Werner Benger Center for Computation & Technology Louisiana State University 1LCI 2010 F5 Tutorial.

LCI 2010 F5 Tutorial 1

FIBERBUNDLE HDF5

Werner Benger

Center for Computation & Technology

Louisiana State University


Data Model Motivation Often as hard to communicate as

technical issues People often don’t see the point Hard to convince people working within

a closed application context about necessity of a semantic layer:“just write the data somehow”“just create a compatible data reader”


Example: “Uniform Grid”

Is an precise mathematical concept:A data box with points uniformly distributed

in some coordinate spaceBasically a multidimensional data array with

bounding box information Occurs in many applications:

Simulation programsVisualization programs


Modeling a Uniform Grid Problem: every person implementing the

concept of a “uniform grid” implements it differentlyUniform grid written by application A is almost

certainly incompatible to the layout expected by some application B

Not a problem within application A’s context, but problematic when exchanging data with application B

are we sure we never want such data exchange?


The n2 problem

Equip application B with interface for A? Or application A with B interface? Then what with application C, D, E,…? Problem is an n2 effort Common data model counts in the

long term, even if short term overhead


Custom-made HDF5


The n2 problem

Application X can read HDF5 written by application YBut can it also understand it??

“application X can read HDF5”“which HDF5?”


Ideally: Unified layer


Data Format vs. Data Model HDF5 does not solve the problem: HDF5 is an container for

multidimensional arrays with attributes○ Keeps away the burden of low-level I/O○ But does not uniquely specify how to

formulate the concept of a “uniform grid”○ Many alternatives possible, each of them

equally appropriate for a certain problem


HDF5 vs. F5

HDF5 is a container for multidimensional arrays, but leaves semantics of data open (“local” information, low-level description):

○ Have an array of 200x200x200 single-precision floats○ This dataset has an attribute named “time”

F5 provides means to describe relationships among data sets (arrays), (“global” information, high-level description) on top of HDF5

○ Have the evolution of a vertex-centered velocity vector field on a uniform grid in Cartesian coordinates

○ Have a scalar field on a surface (e.g. Gaussian curvature on curved surfaces)


Concept of the “F5” F5 data model approach:

Select and specify the only unique way of modeling that is most compatible within similar formulations within a larger context, e.g. “regular grids”, “curvilinear grids”, …

Not necessarily the most straightforward modeling for a specific problem, but only gradual increase of complexity for closely related problem

Not a list of myriads of independent cases – similar cases are modeled similarly

Inspired by mathematical concept of fiber bundles


What is a “fiber bundle”?

Short: a space E that can be written as the product of a base space B and a fiber space F, e.g. E = B × F (trivial bundle)

base space

fiber space at each point of base space


Gains of fiber bundle model Operations on the fiber space can be

performed independent from the base space

○ Vector operations on vector bundles: adding fields, subtracting fields, …

○ Data conversions and transformations, … Operations on the base space

independent from fiber space○ Selecting subsets, cropping and merging

regions…○ Topological relations among points, …


F5 concepts Nested fiber bundles:

Parameter space fiber bundleFiber bundle on discrete pointsFiber bundle on cellsFiber bundle on cell complexes

Support for multiple representations (redundant, but not trivial reproduction)

“Relative” information


Organizational Structure

F5 uses HDF5 grouping capabilities organize objects of equal propertiesAllows to iterate over groups of datasetsAllows to identify important informationMore independence from naming conventions

Information content per Fileall required information can be contained in a single

HDF5 file data can also be spread among multiple files and

uniquely merged file split possible on adjustable granularityOne or many simulations per file


F5 Hierarchy HDF5: Hierarchical Data Format HDF5 Formulation involves five hierarchy

levels (groups):○ Time slices group (generalized: parameter slices)○ Grid group○ Topology group○ Representation group○ Field group (with optional substructure)

/Time/Grid/Topology/Representation/Field/(fragment)/(components)


F5 Hierarchy Levels

Only two levels visible to end-user: “grid group” and “field group”

/Time/Grid/Topology/Representation/Field/

Substructure (fragment)/(components) is internalMight be implemented in low-level HDF5HDF5 might change, F5 API will not


Time Group/Time/Grid/Topology/Representation/Field/

Contains time attribute (textual name not used), groups all information that refers to this physical time

NO integer timestep! Data synchronization by physical time Compare different simulations

○ Exploring parameter space, e.g. weak and strong brill waves○ T=10M is 100 iteration steps on one run, but 150 iterations in

another run.○ Data features and evolution data

Non-equidistant time steps Generalization: multidimensional parameter space


Grid Group


Denotes a geometrical entity at a certain time step (static information)

Freely selectable name Information beyond Grid group is related Arbitrary number of Grid groups per time Optional integer timestep


F5 “Grid” group A geometrical entity at a certain point within

a parameter space, e.g. a uniform grid at t=10.0

Fibers over a parameter space

Is the base space of multiple fibers describing its properties

“topology” groups, e.g.Vertices, edges, faces, cells


Grid propertiesDescribe Grid as a set of points with

neighbourhood information

positional information for each coordinate system

data values for fields per coordinate system

multiple charts, supporting coordinate transformations

Derived information:

connectivity

edges, faces, ...


