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====
Payu
====
:subtitle: A climate model workflow manager
:author: Marshall Ward and Aidan Heerdegen
:description: A Payu training course
:date: 25th May 2021
What is Payu?
=============
Payu is a climate model workflow manager
It is open source, the code is available on GitHub
https://github.com/payu-org/payu
and there is full documentation
https://payu.readthedocs.io/en/latest/
What is a climate model workflow manager?
-----------------------------------------
That means it runs your model for you. In short:
* Setup model run directory (``work``)
* Run the model
* Move outputs/restarts to ``archive`` directory
* Clean up the run directory
* Run again (if instructed to do so)
Features
--------
* Simple YAML based configuration
* Full automatic version control of experimental configuration using ``git``
* Hash based versioning of all model inputs and executables
* Supports many models: MOM5, MOM6, ACCESS-OM, ACCESS-ESM, MITgcm, CICE4, CICE5, Qgcm ...
* Driver based architecture allows support for other models to be added
Etymology
---------
* *P*\ ython on v\ *AYU*
Vayu was Gadi's two times antecedent and though it has passed away...
...Payu lives on!
Motivation
----------
.. notes::
Not only were we using scripts for all of our models, but we also were using
more and more variations of scripts for various tasks.
Version control had not quite caught on yet, but I don't think it would have
addressed our problems anyway.
Long ago, we managed many, many jobscripts.
Many kinds of scripts:
bash, tcsh, ksh, ...
Many different models:
MOM, MITgcm, Q-GCM, ACCESS, ...
Juggling and sharing scripts was becoming a problem. Many of steps were duplicated
between different scripts for the various models. Payu is an attempt to generalise
the task of running a model.
----
.. notes::
Andy Hogg is probably the progenitor of Payu. As Python became more popular
in the group we started using it for non-scientific tasks, Andy asked me
why we don't just use Python for everything?
I probably took this suggestion too literally.
Here is a picture of Andy doing some important scientific computing.
.. image:: img/andy_at_nci.png
"Why not just do everything in Python?"
Prehistoric Payu
----------------
.. notes::
There were even older versions which looked like bash scripts written in
Python, which are so terrible that they're not even worth sharing.
.. code:: python
from payu import gold
def main():
expt = gold(forcing='andrew')
expt.setup()
expt.run()
expt.archive()
if expt.counter < expt.max_counter:
expt.resubmit()
if __name__ == '__main__':
main()
Using Payu
==========
Load the CMS conda environment containing payu::
module use /g/data3/hh5/public/modules
module load conda
Invoking payu
-------------
payu has multiple subcommands. Invoking with the ``-h`` option will print helpful usage message
.. code::sh
$ payu -h
usage: payu [-h] [--version] {archive,build,collate,ghsetup,init,list,profile,push,run,setup,sweep} ...
positional arguments:
{archive,build,collate,ghsetup,init,list,profile,push,run,setup,sweep}
optional arguments:
-h, --help show this help message and exit
--version show program's version number and exit
Subcommands
-----------
============== =============================================================
``init`` Initialise laboratory directories
``setup`` Initialise work directory
``sweep`` Remove ephemeral work directory and copy logs to archive
``run`` Submit model to queue to run
``collate`` Join tiled outputs (and potentially restarts). Not all models
============== =============================================================
-----
Less used
============== =============================================================
``list`` List all supported models
``archive`` Clean up work directory and copy files to archive
``ghsetup`` Setup GitHub repository
``push`` Push local repo to GitHub
============== =============================================================
Never typically used
============== =============================================================
``profile`` Profile model (not typically used)
``build`` Build model executable (not currently supported)
============== =============================================================
------
Pass ``-h`` to subcommands for subcommand specific help and options
.. code::sh
$ payu run -h
usage: payu run [-h] [--model MODEL_TYPE] [--config CONFIG_PATH] [--initial INIT_RUN] [--nruns N_RUNS] [--laboratory LAB_PATH] [--reproduce] [--force]
Run the model experiment
optional arguments:
-h, --help show this help message and exit
--model MODEL_TYPE, -m MODEL_TYPE
Model type
--config CONFIG_PATH, -c CONFIG_PATH
Configuration file path
--initial INIT_RUN, -i INIT_RUN
Starting run counter
--nruns N_RUNS, -n N_RUNS
Number of successive experiments ro run
--laboratory LAB_PATH, --lab LAB_PATH, -l LAB_PATH
The laboratory, this will over-ride the value given in config.yaml
--reproduce, --repro, -r
Only run if manifests are correct
--force, -f Force run to proceed, overwriting existing directories
Clone Experiment
================
* The payu configuration file, ``config.yaml``, the model configuration files
and manifests are tracked directly by ``git``
* When an experiment is cloned only the files tracked by ``git`` are copied
* Other files can be added and changes to those files will be automatically added
to the experiment repo
-----
Clone an existing experiment (usually in a subdirectory in ``$HOME``):
.. code:: sh
cd $HOME
mkdir -p payu/mom
cd payu/mom
git clone https://github.com/payu-org/bowl1.git
cd bowl1
This is the "*control directory*" for ``bowl1``
Your experiment
---------------
* The newly cloned experiment consists of the ``config.yaml``, the config files for
this model (MOM) and, optionally, file manifests
.. code:: sh
bowl1/
├── config.yaml
├── data_table
├── diag_table
├── field_table
├── input.nml
└── manifests
├── exe.yaml
├── input.yaml
└── restart.yaml
Experiment Configuration
------------------------
.. code:: yaml
# PBS
queue: express
ncpus: 4
walltime: 0:10:00
mem: 1GB
jobname: bowl1
# Model
model: mom
input: /g/data/hh5/tmp/mom-test/input/bowl1
exe: /g/data/hh5/tmp/mom-test/bin/mom51_solo_default
# Config
collate: False
Run the experiment
------------------
* This job is pre-configured, so can just run it!
