Merge branch 'release_v0.1.1'

.gitignore

@@ -1,4 +1,7 @@
 HPhi
+makefile
+Makefile
+make.sys
 *backup*
 *cisajs*.dat
 *Time*
@@ -15,4 +18,9 @@ HPhi
 *.synctex.gz
 *.toc
 *~
+build
 #*
+html/
+GPATH
+GRTAGS
+GTAGS

CMakeLists.txt

@@ -0,0 +1,29 @@
+cmake_minimum_required(VERSION 2.8.0 FATAL_ERROR)
+project(HPhi NONE)
+
+if(CONFIG)
+  message(STATUS "Loading configration: " ${PROJECT_SOURCE_DIR}/config/${CONFIG}.cmake)
+  include(${PROJECT_SOURCE_DIR}/config/${CONFIG}.cmake)
+endif(CONFIG)
+if(NOT CMAKE_BUILD_TYPE)
+  set(CMAKE_BUILD_TYPE "Release" CACHE STRING "Type of build" FORCE)
+endif(NOT CMAKE_BUILD_TYPE)
+message(STATUS "Build type: " ${CMAKE_BUILD_TYPE})
+
+enable_language(C)
+
+find_package(OpenMP)
+if(OPENMP_FOUND)
+  set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
+endif(OPENMP_FOUND)
+
+find_package(MPI)
+if(MPI_FOUND)
+  include_directories(${MPI_C_INCLUDE_PATH})
+  add_definitions(-DMPI)
+  set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${MPI_C_LINK_FLAGS}")
+endif(MPI_FOUND)
+
+find_package(LAPACK)
+
+add_subdirectory(src)