Topology Group


Denotes information on a topological component of a Grid

Internal naming scheme & attributesVertices, cells, edges, facesRefinement levelsInvisible to end-user (only via parameters)

Data below Topology group MUST be of same data space (number of elements)


Representation Group/Time/Grid/Topology/Representation/Field/

Denotes information related to a topological entityRelative to a chart (coordinate expressions)Relative to another Topology group

○ Spacelike: refinement information○ Timelike: evolution information (splitup/merge)

Naming scheme determined by relation object/CartesianChart3D//SphericalChart2D//VertexLevel0/


Field Group


Contains actual or procedural data setsType information: scalar, vector, tensor, covectorPositional information

○ Coordinate locations, vertices per cell, edges per cell, …

DATA sets or procedural field information:Components of compound expressionsCoefficients for procedural evaluationPartially covered data sets (Fragments)


Information provided by F5 Field type, e.g. vector, covector, …

no need to guess what the application has donedirectly specifiable in the file format

Coordinate system information, memory order (C-arrays, Fortran-arrays),…

Versioning informationEnables reading old files (ensured backward

compatibility)May also mix older and newer versions in same

file


Grid Types under Consideration

● Point Sets

● Unstructured Cell Data

● Tetrahedral Grids

● Regular Grids

● Uniform Grids

● Uniform Cartesian Grids

● Uniform Polar Grids

● Triangular Surfaces

● Quad-based Surfaces

● Irregular Surfaces

● Hierarchical Grids (AMR)

● Streamlines, Particle Trajectories, Geodesics

● Apparent Horizons

● Embedding Surfaces


Practice: Using F5 Currently source code is hosted at

http://f5.origo.ethz.ch/International/Swiss version of sourgeforgeF5 originally stems from a Germany-based project at the

Max-Planck Institute for Gravitational Physics (Albert-Einstein Institute Potsdam)

Need SVN client software http://subversion.apache.org/

F5 checkout (complete, w. HDF5 & examples)svn co https://svn.origo.ethz.ch/f5/apps/

http://f5.origo.ethz.ch/

http://subversion.apache.org/

https://svn.origo.ethz.ch/f5/apps/


Compiling F5

No “configure” required, just checkout & compile

~:$ svn co https://svn.origo.ethz.ch/f5/apps/ ~:$ cd appsapps:$ make

apps:$ make[1]: Leaving directory `…/apps/tools'

The Fiber Bundle HDF5 Library has been built successfully.

apps:$

… lots of stuff happens…

https://svn.origo.ethz.ch/f5/apps/


Directory Structurebin/ executables, add this to your $PATH

converters/ file converter source code

examples/ examples source code

F5/ the F5 library

GNUmakefile.rules part of the make system

hdf5-src/ snapshot of HDF5 library

lib/ shared libraries

make/ part of the make system

Makefile main make file

obj/ temporary files used for compilation

SVNLINKS SVN internal file

tools/ tools for F5

zlib123/ snapshot of the zlib library


Example: Galaxy Collision



Set up a collectionof “particles”

Radial distributionaround a mass center

Mass centerForIntruder galaxy



Set up particlesin “orbit” aroundgalaxy center

All velocities areTangential

High velocity in theCenter (Kepler rotation)Slow momentum

For intruder galaxy“shooting” to target galaxy


Coding the Galaxy Collisionmain()

{#define N 511 F5_vec3_point_t P[N]; F5_vec3_float_t V[N]; F5_vec3_float_t A[N]; float mass[N], weirdness[N]; for(i=2;i<N;i++) /* Initialize Kepler rotation */ {}

FileID = H5Fcreate("Particles.f5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);

/* Time iteration (euler integration) */ for(t = 0; t<t_end; t+= dt, iteration++) {

for(i=0;i<N;i++) /* Outer Loop: for all particles */ { … euler integration …}/* Write the Data */ F5write_particle_cartesian3Dv(FileID, t*0.01, "GalaxyStars", P, N, 0,

"Velocity", F5T_VEC3_FLOAT, V, "Acceleration", F5T_VEC3_FLOAT, A, "mass", H5T_NATIVE_FLOAT, mass, "weirdness", H5T_NATIVE_FLOAT, weirdness, 0);

} } /* Close the File */ F5Xclose(FileID);}

apps/examples/Particles

http://svn.origo.ethz.ch/wsvn/f5/doc/group__particles.html#g8542a3741d24e09fe62b0dd8653b5c24

http://svn.origo.ethz.ch/wsvn/f5/doc/group__extensions.html#gc75ed193a470fd81e2bf38cdb743e492


Output: “Particle System”

~ $ cd apps/examples/Particles~/apps/examples/Particles $ makemkdir -p /home/apps/obj/arch-Linuxx86_64-Debug.el5/Particlesgcc -I/home/apps -I/home/apps/lib/arch-Linuxx86_64-Debug.el5 -DWITH_hdf5 -I/home/apps/hdf5-src -DWITH_zlib123 "-I/home/l/apps/zlib123/" -MD -shared -fPIC -DHAVE_LIBS_H -DFORTRAN_UNDERLINE -fPIC -ggdb -c /home//apps/examples/Particles/Particles.c -o Particles.orm -f /home/apps/bin/arch-Linuxx86_64-Debug.el5/Particlesunset MAKEFLAGS; g++ Particles.o -L/home/apps/lib/arch-Linuxx86_64-Debug.el5 -L/home/apps/lib/arch-Linuxx86_64-Debug.el5 -o /home/apps/bin/arch-Linuxx86_64-Debug.el5/Particles -lF5 -lhdf5 -lpthread -lzlib123 -lF5 -lhdf5 -lpthread -lzlib123 -lstdc++

Type 'make exec' to execute shared binary Particles


Output: “Particle System”~/apps/examples/Particles $ make execmake[1]: Nothing to be done for `vpath_Particles-bin'.

