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<body class="article">
<div id="header">
<h1>PPM core package README</h1>
<span id="author">v1.2.2, May 2016</span><br />
</div>
<div id="content">
<div class="sect1">
<h2 id="_introduction">Introduction</h2>
<div class="sectionbody">
<div class="paragraph"><p>This is the PPM core source package.</p></div>
</div>
</div>
<div class="sect1">
<h2 id="_changes">Changes</h2>
<div class="sectionbody">
<div class="sidebarblock">
<div class="content">
<div class="title">1.2.2p2</div>
<div class="paragraph"><p>This is the last release of PPM core before introducing the new PPM core
abstraction types. Several new features and a number of critical fixes are
hereby made available the PPM users.</p></div>
<div class="ulist"><div class="title">New features:</div><ul>
<li>
<p>
Added support for adaptive resolution neighbor liists
(<a href="http://dx.doi.org/10.1016/j.cpc.2012.01.003">http://dx.doi.org/10.1016/j.cpc.2012.01.003</a>).
</p>
</li>
<li>
<p>
Added support for VTK file format writing for particles and meshes.
</p>
</li>
<li>
<p>
Updated the PPM build system to include a more robust file dependency
checking.
</p>
</li>
</ul></div>
<div class="ulist"><div class="title">Fixes</div><ul>
<li>
<p>
Fixed more critical bugs in the ghost mapping routines.
</p>
</li>
<li>
<p>
Fixed a critical bug in the communication scheduling routine.
</p>
</li>
<li>
<p>
Fixed bugs in the homogeneous symmetric boundary condition code.
</p>
</li>
<li>
<p>
Fixed <tt>make</tt> to copy the ppm_param.h to the include folder
</p>
</li>
</ul></div>
</div></div>
<div class="sidebarblock">
<div class="content">
<div class="title">1.2.1</div>
<div class="paragraph"><p>This versions brings many bug fixes and several new features</p></div>
<div class="ulist"><div class="title">New features:</div><ul>
<li>
<p>
Implemented Brelaz' graph coloring algorithm in Fortran, replacing the C++
Vizing implementation.
</p>
</li>
<li>
<p>
Added support for homogeneous symmetric boundary conditions
(Dirichlet, Neumann). The ghost mapping and neighbor list routines
properly support boundary conditions now. (Note: The user still has to make
sure the properties of boundary condition ghost particles reflect the correct
boundary condition value.)
</p>
</li>
<li>
<p>
Added Unit testing support using funit (<a href="http://nasarb.rubyforge.org/funit/">http://nasarb.rubyforge.org/funit/</a>).
</p>
</li>
<li>
<p>
Added a control file and argument handling module to simplify the process
of reading, parsing and evaluating the parameters passed to ppm clients.
</p>
</li>
<li>
<p>
Added ppm topology query routines and shortened ppm_mktopo argument list.
There should be in most cases no need to call ppm_topo_get anymore.
</p>
</li>
<li>
<p>
The user can now mange cell lists himself to save unnecessary computations.
</p>
</li>
<li>
<p>
Added a tool to help PPM client developers with debugging. This tool
visualizes domain decompositions and particle positions
</p>
</li>
<li>
<p>
Renamings: ppm_module_user → ppm_module_core,
ppm_module_user_util → ppm_module_core_util
</p>
</li>
</ul></div>
<div class="ulist"><div class="title">Fixes</div><ul>
<li>
<p>
Fixed several critical bugs in the ghost mapping routines
</p>
</li>
<li>
<p>
Fixed ppm_mesh_block_intersect
</p>
</li>
<li>
<p>
Fixed bugs in error handling and reporting
</p>
</li>
<li>
<p>
Fixed <tt>make install</tt> to copy all modules to <tt>$prefix/include/ppm/</tt>
</p>
</li>
<li>
<p>
Several minor fixes and improvements in the ppm build system.