HPhiconfig.sh

@@ -0,0 +1,119 @@
+#!/bin/bash
+if [ -z ${1} ] || [ ${1} = "help" ]; then
+    echo ""
+    echo "Usage:"
+    echo "./HPhiconfig.sh system_name"
+    echo " system_name should be choosen from below:"
+    echo "     sekirei : ISSP system-B"
+    echo "        maki : ISSP system-C"
+    echo "       intel : Intel compiler + Linux PC"
+    echo " mpicc-intel : Intel compiler + Linux PC + mpicc"
+    echo "         gcc : GCC + Linux"
+    echo "     gcc-mac : GCC + Mac"
+    echo "      manual : Manual configuration. See below."
+    echo ""
+    echo "In manual HPhi configtion, please type, for example,  "
+    echo "./HPhiconfig.sh CC=icc LAPACK_FLAGS=\"-Dlapack -mkl=parallel\" \\"
+    echo "   FLAGS=\"-qopenmp  -O3 -xCORE-AVX2 -mcmodel=large -shared-intel\""
+    echo " where"
+    echo "            CC : Compilation command for C"
+    echo "  LAPACK_FLAGS : Compile option for LAPACK"
+    echo "         FLAGS : Other Compilation options"
+    echo ""
+else
+    if [ ${1} = "sekirei" ]; then
+        cat > src/make.sys <<EOF
+CC = icc
+LAPACK_FLAGS = -Dlapack -mkl=parallel 
+FLAGS = -qopenmp  -O3 -xCORE-AVX2 -mcmodel=large -shared-intel
+MTFLAGS = -DDSFMT_MEXP=19937 \$(FLAGS)
+INCLUDE_DIR=./include
+EOF
+    elif [ ${1} = "maki" ]; then
+        cat > src/make.sys <<EOF
+CC = fccpx
+LAPACK_FLAGS = -Dlapack -SSL2BLAMP
+FLAGS = -Kfast,openmp,SPARC64IXfx,parallel -Kmemalias,alias_const
+MTFLAGS = -DDSFMT_MEXP=19937 \$(FLAGS)
+INCLUDE_DIR=./include
+EOF
+    elif [ ${1} = "intel" ]; then
+        cat > src/make.sys <<EOF
+CC = icc
+LAPACK_FLAGS = -Dlapack -mkl=parallel 
+FLAGS = -openmp -O3 -DHAVE_SSE2
+MTFLAGS = -DDSFMT_MEXP=19937 \$(FLAGS)
+INCLUDE_DIR=./include
+EOF
+    elif [ ${1} = "mpicc-intel" ]; then
+        cat > src/make.sys <<EOF
+CC = mpicc
+LAPACK_FLAGS = -Dlapack -mkl=parallel 
+FLAGS = -openmp -O3 -DHAVE_SSE2 -D MPI
+MTFLAGS = -DDSFMT_MEXP=19937 \$(FLAGS)
+INCLUDE_DIR=./include
+EOF
+    elif [ ${1} = "gcc-mac" ]; then
+        cat > src/make.sys <<EOF
+CC = gcc
+LAPACK_FLAGS = -framework Accelerate 
+FLAGS = -fopenmp 
+MTFLAGS = -DDSFMT_MEXP=19937 \$(FLAGS)
+INCLUDE_DIR=./include
+EOF
+    elif [ ${1} = "gcc" ]; then
+        cat > src/make.sys <<EOF
+CC = gcc
+LAPACK_FLAGS = -Dlapack -llapack -lblas
+FLAGS = -fopenmp  -lm
+MTFLAGS = -DDSFMT_MEXP=19937 \$(FLAGS)
+INCLUDE_DIR=./include
+EOF
+    elif [ ${1} == "manual" ]; then
+echo " C compiler ?"
+read CC
+echo " LAPACK option ?"
+read LAPACK_FLAGS
+echo " Other compilation flags ?"
+read FLAGS
+        cat > src/make.sys <<EOF
+CC = ${CC}
+LAPACK_FLAGS = ${LAPACK_FLAGS}
+FLAGS = ${FLAGS}
+MTFLAGS = -DDSFMT_MEXP=19937 \$(FLAGS)
+INCLUDE_DIR=./include
+EOF
+    else
+        echo ""
+        echo "Unsupported system. Please type"
+        echo "./HPhiconfig.sh help"
+        echo ""
+        exit
+    fi
+
+    echo "cat src/make.sys"
+    cat src/make.sys
+
+    echo
+    echo "HPhiconfig DONE"
+    echo
+
+    cat > makefile <<EOF
+HPhi:
+	cd src;make -f makefile_src
+
+userguide:
+	cd doc/jp/;make -f makefile_doc_jp;mv userguide_jp.pdf ../
+	cd doc/en/;make -f makefile_doc_en;mv userguide_en.pdf ../
+
+clean:
+	cd src; make -f makefile_src clean
+	cd doc/jp; make -f makefile_doc_jp clean
+	cd doc/en; make -f makefile_doc_en clean
+	rm -f doc/userguide_??.pdf
+
+veryclean:
+	make clean
+	rm -f src/make.sys makefile
+EOF
+fi

config/fujitsu.cmake

@@ -0,0 +1,7 @@
+# for Fujitsu Compiler
+set(CMAKE_C_COMPILER "mpifccpx" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_RELEASE "-DNDEBUG -Kfast,parallel -Kmemalias,alias_const" CACHE STRING "" FORCE)
+set(OpenMP_C_FLAGS "-Kopenmp" CACHE STRING "" FORCE)
+
+# for SSL2
+set(BLAS_LIBRARIES "-SSL2 --linkfortran" CACHE STRING "" FORCE)

config/gcc.cmake

@@ -0,0 +1,2 @@
+# for GCC Compiler
+set(CMAKE_C_COMPILER "gcc" CACHE STRING "" FORCE)

config/intel.cmake

@@ -0,0 +1,6 @@
+# for Intel Compiler
+set(CMAKE_C_COMPILER "icc" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG -DHAVE_SSE2" CACHE STRING "" FORCE)
+
+# for Intel MKL
+set(BLA_VENDOR "Intel10_64lp" CACHE STRING "" FORCE)

config/sekirei.cmake

@@ -0,0 +1,6 @@
+# for Intel Compiler
+set(CMAKE_C_COMPILER "icc" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS "-O3 -DNDEBUG -xCORE-AVX2 -mcmodel=large -shared-intel" CACHE STRING "" FORCE)
+
+# for Intel MKL
+set(BLA_VENDOR "Intel10_64lp" CACHE STRING "" FORCE)

doc/en/chap02_1_en.tex

@@ -1,45 +1,63 @@
 % !TEX root = userguide_en.tex
 %----------------------------------------------------------
-\begin{enumerate}
-
-\item You can download $\HPhi$ in the following place.\\
+You can download $\HPhi$ in the following place.\\
 \url{https://github.com/QLMS/HPhi/releases}
 