Type 'make exec' to execute shared binary Particles

/home/apps/bin/arch-Linuxx86_64-Debug.el5/Particles/home/apps/bin//Particles

~/apps/examples/Particles $ ls -ltotal 24M-rw-r--r-- 1 werner internalusers 149 Feb 25 08:22 Makefile-rw-r--r-- 1 werner internalusers 3.2K Feb 25 08:22 Particles.c-rw-r--r-- 1 werner internalusers 4.3K Feb 25 08:22 Particles.dsp-rw-r--r-- 1 werner internalusers 24M Feb 25 09:03 Particles.f5

~/apps/examples/Particles $


Inspecting the File

~/apps/examples/Particles $ h5ls Particles.f5Charts GroupTableOfContents Groupt=000000000.0000000000 Groupt=000000000.0100000000 Groupt=000000000.0200000000 Groupt=000000000.0300000000 Groupt=000000000.0400000000 Groupt=000000000.0500000000 Groupt=000000000.0600000000 Groupt=000000000.0700000000 Groupt=000000000.0800000000 Groupt=000000000.0900000000 Groupt=000000000.1000000000 Group


Inspecting 1st Time Slice~/apps/examples/Particles $ h5ls –r Particles.f5/t=000000000.0000000000

/t=000000000.0000000000/GalaxyStars Group/t=000000000.0000000000/GalaxyStars/Charts Group/t=000000000.0000000000/GalaxyStars/Charts/StandardCartesianChart3D Group/t=000000000.0000000000/GalaxyStars/Charts/StandardCartesianChart3D/GlobalChart -> /Charts/Cartesian3D/StandardCartesianChart3D/t=000000000.0000000000/GalaxyStars/Points Group/t=000000000.0000000000/GalaxyStars/Points/StandardCartesianChart3D Group/t=000000000.0000000000/GalaxyStars/Points/StandardCartesianChart3D/Acceleration Dataset {511}/t=000000000.0000000000/GalaxyStars/Points/StandardCartesianChart3D/Positions Dataset {511}/t=000000000.0000000000/GalaxyStars/Points/StandardCartesianChart3D/Velocity Dataset {511}/t=000000000.0000000000/GalaxyStars/Points/StandardCartesianChart3D/mass Dataset {511}/t=000000000.0000000000/GalaxyStars/Points/StandardCartesianChart3D/weirdness Dataset {511}

/Time / Grid / Topology / Coord / Field


Inspecting the File’s Fields

$ h5ls -rv Particles.f5/t=000000000.0000000000/GalaxyStars/Points/StandardCartesianChart3D/Positions

Opened "Particles.f5" with sec2 driver./t=000000000.0000000000/GalaxyStars/Points/StandardCartesianChart3D/Positions Dataset {511/511}Attribute: TypeInfo scalar Type: shared-0:1:0:19496 enum native int { UnknownArrayType = 0 Contiguous = 1 SeparatedCompound = 2 Constant = 3 FragmentedContiguous = 4 FragmentedSeparatedCompound = 5 DirectProduct = 6 IndexPermutation = 7 UniformSampling = 8 FragmentedUniformSampling = 9 } Data: Contiguous Location: 0:1:0:19968 Links: 1 Modified: 2010-02-25 10:13:14 CST Comment: "Contiguous" Storage: 6132 logical bytes, 6132 allocated bytes, 100.00% utilization Type: shared-0:1:0:15464 struct { "x" +0 native float "y" +4 native float "z" +8 native float } 12 bytes

Type: struct { float x,y,z; };


Named Datatypes$ h5ls -rv Particles.f5/t=000000000.0000000000/GalaxyStars/Points/StandardCartesianChart3D/Positions

Opened "Particles.f5" with sec2 driver./t=000000000.0000000000/GalaxyStars/Points/StandardCartesianChart3D/Positions Dataset {511/511}Attribute: TypeInfo scalar Type: shared-0:1:0:19496 enum native int { UnknownArrayType = 0 Contiguous = 1 SeparatedCompound = 2 Constant = 3 FragmentedContiguous = 4 FragmentedSeparatedCompound = 5 DirectProduct = 6 IndexPermutation = 7 UniformSampling = 8 FragmentedUniformSampling = 9 } Data: Contiguous Location: 0:1:0:19968 Links: 1 Modified: 2010-02-25 10:13:14 CST Comment: "Contiguous" Storage: 6132 logical bytes, 6132 allocated bytes, 100.00% utilization Type: shared-0:1:0:15464 struct { "x" +0 native float "y" +4 native float "z" +8 native float } 12 bytes

Type attributes shared among all datasetse.g. coordinate system


Inspecting the File’s Field Data

$ h5ls -d Particles.f5/t=000000000.0000000000/GalaxyStars/Points/StandardCartesianChart3D/Positions

