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<div class="slides">
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<h1 class="title">Running ACCESS-OM2 Models at NCI</h1>
<p class="subtitle" style="text-align: left;"><p>Using payu to run ACCESS-OM2 models</p></p>
<p class="author" style="text-align: right;">Aidan Heerdegen</p>
<p class="date" style="text-align: right;">18 May 2021</p>
</section>
<section id="outline" class="title-slide slide level1">
<h1>Outline</h1>
<ul>
<li>ACCESS-OM2 Model</li>
<li>Configurations</li>
<li>Running the model</li>
<li>Other useful stuff</li>
</ul>
</section>
<section>
<section id="access-om2" class="title-slide slide level1">
<h1>ACCESS-OM2</h1>
<p>Model suite includes 1, 0.25 and 0.1 degree global Ocean/Sea Ice models forced with atmospheric data and almost identical model parameters.</p>
<p>Single <code>access-om2</code> repository with all code and configs</p>
<p><a href="https://github.com/COSIMA/access-om2">https://github.com/COSIMA/access-om2</a></p>
<p>Well documented in wiki</p>
<p><a href="https://github.com/COSIMA/access-om2/wiki">https://github.com/COSIMA/access-om2/wiki</a></p>
</section>
<section id="components" class="slide level2">
<h2>Components</h2>
<p>The model consists of separate component models that run independently and share information via a coupler</p>
<table>
<tbody>
<tr class="odd">
<td>Ocean</td>
<td><code>MOM5</code></td>
</tr>
<tr class="even">
<td>Ice</td>
<td><code>CICE5</code></td>
</tr>
<tr class="odd">
<td>Atmosphere</td>
<td><code>libaccessom2</code> + <code>yatm</code></td>
</tr>
<tr class="even">
<td>Coupler</td>
<td><code>OASIS3-MCT</code></td>
</tr>
</tbody>
</table>
</section>
<section id="code" class="slide level2">
<h2>Code</h2>
<p>All models are open source</p>
<table>
<tbody>
<tr class="odd">
<td><code>MOM5</code></td>
<td><a href="https://github.com/mom-ocean/MOM5">https://github.com/mom-ocean/MOM5</a></td>
</tr>
<tr class="even">
<td><code>CICE5</code></td>
<td><a href="https://github.com/COSIMA/cice5">https://github.com/COSIMA/cice5</a></td>
</tr>
<tr class="odd">
<td><code>libaccessom2</code></td>
<td><a href="https://github.com/COSIMA/libaccessom2">https://github.com/COSIMA/libaccessom2</a></td>
</tr>
<tr class="even">
<td><code>OASIS3-MCT</code></td>
<td><a href="https://github.com/COSIMA/oasis3-mct">https://github.com/COSIMA/oasis3-mct</a></td>
</tr>
</tbody>
</table>
</section>
<section id="forcing-data" class="slide level2">
<h2>Forcing Data</h2>
<ul>
<li>Atmosphere is not free-running model</li>
<li>Atmospheric forcing from data source. Read by <code>libaccessom2+yatm</code>, passed to ice model</li>
<li>Atmosphere uses JRA55 reanalysis derivative product JRA55-do v1.4</li>
</ul>
<p><a href="http://jra.kishou.go.jp/JRA-55/index_en.html">http://jra.kishou.go.jp/JRA-55/index_en.html</a> <a href="https://www.sciencedirect.com/science/article/pii/S146350031830235X">https://www.sciencedirect.com/science/article/pii/S146350031830235X</a></p>
<ul>
<li>IAF (Interannual Forcing) : JRA55-do (1955-present)</li>
<li>RYF (Repeat Year Forcing) : RYF9091 (RYF8485, RYF0304 also available)</li>
</ul>
</section></section>
<section>
<section id="configurations" class="title-slide slide level1">
<h1>Configurations</h1>
<p>All model configurations are global, and there are three supported resolutions</p>
