Re: SOCIS 2013

[Bart Janssens]

On Thu, Jul 25, 2013 at 3:47 PM, Lukáš Svatý <svaty...@gmail.com> wrote:
> I got interested in
> Structured mesh generation
> mainly because I am working in C/C++ all the time and I got some basic experience with NURBS curves.
> Can you provide me some usefull links what to look at if I would like to contribute to this project by SOCIS 2013.

Hi Lukáš,

The most interesting thing to try first would be to install the
coolfluid software (latest master from our git repo) following
http://coolfluidsrv.vki.ac.be/webfiles/coolfluid3/api/nightly/installation.html

Once you compiled the source code, you can run the blockmesher unit
tests. These are in the test/mesh/BlockMesh directory:
https://github.com/coolfluid/coolfluid3/tree/master/test/mesh/BlockMesh

You can run these using ctest -V -R <test name> from the binary dir,
and this will generate .pvtu files that can be opened using ParaView.
This will allow you to get a feel on how the current mesher works. It
is very similar to the OpenFoam BlockMesh format, which is described
here:
http://www.openfoam.org/docs/user/blockMesh.php

The main limitation of our mesher is that it doesn't support curved
surfaces, which would be solved using an extension to NURBS. The code
for the current mesher is at
https://github.com/coolfluid/coolfluid3/blob/master/cf3/mesh/BlockMesh/BlockData.cpp
with the interpolation happening near line 558 in the 3D case.

I noticed that I forgot to add these references to the ideas list, so
I've updated the page now.

I'll be online tomorrow night (Friday) starting 20:00 (CEST) so if you
want to meet on IRC just send me the details of what server to connect
to and your nick.

Cheers,

Bart

[Lukáš Svatý]

Currently im building coolfuid src on my system 

 Linux stluke-pc 3.10.5-1-ARCH x86_64 GNU/Linux

and on 

[ 81%] Building CXX object test/math/CMakeFiles/utest-math-integrate.dir/utest-math-integrate.cpp.o

I get this error:

In file included from /home/stluke/git/coolfluid3/kernel/include/boost/numeric/quadrature/adaptive.hpp:28:0,

                 from /home/stluke/git/coolfluid3/kernel/cf3/math/Integrate.hpp:16,

                 from /home/stluke/git/coolfluid3/kernel/test/math/utest-math-integrate.cpp:17:

/home/stluke/git/coolfluid3/kernel/include/boost/numeric/quadrature/error_estimator.hpp: In function ‘void boost::numeric::quadrature::detail::output(const Value&, typename boost::enable_if<boost::numeric::quadrature::is_arithmetic_scalar<Value> >::type*)’:

/home/stluke/git/coolfluid3/kernel/include/boost/numeric/quadrature/error_estimator.hpp:65:25: error: ‘setprecision’ is not a member of ‘std’

            std::cout << std::setprecision(15);

                         ^

/home/stluke/git/coolfluid3/kernel/include/boost/numeric/quadrature/error_estimator.hpp: In function ‘void boost::numeric::quadrature::detail::output(const OutputRange&, typename boost::disable_if<boost::numeric::quadrature::is_arithmetic_scalar<Value> >::type*)’:

/home/stluke/git/coolfluid3/kernel/include/boost/numeric/quadrature/error_estimator.hpp:74:25: error: ‘setprecision’ is not a member of ‘std’

            std::cout << std::setprecision(15);

                         ^

thats because of the line

#include "boost/math/tools/precision.hpp"

and boost/math folder doesnt actually exist... neither in my forked version of coolfluid3...

I added boost/math/tools/precision but the same error occured

is there some kind of workaround?

[Lukáš Svatý]

I've added boost/math to default package hopefully it will fix this problem... (building atm) 

[Lukáš Svatý]

Currently Im unable to compile on Archlinux, so Im continueing on Fedora 19

but while building via cmake-gui im getting this error:

 !!! ERROR !!!