-\item After expanding downloaded files, 
-move into \verb|src| in the expanded directory.
+You can obtain the $\HPhi$ directory by tiping
 \begin{verbatim}
-$ tar xzvf 
-$ cd /src/
+$ tar xzvf HPhi-xxx.tar.gz
 \end{verbatim}
 
-\item Configure the environment for the installation;
-  please edit \verb|make.sys| and specify the compiler and the option.
-  For some known system, 
-  you can find prepared settings as comments in \verb|make.sys| and use them.
-  For example, when you install $\HPhi$ into the ISSP System-B(sekirei),
-  find 
-\begin{verbatim}
-#####  ISSP System-B "sekirei" #####|
+There are two kind of procedures to install $\HPhi$.
 
-# CC = icc
-# LAPACK_FLAGS = -Dlapack -mkl=parallel 
-# FLAGS = -qopenmp  -O3 -xCORE-AVX2 -mcmodel=large -shared-intel
-# MTFLAGS = -DDSFMT_MEXP=19937 $(FLAGS)
-# INCLUDE_DIR=./include
+\subsection{Using \texttt{HPhiconfig.sh}}
+
+Please run \verb|HPhiconfig.sh| script in the $\HPhi$ directory as follow
+(for ISSP system-B ''sekirei''):
+\begin{verbatim}
+$ bash HPhiconfig.sh sekirei
 \end{verbatim}
-and uncomment it.
+Then environmental configuration file \verb|make.sys| is generated in 
+\verb|src/| directory.
+The command-line argment of \verb|HPhiconfig.sh| is as folows:
+\begin{itemize}
+\item \verb|sekirei| : ISSP system-B ''sekirei''
+\item \verb|maki| : ISSP system-C ''maki''
+\item \verb|intel| : intel compiler + Linux PC
+\item \verb|gcc| : GCC + Linux PC
+\item \verb|gcc-mac| : GCC + Mac
+\end{itemize}
 
-\item Save the modified \verb|make.sys| and type \verb|make| as follows:
+\verb|make.sys| is as follows (for ISSP-system-B ''sekirei''):
 \begin{verbatim}
-$ make all
+ CC = icc
+ LAPACK_FLAGS = -Dlapack -mkl=parallel 
+ FLAGS = -qopenmp  -O3 -xCORE-AVX2 -mcmodel=large -shared-intel
+ MTFLAGS = -DDSFMT_MEXP=19937 $(FLAGS)
+ INCLUDE_DIR=./include
 \end{verbatim}
+We explatin macros of this file as: 
+\begin{itemize}
+\item \verb|CC| : The Compilation command (\verb|icc|, \verb|gcc|, \verb|fccpx|)
+\item \verb|LAPACK_FLAGS| : Compilation options for LAPACK. \verb|-Dlapack| can not be removed.
+\item \verb|FLAGS| : Other compilation options.
+  OpenMP utilization option (\verb|-openmp|, \verb|-fopenmp|, \verb|-qopenmp|, etc.)
+  must be specified.
+\item \verb|MTFLAGS|, \verb|INCLUDE_DIR| : Options for the Mersenne Twister
+  and additional include directory. You do not have to modify them.
+\end{itemize}
 
-Then an executable \verb|HPhi| in the current directory;
-you should add this directory to the \verb|$PATH| or
-make a symbolic link in a place belonging \verb|$PATH|.
+
+Then you are ready to compile HPhi.
+Please type
 \begin{verbatim}
-$ sudo ln -fs `pwd`/HPhi /usr/local/bin/
+$ make HPhi
 \end{verbatim}
+and obtain an executable \verb|HPhi| in \verb|src/| directory;
+you should add this directory to the \verb|$PATH|.
+
+\subsection{Using \texttt{cmake}}
+
 
 \begin{screen}
 \Large 
@@ -55,4 +73,3 @@
 
 \end{screen}
 
-\end{enumerate}