oasis3 and oasis4 : the prism couplers g. berti, p. bourcier, a. caubel, d. declat, m.-a. foujols,...
TRANSCRIPT
FLUME-PRISM Workshop Met Office, Exeter, March 15-16, 2004
OASIS3 and OASIS4 : the PRISM couplers
G. Berti, P. Bourcier, A. Caubel, D. Declat, M.-A. Foujols, J. Latour, S. Legutke,
J. Polcher, R. Redler, H. Ritzdorf, T. Schoenemeyer, S. Valcke and R. Vogelsang
FLUME-PRISM workshop – Met Office, Exeter, 15-16, 2004 Slide 2
Outline
OASIS historicOASIS community todayPRISM first coupler: Oasis3
•model adaptation•coupled model configuration•communication•interpolations/transformations
PRISM final coupler: Oasis4•model adaptation•the Driver•communication•interpolations/transformations•in the prototype•still to be done
Conclusions
FLUME-PRISM workshop – Met Office, Exeter, 15-16, 2004 Slide 3
OASIS: Ocean Atmosphere Sea Ice Soil
OASIS historic
Developed since 1991 in CERFACS to couple existing GCMs. At the time:
•Models at relatively low resolution (~10000-20000 pts)
•Small number of 2D coupling fields (~10) •Low coupling frequency (~once/day)
flexibility was very important, efficiency not so much!
FLUME-PRISM workshop – Met Office, Exeter, 15-16, 2004 Slide 4
1993: OASIS 1.0 (CRAY pipes & files)
1995: OASIS 2.0 (PVM3): Heterogeneous coupling (Cathode)
1996: OASIS 2.1: Global warning scenario (SIDDACLICH)
1998: OASIS 2.2 (SIPC): Seasonal forecasting (Demeter)
1999: OASIS 2.3 (GMEM - NEC): Intercomparison (SINTEX)
2000: OASIS 2.4 (MPI2): Climate Natural variability (Predicate)
2003: OASIS 3 (MPI2-MPI1 + PSMILe + I/O): PRISM
=> new Oasis3 (oasis3_prism_2-1) now available !
OASIS historic
FLUME-PRISM workshop – Met Office, Exeter, 15-16, 2004 Slide 5
•CERFACS (France) ARPEGE3 - ORCA2LIM ARPEGE3 - OPA 8.1 ARPEGE3 - OPAICE
•METEO-FRANCE (France)ARPEGE4 - ORCA2 ARPEGE medias -OPAmed ARPEGE3 - OPA8.1 ARPEGE2 - OPA TDH
•IPSL- LODYC, LMD, LSCE (France) LMDz - ORCA2LIMLMDz - ORCA4 LMDz - OPA ATL3/ATL1 IFS
- OPA 8.1 ECHAM4 - ORCA2
•MERCATOR (France) PAM(OPA)
•MPI - M&D (Germany)ECHAM5 - MPI-OM ECHAM5 - C-HOPE PUMA - C-HOPE EMAD - E-HOPE ECHAM5 - E-HOPE
ECHAM4 - E-HOPE
•ECMWF (UK)IFS Cy23r4 - E-HOPE IFS Cy15r8 - E-HOPE
OASIS community today
FLUME-PRISM workshop – Met Office, Exeter, 15-16, 2004 Slide 6
•CGAM-Reading (UK) HadAM3 - ORCA2
•Southampton University (UK) Inter. Atm - OCCAM lite
•UCL (Belgium) LMDz - CLIO
•SMHI (Sweden) ECHAM - RCA RCA(region.) – RCO(region.)
