please spend sometime before the workshop to read and watch the video from the
previous ACCESS training workshop done by Chloe and Holger.
** note **
https://confluence.csiro.au/display/ACCESS/ACCESS+Training
**1. ACCESS-CM2 Training
**2. ACCESS-ESM1.5 Training https://confluence.csiro.au/display/ACCESS/ACCESS-ESM1.5+Training
**3. Setting up for ACCESS-ESM1.5 https://confluence.csiro.au/display/ACCESS/Setting+up+for+ACCESS-ESM1.5
**4. Archiver https://git.nci.org.au/cm2704/ACCESS-Archiver.git
** note ** Please Please Please make sure you can git clone and run the ESM before the workshop!!!
**1. Read throught the instruction but git clone the following link:
https://github.com/ars599/PI-DEMO
This is the one particullary used for the training!!!
**1. conver the atmosphere output file name from Jan to 001 (not necessary) ...
please use change_unext_esm_ars599.sh $job_id
**2. xconv Download
/g/data/access/projects/access/apps/xconv/1.94/xconv
**3. ACCESS Archiver
** note **
Check out from Tammas Loughran:
https://git.nci.org.au/tfl561/ACCESS-Archiver/-/tree/main
Usage is detailed unger nci git. (NCI account needed)
- to convert UM format to netCDF
- to move wrap data from archive to gdata (easy for OOD)
alternately can use from:
https://github.com/ars599/ACCESS-Archiver_tfl561
It was based on tfl561, and modify to fit AMOS 2022 demo activity
** to do list and a quick Q&A to help you setup and run Archiver**
Issue #4 #4
**3-0. Modify under wrap_ACCESS_Archiver.sh
**3-1. make sure the base outputs files (forexample user: ars599)
base_dir=/scratch/nf33/ars599/access-esm/archive
**3-2. output directory
arch_dir=/g/data/nf33/ars599/archive/CMIP6/ACCESS-ESM1-5/
**3-3. setup run type
#access_version = [cm2, cm2amip, cm2chem, esmscript, esmpayu, om2]
old ESM k shell script
access_version=esmscript
now payu ESM
access_version=esmpayu
basic knowledge of the namelist file for each module
**3-4. atm outputs need to convert to netCDF (xconv can only deal with single file)
#ncexists = [true, false]
#true: Copy netcdf version of file if it exists; false: Always use UM pp-file if it exists, whether or not netcdf version exists
ncexists=true
**3-5. convert subdaily 3h 6h data ?
#subdaily = [true, false]; convert subdaily atm files?
subdaily=false
**3-6. multiple job list
#loc_exps = list of local experiment names (stored in 'base_dir') to archive
loc_exps=(
HI-00
HI-02
)
HI-00 origin need to read all files and then save to a single variable file
https://github.com/ars599/ACCESS-AMOS22/blob/main/scripts/plot_ts_concat_demo3.ipynb
Now just use existing files:
fn1 = 'sst_HI-00_output.nc'
fn2 = 'sst_HI-02_output.nc'
The files have been copied to
idir = '/g/data/access/access_amos22/archive/'
ext1 = idir+"sst_HI-00_output.nc"
ext2 = idir+"sst_HI-02_output.nc"
ext3 = idir+"pr_HI-00_output.nc"
ext4 = idir+"pr_HI-02_output.nc"
https://github.com/ars599/ACCESS-AMOS22/blob/main/scripts/plot_ts_concat_demo.ipynb
** Before submitting your job:
Login via ssh
ssh -X UserID@gadi.nci.org.au
Need to switch project to nf33 (check with echo $PROJECT)
switchproj nf33
echo $PROJECT
Create and cd into /scratch/nf33/userid/access-esm (mkdir)
mkdir /scratch/nf33/UserID
mkdir /scratch/nf33/UserID/access-esm
cd /scratch/nf33/UserID/access-esm
** Load modules
module use /g/data/hh5/public/modules
module load conda/analysis3-unstable
*** Checkout code git clone
git clone https://github.com/ars599/PI-DEMO
cd PI-DEMO
** Explain settings in config file (Tilo/Arnold to explain settings)
cat config.yml
Also readme file, but please follow our instructions today
cat README.md
submit model simulation to queue
payu run
** After submitting your job:
Check status of run
qstat -wau UserID
** New folder (and link) will be created, contains output for 3 main components and coupler including information for each processor in atmosphere + copy of all configuration files (Tilo/Arnold to explain files and output in work folder)
/scratch/nf33/UserID/access-esm/work/PI-DEMO
cat /scratch/nf33/UserID/access-esm/work/PI-DEMO/atmosphere/atm.fort6.pe0
cat /scratch/nf33/UserID/access-esm/work/PI-DEMO/atmosphere/STASHC
** output files for atmoshpere created for monthly and daily output
aiihca.paa1jan and aiihca.pea1jan
New folder “archive” created when run complete, contains model output
/scratch/nf33/txz599/access-esm/archive/PI-DEMO/output000
** Look at monthly and daily output with xconv and/or ferret, convert one field to netcdf with xconv and then load with ferret (Tilo/Arnold to explain analysis of output)
module use ~access/modules
module load xconv
module load ferret
xconv aiihca.paa1jan
Please finish the Survey and if you have any qestion please leave your concern at the following link
** AMOS ACCESS ESM workhop discussion
https://github.com/ars599/ACCESS-AMOS22/issues
** AMOS ACCESS Survey
