First commit OpenFPM_vcluster

INSTALL

+Installation Instructions
+*************************
+
+Copyright (C) 1994-1996, 1999-2002, 2004-2013 Free Software Foundation,
+Inc.
+
+   Copying and distribution of this file, with or without modification,
+are permitted in any medium without royalty provided the copyright
+notice and this notice are preserved.  This file is offered as-is,
+without warranty of any kind.
+
+Basic Installation
+==================
+
+   Briefly, the shell commands `./configure; make; make install' should
+configure, build, and install this package.  The following
+more-detailed instructions are generic; see the `README' file for
+instructions specific to this package.  Some packages provide this
+`INSTALL' file but do not implement all of the features documented
+below.  The lack of an optional feature in a given package is not
+necessarily a bug.  More recommendations for GNU packages can be found
+in *note Makefile Conventions: (standards)Makefile Conventions.
+
+   The `configure' shell script attempts to guess correct values for
+various system-dependent variables used during compilation.  It uses
+those values to create a `Makefile' in each directory of the package.
+It may also create one or more `.h' files containing system-dependent
+definitions.  Finally, it creates a shell script `config.status' that
+you can run in the future to recreate the current configuration, and a
+file `config.log' containing compiler output (useful mainly for
+debugging `configure').
+
+   It can also use an optional file (typically called `config.cache'
+and enabled with `--cache-file=config.cache' or simply `-C') that saves
+the results of its tests to speed up reconfiguring.  Caching is
+disabled by default to prevent problems with accidental use of stale
+cache files.
+
+   If you need to do unusual things to compile the package, please try
+to figure out how `configure' could check whether to do them, and mail
+diffs or instructions to the address given in the `README' so they can
+be considered for the next release.  If you are using the cache, and at
+some point `config.cache' contains results you don't want to keep, you
+may remove or edit it.
+
+   The file `configure.ac' (or `configure.in') is used to create
+`configure' by a program called `autoconf'.  You need `configure.ac' if
+you want to change it or regenerate `configure' using a newer version
+of `autoconf'.
+
+   The simplest way to compile this package is:
+
+  1. `cd' to the directory containing the package's source code and type
+     `./configure' to configure the package for your system.
+
+     Running `configure' might take a while.  While running, it prints
+     some messages telling which features it is checking for.
+
+  2. Type `make' to compile the package.
+
+  3. Optionally, type `make check' to run any self-tests that come with
+     the package, generally using the just-built uninstalled binaries.
+
+  4. Type `make install' to install the programs and any data files and
+     documentation.  When installing into a prefix owned by root, it is
+     recommended that the package be configured and built as a regular
+     user, and only the `make install' phase executed with root
+     privileges.
+
+  5. Optionally, type `make installcheck' to repeat any self-tests, but
+     this time using the binaries in their final installed location.
+     This target does not install anything.  Running this target as a
+     regular user, particularly if the prior `make install' required
+     root privileges, verifies that the installation completed
+     correctly.
+
+  6. You can remove the program binaries and object files from the
+     source code directory by typing `make clean'.  To also remove the
+     files that `configure' created (so you can compile the package for
+     a different kind of computer), type `make distclean'.  There is
+     also a `make maintainer-clean' target, but that is intended mainly
+     for the package's developers.  If you use it, you may have to get
+     all sorts of other programs in order to regenerate files that came
+     with the distribution.
+
+  7. Often, you can also type `make uninstall' to remove the installed
+     files again.  In practice, not all packages have tested that
+     uninstallation works correctly, even though it is required by the
+     GNU Coding Standards.
+
+  8. Some packages, particularly those that use Automake, provide `make
+     distcheck', which can by used by developers to test that all other
+     targets like `make install' and `make uninstall' work correctly.
+     This target is generally not run by end users.
+
+Compilers and Options
+=====================
+
+   Some systems require unusual options for compilation or linking that
+the `configure' script does not know about.  Run `./configure --help'
+for details on some of the pertinent environment variables.
