cross-sections.
 Thanks to a suitable threshold parameter in the FARM program these problematic energies may possibly 
 be skipped. 
 Instead of investigating deeper the choice of such a parameter for the medium case, we analyze the 
 be computed by the FARM program for some cross-sections.
 Thanks to a suitable threshold parameter in the FARM program these problematic energies may possibly 
 be skipped. 
 Instead of investigating deeper the choice of such a parameter for the medium case, we analyze the 

-single precision computation  in a more
+single precision\index{precision!single precision} computation  in a more

 realistic case in Sect.~\ref{huge}. 
 \begin{comment}
 The conclusion of the medium case study is that running PROP in single
 realistic case in Sect.~\ref{huge}. 
 \begin{comment}
 The conclusion of the medium case study is that running PROP in single


@@ -572,7 +571,7 @@ precision gives relatively stable results provided that suitable
 parameter values are used in the FARM program in order to skip the
 problematic energies that are too close to the pseudo-state
 thresholds.  To verify if this conclusion is still valid with a larger
 parameter values are used in the FARM program in order to skip the
 problematic energies that are too close to the pseudo-state
 thresholds.  To verify if this conclusion is still valid with a larger

-data set, the single precision computation is analyzed in a more
+data set, the single precision\index{precision!single precision} computation is analyzed in a more

 realistic case in Sect.~\ref{huge}.
 \end{comment}
 
 realistic case in Sect.~\ref{huge}.
 \end{comment}
 


@@ -592,7 +591,7 @@ realistic case in Sect.~\ref{huge}.
 \end{figure}
 
 We study here the impact on FARM of the PROP program run in
 \end{figure}
 
 We study here the impact on FARM of the PROP program run in

-single precision for the huge case (see Table~\ref{data-sets}).
+single precision\index{precision!single precision} for the huge case (see Table~\ref{data-sets}).

 The cross-sections
 corresponding to all
 atomic target states 1s \dots 7i are explored, which
 The cross-sections
 corresponding to all
 atomic target states 1s \dots 7i are explored, which


@@ -602,24 +601,24 @@ It should be noted that in this case, over the same energy range above the ioniz
 As expected, all the plots exhibit large differences between single and double
 precision cross-sections. 
 For example Fig.~\ref{1s2pHT} and  \ref{1s4dHT} present the 1s2p and 1s4d cross-sections computed in
 As expected, all the plots exhibit large differences between single and double
 precision cross-sections. 
 For example Fig.~\ref{1s2pHT} and  \ref{1s4dHT} present the 1s2p and 1s4d cross-sections computed in

-single and double precision for the huge case.  
-We can conclude that PROP in single precision gives invalid results 
+single and double precision\index{precision!double precision} for the huge case.  
+We can conclude that PROP in single precision\index{precision!single precision} gives invalid results 

 for realistic simulation cases above the ionization threshold.
 Therefore the  deployment of PROP on GPU, described in Sect.~\ref{gpu-implem},
 for realistic simulation cases above the ionization threshold.
 Therefore the  deployment of PROP on GPU, described in Sect.~\ref{gpu-implem},

-has been carried out in double precision. 
+has been carried out in double precision\index{precision!double precision}. 

 
 \section{Towards a complete deployment of PROP on GPUs} 
 \label{gpu-implem}
 
 We now detail how PROP has been progressively deployed on
 
 \section{Towards a complete deployment of PROP on GPUs} 
 \label{gpu-implem}
 
 We now detail how PROP has been progressively deployed on

-GPUs in double precision in order to avoid the
+GPUs in double precision\index{precision!double precision} in order to avoid the

 expensive memory transfers between the host and the GPU.
 Different versions with successive improvements and optimizations are presented.
 We use CUDA~\cite{CUDA_ProgGuide} for GPU programming, as well as the
 expensive memory transfers between the host and the GPU.
 Different versions with successive improvements and optimizations are presented.
 We use CUDA~\cite{CUDA_ProgGuide} for GPU programming, as well as the

-CUBLAS~\cite{CUBLAS} 
+CUBLAS\index{CUBLAS}~\cite{CUBLAS} 

 and MAGMA \cite{MAGMA} libraries for linear algebra operations.
 and MAGMA \cite{MAGMA} libraries for linear algebra operations.