.. code:: sh
cd bowl1
payu run
* Model will run in ``work/`` (an ephemeral directory created in the laboratory just for that model run)
* Output moved to ``archive/`` when run completes without error
Inspecting the output
---------------------
.. notes::
Not all the files exist in these locations at all time. Model output and error
files will reside in control while model is running, but will be archived when
a run succesfully finishes.
PBS output files won't appear until job completed
====================== ======================
``mom.out`` Model output
``mom.err`` Model error
``bowl1.o${jobid}`` PBS (payu) output
``bowl1.e${jobid}`` PBS (payu) error
``archive/output000`` Model output files
``archive/restart000`` Restart (pickup) files
``manifests`` Manifest files for tracking executables and inputs
====================== ======================
Cleaning up
-----------
To clear ``work/`` and save PBS logs::
payu sweep
Or to completely delete the experiment::
payu sweep --hard
This wipes output, restarts, and logs! (``archive/$expt``)
Anatomy of an Experiment
========================
Control vs Laboratory
---------------------
Control path: ``${HOME}/mom/bowl1``
User-configured (text) input
Laboratory: ``/scratch/$PROJECT/$USER/$MODEL/``
Executables, data input, output, etc.
You "control" the laboratory externally
Laboratory overview
-------------------
.. notes::
work is where the ephemeral work directories are created. Named for the experiment
name, usually the same as the directory name.
archive where outputs/restarts saved in directory same as experiment name
means experiment names must be unique for each laboratory, which typically means
for each model
codebase not typically used by payu, for convenience.
bin and input for user convenience, a place where payu looks
============ ===============================
``archive`` Experiment output and restarts
``bin`` Model executables
``codebase`` Model Source code repository
``input`` Static input files
``work`` Ongoing (or failed) experiments
============ ===============================
"``payu init -m mom``" will create these directories
Configuring your experiment
---------------------------
========= =============== ==============
Config Description Default
========= =============== ==============
``model`` Model type (required!)
``name`` Experiment name Expt directory
``exe`` Executable Set by driver
``input`` Model inputs -
========= =============== ==============
Paths can be absolute or relative to the lab path
Scheduler configuration
-----------------------
============ ============== ============
Config Description Default
============ ============== ============
``queue`` PBS Queue ``normal``
``project`` SU Account ``$PROJECT``
``jobname`` Queue job name ``name``
``walltime`` Time request (From PBS)
``ncpus`` CPU request 1
``mem`` RAM request Max node mem
============ ============== ============
``qsub_flags`` for everything else
CPU requests
------------
Normally ``ncpus`` will increase itself to match the node, but more control is
available:
+-----------+-------------+----------+
| Config | Description | Default |
+-----------+-------------+----------+
| platform |
+-----------+-------------+----------+
| →nodesize | Node CPUs | 48 |
+-----------+-------------+----------+
| →nodemem | Node RAM | 192 (GB) |
+-----------+-------------+----------+
-------------
This is currently required to use the Broadwell nodes:
.. code:: yaml
platform:
nodesize: 28
nodemem: 128
.. others
npernode CPUs per node (
``jobfs``
``priority``
``join`` Merge stdout/err ``n``
The work directory
------------------
Run the following to inspect (and test) the setup of your run:
.. code:: sh
payu setup
This will create your ``work`` directory in the laboratory and a symbolic link
to it in your control directory.