+
+   You can give `configure' initial values for configuration parameters
+by setting variables in the command line or in the environment.  Here
+is an example:
+
+     ./configure CC=c99 CFLAGS=-g LIBS=-lposix
+
+   *Note Defining Variables::, for more details.
+
+Compiling For Multiple Architectures
+====================================
+
+   You can compile the package for more than one kind of computer at the
+same time, by placing the object files for each architecture in their
+own directory.  To do this, you can use GNU `make'.  `cd' to the
+directory where you want the object files and executables to go and run
+the `configure' script.  `configure' automatically checks for the
+source code in the directory that `configure' is in and in `..'.  This
+is known as a "VPATH" build.
+
+   With a non-GNU `make', it is safer to compile the package for one
+architecture at a time in the source code directory.  After you have
+installed the package for one architecture, use `make distclean' before
+reconfiguring for another architecture.
+
+   On MacOS X 10.5 and later systems, you can create libraries and
+executables that work on multiple system types--known as "fat" or
+"universal" binaries--by specifying multiple `-arch' options to the
+compiler but only a single `-arch' option to the preprocessor.  Like
+this:
+
+     ./configure CC="gcc -arch i386 -arch x86_64 -arch ppc -arch ppc64" \
+                 CXX="g++ -arch i386 -arch x86_64 -arch ppc -arch ppc64" \
+                 CPP="gcc -E" CXXCPP="g++ -E"
+
+   This is not guaranteed to produce working output in all cases, you
+may have to build one architecture at a time and combine the results
+using the `lipo' tool if you have problems.
+
+Installation Names
+==================
+
+   By default, `make install' installs the package's commands under
+`/usr/local/bin', include files under `/usr/local/include', etc.  You
+can specify an installation prefix other than `/usr/local' by giving
+`configure' the option `--prefix=PREFIX', where PREFIX must be an
+absolute file name.
+
+   You can specify separate installation prefixes for
+architecture-specific files and architecture-independent files.  If you
+pass the option `--exec-prefix=PREFIX' to `configure', the package uses
+PREFIX as the prefix for installing programs and libraries.
+Documentation and other data files still use the regular prefix.
+
+   In addition, if you use an unusual directory layout you can give
+options like `--bindir=DIR' to specify different values for particular
+kinds of files.  Run `configure --help' for a list of the directories
+you can set and what kinds of files go in them.  In general, the
+default for these options is expressed in terms of `${prefix}', so that
+specifying just `--prefix' will affect all of the other directory
+specifications that were not explicitly provided.
+
+   The most portable way to affect installation locations is to pass the
+correct locations to `configure'; however, many packages provide one or
+both of the following shortcuts of passing variable assignments to the
+`make install' command line to change installation locations without
+having to reconfigure or recompile.
+
+   The first method involves providing an override variable for each
+affected directory.  For example, `make install
+prefix=/alternate/directory' will choose an alternate location for all
+directory configuration variables that were expressed in terms of
+`${prefix}'.  Any directories that were specified during `configure',
+but not in terms of `${prefix}', must each be overridden at install
+time for the entire installation to be relocated.  The approach of
+makefile variable overrides for each directory variable is required by
+the GNU Coding Standards, and ideally causes no recompilation.
+However, some platforms have known limitations with the semantics of
+shared libraries that end up requiring recompilation when using this
+method, particularly noticeable in packages that use GNU Libtool.
+
+   The second method involves providing the `DESTDIR' variable.  For
+example, `make install DESTDIR=/alternate/directory' will prepend
+`/alternate/directory' before all installation names.  The approach of
+`DESTDIR' overrides is not required by the GNU Coding Standards, and
+does not work on platforms that have drive letters.  On the other hand,
+it does better at avoiding recompilation issues, and works well even
+when some directory options were not specified in terms of `${prefix}'
+at `configure' time.
+
+Optional Features
+=================
+
+   If the package supports it, you can cause programs to be installed
+with an extra prefix or suffix on their names by giving `configure' the
+option `--program-prefix=PREFIX' or `--program-suffix=SUFFIX'.
