PPM core package README ======================= v1.2.2, May 2016 Introduction ------------ This is the PPM core source package. Changes ------- .1.2.2p2 ************************************************************************ 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. .New features: - Added support for adaptive resolution neighbor liists (http://dx.doi.org/10.1016/j.cpc.2012.01.003). - Added support for VTK file format writing for particles and meshes. - Updated the PPM build system to include a more robust file dependency checking. .Fixes - Fixed more critical bugs in the ghost mapping routines. - Fixed a critical bug in the communication scheduling routine. - Fixed bugs in the homogeneous symmetric boundary condition code. - Fixed `make` to copy the ppm_param.h to the include folder ************************************************************************ .1.2.1 ************************************************************************ This versions brings many bug fixes and several new features .New features: - Implemented Brelaz' graph coloring algorithm in Fortran, replacing the C++ Vizing implementation. - 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.) - Added Unit testing support using funit (http://nasarb.rubyforge.org/funit/). - Added a control file and argument handling module to simplify the process of reading, parsing and evaluating the parameters passed to ppm clients. - 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. - The user can now mange cell lists himself to save unnecessary computations. - Added a tool to help PPM client developers with debugging. This tool visualizes domain decompositions and particle positions - Renamings: ppm_module_user -> ppm_module_core, ppm_module_user_util -> ppm_module_core_util .Fixes - Fixed several critical bugs in the ghost mapping routines - Fixed ppm_mesh_block_intersect - Fixed bugs in error handling and reporting - Fixed `make install` to copy all modules to `$prefix/include/ppm/` - Several minor fixes and improvements in the ppm build system. ************************************************************************ .1.2_p1 ************************************************************************ This is a bug fix release, we fixed several important bugs: - Fixed several critical bugs in mesh mapping routines - Fixed bugs in remeshing routines that prevented clients using those routines from compiling properly - Fixed a bug in the cartesian communication scheduling routine - Fixed build system to not link against GNU math library when compiling with ifort - cleaned many annoying compiler warnings ************************************************************************ .1.2 ************************************************************************ Initial release of new PPM library ************************************************************************ Package contents ---------------- The `.tar.gz` package you have downloaded should contain on the toplevel the following files and directories: ----------------------------------- 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 ---------------------------------- After you compile PPM core there will be further directories for the binaries and include files. Requirements for building PPM core ---------------------------------- - METIS 4: You may download the latest release of METIS 4 from http://glaros.dtc.umn.edu/gkhome/metis/metis/download, alternatively you can get from the PPM website the version of METIS that has been extensively tested with our code. - 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. Make sure that all requirements are compiled with the same compiler that you will be using to build PPM core. Building PPM core ----------------- PPM core is built in 3 simple steps: Step 1: Confguring PPM core ~~~~~~~~~~~~~~~~~~~~~~~~~~~ Run the `configure` script to allow the build system to determine the correct options to compile PPM core. It is very important to give `configure` the correct settings to make sure PPM core is compiled correctly. To find out which settings are supported type ~~~~~~~~~~ $ ./configure --help ~~~~~~~~~~ This is what will be returned: ~~~~~~~~~~~~~~~~~~~~~~~~~~~ `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. ~~~~~~~~~~~~~~~~~~~~~~~~~~~ Following options are especially important: - `--enable-mpi`: 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 `FC` and `LDFLAGS` respectively. - `--enable-linux`: Set this if you're compiling/running on a Linux system - `--prefix`: If you like to install PPM and the target directory is not the system's standard directory (`/usr/`) 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. - `FC` 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. - `LDFLAGS`: If metis was not installed in one of the system's standard library directories (e.g. `/usr/lib`) you must specify the directory to the libmetis.a file here. Here two examples on how you could run the configure command `.configure` on Linux cluster using OpenMPI (and intel compilers, wrapped) ~~~~~~~~~~~~~~~~~~~~~~~~~~~ $ ./configure --enable-mpi=openmpi LDFLAGS=-L../../metis/lib --enable-linux ~~~~~~~~~~~~~~~~~~~~~~~~~~~ `./configure` on Mac OS X workstation with the MacPorts gcc compilers ~~~~~~~~~~~~~~~~~~~~~~~~~~~ $ ./configure FC=gfortran-mp-4.4 LDFLAGS=-L../../metis/gcc/lib ~~~~~~~~~~~~~~~~~~~~~~~~~~~ `./configure` on a computer with OpenMPI installed in a non-standard location ~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./configure --enable-mpi=openmpi FC=/opt/openmpi/1.5/bin/mpif90 \ LDFLAGS=-L../../metis/gcc/lib ~~~~~~~~~~~~~~~~~~~~~~~~~~~ Step 2: Compiling PPM core ~~~~~~~~~~~~~~~~~~~~~~~~~~ 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). Now you can simply run make to compile PPM core: ~~~~~~~~~~~~~~~~~~~~~~~~~~~ $ make ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 `config.log` file and the output of `export`. Finally, if yu are using MPI, please include which MPI library you are using. Step 3: Installing PPM core (optional) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ If you wish to install PPM core you can now use the `make install` command to do so: ~~~~~~~~~~~~~~~~~~~~~~~~~~~ $ make install ~~~~~~~~~~~~~~~~~~~~~~~~~~~ If the target directory is part of the system, you will most probably get a message that you have insufficient rights. If you have a root account you can use in this case the sudo command to override this security setting. ~~~~~~~~~~~~~~~~~~~~~~~~~~~ $ sudo make install ~~~~~~~~~~~~~~~~~~~~~~~~~~~ Your PPM core distribution is installed. Compiling PPM client code against PPM core ------------------------------------------ When compiling your PPM client code you need to first include the PPM core modules: - in `include/ppm/` relative to this directory. Check which compiler flag needs to be used to include Fortran module directories. and link against libppm.a: - in `lib/` relative to this directory. Add -L[path to lib] -lppm to the linking command of your compilation process. Enjoy the PPM experience! Contributors ------------ The PPM library is being maintained and developed by the CSE-lab (group of Professor Petros Koumoutsakos), the MOSAIC group at MPI-CBG Dresden (group of Prfessor Ivo F.Sbalzarini) and the Center for Fluid Dynamics at DTU (group of Professor Jens Walther). PPM core package maintainer: Yaser Afshar <afshar@mpi-cbg.de>
PPMLibrary/ppm
The Parallel Particle Mesh (PPM) library provides a transparent parallelization middleware for particle-mesh simulations.
FORTRANLGPL-3.0