access_re_access_x_vn7.8_1.5km_detail - ACCESS-NRI/accessdev-Trac-archive GitHub Wiki
Model in Details
access_x_vn7.8_1.5km shares the same executable with access_c_vn7.8_1.5km. Please go to
https://trac.nci.org.au/trac/access/wiki/access_c_vn7.8_1.5km_detail
for the instructions on compiling the source code. We will focus on detailing ACCESS-X
system, suite and design in this section.
The standard experiment access_x_vn7.8_1.5km
consists of four parts,
- System files: located on
raijin:$HOME/roses/access_x_vn7.8_1.5km
, copied by the installation script. - Suite files: located on
accessdev:$HOME/roses/access_x_vn7.8_1.5km
, copied by the installation script. - Data output: located on
raijin:/short/$PROJECT/$USER/access_x_vn7.8_1.5km_S
and
raijin:/short/$PROJECT/$USER/ncdata/access_x_vn7.8_1.5km_S
;
those are the forecast data produced by the UM run jobs.
- Source code: located on
raijin:/short/$PROJECT/$USER/access_x_vn7.8_1.5km_src
, copied by the installation script
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.
access_x_vn7.8_1.5km in Details
The structure of access_x_vn7.8_1.5km
system files is detailed here for deeper understanding of the system.
After grabbing those knowledge, users may be able to engage in advanced research activities.
- System files:
raijin:$HOME/roses/access_x_vn7.8_1.5km
beans
:ancil
: executable/scripts for producing ancillary filesmakebc
: executable/scripts for making lateral boundary conditionmars
: executable/scripts for converting/archiving dataum
: executable/scripts for um forecastingum_components
: advanced users may modify the configuration files inside the two following components
for research
* xbcjx
: um component called by recon
and um_run
jobs; shared by 6 domains.
* xbdmx
: um component called by recon_lores
; shared by 6 domains.
umr
: executable/scripts for making initial conditionutil
: utility Python scriptsbin
:env.access_x_vn7.8_1.5km
: settings for the system, such as data input and output directory, log directory,
working directory, archiving options, locations of dump and pi files etc;
you may configure settings as you wish
produceLinks.ksh
: script to create soft links toCylc
scriptsCylc
scripts:Cylc
job script; you may check what is really done by investigating scripts closelyconf
(only advanced users may need to modify some of the configuration files if users understand
what they are doing):
-
ANCILmaster
: -
PS25
: -
STASHmaster
: -
ancil
: ancillay files, including land-sea-mask, landfrac and orog produced on fly -
spectral
: -
log.S
: log files from all tasks of the suite when running -
Cylc
Suite:accessdev:$HOME/roses/access_x_vn7.8_1.5km
-
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/access_x_vn7.8_1.5km_S
conatins 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 usageSW1
: IC fileastart.BN
, LBC filelbc.BN
and forecast pp filesSW2
: similar toSW1
- Note: The directory
raijin:/short/$PROJECT/$USER/access_x_vn7.8_1.5km_S/YYYYMMDDHH
will be moved to
raijin:/short/$PROJECT/$USER/access_x_vn7.8_1.5km_S/previous_dates/YYYYMMDDHH.$$
after suite completes.
$$
is the run ID for the specific job does the move
raijin:/short/$PROJECT/$USER/ncdata/access_x_vn7.8_1.5km_S
contains all forcast data in nectCDF format;
go to YYYYMMDDHH/DOMAIN
, e.g., 2014011800/SW1
for SW1 forecasting data at 2014011800Z run.
- Source codes:
raijin:/short/$PROJECT/$USER/access_x_vn7.8_1.5km_src
;
see https://trac.nci.org.au/trac/access/wiki/access_c_vn7.8_1.5km_detail
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_x_vn7.8_1.5km Cylc Suite in Details
The suite defintion file suite.rc
of access_x_vn7.8_1.5km
is located at accessdev:$HOME/roses/access_x_vn7.8_1.5km/
.
The suite definition file defines all the jobs of access_x_vn7.8_1.5km
standard experiment.
You may modify the suite definition file for the following purposes,
- add or remove tasks from the
suite.rc
- update the cycle time by modifying
initial cycle time
andfinal cycle time
;
in the standard experiment, initial cycle time
and final cycle time
are both set at
2014011800: it only does one run at 2014011800Z
- tune the resources, such as number of cores and memory, for each task in the directive item
We use a tree-like structure to display all tasks in suite.rc
and their descriptions.
Note that tasks are listed in logically running order, which may not be the case in some Cylc
views which may
use alphabetical order.
- -->
setup
AC_setup
: setup the folders for all jobs; Please go to
DATADIR=/short/$PROJECT$USER/access_x_vn7.8_1.5km_S
to check the output
wait_for
: triggered by completion ofAC_setup
; check the availability of
the input data for creating initial and LB conditions
AC_get_initial_conditions
: triggered bywait_for
; get the dump fileAC_get_LB_conditions
: triggered bywait_for
; get the pi files
(in most cases produce soft links to pi files to save disk usage)
- -->
SW1
- ancil_nml: read
raijin:$HOME/roses/access_x_vn7.8_1.5km/SW1
orSW2
and
produce the ancil namelist to raijin:$HOME/roses/access_x_vn7.8_1.5km/beans/ancil
;
the output is grid.SW1.nml
or grid.SW2.nml
.
- ancil: read ancil namelist and create the ancillary files onto
raijin:$HOME/roses/access_x_vn7.8_1.5km/conf/ancil/SW1
or SW2
;
ancillary files include qrparm.landfrac
, qrparm.mask
and qrparm.orog
.
- makebc_nml: read
grid.SW1.nml
orgrid.SW2.nml
and produce the makebc namelist;
output is makebc.SW1.nml
or makebc.SW2.nml
in raijin:$HOME/roses/access_x_vn7.8_1.5km/beans/makebc
- um_nml: read ancillary files and produce um namelist; output is
SW1.um.nml
orSW2.um.nml
in
raijin:$HOME/roses/access_x_vn7.8_1.5km/beans/um
make_lbc
: producing the lateral boundary conditionrecon
: reconfiguration step to produce the initial condition at ACCESS-X resolutionrecon_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
-
finalise_recon
: copy wind fields from the IC of steprecon_lores
to that ofrecon
-
um_run
: UM forecasting job -
um2grb
: convert forecast data fromPP
format togrib
as requested -
ncdf
: convert forecast data fromPP
format tonetCDF
as requested -
-->
SW2
-
-->
finalise
-
AC_cleanup
: clean up unnecessary files after forecasts finish
Note:
- Jobs under each domain are same, i.e. as shown for
SW1
domain. - Please refer to the
Cylc
scripts located inraijin:$HOME/roses/access_x_vn7.8_1.5km/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.