-Since PROP is written in Fortran 90, {\em wrappers} in C are used to
-enable calls to CUDA kernels from PROP routines.
+Since PROP is written in Fortran 90, {\em wrappers\index{wrapper}} in C are used to
+enable calls to CUDA kernels from PROP routines. 

 
 
 \subsection{Computing the output $R$-matrix on GPU}
 
 
 \subsection{Computing the output $R$-matrix on GPU}


@@ -647,7 +646,7 @@ Fig.~\ref{offdiagonal} for an off-diagonal sector.
   These copies, along with possible scalings or transpositions, are
   implemented as CUDA kernels which can be applied to two
   matrices of any size and starting at any offset. 
   These copies, along with possible scalings or transpositions, are
   implemented as CUDA kernels which can be applied to two
   matrices of any size and starting at any offset. 

-  Memory accesses are coalesced \cite{CUDA_ProgGuide} in order to
+  Memory accesses are coalesced\index{coalesced memory accesses} \cite{CUDA_ProgGuide} in order to

   provide the best performance for such memory-bound kernels.
 \item[Step 2] (``Local copies''):~data are copied from
   local $R$-matrices to temporary arrays ($U$, $V$) and to $\Re^{O}$.
   provide the best performance for such memory-bound kernels.
 \item[Step 2] (``Local copies''):~data are copied from
   local $R$-matrices to temporary arrays ($U$, $V$) and to $\Re^{O}$.


@@ -656,13 +655,13 @@ Fig.~\ref{offdiagonal} for an off-diagonal sector.
   is added to matrix $A$ (via a CUDA kernel) and zeroes are written in
    $\Re^{O}$  where required.
 \item[Step 3] (``Linear system solving''):~matrix $A$ is factorized
   is added to matrix $A$ (via a CUDA kernel) and zeroes are written in
    $\Re^{O}$  where required.
 \item[Step 3] (``Linear system solving''):~matrix $A$ is factorized

-  using the MAGMA DGETRF 
+  using the MAGMA DGETRF\index{MAGMA functions!DGETRF} 

    routine and the result is stored in-place.
 \item[Step 4] (``Linear system solving'' cont.):~the matrix system
    routine and the result is stored in-place.
 \item[Step 4] (``Linear system solving'' cont.):~the matrix system

- of linear equations  $AW$ = $V$ is solved using the MAGMA DGETRS 
+ of linear equations  $AW$ = $V$ is solved using the MAGMA DGETRS\index{MAGMA functions!DGETRS} 

 routine. The  solution is stored in matrix $V$.
 \item[Step 5] (``Output matrix product''):~matrix $U$
 routine. The  solution is stored in matrix $V$.
 \item[Step 5] (``Output matrix product''):~matrix $U$

-  is multiplied by matrix $V$ using the CUBLAS DGEMM 
+  is multiplied by matrix $V$ using the CUBLAS\index{CUBLAS} DGEMM 

   routine. The result is stored in a temporary matrix~$t$.
 \item[Step 6] (``Output add''):~$t$ is added to $\Re^{O}$ (CUDA
   kernel).
   routine. The result is stored in a temporary matrix~$t$.
 \item[Step 6] (``Output add''):~$t$ is added to $\Re^{O}$ (CUDA
   kernel).


@@ -696,11 +695,11 @@ presented in Fig.~\ref{amplitudes},
 is a matrix product between
 one $i$ amplitude array and one transposed $j$ amplitude array 
 which is performed by a single DGEMM 
 is a matrix product between
 one $i$ amplitude array and one transposed $j$ amplitude array 
 which is performed by a single DGEMM 

-BLAS call. 
+BLAS\index{BLAS} call. 

 In this version, hereafter referred to as GPU
 V2\label{gpuv2}, $i$ and $j$ amplitude arrays are transferred to the
 GPU memory and the required matrix multiplications are performed on
 In this version, hereafter referred to as GPU
 V2\label{gpuv2}, $i$ and $j$ amplitude arrays are transferred to the
 GPU memory and the required matrix multiplications are performed on

-the GPU (via CUBLAS routines).
+the GPU (via CUBLAS\index{CUBLAS} routines).

 
 
 The involved matrices having medium sizes (either $3066 \times 383$ or
 
 
 The involved matrices having medium sizes (either $3066 \times 383$ or


@@ -734,7 +733,7 @@ Moreover, scaling $j$ amplitude arrays is expected to be faster on the
 GPU than on the CPU, thanks to the massively parallel architecture of
 the GPU and thanks to its higher internal memory bandwidth.
 
