April 15, 2011

The new release of ACES III, release 3.0.6, has been installed on the Altix 4700. ACES III performs Coupled Cluster Methods for parallel computers. Analytic Gradient are implemented in ACES III for SCF and the correlated levels of theory, MBPT(2), MBPT(3), MBPT(4), CCD, QCISD, CCSD, QCISD(T), and CCSD(T). There are analytic gradients for both restricted and unrestricted Hartree-Fock (RHF and UHF, respectively) reference functions. In addition, for the MBPT(2), MBPT(3), CCSD, and CCSD(T) methods, analytic gradients are available for restricted open-shell Hartree-Fock (ROHF) reference functions. They are also available for certain CCSD calculations based on quasi-restricted Hartree-Fock (QRHF) reference functions, namely those for high-spin doublet cases and two-determinant CCSD (TD-CCSD) calculations for open-shell singlet states, in which the open-shell orbitals have different symmetries. A script "runacesIII" is provided that will generate a job file that can be submitted to LSF. This script can be found in the directory:

/usr/local/apps/chemistry_scripts/acesIII


April 15, 2011

The software package ACES II, release 2.8, has been installed on the Altix 4700. ACES II performs Coupled Cluster Methods for parallel computers. Analytic Gradient are implemented in ACES II for SCF and the correlated levels of theory, MBPT(2), MBPT(3), MBPT(4), CCD, QCISD, CCSD, QCISD(T), and CCSD(T). There are analytic gradients for both restricted and unrestricted Hartree-Fock (RHF and UHF, respectively) reference functions. In addition, for the MBPT(2), MBPT(3), CCSD, and CCSD(T) methods, analytic gradients are available for restricted open-shell Hartree-Fock (ROHF) reference functions. They are also available for certain CCSD calculations based on quasi-restricted Hartree-Fock (QRHF) reference functions, namely those for high-spin doublet cases and two-determinant CCSD (TD-CCSD) calculations for open-shell singlet states, in which the open-shell orbitals have different symmetries. A script "runacesII" is provided that will generate a job file that can be submitted to LSF. This script can be found in the directory:

/usr/local/apps/chemistry_scripts/acesII


November 1, 2010

The October 2010 version of GAMESS has been installed in the Altix 4700. GAMESS performs ab initio electronic structure calculations. A script, "run_gamess.sh", is provided to generate a job file that can be submitted to LSF. This script can be found in the directory:

/usr/local/apps/chemistry_scripts/gamess


August 30, 2010

The hybrid MPI/OpenMP version of MrBayes v3.1.2 by Alexis Stamatakis and Wayne Pfeiffer has been installed on the SGI Altix 4700. Information about this version of MrBayes and how to cite the program can be found at http://wwwkramer.in.tum.de/exelixis/software.html.

MrBayes is a program for the Bayesian estimation of phylogeny. Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes's theorem. The posterior probability distribution of trees is impossible to calculate analytically; instead, MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees. A script to run the hybrid Mrbayes can be found:

/usr/local/apps/chemistry_scripts/mrbayes/mrbayes_mpi_omp.csh


August 23, 2010

Gaussian 09, Revision B.01 has been installed on all HPC computers. Gaussian provides state-of-the-art computational algorithms for performing advanced electronic structure modeling. A complete description of the capabilities of the popular computational chemistry software can be found by clicking on the above link. A script "g09run" is provided to generate a job file that can be submitted to LSF. This script can be found in the directory:

/usr/local/apps/chemistry_scripts/gaussian


July 26, 2010

The new release of ACES III, release 3.0.4, has been installed on the Altix 4700. ACES III performs Coupled Cluster Methods for parallel computers. Analytic Gradient are implemented in ACES III for SCF and the correlated levels of theory, MBPT(2), MBPT(3), MBPT(4), CCD, QCISD, CCSD, QCISD(T), and CCSD(T). There are analytic gradients for both restricted and unrestricted Hartree-Fock (RHF and UHF, respectively) reference functions. In addition, for the MBPT(2), MBPT(3), CCSD, and CCSD(T) methods, analytic gradients are available for restricted open-shell Hartree-Fock (ROHF) reference functions. They are also available for certain CCSD calculations based on quasi-restricted Hartree-Fock (QRHF) reference functions, namely those for high-spin doublet cases and two-determinant CCSD (TD-CCSD) calculations for open-shell singlet states, in which the open-shell orbitals have different symmetries. A script "runaces" is provided that will generate a job file that can be submitted to LSF. This script can be found in the directory:

