Implementation of the ABC Quantum Mechanical Reactive Scattering Program on the EGEE Grid Platform Alessandro Costantini 1, Dimitrios Skouteris 1, Osvaldo Gervasi 1, Antonio Lagana 1, Gergely Sipos 2, Akos Balasko 2, Peter Kacsuk 2, Aurelio Rodriguez 3, Eduardo Gutierrez 3, Andres Gomez 3 1 University of Perugia, Perugia, Italy 2 MTA SZTAKI, Budapest, Hungary 3 CESGA, Santiago de Compostela, Spain GRID Tutorial Trieste, Italy September 2008

2 A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 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

3 A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 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

4 A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 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) ldd abc not a dynamic executable  Executable: 1.5MB

5 A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 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"}; cat abc.sh #!/bin/bash EXE=abc date echo "*********************************" echo "Executing $EXE" chmod 755 $EXE ls -l time./$EXE abc.out echo "*********************************" echo "List directory after Executing" ls -l date exit 0

6 A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) September 2008 Step I: VOMS Proxy Create a valid VOMS proxy: 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:

7 A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) September 2008 Step II: Delegation Delegate your proxy to the WMProxy service: glite-wms-job-delegate-proxy –d delID1234 Connecting to the service ================== glite-wms-job-delegate-proxy Success ================== Your proxy has been successfully delegated to the WMProxy: with the delegation identifier: delID1234 ================================================================

8 A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) September 2008 Step III: Submission Submit a job to the WMProxy: glite-wms-job-submit –d delID1234 –o idjob test.jdl Connecting to the service ====================== glite-wms-job-submit Success ====================== The job has been successfully submitted to the WMProxy Your job identifier is: The job identifier has been saved in the following file: /home/alex/idjob ==================================================================

9 A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) September 2008 Step IV: Monitoring Monitor the status of the job: glite-wms-job-status –i idjob ************************************************************* BOOKKEEPING INFORMATION: Status info for the Job : Current Status: Running Status Reason: Job successfully submitted to Globus Destination: ce.grid.unipg.it:2119/jobmanagerlcgpbsshort Submitted: Mon Oct 8 13:03: CEST *************************************************************

10 A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) September 2008 Step V: Collect the output Retrieve the output: glite-wms-job-output --dir /home/alex/test –i idjob =============================================================== JOB GET OUTPUT OUTCOME Output sandbox files for the job: have been successfully retrieved and stored in the directory: /home/alex/test ================================================================

11 A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 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

12 A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 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

13 A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) September 2008 P-GRADE Grid Portal 2.7

14 A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) September 2008 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

15 A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) September 2008 ABC workflow: modify input parameters Double Click on Generator

16 A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 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.

17 A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 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

18 A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) September 2008 ABC workflow: modify Grid parameters Double Click on directory name

19 A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 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

20 A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) September 2008 ABC workflow: modify Grid parameters Double Click on Executor

21 A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) September 2008 ABC workflow: modify Grid parameters

22 A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 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)

23 A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) September 2008 ABC workflow: modify Grid parameters Double Click on file name

24 A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) September 2008 Directory path and file name of the output files stored on the SE ABC workflow: modify Grid parameters

25 A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 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

26 A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 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

27 A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) September 2008 Workflow selection Job selection ABC Reaction Probabilities Graph P-GRADE Portlet: ABC

28 A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 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

29 A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) September 2008

30 A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) September 2008 Directory path for the STDOUT and STDERROR files ABC workflow: modify Grid parameters

31 A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 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

32 A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) September 2008 Technical University of Wien (AT) Johannes Froehlich E-Learning Web Services

33 A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) September 2008 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).

34 A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 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 )

35 A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) September

36 A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) September 2008 The CompChem users

37 A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) September 2008 Jobs submitted per week

38 A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) September 2008 Hours of CPU per week

39 A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) September 2008

40 A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 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.

41 A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 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

42 A.Costantini, A.Laganà et al. GRID Tutorial, Trieste (Italy) 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