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CGNS Tutorial

1) The document discusses using Python and in-memory CGNS trees for code coupling and processing Computational Fluid Dynamics (CFD) data. 2) It introduces pyCGNS, a Python wrapper for CGNS that allows working with CGNS files and data in memory using native Python data types and objects. 3) Examples are given for using pyCGNS to write CGNS files, perform preprocessing and postprocessing tasks, prototype code, and facilitate code coupling between CFD codes through an in-memory representation of the CGNS tree.

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henry ford
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© © All Rights Reserved
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Download as PDF, TXT or read online on Scribd
451 views

CGNS Tutorial

1) The document discusses using Python and in-memory CGNS trees for code coupling and processing Computational Fluid Dynamics (CFD) data. 2) It introduces pyCGNS, a Python wrapper for CGNS that allows working with CGNS files and data in memory using native Python data types and objects. 3) Examples are given for using pyCGNS to write CGNS files, perform preprocessing and postprocessing tasks, prototype code, and facilitate code coupling between CFD codes through an in-memory representation of the CGNS tree.

Uploaded by

henry ford
Copyright
© © All Rights Reserved
Available Formats
Download as PDF, TXT or read online on Scribd
You are on page 1/ 20

AIAA SF 2006

CGNS Tutorial Session

Python & In-memory CGNS trees


Using CGNS trees for Code-coupling

Marc Poinot

Marc Poinot ONERA/DSNA


AIAA-SF-2006/CGNS-Tutorial

Computational Fluid Dynamics


and
Aeroacoustics dept.

France

Python & In-memory CGNS trees


Slide 1/20

Code life cycle

Idea/Code/Test/Change

All

Prototype
Test
Pre/Post processing
Code-coupling
Parallel

you can do with another programming language

Interpreted
Actually dedicated to code gluing
Script languages are easily extensible

Baseline for an Open System


Marc Poinot ONERA/DSNA
AIAA-SF-2006/CGNS-Tutorial

Python & In-memory CGNS trees


Slide 2/20

Python

Object-oriented interpreted language


Very

easy to learn

Clear

syntax

Powerful

numerical extensions

Python/C/C++/Fortran arrays

Good candidate for code gluing


Pre
A

& post processing on CGNS data

scripting language

Marc Poinot ONERA/DSNA


AIAA-SF-2006/CGNS-Tutorial

Python & In-memory CGNS trees


Slide 3/20

pyCGNS

Python wrapper on CGNS MLL and ADF


Straightforward
Use

mapping

100% python types

Lists, strings, integers, floats


Numerical array

Contiguous C/Fortran array


Points to actual memory zone

Easy scripting
Perform

CGNS calls on-the-fly

Marc Poinot ONERA/DSNA


AIAA-SF-2006/CGNS-Tutorial

Python & In-memory CGNS trees


Slide 4/20

Python/CGNS tree

Tree representation
List

of nodes

Each

node has...
A Name
A Type
A Value
A list of sons

Generic CGNS low level node requirements (ADF/HDF5)

['Transform',(1, 2, 3),[],'int[IndexDimension]'],
['PointRange',((1, 1, 1), (1, 9, 9)),[],'IndexRange_t'],
['PointRangeDonor',((21, 1, 1), (21, 9, 9)),[],'IndexRange_t']
Marc Poinot ONERA/DSNA
AIAA-SF-2006/CGNS-Tutorial

Python & In-memory CGNS trees


Slide 5/20

File and memory

ADF/HDF5 file

open/read/write/close
MLL keeps private tree structure in memory
ADF is per-node but still private data structure

PyCGNS

only maps to this behaviour

Python tree

The Python/CGNS tree is just another implementation


Structure in memory but not a proprietary one

Same

interface/Different implementation

Marc Poinot ONERA/DSNA


AIAA-SF-2006/CGNS-Tutorial

Python & In-memory CGNS trees


Slide 6/20

File & memory workflow

ADF

Numeric

MPI

MLL

Python

End-user
Python
script

pyCGNS

The LOGICAL data model is unchanged: SIDS


Marc Poinot ONERA/DSNA
AIAA-SF-2006/CGNS-Tutorial

Python & In-memory CGNS trees


Slide 7/20

pyCGNS example
import CGNS
import numarray as N
x=y=z=N.zeros((3,5,7),'d')
a=CGNS.pyCGNS("newfile.cgns",CGNS.MODE_WRITE)
print a.error
idb=a.basewrite("Base",3,3)
idz=a.zonewrite(idb,"Zone 01",[3,5,7],CGNS.Structured)
a.coordwrite(idb,idz,CGNS.RealDouble,CGNS.CoordinateX,x)
a.coordwrite(idb,idz,CGNS.RealDouble,CGNS.CoordinateY,y)
a.coordwrite(idb,idz,CGNS.RealDouble,CGNS.CoordinateZ,z)
a.close()

