VisIVO Science Gateway User Manual - VisIVO Gateway
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1. Shape Pixel Scale Shape View Azimuth 0 Elevation 0 Zoom 1 FRONT LEFT RIGHT DOWN UP BACK Change Azimuth and Elevation values using your mouse to drag the 3 d cube To zoom in and out hold the shift button and again drag the model Azimuth Elevation Zoom Position and zoom factor of the camera The camera position Azimuth 0 Elevation 0 is looking the box from the top i e the last z plane Scale The axes are scaled To be checked for not uniform system coordinates Basic Palette Check the box to choice a pre defined palette color table Color Table Color Scalar Table The Palette is associated to a field of a table Log Scale Applies a logarithmic scale for the palette Advanced Palette Check the box to create or to upload a customized color palette Palette Range Set the limits for the palette color range Default values are the minimum and maximum value of the Color Scalar Table field Opacity Assign an opacity factor to the displayed elements from 0 0 to 1 0 It is suggested to use a low opacity factor when many data points are requested to be displayed Shape Points are displayed as Pixel Others geometrical forms can be requested In this case the Radius and Height values could be requested Shape is ignored for more than 1000 points to be displayed Scale Shapes If geometrical forms are requested the radius and height may be scaled with a field of the table Radius Scalar and2. Rho Rho New Table Submit The following filter operations are available Add Identifier adds a column tag to a table This filter adds a new column with a sequence of Ids in the input data table Default start value is 0 Only an int value can be given Column name of the new id column should be given Default name is Id Append Tables creates e new table appending data from a list of existing tables Append Filter can append up to 100 tables with the same number of Columns The column names are copied from the first table An error is given if tables contain different numbers of columns Cartesian2polar creates three new fields as the result of the polar transformation This operation creates three new fields in a data table as the result of the spherical polar transformation of three existing fields Column name of the new fields should be given Default names are rho theta and phi Coarse Volume produces a coarse sub volume with plane extraction from the original volume A percentage from 0 0 to 100 0 sub volume will be produced Default value produces a sub volume that could be directly uploaded and visualized with VislVOViewer List of columns contained in the original file should be given Default all columns will be extracted A sub volume with new resolution will be produced No default is given This parameter is ignored if percentage option is given Cut sets to a given threshold column values included in a
3. Image Id 397 Image Id 398 Image Id 399 Select Select Select Select Select Select Select Azimuth 0 Azimuth 31 Azimuth 0 Azimuth 0 Azimuth 0 Azimuth 0 Azimuth 0 Elevation 0 Elevation 12 Elevation 0 Elevation 0 Elevation 0 Elevation 0 Elevation 0 Zoom 1 Zoom 1 000 Zoom 1 Zoom 1 Zoom 1 Zoom 1 Zoom 1 Submit Dynamic Movies can be created by interpolating several steps of a time evolution of a cosmological dataset The user can browse a cosmological time evolution and choose two or more coherent datasets The designed workflow will then produce the necessary number of intermediate VBTs by calculating particle positions and applying boundary conditions as necessary This approach can be very useful e g in revealing galaxy formation or large scale structures such as galaxy clusters 23 VISIVO The creation of a movie represents a significant challenge for the underlying computational resources as often hundreds or thousands high quality images must be produced For this reason Parameter Sweep PS workflows are employed PS workflows are executed in distributed parallel computations The gUSE WS PGRADE infrastructure supports special ports generator and collector ports which enables the PS elaboration of a workflow a single set of input files containing more than one element associated by a port or several input ports having this feature may trigger the proper number of submissions of the associa
4. and exploration of astrophysical datasets within a collaborative visualization environment 2 1 WS PGrade gUSE WS PGRADE gUSE provides a collaborative community oriented application development environment where developers and end users can share layered and parameter sweep enabled workflows workflow graphs workflow templates and ready to run workflow applications via a repository It is integrated with the popular portal framework Liferay which is highly customizable thanks to the adoption of the portlet technology defined in the Java Specification Request JSR 168 and 286 and it is compatible with the most modern web applications gUSE is a virtualization environment providing a large set of high level Distributed Computing Infrastructures DCI services by which interoperation among classical service and desktop grids clouds and clusters unique web services and user communities can be achieved in a scalable way Internally gUSE is implemented as set of Web services which dynamically provide user services in DCI and or Web services environments WS PGRADE uses the client APIs of gUSE services to turn user requests into sequences of gUSE specific Web service calls WS PGRADE hides the communication protocols and sequences behind portlets and its GUI can be accessed via Web browsers Please refer to WS PGRADE gUSE web page and sourceforge project for a detailed users guide The tools to create configure and submit workflows are ava
