NCAS Unified Model (UM) Introductioncms.ncas.ac.uk/documents/training/May2013/um_intro_nov.2012.pdf · UM Course, Reading, Nov. 2012 1 NCAS Unified Model (UM) Introduction Part 1

UM Course, Reading, Nov. 2012 1

NCAS

Unified Model (UM) Introduction

Part 1 – Overview of the UM System


- What is the UM?

- UM User Interface (UMUI)

- Running the UM


The Unified Model (UM) is

owned and developed by UK Met Office, used for both

commercial weather forecasts as well as climate research and advice

to government, for example IPCC reports

PUM (Ported UM) is used under licence by UK academic

community for weather and climate research

used under licence by forecast/climate agencies around the world

[Norway, South Africa, Australia…]

The UM is used by a large and diverse community of users.

The UM is expected to run on a diverse range of computers.


At the UK Met Office

Unified Model code

Atmosphere

Ocean

Data assimilation

system

UKMO Data

archive Observations

UMUI SCS CAP


Ported Unified Model (PUM)

Unified Model code

Atmosphere

Ocean

UMUI

Contains

1) UM code + fixes

2) UM User guide +

documentation + code

browser

3) UM Tools

4) Installation examples

+ 2 or 3 example jobs

tested on 2 or 3

computers+compilers


NCAS supported PUM on HPC services (HECToR, MONSooN)

Unified Model code

Atmosphere

Ocean

UMUI

Contains

1) UM code installed,

optimised, tested and

fixed

2) Changes to UMUI and

archiving mechanism

3) Tools and utilities both

from UKMO and NCAS

4) Managed data from Met

Office and ECMWF

+ many user jobs, both

climate and NWP

HPC Data

archive


UM Versions

Old Dynamics New Dynamics

UKMO 4.5 4.7 5.5 6.0 6.1 6.3 6.6 7.1 7.3…8.2

NCAS + + ? + + + HECToR Y Y Y Y Y

MONSooN Y Y Y Y

Code maintenance nupdate nupdate pumscm FCM

Ocean code old old old NEMO

The Met Office (UKMO) release new versions regularly.

Each version is independent and stands alone.

NCAS may not always port each new version to HECToR or Monsoon

NCAS has very limited effort to port new versions to external systems

NCAS carries out limited testing and provides only sample jobs for users


Unified Model (UM)

versions 4.5 6.1 7.3

configurations

Hadcm3 Hadgam1 Hadgem3-AO

experiments

Nugam

IPCC scenario A3

The UM is not a single fixed piece of code.

In the UK academic community there is a broad UM spectrum as

multiple UM versions are used

new UM configurations are developed

a large variety of UM experiments are performed

QESM

PS18

6.6.3

Hadgem2-ES

7.6


The Unified Model (UM) is a collection of numerical

modelling software which

• can be used in atmosphere only, ocean only, or coupled or with a slab

ocean

• can be coupled to other ocean models via OASIS eg Hadopa , or

other components NEMO, CICE, JULES eg HadGEM3

• may be run in many different modes

aquaplanet

global or meso-scale

regional coupling

in an NCAS ensemble framework UMCET


• runs at different resolutions

Global climate (N48, N96, N144, N216, N512)

LAM (Limited Area Model) (UK 12 km, 4 km)

L38 - L60 – increased vertical resolution

Higem – N144 atmosphere + 1/3⁰ ocean

N48 N96 N144 N216

270 km 135 km 90 km 60 km

96 x 73 192 x 145 288 x 217 432 x 325

3.75º x 2.4º 1.88º x 1.24º 1.25º x 0.83º 0.83º x 0.56º


- What is the UM?


- Running the UM


UMUI - UM User Interface

The UMUI

• is a windows interface to the UM

• is written in Tcl/Tk

• is currently offered via the PUMA service

•which provides all the latest UMUI changes

•centralised access to local files (hand edits etc)

•common job database for ALL academic users

•creates the scripts which control the UM run

(some changes to these scripts may be needed for certain new

bits of code – hand edits)

• has been extended to accommodate non-UKMO users

• assigns values to namelist switches used by the UM at runtime

• selects branches used to build the model (later versions)

• is different for the old and new dynamics but both can be

accommodated within the same UMUI.


