WRF code

Download Report

Transcript WRF code

Some Coding Structure in WRF

Software Architecture



Features

F90 w/ structures and dynamic memory allocation Modules Run-time configurable Hierarchical Software Design Multi-level parallel decomposition

shared-, distributed-, hybrid

Multi-level parallel decomposition

Logical domain 1 Patch, divided into multiple tiles 

Single version of code for efficient execution on:



Distributed-memory



Shared-memory



Hybrid-memory

Model domains are decomposed for parallelism on two-levels

Patch:

section of model domain allocated to a distributed memory node

Tile:

section of a patch allocated to a shared-memory processor within a node; this is also the scope of a model layer subroutine.

Distributed memory parallelism is over patches; shared memory parallelism is over tiles within patches

Three Sets of Dimensions Domain size: ids, ide, jds, jde, kds, kde Memory size: Tile size: ims, ime, jms, jme, kms, kme its, ite, jts, jte, kts, kte

template for model layer subroutine

SUBROUTINE model ( & arg1, arg2, arg3, … , argn, & ids, ide, jds, jde, kds, kde, & ! Domain dims ims, ime, jms, jme, kms, kme, & ! Memory dims its, ite, jts, jte, kts, kte ) ! Tile dims IMPLICIT NONE ! Define Arguments (S and I1) data REAL, DIMENSION (ims:ime,kms:kme,jms:jme) :: arg1, . . .

REAL, DIMENSION (ims:ime,jms:jme) :: arg7, . . .

. . .

! Define Local Data (I2) REAL, DIMENSION (its:ite,kts:kte,jts:jte) :: loc1, . . .

. . .

! Executable code; loops run over tile ! dimensions DO j = jts, jte DO k = kts, kte DO i = MAX(its,ids), MIN(ite,ide) loc(i,k,j) = arg1(i,k,j) + … END DO END DO END DO • Domain dimensions • Size of logical domain • Used for bdy tests, etc.

template for model layer subroutine

REAL, DIMENSION (ims:ime,jms:jme) :: arg7, . . .

. . .

! Define Local Data (I2) REAL, DIMENSION (its:ite,kts:kte,jts:jte) :: loc1, . . .

. . .

! Executable code; loops run over tile ! dimensions DO j = jts, jte DO k = kts, kte DO i = MAX(its,ids), MIN(ite,ide) loc(i,k,j) = arg1(i,k,j) + … END DO END DO END DO • Domain dimensions • • Size of logical domain Used for bdy tests, etc.

logical patch

Example code fragment that requires communication between patches Note the tell-tale +1 and –1 expressions in indices for rr and H1 arrays on right-hand side of assignment. These are horizontal data dependencies because the indexed operands may lie in the patch of a neighboring processor. That neighbor’s updates to that element of the array won’t be seen on this processor. We have to communicate. (dyn_eh/module_diffusion.F ) SUBROUTINE horizontal_diffusion_s (tendency, rr, var, . . .

. . .

DO j = jts,jte DO k = kts,ktf DO i = its,ite mrdx=msft(i,j)*rdx mrdy=msft(i,j)*rdy tendency(i,k,j)=tendency(i,k,j) (mrdx*0.5*((rr( i+1 ,k,j)+rr(i,k,j))*H1( i+1 ,k,j) & & (rr( i-1 ,k,j)+rr(i,k,j))*H1(i ,k,j))+ & mrdy*0.5*((rr(i,k, j+1 )+rr(i,k,j))*H2(i,k, j+1 ) & (rr(i,k, j-1 )+rr(i,k,j))*H2(i,k,j )) & msft(i,j)*(H1avg(i,k+1,j)-H1avg(i,k,j)+ & H2avg(i,k+1,j)-H2avg(i,k,j) & )/dzetaw(k) & ) ENDDO ENDDO ENDDO . . .

template for model layer subroutine

REAL, DIMENSION (ims:ime,jms:jme) :: arg7, . . .

. . .

! Define Local Data (I2) REAL, DIMENSION (its:ite,kts:kte,jts:jte) :: loc1, . . .

. . .

! Executable code; loops run over tile ! dimensions DO j = jts, jte DO k = kts, kte DO i = MAX(its,ids), MIN(ite,ide) loc(i,k,j) = arg1(i,k,j) + … END DO END DO END DO • Domain dimensions • • Size of logical domain Used for bdy tests, etc.

logical patch

template for model layer subroutine

REAL, DIMENSION (ims:ime,jms:jme) :: arg7, . . .