5. by VisIVO Filters for data processing and the VisIVO Viewer for display The conversion is independent of data dimensionality VislVO Importer VislWO Filters VislVO Viewer BINARY A BINARY file called filename bin that is just a sequence of values n1 n2 values in the example all X values all Y values and so on Note n1 represents the number ofcolumns filed in the data table Es n1 8 nz represents the number of elemnts of each fileld Es n2 262144 A Z optional represent the number of cells in each dimension of the mesh size used only for Volumes Es X Y 2 84 64 64 DX DY DZ optional represent the real unit of each cell used only for Volumes Es DX DY DZ 0 1 1 0 2 0 Select the type of your input data Set parameter of your simulation Select a File to Upload Ascii Csv VoTable EEN T Remote Binary Fly Fits Gadget HO Raw Bin Table Select Header File Volume Number of Computational Cells surface bin head File uploaded ee Select File surface bin Cell Sizes AS dim Submit The following file formats can be imported ASCII files are expected to be in tabular form An ASCII file may contain values for N variables organized in columns The columns are typically separated by whitespace characters e g spaces or tabs The first row of an ASCII file lists the N variables names explicitly CSV is a delimited data format that has fields columns separated by the comma character and records rows
6. for inspection 2 http www erflow eu 27 SP ISIXQ users Guide Muon Portal Workflow ba x Select the Muon Portal simulation files to Upload Local Upload Remote Upload Select data Select the visualization parameters The Figure above shows the most recent development and results of the entire computational process starting from a parameter setting through the supplied portlet then b submitting the implemented workflow and finally C outputting resulting images obtained using isosurface rendering for the filtered top image and raw bottom image datasets respectively 6 2 LaSMoG The acceleration of the Universe is one of the most challenging problems in cosmology In the framework of general relativity GR the acceleration originates from dark energy However to explain the current acceleration of the Universe the required value of dark energy must be incredibly small Recently efforts have been made to construct models for modified gravity i e without introducing dark energy as an alternative to dark energy models Observing the large scale structure of the universe could in principle provide new test of GR on cosmic scales This kind of test cannot be done without the help of simulations as the structure formation process is highly non linear Large scale simulations are thus performed for modified gravity models e g from the Large Simulation for Modified Gravity LaSMo
7. given interval gt XISIXO Decimator creates a sub table as a regular subsample from the input table Values are extracted in a regular sequence skipping step element every time The skip value is an integer number gt 1 and represents the number of skipped values In the above example only one element every 10 elements will be reported in the output file Extract Subregion creates a new table from an input table of a sub box or of a sphere The extraction mode and the sub volume size are RADIUS a sphere centered in the given values will be extracted CORNER a rectangular region having the lower corner at the given values will be extracted BOX a rectangular region centered in the given values will be extracted Extract Subvolume produces a table which represents a sub volume from the original volume Grid2Point distributes the values of an input grid to a point distribution in the same domain using the NGP CIC TSC algorithm This operation distributes a volume property to a point data set on the same computational domain using a field distribution CIC NGP TSC algorithm on a regular mesh CIC is the default adopted algorithm The Cell geometry is considered only to compute the cell volume value in this operation This filter produces a new table or adds a new field to the input table The operation performs the following 1 It loads a volume input volume data table and a table with a point distribution in the same
8. gt RI VisIVO Science Gateway User Manual VisIVO Team INAF Osservatorio Astrofisico di Catania Version 2 0 VISIVO Table of Contents E ele Ee sica ADOUSI iii eran pae ISO IE Lia EE EES Release Notes Version ZU Melease NOIGS V CISION Ile LEE Ce Cl nb ee EE CN NEE Lee UR E ene ee ne nee E ee ne ee ee ee eee 22 WISIVO Kee RR EA 3 Who Can Se Mie eg cnn 3 1 Registering and logging iN A MISTING UNS een TEE 11 AM VISIVOAINIPON Enti i 11 42 VislVO FIS RA e int 14 e WISI OC VON E 17 4 3 1 Data Points Visualization ee 18 4 3 2 V CCIOIS VISUANZA NO E 19 4 3 3 Splotch VisualizatioN 19 4 3 4 Volume We E 21 44 Scientific MOVIES aaa iaia 23 5 Data Management 25 DI 27 Onl MUON Ol EE 27 e2 a MO 28 SE FRANE Ca EE ERE O E E 30 T MISIVO MIODI Carrisi ROER I OEO 33 Cc a E E E S 34 VISIVO Users Guide INAF OACT Val About this manual The VisIVO Science Gateway User Manual is a detailed guide and description of VislVO Science Gateway at user level The VisIVO Science Gateway developed by INAF Osservatorio Astrofisico di Catania supported by the SCI BUS project which provides the generic purpose gateway technology as a toolset to access to the major computing data and networking infrastructures and services in Europe including clusters supercomputers grids desktop grids academic and commercial clouds VisIVO Science Gateway is
9. library command line utilities test suite source Java interface and the Java based HDF Viewer HDFView HDF supports several different data models including multidimensional arrays raster images and tables Each defines a specific aggregate data type and provides an API for reading writing and organizing data and metadata New data models can be added by the HDF developers or users This importer can be used with the datasetlist option When the datasetlist option is not given all datasets in the hdf5 will be considered forming the VBT The options must be given as follows The hyperslab option must be given as nameOfDataset offset count where offset and counts are the same of the hdf5 file and must be comma separated values If count exceeds the size of dataset it is automatically adjusted up to the end of hyperslab If offset and or count contains lower values than the dataset dimension not specified offset are put to 0 and count to the dimension of the dataset But this fact could give some unexpected behaviors and it is strongly recommended giving all parameters of offset and dimension The offset and dimension values must be equal to the number of rank If rank 3 offset dimension must contain 3 separated comma values one for each rank if offset dimension contains only two values the third value is assumed to be equal to the size of the dataset NOTE in case of volume with more than one hyperslab users are strongly suggeste