•U. of Bergen (Norway) MM5 - ROMS
•KNMI (Netherlands) ECHAM5 - MPI-OM
•DMI (Danemark) ECHAM - HIRLAM
•INGV (Italy) ECHAM5 – MPI-OM
•IRI (USA) ECHAM4 - MOM3
•JAMSTEC (Japan) ECHAM4 - OPA 8.2
•BMRC (Australia) BAM - MOM4 BAM3 - ACOM2
•U. of Tasmania (Australia) Data Atm. - MOM4
•CAS,IIT Delhi (India) MM5 - POM
OASIS community today
FLUME-PRISM workshop – Met Office, Exeter, 15-16, 2004 Slide 7
PRISM first coupler: Oasis3
Mono-process coupler + parallel coupling library (PSMILe)
• synchronisation of the component models • coupling fields exchange • I/O actions• mono-process interpolation
Flexibility, modularity:• Arbitrary number of models and coupling fields • Different coupling frequencies for each field• Different transformations for each field
Static coupling: all coupling parameters defined initially.
FLUME-PRISM workshop – Met Office, Exeter, 15-16, 2004 Slide 8
Oasis3: model adaptation (1/3)
PRISM System Model Interface Library (PSMILe) API :
•Initialization: call prism_init_comp (comp_id, comp_name, ierr)
•Retrieval of component local communicator:call prism_get_localcomm (local_comm, ierr)
•Global grid definition (master process only)
call prism_write_grid (grd_name, nx, ny, lon, lat)call prism_write_corner (grd_name, nx, ny, nc, clon, clat)call prism_write_mask (grd_name, nx, ny, mask)call prism_write_areas (grd_name, nx, ny, area)
FLUME-PRISM workshop – Met Office, Exeter, 15-16, 2004 Slide 9
Oasis3: model adaptation (2/3)
PRISM System Model Interface Library (PSMILe) API :
•Local partition definition (by each process in the global index space)
call prism_def_partition (part_id, ig_paral, ierr)
•Coupling or I/O field declaration (name, partition id, status, shape, type)
call prism_def_var (var_id, var_name, part_id, var_nbrdims, var_inout,
var_shape, var_type, ierr)
•End of definitioncall prism_enddef (ierr)
FLUME-PRISM workshop – Met Office, Exeter, 15-16, 2004 Slide 10
Oasis3: model adaptation (3/3)
•Coupling or I/O field sending and receiving:in model time stepping loop depending on user’s specifications in namcouple:
•user’s defined source or target (end-point communication)•coupling or I/O sending or receiving at appropriate times•automatic averaging/accumulation•automatic writing of coupling restart file at end of run
call prism_put (var_id, time, var_array, ierr) call prism_get (var_id, time, var_array, ierr)
•Termination:call prism_terminate (ierr)
•Auxiliary routines:call prism_put_inquire (var_id, time, info)call prism_put_restart (var_id, time, info)
PRISM System Model Interface Library (PSMILe) API: :
FLUME-PRISM workshop – Met Office, Exeter, 15-16, 2004 Slide 11
Oasis3: coupled model configuration
•In text file namcouple, read by Oasis3 main process, and distributed to component model PSMILes at beginning of run:
•total run time
•component models
•number of coupling fields
•for each coupling field:
•source and target names (end-point communication) (var_name)
•grid acronym (grid_name)
•coupling and/or I/O status
•coupling or I/O period
•transformations/interpolations
FLUME-PRISM workshop – Met Office, Exeter, 15-16, 2004 Slide 12
Oasis3: communication
PSMILe based on MPI1 or MPI2 message passing
•End-point communication; one-to-one
A
A
A
B
B
B
•Direct communication between models with same grid and partitioning
A
A
A
file
•I/O functionality (automatic switch between coupled and forced mode): GFDL mpp_io library
A
A
A
O
O
O
O