/usr/local/apps/chemistry_scripts/acesIII


June 15, 2010

The latest version (version 1) of the coupled cluster program CFOUR has been installed on the Altix 4700. CFOUR (Coupled-Cluster techniques for Computational Chemistry) is a quantum mechanical suite of programs for performing high-level quantum mechanical calculations on atoms and molecules. Most of the Møller-Plesset (MP) and coupled-cluster (CC) approximations are available and most have complementary analytic derivative approaches within the package. A script "run_cfour" is provided that will generate a job file that can be submitted to LSF. This script can be found in the directory:

/usr/local/apps/chemistry_scripts/cfour


March 23, 2010

GROMACS version 4.0.7 has been installed on the SGI Altix 4700 in the directory /usr/local/apps/gromacs. GROMACS is a molecular dynamics software package, designed biochemical molecules, such as proteins, lipids and nucleic acids. Information, documentation and tutorials can be found on the GROMACS web site.


March 17, 2010

NAMD version 2.7b2 has been installed on the SGI Altix 4700 in the directory /usr/local/apps/namd. NAMD is a molecular dynamics software package, designed for high performance simulations of large biological molecules. Information, documentation and tutorials can be found on the NAMD web site.


February 10, 2010

The latest release of ACES III release 3.0.3) has been installed on the Altix 4700. ACES III performs Coupled Cluster Methods for parallel computers. Analytic Gradient are implemented in ACES III for SCF and the correlated levels of theory, MBPT(2), MBPT(3), MBPT(4), CCD, QCISD, CCSD, QCISD(T), and CCSD(T). There are analytic gradients for both restricted and unrestricted Hartree-Fock (RHF and UHF, respectively) reference functions. In addition, for the MBPT(2), MBPT(3), CCSD, and CCSD(T) methods, analytic gradients are available for restricted open-shell Hartree-Fock (ROHF) reference functions. They are also available for certain CCSD calculations based on quasi-restricted Hartree-Fock (QRHF) reference functions, namely those for high-spin doublet cases and two-determinant CCSD (TD-CCSD) calculations for open-shell singlet states, in which the open-shell orbitals have different symmetries. A script "runaces" is provided that will generate a job file that can be submitted to LSF. This script can be found in the directory:

/usr/local/apps/chemistry_scripts/acesIII


February 10, 2010

The latest version of the coupled cluster program CFOUR has been installed on the Altix 4700. CFOUR (Coupled-Cluster techniques for Computational Chemistry) is a quantum mechanical suite of programs for performing high-level quantum mechanical calculations on atoms and molecules. Most of the Møller-Plesset (MP) and coupled-cluster (CC) approximations are available and most have complementary analytic derivative approaches within the package. A script "run_cfour" is provided that will generate a job file that can be submitted to LSF. This script can be found in the directory:

/usr/local/apps/chemistry_scripts/cfour


January 3, 2010

CFOUR (Coupled-Cluster techniques for Computational Chemistry) is a quantum mechanical suite of programs for performing high-level quantum mechanical calculations on atoms and molecules. Most of the Møller-Plesset (MP) and coupled-cluster (CC) approximations are available and most have complementary analytic derivative approaches within the package. A script "run_cfour" is provided that will generate a job file that can be submitted to LSF. This script can be found in the directory:

/usr/local/apps/chemistry_scripts/cfour


October 19, 2009

NWChem on the SGI ALTIX 4700 has been upgraded to version 5.1.1. A script for running NWChem can be found in the directory

/usr/local/apps/chemistry_scripts/nwchem


October 3, 2009

ACES III (release 3.0.1 is ready July 21, 2009) has been installed on the SGI ALTIX 4700. ACES III performs Coupled Cluster Methods for parallel computers. Analytic Gradient are implemented in ACES III for SCF and the correlated levels of theory, MBPT(2), MBPT(3), MBPT(4), CCD, QCISD, CCSD, QCISD(T), and CCSD(T). There are analytic gradients for both restricted and unrestricted Hartree-Fock (RHF and UHF, respectively) reference functions. In addition, for the MBPT(2), MBPT(3), CCSD, and CCSD(T) methods, analytic gradients are available for restricted open-shell Hartree-Fock (ROHF) reference functions. They are also available for certain CCSD calculations based on quasi-restricted Hartree-Fock (QRHF) reference functions, namely those for high-spin doublet cases and two-determinant CCSD (TD-CCSD) calculations for open-shell singlet states, in which the open-shell orbitals have different symmetries. A script "runaces" is provided that will generate a job file that can be submitted to LSF. This script can be found in the directory:

/usr/local/apps/chemistry_scripts/acesIII


June 1, 2009

Gaussian 2009 has been installed. A script "g09run" is provided to generate a job file that can be submitted to LSF. This script can be found in the directory:

/usr/local/apps/chemistry_scripts/gaussian


March 15, 2009

Gamess has been updated to the January 2009 version. A script, "run_gamess.sh", is provided to generate a job file that can be submitted to LSF. This script can be found in the directory:

/usr/local/apps/chemistry_scripts/gamess


January 24, 2009

Version 4.4 of DMol3 has been installed on the SGI Altix 4700. A script to setup your DMOl3 jobs for submission to LSF can be found:

/usr/local/apps/chemistry_scripts/prp_ms_44

Note: DMol3 is no longer supported under IRIX.