10. parameters concerning the numerical evolutionary code In this way it is possible to store and easily search and retrieve the obtained data by many set of stellar simulations and also get access to a huge amount of homogeneous data such as tracks and isochrones computed by using FRANEC From the FRANEC portlet see the following Figure the FRANEC Workflow will be submitted Franec Workflow Select the workflow parameters Initial Mass Solar Units 0 5 10 Mass Fraction 0 0001 0 04 4 0 0010 Initial He Mass Fraction 0 2 0 5 Alpha Mixing Length 0 5 3 0 3 2 Mass Loss Eta 0 0 4 Lambda Overshooting 0 0 3 0 2 0 1 Diffusion index Evolutionary Stage index 20 ch a2 Structure index Submit Figure 1 FRANEC Portlet The following input parameters are required e Initial Mass Solar Units 0 5 10 It is the mass in Solar Units of the structure Initial He Mass Fraction 0 2 0 5 The mass fraction of the initial helium Z Mass Fraction 0 0001 0 04 The mass fraction of the heavy elements abundance e Alpha Mixing Length 0 5 3 The efficiency of superadibatic convection Mass Loss Eta 0 0 4 Mass loss according to the Reimers 1975 law 30 5 VISIVO Lambda Overshooting 0 0 3 Core convective overshooting during the H burning phase The value adopted for the overshoot is taken from the classical Schwarzschild convective boundary Diffusion index Check to i
11. volume 2 It computes using a CIC or NGP or TSC algorithm a value assumed density for each data point considering the cells value where the point is spread The grid points density values are multiplied for the cell volume and assigned to the point If the density option is given the cell volume is assumed 1 Math Operations creates a new field in a data table as the result of a mathematical operation between the existing fields It is based on Function parser for C v2 83 by Warp http iki filwarp FunctionParser with some minor modifications Merge Tables creates a new table from two or more existing data tables Point Distribute creates a volume using a field distribution CIC NGP TSC algorithm on a regular mesh Point Property assigns a property to each data point on the table Randomizer creates a random subset from the original data table Select Columns creates a new table using one or more columns of a data table VISIVO Select Rows creates a new table using limits on one or more fields of a data table Sigma Contours creates a new table where one or more fields of a data table have values within N sigma contours The filter can be applied on fields that have a Gaussian distribution For the selected fields the filter prints in the stdout the average and the sigma values of the distributions Split Table splits an existing table into two or more tables XIX 4 3 VisIVO Viewer VisIVO
12. 561E 4 Max Color 63 9992 HSML field X Le HSML Factor 1 0 HSML SL 0 125 Gray absorption 0 2 Brightness 1 0 Window resolution X 800 YT 800 Boost colors Color bar Palette Default View X Y and Z are columns of X Y Z Table The X Y Z Tables must have the same number of rows Intensity field It is the name of column to be used for Intensity aA Vish gt lb Log Intensity If it s checked use the logarithm scale for Intensity field Min Max Intensity This value fix the extreme values for intensity Default value are obtained through VisIVO Filtert statistic op Color field It is the name of column to be used to give the color to the particles using the palette Log Color If it s checked use the logarithm scale for Color field Min Max Intensity This value fix the extreme values for color Default value are obtained through VisIVO Filtert statistic op HSML field Column name of the quantity to use for the smoothing of particles HSML Factor It is the fixed smoothing length If this value is gt 0 use this value as radius for particles HSML SL It is the scale factor applied for the smoothing of particles Palette It is the color table used to give the color to the particles Advanced Palette Clicking this button user can create or upload customized color palette Gray absorption It is the opacity factor Brightness It is a factor applied to the intensity increase the brightness for eac
13. G consortium 28 VISIVO LasMOG Workflow Fa x Select the gravity simulation files to Upload Local Upload Remote Upload standard tar modified tar Select the simulation parameters Particle decimation for visualization Resolution ARes Y Res Z Res PointDistribute Algorithm Grid2P oint Aigonthm CIC CIC Select Standard Simulation tar Select Modified Simulation tar i 1 a ER TT a Um N lodel o 3 d ER cessine bt et w A gt ke Ai si gt A The workflow shown in Figure above implements a customized visualization for aiding analysis of modified GR simulations more specifically inspecting datasets to discover anomalies by comparing appropriately with datasets coming from standard GR models The main computational steps are summarised as follows Two datasets corresponding to snapshots of standard gravity Ds and modified gravity Dm model simulations are processed Sub samples of the point distributions with a reduced number of points in the two datasets are generated Then for each of these sub samples a panoramic movie is created as shown in the resulting top image of Figure A point distribute operation is performed on Ds and Dy to create new volume datasets Vs and Vm respectively using a field distribution algorithm on a regular mesh A volume property on the same computational domain is distributed on a regular mesh producing a density field A n
14. Height Scalar Backcolor Background color of the image VISIVO Forecolor Foreground color when the color palette is not selected Show Palette Show Box and Show Axes Create the image with Palette Box and Axes Image Size Set the image dimension 4 3 2 Vectors Visualization VisIVOViewer creates a view of vectors created from the input data file that contains data points The input data file must fit the available RAM If Vectors is selected the vectors are displayed X Y and Z are the application point coordinates and Vx Vy and Vz are the three vector components Vectors Parameters Vor X lm Vy Y lm Vz Z e Vector Line dl Vector Scale za 1 0 Scale width a Vector Line enables vector representation with lines Default representation is the arrows Vector Scale is a scale factor for vector representation It is suggested to don t use this field or to use it carefully A number is expected in this field Scale with vectors may be not scaled default or scaled with the vector magnitude or with another field of the first table Active Scalar 4 3 3 Splotch Visualization This section creates 3D view from the input tables using Splotch a ray tracing rendering tool Select the coordinates i6 A X Log Scale ul vw ze Log scale DD LIZ Log Scale Intensity field X Le Log Intensity L Min Intensity 2 44561E 4 Max Intensity 63 9992 Color field A Log Color L Min Color 2 44