UMUI – creating UM jobs

• choose a UM job which is close to the one you want to

run either from a colleague, UKMO or from NCAS

- either copy the job into your own job if they are in the

same local database

- or upload a basis file, the full description of a UM job

which has come from another UMUI database,

into your own job

• NCAS standard jobs should be available under the userid umui

Basis files can be downloaded from the UMUI and emailed.


UMUI - vocabulary

Experiments : xxab

- a grouping of UM jobs

- identified by a description in the UMUI

- only your experiments are displayed by the UMUI,

unless otherwise requested

- experiments can be created, copied and deleted

Jobs : xxabc

- up to 26 jobs can be grouped in an experiment

- jobs can be created, copied and deleted

- 2 jobs can be differenced

Navigation windows input windows



UM – Submitting the model

UMUI

scripts

namelists

code

MONSooN

HECToR

submit

What do you need to know about the system where the UM is installed?

• directory structure and disk space setup

• job submission mechanism and queue structures

• input files available e.g. modsets, start files, ancillary files

The UM uses namelists for setting parameters at runtime, these

are set in the UMUI.


- What is the UM?


- Running the UM


Running a UM job

Stage 1 - Compilation

UMUI – what options? Sub_model_independent -> Compilation and Modification -> Compile options

Options : compile only, compile and run, run from a named executable

Compile Overrides: Used on some computers for compiler options

to speed up some sections of the code or to overcome problems.

• FCM manages code components

• [uses nupdate/pumscm to extract and change code • gathers all subroutines] • creates makefiles for compilation and loading

• compiles and links the code according to options selected

• creates an executable


Running a UM job

Stage 2 - Reconfiguration

Reconfiguration is a standalone program which modifies (reconfigures)

UM atmosphere or ocean start files

• FMC code management

• uses nupdate/pumscm for any modifications to the code

• compiles the code

• runs the reconfiguration in parallel for new dynamics

in the serial queue for the old dynamics

• produces new start files

UMUI – what options?

Sub_model_independent -> compilation and modifications

-> modification to the reconfiguration

Options: run from a standard executable, run from an existing

executable, compile and create an executable


Running a UM job

Stage 3 - Running

UMUI – what options?

Sub_model_independent ->

Start date and run length

For length of model run and the number of processors to use

you need to understand the computer’s queue structure and the

performance of your job.

Job submission

• qsub for Cray XT4, XT6

• QSUBII for NEC at Hamburg, Earth Simulator

• LSF for SGIs

• Load leveller for IBMs

• @ for PCs and workstations


UM output

STASH

Output Filenames

Job output


Spatial and Temporal Averaging and Storage Handling

Atmosphere Ocean STASH STASH

1) select diagnostic from Load New Diagnostic section 2) Time profile when diagnostic will be output (start and end time and frequency) whether time processing required (accumulation, mean, time series) 3) Domain profile vertical (specify which levels) horizontal (limited area, meaning [ zonal, vertical, meridional, horizontal], weighting) 4) Usage profile select output unit for the diagnostic

STASH



STASH in the UMUI

The UMUI windows for STASH are different from model windows.

Available diagnostics are organised in sections. Some diagnostics

have HELP information, a lot don’t!

Diagnostics -> load new diagnostics -> (double click on the section)

Each internal model has it’s own diagnostics

Atmosphere -> STASH

Ocean -> STASH

Slab ocean -> STASH

Wave -> STASH

Just because a diagnostic is available doesn’t mean it works!

UM Course, Reading, Nov. 2012 25 Verify diagnostics (Ctl V)

Package switched on Package switched off


UM - STASHmaster file

Contains all the information on all the diagnostics available

One STASHmaster file for each internal model H1| SUBMODEL_NUMBER=1

H2| SUBMODEL_NAME=ATMOS

H3| UM_VERSION=4.5

#

#|Model |Sectn | Item |Name |

#|Space |Point | Time | Grid |LevelT|LevelF|LevelL|PseudT|PseudF|PseudL|LevCom|

#| Option Codes | Version Mask |

#|DataT |DumpP | PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8 PC9 PCA |