Marc Poinot ONERA/DSNA


AIAA-SF-2006/CGNS-Tutorial

Python & In-memory CGNS trees


Slide 8/20

Scripting example: Prototypes

Can I do this and that with CGNS ?

Just try it !
Versatile testing support

import CGNS
f=CGNS.pyCGNS("hydro-result.cgns",CGNS.MODE_WRITE)
f.basewrite("MASS2",3,3)
f.zonewrite(1,"Block01",(2,3,4,1,2,3,0,0,0),CGNS.Structured)
f.solwrite(1,1,"07-01-1944 06:00:00",CGNS.CellCenter)
f.fieldwrite(1,1,1,CGNS.RealDouble,"sediment",w)
f.goto(1,[(CGNS.Zone_t,1),(CGNS.FlowSolution_t,1),(CGNS.DataArray_t,1)])
f.descriptorwrite("Description","Text here")
f.descriptorwrite("Units","Text here")
f.close()

Marc Poinot ONERA/DSNA


AIAA-SF-2006/CGNS-Tutorial

Python & In-memory CGNS trees


Slide 9/20

Scripting example: post-processing

Add links to actual grids

The computation sessions results are sharing the same grid


No duplicates
Post-processing adds links to the actual grid
True MLL/ADF calls performed on file

from CGNS import *


a=pyCGNS("result-001.cgns",MODE_MODIFY)
a.goto(1,[(Zone_t,1)])
a.linkwrite("GridCoordinates","grid.cgns","/Base/Zone/GridCoordinates"
)
a.close()
Marc Poinot ONERA/DSNA
AIAA-SF-2006/CGNS-Tutorial

Python & In-memory CGNS trees


Slide 10/20

Scripting example: pre-processing

Structured grid seen as unstructured

Generates connectivity
Read the file/Change in-memory tree/Send to code
Python
Numeric

ADF
pyCGNS

End-user
Python
script

Marc Poinot ONERA/DSNA


AIAA-SF-2006/CGNS-Tutorial

Python & In-memory CGNS trees


Slide 11/20

Code-coupling

Blind connection to peer code


Open

Use

System: Public interface

Common baseline
Restriction input/output

Bct for data exchange

Input/Output: BCDataset
Contact surface
Strong requirements for an arbitrary exchange mean

Efficiency

Memory +no data duplication


Easy stub & proto

Marc Poinot ONERA/DSNA


AIAA-SF-2006/CGNS-Tutorial

Python & In-memory CGNS trees


Slide 12/20

Code-coupling CGNS tree

Marc Poinot ONERA/DSNA


AIAA-SF-2006/CGNS-Tutorial

Python & In-memory CGNS trees


Slide 13/20

Scripting example: code-coupling


import MpCCI
pathB="/FlatPlate/Fluid/ZoneBC/Wall:Heat/DataSet#01/NeumannData"
pathI=pathB+"/Temperature"
pathO=pathB+"/NormalHeatFlux"
it=E.iteration()
fqx=mcci.Parameter_info("Simulation_Fluid_2_Therm_Ratio",MpCCI.CCI_INT)
xp=xw.get(E.RUNTIME_TREE)
xf=X.retrieve(pathO,xp)
if ( xf and ((it % fqx ) == 0 )):
sd1=mcci.Parameter_info("Fluid_Private_Synchro_ID",MpCCI.CCI_INT)
ZID=mcci.Parameter_info("Global_Mesh_ID",MpCCI.CCI_INT)
BID=1
nnodes=len(xf[1].flat)
if ( (it % fqx ) == 0 ):
mcci.Put_nodes(ZID,BID,171,1,nnodes,0,None,MpCCI.CCI_DOUBLE,xf)
mcci.Reach_sync_point(sd1)
(rC,nC)=mcci.Get_nodes(ZoneID,BoundaryID,154,1,nnodes,0,None,MpCCI.CCI_DOUBLE)
...
E.update((E.RUNTIME_TREE,rt)
Marc Poinot ONERA/DSNA
AIAA-SF-2006/CGNS-Tutorial