 GPU than on the CPU, thanks to the massively parallel architecture of
 the GPU and thanks to its higher internal memory bandwidth.
 

-\subsection{Using double-buffering to overlap I/O and computation}
+\subsection{Using double-buffering\index{double-buffering} to overlap I/O and computation}

 
 \begin{figure}[t]
   \centering
 
 \begin{figure}[t]
   \centering


@@ -761,7 +760,7 @@ time for the first sectors. But this evaluation time grows
 linearly with the strip number, and rapidly exceeds the I/O 
 time.
 
 linearly with the strip number, and rapidly exceeds the I/O 
 time.
 

-It is thus interesting to use a double-buffering technique to overlap the
+It is thus interesting to use a double-buffering\index{double-buffering} technique to overlap the 

 I/O time with the evaluation time:
 for each sector, the evaluation of sector $n$ is performed
 (on GPU) simultaneously with the reading of data for sector
 I/O time with the evaluation time:
 for each sector, the evaluation of sector $n$ is performed
 (on GPU) simultaneously with the reading of data for sector


@@ -769,7 +768,7 @@ $n+1$ (on CPU). This requires the duplication in the CPU memory of all the
 data structures
 used for storing data read from I/O files for each sector.
 This version, hereafter referred to as GPU
 data structures
 used for storing data read from I/O files for each sector.
 This version, hereafter referred to as GPU

-V4\label{gpuv4}, uses POSIX threads. Two threads are
+V4\label{gpuv4}, uses POSIX threads\index{POSIX threads}. Two threads are

 executed concurrently: an I/O thread that reads data from I/O files
 for each sector, and a computation thread, dedicated to the propagation
 of the global $R$-matrix, that performs successively for each sector
 executed concurrently: an I/O thread that reads data from I/O files
 for each sector, and a computation thread, dedicated to the propagation
 of the global $R$-matrix, that performs successively for each sector


@@ -782,9 +781,9 @@ the computation thread which are implemented through standard POSIX
 thread mechanisms.
 
 
 thread mechanisms.
 
 

-\subsection{Matrix padding}
+\subsection{Matrix padding\index{padding}}

 The CUBLAS DGEMM 
 The CUBLAS DGEMM 

-performance and the MAGMA DGETRF/DGETRS 
+performance and the MAGMA DGETRF\index{MAGMA functions!DGETRF}/DGETRS\index{MAGMA functions!DGETRS} 

 performance is reduced when the sizes (or
 the leading dimensions) of the matrix are not multiples of the inner blocking size \cite{NTD10a}.
 This inner blocking size can be 32 or 64, depending on the computation
 performance is reduced when the sizes (or
 the leading dimensions) of the matrix are not multiples of the inner blocking size \cite{NTD10a}.
 This inner blocking size can be 32 or 64, depending on the computation


@@ -797,9 +796,9 @@ multiples of 64.
 This corresponds indeed to the optimal size for the matrix product on the
 Fermi architecture \cite{NTD10b}. And as far as linear system solving is
 concerned, all the matrices have sizes which are multiples of 383: we
 This corresponds indeed to the optimal size for the matrix product on the
 Fermi architecture \cite{NTD10b}. And as far as linear system solving is
 concerned, all the matrices have sizes which are multiples of 383: we

-therefore use padding to obtain multiples of 384 (which are 
+therefore use padding\index{padding} to obtain multiples of 384 (which are 

 again  multiples of 64). 
 again  multiples of 64). 

-It can be noticed that this padding has to be performed dynamically
+It can be noticed that this padding\index{padding} has to be performed dynamically

 as the matrices increase in size during the propagation 
 (when possible the
  maximum required storage space is however allocated only once in the
 as the matrices increase in size during the propagation 
 (when possible the
  maximum required storage space is however allocated only once in the


@@ -897,7 +896,7 @@ one C2050 (Fermi) GPU, located at
  UPMC (Universit\'e Pierre et Marie Curie, Paris, France). 
 As a remark, the execution times measured on the C2050 would be the same 
 on the C2070 and on  the C2075, the only difference between these GPUs 
  UPMC (Universit\'e Pierre et Marie Curie, Paris, France). 
 As a remark, the execution times measured on the C2050 would be the same 
 on the C2070 and on  the C2075, the only difference between these GPUs 

-being their memory size and their TDP (Thermal Design Power). 
+being their memory size and their TDP (Thermal Design Power)\index{TDP (Thermal Design Power)}. 

