diff --git a/CHANGES b/CHANGES index e72fc4760..a102d7962 100644 --- a/CHANGES +++ b/CHANGES @@ -4,6 +4,7 @@ Simulation, and Optimization. ----------------------------------------------------- Version 0.51.0 + * Add canned likelihood for scalar GPMSA use-case a la Higdon et al * Add a logit-transformed transition kernel for more efficient proposals * Adding jeffreys distribution as an available prior distribution * Adding likelihood value caching to ML sampler diff --git a/configure.ac b/configure.ac index 983c13d77..6f39f8bb0 100644 --- a/configure.ac +++ b/configure.ac @@ -2,7 +2,7 @@ # Process this file with autoconf to produce a configure script. AC_PREREQ(2.65) -AC_INIT([queso], [0.50.1], [queso-users@googlegroups.com]) +AC_INIT([queso], [0.51.0], [queso-users@googlegroups.com]) PACKAGE_DESCRIPTION="The parallel C++ statistical library QUESO: Quantification of uncertainty for estimation, simulation and optimization" AC_SUBST([PACKAGE_DESCRIPTION]) PACKAGE_URL="https://github.com/libqueso/queso" diff --git a/manual/users/users.tex b/manual/users/users.tex index 6986cee17..0e0aee367 100644 --- a/manual/users/users.tex +++ b/manual/users/users.tex @@ -78,7 +78,7 @@ \newcommand{\D}{ {\bf D}} \newcommand{\myverb}[1]{ \indent{ \begin{verbatim} #1 \end{verbatim} } } -\newcommand{\QUESOversion}{0.50.0} +\newcommand{\QUESOversion}{0.51.0} \usepackage{color} \definecolor{dkgreen}{rgb}{0,0.6,0} diff --git a/manual/users/users_2_installation.tex b/manual/users/users_2_installation.tex index 1c2e3c2f0..683c27584 100644 --- a/manual/users/users_2_installation.tex +++ b/manual/users/users_2_installation.tex @@ -177,16 +177,16 @@ \section{Configure QUESO Building Environment}\label{sec:Queso_configure} -Therefore, the basic steps to configure QUESO using Boost, GSL (required), HDF5 and Trilinos (optional) for installation at `\verb+$HOME/LIBRARIES/QUESO-0.50.0+' are: +Therefore, the basic steps to configure QUESO using Boost, GSL (required), HDF5 and Trilinos (optional) for installation at `\verb+$HOME/LIBRARIES/QUESO-0.51.0+' are: \begin{lstlisting}[{basicstyle=\footnotesize\ttfamily}] -$ ./configure --prefix=$HOME/LIBRARIES/QUESO-0.50.0 \ +$ ./configure --prefix=$HOME/LIBRARIES/QUESO-0.51.0 \ --with-boost=$HOME/LIBRARIES/boost-1.53.0 \ --with-gsl=$HOME/LIBRARIES/gsl-1.15 \ --with-hdf5=$HOME/LIBRARIES/hdf5-1.8.10 \ --with-trilinos=$HOME/LIBRARIES/trilinos-11.2.4 \end{lstlisting} -Note: the directory `\verb+$HOME/LIBRARIES/QUESO-0.50.0+' does not need to exist in advance, since it will be created by the command \verb+make install+ described in Section \ref{sec:install_Queso_make}. +Note: the directory `\verb+$HOME/LIBRARIES/QUESO-0.51.0+' does not need to exist in advance, since it will be created by the command \verb+make install+ described in Section \ref{sec:install_Queso_make}. \section{Compile, Check and Install \Queso{}}\label{sec:install_Queso_make} @@ -266,7 +266,7 @@ \section{Summary of Installation Steps}\label{sec:summary} Supposing you have downloaded the file `queso-0.47.1.tar.gz' into \texttt{\$HOME/queso\_download/}. % In a BASH shell, the basic steps to configure QUESO using GRVY, Boost and GSL for installation at -`\verb+$HOME/LIBRARIES/QUESO-0.50.0+' are: +`\verb+$HOME/LIBRARIES/QUESO-0.51.0+' are: \begin{lstlisting}[{basicstyle=\footnotesize\ttfamily}] $ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:\ @@ -283,7 +283,7 @@ \section{Summary of Installation Steps}\label{sec:summary} $ cd $HOME/queso_download/ #enter source dir $ gunzip < queso-0.47.1.tar.gz | tar xf - $ cd $HOME/queso_download/queso-0.47.1 #enter the build dir -$ ./configure --prefix=$HOME/LIBRARIES/QUESO-0.50.0 \ +$ ./configure --prefix=$HOME/LIBRARIES/QUESO-0.51.0 \ --with-boost=$HOME/LIBRARIES/boost-1.53.0 \ --with-gsl=$HOME/LIBRARIES/gsl-1.15 \ --with-hdf5=$HOME/LIBRARIES/hdf5-1.8.10 \ @@ -292,13 +292,13 @@ \section{Summary of Installation Steps}\label{sec:summary} $ make check $ make install $ make docs -$ ls $HOME/LIBRARIES/QUESO-0.50.0 #listing QUESO installation dir +$ ls $HOME/LIBRARIES/QUESO-0.51.0 #listing QUESO installation dir >> bin include lib examples \end{lstlisting} % % \paragraph*{Note:} According to Section \ref{sec:Queso_tree}, \texttt{\$HOME/queso\_download/} is the source tree, \\ \verb+$HOME/queso_download/queso-0.47.1+ is the build tree, and \newline -% \verb+$HOME/LIBRARIES/QUESO-0.50.0+ is the installation tree. +% \verb+$HOME/LIBRARIES/QUESO-0.51.0+ is the installation tree. % @@ -361,7 +361,7 @@ \section{The Installed Directory Structure} \label{sc-installed-dir-structure} \item \verb+bin+: contains the executable \verb+queso_version+, which provides information about the installed library. The code bellow presents a sample output: \begin{lstlisting}[{basicstyle=\footnotesize\ttfamily}] -kemelli@margarida:~/LIBRARIES/QUESO-0.50.0/bin$ ./queso_version +kemelli@margarida:~/LIBRARIES/QUESO-0.51.0/bin$ ./queso_version --------------------------------------------------------------- QUESO Library: Version = 0.47.1 (47.1) @@ -381,13 +381,13 @@ \section{The Installed Directory Structure} \label{sc-installed-dir-structure} GLPK DIR = HDF5 DIR = --------------------------------------------------------------- -kemelli@margarida:~/LIBRARIES/QUESO-0.50.0/bin$ +kemelli@margarida:~/LIBRARIES/QUESO-0.51.0/bin$ \end{lstlisting} - \item \verb+lib+: contains the static and dynamic versions of the library. The full to path to this directory, e.g., \verb+$HOME/LIBRARIES/QUESO-0.50.0/lib+ should be added to the user's \verb+LD_LIBRARY_PATH+ environmental variable in order to use QUESO library with his/her application code: + \item \verb+lib+: contains the static and dynamic versions of the library. The full to path to this directory, e.g., \verb+$HOME/LIBRARIES/QUESO-0.51.0/lib+ should be added to the user's \verb+LD_LIBRARY_PATH+ environmental variable in order to use QUESO library with his/her application code: \begin{lstlisting}[{basicstyle=\footnotesize\ttfamily}] $ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:\ - $HOME/LIBRARIES/QUESO-0.50.0/lib + $HOME/LIBRARIES/QUESO-0.51.0/lib \end{lstlisting} @@ -410,13 +410,13 @@ \section{Create your Application with the Installed QUESO} \label{sc-use-queso} your \verb+.bashrc+ (supposing you have a BASH-shell): \begin{lstlisting}[{basicstyle=\footnotesize\ttfamily}] $ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:\ - $HOME/LIBRARIES/QUESO-0.50.0/lib + $HOME/LIBRARIES/QUESO-0.51.0/lib \end{lstlisting} % or into your \verb+.cshrc+ file (supposing you have a C-shell): % \begin{lstlisting}[label={},caption={}] % setenv LD_LIBRARY_PATH \$LD_LIBRARY_PATH: -% $HOME/LIBRARIES/QUESO-0.50.0/lib +% $HOME/LIBRARIES/QUESO-0.51.0/lib % \end{lstlisting} @@ -426,7 +426,7 @@ \section{Create your Application with the Installed QUESO} \label{sc-use-queso} library through a Makefile such as the one displayed as follows: \begin{lstlisting}[basicstyle={\footnotesize\ttfamily},deletekeywords={export,rm}] -QUESO_DIR = $HOME/LIBRARIES/QUESO-0.50.0/ +QUESO_DIR = $HOME/LIBRARIES/QUESO-0.51.0/ BOOST_DIR = $HOME/LIBRARIES/boost-1.53.0/ GSL_DIR = $HOME/LIBRARIES/gsl-1.15/ GRVY_DIR = $HOME/LIBRARIES/grvy-0.32.0 diff --git a/manual/users/users_5a_example_sip.tex b/manual/users/users_5a_example_sip.tex index a5d495862..a1cb904ca 100644 --- a/manual/users/users_5a_example_sip.tex +++ b/manual/users/users_5a_example_sip.tex @@ -98,7 +98,7 @@ \subsection{Running the Example}\label{sec:sip-run} To run the executable provided (available after QUESO installation), enter the following commands: \begin{lstlisting}[label={},caption={}] -$ cd $HOME/LIBRARIES/QUESO-0.50.0/ +$ cd $HOME/LIBRARIES/QUESO-0.51.0/ $ cd examples/simpleStatisticalInverseProblem $ rm outputData/* $ ./exSimpleStatisticalInverseProblem_gsl example.inp @@ -178,12 +178,12 @@ \subsection{Create your own Makefile}\label{sec:sip-makefile} Thus, to compile, build and execute the code, the user just needs to run the following commands in the same directory where the files are: \begin{lstlisting} -$ cd $HOME/LIBRARIES/QUESO-0.50.0/examples/simpleStatisticalInverseProblem/ +$ cd $HOME/LIBRARIES/QUESO-0.51.0/examples/simpleStatisticalInverseProblem/ $ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:\ $HOME/LIBRARIES/gsl-1.15/lib/:\ $HOME/LIBRARIES/boost-1.53.0/lib/:\ $HOME/LIBRARIES/hdf5-1.8.10/lib:\ - $HOME/LIBRARIES/QUESO-0.50.0/lib + $HOME/LIBRARIES/QUESO-0.51.0/lib $ make -f Makefile_example_margarida $ ./simple_sip_example example.inp \end{lstlisting} diff --git a/manual/users/users_5b_example_sfp.tex b/manual/users/users_5b_example_sfp.tex index 382cd42de..0b3287e1d 100644 --- a/manual/users/users_5b_example_sfp.tex +++ b/manual/users/users_5b_example_sfp.tex @@ -50,7 +50,7 @@ \subsection{Running the Example}\label{sec:sfp-run} To run the executable provided (available after QUESO installation), enter the following commands: \begin{lstlisting}[label={},caption={}] -$ cd $HOME/LIBRARIES/QUESO-0.50.0/ +$ cd $HOME/LIBRARIES/QUESO-0.51.0/ $ cd examples/simpleStatisticalForwardProblem $ rm outputData/* $ ./exSimpleStatisticalForwardProblem_gsl example.inp @@ -117,12 +117,12 @@ \subsection{Create your own Makefile}\label{sec:sfp-makefile} Thus, to compile, build and execute the code, the user just needs to run the following commands in the same directory where the files are: \begin{lstlisting} -$ cd HOME/LIBRARIES/QUESO-0.50.0/examples/simpleStatisticalForwardProblem +$ cd HOME/LIBRARIES/QUESO-0.51.0/examples/simpleStatisticalForwardProblem $ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:\ $HOME/LIBRARIES/gsl-1.15/lib/:\ $HOME/LIBRARIES/boost-1.53.0/lib/:\ $HOME/LIBRARIES/hdf5-1.8.10/lib:\ - $HOME/LIBRARIES/QUESO-0.50.0/lib + $HOME/LIBRARIES/QUESO-0.51.0/lib $ make -f Makefile_sfp_example_margarida $ ./simple_sfp_example simple_sfp_example.inp \end{lstlisting} diff --git a/manual/users/users_5c_example_gravity.tex b/manual/users/users_5c_example_gravity.tex