implementation of the abc quantum mechanical reactive scattering program on the egee grid platform...
TRANSCRIPT
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
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
3A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 15-18 September 2008
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
4A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 15-18 September 2008
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
5A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 15-18 September 2008
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
6A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 15-18 September 2008
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
7A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 15-18 September 2008
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
================================================================
8A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 15-18 September 2008
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
==================================================================
9A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 15-18 September 2008
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
*************************************************************
10A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 15-18 September 2008
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
===============================================================
=
11A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 15-18 September 2008
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
12A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 15-18 September 2008
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
13A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 15-18 September 2008
P-GRADE Grid Portal 2.7
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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
15A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 15-18 September 2008
ABC workflow: modify input parameters
Double Click on
Generator
16A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 15-18 September 2008
ABC workflow: modify input parameters
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.
17A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 15-18 September 2008
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 input parameters
18A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 15-18 September 2008
ABC workflow: modify Grid parameters
Double Click on directory
name
19A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 15-18 September 2008
ABC workflow: modify Grid parameters
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
20A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 15-18 September 2008
ABC workflow: modify Grid parameters
Double Click on Executor
21A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 15-18 September 2008
ABC workflow: modify Grid parameters
22A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 15-18 September 2008
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)
23A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 15-18 September 2008
ABC workflow: modify Grid parameters
Double Click on file name
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Directory path and file name of the output files stored on the SE
ABC workflow: modify Grid parameters
25A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 15-18 September 2008
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
26A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 15-18 September 2008
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
27A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 15-18 September 2008
Workflow selection
Job selection
ABC Reaction ProbabilitiesGraph
P-GRADE Portlet: ABC
28A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 15-18 September 2008
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
29A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 15-18 September 2008
30A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 15-18 September 2008
Directory path for the STDOUT and STDERROR files
ABC workflow: modify Grid parameters
31A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 15-18 September 2008
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
32A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 15-18 September 2008
Technical University of Wien (AT)
Johannes Froehlich
E-Learning
Web Services
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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).
34A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 15-18 September 2008
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 )
35A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 15-18 September 2008
http://compchem.unipg.it
36A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 15-18 September 2008
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
37A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 15-18 September 2008
Jobs submitted per week
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Hours of CPU per week
39A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 15-18 September 2008
40A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 15-18 September 2008
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.
41A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 15-18 September 2008
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
42A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 15-18 September 2008
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