GT Home : : Campus Maps : : GT Directory

New and Updated Software: BLAST, COMSOL, Mathematica, VASP

This entry was posted by on Friday, 7 December, 2012 at

All of the software detailed below is available through the “modules” system installed on all PACE-managed Redhat Enterprise 6 computers.
For basic usage instructions on PACE systems see the Using Software Modules page.

NCBI BLAST 2.2.25 – Added multithreading in new GCC 4.6.2 version

The 2.2.25 version of BLAST that was compiled with GCC 4.4.5 has multithreading (i.e. multi-CPU execution) disabled.
A new version of BLAST with multithreading enabled has been compiled with the GCC 4.6.2 compiler.

Using it

#First, load the required compiler 
$ module load gcc/4.6.2
#Now load BLAST
$ module load ncbi_blast/2.2.25
#Setup the environment so that blast can find the database
$ export BLASTDB=/path/to/db
#Run a nucleotide-nucleotide search
$ blastn -query /path/to/query/file -db <db_name> -num_threads <number of CPUS allocated to job>

COMSOL 4.3a – Student and Research versions

COMSOL Multiphysics version 4.3a contains many new functions and additions to the COMSOL product suite. These Release Notes provide information regarding new functionality in existing products and an overview of new products.
See the COMSOL Release Notes for information on updates to this version of COMSOL.

Using it

#Load the research version of comsol 
$ module load comsol/4.3a-research
$ comsol ...
#Use the matlab livelink
$ module load matlab/r2011b
$ comsol -mlroot ${MATLAB}

Mathematica 9.0

Mathematica 9 is a major update to the Mathematica software.

Using it

$ module load mathematica/9.0 
$ mathematica

VASP 5.2.12

The pre-calculated kernel for the vdW-DF functional has been installed into the same directory as the vasp binary.
This precalculated kernel is contained in the file “vdw_kernel.bindat”

Using it

#First, load the vasp module (and all the prerequisites) 
$ module load intel/12.1.4 mvapich2/1.6 mkl/10.2 fftw/3.3 vasp/5.2.12
#Copy the kernel to where vasp expects (normally the working directory)
$ cp ${VDW_KERNEL} .
# Run vasp
$ mpirun vasp

Comments are closed.