PACE A Partnership for an Advanced Computing Environment

August 14, 2012

New Software: HDF5(1.8.9), OBSGRID (April 2, 2010), ABINIT(6.12.3), VMD(1.9.1), and NAMD(2.9)

Filed under: tech support — Semir Sarajlic @ 1:33 pm

Several new software packages have been installed on all RHEL6 clusters.


HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data.
A previous version of HDF5 (1.8.7) has existed on the RHEL6 clusters for many months.
The 1.8.9 version includes many bug fixes and some new utilities.

The hdf5/1.8.9 module is used differently than the 1.8.7 module.
The 1.8.9 module is able to detect whether an MPI module has been previously loaded and will support the proper serial or MPI version of the library.
The 1.8.7 module was not able to automatically detect MPI vs. non-MPI.

Here are two examples of how to use the new HDF5 module (note that all compilers and MPI installations are usable with HDF5):

$ module load hdf5/1.8.9


$ module load intel/12.1.4 mvapich2/1.6 hdf5/1.8.9


OBSGRID is an objective re-analysis package for WRF designed to lower the error of analyses that are used to nudge the model toward the observed state.
The analyses input to OBSGRID as the first guess are analyses output from the METGRID part of the WPS package
Here is how to use obsgrid:

$ module load intel/12.1.4 hdf5/1.8.7/nompi netcdf/4.1.3 ncl/6.1.0-beta obsgrid/04022010
$ obsgrid.exe


ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis.
ABINIT 6.8.1 is already installed on the RHEL6 clusters.
There are many changes from 6.8.1 to 6.12.3. See the 6.12.3 release notes for more information.

Here are a few examples of how to use ABINIT in a job script:

#PBS ...
#PBS -l walltime=8:00:00
#PBS -l nodes=64:ib

module load intel/12.1.4 mvapich2/1.6 hdf5/1.8.9 netcdf/4.2 mkl/10.3 fftw/3.3 abinit/6.12.3
mpirun -rmk pbs abinit < abinit.input.file > abinit.output.file


VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
VMD has been installed with support for the GCC compilers (versions 4.4.5, 4.6.2, and 4.7.0), NetCDF, Python+NumPy, TCL, and OpenGL.
Here is an example of how to use it:

  1. Login to a RHEL6 login node (joe-6, biocluster-6, atlas-6, etc.) with X-Forwarding enabled (X-Forwarding is critical for VMD to work).
  2. Load the needed modules:
    $ module load gcc/4.6.2 python/2.7.2 hdf5/1.8.7/nompi netcdf/4.1.3 vmd/1.9.1
  3. Execute “vmd” to start the GUI


NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
Version 2.9 of NAMD has been installed with support for GNU and Intel compilers, MPI, FFTW3.
CUDA support in NAMD has been disabled.

Here is an example of how to use it in a job script in a RHEL6 queue (biocluster-6, atlas-6, ece, etc.):

#PBS -N NAMD-test
#PBS -l nodes=32
#PBS -l walltime=8:00:00
module load gcc/4.6.2 mvapich2/1.7 fftw/3.3 namd/2.9

mpirun -rmk pbs namd2 input.file

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