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ENDyne Software 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. ENDyne agenda. What is the application? Why it's important to grid-enable?

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ENDyne

Software 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


Endyne agenda
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.


What is the application
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 [email protected] for more information.


Why it s important to grid enable
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.


Why it s important to grid enable1
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


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


Grid enabling applications for the grid endyne
Grid Enabling Applications for the Grid: ENDYNE

z

Hydrogen 2

Carbon 2

C2H2 Target

Carbon 1

a

x

d=15 a.u.

[a, b] Orientation

Hydrogen 1

b

p

b

H+ Projectile, Hydrogen 3

y


How does endyne run on a cluster
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.


How does endyne run on a cluster1
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 files

6. modify the  endynejob file to handle output files

7. type "./run" to submit the job

8. type "qstat" to see the job


Grid enabling endyne on a cycle scavenging grid
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.


Grid enabling endyne on a globus grid
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


Discussion detailing of next steps towards suragrid deployment
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?


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

  • 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!


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