<p>At each resolution interannual and repeat year forcing is supported</p>
</section>
<section class="slide level2">
<p>COSIMA Model name: ACCESS-OM2</p>
<ul>
<li>Nominal 1 degree global resolution</li>
<li>JRA55 RYF and IAF</li>
</ul>
<p><a href="https://github.com/COSIMA/1deg_jra55_iaf">https://github.com/COSIMA/1deg_jra55_iaf</a> <a href="https://github.com/COSIMA/1deg_jra55_ryf">https://github.com/COSIMA/1deg_jra55_ryf</a></p>
</section>
<section class="slide level2">
<p>COSIMA Model name: ACCESS-OM2-025</p>
<ul>
<li>Nominal 0.25 degree global resolution</li>
<li>JRA55 RYF and IAF configurations</li>
</ul>
<p><a href="https://github.com/COSIMA/025deg_jra55_ryf">https://github.com/COSIMA/025deg_jra55_ryf</a> <a href="https://github.com/COSIMA/025deg_jra55_iaf">https://github.com/COSIMA/025deg_jra55_iaf</a></p>
</section>
<section class="slide level2">
<aside class="notes">
<p>Don't suggest anyone runs this without contacting COSIMA as runs are expensive</p>
</aside>
<p>COSIMA Model name: ACCESS-OM2-01</p>
<ul>
<li>Nominal 0.1 degree global resolution</li>
<li>JRA55 RYF and IAF configurations</li>
</ul>
<p><a href="https://github.com/COSIMA/01deg_jra55_iaf">https://github.com/COSIMA/01deg_jra55_iaf</a> <a href="https://github.com/COSIMA/01deg_jra55_ryf">https://github.com/COSIMA/01deg_jra55_ryf</a></p>
</section></section>
<section>
<section id="running-the-model" class="title-slide slide level1">
<h1>Running the model</h1>
<aside class="notes">
<p>Can run in a branch to keep config clean Can fork on GitHub and push config changes back to fork</p>
</aside>
<p>Follow the Quick Start instructions in the ACCESS-OM2 Wiki on github</p>
<p><a href="https://github.com/COSIMA/access-om2/wiki/Getting-started#quick-start">https://github.com/COSIMA/access-om2/wiki/Getting-started#quick-start</a></p>
</section>
<section class="slide level2">
<p>As an example, using the 1 deg JRA55 IAF configuration:</p>
<pre class="bash"><code>module use /g/data3/hh5/public/modules
module load conda
git clone https://github.com/COSIMA/1deg_jra55_iaf
cd 1deg_jra55_iaf </code></pre>
</section>
<section class="slide level2">
<pre class=""><code>1deg_jra55_iaf/
|-- accessom2.nml
|-- atmosphere
| |-- atm.nml
| `-- forcing.json
|-- config.yaml
|-- doc
| `-- Fabio2018_Namelist_meeting_final.pdf
|-- ice
| |-- cice_in.nml
| |-- input_ice_gfdl.nml
| |-- input_ice_monin.nml
| `-- input_ice.nml
|-- manifests
| |-- exe.yaml
| |-- input.yaml
| `-- restart.yaml
|-- metadata.yaml
|-- namcouple
|-- nmltab.py
|-- ocean
| |-- data_table
| |-- diag_table
| |-- diag_table_source.yaml
| |-- field_table
| |-- input.nml
| `-- make_diag_table.py
|-- README.md
|-- resub.sh
|-- run_summary.py
|-- sync_data.sh
`-- tidy_restarts.py</code></pre>
</section>
<section class="slide level2">
<p>The <code>libaccessom2</code> namelist <code>accessom2.nml</code> controls logging, timesetp, forcing dates and model run length (<code>restart_period</code>)</p>
<pre class="yaml"><code>&accessom2_nml
log_level = 'DEBUG'
! ice_ocean_timestep defines the MOM baroclinic timestep, CICE thermodynamic timestep
! and MOM-CICE coupling interval, in seconds.
! ice_ocean_timestep is normally a factor of the JRA55-do forcing period of 3hr = 10800s,
! e.g. one of 100, 108, 120, 135, 144, 150, 180, 200, 216, 225, 240, 270, 300, 360, 400, 432,
! 450, 540, 600, 675, 720, 900, 1080, 1200, 1350, 1800, 2160, 2700, 3600 or 5400 seconds.
