Implementation of the ABC Quantum Mechanical Reactive Scattering Program on the EGEE Grid Platform...

Implementation of the ABC Quantum

Mechanical Reactive Scattering Program on

the EGEE Grid Platform

Alessandro Costantini1, Dimitrios Skouteris1, Osvaldo Gervasi1, Antonio Lagana1,

Gergely Sipos2, Akos Balasko2, Peter Kacsuk2,

Aurelio Rodriguez3, Eduardo Gutierrez3, Andres Gomez3

1 University of Perugia, Perugia, Italy2 MTA SZTAKI, Budapest, Hungary

3 CESGA, Santiago de Compostela, Spain

[email protected]

GRID TutorialTrieste, Italy

15-18 September 2008

2A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 15-18 September 2008

Summary

ABC reactive scattering code: computational aspects

Gridification and submission:

– CLI on a UI machine

Services and web visualization tools for ABC code

– P-GRADE Grid Portal

Conclusions


ABC code

Significant Memory demands (>1GB)

Large request of CPU time (2 days for a set of 30 E)

Each simulation is independent from the other

– Must be executed several times for different sets of input parameters (parameter study job)

Executed via the classical command line interface


Prepare for Gridification

Very easy Gridification

-Right libraries (Blas, Lapack, libg2c)

-Right compiler (ifort, g95)

-Right option for compiler (-static, -Bstatic, -static-libcxa)

[alex@ui:~/ABC]$ ldd abc

not a dynamic executable

Executable: 1.5MB


Prepare JDL file

Type = "Job";

JobType = "Normal";

Executable = "abc.sh";

StdOutput = "std.out";

StdError = "std.err";

InputSandbox = {"abc.sh","abc","clhd.d","BW.3p","SW.2p","SW.3p"};

OutputSandbox = {"std.out","std.err","abc.out","clhd.d"};

alex@ui:~/ABC$ cat abc.sh

#!/bin/bash

EXE=abc

date

echo

"*********************************"

echo "Executing $EXE"

chmod 755 $EXE

ls -l

time ./$EXE < clhd.d > abc.out

echo

"*********************************"

echo "List directory after Executing"

ls -l

date

exit 0


Step I: VOMS Proxy

Create a valid VOMS proxy:

alex@ui:~$ glite-voms-proxy-init -voms compchem

Your identity: /C=IT/O=INFN/OU=Personal Certificate/L=University of Perugia Dept

Maths and CompSci/CN=Alessandro Costantini

Cannot find file or dir: /home/alex/.glite/vomses

Creating temporary proxy ................................................................... Done

Contacting voms.cnaf.infn.it:15003

[/C=IT/O=INFN/OU=Host/L=CNAF/CN=voms.cnaf.infn.it]

"compchem" Done

Creating proxy ................................................................................... Done

Your proxy is valid until Tue Oct 9 00:56:49 2007


Step II: Delegation

Delegate your proxy to the WMProxy service:

alex@ui:~$ glite-wms-job-delegate-proxy –d delID1234

Connecting to the service https://gliterb00.cnaf.infn.it:7443/glite_wms_wmproxy_server

================== glite-wms-job-delegate-proxy Success ==================

Your proxy has been successfully delegated to the WMProxy:

https://gliterb00.cnaf.infn.it:7443/glite_wms_wmproxy_server

with the delegation identifier: delID1234

================================================================


Step III: Submission

Submit a job to the WMProxy:

alex@ui:~$ glite-wms-job-submit –d delID1234 –o idjob test.jdl

Connecting to the service https://gliterb00.cnaf.infn.it:7443/glite_wms_wmproxy_server

====================== glite-wms-job-submit Success ======================

The job has been successfully submitted to the WMProxy

Your job identifier is:

https://gliterb00.cnaf.infn.it:9000/wJbzJtuHdkLXNbIxmLV0Uw

The job identifier has been saved in the following file:

/home/alex/idjob

==================================================================


Step IV: Monitoring

Monitor the status of the job:

alex@ui:~$ glite-wms-job-status –i idjob

*************************************************************

BOOKKEEPING INFORMATION:

Status info for the Job : https://gliterb00.cnaf.infn.it:9000/wJbzJtuHdkLXNbIxmLV0Uw

Current Status: Running

Status Reason: Job successfully submitted to Globus

Destination: ce.grid.unipg.it:2119/jobmanagerlcgpbsshort

Submitted: Mon Oct 8 13:03:57 2007 CEST

*************************************************************


Step V: Collect the output

Retrieve the output:

alex@ui:~$ glite-wms-job-output --dir /home/alex/test –i idjob

===============================================================

JOB GET OUTPUT OUTCOME

Output sandbox files for the job:

https://gliterb00.cnaf.infn.it:9000/wJbzJtuHdkLXNbIxmLV0Uw

have been successfully retrieved and stored in the directory:

/home/alex/test

===============================================================

=


The Gridification of the ABC code

The porting has been carried out using the P-GRADE Grid Portal 2.7 implemented in COMPCHEM

– Open source tool (based on GridSphere)– Provides intuitive graphical interface for porting– Collect Grid resources– Observe and supervise the execution


The Gridification of the ABC code

P-GRADE Grid Portal 2.7

– The generic application structure is a workflow– Define parameter study application– Specific graphical web tools can be added:

Portlets– Does not require the modification of the original

code for execution


P-GRADE Grid Portal 2.7


Executor: executed as many times in parallel as many parameters are generated by

“Generator”Collector: collects all

output files into a single TAR file

Generator: generates input files with different parameters

ABC workflow: explanation of job flow


ABC workflow: modify input parameters

Double Click on

Generator



Hitting on a key opens the value

definition window for that key. Template text with keys. Keys

will be replaced with actual numbers by the Generator during the execution of the workflow.