. . .

! Define Local Data (I2) REAL, DIMENSION (its:ite,kts:kte,jts:jte) :: loc1, . . .

. . .

! Executable code; loops run over tile ! dimensions DO j = jts, jte DO k = kts, kte DO i = MAX(its,ids), MIN(ite,ide) loc(i,k,j) = arg1(i,k,j) + … END DO END DO END DO • • Domain dimensions • Size of logical domain • Used for bdy tests, etc.

Memory dimensions • Used to dimension dummy arguments • Do not use for local arrays

1 node

logical patch jme halo ims ime jms

template for model layer subroutine

REAL, DIMENSION (ims:ime,jms:jme) :: arg7, . . .

. . .

! Define Local Data (I2) REAL, DIMENSION (its:ite,kts:kte,jts:jte) :: loc1, . . .

. . .

! Executable code; loops run over tile ! dimensions DO j = jts, jte DO k = kts, kte DO i = MAX(its,ids), MIN(ite,ide) loc(i,k,j) = arg1(i,k,j) + … END DO END DO END DO •

ims

• • Domain dimensions • Size of logical domain • Used for bdy tests, etc.

Memory dimensions • Used to dimension dummy arguments • Do not use for local arrays Tile dimensions • Local loop ranges • Local array dimensions

jme jte tile its halo ite jts ime jms

Data structure

 WRF Data Taxonomy  State data  Intermediate data type 1 (L1)  Intermediate data type 2 (L2)

Data structure State data

      Persist for the duration of a domain Represented as fields in domain data structure Arrays are represented as dynamically allocated pointer arrays in the domain data structure Declared in Registry using

state

keyword Always

memory

dimensioned; always

thread shared

Only state arrays can be subject to I/O and Interprocessor communication

template for model layer subroutine

REAL, DIMENSION (ims:ime,jms:jme) :: arg7, . . .

. . .

! Define Local Data (I2) REAL, DIMENSION (its:ite,kts:kte,jts:jte) :: loc1, . . .

. . .

Memory dimensions • Used to dimension dummy arguments • Do not use for local arrays

1 node

logical patch jme halo ims ime jms

Data structure L1 Data

 Data that persists for the duration of 1 time step on a domain and then released  Declared in Registry using

keyword  Typically automatic storage (program stack) in solve routine  Typical usage is for tendency or temporary arrays in solver  Always

memory

dimensioned and

thread shared

 Typically

not

communicated or I/O

Data structure L2 Data

 L2 data are local arrays that exist only in model-layer subroutines and exist only for the duration of the call to the subroutine  L2 data is not declared in Registry, never communicated and never input or output  L2 data is

tile

dimensioned and

thread local

; over dimensioning within the routine for redundant computation is allowed  the responsibility of the model layer programmer  should always be limited to thread-local data

template for model layer subroutine

REAL, DIMENSION (ims:ime,jms:jme) :: arg7, . . .

. . .

! Define Local Data (I2) REAL, DIMENSION (its:ite,kts:kte,jts:jte) :: loc1, . . .

. . .

! Executable code; loops run over tile ! dimensions DO j = jts, jte DO k = kts, kte DO i = MAX(its,ids), MIN(ite,ide) loc(i,k,j) = arg1(i,k,j) + … END DO END DO END DO •

ims

• • Domain dimensions • Size of logical domain • Used for bdy tests, etc.

Memory dimensions • Used to dimension dummy arguments • Do not use for local arrays Tile dimensions • Local loop ranges • Local array dimensions

jme jte tile its halo ite jts ime jms

The Registry

    

"Active data dictionary” for managing WRF data structures



Database describing attributes of model state, intermediate, and configuration data

  

Dimensionality, number of time levels, staggering Association with physics I/O classification (history, initial, restart, boundary)

 

Communication points and patterns Configuration lists (e.g. namelists)



Program for auto-generating sections of WRF from database:



570 Registry entries



30-thousand lines of automatically generated WRF code



Allocation statements for state data, I1 data

 

Argument lists for driver layer/mediation layer interfaces Interprocessor communications: Halo and periodic boundary updates, transposes