! The model is usually stable with a 5400s timestep, including in the initial spinup from rest.
ice_ocean_timestep = 5400
&end
&date_manager_nml
forcing_start_date = '1958-01-01T00:00:00'
forcing_end_date = '2019-01-01T00:00:00'
! Runtime for a single segment/job/submit, format is years, months, seconds,
! two of which must be zero.
restart_period = 5, 0, 0
&end</code></pre>
</section>
<section class="slide level2">
<p>To run the model as a test change model run time from 5 years to 1 month: in <code>accessom2.nml</code></p>
<pre class="yaml"><code>restart_period = 0, 1, 0</code></pre>
<p>Run the model</p>
<pre class="bash"><code>payu run</code></pre>
</section>
<section class="slide level2">
<ul>
<li>payu prints the the command it submits and other information</li>
<li>Some errors visible by inspection: incorrect payu path, incorrect storage flags, inefficient processor count</li>
</ul>
<pre class="sh"><code>$ payu run -f
payu: warning: Job request includes 47 unused CPUs.
payu: warning: CPU request increased from 241 to 288
Loading input manifest: manifests/input.yaml
Loading restart manifest: manifests/restart.yaml
Loading exe manifest: manifests/exe.yaml
payu: Found modules in /opt/Modules/v4.3.0
qsub -q normal -P w97 -l walltime=10800 -l ncpus=288 -l mem=1000GB -N 1deg_jra55_iaf -l wd -j n -v PAYU_PATH=/g/data3/hh5/public/apps/miniconda3/envs/analysis3-21.04/bin,PAYU_FORCE=True,MODULES
HOME=/opt/Modules/v4.3.0,MODULES_CMD=/opt/Modules/v4.3.0/libexec/modulecmd.tcl,MODULEPATH=/g/data3/hh5/public/modules:/opt/Modules/modulefiles:/opt/Modules/v4.3.0/modulefiles:/apps/Modules/modu
lefiles -W umask=027 -l storage=gdata/hh5+gdata/ik11+gdata/qv56+scratch/w97 -- /g/data3/hh5/public/apps/miniconda3/envs/analysis3-21.04/bin/python3.8 /g/data3/hh5/public/apps/miniconda3/envs/an
alysis3-21.04/bin/payu-run </code></pre>
</section>
<section class="slide level2">
<p>The PBS options for <code>normal</code> queue</p>
<pre class="yaml"><code># PBS configuration
queue: normal
walltime: 3:00:00
jobname: 1deg_jra55_iaf
mem: 1000GB</code></pre>
</section>
<section class="slide level2">
<p>The model options</p>
<pre class="yaml"><code># Model configuration
name: common
model: access-om2
input: /g/data/ik11/inputs/access-om2/input_20201102/common_1deg_jra55
submodels:
- name: atmosphere
model: yatm
exe: /g/data/ik11/inputs/access-om2/bin/yatm_5b6c697d.exe
input:
- /g/data/ik11/inputs/access-om2/input_20201102/yatm_1deg
- /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/atmos/3hr/rsds/gr/v20190429
- /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/atmos/3hr/rlds/gr/v20190429
- /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/atmos/3hr/prra/gr/v20190429
- /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/atmos/3hr/prsn/gr/v20190429
- /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/atmos/3hrPt/psl/gr/v20190429
- /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/land/day/friver/gr/v20190429
- /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/atmos/3hrPt/tas/gr/v20190429
- /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/atmos/3hrPt/huss/gr/v20190429
- /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/atmos/3hrPt/uas/gr/v20190429
- /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/atmos/3hrPt/vas/gr/v20190429
- /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/landIce/day/licalvf/gr/v20190429
ncpus: 1
- name: ocean
model: mom
exe: /g/data/ik11/inputs/access-om2/bin/fms_ACCESS-OM_af3a94d4_libaccessom2_5b6c697d.x
input: /g/data/ik11/inputs/access-om2/input_20201102/mom_1deg
ncpus: 216
- name: ice
model: cice5
exe: /g/data/ik11/inputs/access-om2/bin/cice_auscom_360x300_24p_2572851d_libaccessom2_5b6c697d.exe
input: /g/data/ik11/inputs/access-om2/input_20201102/cice_1deg
ncpus: 24</code></pre>
</section>
<section class="slide level2">
<p>Collation options include collating restarts, and using multiple CPUs to speed up collation</p>
<pre class="yaml"><code># Collation
collate:
restart: true
walltime: 1:00:00
mem: 30GB
ncpus: 4
queue: normal
exe: /g/data/ik11/inputs/access-om2/bin/mppnccombine</code></pre>
</section>
<section class="slide level2">
<p>Miscellaneous options</p>
<pre class="yaml"><code># Misc
runlog: true
stacksize: unlimited
restart_freq: 1 # use tidy_restarts.py instead
mpirun: --mca io ompio --mca io_ompio_num_aggregators 1
qsub_flags: -W umask=027
# set number of cores per node (28 for normalbw, 48 for normal on gadi)
platform:
nodesize: 48
# sweep and resubmit on specific errors - see https://github.com/payu-org/payu/issues/241#issuecomment-610739771
userscripts:
error: resub.sh
run: rm -f resubmit.count
# DANGER! Do not uncomment this without checking the script is syncing to the correct location!
# postscript: sync_data.sh</code></pre>
</section>
<section id="restart-from-another-experiment" class="slide level2">
<h2>Restart from another experiment</h2>
<ul>
<li>payu will use any existing restart in the <code>archive</code> directory</li>
<li>restart option in <code>config.yaml</code> is best, but doesn't currently work for ACCESS-OM2</li>
<li>Copy or link previous restart and output directories into your <code>archive</code>. See the <a href="https://github.com/COSIMA/access-om2/wiki/Tutorials#starting-a-new-experiment-using-restarts-from-a-previous-experiment">ACCESS-OM2 wiki for details</a></li>
</ul>
</section>
<section id="has-my-model-crashed" class="slide level2">
<h2>Has my model crashed?</h2>
<p>Signs your model has crashed:</p>
<ul>
<li><code>work/</code> directory still present in control directory</li>
<li><code>access-om2.out</code> and <code>access-om2.err</code> still present in control directory</li>
<li>Non-zero <code>Exit Status</code> in PBS log file</li>
</ul>
<pre class=""><code>======================================================================================
Resource Usage on 2021-05-25 17:02:12:
Job Id: 22990186.gadi-pbs
Project: w97
Exit Status: 1
Service Units: 6.88
NCPUs Requested: 288 NCPUs Used: 288
CPU Time Used: 00:21:24
Memory Requested: 1000.0GB Memory Used: 121.07GB
Walltime requested: 03:00:00 Walltime Used: 00:00:43
JobFS requested: 600.0MB JobFS used: 0B
======================================================================================</code></pre>
</section>
<section id="diagnosing-a-crash" class="slide level2">
<h2>Diagnosing a crash</h2>
<aside class="notes">
<p>The code was compiled to include human readable source code names which makes it easier to debug</p>
<p>This is an MPI program running multiple copies of the models, and each will be signalled to "die" when there is a fatal error</p>
</aside>
<ul>
<li>Check <code>access-om2.err</code> and find the first error message that looks like this</li>
</ul>
<pre class="sh"><code>FATAL from PE 178: ==>Error: time step instability detected for baroclinic gravity waves in ocean_model_mod
Image PC Routine Line Source
fms_ACCESS-OM_af3 0000000001C458BA Unknown Unknown Unknown
fms_ACCESS-OM_af3 0000000001825DAC mpp_mod_mp_mpp_er 58 mpp_util_mpi.inc
fms_ACCESS-OM_af3 0000000000D8FF91 ocean_velocity_mo 886 ocean_velocity.F90
fms_ACCESS-OM_af3 0000000000466493 ocean_model_mod_m 1258 ocean_model.F90
fms_ACCESS-OM_af3 0000000000410FDB MAIN__ 358 ocean_solo.F90
fms_ACCESS-OM_af3 000000000040F662 Unknown Unknown Unknown
libc-2.28.so 000014E858A3D7B3 __libc_start_main Unknown Unknown
fms_ACCESS-OM_af3 000000000040F56E Unknown Unknown Unknown</code></pre>
<ul>
<li>Backtrace (or stacktrace) shows location in the code where error occurred</li>
<li>A stack trace for every cpu (rank)</li>
</ul>
</section>
<section class="slide level2">
<p>Another example of an error</p>
<pre class="sh"><code>FATAL from PE 142: Error: salinity out of range with value -9.223462738696E-01 at (i,j,k) = ( 214, 184, 21), (lon,lat,dpt) = ( -66.5000, 17.8501, 261.0993 m)
Image PC Routine Line Source
fms_ACCESS-OM_af3 0000000001C458BA Unknown Unknown Unknown
fms_ACCESS-OM_af3 0000000001825DAC mpp_mod_mp_mpp_er 58 mpp_util_mpi.inc
fms_ACCESS-OM_af3 00000000005EC1D5 ocean_tempsalt_mo 1360 ocean_tempsalt.F90
fms_ACCESS-OM_af3 00000000008440CC ocean_tracer_mod_ 2540 ocean_tracer.F90
