COSIMA 2018 Report

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Aims & Goals

The third meeting of the Consortium for Ocean Sea Ice Modelling in Australia (COSIMA) was held in Canberra on 7-8 May 2018. This annual COSIMA workshop aims to:

  • Establish a community around ocean-sea ice modelling in Australia;
  • Discuss recent scientific advances in ocean and sea ice research in a forum that is inclusive and model-agnostic, particularly including observational programs;
  • Agree on immediate next steps in the COSIMA model development plan; and
  • Develop a long-term vision for Australian scientific advances in this area.

Participants

The 2018 workshop is our largest workshop yet, with 30 talks and 49 participants.

Attendees included:

Gary Brassington (Bureau of Meteorology), Matt Chamberlain (CSIRO), Chris Chapman (CSIRO), Fabio Dias (UTAS/CSIRO), Prasanth Divakaran (Bureau of Meteorology), Peter Dobrohotoff (CSIRO), Catia Domingues (UTAS), Matthew England (UNSW), Russ Fiedler (CSIRO), Annie Foppert (CSIRO), Leela Frankcombe (UNSW), Bishakhdatta Gayen (ANU), Angus Gibson (ANU), Stephen Griffies (NOAA/GFDL), Nicholas Hannah (COSIMA), Aidan Heerdegen (ANU/CLEX), Petra Heil (AAD & ACE CRC), Andy Hogg (ANU), Ryan Holmes (UNSW), Shane Keating (UNSW), Andrew Kiss (ANU), Vassili Kitsios (CSIRO), Veronique Lago (UNSW), Clothilde Langlais (CSIRO), Andrew Lenton (CSIRO), Kewei Lyu (CSIRO), Jie Ma (CSIRO), Simon Marsland (CSIRO), Paige Martin (University of Michigan), Josue Martinez Moreno (ANU), Richard Matear (CSIRO), Laurie Menviel (UNSW), Mainak Mondal (ANU), Ruth Moorman (ANU), Adele Morrison (ANU), Terry O’Kane (CSIRO), Peter Oke (CSIRO), Ramkrushnbhai Patel (UTAS), Paul Sandery (CSIRO), Abhishek Savita (UTAS-CSIRO), Kate Snow (NCI), Paul Spence (UNSW), Kial Stewart (ANU/UNSW), Veronica Tamsitt (UNSW/CSIRO), Mirko Velic (Bureau of Meteorology), Marshall Ward (NCI), Luwei Yang (IMAS, UTAS), Rui Yang (NCI), Jan Zika (UNSW)

Status

The workshop was structured to focus on scientific questions on Day 1, particularly in the first two sessions. In these sessions, topics ranged from from Antarctic shelf processes to oceanic convection, from reversibility of the Earth system to frictional drag. The final session on day 1 focussed more on technical issues, including assessment of the optimisation status of existing models. On Day 2, talks focussed more on strategic issues, including an outline of Bluelink, ACCESS, CAFE and coastal programs. These strategic talks transitioned to small-group discussions (see synthesis below). The workshop finished with a tutorial on the COSIMA Cookbook framework for model analysis.

The Australian landscape in ocean-sea ice research involves a number of interleaving programs, each of which was represented at this workshop.  The figure below outlines the linkages between these programs:

By way of explanation:

ACCESS-CM2/-ESM1.5 will be Australia’s input to CMIP6, and use MOM5 and CICE at 1°.

CAFE is the decadal prediction system in development, which uses MOM5.

ARCCSS/CLEX, ARC CoE programs, use high-resolution ocean-sea ice models for process studies.

Bluelink/OFAM is the ocean forecasting and reanalysis system which will adopt ACCESS-OM2-01 in future versions.

CSHOR is the Centre for Southern Hemisphere Oceanographic Research; it focuses on observational studies but we hope to establish two-way interactions with this program.

Coastal Modelling includes the Australian coastal oceanography community, as well as Antarctic nearshore programs within AAD and ACE-CRC.

A major theme of the workshop was to review the status of the ACCESS-OM2 model which is the focus of COSIMA. In short, we have had success with model releases at 1° and 0.25° resolution – these models are now actively being used for scientific runs, and are available for download and use by the community. They include a recent upgrade to the file-based atmosphere (YATM) and new JRA55-do forcing datasets. The 0.1° version of the model has progressed significantly in the last year; there are outstanding tasks to evaluate model output and further optimise the model configuration.