 

Code for defining and managing run-time configuration information Code for forcing, feedback and interpolation of nest data Automates time consuming, repetitive, error-prone programming Insulates programmers and code from package dependencies Allow rapid development Documents the data

Registry data base

  Currently implemented as a text file: Registry/Registry Types of entry: 

State

– Describes state variables and arrays in the domain structure

 

Dimspec

– Describes dimensions that are used to define arrays in the model

– Describes local variables and arrays in solve



Typedef

– Describes derived types that are subtypes of the domain structure

 

Rconfig

– Describes a configuration (e.g. namelist) variable or array

Package

– Describes attributes of a package (e.g. physics)

 

Halo

– Describes halo update interprocessor communications

Period

– Describes communications for periodic boundary updates



Xpose

– Describes communications for parallel matrix transposes

State/L1 Entry (Registry)



Elements

 

Entry :

The keyword “state”

Type :

The type of the state variable or array (real, double, integer, logical, character, or derived)   

Sym :

The symbolic name of the variable or array

Dims

Use :

A string denoting the dimensionality of the array or a hyphen (-) A string denoting association with a solver or 4D scalar array, or a hyphen     

NumTLev :

An integer indicating the number of time levels (for arrays) or hypen (for variables)

Stagger : IO :

String indicating staggered dimensions of variable (X, Y, Z, or hyphen) String indicating whether and how the variable is subject to I/O and Nesting

DName : Descrip :

Metadata name for the variable Metadata description of the variable 

Example

# Type Sym Dims Use Tlev Stag IO Dname Descrip # definition of a 3D, two-time level, staggered state array state real ru ikj dyn_em 2 X irh "RHO_U" "X WIND COMPONENT“ i1 real ww1 ikj dyn_em 1 Z

State Entry

–

different output times

 Example

In Registry

state real ru ikj dyn_em 2 X irh0

"RHO_U" "XX“

In namelist.input

auxhist

_outname = 'pm_output_d_' auxhist

_interval = 10000, 10000, 5 frames_per_auxhist

= 30, 30, 24 auxhist

_begin_y = 0 auxhist

_begin_mo = 0 auxhist

_begin_d = 1 auxhist

_begin_h = 0 auxhist

_begin_m = 0 auxhist

_begin_s = 0 io_form_auxhist

= 2,

This will give you a five minute output interval on domain 3 starting after 1 day simulation.

Dimspec entry



Elements



Entry :

The keyword “dimspec”  

DimName : Order :

The name of the dimension (single character) The order of the dimension in the WRF framework (1, 2, 3, or ‘ ‘)   

HowDefined : CoordAxis :

specification of how the range of the dimension is defined which axis the dimension corresponds to, if any (X, Y, Z, or C)

DatName :

metadata name of dimension 

Example

dimspec i 1 standard_domain x west_east dimspec j 3 standard_domain y south_north dimspec k 2 standard_domain z bottom_top dimspec l 2 namelist=num_soil_layers z soil_layers

Package Entry (Registry)



Elements

    

Entry

: the keyword “package”,

Package name

: the name of the package: e.g. “kesslerscheme”

Associated rconfig choice :

the name of a rconfig variable and the value of that variable that choses this package

Package state vars :

unused at present; specify hyphen (-)

Associated 4D scalars :

the names of 4D scalar arrays and the fields within those arrays this package uses 

Example

# specification of microphysics options package passiveqv mp_physics==0 package kesslerscheme mp_physics==1 package linscheme mp_physics==2 package ncepcloud3 mp_physics==3 package ncepcloud5 mp_physics==4 moist:qv moist:qv,qc,qr moist:qv,qc,qr,qi,qs,qg moist:qv,qc,qr moist:qv,qc,qr,qi,qs # namelist entry that controls microphysics option rconfig integer mp_physics namelist,namelist_04 max_domains 0

Comm entries: halo and period



Elements

 

Entry :

keywords “halo” or “period”

Commname :

name of comm operation 

Description :

 For halo: defines the halo or period operation npts:f1,f2,...[;npts:f1,f2,...]*  For period: width:f1,f2,...[;width:f1,f2,...]* 

Example

# first exchange in eh solver halo HALO_EH_A dyn_em 24:u_2,v_2,ru_1,ru_2,rv_1,rv_2,w_2,t_2;4:pp,pip # a periodic boundary update period PERIOD_EH_A dyn_em 2:u_1,u_2,ru_1,ru_2,v_1,v_2,rv_1,rv_2,rw_1,rw_2

4D Tracer Arrays

    State arrays, used to store arrays of 3D fields such as moisture tracers, chemical species, ensemble members, etc.