 We emphasize that the execution times correspond to the
 complete propagation for all six energies of the large case (see
 Table~\ref{data-sets}), that is to say to the complete execution of
 We emphasize that the execution times correspond to the
 complete propagation for all six energies of the large case (see
 Table~\ref{data-sets}), that is to say to the complete execution of


@@ -906,7 +905,7 @@ Since energies are independent, execution times for more energies
 (e.g. the huge case) should be proportional
 to those reported in Table~\ref{table:time}.  
 
 (e.g. the huge case) should be proportional
 to those reported in Table~\ref{table:time}.  
 

-These tests, which have been performed with CUDA 3.2, CUBLAS 3.2 and 
+These tests, which have been performed with CUDA 3.2, CUBLAS\index{CUBLAS} 3.2 and 

 MAGMA 0.2, 
 show that the successive GPU versions of PROP offer 
 increasing, and at the end interesting, speedups.
 MAGMA 0.2, 
 show that the successive GPU versions of PROP offer 
 increasing, and at the end interesting, speedups.


@@ -919,21 +918,21 @@ reduced thanks to~V3,
 which also accelerates the computation of
 amplitude arrays thanks to the GPU. 
 The 
 which also accelerates the computation of
 amplitude arrays thanks to the GPU. 
 The 

-double-buffering technique implemented in V4
+double-buffering\index{double-buffering} technique implemented in V4

  effectively enables the overlapping of 
 I/O operations with computation, while the 
  effectively enables the overlapping of 
 I/O operations with computation, while the 

-padding implemented in V5 also improves the computation times.
+padding\index{padding} implemented in V5 also improves the computation times.

 It 
 It 

-is noticed that the padding 
+is noticed that the padding\index{padding}  

 does offer much more performance gain with,  
 does offer much more performance gain with,  

-for example,  CUDA 3.1 and the MAGMA DGEMM~\cite{NTD10b}:  the
+for example,  CUDA 3.1 and the MAGMA DGEMM\index{MAGMA functions!DGEMM}~\cite{NTD10b}:  the

 speedup with respect to one 
 CPU core was increased from 6.3 to 8.1 on C1060, and from 9.5 to 14.3
 on C2050. 
 speedup with respect to one 
 CPU core was increased from 6.3 to 8.1 on C1060, and from 9.5 to 14.3
 on C2050. 

-Indeed since CUBLAS 3.2 performance has been improved for non block multiple
+Indeed since CUBLAS\index{CUBLAS} 3.2 performance has been improved for non block multiple

 matrix sizes through MAGMA code~\cite{NTD10a}. 
 Although for all versions the C2050 (with its improved
 matrix sizes through MAGMA code~\cite{NTD10a}. 
 Although for all versions the C2050 (with its improved

-double precision performance) offers up to almost 
+double precision\index{precision!double precision} performance) offers up to almost 

 double speedup compared to 
 the C1060, the performance obtained with both architectures justifies the use of 
 the GPU for such an application.
 double speedup compared to 
 the C1060, the performance obtained with both architectures justifies the use of 
 the GPU for such an application.


@@ -1009,33 +1008,32 @@ obtained for all operations, except for the
 CPU-GPU transfers and the linear system solving.
 The CPU-GPU transfers are mainly due to the $j$ amplitude arrays, and
 currently still correspond to minor times. When required, the
 CPU-GPU transfers and the linear system solving.
 The CPU-GPU transfers are mainly due to the $j$ amplitude arrays, and
 currently still correspond to minor times. When required, the

-double-buffering technique may also be used to overlap such transfers
-with computation on the GPU.
+double-buffering\index{double-buffering} technique may also be used to overlap such transfers with computation on the GPU.