fms_ACCESS-OM_af3 000000000044795F ocean_model_mod_m 1864 ocean_model.F90
fms_ACCESS-OM_af3 0000000000416592 MAIN__ 468 ocean_solo.F90
fms_ACCESS-OM_af3 000000000040F662 Unknown Unknown Unknown
libc-2.28.so 0000148096D7A7B3 __libc_start_main Unknown Unknown
fms_ACCESS-OM_af3 000000000040F56E Unknown Unknown Unknown</code></pre>
<ul>
<li>If the cause of the crash isn't obvious might have to dig into log files within the model subdirectories in <code>work/</code></li>
</ul>
</section></section>
<section>
<section id="other-useful-stuff" class="title-slide slide level1">
<h1>Other Useful Stuff</h1>
</section>
<section id="diagnostics" class="slide level2">
<h2>Diagnostics</h2>
<ul>
<li>Only a fraction of the possible diagnostic (and tracer) fields are output</li>
<li>MOM diagnostics determined by the <code>diag_table</code> which is generated programmatically</li>
<li>CICE diagnostics are definted in <code>cice_in.nml</code></li>
</ul>
</section>
<section id="perturbations" class="slide level2">
<h2>Perturbations</h2>
<p>Add offsets or scale atmospheric forcing fields. Either single value, spatially and/or temporally varying e.g.</p>
<pre class="json"><code>{
"description": "JRA55-do V1.3 RYF 1990-91 forcing",
"inputs": [
{
"filename": "/g/data/ua8/JRA55-do/RYF/v1-3/RYF.rsds.1990_1991.nc",
"fieldname": "rsds",
"cname": "swfld_ai",
"perturbations": [
{
"type": "scaling",
"dimension": "spatiotemporal",
"value": "../test_data/scaling.RYF.rsds.1990_1991.nc",
"calendar": "forcing"
},
{
"type": "offset",
"dimension": "constant",
"value": 5,
"calendar": "forcing"
}
]
}
]
}</code></pre>
<p>See the wiki for details</p>
<p><a href="https://github.com/COSIMA/access-om2/wiki/Tutorials#Scaling-the-forcing-fields">https://github.com/COSIMA/access-om2/wiki/Tutorials#Scaling-the-forcing-fields</a></p>
</section>
<section id="available-data" class="slide level2">
<h2>Available data</h2>
<ul>
<li>Some data is published and available via THREDDS from NCI</li>
</ul>
<p><a href="http://dx.doi.org/10.4225/41/5a2dc8543105a">http://dx.doi.org/10.4225/41/5a2dc8543105a</a></p>
<ul>
<li>Always preferable (faster) to access directly on disk</li>
<li>Need to join groups: <code>hh5</code>, <code>ik11</code>, <code>cj50</code> and <code>qv56</code> at <a href="https://my.nci.org.au">https://my.nci.org.au</a></li>
</ul>
</section>
<section id="analysis" class="slide level2">
<h2>Analysis</h2>
<p>COSIMA provides the <a href="https://github.com/COSIMA/cosima-cookbook">COSIMA Cookbook</a>, a database to find and load COSIMA datasets</p>
<p><a href="https://cosima-recipes.readthedocs.io/en/latest/">COSIMA Recipes repository</a> contains Tutorials and Documented Examples</p>
<p>Cookbook includes interactive <a href="https://cosima-recipes.readthedocs.io/en/latest/tutorials/Using_Explorer_tools.html#gallery-tutorials-using-explorer-tools-ipynb">Data Explorer tool</a> to find and load COSIMA datasets at NCI</p>
</section>
<section id="compiling-executables" class="slide level2">
<h2>Compiling Executables</h2>
<ul>
<li>The models are compiled and then published to a shared area in <code>ik11</code></li>
<li>Build scripts Andrew Kiss has developed link the codebase to the executable name via <code>git</code> commit hashes</li>
<li>Best to use published executables with known provenance</li>
<li>If compiling executables keep <code>access-om2</code> source tree separate from your control directories</li>
</ul>
</section></section>
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