Oasis3•Parallel communication between parallel models and Oasis3 interpolation process
FLUME-PRISM workshop – Met Office, Exeter, 15-16, 2004 Slide 13
Oasis3: interpolations/transformations
separate sequential processneighbourhood searchweight calculationinterpolation per se during the run
A
A
A
O
O
O
O
Oasis3
Oasis3
on 2D scalar fields only
• Interfacing with RPN Fast Scalar INTerpolator package
• nearest-neighbour, bilinear, bicubic for regular Lat-Lon grids
• Interfacing with SCRIP1.4 library •nearest-neighbour, 1st and 2nd order conservative remapping for all grids • bilinear and bicubic interpolation for «logically-rectangular» grids
• Bilinear and bicubic interpolation for reduced atmospheric grids• Other spatial transformations: flux correction, merging, etc.• General algebraic operations
FLUME-PRISM workshop – Met Office, Exeter, 15-16, 2004 Slide 14
PRISM final coupler: Oasis4
Situation today:
•Higher resolution, parallel and scalable models
•Higher coupling frequencies desirable
•Higher number of models and (3D) coupling fields
•Massively parallel platformsNeed to optimise and parallelise the coupler
Oasis4 is composed of: •a Driver•a Transformer•a new PRISM System Model Interface Library
FLUME-PRISM workshop – Met Office, Exeter, 15-16, 2004 Slide 15
PRISM final coupler: Oasis4
Some keynotes: Developers:
Sophie Valcke (CERFACS) - Design, XML inputDamien Declat (CERFACS) - Driver, transformer, XML inputRené Redler (NEC CCRLE) - PSMIle, portability to Linux PC cluster Hubert Ritzdorf (NEC CCRLE) - Parallel search, transformer interaction Reiner Vogelsang (SGI) - I/O, portability to SGITh. Schoenemeyer (NEC HPCE) - Parallelisation, portability to NEC SX Jean Latour (Fujitsu ) - Portability to Fujitsu VPP and PC cluster
Public domain; open source license (LGPL)
All external libraries and modules used exist in public domain versions; vendor optimized versions may also exist:
• MPI1 and/or MPI2 • mpp_io; NetCDF/parallel NetCDF• libXML• SCRIP
Programming language: Fortran 90 and C
FLUME-PRISM workshop – Met Office, Exeter, 15-16, 2004 Slide 16
Oasis4: model adaptation (1/5)
New PSMILe API:
•Application initialization (1 call/application) : call prism_init
(appl_name, ierr)
•Component application (1 call/component) :
call prism_init_comp (comp_id, comp_name, ierr)
•Retrieval of component local communicator (1 call/component):
call prism_get_localcomm
(comp_id, local_comm, ierr)
•Inquire SCC or SMIOCs persistent values:
call prism_get_persist (…)
FLUME-PRISM workshop – Met Office, Exeter, 15-16, 2004 Slide 17
Oasis4: model adaptation (2/5)
•Definition of grid (3D)
call prism_def_grid (grd_id, grd_name, comp_id, grd_shape, type, ierr)
call prism_set_corners (grd_id, nbr_crnr, crnr_shape, crnr_array, ierr)
•Placement of scalar points, vector points, subgrids on the grid:
call prism_set_points(pt_id, pt_name, grd_id, pt_shape, pt_lon, pt_lat, pt_vert ,ierr)
call prism_set_vector(vct_id, vct_name, array_of_pt_ids,ierr)
call prism_set_subgrid(sgrd_id, sgrd_name, grd_id, n_sgrd, sgrd_shape, sgrd_array, ierr)
Function overloading to keep the interface concise and flexible
FLUME-PRISM workshop – Met Office, Exeter, 15-16, 2004 Slide 18
Oasis4: model adaptation (3/5)
•Definition of grid cell dimension
call prism_set_scalefactors(grd_id, scale_shape, scale_array, ierr)
•Definition of grid cell mask
call prism_set_mask(msk_id, grd_id, msk_shape, msk_array, ierr)
•Definition of point local coordinate system angle