15. The FLY output format is a binary sequence of values of n data points as follows X1 Y1 Z1 X2 Y2 Z2 Xn Yn Zn Vx1 Vy1 Vz1 Vx2 Vy2 Vz2 Vxn Vyn Vzn FITS table format is a codification into a formal standard by the NASA Science Office of Standards and Technology NOST of the FITS rules http fits gsfc nasa gov endorsed by the IAU FITS supports tabular data with named columns and multidimensional rows Both binary and ASCII FITS table versions have been specified The data in a column of a FITS table can be in a different format from the data in other columns Together with the ability to string multiple header data blocks together by using FITS files it is possible to represent entire relational databases GADGET is freely available code for cosmological N body SPH simulations on massively parallel computers with distributed memory GADGET uses an explicit communication model that is implemented with the standardized MPI communication interface The code can be run on essentially all Supercomputer systems presently in use including clusters of workstations or individual PCs VisIVO Importer will produce a VBT for each species in the gadget file supplied The HDF5 FORMAT hierarchical Data Format is a library and multi object file format for the transfer of graphical and numerical data between computers lt was created by the NCSA but is currently maintained by The HDF Group The freely available HDF distribution consists of the
16. Viewer creates views from the input data file The input data file must be in the Internal Binary format The input data file must fit the available RAM VisIVOViewer produces png images given camera position values of Azimuth Elevation and Zoom NOTE the camera of the Viewer at the default position Azimuth 0 Elevation 0 is looking the box from the top z plane VislVo Viewer WislYO Importer VislVO Filters VislVO Viewer di View your data into VislCweb portal surface bin Field density Le Basic Palette 3 Volume rendering Shadow Isesurface 2 Backcolor Black 3 Forecolor White sl SRI Show Palette _ Show Box Show Axes I Stereo Isosurface Counter Value 0 gt 255 125 Image size Medium View Azimuth A5 Elevation 45 Zoom FRONT LEFT RIGHT DOWN UP BACK Viewer Param File Change Azimuth and Elevation values using your mouse to drag the 3d cube To zoom in and out hoki the shift button and again drag the model gt NR 4 3 1 Data Points Visualization When the imported datasets is a table the following options should be selected amp View your data into VisIVOweb portal eva Points L Vectors _ Splotch Select the coordinates X X Log Scale Moni Log Scale BR EC Basic Palette Advanced Palette Palette Backcolor Black Le Forecolor White EN Scale Show Palette _ Show Box _ Show Axes Stereo Opacity 0 666 Image size Medium
17. a web based workflow enabled portal for integrating large scale multidimensional datasets and applications for visualization and data filtering on Distributed Computing Infrastructures DCls Advanced users are enabled to create change invoke and monitor workflows while standard users are provided with easy to use specific web based user interfaces hiding all the technical aspects of the visualization software and DCls configurations and settings 1 http www sci bus eu gt XISIXO Release Notes Release Notes Version 2 0 The current version of the portal supports the usage of WS P Grade gUSE Version 3 5 2 It contains the following new portlets under the menu Community Muon Portal this portlet was developed to support the Muon Portal project which aims at detecting nuclear threat carried into cargo containers exploiting the muon particles coming from the secondary radiation of the sun LasMoG this portlet was designed to submit a workflow comparing the modified gravity models i e without introducing dark energy with the standard dark energy models FRANEC this portlet was designed to run FRANEC numerical code This code is perfectly suited for computing evolutions of stars on the basis of a number of different physical inputs and parameters Release Notes Version 1 0 The version 1 0 of the portal supports the usage of WS P Grade gUSE Version 3 4 4 It contains the following portlets VisIVO Importer c
18. d to give the same hyperlab extension count In case of volume with specified hyperslab the computational cells x y z values are ignored Datasets with different numbers of rows will 12 gt XISIXO produce columns with the number of rows equal to the maximum number of rows The rows will be pads with missingvalue parameter Datasets with rank greater than 1000 cannot be read Datasets can represent tables or volumes If a dataset represents a volume the dataset rank must be equal to 3 and the volume option must be given A table dataset with rank gt 1 will produce different columns in the VBT If a dataset is a table and it has rank 3 and hyperslab offset 0 0 0 count 15 10 1000 it will produce 15 10 columns each having 1000 elements The columns names will be datasetname_O 0 datasetname 0 1 datasetname 0 2 datasetname 14 9 The volume dataset rank must be equal to 3 If the dataset represents a volume the volume option must be given In this case the hyperslab dimension if given represents the volume dimension and the compx compy compz options are ignored More datasets can be given but in this case they must have the same hyperslab dimension the first hyperslab sets the volume resolution RAW Binary FORMAT files are simply a binary dump of the memory for data points The content of the Raw Binary data points file is a sequence of x y and z coordinate for each point then a sequence of fields one scalar
