How To's

First and foremost, to have a complete and detailed description of the system, read the wiki page dedicated to CCMS Blackhole cluster (http://www.mech.uq.edu.au/hpcwiki). For the login and the password, read the email you got from the admin when your account was created.

Installing FFTW (2.1.5)

Load PGI (7.0-2) and OpenMPI (1.2-pgi-7.0-2). They are the default modules. The installation process is basic: ./configure/make/make install. You may install FFTW with single and double precision.

./configure --prefix=/MyDirectory/FFTW-2.1.5 --enable-mpi --enable-fortran --enable-threads --enable-type-prefix --enable-float

Note the last flag (--enable-float) is for single precision. You can add the options F77, CC, FFLAGS, CFLAGS, CPPFLAGS and LDFLAGS to relate to compiler commands and flags if configure cannot find them. In this case, they would be (for the versions of the module cited above):

F77=/opt/openmpi-1.2/pgi-7.0-2/bin/mpif77
CC=/opt/openmpi-1.2/pgi-7.0-2/bin/mpicc
FFLAGS=-L/opt/openmpi-1.2/pgi-7.0-2/lib
CFLAGS=-I/opt/openmpi-1.2/pgi-7.0-2/bin
CPPFLAGS=-I/opt/openmpi-1.2/pgi-7.0-2/include
LDFLAGS=-L/opt/openmpi-1.2/pgi-7.0-2/lib

You can always try ./configure -help to have more details on the options.

Installing GROMACS (3.2.1)

You can advice some pieces of advices on the GROMACS website abouse installation (at http://www.gromacs.org/content/view/19/32/). Don't forget to add the environment variables CPPFLAGS and LDFLAGS!

export CPPFLAGS=-I/opt/openmpi-1.2/pgi-7.0-2/include
export LDFLAGS=-L/opt/openmpi-1.2/pgi-7.0-2/lib

(For a Bash shell)

You only need mdrun with MPI. So you can install everything without MPI (single and double precision if you like), and then install mdrun only with MPI enable (it is an all static installation! turn it off if you don't want it).

./configure --prefix=/home1/poger/PROGS/GROMACS/3.2.1 --with-fft=fft --enable-all-static

Then:

make
make install

For mdrun with MPI:

./configure --prefix=/home1/poger/PROGS/GROMACS/3.2.1 --with-fft=fft --enable-all-static --enable-mpi --program-suffix=_mpi

Followed by:

make mdrun
make install-mdrun

Options you can add:

F77=/opt/openmpi-1.2/pgi-7.0-2/bin/mpif77
CC=/opt/openmpi-1.2/pgi-7.0-2/bin/mpicc
FFLAGS=-L/opt/openmpi-1.2/pgi-7.0-2/lib
CFLAGS=-I/opt/openmpi-1.2/pgi-7.0-2/bin

Using rsync

An efficient way to transfer files or directory between computers:

rsync -avzP --delete -e 'ssh -p20' ikass@guava.md.smms.uq.edu.au:/data8/ikass/projects/polarizability/alcohols_classic/ethanol/pure_ethanol_1k_mol/MD_NVT_298K/ /Users/ikass/projects/polarizability/alcohols_classic/ethanol/pure_ethanol_1k_mol/MD_NVT_298K/