</p>
</li>
</ul></div>
</div></div>
<div class="sidebarblock">
<div class="content">
<div class="title">1.2_p1</div>
<div class="paragraph"><p>This is a bug fix release, we fixed several important bugs:</p></div>
<div class="ulist"><ul>
<li>
<p>
Fixed several critical bugs in mesh mapping routines
</p>
</li>
<li>
<p>
Fixed bugs in remeshing routines that prevented clients using those
routines from compiling properly
</p>
</li>
<li>
<p>
Fixed a bug in the cartesian communication scheduling routine
</p>
</li>
<li>
<p>
Fixed build system to not link against GNU math library when compiling
with ifort
</p>
</li>
<li>
<p>
cleaned many annoying compiler warnings
</p>
</li>
</ul></div>
</div></div>
<div class="sidebarblock">
<div class="content">
<div class="title">1.2</div>
<div class="paragraph"><p>Initial release of new PPM library</p></div>
</div></div>
</div>
</div>
<div class="sect1">
<h2 id="_package_contents">Package contents</h2>
<div class="sectionbody">
<div class="paragraph"><p>The <tt>.tar.gz</tt> package you have downloaded should contain on the toplevel the
following files and directories:</p></div>
<div class="listingblock">
<div class="content">
<pre><tt> 34K COPYING The License
7.5K COPYING.LESSER
4.2K Makefile.in The Makefile template used by configure
610B NOTICE
14K README This file
28K README.html The HTML version of this file
717B aclocal.m4
44K config.guess
25K config.status
33K config.sub
205K configure The build configure script
8.5K configure.ac Thie build configure script template
14K install-sh
16K m4 Contains build scripts
4.7M src Contains the source code
292K utils Contains the PPM debug utility and FUnit</tt></pre>
</div></div>
<div class="paragraph"><p>After you compile PPM core there will be further directories for the binaries
and include files.</p></div>
</div>
</div>
<div class="sect1">
<h2 id="_requirements_for_building_ppm_core">Requirements for building PPM core</h2>
<div class="sectionbody">
<div class="ulist"><ul>
<li>
<p>
METIS 4: You may download the latest release of METIS 4 from
<a href="http://glaros.dtc.umn.edu/gkhome/metis/metis/download">http://glaros.dtc.umn.edu/gkhome/metis/metis/download</a>, alternatively you can
get from the PPM website the version of METIS that has been extensively tested
with our code.
</p>
</li>
<li>
<p>
An MPI distribution (optional): Either get OpenMPI, mpich2 or any other MPI 2
compliant MPI library. If you are compiling PPM on a cluster, most likely your
sysadmin will have already an MPI installed on the system.
</p>
</li>
</ul></div>
<div class="paragraph"><p>Make sure that all requirements are compiled with the same compiler that you
will be using to build PPM core.</p></div>
</div>
</div>
<div class="sect1">
<h2 id="_building_ppm_core">Building PPM core</h2>
<div class="sectionbody">
<div class="paragraph"><p>PPM core is built in 3 simple steps:</p></div>
<div class="sect2">
<h3 id="_step_1_confguring_ppm_core">Step 1: Confguring PPM core</h3>
<div class="paragraph"><p>Run the <tt>configure</tt> script to allow the build system to determine the correct
options to compile PPM core.</p></div>
<div class="paragraph"><p>It is very important to give <tt>configure</tt> the correct settings to make sure PPM
core is compiled correctly. To find out which settings are supported type</p></div>
<div class="listingblock">
<div class="content">
<pre><tt>$ ./configure --help</tt></pre>
</div></div>
<div class="paragraph"><p>This is what will be returned:</p></div>
<div class="listingblock">
<div class="content">
<pre><tt>`configure' configures PPM 1.2.2 to adapt to many kinds of systems.
Usage: ./configure [OPTION]... [VAR=VALUE]...
To assign environment variables (e.g., CC, CFLAGS...), specify them as
VAR=VALUE. See below for descriptions of some of the useful variables.
Defaults for the options are specified in brackets.
