Commit 49707e8a authored by Paolo Tricerri's avatar Paolo Tricerri
Browse files

Merge branch 'master' into TimeAdvanceFSI

Conflicts:
	examples/Makefile.am
	examples/benchmark_HPCNavierStokes/benchmark_HPCNavierStokes.cpp
	examples/benchmark_RossEthierSteinman/ethiersteinman.cpp
	examples/example_ML/MLTester.hpp
	examples/example_NavierStokesRestart/Makefile.am
	examples/example_NavierStokesRestart/cylinder.cpp
	examples/example_NavierStokesRestart/data
	examples/example_cavity/main.cpp
	examples/example_nsResistanceBC/resistance.cpp
	examples/example_ns_flux/cylinder.cpp
	examples/unmaintained_ct/ChorinTemam.hpp
	examples/unmaintained_masstransport/masstransport.cpp
	testsuite/data/mesh/inria/Makefile.am
	testsuite/testsuite.at
parents 459792ac 23a0f806
# @HEADER
# *******************************************************************************
#
#
# Copyright (C) 2004, 2005, 2007 EPFL, Politecnico di Milano, INRIA
# Copyright (C) 2010 EPFL, Politecnico di Milano, Emory University
#
# Copyright (C) 2011,2012,2013 EPFL, Politecnico di Milano, Emory University
#
# This file is part of LifeV.
#
#
# LifeV is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
#
# LifeV is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# Lesser General Public License for more details.
#
#
# You should have received a copy of the GNU Lesser General Public License
# along with LifeV. If not, see <http://www.gnu.org/licenses/>.
#
# *******************************************************************************
# @HEADER
\ No newline at end of file
# @HEADER
......@@ -5,58 +5,22 @@ HOWTO to make a release X_Y_Z
(this is a preliminary version for git)
cd top_srcdir
1- branch HEAD with the branchname LIFEV_X_2Y_BRANCH
git branch LIFEV_X_2Y_BRANCH
git checkout LIFEV_X_2Y_BRANCH
and
tag LIFEV_X_2Y_BRANCH with the tag LIFEV_X_2Y_Z
git tag LIFEV_X_2Y_Z
git push --tags
2- update configure.in.in VERSION
3- update NEWS
4- run make distcheck
o you can try the following command to speed up this check
make distcheck DISTCHECK_CONFIGURE_FLAGS="--enable-opt2" AM_MAKEFLAGS="-j <n>"
git remote add github git@github.com:lifev/lifev.git
where <n> is the number of processes you want to launch concurrently
e.g.:
nohup make distcheck DISTCHECK_CONFIGURE_FLAGS="--with-trilinos=/u/cmcs/deparis/local/debug64-openmpi/trilinos-9 --prefix=/usr/scratch/deparis/lifev-clean/local --enable-debug --disable-shared --enable-static --with-hdf5=/usr --with-mpi --with-mpi=/usr/lib/openmpi --with-superlu=/usr --with-umfpack-include=-I/usr/include/suitesparse --with-libs='-lsuperlu -lumfpack -lamd' F77=gfortran"
e.g.:
nohup make distcheck DISTCHECK_CONFIGURE_FLAGS="--prefix=/Users/simone/local/debug/lifev --with-trilinos=/Users/simone/local/debug/trilinos10.6 --with-mpi=/usr --with-parmetis=/Users/simone/local/opt/parmetis/ --with-boost-include=/Users/simone/local/opt/boost1.45.0/include --with-boost-lib=/Users/simone/local/opt/boost1.45.0/lib --with-hdf5=/Users/simone/local/opt/hdf5-1.8.5/ GCC=gcc-4.2 GXX=g++-4.2 F77=gfortran CPPFLAGS=-DH5_USE_16_API"
o ensures that the generated tarball is complete
o runs all tests from the tarball
If step 3 went fine then
cd top_srcdir
5- if any changes/updates/bugfixes : tag again and go to 2
1- update Version.cmake
tag LIFEV_X_2Y_BRANCH with the tag LIFEV_X_2Y_Z
cd top_srcdir
git tag LIFEV_X_2Y_Z
2- update NEWS
6- merge fixes to HEAD: cd lifev-head
(to do)
3- tag master with the tag RELEASE_X_Y_Z
X_Y_Z=3_2_0
7- upload the tarball on cmcsforge.epfl.ch
git tag RELEASE_${X_Y_Z}
git push github RELEASE_${X_Y_Z}
git push origin RELEASE_${X_Y_Z}
8- add news on cmcsforge.epfl.ch and www.lifev.org
4- add news on cmcsforge.epfl.ch and www.lifev.org
9- send email on lifev-dev@ and eventually other lists like
cmcs.personnel@
5- send email on lifev-dev@
Copyright (C) 1994, 1995, 1996, 1999, 2000, 2001, 2002 Free Software
Foundation, Inc.
