VisIVO: data VisIVO: data visualization on the gridvisualization on the grid

Scientific Multidimensional Data Scientific Multidimensional Data ExplorationExploration

4th EGEE User Forum/OGF 25 and OGF Europe's 2nd International Event 2-6 March 2009Catania

Ugo Becciani, A. Costa, G. Caniglia, C. Gheller

M. Comparato, P. Massimino, M. Krokos, L. Zef Han

--fformat votable /home/user/demo/vizier.xml.....--x x --y y --z z --color --colortable --colorscalar scalar0 --glyphs sphere

VisIVODesktop

VisIVOServerVisIVOWeb

Closely integrated, complementary and independent !

Pc GNU/Linux

Grid environment

Interactive fast navigation

VisIVO Desktop VisIVO desktop is a visualisation package developed in collaboration

between INAF (Catania Astrophysical Observatory), CINECA (the largest Italian academic supercomputing center) and University of Portsmouth, with the specific object of supporting visualisation and analysis of astrophysical data. It was developed in the Italian participation in the VO-TECH project.

• Free Software

• Cross Platform: MacOSX Windows and Linux (Ubuntu , Debian, Fedora),

• N-Dim (>3) Visualization of Astrophysical data (lut and glyphs =>

scalar properties of each element)

• Point, Volume and Vector Visualization

• Astrophysical Data Analysis

• VO (Virtual Observatory) compliance (Interoperability: VOT,

PLASTIC,VizieR)

• Easy to use: intuitive menu drives the user.

➲ Input file formats

Ascii, CSV Binary HDF5 FITS Gadget VOTable

Uniform management

All internal data are represented like a table, a sequence of float values (VisIVO Binary Table - VBT)

VisIVO Desktop

Visualisations Navigation -- Zoom -- Lookup table -- Algorithms -- Data selection -- Picker op. --

Interoperability

LODLevel Of Detail: while interacting with the visualized data (i.e.

zooming and rotating) a simplified graphical representation is used in order to keep the manipulation interactive

Data manipulation New Fields can be created as

mathematical functions of existing fields

Tables can be merged

Subsets can be extracted using different sampling techniques

Vectors

Vector Fields can be created from a VBT selecting any loaded fields as its three components

VisIVO Server on the Grid Non-interactive command line application that implements

visualisation functionalities; its output is a static 2D image of a 3D object

Easy integration in Virtual Observatory complaint Web Services and in the Grid environment

It will provide the user with a 3D preview of huge data exploiting the powerful facilities of the Grid environment

Easy to use

Open Source code: project maintained on sourceforge. NO LIMIT on data size !

VisIVO ServerBasic Architecture

TVO XML Document

Local or Remote (http ref) User Data

VBT: VisIVO Binary TableVBT: VisIVO Binary Table

New VBTNew VBT

VisIVO ImporterInput: Local or Remote file: ASCII-CSV, Binary, VOTable, FLY, Gadget, TVO XML Document , Fits Table, HDF5

Op: Data format conversion: VBTs creation

Output: VBTs (optimised for VisIVO Filters and Viewer).

NOTE: No limit on data dimension for input data

float616777216littleXYZVx...

float616777216littleXYZVx...

VBT: VisIVO Binary Table Ascii Header (.bin.head):contains basic metadata information.

Internal data rappresentation: floatNumber of fieldsNumber of elements of each field (including mesh data for volumes)Data format identifier: little endianList of field names

VisIVO Server

Binary File (.bin):a sequence of binary arrays (fields).

VisIVO Importer VisIVOImporter  --fformat filetype  [--out name] [--volume] [--compx X --compy Y --compz Z] [--sizex DX --sizey DY --sizez DZ] [--bigendian] [--double] [--npoints N] filename

--fformat specifies the input file data format--out [name] (optional) output filename. Default name VisIVOServerBinary.bin--volume (optional) used to create a table that contains Volume data--compx [double] --compy [double] --compz [double] (optional)  If data is a Volume the user must enter the mesh geometry. If data size fits a cubic mesh these valuesare automatically computed.

--sizex [double] --sizey [double] --sizez [double] (optional). Cell geometry  Default values 1.0 1.0 1.0

--bigendian (optional) Used only for big Endian Gadget and FLY input  file. Default files are little Endian.

--double (optional) Used only for double data of FLY input  file. Default value is float--npoints (optional) Used only for  FLY input  file. Number of data points.