September 27, 2008

Amber version 10 has been installed on the Altix 4700. It is located

/usr/local/apps/amber10

Older version of amber remain on the system. To use the new version, set the environment variable AMBERHOME to the above location.


August 29, 2008

scilab-4.1.2 has been installed on coffee.ecu.edu. Scilab is a scientific software package for numerical computations providing a powerful open computing environment for engineering and scientific applications. For more information visit the scilab web page:

http://www.scilab.org/


July 5, 2008

The 2008 version of GAMESS has been installed. A script, "run_gamess.sh", generates a job file that you submit to LSF can be found in the directory:

/usr/local/apps/chemistry_scripts/gamess


June 23, 2008

GULP is a program for performing a variety of types of simulation on materials using boundary conditions of 0-D (molecules and clusters), 1-D (polymers), 2-D (surfaces, slabs and grain boundaries), or 3-D (periodic solids). The focus of the code is on analytical solutions, through the use of lattice dynamics, where possible, rather than on molecular dynamics. A variety of force fields can be used within GULP spanning the shell model for ionic materials, molecular mechanics for organic systems, the embedded atom model for metals and the reactive REBO potential for hydrocarbons. Analytic derivatives are included up to at least second order for most force fields, and to third order for many.

If you want a graphical interface to GULP, look here:

http://gdis.sourceforge.net

Accelry's Materials Studio may also be used to setup GULP input files. These can then be transferred the Altix and submitted to LSF to run.

A script to run GULP can be found in the directory

/usr/local/apps/chemistry_scripts/gulp

If you have never used GULP, we direct you to the GULP web site:

http://www.ivec.org/gulp



April 4, 2008

Version 4.0 of POY has been installed on the SGI Altix 4700. POY is a program for phylogenetic analysis of DNA and other data using dynamic homology. The new executable is

/usr/local/apps/poy/mpoy_4.0


April 3, 2008

Version 4.3 of Materials Studio has been installed. The script to run the new version of DMol3 on the Altix 4700 can be found:

/usr/local/apps/chemistry_scripts/dmol3/prp_ms_43

Those interesed in installing the new Materials Studio interface on their PC should contact Lee Bartolotti.

Note: Version 4.3 of DMol3 is not available on the Origin 350.


March 25, 2008

The latest version of gamess has been installed. This is the March 2007 version.

/usr/local/apps/chemistry_scripts/gamess


November 8, 2007

Gaussian has been upgraded to Revision E.01. This release has some important new features. A description of the changes and additions can be found in the release notes. A script for running Gaussian on the Origin 350 can be found in the directory

/usr/local/apps/chemistry_scripts/gaussian


August 8, 2007

Version 4.2 of MaterialsStudio has been installed on the Altix 4700. The modules included are: DMol3, Discover, Amorphous Cell, and Castep. The new script to set up the DMol3 LSF job file can be found

/usr/local/apps/chemistry_scripts/dmol3/prp_ms_42

May 1, 2007

SGI announces the installation of a 128 processor SGI Altix 4700 high performance computer at East Carolina University. This computer was purchased, in part, from a grant from the National Science Foundation. Read the news article at the link below:

http://www.hpcwire.com/hpc/1546025.html

March 30, 2007

Licenses for the Accelrys Life and Material Sciences software Licenses has been installed. They are valid for one year. A complete listing of the available software can be found:

http://www.ecu.edu/cacs/frames_cacs/software.html

February 6, 2007

Installed AMBER version 9 on the ECU computers. Sample batch job files for running this version of AMBER can be found:

/usr/local/apps/chemistry_scripts/amber

February 5, 2007

Gamess 2006 has been installed on the ECU computers. Scripts for running gamess can be found in the directory

/usr/local/apps/chemistry_scripts/gamess

January 8, 2007

MaterialStudio 4.1 has been installed on the SGI Origin 350. This is also an upgrade of DMol3 with the following enhancements:

  • COSMO solvation model for periodic systems.
  • Unit cell optimization.
  • Support for larger (triple) basis sets.
  • Plotting of charge densities for periodic systems.
The script for running this version of DMol3 can be found:

/usr/local/apps/chemistry_scripts/dmol3/prp_ms_4

November 26, 2006

A new web tutorial has been added to the CACS web page. This tutorial provides instructions for using the Nudged Elastic Band method to calculate the minimum energy path of a chemical reaction. Using the associated extremals from the calculated reaction minimum energy path, thermodynamic and kinetic data are calculated for the various steps of the chemical reaction.

