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HDF

Software Description: 

HDF is a library and a multi-object file format that facilitates the transfer of various types of scientific data between machines and operating systems. HDF5 also has a collection of utilities for manipulating data.

Software Support Level: 
Secondary Support
Itasca Documentation: 

Itasca

To run HDF5 interactively in a Linux environment run the command:

 module load hdf5/hdf5-1.8.7-intel-pmpi

or

 module load hdf5/hdf5-1.8.7-intel-serial

On Itasca, examples can be found in

 /soft/hdf5/hdf5-1.8.7-intel-serial/share/hdf5_examples

 /soft/hdf5/hdf5-1.8.7-intel-pmpi/share/hdf5_examples

 

Software Access Level: 
Open Access
Software Categories: 
Lab Documentation: 

Labs

 To run HDF5 interactively in a Linux environment run the command:

module load hdf5

Examples

Examples of how to use HDF5 routines can be found on the Lab Linux systems in

/soft/hdf5/1.8.5-patch1/share/hdf5_examples/
 
Software Interactive/GUI: 
No

GROMACS

Software Description: 

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.

Software Support Level: 
Primary Support
Itasca Documentation: 

Itasca has GROMACS builds that utilize Platform MPI as well as Open MPI. While the Open MPI builds are easier to use, the binaries built with Platform MPI generally offer better performance. "module avail gromacs" entered on the command line will print the versions of GROMACS available on Itasca. Any modules with an "-ompi" suffix were built using Open MPI, while modules with no suffix or a "-pmpi" suffix were built with Platform MPI.

A sample submission script for a Platform MPI build is below. You must load the module you are using in your submission script in your .bashrc file for Platform MPI Gromacs jobs to function properly.

#!/bin/bash -l 
#PBS -l walltime=24:0:0
#PBS -l mem=64GB
#PBS -l nodes=8:ppn=8

module load gromacs
cd $PBS_O_WORKDIR

mpirun -np 64 -hostfile $PBS_NODEFILE mdrun -s topol

It is not necessary to load any modules in your .bashrc file if using the Open MPI builds. A sample submission script that would run an Open MPI build of Gromacs 4.5.1 is below.

#!/bin/bash -l 
#PBS -l walltime=24:0:0
#PBS -l mem=64GB
#PBS -l nodes=8:ppn=8

module load gromacs/4.5.1-ompi
cd $PBS_O_WORKDIR

mpirun mdrun -s topol
Software Access Level: 
Open Access
Lab Documentation: 

To run this software interactively in a Linux environment run the command:

module load gromacs
Software Interactive/GUI: 
No

BFAST

Software Description: 

BFAST facilitates the fast and accurate mapping of short reads to reference sequences, where mapping billions of short reads with variants is of utmost importance.

Software Support Level: 
Secondary Support
Software Access Level: 
Open Access
Software Categories: 
Software Interactive/GUI: 
No
General Linux Documentation: 

To run this software interactively in a Linux environment run the commands:

module load bfast
bfast command [options]

manual can be found at:

/soft/bfast/VER/share/doc/bfast/bfast-book.pdf

Where VER is the current version of bfast that you're interested in.

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Matlab

Software Description: 

Matlab is a high level technical computing language and interactive environment for data visualization, data analysis, numerical computation, and algorithm development.

Software Support Level: 
Primary Support
Software Access Level: 
Limited Licenses
PBS Example: 

Matlab programs can be submitted to a queue using PBS script such as the one below. 

#PBS -l nodes=1:ppn=1,mem=1gb,walltime=4:00:00
#PBS -m abe
cd /location/of/the/script
module load matlab
matlab -nodisplay -r "maxNumCompThreads(1)" < my.m

where maxNumCompThreads(1) sets one thread (or one core) for running my.m (the matlab job). The number of threads can have a value up to the number of cores in that node.   The variable maxNumCompThreads must be specified. Otherwise, the job will request twice as many cores as there are available on a computing node. This can cause problems for all jobs running on the same node.

Software Interactive/GUI: 
No
General Linux Documentation: 

To run this software interactively in a Linux environment run the commands:

module load matlab
matlab

Several versions of Matlab are available, but the versions may be different on different platforms.To list all versions of Matlab available on the machine, type

module avail matlab

When running on the elmob nodes use this module instead:

module load matlab/R2010b
matlab

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AMBER

Software Description: 

AMBER. Assisted Model Building with Energy Refinement. AMBER refers to two things: a molecular mechanical force field for the simulation of biomolecules (which is in general use in a variety of simulation programs)- and a package of molecular simulation programs which includes source code and demos.