Configuration:
-h, --help display this help and exit
--help=short display options specific to this package
--help=recursive display the short help of all the included packages
-V, --version display version information and exit
-q, --quiet, --silent do not print `checking ...' messages
--cache-file=FILE cache test results in FILE [disabled]
-C, --config-cache alias for `--cache-file=config.cache'
-n, --no-create do not create output files
--srcdir=DIR find the sources in DIR [configure dir or `..']
Installation directories:
--prefix=PREFIX install architecture-independent files in PREFIX
[/usr/local]
--exec-prefix=EPREFIX install architecture-dependent files in EPREFIX
[PREFIX]
By default, `make install' will install all the files in
`/usr/local/bin', `/usr/local/lib' etc. You can specify
an installation prefix other than `/usr/local' using `--prefix',
for instance `--prefix=$HOME'.
For better control, use the options below.
Fine tuning of the installation directories:
--bindir=DIR user executables [EPREFIX/bin]
--sbindir=DIR system admin executables [EPREFIX/sbin]
--libexecdir=DIR program executables [EPREFIX/libexec]
--sysconfdir=DIR read-only single-machine data [PREFIX/etc]
--sharedstatedir=DIR modifiable architecture-independent data [PREFIX/com]
--localstatedir=DIR modifiable single-machine data [PREFIX/var]
--libdir=DIR object code libraries [EPREFIX/lib]
--includedir=DIR C header files [PREFIX/include]
--oldincludedir=DIR C header files for non-gcc [/usr/include]
--datarootdir=DIR read-only arch.-independent data root [PREFIX/share]
--datadir=DIR read-only architecture-independent data [DATAROOTDIR]
--infodir=DIR info documentation [DATAROOTDIR/info]
--localedir=DIR locale-dependent data [DATAROOTDIR/locale]
--mandir=DIR man documentation [DATAROOTDIR/man]
--docdir=DIR documentation root [DATAROOTDIR/doc/ppm]
--htmldir=DIR html documentation [DOCDIR]
--dvidir=DIR dvi documentation [DOCDIR]
--pdfdir=DIR pdf documentation [DOCDIR]
--psdir=DIR ps documentation [DOCDIR]
Optional Features:
--disable-option-checking ignore unrecognized --enable/--with options
--disable-FEATURE do not include FEATURE (same as --enable-FEATURE=no)
--enable-FEATURE[=ARG] include FEATURE [ARG=yes]
--enable-mpi[=impl.] use MPI (default is no), If the MPI implementation
of your choice provides compile wrappers that are in
PATH, I can set them myself, choose: guess (I will
choose the first implementation I can find),
openmpi, lammpi, mpich, mpich2, intelmpi_gnu
(Intel's MPI with GNU Compilers), intelmpi_intel
(Intel's MPI with Intel Compilers), sun (Sun MPI),
ibm (IBM AIX POE). Else, set this flag with no value
and set CC, CXX and FC to the appropriate compiler
wrappers (safest)
--enable-linux compile for linux (default is no)
--enable-etime use etime (default is no)
--enable-vector enable __VECTOR (default is no)
--enable-mathkeisan enable __MATHKEISAN (default is no)
--enable-sxf90 enable __SXF90 (default is no)
--enable-crayfishpack enable __CRAYFISHPACK (default is no)
--enable-hypre enable __HYPRE (default is no)
--enable-no-microinstr enable __NOMICROINSTRUCTIONS (default is no)
--enable-dev enable development mode (default is no)
--enable-debug enable debug mode (default is no)
Some influential environment variables:
CXX C++ compiler command
CXXFLAGS C++ compiler flags
LDFLAGS linker flags, e.g. -L<lib dir> if you have libraries in a
nonstandard directory <lib dir>
LIBS libraries to pass to the linker, e.g. -l<library>
CPPFLAGS (Objective) C/C++ preprocessor flags, e.g. -I<include dir> if
you have headers in a nonstandard directory <include dir>
CC C compiler command
CFLAGS C compiler flags
CPP C preprocessor
FC Fortran compiler command
FCFLAGS Fortran compiler flags
Use these variables to override the choices made by `configure' or to help
it to find libraries and programs with nonstandard names/locations.