The COSIMA Cookbook tutorial was attended by about a third of participants, and some progress was made. The aim of this tutorial was to entrain more active users to the system and encourage input from those users. The Cookbook is similar in style to the analysis system being developed for CAFE and it may be possible to merge elements of each framework at some stage in the future.

Program

Where available, talk files are linked from the presenter’s name.

Monday 7 May
10:00 Arrival & Morning tea
10:30 Session 1 (Chair – Andy Hogg)
Stephen M Griffies (NOAA/GFDL): Understanding and projecting global and regional sea level: More reasons to include refined ocean resolution in global climate models
Andrew Kiss (ANU): Overview of the ACCESS-OM2 model suite
Andrew Lenton (CSIRO): Ocean Reversibility in ACCESS-ESM
Catia Domingues (UTAS): Global and spatial temporal changes in upper-ocean thermometric sea level
Fabio Dias (UTAS/CSIRO): Mean and seasonal states of the ocean heat and salt budgets in ACCESS-OM2
Adele Morrison (ANU): Circumpolar Deep Water transport towards Antarctica driven by dense water export
Jan Zika (UNSW): Getting an ocean model to obey: Prescribing and perturbing exact fluxes of heat and fresh water
12:30 Lunch
13:30 Session 2 (Chair – Clothilde Langlais)
Petra Heil (AAD & ACE CRC): ACCESS-OM2-01 sea ice
Paul Sandery (CSIRO): Sea-ice data assimilation and forecasting using an Ensemble Transform Kalman Filter
Paul Spence (UNSW): Does the Southern Ocean have sleep apnea?
Veronique Lago (UNSW): Impact of projected amplification of Antarctic meltwater on Antarctic Bottom Water formation
Ryan Holmes (UNSW): Numerical Mixing in the COSIMA Models
Luwei Yang (IMAS, UTAS): The impacts of bottom frictional drag on the sensitivity of the Southern Ocean circulation to changing wind
Vassili Kitsios (CSIRO): Stochastic subgrid turbulence parameterisation of eddy-eddy, eddy-topographic, eddy-meanfield and meanfield-meanfield interactions
Matt Chamberlain (CSIRO): Using transport matrices to probe circulation in ocean models
15:30 Afternoon tea
16:00 Session 3 (Chair – Petra Heil)
Nicholas Hannah (COSIMA): ACCESS-OM2 Software Development
Marshall Ward (NCI): ACCESS-OM2 performance analysis
Rui Yang (NCI): Parallel IO in MOM5
Angus Gibson (ANU): Towards an adaptive vertical coordinate in MOM6
Jie Ma (CSIRO ): Investigating interannual-decadal variability of Indian Ocean temperature transport in an eddy-resolving model
Paige Martin (University of Michigan): Frequency-domain analysis of energy transfer in an idealized ocean-atmosphere model
17:30 Close
19:00 Workshop dinner (Debacle – 24 Lonsdale St Braddon)
Tuesday 8 May
9:00 Session 4 (Chair – Andrew Kiss)
Andy Hogg (ANU): Are we Redi for 0.25° ocean-climate models?
Kial Stewart (ANU): The Repeat Year Forcing for JRA55-do
Terry O’Kane (CSIRO): Coupled data assimilation and ensemble initialization with application to multi-year ENSO prediction
Gary Brassington (Bureau of Meteorology): Ocean forecasting status and outlook
Peter Oke (CSIRO): Bluelink activities and plans
Matthew England (UNSW): A proposal for future projection simulations using COSIMA ocean-ice models
Richard Matear (CSIRO): CSIRO Decadal Climate Forecasting, update of the project’s progress
Simon Marsland (CSIRO): Preparing ACCESS for CMIP6
Clothilde Langlais (CSIRO): Downscaling towards the coast – a perspective on where the coastal modelling group would like to go
11:00 Morning tea
11:30 Discussion: COSIMA planning and strategy
13:00 Lunch
14:00 Strategy and planning summary
14:30 COSIMA Cookbook tutorial
16:00 Close

Synthesis of Discussion

Tuesday afternoon included discussions of present and future needs and directions of the COSIMA community, via breakout sessions on the topics Sea Ice, Coastal / Forecasting, Coupled Modelling, Process Modelling, Biogeochemistry, and Technical. The overall threads of  these discussions are summarised here.