t=000000000.0000000000/GalaxyStars/Points/StandardCartesianChart3D/Positions Dataset {511} Data: (0) {-0.002, -0.002, 9.995}, {0, 0, 1e-06}, {0.0509902, 0.136946, 9.99645e-07}, {0.0926937, 0.11297, 9.99645e-07}, {0.124352, 0.0767509, 9.99645e-07}, {0.142536, 0.0322152, 9.99645e-07}, (6) {0.145273, -0.0158116, 9.99645e-07}, {0.132268, -0.062125, 9.99645e-07}, {0.104929, -0.101706, 9.99645e-07}, {0.0662198, -0.130266, 9.99645e-07}, {0.0203346, -0.144709, 9.99645e-07}, (11) {-0.0277542, -0.143471, 9.99645e-07}, {-0.0728353, -0.126686, 9.99645e-07}, {-0.110024, -0.0961719, 9.99645e-07}, {-0.135289, -0.0552364, 9.99645e-07}, {-0.145894, -0.00831518, 9.99645e-07}, (16) {-0.140689, 0.0395071, 9.99645e-07}, {-0.120238, 0.0830482, 9.99645e-07}, {-0.0867577, 0.11759, 9.99645e-07}, {-0.0438756, 0.139389, 9.99645e-07}, {0.00376106, 0.146083, 9.99645e-07}, (21) {0.0360555, 0.303467, 9.98582e-07}, {0.132638, 0.275317, 9.98582e-07}, {0.214846, 0.217333, 9.98582e-07}, {0.273773, 0.135796, 9.98582e-07}, {0.303032, 0.0395446, 9.98582e-07}, (26) {0.299453, -0.0609925, 9.98582e-07}, {0.263424, -0.15492, 9.98582e-07}, {0.198848, -0.23206, 9.98582e-07}, {0.112725, -0.284052, 9.98582e-07}, {0.0143853, -0.305263, 9.98582e-07}, (31) {-0.0855128, -0.293394, 9.98582e-07}, {-0.176144, -0.249731, 9.98582e-07}, {-0.247688, -0.179006, 9.98582e-07}, {-0.292391, -0.0888827, 9.98582e-07}, {-0.305408, 0.0108722, 9.98582e-07}, (36) {-0.28533, 0.109449, 9.98582e-07}, {-0.234332, 0.196165, 9.98582e-07}, {-0.157941, 0.261624, 9.98582e-07}, {-0.0644337, 0.298732, 9.98582e-07}, {0.0294392, 0.459661, 9.96813e-07},


Animation


F5ls – list F5 semantics

F5ls Particles.f5

----------- [Particles.f5] --------------

******* Timeslice for t=0 ******* Grid `GalaxyStars' (no timestep information) Root level vertex fields: Acceleration : Contiguous <0.1.4> Size: 511 vector (32bit) Positions : Contiguous <0.1.4> Size: 511 cartesian coordinates [float] (no range) Velocity : Contiguous <0.1.4> Size: 511 vector (32bit) mass : Contiguous <0.1.4> Size: 511 scalar (float) weirdness : Contiguous <0.1.4> Size: 511 scalar (float)

******* Timeslice for t=0.01 ******* Grid `GalaxyStars' (no timestep information) Root level vertex fields: Acceleration : Contiguous <0.1.4> Size: 511 vector (32bit) Positions : Contiguous <0.1.4> Size: 511 cartesian coordinates [float] (no range) Velocity : Contiguous <0.1.4> Size: 511 vector (32bit) mass : Contiguous <0.1.4> Size: 511 scalar (float) weirdness : Contiguous <0.1.4> Size: 511 scalar (float)

******* Timeslice for t=0.02 *******

make –C ~/apps/tools/F5ls/


2nd Example: Uniform Grid„Data Cube“


2nd Example: Uniform Grid„Data Cube“

Time-dependent?

Same cube,

Many fields?


Coding the Uniform Grid, Imain()

{int NumOfDataValues = NumOfDataValuesX*NumOfDataValuesY*NumOfDataValuesZ; hid_t FileID, DataID; /* HDF5-Identifiers for opened File and opened DataSet */ hsize_t dims[3]; /* Number of Values in each dimension */ F5_vec3_point_t Origin; /* Starting Point of the Volume */ F5_vec3_float_t Delta; /* Stepsize between two Points on the Grid */ F5Path *fpath; float ScalarData[NumOfDataValuesX*NumOfDataValuesY*NumOfDataValuesZ];

/* Init Data */

/* Create the File */ FileID = H5Fcreate(FileName, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);


Coding the Uniform Grid, II

fpath = F5Fwrite_uniform_cartesian3D( FileID, /* File identifier given by HDF5 */ 3.141592, /* Time Value of the field */ "SimpleScalar", /* Name of the Grid */ &Origin, /* Starting Point of the Volume */ &Delta, /* Spacing between Grid points */ dims, /* Number of Values in each direction */ "TestField", /* Name of the Field */ H5T_NATIVE_FLOAT, /* Type of the Values in the Field */ ScalarData, /* Pointer to the Data */ NULL, /* Coordinate System (default) */ F5P_DEFAULT); /* Default dataset properties */

F5close(fpath); H5Fclose(FileID);


Run: “Uniform Grid”

~ $ cd apps/examples/ScalarSimple~/apps/examples/ScalarSimple $ make… … … … … …

Type 'make exec' to execute shared binary ScalarSimple

/home/apps/bin/arch-xxxx-Debug/ScalarSimple

~/apps/examples/ScalarSimple $ make execmake[1]: Nothing to be done for `vpath_ScalarSimple-bin'.

Type 'make exec' to execute shared binary ScalarSimple

/home/apps/bin/arch-msys-Debug/ScalarSimple/home/apps/bin//ScalarSimple


Output: “Uniform Grid”

apps/examples/ScalarSimple $ ls -l

-rw-r--r-- 1 werner 24824 Feb 26 15:36 CellScalar.f5-rw-r--r-- 1 werner 184 Feb 25 08:22 Makefile-rw-r--r-- 1 werner 12930192 Feb 26 15:36 ManyGridMultiScalar.f5-rw-r--r-- 1 werner 4330832 Feb 26 15:36 MultiScalar.f5-rw-r--r-- 1 werner 16322 Feb 25 08:22 ScalarSimple.c-rw-r--r-- 1 werner 4802 Feb 25 08:22 ScalarSimple.dsp-rw-r--r-- 1 werner 153328 Feb 26 15:36 StaticScalar.f5-rw-r--r-- 1 werner 1526600 Feb 26 15:36 TimeDependentScalar.f5


