February 22-23, Washington D.C.SURA

ENDyneSoftware for Dynamics of Electrons and Nuclei in

Molecules. Developed by Dr. Yngve Öhrn and Dr. Erik Deumens,

University of Florida. Presented by Jerry Perez

Texas Tech University

February 22-23, Washington D.C.SURA

ENDyne agenda

• What is the application? • Why it's important to grid-enable?• Description of the grid-enabling

that's been done so far.• Discussion/detailing of next steps

towards SURAgrid deployment• Steps to be undertaken on Day 2

or plans or beyond.

February 22-23, Washington D.C.SURA

What is the application?• ENDyne is an application that implements the

Electron Nuclear Dynamics (END) theory for studying the interaction between molecular geometry and electronic structure in a time-dependent and self-consistent way.

• The theory is somewhat unfamiliar to most people and the software is not very user friendly

• For that reason we do not make the code available to a general audience at this time.

• However, if someone is interested in the code, they can come and study with us for about a month and they get to take the code with them at the end. Please send e-mail to jorge.morales@ttu.edu for more information.

February 22-23, Washington D.C.SURA

Why it's important to grid-enable?

• The code we use is ENDyne 2.7 coded by Dr. Erik Deumens, University of Florida.

• A new code call CSTechG, having novel Coherent States applications, novel Dynamic Field Theory implementations and our Compute Grid implementations, is under development in the Morales group.

• ENDyne scales nicely with grids.• ENDyne requires many runs.

February 22-23, Washington D.C.SURA

Why it's important to grid-enable?

• Calculate electron transfer processes in large molecules of biological interest

• Simulate gas-phase molecular collisions

• Nanotechnology – Quantum Computing

February 22-23, Washington D.C.SURA

Description of the grid-enabling that's been done so far.

• Grid enabling has been done on campus grid level.

• Grid enabling has been tested using Condor.

• Grid enabling has been tested using Globus.

February 22-23, Washington D.C.SURA

Grid Enabling Applications for the Grid: ENDYNE

C2H2 TargetCarbon 1

Carbon 2

d=15 a.u.

b

p

x

z

H+ Projectile, Hydrogen 3

[] Orientation

y

Hydrogen 2

Hydrogen 1

February 22-23, Washington D.C.SURA

How does ENDYNE run on a cluster?

• A batch file was written for the ENDYNE users and stored in an environment variable called DYNROOT$

• The batch file that ran single processor jobs was called “endyne”.

• The batch file called “run” submits multiple ENDYNE jobs into the queue by reading multiple input files from the directory “run” is ran in.

February 22-23, Washington D.C.SURA

How does ENDYNE run on a cluster?

Before any jobs are submitted, the files must be prepared for running:

1. prepare the "endyne_H+HF_opt_pvdz.90-00.in"2. optimize the "endyne_H+HF_opt_pvdz.90-00.in"

by command "endyne endyne_H+HF_opt_pvdz.90-00.in > inin"

3. collect the zoca parameters by using collect.pe program and command "./collect.pe >outout"

4. prepare the "endyne_H+HF_run_pvdz.90-00.tmpl.in" and insert the zoca parameters from "outout" file

5. modify the "run" file to program path of input files6. modify the  endynejob file to handle output files7. type "./run" to submit the job8. type "qstat" to see the job

February 22-23, Washington D.C.SURA

Grid enabling ENDYNE on a Cycle Scavenging Grid

• Had to remove environment dependencies (DYNROOT$).

• Had to recompile ENDYNE for uniprocessor capabilities.

• TEST recompiled program locally before moving it onto the grid!!!

• Had to register libraries and necessary input files with the grid.

• Had to teach researchers how to use TechGrid campus-wide grid.

• Approx 3 hours of instruction with added documentation was necessary to get them on their feet.

February 22-23, Washington D.C.SURA

Grid enabling ENDYNE on a Globus Grid

• If all sites wish to use ENDYNE, one way is to create an environment variable called DYNROOT$.

• Another way to run ENDYNE is to do away with environmental dependencies and recompile for static execution.

• globus-url-copy -vb -p 20 –dbg gsiftp://antaeus.hpcc.ttu.edu:2811/home/addepall/GRID/endyne  gsiftp://buda.tacc.utexas.edu:2811/home/addepall/endyne

February 22-23, Washington D.C.SURA

Discussion/detailing of next steps towards SURAgrid

deployment

• Create accounts for ENDyne researchers on other SURAgrid machines.

• Jobs are ready to run.• Which machines in SURA are cross

certified?• How many CPU’s are available?

February 22-23, Washington D.C.SURA

Steps to be undertaken on Day 2 or plans or beyond.

• Create certificates for Dr. Maiti and Dr. Yan of Texas Tech.

• Create accounts.• Transfer input files. • Create scripts and instructions for

new grid users.• ENDyne creates about 1.5 Gigs of

output per run. We need to run thousands!