Report bugs to the package provider.</tt></pre>
</div></div>
<div class="paragraph"><p>Following options are especially important:</p></div>
<div class="ulist"><ul>
<li>
<p>
<tt>--enable-mpi</tt>: If you will be running PPM clients on a parallel environment
(a cluster) using MPI, you must specify which MPI implementation you are
using. If your system is properly configured then this should be enough
information for PPM core build system to find the MPI libraries and compiler
wrappers needed. If this goes wrong, you may ommit this option and set
compiler wrapper and libraries in <tt>FC</tt> and <tt>LDFLAGS</tt> respectively.
</p>
</li>
<li>
<p>
<tt>--enable-linux</tt>: Set this if you’re compiling/running on a Linux system
</p>
</li>
<li>
<p>
<tt>--prefix</tt>: If you like to install PPM and the target directory is not the
system’s standard directory (<tt>/usr/</tt>) then you have to define this directory
here. You must provide the full path. It is not necessary to install PPM.
Building it and leaving it in the compilation directory is sufficient. If you
provide a directory here it must already exist - it will not be created by the
build system.
</p>
</li>
<li>
<p>
<tt>FC</tt> etc.: If you wish to not use MPI or you have to specify exactly which
compiler executable should be used, then you can use this flag to set your
compiler.
</p>
</li>
<li>
<p>
<tt>LDFLAGS</tt>: If metis was not installed in one of the system’s standard library
directories (e.g. <tt>/usr/lib</tt>) you must specify the directory to the libmetis.a
file here.
</p>
</li>
</ul></div>
<div class="paragraph"><p>Here two examples on how you could run the configure command</p></div>
<div class="paragraph"><p><tt>.configure</tt> on Linux cluster using OpenMPI (and intel compilers, wrapped)</p></div>
<div class="listingblock">
<div class="content">
<pre><tt>$ ./configure --enable-mpi=openmpi LDFLAGS=-L../../metis/lib --enable-linux</tt></pre>
</div></div>
<div class="paragraph"><p><tt>./configure</tt> on Mac OS X workstation with the MacPorts gcc compilers</p></div>
<div class="listingblock">
<div class="content">
<pre><tt>$ ./configure FC=gfortran-mp-4.4 LDFLAGS=-L../../metis/gcc/lib</tt></pre>
</div></div>
<div class="paragraph"><p><tt>./configure</tt> on a computer with OpenMPI installed in a non-standard location</p></div>
<div class="listingblock">
<div class="content">
<pre><tt>./configure --enable-mpi=openmpi FC=/opt/openmpi/1.5/bin/mpif90 \
LDFLAGS=-L../../metis/gcc/lib</tt></pre>
</div></div>
</div>
<div class="sect2">
<h3 id="_step_2_compiling_ppm_core">Step 2: Compiling PPM core</h3>
<div class="paragraph"><p>If the configure process finished successfully you should see on your screen a
message that the Makefile has been generated (and you can now find this
Makefile in this directory).</p></div>
<div class="paragraph"><p>Now you can simply run make to compile PPM core:</p></div>
<div class="listingblock">
<div class="content">
<pre><tt>$ make</tt></pre>
</div></div>
<div class="paragraph"><p>If you encounter problems in the compilation process (compile errors) please,
first check if you have set everything correctly in your environment. If the
error persists, please send us a bug-report detailing the previous steps you
have performed. Also, please include the <tt>config.log</tt> file and the output of
<tt>export</tt>. Finally, if yu are using MPI, please include which MPI library you are
using.</p></div>
</div>
<div class="sect2">
<h3 id="_step_3_installing_ppm_core_optional">Step 3: Installing PPM core (optional)</h3>