First 3 indices are over grid dimensions; last dimension is the tracer index Each tracer is declared in the Registry as a separate

state

array but with

and optionally also

modifiers to the dimension field of the entry The field is then added to the 4D array whose name is given by the use field of the Registry entry

Package Entry (Registry)

state real qv ikjft moist 2 \ i01rhusdf=(bdy_interp:dt,rqv_b,rqv_bt) "QVAPOR" "Water vapor mixing ratio" "kg kg-1" state real qc ikjft moist 2 \ i01rhusdf=(bdy_interp:dt,rqc_b,rqc_bt) "QCLOUD" "Cloud water mixing ratio" "kg kg-1" state real qr ikjft moist 2 \ i01rhusdf=(bdy_interp:dt,rqr_b,rqr_bt) "QRAIN" "Rain water mixing ratio" "kg kg-1" state real qi ikjft moist 2 \ i01rhusdf=(bdy_interp:dt,rqi_b,rqi_bt) "QICE" "Ice mixing ratio" "kg kg-1" state real qs ikjft moist 2 \ 1" i01rhusdf=(bdy_interp:dt,rqs_b,rqs_bt) "QSNOW" "Snow mixing ratio" "kg kg state real qg ikjft moist 2 \ i01rhusdf=(bdy_interp:dt,rqg_b,rqg_bt) "QGRAUP" "Graupel mixing ratio" "kg kg-1"

4D

Tracer

Arrays

 The extent of the last dimension of a tracer array is from PARAM_FIRST_SCALAR to num_

tracername

 Both defined in Registry-generated frame/module_state_description.F

 PARAM_FIRST_SCALAR is a defined constant (2)  Num_

tracername

is computed at run-time in set_scalar_indices_from_config (module_configure)  Calculation is based on which of the tracer arrays are associated with which specific packages in the Registry and on which of those packages is active at run time (namelist.input)

4D

Tracer

Arrays

   Each tracer index (e.g. P_QV) into the 4D array is also defined in module_state_description and set in set_scalar_indices_from_config Code should always test that a tracer index greater than or equal to PARAM_FIRST_SCALAR before referencing the tracer (inactive tracers have an index of 1) Loops over tracer indices should always run from PARAM_FIRST_SCALAR to num_

tracername --

EXAMPLE

4D

Tracer

Array Example

• 4D moisture field, moist_1(i,k,j,?) ? =

P_QV (water vapor) P_QC (cloud water) P_QI (cloud ice) P_QR (rain) P_QS (snow) P_QG (graupel)

IF (qi_flag) then (the memory of cloud ice is allocated) . . .

Directory Structure

Registry

WRF Mass-Coordinate Model Integration Procedure

WRFV3/dyn_em/solve_em.F

Begin time step Runge-Kutta loop (steps 1, 2, and 3) (i) advection, p-grad, buoyancy using  

,   ,     (ii) if step 1 (first_rh_part1/part2) physics, save for steps 2 and 3 (iii) assemble dynamics tendencies Acoustic step loop (i) advance U,V, then then w, (ii) time-average U,V,  ,  ,   End acoustic loop Advance scalars using time-averaged U,V,  End Runge-Kutta loop Other physics (currently microphysics) End time step

… phy_init phy_prep radiation_driver surface_driver pbl_driver cumulus_driver WRF … solve_em part1 DYNAMICS .

moist_physics_prep microphysics_driver

Physics Calculate decoupled variable tendencies • Cumulus parameterization • Boundary layer parameterization • Radiation parameterization Update decoupled variables directly • Microphysics

Physics three-level structure

solve_em Physics_driver SELECT CASE (CHOICE)

CASE ( NOPHY ) CASE ( SCHEME1 ) CALL XXX CASE ( SCHEME2 )

CALL YYY CASE DEFAULT

END SELECT Individual physics scheme (

XXX

)

Rules for WRF physics

 Naming rules module_ yy _

xxx

(module) yy = ra is for radiation bl is for PBL sf is for surface and surface layer cu is for cumulus mp is for microphysics.

xxx

= individual scheme ex, module_ cu _

grell

Rules for WRF physics

 Naming rules R XX

YY

TEN (tendencies) XX = variable (th, u, v, qv, qc, … )

YY

= ra is for radiation bl is for PBL cu is for cumulus ex, R TH

BL

TEN

Rules for WRF physics

 Naming rules  

One scheme one module Coding rules (later)

WRF Physics Features

• Unified global constatnts

(module_model_constants.F)

REAL , PARAMETER :: r_d = 287.

