Getafix

This cluster uses the module system for additional packages. To compile the toolkit with the optimized MKL libraries you will need:

module add gnu gnutools boost intel/2019.5.0
unset CPATH

export LD_LIBRARY_PATH="/opt/gnu/gcc/lib64:$LD_LIBRARY_PATH"

../mptoolkit/configure --with-lapack=-llapack --with-boost=$BOOSTROOT \
--with-blas="-L${MKLROOT}/lib/intel64 -Wl,--no-as-needed -lmkl_gf_lp64 -lmkl_sequential -lmkl_core -lpthread -lm -ldl" \
CXXFLAGS="-O2 -march=core2 -mtune=native -flto"

You will need to add these modules and the export line to your .bashrc file or to the top of your job script to ensure that the paths are set up to properly load the shared libraries.

Do not use the mkl module. Versions of MKL prior to 2019.5 contain bugs in the complex SVD and eigensolvers that affect the toolkit. The version of MKL-2019.5 is designed for the Intel C++ compiler, which is why there is a bit of juggling with the configure options to get it to work with the GNU compiler.

The unset CPATH line is necessary because the intel/2019.5.0 module is not well behaved, and it configures the include paths for the Intel C++ compiler using the CPATH variable. This is also used by gcc, so that causes gcc to attempt to link against the Intel standard libraries.

Summary of all commands to download and install to $HOME/bin

module add gnu gnutools boost intel/2019.5.0
unset CPATH
git clone git://git.science.uq.edu.au/mptoolkit
mptoolkit/fix-timestamp.sh
mkdir build
cd build
../mptoolkit/configure --prefix=$HOME --with-lapack=-llapack --with-boost=$BOOSTROOT \
--with-blas="-L${MKLROOT}/lib/intel64 -Wl,--no-as-needed -lmkl_gf_lp64 -lmkl_sequential -lmkl_core -lpthread -lm -ldl" \
CXXFLAGS="-O2 -march=core2 -mtune=native -flto"
make all models
make install install-models

You will also want to add the line

export PATH="$HOME/bin:$PATH"

to the .bashrc file in your home directory.

Relevant links

Some of these links will require connecting to the UQ VPN.

getafix website https://research.smp.uq.edu.au/computing/index.php?n=Getafix.Getafix?from=Main.Getafix
System usage reports http://faculty-cluster.soe.uq.edu.au/ganglia/
Hardware setup and available queues https://research.smp.uq.edu.au/computing/index.php?n=Howto.Sge-slurm
See https://research.smp.uq.edu.au/computing/index.php?n=Howto.Slurm for some documentation on the Slurm queue manager.