Content: “Uniform Grid”

apps/examples/ScalarSimple $ h5ls StaticScalar.f5 Charts GroupTableOfContents Groupt=000000003.1415920000 Group

apps/examples/ScalarSimple $ h5ls -r StaticScalar.f5/t=000000003.1415920000 /t=000000003.1415920000/SimpleScalar Group/t=000000003.1415920000/SimpleScalar/Charts Group/t=000000003.1415920000/SimpleScalar/Charts/StandardCartesianChart3D Group/t=000000003.1415920000/SimpleScalar/Charts/StandardCartesianChart3D/GlobalChart -> /Charts/Cartesian3D/StandardCartesianChart3D/t=000000003.1415920000/SimpleScalar/Fields Group/t=000000003.1415920000/SimpleScalar/Fields/Positions Group/t=000000003.1415920000/SimpleScalar/Points Group/t=000000003.1415920000/SimpleScalar/Points/StandardCartesianChart3D Group/t=000000003.1415920000/SimpleScalar/Points/StandardCartesianChart3D/Positions Group/t=000000003.1415920000/SimpleScalar/Points/StandardCartesianChart3D/TestField Dataset {30, 20, 53}


Positions: “Uniform Grid”apps/examples/ScalarSimple $ $ h5ls -vr StaticScalar.f5/t=000000003.1415920000/SimpleScalar/Points/StandardCartesianChart3DOpened "StaticScalar.f5" with sec2 driver./t=000000003.1415920000/SimpleScalar/Points/StandardCartesianChart3D/Positions Group Attribute: DataspaceDims {3} Type: native int Data: 30, 20, 53 Attribute: base scalar Type: shared-0:1:0:15464 struct { "x" +0 native float "y" +4 native float "z" +8 native float } 12 bytes Data: {-1, -1, -1} Attribute: delta scalar Type: shared-0:1:0:15464 struct { "x" +0 native float "y" +4 native float "z" +8 native float } 12 bytes Data: {0.0377358, 0.1, 0.0666667}

Type: struct { float x,y,z; };

ResolutionBounding Box originCell size


Positions: “Uniform Grid”apps/examples/ScalarSimple $ $ h5ls -vr StaticScalar.f5/t=000000003.1415920000/SimpleScalar/Points/StandardCartesianChart3D/TestField Dataset {30/30, 20/20, 53/53} Attribute: TypeInfo scalar Type: shared-0:1:0:19496 enum native int { UnknownArrayType = 0 Contiguous = 1 SeparatedCompound = 2 Constant = 3 FragmentedContiguous = 4 FragmentedSeparatedCompound = 5 DirectProduct = 6 IndexPermutation = 7 UniformSampling = 8 FragmentedUniformSampling = 9 } Data: Contiguous


Positions: “Uniform Grid”apps/examples/ScalarSimple $ $ ../../bin/F5ls StaticScalar.f5 ----------- [StaticScalar.f5] --------------

******* Timeslice for t=3.14159 ******* Grid `SimpleScalar' (no timestep information) Root level vertex fields: Positions : UniformSampling <0.1.4> Size: 53x20x30 cartesian coordinates Range: [-1,-1,-1]-[0.962264,0.9,0.933333] TestField : Contiguous <0.1.4> Size: 53x20x30 scalar (float)


More Layout examples:a Uniform Grid

Information available:Data at time T=0.0grid name selected as “minkowski” data defined on verticesUsing default cartesian coordinates

/T=0/minkowski/Points/StandardCartesianChart3D/*


Constructing a Uniform Grid, II

Bounding box information is stored as procedural field called “Positions”Contains min/max information, or base and

delta

/T=0/minkowski/Points/StandardCartesianChart3D/Positions


Constructing a Uniform Grid, III

Defining a scalar field:

/T=0/minkowski/Points/StandardCartesianChart3D/ADMBASE::LAPSE Dataset {43, 37, 19}

Defining a vector field:Optional field of struct or struct of fields

/T=0/minkowski/Points/StandardCartesianChart3D/STATICCONFORMAL::CONFAC_1DERIVS Group

/T=0/minkowski/Points/StandardCartesianChart3D/STATICCONFORMAL::CONFAC_1DERIVS/Dx Dataset {43, 37, 19}

/T=0/minkowski/Points/StandardCartesianChart3D/STATICCONFORMAL::CONFAC_1DERIVS/Dy Dataset {43, 37, 19}

/T=0/minkowski/Points/StandardCartesianChart3D/STATICCONFORMAL::CONFAC_1DERIVS/Dz Dataset {43, 37, 19}


F5 API Demo: static scalarF5Path*fpath;Hid_t FileID;

FileID = H5Fcreate(“Filename.f5”,H5F_ACC_TRUNC, /* Creation Flags */H5P_DEFAULT, /* File creation property list identifier */H5P_DEFAULT); /* File access property list identifier */

/* Write the Data */fpath = F5Fwrite_uniform_cartesian3D(FileID, /* File identifier given by HDF5 */

3.141592, /* Time Value of the field */"SimpleScalar", /* Name of the Grid */&Origin, /* Starting Point of the Volume */&Delta, /* Spacing between Grid points */dims, /* Number of Values in each direction */"TestField", /* Name of the Field */H5T_NATIVE_FLOAT, /* Type of the Values in the Field */ScalarData, /* Pointer to the Data */NULL, /* Coordinate System - We use a standard chart

here. */F5P_DEFAULT); /* Default dataset properties */

F5close(fpath); /* Close the DataSet */

/* Close the File */H5Fclose(FileID);