All the possible combinations of the replaced template are written into separate files.

Generator job is a macro processor that generates text files by replacing keys with actual values in a template which is defined by the user.

In the current workflow p_1 parameter defines values for “jmax” and p_2 defines values for “rmax” parameters of

ABC.


In this form you can define actual values for the selected

parameter.

Using this frame the user can modify the range for each variable in order to

define larger parameter sets.



ABC workflow: modify Grid parameters

Double Click on directory

name



Path syntax is (EGEE): /grid/VONAME/YourUsernameInVO/custom_dir

You must change ABC_AGEN_files10 to any other directory name to avoid data-rewrite on the grid



Double Click on Executor




ABC workflow: input and output files

The result of the parallel ABC simulation jobs are files that are saved on the Storage Elements. The files are

registered in the File Catalog with Logical File Names.

Input files that are the same for every execution of the ABC simulation (ABC binary executable, PESs)



Double Click on file name


Directory path and file name of the output files stored on the SE



ABC job status

The User can download the output files coming from the calculations

Status of each job in the Executor

Status of the submitted workflow

Status of the Collector

Status of the Generator


Added value on P-GRADE (Prototype)

Prototypical visualization tool has been implemented on

P-GRADE using Portlet

– UI components managed and displayed in a web

portal

2D-Graph rendering of the Reaction Probabilities of a

selected output file for the ABC code

Reaction Probabilities Rendering


Workflow selection

Job selection

ABC Reaction ProbabilitiesGraph

P-GRADE Portlet: ABC


Conclusions

Gridification can be a very easy process (it depends on the complexity of your application)

Job submission

• CLI (flexible)

• Web-Portals (P-GRADE)

•-user-friendly interfaces

The ABC workflow can be improved and exported to other applications



Directory path for the STDOUT and STDERROR files



The Molecular Science community and the Grid

The Grid environment allows us to carry out simulation of molecular systems increasing the quality and the quantity of properties investigated

The researcher is able to perform computational campaign:– Massive submission of sequential jobs running on

different input datasets

– Submission of parallel jobs running on huge pool of nodes

Offers efficient data management facilities– Storage of large amount of data


Technical University of Wien (AT)

Johannes Froehlich

E-Learning

Web Services


Molecular Virtual Reality

The use of Molecular Virtual Reality (Visualization + Virtual Reality techniques applied at the nanometer level) helps the researchers to better understand the molecular processes

We have implemented some virtual monitors of GEMS creating Virtual Worlds based on atoms positions saved during the trajectory calculations (MVR animations)

A Virtual World may be created also from a static description of the system in the initial or in the final configuration (mol2, PDB, etc).


CompChem VO in EGEE III

In EGEE the Computational Chemistry community is represented by two VO’s:– CompChem VO (public domain, shareware software,

managed by University of Perugia, Italy)– GAUSSIAN VO (commercial software, managed by

Cyfronet, PL) A Center of Excellence grouping the labs of both

VOs will be established in EGEE III We participated to

– the MPI working group to promote the use of MPI and parallel software in EGEE (EGEE/int.eu.grid MPI international workshop, Dublin, Dec 11th-12th, 2006)

– the User Support working group to promote and improve the User Support systems available in EGEE (EGEE Workshop for VO’s,

Karlshrue, Germany, March 1st-2nd, 2007 )


http://compchem.unipg.it


The CompChem users

Organization User Contact email

University of Barcelona Margarita Alberti maw <at> qf .ub.es

University of the Basque Country Ernesto Garcia qfpgapae <at> vc.ehu.es

University of PerugiaDimitris Skouteris. Leonardo

Arteconi, Alessandro Costantini

{dimitris, bodynet, alex} <at>

dyn.unipg.it

Cyf ronet, Poland Mariusz Sterzel m.sterzel <at> cyf ronet.pl

I MI P- I talian National Research Council Domenico Bruno d.bruno <at> area.ba.cnr.it

CESGA, Spain J avier Lopez j lopez <at> cesga.es

University of Vienna Matthias Ruckenbauer hans.lischka <at> univie.ac.at

UCY, Cyprus Constantinos Zeinalipour-Yazdi

ENEA, I taly Carlo Scio

chf .vu Gintaras Urbelis

pdc.kth.se Olav Vatras @ pdc.kth.se

University of Crete Stavros C Farantos f arantos <at> iesl.f orth.gr


Jobs submitted per week


Hours of CPU per week



ABC workflow: explanation of job flow

Represent the input files that are the same for every execution of the ABC simulation (ABC binary executable,

PESs)

The result of the parallel ABC simulation jobs are files that are saved on the Storage Elements. The files are

registered in the File Catalog with Logical File Names.

Represent the compressed output files (abc.outs)

Represents the input files that differ for the ABC

simulations.


ABC code

Quantum mechanical atom-diatom reactive scattering program

– Carries out accurate calculations of the quantum S matrix elements

– Evaluates reaction probabilities as well as state to state integral and differential cross sections


ABC code II

The program integrates the Schrödinger equation using:

– Delves hyperspherical coordinates

– A coupled channel method

– A time independent technique to integrate the atom-diatom nuclear Schrödinger eq.

[Ĥ-E] ψ = 0

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Implementation of the ABC Quantum Mechanical Reactive Scattering Program on the EGEE Grid Platform...

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