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Model for 1D/2D wave propagation, sediment transport and morphological changes |
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- Go to the directory where your source code is avalaible
- Update the source code with command:
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svnupdatesvn update |
- Clean up your directory by typing:
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make distcleanclean |
- In here build a Makefile with the command:
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- type ./configure --help for detailed options; i.e to build mpi executable you can use one of the following commands:
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FC=gfortran44 ./configure --with-mpi
FC=gfortran44 MPIFC=/opt/mpich2-1.0.8-gcc44-x86_64/bin/mpif90 ./configure --with-mpi
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- You can also use the gfortan44 compiler to build a Makefile with netcdf output:
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FC=gfortran44 PKG_CONFIG_PATH=/opt/netcdf-4.1.1/gfortran/lib/pkgconfig ./configure --with-netcdf |
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FC=gfortran44 MPIFC=/opt/mpich2-1.0.8-gcc44-x86_64/bin/mpif90 PKG_CONFIG_PATH=/opt/netcdf-4.1.1/gfortran/lib/pkgconfig ./configure --with-netcdf --with-mpi |
- Build you XBeach executable by running you make file and typing:
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### ********************************************************************
### ********************************************************************
### ** **
### ** Example shell script to run XBeach executable in parallel **
### ** with MPICH2 via SGE on linux cluster. **
### ** c 2009 Deltares **
### ** author: Menno Genseberger **
### ** Changes: Leroy van Logchem 24 Nov 2010 **
### ** -- Use tight integrated mpich2 PE. Requires secret file: **
### ** ~/.mpd.conf **
### ** secretword=mys3cret **
### ** **
### ********************************************************************
### ********************************************************************
### The next line species the shell "/bin/sh" to be used for the execute
### of this script.
#!/bin/sh
### The "-cwd" requests execution of this script from the current
### working directory; without this, the job would be started from the
### user's home directory.
#$ -cwd
### The name of this SGE job is explicitly set to another name;
### otherwise the name of the SGE script itself would be used. The name
### of the job also determines how the jobs output files will be called.
#$ -N XB_ZandMotor
### The next phrase asks for a "parallel environment" called "mpich2",
### to be run with 4 slots (for instance 4 cores).
### "mpich2" is a specific name for H3/H4 linux clusters (this name is
### for instance "mpi" on DAS-2/DAS-3 linux clusters).
#$ -pe distrib 3
### Start SGE.
. /opt/sge/InitSGE
### Code compiled with Intel 11.0 compiler.
export LD_LIBRARY_PATH=/opt/intel/Compiler/11.0/081/lib/ia32:$LD_LIBRARY_PATH
### Specific setting for H3/H4 linuxclusters, needed for MPICH2
### commands (mpdboot, mpirun, mpiexed, mpdallexit etc.).
export PATH="/opt/mpich2/bin:${PATH}"
xbeach_bin_dir=/u/thiel/checkouts/trunk
cp $xbeach_bin_dir/xbeach xbeach.usedexe
### Some general information available via SGE. Note that NHOSTS can be
echo ----------------------------------------------------------------------
echo Parallel run of XBeach with MPICH2 on H4 linuxcluster.
echo SGE_O_WORKDIR: $SGE_O_WORKDIR
echo HOSTNAME : $HOSTNAME
echo NHOSTS : $NHOSTS
echo NQUEUES : $NQUEUES
echo NSLOTS : $NSLOTS
echo PE_HOSTFILE : $PE_HOSTFILE
echo Contents of auto generated machinefile:
cat $TMPDIR/machines
echo ----------------------------------------------------------------------
### General, start XBeach in parallel by means of mpirun.
mpirun -np $NSLOTS $xbeach_bin_dir/xbeach >> output_xbeach_mpi 2>&1
### General for MPICH2, finish your MPICH2 communication network.
mpdallexit
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Note for Jaap and Jamie type "mpd &" and follow instructions:
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cn $HOME
touch .mpd.conf
chmod 600 .mpd.configconf
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Now edit the .mpd.config file and add the text:
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