.. notes::
This is the first step once a model run begins, but it is exposed separately to allow
testing all input and executable paths are correct without having to actually run the model.
By default payu will not submit a job if there is an existing ``work/`` directory. After running
``payu setup`` you must run ``payu sweep`` or use the ``-f`` option to run the model ``payu run -f``
Inside the work directory
-------------------------
.. notes::
Executable linked into work: for tracking and so obvious which exe being used
Inspect the symbolic link to ``work`` and its contents::
work
├── config.yaml
├── data_table
├── diag_table
├── field_table
├── INPUT
│ ├── gotmturb.inp -> /g/data/hh5/tmp/mom-test/input/bowl1/gotmturb.inp
│ ├── grid_spec.nc -> /g/data/hh5/tmp/mom-test/input/bowl1/grid_spec.nc
│ ├── ocean_barotropic.res.nc -> /scratch/w97/aph502/mom/archive/bowl1/restart000/ocean_barotropic.res.nc
│ ├── ocean_bih_friction.res.nc -> /scratch/w97/aph502/mom/archive/bowl1/restart000/ocean_bih_friction.res.nc
│ ├── ocean_density.res.nc -> /scratch/w97/aph502/mom/archive/bowl1/restart000/ocean_density.res.nc
│ ├── ocean_pot_temp.res.nc -> /scratch/w97/aph502/mom/archive/bowl1/restart000/ocean_pot_temp.res.nc
│ ├── ocean_sbc.res.nc -> /scratch/w97/aph502/mom/archive/bowl1/restart000/ocean_sbc.res.nc
│ ├── ocean_solo.res -> /scratch/w97/aph502/mom/archive/bowl1/restart000/ocean_solo.res
│ ├── ocean_temp_salt.res.nc -> /scratch/w97/aph502/mom/archive/bowl1/restart000/ocean_temp_salt.res.nc
│ ├── ocean_thickness.res.nc -> /scratch/w97/aph502/mom/archive/bowl1/restart000/ocean_thickness.res.nc
│ ├── ocean_tracer.res -> /scratch/w97/aph502/mom/archive/bowl1/restart000/ocean_tracer.res
│ ├── ocean_velocity_advection.res.nc -> /scratch/w97/aph502/mom/archive/bowl1/restart000/ocean_velocity_advection.res.nc
│ └── ocean_velocity.res.nc -> /scratch/w97/aph502/mom/archive/bowl1/restart000/ocean_velocity.res.nc
├── input.nml
├── log
├── manifests
│ ├── exe.yaml
│ ├── input.yaml
│ └── restart.yaml
├── mom51_solo_default -> /g/data/hh5/tmp/mom-test/bin/mom51_solo_default
└── RESTART
Your config files are copied, and sometimes modified. Your input data is symlinked.
A simple configuration
----------------------
The configuration file (``config.yaml``) uses the YAML format
.. code:: yaml
model: mom6
name: om4_gm_test
queue: normal
jobname: mom6_om4
walltime: 20:00
ncpus: 960
mem: 1500GB
exe: mom6_intel17
input:
- om4_grid
- om4_atm
Most variables have "sensible" defaults
A more complex configuration
----------------------------
.. code:: yaml
# PBS configuration
queue: normal
project: fp0
walltime: 02:30:00
jobname: om2_jra55
ncpus: 1153
mem: 2000GB
#platform:
# nodesize: 28
laboratory: /scratch/fp0/mxw900/cosima
repeat: True
collate:
walltime: 4:00:00
mem: 30GB
ncpus: 4
queue: express
flags: -n4 -z -m -r
# Model configuration
model: access
submodels:
- name: coupler
model: oasis
input: oasis_025
ncpus: 0
- name: atmosphere
model: matm
exe: matm
#input: jra55-0.8_025
input: /scratch/v45/mxw900/cosima/nc64
ncpus: 1
- name: ocean
model: mom
exe: mom
input:
- mom
# - iaf-sw21d
ncpus: 960
- name: ice
model: cice
exe: cice_nohalo
input: cice
ncpus: 192
calendar:
runtime:
years: 0
months: 0
days: 30
start:
year: 1
month: 1
days: 1
Feature overview
================
Multiple runs
-------------
.. notes::
This does not affect the total number of runs which is goverened entirely by the value passed
to the ``-n`` option.
* To do multiple runs in sequence:
.. code::
payu run -n 20
* We save every output, and every 5th restart. To change the rate restart files are saved::
restart_freq: 1
* To run the model multiple times for each submission to the queue::
runspersub: 5
will run the model 5 times during each queued job. Can help reduce overhead spent waiting in queue
Path control
------------
.. notes::
Just about every path can be explicitly set, though at some point it does
get a bit weird to, say, change the control path...