F5 API Demo: dynamic scalar

/* Step through the Time */for(j=0;j<NumOfTimeSteps;j++,Time+=0.5){

/* Init the Field for each time step */for(i=0;i<NumOfDataValues;i++){

ScalarData[i] = (float)i + Time; /* This is really simple and stupid... */}

fpath = F5Fwrite_uniform_cartesian3D(FileID, /* File identifier given by HDF5 */ Time, /* Time Value of the field */ "TimeScalar", /* Name of the Grid */ &Origin, /* Starting Point of the Volume */ &Delta, /* Spacing between Grid points */ dims, /* Number of Values in each direction */ "TestField", /* Name of the Field */ H5T_NATIVE_FLOAT, /* Type of the Values in the Field */ ScalarData, /* Pointer to the Data */ NULL, /* Coordinate System - We use a standard chart

here. */ F5P_DEFAULT); /* Default dataset properties */

F5close(fpath); /* Close the DataSet */}


F5 API demo: many fields F5write_uniform_cartesian3Dv(FileID, /* File identifier given by HDF5 */

Time, /* Time Value of the field */"TimeScalar", /* Name of the Grid */&Origin, /* Starting Point of the Volume */&Delta, /* Spacing between Grid points */dims, /* Number of Values in each direction */NULL, /* Coordinate System - We use a standard chart

here. */F5P_DEFAULT, /* Default dataset properties */"TestField", /* Name of the first Field */H5T_NATIVE_FLOAT, /* Type of the Values in the Field */ScalarData, /* Pointer to the Data */"TestField2", /* Name of the second Field */H5T_NATIVE_DOUBLE, /* Type of the Values in the Field */ScalarData2, /* Pointer to the Data */NULL, /* To end the List of Fields */H5T_NATIVE_DOUBLE, /* Whatever - does not matter */NULL /* To end the List of Fields */);


Example: Uniform Grid with many fields (h5ls)

H5ls minkowski-0000.f5

Charts Group

T=0 Group

T=0.119047619047619041010577234374 Group

T=0.238095238095238193043456931264 Group

T=0.357142857142857372831912243782 Group

T=0.476190476190476552620367556301 Group

T=0.595238095238095232808461787499 Group

TableOfContents Group

Note: actual time information is specified as float attribute, not via group names.


Example: Uniform Grid with many fields (h5ls -r)H5ls -r minkowski-0000.f5

/T=0/minkowski/Points/StandardCartesianChart3D Group

/T=0/minkowski/Points/StandardCartesianChart3D/ADMBASE::CURV Group

/T=0/minkowski/Points/StandardCartesianChart3D/ADMBASE::CURV/gxx Dataset {43, 37, 19}

/T=0/minkowski/Points/StandardCartesianChart3D/ADMBASE::CURV/gxy Dataset {43, 37, 19}

/T=0/minkowski/Points/StandardCartesianChart3D/ADMBASE::CURV/gxz Dataset {43, 37, 19}

/T=0/minkowski/Points/StandardCartesianChart3D/ADMBASE::CURV/gyy Dataset {43, 37, 19}

/T=0/minkowski/Points/StandardCartesianChart3D/ADMBASE::CURV/gyz Dataset {43, 37, 19}

/T=0/minkowski/Points/StandardCartesianChart3D/ADMBASE::CURV/gzz Dataset {43, 37, 19}

/T=0/minkowski/Points/StandardCartesianChart3D/ADMBASE::LAPSE Dataset {43, 37, 19}

/T=0/minkowski/Points/StandardCartesianChart3D/ADMBASE::METRIC Group

/T=0/minkowski/Points/StandardCartesianChart3D/ADMBASE::METRIC/gxx Dataset {43, 37, 19}

/T=0/minkowski/Points/StandardCartesianChart3D/ADMBASE::METRIC/gxy Dataset {43, 37, 19}

/T=0/minkowski/Points/StandardCartesianChart3D/ADMBASE::METRIC/gxz Dataset {43, 37, 19}

/T=0/minkowski/Points/StandardCartesianChart3D/ADMBASE::METRIC/gyy Dataset {43, 37, 19}

/T=0/minkowski/Points/StandardCartesianChart3D/ADMBASE::METRIC/gyz Dataset {43, 37, 19}

/T=0/minkowski/Points/StandardCartesianChart3D/ADMBASE::METRIC/gzz Dataset {43, 37, 19}

/T=0/minkowski/Points/StandardCartesianChart3D/Positions Group

/T=0/minkowski/Points/StandardCartesianChart3D/STATICCONFORMAL::CONFAC Dataset {43, 37, 19}

/T=0/minkowski/Points/StandardCartesianChart3D/STATICCONFORMAL::CONFAC_1DERIVS Group

/T=0/minkowski/Points/StandardCartesianChart3D/STATICCONFORMAL::CONFAC_1DERIVS/Dx Dataset {43, 37, 19}

/T=0/minkowski/Points/StandardCartesianChart3D/STATICCONFORMAL::CONFAC_1DERIVS/Dy Dataset {43, 37, 19}

/T=0/minkowski/Points/StandardCartesianChart3D/STATICCONFORMAL::CONFAC_1DERIVS/Dz Dataset {43, 37, 19}

/T=0.119047619047619041010577234374 Group

/T=0.119047619047619041010577234374/minkowski Group


F5ls (data semantics)

F5ls minkowski-0000.f5 minkowski-0060.f5 minkowski-0120.f5 minkowski-0180.f5

******* Timeslice for t=0 *******

Grid `minkowski', showing vertex fields:

ADMBASE::CURV : SeparatedCompound <0.1.0> 43x37x19 metric tensor

ADMBASE::LAPSE : Contigous <0.1.0> 43x37x19 scalar

ADMBASE::METRIC : SeparatedCompound <0.1.0> 43x37x19 metric tensor

Positions : UniformSampling <0.1.0> 43x37x19 cartesian coordinates [-0.5,-0.5,-0.5]-[0.5,0.5,0.5]