index 1f84b60b5..8c5e657db 100644 --- a/manual/users/users_5c_example_gravity.tex +++ b/manual/users/users_5c_example_gravity.tex @@ -198,14 +198,14 @@ \subsection{Running the Example}\label{sec:gravity-run} To run the executable provided (available after QUESO installation), enter the following commands: \begin{lstlisting}[label={},caption={}] -$ cd $HOME/LIBRARIES/QUESO-0.50.0/examples/gravity +$ cd $HOME/LIBRARIES/QUESO-0.51.0/examples/gravity $ rm outputData/* $ ./gravity_gsl gravity_inv_fwd.inp \end{lstlisting} The console output of the program is: \begin{lstlisting}[caption={Console output of program \texttt{gravity\_gsl}}, label={code:console_output},language={bash}] -kemelli@violeta:~/LIBRARIES/QUESO-0.50.0/examples/gravity$ ./gravity_gsl gravity_inv_fwd.inp +kemelli@violeta:~/LIBRARIES/QUESO-0.51.0/examples/gravity$ ./gravity_gsl gravity_inv_fwd.inp --------------------------------------------------------------------- QUESO Library: Version = 0.47.1 (47.1) @@ -251,7 +251,7 @@ \subsection{Running the Example}\label{sec:gravity-run} Ending run at Mon Apr 29 17:27:33 2013 Total run time = 1 seconds -kemelli@violeta:~/LIBRARIES/QUESO-0.50.0/examples/gravity$ +kemelli@violeta:~/LIBRARIES/QUESO-0.51.0/examples/gravity$ \end{lstlisting} @@ -334,7 +334,7 @@ \subsection{Running the Gravity Example with Several Processors} \begin{lstlisting}[caption={}, label={},language={bash}] -cd $HOME/LIBRARIES/QUESO-0.50.0/examples/gravity/ +cd $HOME/LIBRARIES/QUESO-0.51.0/examples/gravity/ mpirun -np 8 ./gravity_gsl gravity_inv_fwd.inp \end{lstlisting} diff --git a/manual/users/users_5e_example_ml_modal.tex b/manual/users/users_5e_example_ml_modal.tex index c5a78c965..00d8381d1 100644 --- a/manual/users/users_5e_example_ml_modal.tex +++ b/manual/users/users_5e_example_ml_modal.tex @@ -9,7 +9,7 @@ \section{\texttt{modal}}\label{sec:example_modal} Choosing between a one-mode or a two-mode target distribution is done at execution level, as presented in the following code line: \begin{lstlisting}[label={},caption={}] -$ cd $HOME/LIBRARIES/QUESO-0.50.0/ +$ cd $HOME/LIBRARIES/QUESO-0.51.0/ $ cd examples/modal $ rm outputData/* $ ./modal_gsl example.inp @@ -57,7 +57,7 @@ \subsubsection{Running the One-Mode Example} To run the executable provided considering a \underline{one-mode} distribution, enter the following commands: \begin{lstlisting}[label={},caption={Running the example with a one-mode distribution.}] -$ cd $HOME/LIBRARIES/QUESO-0.50.0/ +$ cd $HOME/LIBRARIES/QUESO-0.51.0/ $ cd examples/modal $ rm outputData/* $ ./modal_gsl example.inp 1 #one mode! @@ -113,7 +113,7 @@ \subsubsection{Running the Two-Mode Example} To run the executable provided considering a \underline{two-modes} distribution, enter the following commands: \begin{lstlisting}[label={},caption={Running the example with a two-mode distribution.