+
+   Some packages pay attention to `--enable-FEATURE' options to
+`configure', where FEATURE indicates an optional part of the package.
+They may also pay attention to `--with-PACKAGE' options, where PACKAGE
+is something like `gnu-as' or `x' (for the X Window System).  The
+`README' should mention any `--enable-' and `--with-' options that the
+package recognizes.
+
+   For packages that use the X Window System, `configure' can usually
+find the X include and library files automatically, but if it doesn't,
+you can use the `configure' options `--x-includes=DIR' and
+`--x-libraries=DIR' to specify their locations.
+
+   Some packages offer the ability to configure how verbose the
+execution of `make' will be.  For these packages, running `./configure
+--enable-silent-rules' sets the default to minimal output, which can be
+overridden with `make V=1'; while running `./configure
+--disable-silent-rules' sets the default to verbose, which can be
+overridden with `make V=0'.
+
+Particular systems
+==================
+
+   On HP-UX, the default C compiler is not ANSI C compatible.  If GNU
+CC is not installed, it is recommended to use the following options in
+order to use an ANSI C compiler:
+
+     ./configure CC="cc -Ae -D_XOPEN_SOURCE=500"
+
+and if that doesn't work, install pre-built binaries of GCC for HP-UX.
+
+   HP-UX `make' updates targets which have the same time stamps as
+their prerequisites, which makes it generally unusable when shipped
+generated files such as `configure' are involved.  Use GNU `make'
+instead.
+
+   On OSF/1 a.k.a. Tru64, some versions of the default C compiler cannot
+parse its `<wchar.h>' header file.  The option `-nodtk' can be used as
+a workaround.  If GNU CC is not installed, it is therefore recommended
+to try
+
+     ./configure CC="cc"
+
+and if that doesn't work, try
+
+     ./configure CC="cc -nodtk"
+
+   On Solaris, don't put `/usr/ucb' early in your `PATH'.  This
+directory contains several dysfunctional programs; working variants of
+these programs are available in `/usr/bin'.  So, if you need `/usr/ucb'
+in your `PATH', put it _after_ `/usr/bin'.
+
+   On Haiku, software installed for all users goes in `/boot/common',
+not `/usr/local'.  It is recommended to use the following options:
+
+     ./configure --prefix=/boot/common
+
+Specifying the System Type
+==========================
+
+   There may be some features `configure' cannot figure out
+automatically, but needs to determine by the type of machine the package
+will run on.  Usually, assuming the package is built to be run on the
+_same_ architectures, `configure' can figure that out, but if it prints
+a message saying it cannot guess the machine type, give it the
+`--build=TYPE' option.  TYPE can either be a short name for the system
+type, such as `sun4', or a canonical name which has the form:
+
+     CPU-COMPANY-SYSTEM
+
+where SYSTEM can have one of these forms:
+
+     OS
+     KERNEL-OS
+
+   See the file `config.sub' for the possible values of each field.  If
+`config.sub' isn't included in this package, then this package doesn't
+need to know the machine type.
+
+   If you are _building_ compiler tools for cross-compiling, you should
+use the option `--target=TYPE' to select the type of system they will
+produce code for.
+
+   If you want to _use_ a cross compiler, that generates code for a
+platform different from the build platform, you should specify the
+"host" platform (i.e., that on which the generated programs will
+eventually be run) with `--host=TYPE'.
+
+Sharing Defaults
+================
+
+   If you want to set default values for `configure' scripts to share,
+you can create a site shell script called `config.site' that gives
+default values for variables like `CC', `cache_file', and `prefix'.
+`configure' looks for `PREFIX/share/config.site' if it exists, then
+`PREFIX/etc/config.site' if it exists.  Or, you can set the
+`CONFIG_SITE' environment variable to the location of the site script.
+A warning: not all `configure' scripts look for a site script.
+
+Defining Variables
+==================
+
+   Variables not defined in a site shell script can be set in the
+environment passed to `configure'.  However, some packages may run
+configure again during the build, and the customized values of these
+variables may be lost.  In order to avoid this problem, you should set
+them in the `configure' command line, using `VAR=value'.  For example:
+
+     ./configure CC=/usr/local2/bin/gcc
+
+causes the specified `gcc' to be used as the C compiler (unless it is
+overridden in the site shell script).