STATICCONFORMAL::CONFAC : Contigous <0.1.0> 43x37x19 scalar

STATICCONFORMAL::CONFAC_1DERIVS : SeparatedCompound <0.1.0> 43x37x19 vector

STATICCONFORMAL::CONFAC_2DERIVS : SeparatedCompound <0.1.0> 43x37x19 metric tensor

******* Timeslice for t=0.119048 *******


ADMBASE::CURV : SeparatedCompound <0.1.0> 43x37x19 metric tensor

ADMBASE::LAPSE : Contigous <0.1.0> 43x37x19 scalar

ADMBASE::METRIC : SeparatedCompound <0.1.0> 43x37x19 metric tensor


STATICCONFORMAL::CONFAC : Contigous <0.1.0> 43x37x19 scalar

STATICCONFORMAL::CONFAC_1DERIVS : SeparatedCompound <0.1.0> 43x37x19 vector

STATICCONFORMAL::CONFAC_2DERIVS : SeparatedCompound <0.1.0> 43x37x19 metric tensor


Storing fragmented data on Uniform Grid Information available:

Data at time T=0.0grid name selected as “minkowski” data defined on verticesUsing default Cartesian coordinatesData are not contiguous but exists in many

fragments – internal structure of fields

/T=0/minkowski/Points/StandardCartesianChart3D/*/?


Constructing fragmented field on Uniform Grid, II Fields are not data sets, but a group

containing data sets, each a fragment

/T=0/minkowski/Points/StandardCartesianChart3D/ADMBASE::LAPSE Group

/T=0/minkowski/Points/StandardCartesianChart3D/ADMBASE::LAPSE/box0 Dataset {10, 37, 19}





Constructing fragmented field data on Uniform Grid, II Positional information per fragment

provided once in the Positions/ component


/T=0/minkowski/Points/StandardCartesianChart3D/Positions/box0 Group w. attrib. (min,max)




Constraint: all fields per representation group must be fragmented same way

Consistent layout ensured


Example: Fragmented data on a Uniform Grid with many fields (h5ls)

h5ls minkowski-0000:0000.f5

Charts Group

T=0 Group

T=0.119047619047619041010577234374 Group

T=0.238095238095238193043456931264 Group

T=0.357142857142857372831912243782 Group

T=0.476190476190476552620367556301 Group

T=0.595238095238095232808461787499 Group

TableOfContents Group

h5ls minkowski-0000:0000.f5/T=0/minkowski/Points/StandardCartesianChart3D

ADMBASE::CURV Group

ADMBASE::LAPSE Group

ADMBASE::METRIC Group

Positions Group

STATICCONFORMAL::CONFAC Group

STATICCONFORMAL::CONFAC_1DERIVS Group

STATICCONFORMAL::CONFAC_2DERIVS Group


Example: Uniform Grid with many fragmented fields (h5ls)H5ls -r minkowski-0000:0000.f5

/T=0 Group

/T=0/minkowski Group

/T=0/minkowski/Points/StandardCartesianChart3D Group

/T=0/minkowski/Points/StandardCartesianChart3D/ADMBASE::CURV Group

/T=0/minkowski/Points/StandardCartesianChart3D/ADMBASE::CURV/node-00000 Group

/T=0/minkowski/Points/StandardCartesianChart3D/ADMBASE::CURV/node-00000/gxx Dataset {23, 20, 19}

/T=0/minkowski/Points/StandardCartesianChart3D/ADMBASE::CURV/node-00000/gxy Dataset {23, 20, 19}

/T=0/minkowski/Points/StandardCartesianChart3D/ADMBASE::CURV/node-00000/gxz Dataset {23, 20, 19}

/T=0/minkowski/Points/StandardCartesianChart3D/ADMBASE::CURV/node-00000/gyy Dataset {23, 20, 19}

/T=0/minkowski/Points/StandardCartesianChart3D/ADMBASE::CURV/node-00000/gyz Dataset {23, 20, 19}

/T=0/minkowski/Points/StandardCartesianChart3D/ADMBASE::CURV/node-00000/gzz Dataset {23, 20, 19}

/T=0/minkowski/Points/StandardCartesianChart3D/ADMBASE::LAPSE Group

/T=0/minkowski/Points/StandardCartesianChart3D/ADMBASE::LAPSE/node-00000 Dataset {23, 20, 19}

/T=0/minkowski/Points/StandardCartesianChart3D/ADMBASE::METRIC Group

/T=0/minkowski/Points/StandardCartesianChart3D/ADMBASE::METRIC/node-00000 Group

/T=0/minkowski/Points/StandardCartesianChart3D/ADMBASE::METRIC/node-00000/gxx Dataset {23, 20, 19}

/T=0/minkowski/Points/StandardCartesianChart3D/ADMBASE::METRIC/node-00000/gxy Dataset {23, 20, 19}

/T=0/minkowski/Points/StandardCartesianChart3D/ADMBASE::METRIC/node-00000/gxz Dataset {23, 20, 19}

/T=0/minkowski/Points/StandardCartesianChart3D/ADMBASE::METRIC/node-00000/gyy Dataset {23, 20, 19}

/T=0/minkowski/Points/StandardCartesianChart3D/ADMBASE::METRIC/node-00000/gyz Dataset {23, 20, 19}

/T=0/minkowski/Points/StandardCartesianChart3D/ADMBASE::METRIC/node-00000/gzz Dataset {23, 20, 19}


…


Fragmented data F5ls (data semantics)