This file is free documentation; the Free Software Foundation gives
unlimited permission to copy, distribute and modify it.
Basic Installation
==================
These are generic installation instructions.
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 only 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. If you're
using `csh' on an old version of System V, you might need to type
`sh ./configure' instead to prevent `csh' from trying to execute
`configure' itself.
Running `configure' takes awhile. 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.
4. Type `make install' to install the programs and any data files and
documentation.
5. 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.
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=c89 CFLAGS=-O2 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 must use a version of `make' that
supports the `VPATH' variable, such as 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 `..'.
If you have to use a `make' that does not support the `VPATH'
variable, you have 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.
Installation Names
==================
By default, `make install' will install the package's files in
`/usr/local/bin', `/usr/local/man', etc. You can specify an
installation prefix other than `/usr/local' by giving `configure' the
option `--prefix=PATH'.
You can specify separate installation prefixes for
architecture-specific files and architecture-independent files. If you
give `configure' the option `--exec-prefix=PATH', the package will use
PATH as the prefix for installing programs and libraries.
Documentation and other data files will still use the regular prefix.
In addition, if you use an unusual directory layout you can give
options like `--bindir=PATH' 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.
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'.
Optional Features
=================
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.
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 `--target=TYPE' option 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
will cause the specified gcc to be used as the C compiler (unless it is
overridden in the site shell script).
`configure' Invocation
======================
`configure' recognizes the following options to control how it
operates.
`--help'
`-h'
Print a summary of the options to `configure', and exit.
`--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.
`configure' also accepts some other, not widely useful, options. Run
`configure --help' for more details.
Please follow the tutorial (visit http://www.lifev.org)
\ No newline at end of file
The copyright header can be found in Copyright.txt in the root folder.
This file contained a link to the licensing section of the Trilinos website.
Do we also need additional licensing information?
The copyright and license information that cover all the files of this sofware
distribution can be found in Copyright.txt in the root folder.
# -*- readme-debian -*-
LifeV 3.2.0:
============
* New modular structure and configuration using CMake similar to Trilinos
* Distribution through GitHub
New features are not described here for brevity.
LifeV 2.2.0:
=============
......
===================================
== OUT OF DATE as of 9.03.2012 ==
== NEEDS UPDATING ! ==
===================================
For configuring and building LifeV with CMake the following variables are of importance
(provide them as arguments to the cmake command -D VARIABLE_NAME:VARIABLE_TYPE=VALUE):
* CMAKE_CXX_COMPILER (STRING) - set this to the desired C++ compiler (g++, c++, mpicxx, mpixlcxx etc.)
By default, this is set to "mpicxx"
* CMAKE_CXX_FLAGS (STRING) - provide a string containing additional compiler flags (this variable
can be used to override the default settings, like optimization level, of the build type
* CMAKE_BUILD_TYPE (STRING) - set this to Debug ( -Wall -g) or Release (-O2).
By default, this is set to "Debug"
* LIFE_EXTRA_LINK_LINE (STRING) - use this to specify flags for the linker or append additional libraries
to the link line
* CMAKE_INSTALL_PREFIX (PATH) - set this to the desired install location for LifeV
Third party library dependencies:
* ParMETIS (required) - if it is installed in a non-standard location, you will need to set
PARMETIS_ROOT (PATH) to the appropriate location
* MPI - if you plan on using the MPI wrappers (mpicxx, mpixlcxx etc.), then you need to set
LIFE_USE_MPI_WRAPPER (BOOL), and no additional information is required about the MPI installation.