Orphan file list:

/home/lsvaty/git/coolfluid3/kernel/cf3/common/PE/Comm.cpp

/home/lsvaty/git/coolfluid3/kernel/cf3/common/PE/CommWrapperMArray.cpp

/home/lsvaty/git/coolfluid3/kernel/cf3/common/PE/ListeningThread.cpp

/home/lsvaty/git/coolfluid3/kernel/cf3/common/PE/ListeningInfo.cpp

/home/lsvaty/git/coolfluid3/kernel/cf3/common/PE/CommPattern.cpp

/home/lsvaty/git/coolfluid3/kernel/cf3/common/PE/WorkerGroup.cpp

/home/lsvaty/git/coolfluid3/kernel/cf3/common/PE/CommWrapper.cpp

/home/lsvaty/git/coolfluid3/kernel/cf3/common/PE/debug.cpp

/home/lsvaty/git/coolfluid3/kernel/cf3/common/PE/Manager.cpp

/home/lsvaty/git/coolfluid3/kernel/cf3/common/PE/debug.hpp

/home/lsvaty/git/coolfluid3/kernel/cf3/common/PE/CommPattern.hpp

/home/lsvaty/git/coolfluid3/kernel/cf3/common/PE/Manager.hpp

/home/lsvaty/git/coolfluid3/kernel/cf3/common/PE/CommWrapper.hpp

/home/lsvaty/git/coolfluid3/kernel/cf3/common/PE/Comm.hpp

/home/lsvaty/git/coolfluid3/kernel/cf3/common/PE/all_reduce.hpp

/home/lsvaty/git/coolfluid3/kernel/cf3/common/PE/datatype.hpp

/home/lsvaty/git/coolfluid3/kernel/cf3/common/PE/Buffer.hpp

/home/lsvaty/git/coolfluid3/kernel/cf3/common/PE/types.hpp

/home/lsvaty/git/coolfluid3/kernel/cf3/common/PE/ListeningInfo.hpp

/home/lsvaty/git/coolfluid3/kernel/cf3/common/PE/all_gather.hpp

/home/lsvaty/git/coolfluid3/kernel/cf3/common/PE/WorkerGroup.hpp

/home/lsvaty/git/coolfluid3/kernel/cf3/common/PE/reduce.hpp

/home/lsvaty/git/coolfluid3/kernel/cf3/common/PE/scatter.hpp

/home/lsvaty/git/coolfluid3/kernel/cf3/common/PE/all_to_all.hpp

/home/lsvaty/git/coolfluid3/kernel/cf3/common/PE/operations.hpp

/home/lsvaty/git/coolfluid3/kernel/cf3/common/PE/broadcast.hpp

/home/lsvaty/git/coolfluid3/kernel/cf3/common/PE/gather.hpp

/home/lsvaty/git/coolfluid3/kernel/cf3/common/PE/CommWrapperMArray.hpp

/home/lsvaty/git/coolfluid3/kernel/cf3/common/PE/ListeningThread.hpp

!!! ERROR !!!

!!! ERROR !!! Orphan files where found during the configuration.

!!! ERROR !!! Check full list in file /home/lsvaty/git/coolfluid3/build/OrphanFiles.txt

!!! ERROR !!!

CMake Error at cmake/ProcessOrphanFiles.cmake:24 (message):

Aborted build system configuration.

Add orphan files to the build system or remove them.

Call Stack (most recent call first):

CMakeLists.txt:201 (include)

do you know where could be a problem?

I'll be actually continueing tomorrow since its 2 in the morning :)

Lukáš Svatý

2013/8/8 Lukáš Svatý <svaty...@gmail.com>

[Bart Janssens]

Hi Lukas,

This error appears when certain files are found in the source tree but
not listed in a CMakeLists.txt file. In this case, the reason is that
MPI is not found. On Fedora, install the openmpi packages to solve
this. Compiling without MPI is untested and clearly doesn't work.

Cheers,

Bart

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[Bart Janssens]

I've never seen this problem, I'll have to look into it. For now, you
should be able to disable the test in the Cmake advanced options, it
has no impact on your work.

[Daan Deconinck]

I had the same issue, adding #include <iomanip> fixed the problem with setprecision.

Hth,
Daan

Sent from my iPhone

[Lukáš Svatý]

I have the openmpi package installed 

lsvaty@dhcp131-239 ~$ rpm -qa | grep openmpi

boost-openmpi-python-1.53.0-8.fc19.x86_64

openmpi-1.6.5-1.fc19.x86_64

boost-graph-openmpi-1.53.0-8.fc19.x86_64

boost-openmpi-devel-1.53.0-8.fc19.x86_64

boost-openmpi-1.53.0-8.fc19.x86_64

openmpi-devel-1.6.5-1.fc19.x86_64

and paths set correctly:

libraries: /usr/lib/openmpi

compilers: /usr/lib64/openmpi/bin/  "mpicxx|mpicc|mpif77"

Lukáš Svatý

2013/8/9 Bart Janssens <ba...@bartjanssens.org>

[Oscar Pérez]

Daan Deconinck is right

regards,
Oscar