Open and accessible code, configurations, output and analysis

Transparency, accessibility and reproducibility of model code development, run configurations and output data were named as priorities by many groups. Nic Hannah’s proposed REDB (Reproducible Experiment Database, http://redb.io) was widely supported as a means to tie together and curate the source code, configurations, output and analysis of model experiments. Using consistent shared codebases was also a priority. Containerisation was suggested as a method to make experiments self-contained. Extension of the database to include idealised experiments was also suggested.

Model evaluation

There is a need for more model evaluation against observations. Several groups highlighted the importance of better integration of observations for model validation and a desire for this functionality to be better supported in the COSIMA Cookbook. Comparison of CICE to SIS-1 at 1 and 1/4 deg was also suggested.

Technical validation is also needed – e.g. BGC, bit reproducibility, broadened test suite, regression testing. Model performance and stability priorities include: resolve crashes, balance load, MPI benchmarks and stress testing.

Usability

Suggestions included a glossary for beginners, an online portal for control runs, and to minimise difficulty of running new model configurations. Standardised output files and naming conventions would facilitate analysis. Improved functionality and versatility of the COSIMA Cookbook was also suggested.

Documentation was a priority for many, in particular an ACCESS-OM2 documentation paper, but also open/evolving documentation as the models develop.

Parameter selection was also a concern for many – how to choose appropriate parameters (e.g. for ice or BGC), how to assess model sensitivity to parameters, how to document why parameters were chosen or altered. Data assimilation was suggested a way to improve ice parameter selection, including assimilation of under-ice observations (e.g. temperature). BGC was suggested as a way to constrain the dynamics.

It was pointed out that the payu run management software underpins model runs, yet formal funding for its continued development is presently lacking.

Model enhancements

Suggestions for enhanced modelling capability included: interannual forcing, WOMBAT BGC, coupling to an atmosphere model, 1-way nesting, coupling to wavewatch, explicit tides, wet/dry cells.

Community coordination, synergies and strategy

Suggestions included a streamlined process for providing community feedback and deciding on priorities, and for community involvement in developing the BGC component. It was also suggested to foster engagement with atmosphere and sea ice specialists, and have a more formalized ice group. The technical team is also seeking more input from scientists, especially regarding sea ice.

Regarding modelling strategy, it was suggested to have intelligent model diversity (not too many versions), a consensus on standard perturbation experiments, and to decide on resources to commit to MOM5 vs. MOM6.

Summary of Priority Tasks

The following list of tasks was identified as a priority for the near term. Volunteers to lead or assist with tasks much appreciated.

  1. IAF Runs: With the addition of YATM, we now have the facility to run Interannual Forcing (IAF) runs from the JRA55-do forcing dataset in ACCESS-OM2. Once YATM has been tested, we will conduct IAF runs at all resolutions, starting with 1°.
  2. Model Documentation: Production of a model documentation paper is a high priority for the coming months. This will be achieved by:
    1. Writing a larger technical documentation report (https://github.com/OceansAus/ACCESS-OM2-1-025-010deg-report) that will be stripped down to feed into a paper; and
    2. Inviting community evaluation of existing model output.
  3. Model evaluation and analysis: We propose the COSIMA Cookbook as a framework for users to contribute model analyses. In particular, we encourage observational comparisons with existing model output, and also encourage users to submit bug reports and feature requests via https://github.com/OceansAus/cosima-cookbook/issues
  4. WOMBAT: In the coming months we will look to implement the WOMBAT biogeochemistry model (already running in MOM5) into the ACCESS-OM2 framework.
  5. Capability gaps: The COSIMA community has been able to leverage expertise from a number of different programs. However, our community as a whole remains subcritical in several areas, including sea ice modelling and atmospheric dynamics.
  6. REDB: Nic Hannah proposed a new system for tracking simulations and the output data. This system was identified by many discussion groups as a potential solution to some of our collaboration roadblocks. We will investigate the viability of such a system.
  7. MOM6: Plan is to begin transition to MOM6, building up experience in the latter half of 2018.