19. data file extension Dun storing actual data values VisIVO Importer converts user supplied datasets into VBTs without imposing any limits on sizes or dimensionality It supports conversion from several popular formats such as ASCII and CSV VOTables or FITS Tables VisIVO Filter is a collection of data processing modules to modify a VBT or to create a new VBT from existing VBTs The filters support a range of operations such as scalar distribution mathematical operations or selections of regions For example decimation or randomization are typically employed for constructing reduced VBTs to perform a sub sampling in order to fit it in the available RAM memory VisIVO Viewer is based on the Visualization ToolKit library for multidimensional visualization It creates 3D images of datasets rendering points volumes and isosurfaces within a bounding box used for representing the coordinate system employed Moreover there is support for customized look up tables for visualization using a variety of glyphs such as cubes spheres or cones The VisIVO Library was developed to port VislVO Server on gLite middleware It allows a job running on a grid node to produce a set of images or movies directly using VisIVO with its internal data arrays without the need to produce intermediate files This is particularly important when running on the grid where the user wants to have a quick look of the results during the data production phase The images in this way ca
20. ew volume V is computed where each of its voxels shows a difference of values in the density between Vs and Vu It is then filtered with a lower bound threshold and all the voxels satisfying the filters are saved in a text file for further analysis purposes as shown in the resulting bottom image of Figure Several renderings of V are performed o Volume rendering 29 VISIVO o lsosurface rendering of the density field to produce panoramic movies using different isovalues as shown in the resulting bottom image of Figure o Ortho slice rendering i e orthogonal slice planes through the volume dataset 6 3 FRANEC FRANEC is a state of art numerical code for stellar astrophysics This code is perfectly suited for computing the evolution of a star on the basis of a number of different physical inputs and parameters Parameters are listed in one input file A single run of FRANEC produces one synthetic model SM To produce an isochrone for a given chemical composition through a FIR Full Isochrone Run it is necessary to execute a large number of SMRs SM runs varying the initial mass of the stellar models Once these evolutionary tracks and isochrones as well as additional data describing the simulated stellar structures are computed they can be distributed in datasets over different sites The simulations of stellar models produce simulation output files with a set of associated metadata Such metadata are linked to all
21. for each data point Vis VOlmporter reads a descriptor file More than one raw data file name can be described VOTable format is an XML standard for the interchange of data represented as a set of tables In this context a table is an unordered set of rows each having a uniform format as specified in the table metadata information Each row in a table is a sequence of table cells and each of these contain either a primitive data type or an array of such primitives It can also contain a link to an external file that the XML part describes No VOTables with binary values are supported in VisIVO The file sizes that can be processed by the VisIVO Server are only limited by the underlying parsing libraries This reader has no limit on VOTable size but can read only ascii data VISIVO 4 2 VisIVO Filters VisIVO Filters convert imported data from an original data table internal data format table into a new one or can create a Volume from a table VislVO Filters VisIVO Importer VisIVO Viewer The selected VBT is starmap out Please select an operation Cartesian 2 Po e Cartesian 2 Polar This filter creates creates three new columns with names given in Column name for fields as the result ofthe spherical polar transformation of three existing columns given in Columns for point coordinates fields Anew table is created if the New Table option is selected Columns for point coordinates X T long v lat Column name for
22. h point Window resolution It is the image size in pixel Color bar If it s checked show color bar in image Azimuth Elevation Zoom Position and zoom factor of the camera The camera position Azimuth 0 Elevation 0 is looking the box from the top i e the last z plane 20 5 Val 4 3 4 Volume Visualization This portlet creates 3D views from Field of the input tables The View button creates the image Volumes are displayed in a new window Field thetaQuadro Volume rendering Shadow Isosurface Basic Palette Advanced Palette Palette Backcolor Black Forecolor White Show Palette Show Box Show Axes Stereo Image size Medium w Slicer lsosurface Counter Value 0 gt 255 125 View Azimuth 0 Elevation 0 Zoom 1 FRONT LEFT RIGHT DOWN UP BACK Change Azimuth and Elevation values using your mouse to drag the 3 d To zoom in and out hold the shift button and again drag the model Azimuth Elevation Zoom Position and zoom factor of the camera The camera position Azimuth 0 Elevation 0 is looking the box from the top i e the last z plane Scale The axes are scaled To be checked for not uniform system coordinates Basic Palette Check the box to choice a pre defined palette color table Color Table Log Scale Applies a logarithmic scale for the palette Advanced Palette Check the box to create or to upload a customized color
23. ies VisIVO Gateway allows users to generate scientific movies Scientific movies are useful not only to scientists to present and communicate their research results but also to museums and science centres to introduce complex scientific concepts to a general public audience Users can create a Panoramic Movie by moving a camera along a motion path of 360 in azimuth and 90 in elevation within the domain of a dataset Generate Movie Panoramic Movie Dynamic Movie A Panoramic Movie creates a movie rotating the camera positions of 360 degrees in azimuth and 180 degrees in elevation Panoramic Movie The movie is being created lt can take several minutes Customized Movies can be produced by intermediate snapshots specified as camera positions orientations and the gateway generates a movie with a camera path containing the specified positions orientations Create Movie f xX Create here your customized movie throught your images Click on the images to view the properties Select the images and then choose their frame position Select ap Position Position Position Position Azimuth 0 Azimuth 0 Azimuth 0 Azimuth 0 Elevation 0 Elevation 0 Elevation 0 Elevation 0 Zoom 1 Zoom 1 Zoom 1 Zoom 1 Submit Create here your customized movie throught your images Click on the images to view the properties Select one image and then setthe slice positions Image Id 289 Image Id 293 Image Id 294 Image Id 296