call prism_set_angle
(pt_id, angle_shape, angle_array, ierr)
FLUME-PRISM workshop – Met Office, Exeter, 15-16, 2004 Slide 19
prism_def_grid
Example
prism_set_mask
prism_set_points
prism_set_pointsprism_set_points
prism-set-corners
Oasis4: model adaptation (4/5)
prism_set_vector
FLUME-PRISM workshop – Met Office, Exeter, 15-16, 2004 Slide 20
Oasis4: model adaptation (5/5)
•Coupling or I/O field declaration
call prism_def_var(var_id, var_name, grd_id, pt_id, msk_id, var_nbrdims,
var_shape, var_type, ierr)
•End of definitioncall prism_enddef (ierr)
•Coupling or I/O field sending and receiving:in model time stepping loop depending on user’s specifications in SMIOC:
•user’s defined source or target, component or file (end-point communication)•coupling or I/O sending or receiving at appropriate times •automatic averaging/accumulation•automatic writing of coupling restart file at end of run
call prism_put (var_id, date, date_bounds, var_array, info, ierr) call prism_get (var_id, date, date_bounds, var_array, info, ierr)
FLUME-PRISM workshop – Met Office, Exeter, 15-16, 2004 Slide 21
Application and component description (XML files):For each application (code):
one Application Description (AD):•possible number of processes•components included
For each component in the application:
one Potential Model Input and Output Description (PMIOD)
•component general characteristics: name, component simulated, …•code general characteristics: lab, documentation, contact, …•grid information: domain, resolution(s), grid type, …
•potential I/O or coupling variables:•local name, standard name •units, valid min and max •numerical type•associated grid and points •intent –input and/or output
•persistent variables: name, units, numerical type, possible values, …
Oasis4: coupled model configuration (1/2)
FLUME-PRISM workshop – Met Office, Exeter, 15-16, 2004 Slide 22
Coupled model configuration (XML files): The user produces
a Specific Coupling Configuration (SCC):• experiment and run start date and end date• start mode (MPI1, MPI2)• applications, components for each application• host(s), number of processes per host, ranks for each component
For each component, a Specific Model Input and Output Configuration (SMIOC)
• PMIOD component and code general characteristics• grid information: chosen resolution, … • I/O or coupling variables:
•local and standard name, units, valid min max, numerical type, grid •activated intent –input and/or output•source and/or target (component and/or file)•coupling or I/O dates•transformations/interpolations/combinations
•persistent variables: name, units, numerical type, chosen value, …
Oasis4: coupled model configuration (2/2)
Driver
TOCE
ATM
LAND
fileV4Definition Phase
OCE PMIODV1: out, metadata V1V2: in, metadata V2
ATM PMIODV1: in, metadata V1V2: out, metadata V2V3: out, metadata V3
LAND PMIODV3: in, metadata V3V4: in, metadata V4
ATM-LAND AD
OCE AD
OCE SMIOCV1 : to ATM, T1 to file V1V2 : from ATM, T2
userATM SMIOC V1 : from OCE, T1V2: to OCE, T2V3 : to LAND
user
LAND SMIOC V3 : from ATMV4 : from fileV4
user
Composition Phase
user
SCC ATM:...OCE:...LAND:...
user
Deployment Phase
V1V1
V2V2
V3
fileV1
V4
FLUME-PRISM workshop – Met Office, Exeter, 15-16, 2004 Slide 24
Oasis4: the Driver
•Manages a static coupling:
all applications are started directly in the run script (MPI1 mode) or launched by the Driver at the beginning of the run (MPI2 mode) for the whole run.
