application porting activities @ infn

EGEE-III INFSO-RI-222667

Enabling Grids for E-sciencE

www.eu-egee.org

EGEE and gLite are registered trademarks

Application Porting activities @ INFN

Giuseppe LA ROCCA

INFN [email protected]

EGEE’09 ConferenceBarcelona, 21-25 Sept 2009


EGEE-III INFSO-RI-222667 G. LA ROCCA – EGEE’09 Conference, 21-25 Sept 2009 - Barcelona

Porting the

Case study from



ASTRA (Ancient instrument Sound/Timbre Reconstruction Application)

Multi-disciplinary project involving archaeologists, musicians, physicists, computer scientists, engineers in an international distributed environment.

• The goal: taking archaeological findings of extinct musical instruments, and lets us play them again.• The idea: recreate a model of the musical instrument and produce the sound by simulating its behavior as a mechanical system.



Modeling and computation on the Grid

Computer

model

The Grid Network

Reconstructed sounds

Archaeological findings

Load the sounds on a piano keyboard and

play

30 sec. of audio sound => 90min. on Pentium @ 3.73Ghz, 2 GB RAM



Musica @ Fisica

• In June 2009, the concert "Musica @ Fisica", was organized by the Catania Division of the Italian National Institute of Nuclear Physics.

• This world premiere showcased the sounds of the Epigonion, an instrument of the past, reconstructed via computer-intensive modelling, being performed alongside real instruments such as baroque cello and percussions

Purcell’s “The Sparrow and the Gentle Dove”, (a reconstructed Epigonion played live with percussion and baroque cello) http://www.youtube.com/watch?v=mnEbtIQkJ-A



Porting

Case study from

VisualGRID with GENIUS: on-line video streaming for application

control & demonstration



Introduction

Several Grid applications produce as output graphical content such as images that can be collected and encoded as a unique video. This feature might be useful for both demonstration and job control job.

VisualGrid is a post-processing tool allowing to show, starting from a list of images sequence, the video output produced by a producer application (e.g. FLUENT).

Fig.: Some frames of the sequence produced by FLUENT and streamed by the VisualGrid tool.



VisualGRID’s workflow

64 cores for 14 CPU daysEnvironment protection



Porting

Case study from

“GROningen MAchine for Chemical Simulations”



GROMACS

• GROMACS is a package for performing molecular dynamics (MD) simulations. – It is widely used by the scientific community.

• MD simulations use Newton's laws of motion to estimate thermodynamic properties and collective motions of molecular systems– Many interesting molecular systems contain several thousands

of atoms: one needs great computational resources for state-of-the-art work

• GROMACS consists of more than 50 programs. They can be divided in 3 major classes:– Preparation of Input– Execution of Simulation (mdrum)– Analysis of Output

• Programs are command-line based, written mostly in C



GROMACS’ workflow

UIVOMS

Server

WMS

User

GROMACS software



Support the



Deployed MPI MrBayes @ UPM

The Submission

The Monitoring

The Visualization

https://ui.biruni.upm.my



INFN Grid Schoolfor site administrators and

applications porting



LocationInternational Center for Theoretical Physics (ICTP)InfoLAB, Adriatic GuesthouseVia Grignano, 934014 Triestewww.ictp.it

Event homepage(s)http://agenda.infn.it/conferenceDisplay.py?confId=723http://agenda.infn.it/conferenceDisplay.py?confId=725

Program webpage(s)http://agenda.infn.it/conferenceOtherViews.py?

view=standard&confId=723http://agenda.infn.it/conferenceOtherViews.py?

view=standard&confId=7235



T-Infrastructure description

• The following commercial sponsors made available some demo units of their servers:

– Sun Microsystems Italy provided us with two powerful 64bit multi-core servers, the Sun Fire X 4600 M2 with 32 cores each one: this unit is based on 8 Quad-Core AMD Opteron, 64 GB of memory, 4 x 146Gb SAS 15000 rpm disk drives;



T-Infrastructure description (cont.)