Otherwise, the scripts will try to determine the location of MPI headers and libraries.
In case of a non standard installation, please provide the location of MPI through the
MPI_INCLUDE_PATH (PATH) and MPI_LIBRARIES (STRING) variables.
* Trilinos (required) - if the Trilinos libraries aren't installed in a standard location,
please set Trilinos_ROOT (PATH) to point to the installation
* UMFPACK (optional) - if planning to compile LifeV with UMFPACK support, please set LIFE_USE_UMFPACK
(BOOL) to TRUE. In the event of a non standard UMFPACK installation, please provide a hint
through UMFPACK_ROOT (PATH). Please note that the scripts expect that both UMFPACK, UFConfig and
AMD are installed in the "include" and "lib" subdirectories of UMFPACK_ROOT.
* LAPACK and BLAS (required) - in the case of non-standard location and name for the LAPACK and BLAS
libraries, they can be specified through the LAPACK_LIBRARIES (STRING) and BLAS_LIBRARIES (STRING)
variables.
* Boost (required) - in the case of a non-standard Boost installation, please provide it's location
through the BOOST_ROOT (PATH) variable
* HDF5 (optional) - the HDF5 support in LifeV can be activated with LIFE_USE_HDF5 (BOOL).
Non standard paths can be provided through HDF5_ROOT (PATH)
* QHULL (optional) - the QHULL support in LifeV is activated with LIFE_USE_QHULL (BOOL).
Non standard paths can be provided with QHULL_ROOT (PATH)
All the optional third party libraries are disabled by default.
After the configuration phase, compile the libraries with "make", tests can be compiled individually with
"make <NAME_OF_TEST>" or collectively with "make all_tests". Running the testsuite is done by issuing
"ctest".
The configure scripts respond to other default CMake variables. These aren't needed in most cases, but
additional information about them can be found on the official CMake website.
The collection of CMake scripts for LifeV is work in progress.
----------------------------------------------------------------------------
Radu Popescu, EPFL - CMCS
<radu.popescu@epfl.ch>
LifeV (pronounced "life five")
the C++ parallel finite element library for the solution of PDEs.
Distributed under LGPL by CMCS – EPFL, E(CM)2 – Emory, MOX – Polimi, REO, ESTIME– INRIA.
about 30 active developers.
