access_aps1_access_c_detail - ACCESS-NRI/accessdev-Trac-archive GitHub Wiki
Model in Details
The ACCESS-C operational standard experiment aps1_access_c consists of four parts,
- System files: located on
raijin:$HOME/roses/aps1_access_c
, copied by the installation script. - Suite files: located on
accessdev:$HOME/roses/aps1_access_c
, copied by the installation script. - Data output: located on
raijin:/short/$PROJECT/$USER/aps1_access_c_S
and
raijin:/short/$PROJECT/$USER/ncdata/aps1_access_c_S
;
those are the forecast data produced by the UM run jobs.
- Source code: located on
raijin:/short/$PROJECT/$USER/aps1_access_c_src
, copied by the installation script
In this sectiom, we will explain the components and the structure of the system files in details; we also
describe the tasks/steps in the suite definition in details for the better understanding of the experiment; and
finally we introduce the compilation of the source code for advanced research activity.
ACCESS-C in Details
As explained, aps1_access_c system file, suite and source codes are copied to either raijin
or accessdev
and
output files are produced when running the suite. The details of these information are illustrated for higher
level of understanding of the whole system. By grabbing those knowledge, users may implement advanced research
by configuring settings, modifying the source codes and some other methods to enhance the forecasting accuracy, running
effieciency etc.
- System files:
raijin:$HOME/roses/aps1_access_c
beans
:makebc
: executable/scripts for making lateral boundary conditionmars
: executable/scripts for converting/archiving dataum
: executable/scripts for um forecastingum_components
: advanced users may modify the configuration files inside the two following components
for research
* xbcjx
: um component called by recon
and um_run
jobs; shared by 6 domains.
* xbdmx
: um component called by recon_lores
; shared by 6 domains.
umr
: executable/scripts for making initial conditionutil
: utility Python scriptsbin
:env.aps1_access_c
: settings for the system, such as data input and output directory, log directory,
working directory, archiving options, locations of dump and pi files etc;
you may configure settings as you wish
produceLinks.ksh
: script to create soft links toCylc
scriptsCylc
scripts:Cylc
job script; you may check what is really done by investigating scripts closelyconf
(only advanced users may need to modify some of the configuration files if users understand
what they are doing):
-
ANCILmaster
: -
PS25
: -
STASHmaster
: -
ancil
: ancillary files, including land-sea-mask, landfrac and orog, for 6 domains; do not need to be modified -
spectral
: -
log.S
: log files from all tasks of the suite when running -
Cylc
Suite:accessdev:$HOME/roses/aps1_access_c
-
suite.rc
: suite definition file which defines jobs, job flow, cycle time, resources for jobs etc;
the command rose suite-run
picks up this file suite.rc
to run the model
-
other files but not important in this case
-
Output data:
raijin:/short/$PROJECT/$USER/
-
raijin:/short/$PROJECT/$USER/aps1_access_c_S
contains all input and output data running the model;
in this folder each run is given an individual directory as YYYYMMDDHH
, such as 2014011800
to
accommodate inputs and outputs. In this directory of YYYYMMDDHH
,
ic
: dump file for producing IC for each domainlbc
: pi files for producing LBC for each domain; usually soft links to pi files to save disk usageBN
: IC fileastart.BN
, LBC filelbc.BN
and forecast pp filesSY
: similar toBN
VT
: similar toBN
AD
: similar toBN
PH
: similar toBN
DN
: similar toBN
- Note: The directory
raijin:/short/$PROJECT/$USER/aps1_access_c_S/YYYYMMDDHH
will be moved to
raijin:/short/$PROJECT/$USER/aps1_access_c_S/previous_dates/YYYYMMDDHH.$$
after suite completes.
$$
is the run ID for the specific job does the move
raijin:/short/$PROJECT/$USER/ncdata/aps1_access_c_S
contains all forecast data in nectCDF format;
go to YYYYMMDDHH/DOMAIN
, e.g., 2014011800/BN
for Brisbane forecasting data at 2014011800Z run.