24. ilable into VislVO Gateway under the Advanced Tools menu 2 2 VisIVO Tools VisIVO is an integrated suite of tools and services for effective visual discovery in currently available and next generation large scale astrophysical datasets gt XISIXO VisIVO consists of VisiVO Desktop a stand alone application for interactive visualization on standard PCs and VisIVO Server a grid enabled platform for high performance visualization The main characteristic of VislVO is to support high performance multidimensional visualization of very large scale astrophysical datasets Users can obtain meaningful visualizations rapidly while preserving full and intuitive control of the relevant visualization parameters This section focuses on VisIVO Server allowing intuitive visual discovery with 3D views being created from data tables VislVO Server can be installed easily on any web server with a database repository VisIVO Server consists of three core components VisIVO Importer VisiVO Filter and VisIVO Viewer To create customized views of 3D renderings from astrophysical data tables a two stage process is employed First VislIVO Importer is utilized to convert user datasets into VisIVO Binary Tables VBTs Then VisIVO Viewer is invoked to display customized views of 3D renderings A VBT is a highly efficient data representation realized through an header file extension bin head containing all necessary metadata and a raw
25. in an interactive and user friendly way by means of the supplied portlets Any user can submit jobs to the underlying DCls without requiring a priori any specific technical expertise related to the particulars of the DCI configuration 6 7 Muon Portal The deflection of muonic particles present in the secondary cosmic radiation results from crossing high atomic number materials such as uranium or other fissile materials This can significantly improve on the success rate of current nuclear threat detection methods which are based on X ray scanners especially in terms of capacity for identification and location of illicit materials inside cargo containers even considering the possibility of screens designed to mask their existence It has been developed a visualisation oriented workflow suitable for inspection of cargo containers carrying high atomic number materials by displaying tomographic images The datasets containing coordinates of the muon tracker planes are first uploaded to our gateway and filtered by using the Point of Closest Approach POCA algorithm to create a representation containing the scattering deflection of cosmic radiations The result is then visualized using point rendering Further processing is then applied based on user defined thresholds followed by conversion into data volumes using the deflection angle field distribution by employing the 3D Cloudin Cell CIC smoothing algorithm Finally a tomography is performed
26. lows have become a popular approach to model and organize such kind of processes explicitly specifying the dependencies between processes within an experiment and orchestrating the distributed resources gt XISIXO 2 Main goal VisIVO Science Gateway is developed on top of WS PGRADE an highly flexible cooperative graphical user interface for the grid User Support Environment The gateway provides access to VislVO Server tools enabling the execution of a comprehensive collection of modules for processing and visualization of astrophysical datasets on DCls Several customized workflows were configured to allow different basic tasks such as datasets local or remote upload and creation of scientific movies These workflows are provided with specific user interface portlets to enable easy parameter setting for standard users to hide the complexity of the underlaying system and infrastructure The advanced users are able to adapt the basic workflows to his her specific problem This modularity achieved by subdividing the workflow into different tasks ensures the re usability of the subtasks and provides more flexibility for the user The gateway is connected to data repositories and workflows via a mobile application for astrophysical visualization named VisIVO Mobile The mobile application share the same accounts of the gateway and offers research groups and communities an exciting possibility to share results and experiences of analysis
27. n be produced directly in the grid catalogue while the user code is running in a system that cannot be directly accessed by the user a worker node VISIVO 3 Who can use the portal VisIVO Science Gateway is suited for scientists aiming to investigate large scale datasets with the possibility to create movies and complex views of multidimensional datasets VisIVO Gateway offers new exciting and easily accessible opportunities not only to specialized users e g astrophysical researchers but also to the wider public e g high school education or innovative citizen science for new scientific developments 3 1 Registering and logging in The VisIVO Science Gateway offers role based authorization modules and supports the login with user name and password gt VISO A Welcome Documentation Pubblications Useful Links Contacts VisIVO Gateway Welcome gt Create Account Return to Full Page First Name Required Birthday January Middle Name Gender Male a et Screen Name Required Text Verification Required Email Address Required Users can also login using their Facebook or OpenID accounts Three main roles are provided guests standard and advanced users Guests lack of any account for the science gateway However they can obtain information about the VisIVO project and the main features offered by the gateway A new account for standard and advanced user can be created b
