Your Federal Quarterly Tax Payments are due April 15th Get Help Now >>

PowerPoint Presentation by k966Xd

VIEWS: 0 PAGES: 13

									                                  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




SURA                                                       February 22-23, Washington D.C.
                  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.

SURA                                      February 22-23, Washington D.C.
               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.

SURA                                               February 22-23, Washington D.C.
       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.
SURA                                       February 22-23, Washington D.C.
       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




SURA                                    February 22-23, Washington D.C.
       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.

SURA                                  February 22-23, Washington D.C.
       Grid Enabling Applications for the
               Grid: ENDYNE
                                     z



                                             Hydrogen 2
                          Carbon 2

                                                 C2H2 Target
                     Carbon 1
                                         a
              d=15 a.u.                                        x

              Hydrogen 1                     [a, b] Orientation

                                     b                   p

                                             b


                                         H+ Projectile, Hydrogen 3
                            y




SURA                                                                 February 22-23, Washington D.C.
       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.
SURA                                    February 22-23, Washington D.C.
       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
SURA
       8. type "qstat" to see the job              February 22-23, Washington D.C.
         Grid enabling ENDYNE on a Cycle
                 Scavenging Grid
       • Had to remove environment dependencies
         (DYNROOT$).
       • Had to recompile ENDYNE for uniprocessor
         capabilities.
       • TEST recompiled program locally before moving it
         onto the grid!!!
       • Had to register libraries and necessary input files with
         the grid.
       • Had to teach researchers how to use TechGrid
         campus-wide grid.
       • Approx 3 hours of instruction with added
         documentation was necessary to get them on their
         feet.
SURA                                                 February 22-23, Washington D.C.
        Grid enabling ENDYNE on a Globus
                       Grid
       • If all sites wish to use ENDYNE, one way is to
         create an environment variable called
         DYNROOT$.
       • 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/adde
         pall/GRID/endyne gsiftp://buda.tacc.utexas.e
         du:2811/home/addepall/endyne

SURA                                         February 22-23, Washington D.C.
         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?

SURA                                 February 22-23, Washington D.C.
        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!
SURA                                       February 22-23, Washington D.C.

								
To top