November 9, 2006

The electron localization function (ELF) program has been installed on zeus. Scripts for running ELF can be found

/usr/local/apps/chemistry_scripts/elf


October 26, 2006

NWChem has been upgraded to version 5.0. This release has some important new features. A script for running NWChem on the Origin 350 can be found in the directory

/usr/local/apps/chemistry_scripts/nwchem


Sept 28, 2006

The computational chemistry training classroom has been upgraded. The 14 SGI Octane II workstations have been replaced by 14 SGI Fuels. This upgrade will ensure that students at ECU continue to be trained with and exposed to the latest in computational tools. The 14 SGI Octane II have been moved to the 5th floor of the Science and Technology Bldg where we have established some student computer labs. Here they continue to be a resource for the student community.


Sept 1, 2006

The ECU HPC community has won its second NSF MRI (Prof Andy Sargent was the PI). This grant will be used to supplement the purchase a 1 teraflop high performance computer. This computer, along with our 32 processor SGI Origin 350, provides the HPC resources for leading edge research and exposes our students to state of the art computational tools.


March 24, 2006

A new version of MaterialsStudio DMol3 4.0 has been installed on zeus. Unfortunately, it requires a different set up than the old version, thus a new setup script is provided. You can find it:

/usr/local/apps/chemistry_scripts/dmol3/prp_ms_4


Feb 14, 2006

NWChem has been upgraded to version 4.7. This release has some important new features. A script for running NWChem on the Origin 350 can be found in the directory

/usr/local/apps/chemistry_scripts/nwchem


Dec 13, 2005

Gaussian has been upgraded to Revision D.01. This release has some important new features. A description of the changes and additions can be found in the release notes. A script for running Gaussian on the Origin 350 can be found in the directory

/usr/local/apps/chemistry_scripts/gaussian


Oct 4, 2005

SeqWeb has been installed on the SGI Origin 350. This is a web interface to the GCG software package. You must have an account on the SGI Origin 350 to use gcg and request a SeqWeb login. SeqWeb is accessed through your browser:

http://zeus.ecu.edu:8030


Aug 31, 2005

GCG software package is now installed on the SGI Origin 350. You must have an account on the Origin 350 to use GCG. To use the software type

source     /usr/local/apps/accelrys/dsgcg/gcgstartup
gcg
gcgsupport


Aug 17, 2005

A LeAP to Amber workshop was given. This workshop provided an introduction to the LeAP interface to the Amber molecular dynamics suite of computer software.


Aug 1, 2005

InsightII 2005 is now installed on the SGI Origin 350. To use the software type

source     /usr/local/apps/accelrys/cshrc
insightII


April 19, 2005

Cerius2 c410 installed on the SGI Origin 350. To use the cerius2 type

source     /usr/local/apps/accelrys/cshrc
/usr/local/apps/accelrys/cerius2/bin/cerius2


April 1, 2005

The number of Accelrys tokens have been increased to 49. This allows ECU to take full advantage of the expansion of the Origin 350.


Dec 16, 2004

The SGI Origin 350 has been upgraded to 32 processors, 32 GB of memory and 1 TB of disk space. Platform Computing's Load Sharing Facility (LSF) is used for scheduling and running all jobs. A LSF tutorial can be found:

http://www.star.bnl.gov/STAR/comp/train/using_lsf.html#Own


Sep 1, 2004

ECU has won a Major Research Instrumentation Grant from the National Science Foundation. This award will allow ECU to double the size of the existing SGI Origin 350. When upgraded, the new configuration of the SGI O350 will be 32 processors, 32 GB of memory and 1 TB of disk space. The Operating System is SGI IRIX (a version of UNIX). A UNIX tutorial can be found:

http://www.isu.edu/departments/comcom/unix/workshop/unixindex.html


June 24, 2004

Gaussian has been upgraded to Revision C.02. This release is mainly a bug fix. A description of the changes and additions can be found in the release notes.


May 2004

A new SGI Origin 350 computer has arrived at ECU. This computer has 16 processors, 16 GB of memory and 0.5 Terabyte of disk space. Also installed on the O350 is the Accelrys suite of software for the Life and Material Sciences. This gives the ECU community a powerful set of resources for exploring scientific problems through computation.


April 2004

A new web page has been established for the molecular viewer and builder "MolStart" written by Dr. Chentegh Lee. MolStart is a molecular viewer and editor written in Java. We are constantly improving the application to create a friendly graphical user interface to view and build molecular structures.