28. nclude diffusion Evolutionary Stage index Set index 0 no limit 1 end phase central burning of H 2 end phase central burning of RGB for small masses Structure index Check to print structures into the file stampe every 30 models otherwise the file will be overwritten FRANEC Workflow When selecting the input parameters clicking on the Submit button the Franec workflow will be submitted The FRANEC workflow as depicted in Figure has a typical modular architecture it is easy to identify its modules that can be reused to build other workflows Modules can be identified on the basis of the function they provide EOS module provides the Equation of State in tabular form The input values are the Metallicity Z and the type of mixture combination of chemical elements heavier than helium OPACITY module produces a table of Opacity from pre calculated tables Given the Metallicity value Z and the type of mixture it obtains a new table of opacity which is interpolated from the pre calculated ones FRANEC is the core module of the workflow It produces the models of stellar evolution starting from the output of the two modules EOS and OPACITY and a set of input parameters given by the user to perform the evolution It produces a set of parameter values varying in relation to time quantities varying in relation to the radius of the model the chemical composition of the core vs time surface chemicals vs time and ene
29. ng figure Properties Edit Meta data Name Type VislvO Table clusterfields4 ascij45 Description Creation Date 2012 07 24 N of Fields 5 N of Elements 262144 Data Type float Endianity little Download Binary and Header Show Table Fields x The Properties portlet is easily reachable clicking on the item from the Data Management portlet 26 gt XISIXO 6 Community A number of challenging workflows has been prototyped to support highly specialised scientific communities mainly in astrophysics This section discusses the visualisation oriented applications Muon Portal and LasMOG and the simulation oriented workflow FRANEC The former are deployed for detecting nuclear threat materials and investigating large scale modified gravity models respectively The latter is exploited for carrying out stellar evolution simulations These workflows will be supported in ER flow project so that they can be stored into the SHIWA workflow repository together with related meta data allowing investigation of their interoperability and dissemination across relevant communities through the SHIWA simulation platform Advanced users can exploit such workflows as templates for building new customized workflows to suit particular requirements of scientific communities e g by modifying appropriately constituent building blocks customized LasMOG workflows can be generated Standard users can then execute these workflows
30. onverts user datasets into VisIVO Binary Tables VBTs internal format and extract all necessary meta data providing the dataset for further exploration to the portal VisIVO Filters converts imported datasets from an original data table into a new one performing several operations e g can create a Volume from a table VisIVO Viewer display customized views of 3D renderings Properties displays the meta data of the imported datasets and produced images Data Management allows the management of imported datasets and produced images and movies and allows the navigation within the different services offered by the portal Panoramic and Dynamic Movie creates scientific movies starting from a produced image Custom Movie creates scientific movies starting from all produced images from an imported dataset gt XISIXO 1 Introduction In astronomy visualization based knowledge discovery occupies a critical role Collaborative visualization enables multiple users to share a visualization experience interacting simultaneously with a dataset giving feedbacks on what the other participants are doing seeing Moreover workflow driven applications allow the reproduction of specific visualization results which represent a challenging task since the election of certain visualization parameter is not usually a straightforward process VisIVO Science Gateway is a web based workflow enabled framework for integrating large scale mul
31. palette Palette Range Set the limits for the palette color range Default values are the minimum and maximum value of the Field Volume Rendering This option creates the image with the volume rendering technique Shadow optional enables shadow view in the image Isosurface This option creates the image of the volume isosurface The Isosurface Contour Value fixes the isocontour Slicer This option creates the image of the intersection plane with the volume ORTHOSLICE the plane is orthogonal to the Volume box Image Creates an image Slice The plane is parallel to the X or Y or Z plane Position Position of the plane inside the volume If the volume is 64X64X64 mesh the plane position 32 is in the box center GENERIC PLANE the plane is inside the Volume box Image Creates an image Point The three coordinates of a point in the plane Orthogonal The three coordinate fixing the normal 21 VISIVO axes to the plane in the point fixed by Point option It is suggested to visualize the Box for a better visualization of the plane in the volume Backcolor Background color of the image Forecolor Foreground color when the color palette is not selected Wireframe optional visualize the isosurface with wireframe Smooth It smooth the isosurface visualization Show Palette Show Box and Show Axes Create the image with Palette Box and Axes Image Size Set the image dimension 22 gt Val 4 4 Scientific Mov
32. rgy resolution Flows vs time TAR produces an archive of the main outputs GNUPLOT produces the output plots When the workflow execution reach the Finished status the output will be stored into the FileManagement Portlet see Figure with a new folder containing the output archive 31 VISIVO Users Guide Out tar and two plots named GraphLogTCLogRC png and GraphLogTELogL png Two exemplificative plots are shown in Figure FileManagement Help Your Files Y FRANEC_1 GraphLogTcLogRC png GraphLogTeLogL png 5 Outtar Y FRANEC_2 e GraphLogTcLogRC png e GraphLogTeLogL png 5 Outtar Y FRANEC_3 phLoa FRANEC Output plots INAF OACT 32 VISIVO 7 VIisIVO Mobile VisIVO Science Gateway is fully integrated with VisIVO Mobile application This application allows smartphone devices to exploit VislVO Gateway functionalities to access large scale astrophysical datasets residing on a server repository for analysis and visual discovery Through interactive widgets customized visualizations images or movies can be generated and stored on the remote server B z Select For Ascii Importer Submit Description alessandro costa oact inaf it 000000000 Remote File Url Username Cancel The application notifies users when requested visualizations are available for retrieving on their smartphones and allows easy sharing of data images and movie