– E4 Company sent us two blades chassis with a total of 10 Quad-Core Intel Xeon blade servers (8 cores each server): each servers was provided with 16Gb of memory and 1 SAS disk drives of 73Gb;

– Dell Computers Italy made available 1 PowerEdge M1000e Blade Enclosure with 8 PowerEdge M600 blade servers featuring 2 Quad-Core Intel Xeon X5460, 8Gb of memory, 2 x 73Gb SAS 15000 rpm disk drives; additionally, one iSCSI SAN disk array, the EqualLogic PS5000, configured with a set of 8x 500Gb SAS 10000 rpm disk drives, has been sent by DELL.



T-Infrastructure description (cont.)

In summary, the local infrastructure provided a total of 208 cores and 6 TeraBytes of storage. To better exploit the available computational power, the natural choice was to take advantage of virtualization technologies, especially needed for the two 32-way Sun servers. At this purpose, it was adopted the software stack from VMware, in particular we used VMware Virtual Infrastructure 3 with ESX Server 3.5.



Training activities organization

• During the first week of the school the installation of the following gLite 3.1 services have been showed:

– User Interface;– Computing Element (LSF Based);– Worker Node (LSF Based);– Computing Element (Torque/Maui based);– Worker Node (Torque/Maui based);– Storage Element (DPM);– Storage Element (dCache);– Storage Element (StoRM);– MON Box;– AMGA Metadata Catalogue.

• In the last two days of the week, a complete grid testbed had to be properly installed and configured to be used on the following two weeks for the Application Porting School.



The selected applications

6 applications have been successfully ported on the local t-Infrastructures during the 2nd week of the school



Porting

Case study from

“Automatic Antenna Design”



Introduction

• The application aims at studying and development of a framework to speed up the design of television antennas.

– Basically, a typical television antennal can be considered composed by a set of cylinders displaced in the space and each cylinder can mathematically be modelled as a set of N lines in the space.

• The main goal of this problem is to detect analytically the best spatial arrangement of a television antenna to satisfies simulation requirements.

• The main software package is based on the Genetic Programming. It uses the ECJ (Evolutionary Computation in Java) library, which provide the basic functionalities to deal with the genetic programming, and the NEC2++ (Numerical Electromagnetic Code) software package written in C++ developed at Lawrence Livermore Laboratory to analyse the television aerials.



Introduction (cont.)

• The software can run in two different ways: stand-alone or master/slave.

In order to take advantages of the computational resources of the Grid and speed up the analysis and the detection of the solution for the problem, the master/slave modality has been chosen.

In this scenario the master is responsible to generate the population of candidate solutions, while the slave nodes, running on different WNs of a Grid, are in charge to evaluate a subset (proportional to Total population / N) of this population.

Each slave at start up opens a socket, based on TCP-connection, with the master node which is running on the UI. Once a connection is established with at least one slave, the master generates the population and then sub-divides the evaluation problems with all the registered slaves.



Performance

SINGLE PC:

•Core 2 Duo E6600 @ 2.4 Ghz•4 GB di RAM•Master-Slave configuration with 1 Slave

GRID:• 1 Master 20 Slaves

≈ 288hrs (12 days) ≈ 7hrs

…



Web interface

Job submission using via Java WMproxy API (ver. 3.1) + Cog jGlobus (ver. 1.4)

GSI support based on Java VOMS API included!



Web interface (cont.)

Job monitoring using via Java LBproxy API



Porting

Case study from

“SimTriplex Application”



Introduction

• This application simulates interactions among immune systems, tumor and tumor vaccine.

• The mammary carcinoma is one of the tumors which can have a genetic origin.

– A biologist group of the University of Bologna has found a vaccine for mammary carcinoma (Triplex Vaccine).

– The vaccine has been tested on genetic modified mice (HER-2/neu mice) which develop the mammary carcinoma.

– Each in vivo experiment takes at least one year and roughly 20 mice.




• An agent based model was built up to simulate the immune response induced by the vaccine.– The model reproduces the result of the in-vivo

experiments.

• Using the model as a virtual lab one can perform experiments on new vaccination schedules and heuristically find better ones.

• Finding a minimal/optimal vaccination schedule is a non trivial problem.– The application run on Linux systems, and has high

computational requirements, specially when selecting a large temporal range o an higher scale is simulated.




• The simulation is usable from a comfortable web interface where runs can be transparently submitted to different infrastructure.



Thank you for your attention!

application porting activities @ infn

Documents