- Source codes:
raijin:/short/$PROJECT/$USER/aps1_access_c_src
;
see the APS1 ACCESS-C Compilation of Source Code for compilation instruction
umbase
: Modify source codes in here for testing new scienceumrecon
: Contains configuration file to compilerecon
executableummodel
: Contains configuration file to compileum
executable
ACCESS-C Cylc Suite in Details
ACCESS-C is a relatively simple forecast-only system compared with the Bureau Global and Regional
operational assimilation and forecast systems. The suite definition file suite.rc
is located at
accessdev:$HOME/roses/aps1_access_c/
. The suite definition file defines all the jobs of aps1_access_c
standard experiment. You may modify the suite definition file for the following purposes,
- add or remove tasks from the
suite.rc
- update the cycle time by modifying
initial cycle time
andfinal cycle time
;
in the standard experiment, initial cycle time
and final cycle time
are both set at
2014011800: it only does one run at 2014011800Z
- tune the resources, such as number of cores and memory, for each task in the directive item
We use a tree-like structure to display all tasks in suite.rc
and their descriptions.
Note that tasks are listed in logically running order, which may not be the case in some Cylc
views which may
use alphabetical order.
- -->
setup
AC_setup
: setup the folders for all jobs; Please go to
DATADIR=/short/$PROJECT$USER/aps1_access_c_S
to check the output
short adminsitration job finishing in seconds
wait_for
: triggered by completion ofAC_setup
; check the availability of
the input data for creating initial and LB conditions
short job finishing in seconds
AC_get_initial_conditions
: triggered bywait_for
; get the dump file
short job finishing within minutes
AC_get_LB_conditions
: triggered bywait_for
; get the pi files
(in most cases produce soft links to pi files to save disk usage)
short job finishing within a minute
- -->
brisbane
make_lbc
: producing the lateral boundary condition
long job finishing within 30-60 minutes
recon
: reconfiguration step to produce the initial condition at ACCESS-C resolution
medium job finishing within few minutes
recon_lores
: reconfiguration step to produce the initial condition at
the original resolution of the nested NWP system, i.e., ACCESS-R (12km) in this case
medium job finishing within few minutes
finalise_recon
: copy wind fields from the IC of steprecon_lores
to that ofrecon
short job finishing within minutes
um_run
: UM forecasting job
long job finishing within 30-60 minutes
um2grb
: convert forecast data fromPP
format togrib
as requested
medium job finishing within few minutes
ncdf
: convert forecast data fromPP
format tonetCDF
as requested
medium job finishing within few minutes
-
-->
sydney
-
-->
victas
-
-->
adelaide
-
-->
perth
-
-->
darwin
-
-->
finalise
-
AC_cleanup
: clean up unnecessary files after forecasts finish
short job finishing within seconds
Note:
- Jobs under each domain are same, i.e. as shown for
brisbane
domain. - Please refer to the
Cylc
scripts located inraijin:$HOME/roses/aps1_access_c/bin
for more information.
In every script, usually the purpose of the script is described at the header section. In addition,
the input data required by the job and the output produced by the job are also recorded at the header
section for reference.
APS1 ACCESS-C Compilation of Source Code
Researchers may need to modify the source codes for testing new Physics, improving efficiency and so on.
The source code is copied by the ~access/AccessModelExperimentLibrary/aps1_access_c/install_aps1_access_c.ksh
to raijin:/short/$PROJECT/$USER/aps1_access_c_src
. The modification on source codes must be done in umbase
place and users may follow the instructions to do the compilation,
- Update the environment,
module purge
module use ~access/modules
module load intel-cc/12.1.8.273
module load intel-fc/12.1.8.273
module load openmpi/1.6.5
module load netcdf/4.3.0
module load fcm/2.3.1
- Go to
raijin:/short/$PROJECT/$USER/aps1_access_c_src/ummodel
and type
fcm build
to produce UM executable. Look for the executable in raijin:/short/$PROJECT/$USER/aps1_access_c_src/ummodel/bin
,
the name of the executable is UM7.6_UK4_EXEC_01.exe
.
- Go to
raijin:/short/$PROJECT/$USER/aps1_access_c_src/umrecon
and type
fcm build
to produce UM Recinfiguration executable. Look for the executable in raijin:/short/$PROJECT/$USER/aps1_access_c_src/umrecon/bin
,
the name of the executable is qxreconf
.