----------------------------------------------------------------------------
Simone Deparis, EPFL - CMCS
<simone.deparis@epfl.ch>
# @HEADER
# *******************************************************************************
#
#
# Copyright (C) 2004, 2005, 2007 EPFL, Politecnico di Milano, INRIA
# Copyright (C) 2010 EPFL, Politecnico di Milano, Emory University
#
#
# This file is part of LifeV.
#
#
# LifeV is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
#
# LifeV is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# Lesser General Public License for more details.
#
#
# You should have received a copy of the GNU Lesser General Public License
# along with LifeV. If not, see <http://www.gnu.org/licenses/>.
#
......@@ -28,14 +28,14 @@
# for release mode and set the version.
#
SET(LifeV_VERSION 3.1.1)
SET(LifeV_VERSION 3.2.0)
SET(LifeV_MAJOR_VERSION 3)
SET(LifeV_MINOR_VERSION 1)
SET(LifeV_MICRO_VERSION 1)
SET(LifeV_MAJOR_MINOR_VERSION 030101)
SET(LifeV_VERSION_STRING "3.1.1")
SET(LifeV_MINOR_VERSION 2)
SET(LifeV_MICRO_VERSION 0)
SET(LifeV_MAJOR_MINOR_VERSION 030200)
SET(LifeV_VERSION_STRING "3.2.0")
SET(LifeV_ENABLE_DEVELOPMENT_MODE_DEFAULT ON) # Change to 'OFF' for a release
# Used by testing scripts and should not be used elsewhere
SET(LifeV_REPOSITORY_BRANCH "master" CACHE INTERNAL "")
SET(LifeV_TESTING_TRACK "Nightly build 3.0" CACHE INTERNAL "")
SET(LifeV_TESTING_TRACK "Nightly build 3.2" CACHE INTERNAL "")
set (EXAMPLE_LIST example_cylinder example_impes)
foreach (component ${EXAMPLE_LIST})
add_subdirectory(${component})
endforeach()
add_custom_target (examples
DEPENDS ${EXAMPLE_LIST})
# -*- makefile; indent-tabs-mode: t -*-
#
#
#
# Copyright (C) 2010 Simone Deparis (simone.deparis@epfl.ch)
#
# Distributed under the GPL(GNU Public License):
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
#
SUFFIXES = .cpp .hpp .idl .c .h .f .F .o .moc
SUBDIRS = benchmark_GreenshieldsWeller \
benchmark_RossEthierSteinman \
example_cavity \
benchmark_HPCNavierStokes \
example_cylinder \
example_heart \
example_impes \
example_ML \
example_NavierStokesRestart \
example_ns_flux \
example_nsResistanceBC \
utility_converterGetPot2Teuchos \
utility_fsiCutter \
utility_meshReorder \
application_aortaFSI \
unmaintained_ct \
unmaintained_masstransport \
unmaintained_rk
$(srcdir)/package.m4: $(top_srcdir)/configure.in.in
{ \
echo '# Signature of the current package.'; \
echo 'm4_define([AT_PACKAGE_NAME], [@PACKAGE_NAME@])'; \
echo 'm4_define([AT_PACKAGE_TARNAME], [@PACKAGE_TARNAME@])'; \
echo 'm4_define([AT_PACKAGE_VERSION], [@PACKAGE_VERSION@])'; \
echo 'm4_define([AT_PACKAGE_STRING], [@PACKAGE_STRING@])'; \
echo 'm4_define([AT_PACKAGE_BUGREPORT], [@PACKAGE_BUGREPORT@])'; \
} >$(srcdir)/package.m4
EXTRA_DIST =
#EXAMPLES = $(srcdir)/examples
check-local:
include $(top_srcdir)/Doxyfile.am
MOSTLYCLEANFILES =
DISTCLEANFILES =
# -*- makefile -*-
###################################################################################################
#
# This file is part of the LifeV Applications
# Copyright (C) 2001-2011 EPFL, Politecnico di Milano, INRIA
#
# Author(s): Gwenol Grandperrin <gwenol.grandperrin@epfl.ch>
# Date: 28-10-2010
# License Terms: GNU GPL
#
###################################################################################################
include $(top_srcdir)/testsuite/Makefile.testsuite
SUFFIXES = .cpp .hpp .idl .c .h .f .F .o .moc
check_HEADERS = # List of all the hpp files
check_PROGRAMS = benchmark_HPCNavierStokes
benchmark_HPCNavierStokes_SOURCES = benchmark_HPCNavierStokes.cpp
link:
test -a Ressources || ln -s $(top_srcdir)/examples/benchmark_HPCNavierStokes/Ressources Ressources
test -a data || ln -s $(top_srcdir)/examples/benchmark_HPCNavierStokes/Ressources/data data
test -a 100170_cm_N2H0.008_fluid_coarse.mesh || ln -s $(top_srcdir)/examples/benchmark_HPCNavierStokes/Ressources/100170_cm_N2H0.008_fluid_coarse.mesh 100170_cm_N2H0.008_fluid_coarse.mesh
scripts:
cp $(top_srcdir)/examples/benchmark_HPCNavierStokes/Scripts/* ./
recheck: clean_PROGRAMS check
clean_PROGRAMS:
-rm $(check_PROGRAMS)
clean-results:
-rm *.vct *.scl *.case *.geo *.xmf *.h5
# -*- getpot -*- (GetPot mode activation for emacs)
#-------------------------------------------------
# Data file for EthierSteinman test case
#-------------------------------------------------
[problem]
mesh_dir = ./
mesh_file = 100170_cm_N2H0.008_fluid_coarse.mesh
viscosity = 0.035
density = 1.0
initial_time = 0.0;
end_time = 1e-2;
timestep = 1e-4;
[exporter]
type = hdf5 # hdf5 (if library compiled with hdf5 support) or ensight
multimesh = false
start = 0
save = 1
[fluid]
[./physics]
density = 1.0 # density
viscosity = 0.035 # viscosity
[../time_discretization]
initialtime = 0.0
endtime = 0.010