Software Support Level: 
Secondary Support
Itasca Documentation: 
Amber 11 is available on Itasca. Calling the sander.MPI binary on more than one node (8 cores) requires the amber module to be loaded in your .bashrc file. If you are running pmemd.MPI this step is not necessary. A sample job script is below.
#!/bin/bash -l
#PBS -l walltime=8:00:00,pmem=1000mb,nodes=8:ppn=8
#PBS -m abe

module load amber/11

cd $PBS_O_WORKDIR

mpirun -np 64 -hostfile $PBS_NODEFILE `which pmemd.MPI` \
  -O -i mdin -c eq200.x -o cellulose.sander.log

Additional Documentation

Software Access Level: 
Open Access
PBS Example: 

An example PBS script for submitting AMBER jobs to the queue is shown below.

#!/bin/bash -l 
#PBS -l walltime=24:00:00,mem=16gb,nodes=2:ppn=8 
#PBS -m abe 

module load amber 

cd $PBS_O_WORKDIR 

mpirun sander.MPI -O -i AMP2md39.in -o AMP2md39.out -p \
  AMP2_wat.prmtop -c AMP2md38.rst -r AMP2md39.rst -x \
  AMP2md39.mdcrd
Software Interactive/GUI: 
No
General Linux Documentation: 

To run this software interactively in a Linux environment run the command:

module avail amber

and choose the most recent version of the software applicable to your research. The exact name of the module will vary from machine to machine, and over time with new updates so be sure to study the list printed with the 'module avail' command demonstrated above. For example,

module load amber/11
The amber module requires and will automatically load several other modules. Pay attention to any error messages or warnings that result from loading the module as conflicts with other packages already loaded in your environment are a common source of error. An example submission script is below. Note that the #PBS lines need to be tuned for each cluster's policies. You may not need to run short jobs through the queue, so the program can be used interactively by loading the module and running the executable directly at the command prompt.
#!/bin/bash -l 
#PBS -l walltime=24:00:00,mem=16gb,nodes=2:ppn=8 
#PBS -m abe 

module load amber 

cd $PBS_O_WORKDIR 

mpirun sander.MPI -O -i AMP2md39.in -o AMP2md39.out -p \
  AMP2_wat.prmtop -c AMP2md38.rst -r AMP2md39.rst -x \
  AMP2md39.mdcrd

Additional Documentation

Allinea MAP

Software Description: 

Allinea MAPis a profiler for serial and parallel applications written in C, C++, FORTRAN 77, Fortran 90. It supports multiple parallel programming paradigms including MPI, and OpenMP.

Software Support Level: 
Secondary Support
Software Access Level: 
Open Access
Software Categories: 
Software Interactive/GUI: 
No
General Linux Documentation: 
To run this software in a Linux environment run the commands:
module load allinea-tools intel/12.0 ompi/1.5.4/intel
map

To profile your application, you need to build it with the MAP libraries, for example:

module load allinea-tools intel/12.0 ompi/1.5.4/intel
C: mpicc -g -O3 your.c -lmap-sampler
C++: mpicxx -g -O3 your.c -lmap-sampler
FORTRAN: mpif90 -g -O3 your.c -lmap-sampler

On the login nodes, you can use MAP only up to the number of cores available. For an MPI job to run across nodes, one need run MAP interactively through a queue by " qsub -I -X -q batch ". Here is the procedure for profiling a MPI job to run over 2 nodes:

qsub -I -X -l nodes=2:ppn=8,mem=20gb,walltime=1:00:00
cd your_work_directory
module load allinea-tools intel/12.0 ompi/1.5.4/intel
map

For Platform MPI, the following commands are used for profiling an MPI application:

module load intel pmpi/8.2.0/intel allinea-tools
export LD_LIBRARY_PATH=/opt/platform_mpi-8.02.00.00-20121216r/MPICH1.2/lib/linux_amd64:$LD_LIBRARY_PATH
export MPICC=mpicc.mpich
mpif90.mpich -g -O3 mpi_hello.f
map -profile -n 4 ./a.out

For Intel MPI, please try the following

module load intel impi/intel allinea-tools
map -n 4 -profile -mpiargs "-r ssh -f nodelist" ./a.out

Where nodelist is a file containing the name of nodes assigned for running the job

node1155

node1156

node1154

node1157

More working examples for building scalar and parallel applications (with a variety of versions of MPI) are in

/soft/allinea-tools/4.1-32296/examples

CRYSTAL

Software Description: 

The CRYSTAL program computes the electronic structure of periodic systems within Hartree Fock, density functional or various hybrid approximations. The Bloch functions of the periodic systems are expanded as linear combinations of atom centred Gaussian functions. Powerful screening techniques are used to exploit real space locality. The code may be used to perform consistent studies of the physical, electronic and magnetic structure of molecules, polymers, surfaces and crystalline solids. 

 

Software Support Level: 
Secondary Support
Software Access Level: 
Open Access
Software Categories: 
Software Interactive/GUI: 
No

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