Python & In-memory CGNS trees


Slide 14/20

Scripting example: parallel


import elsApy
from Scientific

as E
import MPI

communicator=MPI.world.duplicate()
id = communicator.rank
if
( id == 0 ): remoteId=1
elif ( id == 1 ): remoteId=0
datatree=E.get(E.RUNTIME_TREE)
temp=pickle.dumps(datatree)
communicator.nonblocking_send(temp, remoteId, id)
return,rank,tag=communicator.receiveString(None,None)
result=pickle.loads(return)
for l in result:
if (l[0] == "RunTimeTree"):
for ll in l[2]:
if (ll[0] == "Rotor#Output"): ll[0]="Stator#Input"
if (ll[0] == "Stator#Output"): ll[0]="Rotor#Input"
E.update(E.RUNTIME_TREE,result)
Marc Poinot ONERA/DSNA
AIAA-SF-2006/CGNS-Tutorial

Python & In-memory CGNS trees


Slide 15/20

In-memory issues

Dedicated to a platform
One

per platform: requires an API

Translation

mandatory between platforms

XDR-like

Best should be
Use

an existing system

Python/Numeric (+Marshalling)
HDF5 (?)

Marc Poinot ONERA/DSNA


AIAA-SF-2006/CGNS-Tutorial

Python & In-memory CGNS trees


Slide 16/20

Python/CGNS Tree interface

List of Python objects

MLL-like interface

Numeric Python arrays


Input/Output from MLL
Use paths instead of ids

NewBase

NewZone

NewGridCoordinates

NewCoordinates

GetByExactPath

NewDataArray

GetByRegexpPath

GetAllTreePath

T=CGNSTree()
base=newBase(T,"Base",3,3)
print T
getChildrenNameByPath(T,"/Base/Zone-002/GridCoordinates")
[['CGNSLibraryVersion', 2.4, [], 'CGNSLibraryVersion_t'],
['Base', array([3, 3]), [], 'CGNSBase_t']
]
Marc Poinot ONERA/DSNA
AIAA-SF-2006/CGNS-Tutorial

Python & In-memory CGNS trees


Slide 17/20

Script example: Python/CGNS tree


T=C.newCGNS()
base=C.newBase(T,"Base",3,3)
size=(20,10,5)
z1=C.newZone(base,"Zone-001",size)
C.newCoordinates(z1,"CoordinatesX",x)
C.newCoordinates(z1,"CoordinatesY",y)
f=open("T01.py","w+")
f.write(str(T))
f.close()
clist=C.getChildrenNameByPath(T,"/Base/Zone-002/GridCoordinates")
for c in clist:
n=C.getByExactPath(T,"/Base/Zone-002/GridCoordinates/"+c)
print C.nodeName(n)
v=C.nodeValue(n)
print
print
print
print

C.getChildrenType(T,"CGNSBase_t")
C.getAllTreePath(T)
C.getAllTreeType(T,"Zone_t")
C.getAllTreeType(T,"DataArray_t")

Marc Poinot ONERA/DSNA


AIAA-SF-2006/CGNS-Tutorial

Python & In-memory CGNS trees


Slide 18/20

Workflow pre/post processing

Use tools operating on data trees


A

data model is described by a grammar: SIDS

Translate

the grammar for existing tools

Relax-NG, BNF, ...

In-Memory data structre can be used for...


Perform

tree verification

Operate

tree as ADT

Generate code:

MLL/ADF/HDF5/XML/SQL/XDR/...

Marc Poinot ONERA/DSNA


AIAA-SF-2006/CGNS-Tutorial

Python & In-memory CGNS trees


Slide 19/20

More than float arrays...

CGNS is more than a storage mean...


CGNS

Store data the CGNS way

e.g. Map to 100% python objects

Tree with public definition

CGNS

as a data model

as component interface

Code-coupling data model


Transfer whole tree instead of arrays

e.g. Memory buffer based system

Marc Poinot ONERA/DSNA


AIAA-SF-2006/CGNS-Tutorial

Python & In-memory CGNS trees


Slide 20/20

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