development.tex

\section{Development}
\subsection{Building}
\begin{frame}[fragile]
\frametitle{Compiling, Linking and Running Applications}
\framesubtitle{on HPC clusters}
 \begin{description}
    \item [source code] C / C++ / Fortran ( \verb|.c, .cpp, .f90, .h|  )
    \item [compile] Cray/Intel/GNU compilers
    \item [assemble] into machine code (object files: \verb|.o, .obj| )
    \item [link] Static Libraries (\verb|.lib, .a|  ) \\ Shared Library (\verb|.dll, .so| ) \\ Executables (\verb|.exe, .x| )
    \item ~ 
    \item [request allocation] submit job request to SLURM queuing system \\ \verb|salloc/sbatch|
    \item [run] application on scheduled resources \\ \verb|srun/mpirun|
 \end{description}
\end{frame}

\subsection{Modules}
\begin{frame}[fragile]
\frametitle{Modules}
\framesubtitle{The \textit{modules package} allow for dynamic add/remove of installed software packages to the running environment}

\begin{exampleblock}{Loading modules}
  \begin{verbatim}
  module load 	<software_name>
  module add 	<software_name>
  module use 	<software_name>
  \end{verbatim}
\end{exampleblock}

\begin{exampleblock}{Swapping modules}
  \begin{verbatim}
  module swap 	<software_name_1> <software_name_2>
  \end{verbatim}
\end{exampleblock}

\begin{exampleblock}{Unloading modules}
  \begin{verbatim}
  module unload <software_name>
  \end{verbatim}
\end{exampleblock}
\end{frame}


\begin{frame}[fragile]
\frametitle{Modules }
\framesubtitle{Displaying modules}
\begin{exampleblock}{\$ module list}
\scriptsize
\begin{verbatim}
Currently Loaded Modulefiles:
  1) modules/3.2.6.7
  ...
  20) PrgEnv-cray/5.2.56
\end{verbatim}
\end{exampleblock}

\begin{exampleblock}{\$ module avail [\textit{software\_name}]}
\scriptsize
\begin{verbatim}
-------------------------- /opt/modulefiles -----------------------------
gcc/4.8.1     gcc/4.9.1(default)     gcc/4.9.2     gcc/4.9.3    gcc/5.1.0
\end{verbatim}
\end{exampleblock}

\begin{exampleblock}{\$ module show \textit{software\_name}}
\scriptsize
\begin{verbatim}
------------------------- /opt/modulefiles/gcc/4.9.1 ---------------------
conflict	 gcc 
prepend-path	 PATH /opt/gcc/4.9.1/bin 
prepend-path	 MANPATH /opt/gcc/4.9.1/snos/share/man 
prepend-path	 LD_LIBRARY_PATH /opt/gcc/4.9.1/snos/lib64 
setenv		 GCC_PATH /opt/gcc/4.9.1 
-------------------------------------------------------------------
\end{verbatim}
\end{exampleblock}
\end{frame}

\subsection{Programming environments}
\begin{frame}[fragile]
  \frametitle{Programming Environment Modules}
  \framesubtitle{specific to \alert{Beskow}}

\begin{columns}[t]
\column{.7\textwidth}
  \begin{description}
  \item [Cray] \verb|$ module load PrgEnv-cray|
  \item [Intel] \verb|$ module load PrgEnv-intel|
  \item [GNU] \verb|$ module load PrgEnv-gnu|
  \end{description}
   % \item Module cray-libsci provides BLAS, LAPACK, BLACS, and SCALAPACK
   % \item Module cray-mpich provides MPI
\column{.3\textwidth}
    \begin{verbatim}
$ cc	source.c
$ CC	source.cpp
$ ftn	source.F90
  \end{verbatim}
\end{columns}
  \begin{exampleblock}{Compiler wrappers : \alert{\textbf{cc} \textbf{CC} \textbf{ftn}}}
    \alert{Advantages}\\
    Compiler wrappers will automatically 
    \begin{itemize}
      \item link to BLAS, LAPACK, BLACS, SCALAPACK, FFTW\\
      \item use MPI wrappers\\
    \end{itemize}
    \alert{Disadvantage}\\
    Sometimes you need to edit Makefiles which are not designed for Cray 
\end{exampleblock}
\end{frame}


\subsection{Compilers}
\begin{frame}[fragile]
\frametitle{Compiling serial and/or parallel code}
\framesubtitle{specific to \alert{Tegner}}

\begin{columns}[t]
\column{.45\textwidth}
\begin{exampleblock}{GNU Compiler Collection (\textbf{gcc})}
  \scriptsize
  \begin{verbatim}
$ module load 	gcc openmpi
$ gcc	   -fopenmp source.c
$ g++	   -fopenmp source.cpp
$ gfortran -fopenmp source.F90
$ mpicc	   -fopenmp source.c
$ mpicxx   -fopenmp source.cpp
$ mpif90   -fopenmp source.F90
  \end{verbatim}
  \end{exampleblock}

  \begin{exampleblock}{Portland Group Compilers (\textbf{pgi}) }
  \scriptsize
  \begin{verbatim}
$ module load 	pgi
$ pgcc  -mp source.c
$ pgcpp -mp source.cpp
$ pgf90 -mp source.F90
  \end{verbatim}
  \end{exampleblock}

\column{.45\textwidth}

  \begin{exampleblock}{Intel compilers (\textbf{i-compilers})}
  \scriptsize
  \begin{verbatim}
  $ module load i-compilers
  $ icc   -openmp source.c	
  $ icpc  -openmp source.cpp
  $ ifort -openmp source.F90
  $ module load i-compilers intelmpi
  $ mpiicc 	-openmp source.c
  $ mpiicpc 	-openmp source.cpp
  $ mpiifort 	-openmp source.F90
  \end{verbatim}
  \end{exampleblock}

  \begin{exampleblock}{CUDA compilers (\textbf{cuda})}
  \scriptsize
  \begin{verbatim}
  $ module load cuda
  $ nvcc source.cu
  $ nvcc -arch=sm_37  source.cu
  \end{verbatim}
  \end{exampleblock}

\end{columns}
\end{frame}