Default paths can be set explicitly
============== ===================
``shortpath`` Root ("scratch") path
``laboratory`` Laboratory path
``control`` Control path
============== ===================
e.g. to run under multiple project codes but keep all files in the same laboratory location
specify ``shortpath``
MPI support
-----------
MPI support is very explicit at the moment:
.. notes::
We rely on NCI wrapper scripts to fix the MPI module.
Also, these particular settings are nonsense together, they're just various
examples. Usually do not set an explicit mpi module, this is done automatically
by the ``mpirun`` script.
.. code:: yaml
mpi:
module: openmpi/2.1.1-debug
modulepath: /home/157/mxw157/modules
flags:
- -mca orte_output_filename log
- -mca pml yalla
runcmd: map --profile mpiexec
It is not recommended to change these without understanding and good reason
Userscript support
------------------
* Subcommands and scripts can be injected after key steps
.. code:: yaml
userscripts:
init: 'echo "some_data" > input.nml'
setup: patch_inputs.py
run: 'qsub postprocess.sh'
postscript: sync_output_to_gdata.sh
* These will run after the prescribed section.
* ``postscript`` runs when a run finishes, if the output is collated it runs
after that completes.
Supported models
----------------
To see the supported models::
payu list
But expect some atrophy...
File Tracking
-------------
.. notes::
Very early in this job, there was a "dodgy aerosol file" that had
been used in some simulations, but hard/impossible to say which
runs/files were affected
* Track input files used for each model run
* Completely automatic. User intervention not required
* Reproducibly re-run previous experiment
* Share experiments more easily as input files all specified
* Flexibility with specifying path to input files
* Identify all runs using specified file (possible future feature)
What is tracked?
----------------
.. notes::
Executables and inputs are not expected to change. Can specify a flag to either warn
if they do and stop, or update manifest and continue
Restarts are the opposite, and by default are always expected to be different for each
run, unless a flag is specified to reproduce a run, in which case any difference will
flag an error and stop
=========== ===================
Executables ``manifests/exe.yaml``
Inputs ``manifests/inputs.yaml``
Restarts ``manifests/restarts.yaml``
=========== ===================
How is it tracked?
------------------
* Uses `yamanifest <https://github.com/aidanheerdegen/yamanifest>`_
* Creates a manifest file which uses ``YAML`` format
* Each file (symlink) in ``work`` is a dictionary key in manifest file
* Manifests files are tracked by ``git``, so the unique hash for every
tracked file is associated with each run using version control
Example
-------
.. notes::
Note there is a header and a version string, can ignore
All files in work are either config files (which are tracked
by git) or symbolic links to files elsewhere on filesystem
Issues with getting this working has to do with enforcing this
for all models - can be difficult with hardwired paths etc
* ``fullpath`` is the actual location of the file
* The hashes uniquely identify file
.. code::yaml
format: yamanifest
version: 1.0
---
work/mom51_solo_default:
fullpath: /g/data/hh5/tmp/mom-test/bin/mom51_solo_default
hashes:
binhash: 423d9cf92c887fe3145c727c4fbda4d0
md5: 989580773079ede1109b292c2bb2ad17
Hierachy of hashes
------------------
.. notes::
binhash uses datestamp and size combined with first 100MB of a file.
Not guaranteed unique, but likely to detect if the file has changed
* yamanifest supports multiple hashes => hierarchy of hashes
* Unique hashes (md5, sha128) take too long on large files
* Fast hashing to check for file changes
* Use unique hash check when necessary
* Running ``payu setup`` for experiments with large number and size of input files
can be useful: precalculate expensive hashes saves time when job runs on queue
Forking and sharing experiments
===============================
Creating a new experiment
-------------------------
.. notes::
Sharing experiments is new, but we are working on improving this experience
Let's have some **FUN** and increase the timestep::
git clone bowl1 bowl2
cd bowl2
We are in a hurry, so let's make ``dt_ocean`` in ``input.nml`` very large::
&ocean_model_nml
dt_ocean = 86400
Recording your progress
-----------------------
See changes to the run by utilising ``git``::
git log
and responsible people *always* document their changes::
git commit -am "Testing a large timestep"
But if you're lazy then payu will commit upon completion.
Let's run it!
FAILURE
-------
.. image:: img/angry.jpg
Your run crashed!!!