+
+Unfortunately, this technique does not work for `CONFIG_SHELL' due to
+an Autoconf limitation.  Until the limitation is lifted, you can use
+this workaround:
+
+     CONFIG_SHELL=/bin/bash ./configure CONFIG_SHELL=/bin/bash
+
+`configure' Invocation
+======================
+
+   `configure' recognizes the following options to control how it
+operates.
+
+`--help'
+`-h'
+     Print a summary of all of the options to `configure', and exit.
+
+`--help=short'
+`--help=recursive'
+     Print a summary of the options unique to this package's
+     `configure', and exit.  The `short' variant lists options used
+     only in the top level, while the `recursive' variant lists options
+     also present in any nested packages.
+
+`--version'
+`-V'
+     Print the version of Autoconf used to generate the `configure'
+     script, and exit.
+
+`--cache-file=FILE'
+     Enable the cache: use and save the results of the tests in FILE,
+     traditionally `config.cache'.  FILE defaults to `/dev/null' to
+     disable caching.
+
+`--config-cache'
+`-C'
+     Alias for `--cache-file=config.cache'.
+
+`--quiet'
+`--silent'
+`-q'
+     Do not print messages saying which checks are being made.  To
+     suppress all normal output, redirect it to `/dev/null' (any error
+     messages will still be shown).
+
+`--srcdir=DIR'
+     Look for the package's source code in directory DIR.  Usually
+     `configure' can determine that directory automatically.
+
+`--prefix=DIR'
+     Use DIR as the installation prefix.  *note Installation Names::
+     for more details, including other options available for fine-tuning
+     the installation locations.
+
+`--no-create'
+`-n'
+     Run the configure checks, but stop before creating any output
+     files.
+
+`configure' also accepts some other, not widely useful, options.  Run
+`configure --help' for more details.

configure.ac

+#                                               -*- Autoconf -*-
+# Process this file with autoconf to produce a configure script.
+
+
+AC_PREREQ(2.59)
+AC_INIT(FULL-PACKAGE-NAME, VERSION, BUG-REPORT-ADDRESS)
+AC_CANONICAL_SYSTEM
+AC_CONFIG_SRCDIR([src/main.cpp])
+AM_INIT_AUTOMAKE
+AC_CONFIG_HEADER([src/config.h])
+m4_ifdef([MYSQL_FOUND],,[m4_include([m4/ax_lib_mysql.m4])])
+m4_ifdef([AX_CHECK_COMPILER_FLAGS],,[m4_include([m4/ax_check_compiler_flags.m4])])
+m4_ifdef([ACX_PTHREAD],,[m4_include([m4/acx_pthread.m4])])
+m4_ifdef([AX_CHECK_CL],,[m4_include([m4/ax_opencl.m4])])
+m4_ifdef([AX_BOOST_BASE],,[m4_include([m4/ax_boost_base.m4])])
+m4_ifdef([AX_BOOST_PROGRAM_OPTIONS],,[m4_include([m4/ax_boost_program_options.m4])])
+m4_ifdef([AX_BOOST_THREAD],,[m4_include([m4/ax_boost_thread.m4])])
+m4_ifdef([ACX_MPI],,[m4_include([m4/acx_mpi.m4])])
+m4_ifdef([AX_OPENMP],,[m4_include([m4/ax_openmp.m4])])
+m4_ifdef([AX_GCC_X86_CPUID],,[m4_include([m4/ax_gcc_x86_cpuid.m4])])
+m4_ifdef([AX_GCC_ARCHFLAG],,[m4_include([m4/ax_gcc_archflag.m4])])
+m4_ifdef([AX_CUDA],,[m4_include([m4/ax_cuda.m4])])
+
+CXXFLAGS+=" --std=c++11 "
+NVCCFLAGS=" "
+
+# Checks for programs.
