[dune-pdelab] Heat Equation in Parallel

Afshin Loni afshin.loni at gmail.com
Thu Jun 16 19:17:52 CEST 2016


Hi Jö,

Thanks for the reply, Actually I did delete the build directory, I am
making a debug build folder generally and I deleted it. I have an
Install.sh file which takes care of everything and also generates the opt
file , here it is :

#!/bin/bash

ROOT=$(pwd)
if [ ! "$F77" ]; then
  F77=gfortran
fi
if [ ! "$CC" ]; then
CC=gcc
fi
if [ ! "$CXX" ]; then
CXX=g++
fi
if [ ! "$CXXFLAGS" ]; then
CXXFLAGS="-O3 -DNDEBUG"
fi
CFLAGS="$CXXFLAGS"
if [ ! "$MAKE_FLAGS" ]; then
MAKE_FLAGS="-j2"
fi

# To avoid an ugly cmake bug we expand our compiler variables to absolute
paths
export CC=$(which $CC)
export CXX=$(which $CXX)
export F77=$(which $F77)

# Check whether we have built external dependencies
if [ ! -d "$(pwd)/external/ug" ]; then
  ./external.sh
fi


# generate an opts file with debug flags
echo "CMAKE_FLAGS=\"
-DUG_ROOT=$ROOT/external/ug
-DCMAKE_C_COMPILER='$CC'
-DCMAKE_CXX_COMPILER='$CXX'
-DMPI_CC_COMPILER=mpicc.mpich
-DMPI_CXX_COMPILER=mpicxx.mpich
-DCMAKE_CXX_FLAGS='-Wall
-DDUNE_AVOID_CAPABILITIES_IS_PARALLEL_DEPRECATION_WARNING'
-DCMAKE_CXX_FLAGS_DEBUG='-O0 -ggdb'
-DDUNE_SYMLINK_TO_SOURCE_TREE=1
-DCMAKE_BUILD_TYPE=Debug
-DCMAKE_INSTALL_PREFIX=/home/afshin/dunes/installation2
\"" > debug.opts



./dune-common/bin/dunecontrol --opts=debug.opts
--builddir=$(pwd)/debug-build all

#to install
 mkdir /home/afshin/dunes/installation2
 ./dune-common/bin/dunecontrol --opts=debug.opts
--builddir=$(pwd)/debug-build make install


Best,
Afshin

On Thu, Jun 16, 2016 at 4:59 PM, Jö Fahlke <jorrit at jorrit.de> wrote:

> Am Thu, 16. Jun 2016, 12:28:11 +0200 schrieb Afshin Loni:
> > I am trying to solve a heat equation in parallel but it seems impossible
> > for me, So here's the story.
> > I have the tutorials of the course that took place in March. and
> tutorial 3
> > is solving the heat equation. basically the tutorial says you can run the
> > code in parallel by simply running the mpirun. as you know the code
> checks
> > for the mpi with mpihelper and then it prints out e.g. running in
> parallel
> > on 1 process(es). but when I run the heat equation on two processors it
> > prints
> >
> > running in parallel on 1 process(es)
> > running in parallel on 1 process(es)
> >
> > which basically means the code is running sequentially twice.
> > I thought I need to use some flags, so I used the following flags to
> > compile:
> >
> > -DMPI_CC_COMPILER=mpicc.mpich \
> > -DMPI_CXX_COMPILER=mpicxx.mpich
>
> Hi!
>
> You need to delete your build directory and rebuild completely after
> changing
> such configuration flags.
>
> In case you did that already, or in case that did not help:  how exactly
> are
> you specifying those flags?  E.g. if you specify them in your .opts-file,
> please provide it here.
>
> Regards,
> Jö.
>
> > but I got no change.
> > I thought tutorial 3 is incapable of running in parallel so I tried
> > tutorial 6 which is about parallelization. But I got the same results.
> > MPICH is also installed on my ubuntu 15.10 system.
> >
> > Any help would be appreciated.
> >
> > Regards,
> > Afshin
>
> > _______________________________________________
> > dune-pdelab mailing list
> > dune-pdelab at dune-project.org
> > http://lists.dune-project.org/mailman/listinfo/dune-pdelab
>
>
> --
> Jorrit (Jö) Fahlke, Institute for Computational und Applied Mathematics,
> University of Münster, Orleans-Ring 10, D-48149 Münster
> Tel: +49 251 83 35146 Fax: +49 251 83 32729
>
> If God had intended Man to Smoke, He would have set him on Fire.
> -- fortune
>
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