Espresso on CSC

Espresso on CSC

Here you can find a short introduction on how to compile and use ESPResSo on the CSC computer cluster.

Compiling

CSC-I (login.csc.uni-frankfurt.de)

To be done.

CSC-II (drei.csc.uni-frankfurt.de)

You have three different options of compiling Espresso on the CSC-II cluster.

All three options assume that you want to use the recent way of configuring using object directories and have the Espresso sources in the following folder:

$SRCDIR = $HOME/src/Espresso

.

Single Processor

1. Create an object directory

mkdir ~/bin/Espresso/obj-single
cd ~/bin/Espresso/obj-single

2. Create and edit the configuation file 'myconfig.h'

cp $SRCDIR/myconfig-sample.h ./myconfig.h
vi myconfig.h

3. Execute configure

$SRCDIR/configure --without-mpi \
                  CPPFLAGS="-I/opt/fftw3/include -I/opt/tcl8.4.9/include" \
                  LDFLAGS="-L/opt/fftw3/lib -L/opt/tcl8.4.9/lib"

4. Build Espresso

make -j

Multi Processor with Ethernet Communication

As above but exchange step 3 by the following:

3. Execute configure

export PATH=/opt/mpich/gcc323/bin/:$PATH
$SRCDIR/configure --with-mpi=mpich \
                  CC="/opt/mpich/gcc323/bin/mpicc" \
                  CPPFLAGS="-I/opt/fftw3/include -I/opt/tcl8.4.9/include" \
                  LDFLAGS="-L/opt/fftw3/lib -L/opt/tcl8.4.9/lib"

Multi Processor with Myrinet Communication

1. Create an object directory

mkdir ~/bin/Espresso/obj-myri
cd ~/bin/Espresso/obj-myri

2. Create and edit the configuation file 'myconfig.h'

cp $SRCDIR/myconfig-sample.h ./myconfig.h
vi myconfig.h

3. Execute configure

export PATH=/opt/mpich_gm/gcc323/bin/:$PATH
$SRCDIR/configure --with-mpi=mpich \
                  CC="/opt/mpich_gm/gcc323/bin/mpicc" \
                  CPPFLAGS="-I/opt/fftw3/include -I/opt/tcl8.4.9/include" \
                  LDFLAGS="-L/opt/fftw3/lib -L/opt/tcl8.4.9/lib"

4. Build Espresso

make -j

CSC-III (quad.csc.uni-frankfurt.de)

To be done.

Running

All jobs (even single processor jobs) have to be submitted to the queueing system. Do not run time consuming applications (i.e. any kind of simulation) on the head node.

Environment Variables

Make sure that you include

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/fftw3/lib:/opt/tcl8.4.9/lib

in your profile (i.e. ~/.bashrc) in order to find the libraries during runtime.