+AC_PROG_CXX
+
+# Checks g++ flags
+
+AC_CANONICAL_HOST
+
+# Check target architetture
+
+AX_GCC_ARCHFLAG([], [CXXFLAGS="$CXXFLAGS $ax_cv_gcc_archflag"], [])
+
+###### Check for debug compilation
+
+AC_MSG_CHECKING(whether to build with debug information)
+debuger=no
+AC_ARG_ENABLE(debug,
+	AC_HELP_STRING(
+	    [--enable-debug],
+	    [enable debug data generation (def=no)]
+	),
+  	debuger="$enableval"
+)
+
+
+
+AC_MSG_RESULT($debuger)
+if test x"$debuger" = x"yes"; then
+	AC_DEFINE([DEBUG_MODE],[],[Debug])
+	AC_DEFINE([DEBUG],[],[Debug])
+	CXXFLAGS="$CXXFLAGS -g3  -Wall -O0 "
+	NVCCFLAGS+="$NVCCFLAGS -g -O0 "
+else
+	CXXFLAGS="$CXXFLAGS -Wall -O3 -g3 "
+	NVCCFLAGS+="$NVCCFLAGS -O3 "
+fi
+
+####### Checking for GPU support
+
+AX_CUDA
+
+AC_MSG_CHECKING(whether to build with GPU support)
+gpu_support=no
+AC_ARG_ENABLE(gpu,
+	AC_HELP_STRING(
+	    [--enable-gpu],
+	    [enable gpu support]
+	),
+  	gpu_support="$enableval"
+)
+
+
+
+AC_MSG_RESULT($gpu_support)
+if test x"$gpu_support" = x"yes"; then
+	AC_DEFINE([GPU],[],[GPU support])
+fi
+
+
+# Set this conditional if cuda is wanted
+
+AM_CONDITIONAL(BUILDCUDA, test ! x$NVCC = x"no")
+
+###########################
+
+no_avx=no
+no_sse42=no
+no_sse41=no
+no_sse3=no
+no_sse2=no
+no_sse=no
+no_mmx=no
+AX_CHECK_COMPILER_FLAGS([-msse4.2],[CXXFLAGS="$CXXFLAGS -mavx"],[no_avx=yes])
+AX_CHECK_COMPILER_FLAGS([-msse4.2],[CXXFLAGS="$CXXFLAGS -msse4.2"],[no_sse42=yes])
+AX_CHECK_COMPILER_FLAGS([-msse4.1],[CXXFLAGS="$CXXFLAGS -msse4.1"],[no_sse41=yes])
+AX_CHECK_COMPILER_FLAGS([-msse3],[CXXFLAGS="$CXXFLAGS -msse3"],[no_sse3=yes])
+AX_CHECK_COMPILER_FLAGS([-msse2],[CXXFLAGS="$CXXFLAGS -msse2"],[no_sse2=yes])
+AX_CHECK_COMPILER_FLAGS([-msse],[CXXFLAGS="$CXXFLAGS -msse"],[no_sse=yes])
+AX_CHECK_COMPILER_FLAGS([-mmmx],[CXXFLAGS="$CXXFLAGS -mmmx"],[no_mmx=yes])
+AX_CHECK_COMPILER_FLAGS([-Wno-unused-but-set-variable],[CXXFLAGS="$CXXFLAGS -Wno-unused-but-set-variable"],[])
+
+AC_SUBST(NVCCFLAGS)
+
+# Checks for typedefs, structures, and compiler characteristics.
+
+# Checks for library functions.