 
 
 
 
 
 

-\section{Propagation of multiple concurrent energies on GPU}
+\section{Propagation of multiple concurrent energies on GPU}\index{concurrent kernel execution}

 
 Finally, we present here an improvement that can  
 benefit from the Fermi architecture, as well as from the newest Kepler
 architecture, 
 both of which enable the concurrent execution of multiple 
 
 Finally, we present here an improvement that can  
 benefit from the Fermi architecture, as well as from the newest Kepler
 architecture, 
 both of which enable the concurrent execution of multiple 

-CUDA kernels, thus offering additional speedup on  
+CUDA kernels\index{concurrent kernel execution}, thus offering additional speedup on  

 GPUs for small or medium computation grain kernels.
 In our case, the performance gain on the GPU is indeed limited
 since most matrices have small or medium sizes. 
 By using multiple streams within one CUDA context~\cite{CUDA_ProgGuide},
 we can propagate multiple energies
 GPUs for small or medium computation grain kernels.
 In our case, the performance gain on the GPU is indeed limited
 since most matrices have small or medium sizes. 
 By using multiple streams within one CUDA context~\cite{CUDA_ProgGuide},
 we can propagate multiple energies

-concurrently on the Fermi GPU. 
+concurrently\index{concurrent kernel execution} on the Fermi GPU. 

 It can be noticed that all GPU computations for all streams are
 launched by the same host thread. We therefore rely here on the {\em legacy
 It can be noticed that all GPU computations for all streams are
 launched by the same host thread. We therefore rely here on the {\em legacy

-API} of CUBLAS~\cite{CUBLAS} (like MAGMA)
+API} of CUBLAS\index{CUBLAS}~\cite{CUBLAS} (like MAGMA)

 without thread safety problems. 
 A {\em breadth first} issue order is used for kernel
 launchs \cite{CUDA_stream}: for a given GPU kernel, all kernel launchs
 are indeed issued together in the host thread, using one stream for each
 concurrent energy, in order to maximize concurrent kernel
 without thread safety problems. 
 A {\em breadth first} issue order is used for kernel
 launchs \cite{CUDA_stream}: for a given GPU kernel, all kernel launchs
 are indeed issued together in the host thread, using one stream for each
 concurrent energy, in order to maximize concurrent kernel

-execution.  
+execution\index{concurrent kernel execution}.  

 Of course, the memory available on the GPU must be large enough to
 store all data structures required by each energy. 
 Moreover, multiple streams are also used within the
 Of course, the memory available on the GPU must be large enough to
 store all data structures required by each energy. 
 Moreover, multiple streams are also used within the


@@ -1080,7 +1078,7 @@ in order to enable concurrent executions among the required kernels.
 In order to have enough GPU memory to run two or three concurrent
 energies for the large case, we use one C2070 GPU 
 (featuring 6GB of memory) 
 In order to have enough GPU memory to run two or three concurrent
 energies for the large case, we use one C2070 GPU 
 (featuring 6GB of memory) 

-with one Intel X5650 hex-core CPU, CUDA 4.1 and CUBLAS 4.1, as
+with one Intel X5650 hex-core CPU, CUDA 4.1 and CUBLAS\index{CUBLAS} 4.1, as

 well as the latest MAGMA release (version 1.3.0). 
 Substantial changes have been required 
 in the MAGMA calls with respect to the previous versions of PROP that were using MAGMA 0.2. 
 well as the latest MAGMA release (version 1.3.0). 
 Substantial changes have been required 
 in the MAGMA calls with respect to the previous versions of PROP that were using MAGMA 0.2. 


@@ -1093,15 +1091,14 @@ concurrent energies or more.
 With the more realistic large case, the performance gain is lower mainly because of
 the increase in matrix sizes, which implies a better GPU usage
 with only one energy on the GPU. The concurrent execution of multiple
 With the more realistic large case, the performance gain is lower mainly because of
 the increase in matrix sizes, which implies a better GPU usage
 with only one energy on the GPU. The concurrent execution of multiple

-kernels is also limited by other operations on the
+kernels\index{concurrent kernel execution} is also limited by other operations on the

 GPU \cite{CUDA_ProgGuide,CUDA_stream} and by the current MAGMA code which
 prevents concurrent MAGMA calls in different streams. 
 Better speedups can be here expected on the latest Kepler GPUs which
 offer additional compute power, and whose {\em Hyper-Q} feature may help
 improve further the GPU utilization with concurrent energies. 
 On the contrary, the same code on the C1060 shows no speedup
 GPU \cite{CUDA_ProgGuide,CUDA_stream} and by the current MAGMA code which
 prevents concurrent MAGMA calls in different streams. 
 Better speedups can be here expected on the latest Kepler GPUs which
 offer additional compute power, and whose {\em Hyper-Q} feature may help
 improve further the GPU utilization with concurrent energies. 
 On the contrary, the same code on the C1060 shows no speedup

- since the concurrent kernel launches are
-serialized on this previous GPU architecture. 
+ since the concurrent kernel launches are serialized on this previous GPU architecture. 