}] -$ cd $HOME/LIBRARIES/QUESO-0.50.0/ +$ cd $HOME/LIBRARIES/QUESO-0.51.0/ $ cd examples/modal $ rm outputData/* $ ./modal_gsl example.inp 2 # two modes! @@ -194,12 +194,12 @@ \subsection{Create your own Makefile}\label{sec:modal-makefile} Thus, to compile, build and execute the code, the user just needs to run the following commands in the same directory where the files are: \begin{lstlisting} -$ cd $HOME/LIBRARIES/QUESO-0.50.0/examples/modal/ +$ cd $HOME/LIBRARIES/QUESO-0.51.0/examples/modal/ $ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:\ $HOME/LIBRARIES/gsl-1.15/lib/:\ $HOME/LIBRARIES/boost-1.53.0/lib/:\ $HOME/LIBRARIES/hdf5-1.8.10/lib:\ - $HOME/LIBRARIES/QUESO-0.50.0/lib + $HOME/LIBRARIES/QUESO-0.51.0/lib $ make -f Makefile_modal_violeta $ ./modal_gsl example.inp \end{lstlisting} @@ -318,4 +318,4 @@ \subsubsection{Autocorrelation Plots} \vspace{-10pt} \caption{Autocorrelation plots for $\theta_1$, $\theta_2$ and $\theta_3=\sigma^2$. Two-mode distribution.} \label{fig:modal_autocorr_2modes} -\end{figure} \ No newline at end of file +\end{figure} diff --git a/manual/users/users_5f_example_ml_bimodal.tex b/manual/users/users_5f_example_ml_bimodal.tex index 5a7556606..6ee86cdd1 100644 --- a/manual/users/users_5f_example_ml_bimodal.tex +++ b/manual/users/users_5f_example_ml_bimodal.tex @@ -35,7 +35,7 @@ \subsection{Running the Example}\label{sec:bimodal-run} To run the executable provided (available after QUESO installation), and generate figures for the chains, PDFs, CDFs, etc., enter the following commands: \begin{lstlisting}[label={},caption={}] -$ cd $HOME/LIBRARIES/QUESO-0.50.0/examples/bimodal +$ cd $HOME/LIBRARIES/QUESO-0.51.0/examples/bimodal $ rm outputData/* $ ./bimodal_gsl bimodal_1chain.inp $ matlab @@ -113,12 +113,12 @@ \subsection{Create your own Makefile}\label{sec:bimodal-makefile} Thus, to compile, build and execute the code, the user just needs to run the following commands in the same directory where the files are: \begin{lstlisting} -$ cd $HOME/LIBRARIES/QUESO-0.50.0/examples/bimodal/ +$ cd $HOME/LIBRARIES/QUESO-0.51.0/examples/bimodal/ $ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:\ $HOME/LIBRARIES/gsl-1.15/lib/:\ $HOME/LIBRARIES/boost-1.53.0/lib/:\ $HOME/LIBRARIES/hdf5-1.8.10/lib:\ - $HOME/LIBRARIES/QUESO-0.50.0/lib + $HOME/LIBRARIES/QUESO-0.51.0/lib $ make -f Makefile_bimodal_violeta $ ./bimodal_gsl example.inp \end{lstlisting} diff --git a/manual/users/users_5g_example_ml_hysteretic.tex b/manual/users/users_5g_example_ml_hysteretic.tex index 0edc8dad8..13322ef64 100644 --- a/manual/users/users_5g_example_ml_hysteretic.tex +++ b/manual/users/users_5g_example_ml_hysteretic.tex @@ -118,7 +118,7 @@ \subsection{Running the Example}\label{sec:hysteretic-run} To run the executable provided (available after QUESO installation), and generate figures for the chains, KDEs, CDFs, autocorrelation and scatter plots, enter the following commands: \begin{lstlisting}[label={},caption={}] -$ cd $HOME/LIBRARIES/QUESO-0.50.0/examples/example +$ cd $HOME/LIBRARIES/QUESO-0.51.0/examples/example $ rm outputData/* $ ./example_gsl example_1chain.inp $ matlab @@ -178,12 +178,12 @@ \subsection{Create your own Makefile}\label{sec:hysteretic-makefile} Thus to compile, build and execute the code, commands similar to the following should be entered: \begin{lstlisting} -$ cd $HOME/LIBRARIES/QUESO-0.50.0/examples/hysteretic/ +$ cd $HOME/LIBRARIES/QUESO-0.51.0/examples/hysteretic/ $ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:\ $HOME/LIBRARIES/gsl-1.15/lib/:\ $HOME/LIBRARIES/boost-1.53.0/lib/:\ $HOME/LIBRARIES/hdf5-1.8.10/lib:\ - $HOME/LIBRARIES/QUESO-0.50.0/lib + $HOME/LIBRARIES/QUESO-0.51.0/lib $ make -f Makefile_hysteretic_violeta $ ./hysteretic_gsl example.inp \end{lstlisting}