#|Rotate| PPFC | USER | LBVC | BLEV | TLEV |RBLEVV| CFLL | CFFF |

#

#======================================================================

#

1| 1 | 0 | 1 |PSTAR AFTER TIMESTEP |

2| 2 | 0 | 1 | 1 | 5 | -1 | -1 | 0 | 0 | 0 | 0 |

3| 00000000000000000000 | 00000000000000000001 |

4| 1 | 0 | 0 0 0 0 0 16 -99 -99 -99 -99 |

5| 0 | 8 | 0 | 129 | 0 | 0 | 0 | 9999 | 12 |

#

Use Paul Burton’s STASHmaster viewer to look at these files

http://ncas-cms.nerc.ac.uk

http://ncas-cms.nerc.ac.uk/




• Users can add new diagnostics

• Advice via the UM Information Service (STASH User Guide)

• User must provide a STASHmaster file local to the UMUI

STASH - Adding new diagnostics

Users can copy diagnostics setting from one UM job to another

using

copy_stash

and the two UM basis files. The two jobs must be the same version.


Output listing from the UM

Output listing quite large and confusing Output directory $HOME/um/umui_out Output listing filename, e.g. xagmc000.xagmc.o98342.t14136.leave Output listing options controlled by UMUI Submodel Independent -> Output Choices Check output listing for - timings reported at the end of the listing file - key words like ERROR, ABORT "file not found" Check presence of key files, executable after compilation start file after reconfiguration output files after model run


SUMMARY


How a UM experiment (HADAM3, UKMES, UK4km) is

defined.

A standard named UM experiment has

• a defined version of the UM (4.5, 6.1)

• a particular horizontal and vertical resolution

• particular settings in the UMUI

+ hand-edits, which change the settings in the UMUI

• include a controlled list of ‘mods’, which are changes to the UM source

code or particular branches in FCM

• use a defined set of input files, start files, ancillary files and lateral

boundary conditions

=> Named experiments can change and evolve at a different rate to UM

versions


NCAS

Unified Model (UM) Introduction

Part 2 – Code Maintenance


UM Code maintenance is different for

different versions

Version 4.5

a) nupdate (either original Cray version or UKMO C version)

Version 6.1

b) pumscm (almost the same as nupdate written in perl)

Version 6.3 and above

c) FCM Flexible Configuration Management

- written in perl

- based on subversion


UM User Interface

UMUI Local

UM code library

Input files

Output Remote

Analysis

Analysis and

Visualisation Local

2) Running the UM job

3) Analysis of UM output

1) Setting up the UM job

The UMUI produces a set of

scripts to run the UM that

assumes that the UM has been

installed with the structure

created by the installation

procedure.

a),b)


UM - Code

• UM code is written in Fortran with some C

• Fortran 77 with Fortran 90 extensions as well as Fortran 90

• uses NUPDATE (and derivatives) as a code maintenance tool

- either former Cray version now ported to

IBM, Linux, HP, DEC, Sun, SGI

- or UMKO portable version with limited functionality

- or PUMSCM (in perl) for the New Dynamics versions

NUPDATE user guide available on the NCAS-CMS

web site, PUMSCM has nearly the same functionality

but with some extra features.

a),b)


NUPDATE/PUMSCM

• each line in the program library

has a unique identifier

<DECK>.<line number>

• a new program library is only

created for new versions of the UM

DECK FRED

DECK JOE

Use a modification set (modset or mod) to change the program

library.

*IDENT TESTP */ test print statement

*DECLARE FRED

*I FRED.24

print *, ‘ temp in CONVEC’, T

Program Library

a),b)


NUPDATE/PUMSCM

Program Library (for each version of

the UM)

modset (change or modification

of the code)

nupdate or pumscm

*.f (compile file for each

subroutine or deck)

defs (nupdate controlled

definitions) apply

a),b)


From UM 6.3 onwards changes to the Unified Model source

code will be managed using FCM Flexible

Configuration Management

• source code managed through subversion

• full history of source code change using trac and wiki

• code extract system managed through scripts

• build system with scripts and make

c)


UMUI

UM code

Input files Output

Analysis

Analysis and

Visualisation Local

subversion +trac+wiki

User logs in

User

UM code

HPC service

PUMA

NCAS FCM service

is only available on

PUMA.

c)

Documents

NCAS Unified Model (UM) Introductioncms.ncas.ac.uk/documents/training/May2013/um_intro_nov.2012.pdf · UM Course, Reading, Nov. 2012 1 NCAS Unified Model (UM) Introduction Part 1