33. s via e mail or common social networks 33 VISIVO Contacts For general information on the VislVO Science Gateway and support request please contact visivo support oact inaf it If you have any concerns and questions on WS PGRADE gUSE technologies please use the Forum https www sci bus eu message board 34
34. separated by newlines Fields that contain a special character Such as comma newline or double quote must be enclosed in double quotes However if a line contains a single entry that happens to be the empty string it may be enclosed in double quotes If a field s value is a double quote character this is dealt with by placing another double quote character next to it The CSV file format does not require a specific character encoding byte order or line terminator format NOTE The Importer automatically skips all the lines starting with character If the first line contains column names starting with this character will be removed and the columns names will be given without tt Binary format is supposed to be the Internal Binary Table Assuming that a VBT is to be processed Note that the files VBTUserFileName bin and VBTUserFileName bin head must be either local or remote existing files In case this header file resides remotely a complete copy is created within the VisIVO Server output directory gt XISIXO FLY is code that uses the tree N body method for three dimensional self gravitating collisionless systems evolution FLY is a fully parallel code based on the tree Barnes Hut algorithm periodical boundary conditions are implemented by means of the Ewald summation technique FLY is based on the one side communication paradigm for sharing data among processors accessing remotely private data without synchronism
35. ted job 24 5 Data Management VisIVO Science Gateway provide a Data Management portlet which allows users the reusability of their private staging area within the system for managing their datasets as well as images and movies produced from such datasets The interaction with the Data Management portlet allows the navigation within the different services offered by the portal mainly the VisIVO Viewer and Filter portlets and the scientific movie creation portlets f deManagement P x Your File H ROOT v er data J surface bin Custemeids lt asagi Rename Starman out Properties miyData Delete v Pictures Filter pointview View e DIV e di won Customized Movie spiolchview surface bin pno v P Mowe gt datallove gt mitos 2 gt mividonie 1 Different icons differentiate the different items types S for folders m for table datasets point VBTs L i for volume datasets volume VBTs hal for images for scientific movies VISIVO Users can create new folders move items inside and outside a folder rename and delete folders and items Right clicking on an item the user can access the Portal services performing the filtering and visualization actions and accessing to the possibility of creating scientific movies Each imported VBT and generated image is associated to several meta data which can be inspected and edited in the Properties portlet as shown in the followi
36. tidimensional datasets and applications for visualization and data filtering on Distributed Computing Infrastructures DCls Advanced users are enabled to create change invoke and monitor workflows while standard users are provided with easy to use specific web based user interfaces hiding all the technical aspects of the visualization software and DCls configurations and settings Cosmological simulations produce many terabyte of datasets and the highest resolution simulation codes executed on next generation supercomputers will result in petabytes of data Furthermore petabytes of observational data are already stored in archives e g LSST LOFAR or SDSS Such data volumes pose significant challenges for data analysis storage and access and a critical step in understanding interpreting and verifying the outcome is represented by scientific visualization Visualization is lead as an interactive process including qualitative comparative and quantitative stages to analyze data present results and also to engage the public Gaining a comprehensive insight into large scale multi dimensional datasets typically requires very sophisticated statistical and data analysis algorithms Often several data exploration and visualization tools are employed for visual discoveries in order to identify regions of interest These stages involve distributed data and computing resources and require collaboration among astrophysicists Recently scientific workf
37. y an unknown user or an existing Facebook or Openld account can be leveraged to access the portal Standard users are enabled to choose pre defined workflows to become acquainted to the tools and specific workflows The latter are offered via intuitive graphical user interfaces which lowers the barrier for utilizing the tools as well as using them on high performance computing facilities and DCls The users are allowed to change input and parameters to invoke and monitor workflows Advanced users can access to additional features to create and change workflows and to set configurations of grid infrastructures These tools are also available to standard users to not pose any a priori limitation on the workflow technology usage Standard users can upload and manage their datasets through portlets without any knowledge about the totally hidden grid infrastructure and middleware By using interactive 5 VISIVO widgets user can construct customized renderings or storing data analysis and visualization results for future reference The datasets are managed internally through a relational database for preserving their metadata and maintaining data consistency Figure below shows the main portlets of the Gateway connecting to VislVO Importer Filters and Viewer services accessible by the menu VisIVO Tools VISIVO 4 Using the portal 4 1 VisIVO Importer VisIVO Importer converts user supplied datasets into a VBT VBTs are used
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