•Participates to communicator set-up
•Reads the SCC and SMIOcs information and distributes it to the component PSMILes
Driver
FLUME-PRISM workshop – Met Office, Exeter, 15-16, 2004 Slide 25
•More elaborate PSMILe based on MPI1 or MPI2
•Parallel communication including repartitioning:
•based on geographical description of the partitions
•parallel calculation of communication patterns in source PSMILe
OB
OB
OB
C
C
C
O1
O1
C
C
Same grid, different decomposition direct repartitioning:
• for each target point, parallel calculation of source matching point in source PSMILe
Oasis4: communication (1/3)
T
OB
OB
OB
C
C
C
O2
O2
C
C
Different grid and decomposition via Transformer:
• for each target point, parallel calculation of source interpolation neighbours in source PSMILe
FLUME-PRISM workshop – Met Office, Exeter, 15-16, 2004 Slide 26
Oasis4: communication (2/3)
x x x x x x x x x x x x x x x x x x x x
o o oo o oo o o
1/ Envelop exchange 2/ Detailed neighbourhood search
3/ EPIOS and EPIOT definition
Parallel calculation of communication patterns in source PSMILe
For each pair of source and target processes:
x x x x x x x x x
o o oo o o
x x x x x x x x x
o o oo o o
EPIOS1EPIOT1
x x x x x
o o oo o o
x xx xx x
x x x x x
o o oo o o
x xx xx xEPIOS2 EPIOT2
FLUME-PRISM workshop – Met Office, Exeter, 15-16, 2004 Slide 27
• parallel 3D neighbourhood search in each source process PSMILe
• new search algorithm: parallel multigrid technique, higher efficiency
• extraction of useful part of source field only• end-point communication • one-to-one or one-to-many; combination
• source data can be consumed by more than one target model or file and at a different frequencies
Oasis4: communication (3/3)
• parallel I/O (vector, bundles, vector bundles) : GFDL mpp_io, parNetCDF
A
A
A
file
single parallel
A
A
A
file1
file2
file3
distributed
A
A
A
file
FLUME-PRISM workshop – Met Office, Exeter, 15-16, 2004 Slide 28
PSMILe: •time transformations, local transformations•global conservation, combinations
Transformer:
Oasis4: interpolations/transformations
T
OB
OB
OB
C
C
C
O2
O2
C
C•loops over PSMILe requests
•EPIOS and EPIOT definition (source PSMILe)
•For each EPIOT point, neighbours in EPIOS (source PSMILe)
=>Transformer calculates interpolation weights
•Prism_put of EPIOS (source PSMILe)=>Transformer performs interpolation per se
•Prism_get of EPIOT (target PSMILe) •well suited for MPI parallelisation
FLUME-PRISM workshop – Met Office, Exeter, 15-16, 2004 Slide 29
Different interpolation schemes:•nearest-neighbour, bilinear, bicubic, conservative remapping, …
On different types of fields
•1D-2D-3D scalar, vector, bundles, bundles of vectors
On different types of grids
•blockstructured (regular and irregular)
•unstructured
•static or dynamic
Oasis4: interpolations/transformations
FLUME-PRISM workshop – Met Office, Exeter, 15-16, 2004 Slide 30
•Access of XML information •Coupling and I/O of n parallel applications with m components.•Coupling exchange with repartitionning, direct or through the (mono-process) Transformer •Interpolations:
•PSMILe (non-exact) parallel neighborhood search•3D nearest-neighbour
•I/O: •single and parallel mode
•Coupling and I/O exchange from one source to many targets •Local transformations (scatter, gather, add or mult scalar, statistics)
•Basic time transformation (average, accumul, min, max)
Oasis4: in the prototype (03/2004)
FLUME-PRISM workshop – Met Office, Exeter, 15-16, 2004 Slide 31
•Completion of PSMILe calendar routines (internal and external)
•PSMILe API for model access to SCC and SMIOC information
•Interpolation:•More schemes (conservative, 3D, etc.)•Exact parallel neighbour search
•Transformer parallelisation
•Field reduction, combination
•Full support of vector and bundle fields (I/O OK)
•I/O: distributed mode (parNetCDF)
•Adaptative grids
•Unstructured grids
Oasis4: still to be done
FLUME-PRISM workshop – Met Office, Exeter, 15-16, 2004 Slide 32
Conclusions
Calendar:•Oasis3_prism_2-1 available
•Oasis4 prototype available within days
•Oasis4 final PRISM version due 12/2004
Follow-on:•Oasis4 developments will go on after 12/2004 with PRISM sustained support
•FP6 funding (march 2005)?
Static vs dynamic couplers:•In the near and mid future, Oasis4 and Palm (Cerfacs dynamical coupler) will remain separate software
•Fusion may be considered when climate modelling and data assimilation communities will join