Inspecting failed jobs
----------------------
Failed jobs retain output and error files (``mom.out``, ``mom.err`` in this case), and
a ``work/`` directory
From ``mom.err``::
FATAL from PE 2: ==>Error: time step instability detected for baroclinic gravity waves in ocean_model_mod
forrtl: error (78): process killed (SIGTERM)
Errors are saved to ``archive/error_logs`` with PBS job IDs
(Note: Error logs can get big fast!)
GitHub integration
------------------
.. notes::
Here, show off git remote as well as the .ssh directory
You can sync your experiment on GitHub::
payu ghsetup
payu push
Visit your experiment in GitHub!
NOTE: This will create SSH keys in your ``$HOME/.ssh`` directory.
Other GitHub features
---------------------
.. notes::
Remember to do a bit of a tech demo to mxw900-raijin here.
The unmentioned features are:
* name (on github)
* username
* sshid (ssh key path)
* private
* remote name (payu)
You should set a description for your run:
.. code:: yaml
description: A very fun experiment
You can also save jobs to an organization:
.. code:: yaml
runlog:
organization: mxw900-raijin
There are a few other features here, and someday they may be documented!
Currently "``payu push``" is manual, but we could make it automatic.
Coupled Models
==============
Coupled configuration
---------------------
Yes, Payu supports coupled models!
https://github.com/COSIMA/01deg_jra55_iaf
.. code:: yaml
model: access-om2
input: /g/data/ik11/inputs/access-om2/input_08022019/common_01deg_jra55
submodels:
- name: atmosphere
model: yatm
exe: /g/data/ik11/inputs/access-om2/bin/yatm_4198e150.exe
input:
- /g/data/ik11/inputs/access-om2/input_08022019/yatm_01deg
- /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_e837d05d_libaccessom2_4198e150.x
input: /g/data/ik11/inputs/access-om2/input_08022019/mom_01deg
ncpus: 4358
- name: ice
model: cice5
exe: /g/data/ik11/inputs/access-om2/bin/cice_auscom_3600x2700_722p_597e4561_libaccessom2_4198e150.exe
input: /g/data/ik11/inputs/access-om2/input_20200422/cice_01deg
ncpus: 799
Layout of a coupled model
-------------------------
Inputs, work and output are separated by the ``name``::
libom2_1deg
|-- accessom2.nml
|-- archive -> /scratch/fp0/mxw900/access-om2/archive/libom2_1deg
|-- atmosphere
| |-- atm.nml
| |-- checksums.txt
| `-- forcing.json
|-- config.yaml
|-- ice
| |-- cice_in.nml
| |-- input_ice.nml
| |-- input_ice_gfdl.nml
| `-- input_ice_monin.nml
|-- namcouple
|-- ocean
| |-- checksums.txt
| |-- data_table
| |-- diag_table
| |-- field_table
| `-- input.nml
|-- sync_output_to_gdata.sh
`-- sync_restarts_to_gdata.sh
Common files (``accessom2.nml``, ``namcouple``) are in the top directory.
Work directories have a similar structure.
Troubleshooting
===============
Model crashes
-------------
If you see this error in your PBS log::
payu: Model exited with error code 134; aborting."
then it means the model crashed and payu has halted execution.
Check your error logs to figure out the problem.
Various Python errors
---------------------
Sometimes a missing file or misconfigured experiment will cause an error in
Python::
Traceback (most recent call last):
File "/home/157/mxw157/python/payu/bin/payu", line 8, in <module>
cli.parse()
File "/home/157/mxw157/python/payu/payu/cli.py", line 61, in parse
run_cmd(**args)
File "/home/157/mxw157/python/payu/payu/subcommands/setup_cmd.py", line 18, in runcmd
expt.setup(force_archive=force_archive)
File "/home/157/mxw157/python/payu/payu/experiment.py", line 353, in setup
model.setup()
File "/home/157/mxw157/python/payu/payu/models/mom.py", line 69, in setup
super(Mom, self).setup()
File "/home/157/mxw157/python/payu/payu/models/model.py", line 151, in setup
shutil.copy(f_path, self.work_path)
File "/apps/python/2.7.6/lib/python2.7/shutil.py", line 119, in copy
copyfile(src, dst)
File "/apps/python/2.7.6/lib/python2.7/shutil.py", line 82, in copyfile
with open(src, 'rb') as fsrc:
IOError: [Errno 2] No such file or directory: '/home/157/mxw157/mom/course/bowl2_course/input.nml'
Run ``payu setup`` and test that the experiment is set up properly.
Cloning issues
--------------
* Some ``config.yaml`` contain relative paths for inputs and executables, which
can make sharing difficult.
* Either copy (or symlink) their files into your local lab, or modify your
``config.yaml`` to use absolute paths.