+
+AC_CONFIG_FILES([Makefile src/Makefile])
+AC_OUTPUT
+echo ""
+echo   "***********************************"
+echo   "*                                 *"
+arch_str="${ax_cv_gcc_archflag#-march=#-mtune=}"
+arch_str="${arch_str#-mtune=}"
+n_arch_str=${#arch_str}
+for (( X=0; X<23-n_arch_str; X++ ))
+do
+   arch_str="$arch_str "
+done
+echo "*    arch: $arch_str*"
+if [ test x"$no_sse42" = x"no" ]; then
+    echo "*    sse4.2: yes                  *"
+else
+    echo "*    sse4.2: no                   *"
+fi
+if [ test x"$no_sse41" = x"no" ]; then
+    echo "*    sse4.1: yes                  *"
+else
+    echo "*    sse4.1: no                   *"
+fi
+if [ test x"$no_sse3" = x"no" ]; then
+    echo "*    sse3: yes                    *"
+else
+    echo "*    sse3: no                     *"
+fi
+if [ test x"$no_sse2" = x"no" ]; then
+    echo "*    sse2: yes                    *"
+else
+    echo "*    sse2: no                     *"
+fi
+if [ test x"$no_sse" = x"no" ]; then
+    echo "*    sse: yes                     *"
+else
+    echo "*    sse: no                      *"
+fi
+if [ test x"$no_mmx" = x"no" ]; then
+  echo "*    mmx: yes                     *"
+else
+  echo "*    mmx: no                      *"
+fi
+if [ test x"$profiler" = x"yes" ]; then
+  echo "*    profiler: yes                *"
+else
+  echo "*    profiler: no                 *"
+fi
+if [ test x"$debuger" = x"yes" ]; then
+  echo "*    debug: yes                   *"
+else
+  echo "*    debug: no                    *"
+fi
+if [ test x"$no_64" = x"no" ]; then
+  echo "*    64 bit: yes                  *"
+else
+  echo "*    64 bit: no                   *"
+fi
+if [ test x"$gpu_support" = x"no" ]; then
+  echo "*    gpu: no                      *"
+else
+  echo "*    gpu: yes                     *"
+fi
+echo   "*                                 *"
+echo   "***********************************"
+

install_MPI.sh

+#!/bin/bash 
+
+mkdir ${HOME}/MPI
+wget http://www.open-mpi.de/software/ompi/v1.8/downloads/openmpi-1.8.1.tar.bz2
+tar -xvf openmpi-1.8.1.tar.bz2
+cd openmpi-1.8.1
+sh ./configure --prefix=${HOME}/MPI --enable-opal-multi-threads --enable-mpi-f90
+make
+make install

src/Makefile.am

+
+LINKLIBS = $(PTHREAD_LIBS) $(OPT_LIBS) $(BOOST_LDFLAGS) $(BOOST_PROGRAM_OPTIONS_LIB) $(CUDA_LIBS) $(BOOST_THREAD_LIB)
+
+bin_PROGRAMS = ppline
+ppline_SOURCES = main.cpp
+ppline_CXXFLAGS = $(CUDA_CFLAGS)
+ppline_CFLAGS = $(CUDA_CFLAGS)
+ppline_LDADD = $(LINKLIBS) -L/usr/lib64/nvidia-bumblebee/
+
+.cu.o :
+	$(NVCC) $(NVCCFLAGS) -o $@ -c $<

src/TThread.cpp

+//
+//  Project   : ThreadPool
+//  File      : TThread.cc
+//  Author    : Ronald Kriemann
+//  Purpose   : baseclass for a thread-able class
+//
+// arch-tag: aec71576-f8d5-4573-ad31-f3dbddc59934
+//
+
+#include <unistd.h>
+#include <signal.h>
+#include <time.h>
+#include <sched.h>
+#include <string.h>
+
+#include <iostream>
+#include <cmath>
+
+#include "TThread.h"
+
+//
+// routine to call TThread::run() method
+//
+extern "C"
+void *
+_run_thread ( void *arg )
+{
+    if (arg != NULL)
+    {
+        ((TThread*) arg)->run();
+        ((TThread*) arg)->reset_running();
+    }// if
+
+    return NULL;
+}
+
+////////////////////////////////////////////
+//
+// constructor and destructor
+//
+    
+TThread::TThread ( const int thread_no )
+        : _running( false ), _thread_no(thread_no)
+{
+}
+
+TThread::~TThread ()
+{
+    // request cancellation of the thread if running
+    if ( _running )
+        cancel();
+}