REAL , PARAMETER :: r_v = 461.6

REAL , PARAMETER :: cp = 7.*r_d/2.

REAL , PARAMETER :: cv = cp-r_d .

WRF Physics Features

• Unified global constatnts

(module_model_constants.F) • Unified common calculations (saturation mixing ratio) • Vertical index (kms is at the bottom)

Implement a new physics scheme

      Prepare your code Create a new

module

Declare new variables and a new package in

Registry

Modify Do Modify

namelist initialization solve_em.F

 Modify

phy_prep

Implement a new physics scheme

 Modify

cumulus_driver.F

(use cumulus parameterization as an example)  Modify

calculate_phy_ten

 Modify

phy_cu_ten (module_physics_addtendc.F)

 Modify

Makefile

 Compile and test

… phy_init phy_prep radiation_driver surface_driver pbl_driver cumulus_driver WRF … solve_em part1 DYNAMICS .

moist_physics_prep microphysics_driver

Prepare your code

1. F90 a) Replace continuation characters in the 6th column with f90 continuation `&‘ at end of previous line F77 Subroutine kessler(QV, T, + its,ite,jts,jte,kts,kte, + ims,ime,jms,jme,kms,kme, + ids,ide,jds,jde,kds,kde) F90 Subroutine kessler(QV, T, . . . & its,ite,jts,jte,kts,kte, & ims,ime,jms,jme,kms,kme,& ids,ide,jds,jde,kds,kde )

Prepare your code

1. F90 a) Replace continuation characters in the 6th column with f90 continuation `&‘ at end of previous line b) Replace the 1st column `C` for comment with `!` F77 c This is a test F90 ! This is a test

Prepare your code

1. F90 2. No common block common/var1/T,q,p, … WRF Subroutine sub(T,q,p, ….) real,intent(out), & dimension(ims:ime,kms:kme,jms:jme):: T,q,p

Prepare your code

1. F90 2. No common block 3. Use “

implicit none

” 4. Use “

intent

” Subroutine sub(T,q,p, ….) implicit none real,intent(out), & dimension(ims:ime,kms:kme,jms:jme):: T real,intent( in), & dimension(ims:ime,kms:kme,jms:jme):: q real,intent(inout), & dimension(ims:ime,kms:kme,jms:jme):: p

Prepare your code

1. F90 2. No common block 3. Use “

implicit none

” 4. Use “

intent

” 5.Variable dimensions Subroutine sub(global,….) implicit none real,intent(out), & dimension(ims:ime,kms:kme,jms:jme):: global real,dimension(its:ite,kts:kte,jts:jte):: local

Prepare your code

1. F90 2. No common block 3. Use “

implicit none

” 4. Use “

intent

” 5.Variable dimensions 6.Do loops

do j = jts, jte do k = kts, kte do i = its, ite ...

enddo enddo enddo

Implement a new physics scheme

 Create a new module ex,

module_cu_exp.F (plug in all your codes)

 Go Registry and declare a new package (and new variables) (WRFV1/Registry) package kfscheme cu_physics==1 - package bmjscheme cu_physics==2 - -

package expscheme cu_physics==3 - -

Implement a new physics scheme

 Create a new module ex,

module_cu_exp.F (plug in all your codes)

 Go Registry and declare a new package (and new variables) (WRFV1/Registry) Cloud microphysics package kesslerscheme mp_physics==1 - moist:qv,qc,qr package linscheme mp_physics==2 - moist:qv,qc,qr,qi,qs,qg package wsm3 mp_physics==3 - moist:qv,qc,qr package wsm5 mp_physics==4 - moist:qv,qc, qr,qi,qs

Implement a new physics scheme

 Create a new module ex,

module_cu_exp.F (plug in all your codes)

 Go Registry and declare a new package (and new variables) (WRFV1/Registry)  Modify namelist.input and assign cu_physics =

3

WRF

(

dyn_em) (start_em.F)

start_domain_em (phys) (module_physics_init.F) phy_init cu_init …….