 
 
 
 
 
 


@@ -1111,16 +1108,15 @@ serialized on this previous GPU architecture.
 
 
 \section{Conclusion and future work}
 
 
 \section{Conclusion and future work}

-\label{conclusion}
-
+\label{conclusion} 

 
 In this chapter, we have presented our methodology and our results in
 the deployment on 
 a GPU of an application (the PROP program) in atomic physics. 
 
 We have started by studying the numerical stability of PROP using
 
 In this chapter, we have presented our methodology and our results in
 the deployment on 
 a GPU of an application (the PROP program) in atomic physics. 
 
 We have started by studying the numerical stability of PROP using

-single precision arithmetic. This has shown that PROP
-using single precision, while relatively stable for some small cases,
+single precision\index{precision!single precision} arithmetic. This has shown that PROP
+using single precision\index{precision!single precision}, while relatively stable for some small cases,

 gives unsatisfactory results for realistic simulation cases above the
 ionization threshold where there is a 
 significant density of pseudo-states. It is
 gives unsatisfactory results for realistic simulation cases above the
 ionization threshold where there is a 
 significant density of pseudo-states. It is


@@ -1129,25 +1125,25 @@ where the actual target states are less dense. This requires further
 investigation. 
 
 We have 
 investigation. 
 
 We have 

-therefore deployed the PROP code in double precision on 
+therefore deployed the PROP code in double precision\index{precision!double precision} on 

 a GPU, with successive improvements. The different GPU versions 
 each offer increasing speedups over the CPU version.
 Compared to the single (respectively four) core(s) CPU version, the
 optimal GPU implementation 
 gives a speedup of 8.2 (resp. 4.6) on one C1060 GPU,
 and a speedup of 15.9 (resp. 9.0) on one 
 a GPU, with successive improvements. The different GPU versions 
 each offer increasing speedups over the CPU version.
 Compared to the single (respectively four) core(s) CPU version, the
 optimal GPU implementation 
 gives a speedup of 8.2 (resp. 4.6) on one C1060 GPU,
 and a speedup of 15.9 (resp. 9.0) on one 

-C2050 GPU with improved double precision performance.
+C2050 GPU with improved double precision\index{precision!double precision} performance.

 An additional gain of around 15\% 
 can also be obtained on one Fermi GPU
 with large memory (C2070) thanks to concurrent kernel execution. 
 
 Such speedups 
 cannot be directly compared with the 1.15 speedup 
 An additional gain of around 15\% 
 can also be obtained on one Fermi GPU
 with large memory (C2070) thanks to concurrent kernel execution. 
 
 Such speedups 
 cannot be directly compared with the 1.15 speedup 

-obtained with the HMPP version, since in our tests the CPUs are
-different and the CUBLAS versions are more recent.  
+obtained with the HMPP\index{HMPP} version, since in our tests the CPUs are
+different and the CUBLAS\index{CUBLAS} versions are more recent.  

 However, the programming effort required 
 progressively to deploy PROP on GPUs clearly offers improved and interesting speedups for this 
 However, the programming effort required 
 progressively to deploy PROP on GPUs clearly offers improved and interesting speedups for this 

-real-life   application in double precision with varying-size matrices. 
+real-life   application in double precision\index{precision!double precision} with varying-size matrices. 

 
 
 We are currently working on a hybrid CPU-GPU version that spreads the
 
 
 We are currently working on a hybrid CPU-GPU version that spreads the


@@ -1155,7 +1151,7 @@ computations of the independent energies on both the CPU
 and the GPU. This will enable 
 multiple energy execution on the CPU, with 
 one or several core(s) dedicated to each energy (via multi-threaded
 and the GPU. This will enable 
 multiple energy execution on the CPU, with 
 one or several core(s) dedicated to each energy (via multi-threaded

-BLAS libraries). Multiple 
+BLAS\index{BLAS} libraries). Multiple 

 concurrent energies may also be propagated on each Fermi GPU. 
 By merging this work with the current MPI PROP program, we will
 obtain a scalable hybrid CPU-GPU version.
 concurrent energies may also be propagated on each Fermi GPU. 
 By merging this work with the current MPI PROP program, we will
 obtain a scalable hybrid CPU-GPU version.