VisIVO FiltersInput: A VBT data file

Op: It creates a new VBT or gives info on specified fields

Output: a new VBT or other info

NOTE: it must be applied to visualise huge data

General Syntax:

VisIVOFilters --op filterOpCode <options> InputFile (VBT file)

VisIVO FiltersAppend Tables: Creates a new table appending data from a list of existing tables Coarse Volume: Produces a coarsed subvolume with plane extraction from the original volumeDecimator: Creates a subtable as a regular subsample from the input table.Extract Subregion: Creates a new table from an input table: sub-box or sphere extraction.Extract Subvolume: Produces a table which represents a subvolume from the original volumeMath. Operations: Create a new field in a data table as the result of a mathematical operation between existing fieldsMerge Tables: Create a new table from two or more existing data tablesPoint Distribution: Creates a volume using a field distribution (CIC algorithm) on a regular mesh

Point Property: Assigns a property using a field distributionRandomizer: Creates a random subset from the original data tableSelect Fields: Creates a new table using one or more fields of a data table Select Rows: Creates a new table using limits  on one or more fields of a data table Show Table: Produces an ASCII table of selected fields Statistic: Creates and plots an histogram of a scalar field in the table

VisIVO ViewerVisIVO Viewer is a command line application that produces

3D images from the binary internal data format table (VBT)

The user must specify three fields of the table for 3D representation.

The user can also specifiy the following main options:- Camera position (azimuth and elevation)- Zoom level- Transparency / Opacity- Point shape (pixel/sphere, cube, cone etc..)- Lookup table- ..........

VisIVO ViewerGeneral Syntax

VisIVOViewer <options> inputFile (VBT file)

--volume (for volume representation)

Input: A VBT data file

Op: It creates one or more view of data

Output: png files

LIMITS: the input VBT data file must fit the available RAM

- Default Output: 4 Images:

- Az=0 - Elev=0- Az=90 - Elev=0- Az=0 - Elev=90- Az=45 -Elev=45

VisIVO Viewer

Customized Image fixing: Az, Elev, Transparency....

Cometa Consortium

COnsorzio Multi Ente per la promozione e

l'adozione di Tecnologie di calcolo Avanzato

PI2S2 Project

Funded by the Italian MUR using EU funds for Objective 1

The Sicilian Grid in one slide

Available computing and storage resources 1. ~2500 cores AMD Opteron 22182. 2 GB RAM per core 3. LSF as LRMS everywhere4. Infiniband-4X at all sites

1. 200+ TB of raw disk storage 2. Distributed/parallel GPFS filesystem

gLite 3.0 middleware everywhere

PI2S2 infrastructure and HPC

• Each PI2S2 site has a low latency Infiniband network

• Intel fortran and PGI compilers are available

UI “on-board”: share all resources with the WNs available remote login it is possible to compile and test codes

HPC RUN

A special hpc queue is available. It allows the CPU core reservation

It is possible to use ALL nodes of a PI2S2 site (more than 200 CPU cores)

• PI2S2 Grid infrastructure supports the following MPI versions

PI2S2 infrastructure and HPC

each MPI version has been built with different compilers. The supported tags are :

MVAPICH_GCC4 MVAPICH_INTEL9 MVAPICH_PGI706

MVAPICH2_GCC4 MVAPICH2_INTEL9 MVAPICH2_PGI706

MPICH_GCC4 MPICH_INTEL9 MPICH_PGI706

o MPICH_SH_GCC4 o MPICH_SH_INTEL9 o MPICH_SH_PGI706

MPICH2_GCC4 MPICH2_INTEL9 MPICH2_PGI706

Running Using Gigabit Network

Running Using Inifiband 4x Network

Type = "Job";

JobType = "MVAPICH2";

Executable = “MPIparallel_exec”;

NodeNumber = 200;

Arguments = “arg1 arg2 arg3";

StdOutput = "test.out";

StdError = "test.err";

InputSandbox = {“mpi.pre.sh”,“mpi.post.sh”,

“MPIparallel_exec”, “watchdog.sh”};

OutputSandbox = {“test.err”, “test.out” }

PI2S2 infrastructure and HPC

Pre e Post Processing Scripts

Pre e Post Processing Scripts

ExecutableExecutable

It runs during the parallel executionIt runs during the parallel execution

VisIVOServer

HPC and Visualisation on the Grid

- Can be executed on the Grid

- Produces images (on the grid Catalog)

- Visualisation of large dataset during the data production phase

Data Image, obtained with VisIVO Server, of a cosmological half-billion bodies simulation, running since January 9th on the Cometa Grid

Independent job

Sub-process of the watchdog procedure

VisIVOWeb

http://visivoserver.oact.inaf.it

VisIVOWeb

Ugo BeccianiPrincipal InvestigatorAstrophysical Observatory Catania Italy

Mel KrokosCo-Principal InvestigatorUniversity of Portsmouth UK

Claudio Gheller Co-Principal InvestigatorCineca Bologna Italy

Gabriella Caniglia Software Developer Astrophysical Observatory Catania Italy

Marco Comparato Software Manager/Developer Astrophysical Observatory Catania Italy

Alessandro Costa Web Services & TVO Astrophysical Observatory Catania Italy

Zef Han J.Software developerUniversity of Portsmouth UK

Pietro MassiminoWeb developerAstrophysical Observatory Catania Italy

http://visivo.oact.inaf.it

http://visivoserver.oact.inaf.it

Thanks!