(

dyn_em)

solve_em

phys/module_physics_init.F

 Pass new variables down to cu_init (

dyn_em) (start_em.F)

start_domain_em (phys) (module_physics_init.F) phy_init cu_init WRF …….

(

dyn_em)

solve_em

phys/module_physics_init.F

  Pass new variables down to cu_init Go subroutine cu_init Include the new module and create a new SELECT case

phys/module_physics_init.F

Subroutine cu_init(…) .

USE module_cu_kf USE module_cu_bmj USE module_cu_exp cps_select: SELECT CASE(config_flags%cu_physics) CASE (KFSCHEME) CALL kfinit(...) CASE (BMJSCHEME) CALL bmjinit(...) CASE (EXPSCHEME) CALL expinit(...) CASE DEFAULT END SELECT cps_select Match the package name in Registry

phy_prep … phy_init WRF … solve_em part1 DYNAMICS .

moist_physics_prep microphysics_driver

phy_prep/moist_physics_prep

• Calculate required variables • Convert variables from C grid to A grid

… phy_init WRF … solve_em part1 phy_prep radiation_driver surface_driver pbl_driver cumulus_driver Expcps DYNAMICS .

moist_physics_prep microphysics_driver

Three-level structure

solve_em Physics_driver SELECT CASE (CHOICE)

CASE ( NOPHY ) CASE ( SCHEME1 ) CALL XXX CASE ( SCHEME2 )

CALL YYY CASE DEFAULT

END SELECT Individual physics scheme (

XXX

)

cumulus_driver.F

 Go physics driver (cumulus_driver.F) Include the new module and create a new SELECT CASE in driver Check available variables in drivers (variables are explained inside drivers)

Module_cumulus_driver.F

MODULE module_cumulus_driver CONTAINS

Subroutine cumulus_driver (….) .

!-- RQICUTEN Qi tendency due to ! cumulus scheme precipitation (kg/kg/s) !-- RAINC accumulated total cumulus scheme precipitation (mm) !-- RAINCV cumulus scheme precipitation (mm) !-- NCA counter of the cloud relaxation ! time in KF cumulus scheme (integer) !-- u_phy u-velocity interpolated to theta points (m/s) !-- v_phy v-velocity interpolated to theta points (m/s) !-- th_phy potential temperature (K) !-- t_phy temperature (K) !-- w vertical velocity (m/s) !-- moist moisture array (4D - last index is species) (kg/kg) !-- dz8w dz between full levels (m) !-- p8w pressure at full levels (Pa)

Module_cumulus_driver.F

MODULE module_cumulus_driver CONTAINS Subroutine cumulus_driver . USE module_cu_kf USE module_bmj_kf USE module_cu_exp cps_select: SELECT CASE(config_flags%cu_physics) CASE (KFSCHEME) CALL KFCPS(...) CASE (BMJSCHEME) CALL BMJCPS(...)

CASE (EXPSCHEME) CALL EXPCPS(...)

Match the package name in Registry CASE DEFAULT END SELECT cps_select

… phy_init phy_prep radiation_driver surface_driver pbl_driver cumulus_driver WRF … solve_em part1 DYNAMICS .

moist_physics_prep microphysics_driver

solve_em part1 phy_prep cumulus_driver expcps part2 calculate_phy_tend update_phy_ten phy_cu_ten message passing ?

DYNAMICS .

phys/module_physics_addtendc.F

Subroutine phy_cu_ten (… ) .

. CASE(BMJSCHEME) CASE (EXPSCHEME) CALL add_a2a (rt_tendf, RTHCUTEN,… ) CALL add_a2c_u(ru_tendf,RUBLTEN,… ) CALL add_a2c_v(rv_tendf,RVBLTEN,… ) .

if ( QI_FLAG ) & CALL add_a2a(moist_tendf(ims,kms,jms,P_QV),RQVCUTEN, .. & ids,ide, jds, jde, kds, kde, & ims, ime, jms, jme, kms, kme, & its, ite, jts, jte, kts, kte ) .