F5ls minkowski-*.f5

******* Timeslice for t=0 *******


ADMBASE::CURV : FragmentedSeparatedCompound <0.1.0> 43x37x19 metric tensor

ADMBASE::LAPSE : FragmentedContigous <0.1.0> 43x37x19 scalar

ADMBASE::METRIC : FragmentedSeparatedCompound <0.1.0> 43x37x19 metric tensor


STATICCONFORMAL::CONFAC : FragmentedContigous <0.1.0> 43x37x19 scalar

STATICCONFORMAL::CONFAC_1DERIVS : FragmentedSeparatedCompound <0.1.0> 43x37x19 vector

STATICCONFORMAL::CONFAC_2DERIVS : FragmentedSeparatedCompound <0.1.0> 43x37x19 metric tensor

******* Timeslice for t=0.119048 *******


ADMBASE::CURV : FragmentedSeparatedCompound <0.1.0> 43x37x19 metric tensor

ADMBASE::LAPSE : FragmentedContigous <0.1.0> 43x37x19 scalar

ADMBASE::METRIC : FragmentedSeparatedCompound <0.1.0> 43x37x19 metric tensor


STATICCONFORMAL::CONFAC : FragmentedContigous <0.1.0> 43x37x19 scalar

STATICCONFORMAL::CONFAC_1DERIVS : FragmentedSeparatedCompound <0.1.0> 43x37x19 vector

STATICCONFORMAL::CONFAC_2DERIVS : FragmentedSeparatedCompound <0.1.0> 43x37x19 metric tensor

…


Constructing uniform AMR Information available:

Data at time T=0.0grid name selected as “minkowski” data defined on verticesUsing default cartesian coordinatesData are available in multiple refinement levels



Constructing uniform AMR, II Levels specified via Topology group

/T=0/minkowski/VertexLevel0/StandardCartesianChart3D/ADMBASE::LAPSE Dataset {10, 10, 10}/T=0/minkowski/VertexLevel1/StandardCartesianChart3D/ADMBASE::LAPSE Dataset {20, 20, 20}/T=0/minkowski/VertexLevel2/StandardCartesianChart3D/ADMBASE::LAPSE Dataset {40, 40, 40}/T=0/minkowski/VertexLevel3/StandardCartesianChart3D/ADMBASE::LAPSE Dataset {80, 80, 80}

Field substructure still applicable:Field may be fragmentedField fragments may be omittedCompound field may be separated into

componentsField may be procedural (bounding box per

fragment)


Example: AMR, Fragmented Example in:

apps/examples/FragmentedField/

Demonstrates○ Fragmentation○ Refinement○ Time dependency○ Multiple fields


F5ls FragmentedField.f5

F5ls option “-r” displays refinement******* Timeslice for t=0.9 ******* Grid `DemoGrid' [ 10] <<< Points >>> NonsenseScalar : FragmentedContiguous <0.1.3> Size: 129x89x45 scalar (float) Positions : UniformSampling <0.1.3> Size: 129x89x45 cartesian coordinates [float] Range: [-10,-5,-2.5]-[15.6,12.6,6.3] SensitiveVectors : FragmentedContiguous <0.1.3> Size: 129x89x45 vector (32bit) <<< VertexLevel_2x2x2 >>> NonsenseScalar : FragmentedContiguous <0.1.3> Size: 129x89x45 scalar (float) Positions : UniformSampling <0.1.3> Size: 129x89x45 cartesian coordinates [float] Range: [-10,-5,-2.5]-[2.8,3.8,1.9] SensitiveVectors : FragmentedContiguous <0.1.3> Size: 129x89x45 vector (32bit) <<< VertexLevel_3x3x3 >>> NonsenseScalar : FragmentedContiguous <0.1.3> Size: 129x89x45 scalar (float) Positions : UniformSampling <0.1.3> Size: 129x89x45 cartesian coordinates [float] Range: [-10,-5,-2.5]-[-3.6,-0.6,-0.3] SensitiveVectors : FragmentedContiguous <0.1.3> Size: 129x89x45 vector (32bit)


Constructing multipatch data Information available:

Data at time T=0.0grid name selected as “minkowski” data defined on verticesUsing multiple coordinate systems



Constructing multipatch data, II

Coordinate systems specified via Representation group

/T=0/minkowski/Points/CartesianPatch0/ADMBASE::LAPSE Dataset {10, 10, 10}/T=0/minkowski/Points/CartesianPatch1/ADMBASE::LAPSE Dataset {10, 10, 10}/T=0/minkowski/Points/CartesianPatch2/ADMBASE::LAPSE Dataset {10, 10, 10}/T=0/minkowski/Points/StandardCartesianChart3D/ADMBASE::LAPSE Dataset {30, 30, 30}

Field & refinement substructure still applicable

Global coordinate system optional Coordinate transformation information

specified elsewhere (not shown here)


Multipatch / Curvilinear Grid


Viz example: vectors field in curvilinear multiblock data


Features Supported by F5 (II)

Extended data types ○ vector fields ○ tensor fields ○ covariant and contravariant indices ○ coordinate transformation rules for vector and tensor fields

Transparent support for different field layouts ○ arrays of structs ○ struct of arrays

Arbitrary dimensions ○ one-dimensional data ○ two-dimensional data (surfaces) ○ three-dimensional data (volumes) ○ higher dimensions up to HDF5 limit


Features Supported by F5(III)

Structured and unstructured grid types particle systems triangular surfaces regular surfaces uniform grids regular grids adaptive hierarchical meshes (AMR data) curvilinear grids tetrahedral grids (n.i.) hexahedral grids (n.i.) unstructured grids (n.i.)


Further Info

http://www.fiberbundle.net

http://www.fiberbundle.net/

Werner Benger Center for Computation & Technology Louisiana State University 1LCI 2010 F5 Tutorial.

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Transcript of Werner Benger Center for Computation & Technology Louisiana State University 1LCI 2010 F5 Tutorial.