Recommendations for COSIMA 2019 workshop

  • Institute a James Munroe award for contributions to COSIMA
  • Extend to a 2.5-day workshop to allow more time for discussion (not extra talks)

Technical Working Group Meeting, June 2018

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Minutes

Date: 12th June 2018
Attendees:

  • Marshall Ward (MW) (Chair), NCI
  • Aidan Heerdegen (AH) and Andrew Kiss (AK), CLEX ANU
  • Russ Fiedler (RF), Matt Chamberlain (MC), CSIRO Hobart
  • Peter Dobrohotoff (PD), CSIRO Aspendale
  • Justin Freeman (JF) BoM Melbourne
  • Nic Hannah (NH) Double Precision

TWG Meeting

JF:  Would be able to attend more regularly if there was a calendar invite which would enable him to schedule the meeting. How do we integrate calendars for Justin

COSIMA Models

AK: Bathymetry error in tenth model in Cumberland Sound, Baffin Island. Causes model blow ups.
RF: Yes blast it out. Russ will do it today. AH: Do we need any changes to restart/input files? Russ: if below zero  for eta_t, might have to set to zero. Otherwise will complain about penetrating rock.
AK: tenth very unstable over the weekend.
MW: longjmp error means the backtrace is failing. Memory go so severely corrupted that can’t properly debug.
“nearest_index array must be monotonically increasing error”
AK: Sweep and resubmit and works.
AK: More errors since turned on diagnostics for Adele. RF: are these globals? MW: could be FMS bugs because MPI is being strained and things are out of order.
AK: daily outputs in regional area: temp, salt, uhrho_et, vhrho_nt, rho_dzt. RF: spewing output from a lot of processors as regional outputs do not use io_layout, so every affected processor outputting data. AK: only doing for 2 years and then turn it off. It has slowed it down. Become erratic in timing. RF: Some processors not outputting the field, not sure why it should make it unstable.
AK: Put up as an issue.
AH: What is the current model config for tenth, and performance? AK: 4.5K on MOM, 2K on cice. Runs with 450s timestep, 1.5 hr/mo. Now running at 400s. Crash in Baffin Island goes away with shorter timestep.
AH: Try and get tenth running faster. Ice no longer holding back timstep. AK: Was running 540s before Baffin island issues.
MW: netCDF4 v4.4 has FPE turned on. Built by a different person. Historically always had FPE disabled. AK: 4.2.1.1 in MOM. 4.3.2 in CICE. 4.4.1 in matm. OASIS has default. AK: waiting for yatm build to be signed off. Ben M suggested we should be using openmpi/1.10.7 (optionally with debug). Number of bugs fixed between 1.10.2 and 1.10.7.
AK: Want to try out orange layout with CICE. Currently 2000 cores with no landmasking and 1 block / processor. Could be run a lot cheaper. Currently MOM bound. Should be to run well below 2000 cores. Waiting for yatm to be sorted out. Trying some frankenstein builds and back porting to matm.
AK: Timing is very inconsistent. RF: Ocean eta and plot diagnose has a collective. Does a sum. Somewhere it has hung. All depend on this function. MW: Could be load imbalance in CICE.
MW: MPI_Comm_split hangs or fails intermittently.
AK: No stock runs since looking at runtime. MW: thinks his profiling was wrong because of lack of ice. AK: looking at the load imbalance there is ice. MW: ran from rest for 10 days. CICE would normally do work that wasn’t captured. MW: tried to redo profiles and all runs stopped working. Shocking.
MW: moved on to yatm. Putting scorep into yatm had issues, so not redone the profiles with realistic ice.
AK: will spin off run with no diagnostics as point of comparison. MW: at dt=300s, 100s/day seemed reproducible. Andrew’s 50% slower. Maybe more stuff happening. One of two issues that need to be resolved. CICE bound results different, second is MOM slowdown. Matching MOM-SIS important goal.
MC: how much longer running spinup? When switch to IAF? AK: will switch to IAF ASAP. Andy is running RYF @ quarter. Then Paul Spence will run IAF quarter. Currently 34 years of spin-up with 84/85 repeat year. MC: Will start from year zero? AK: there are biases in RYF, so not sure if we should spin off from this run. Might depend on how many years we have to get done.
MC: will there be multiple cycles of IAF? AK: depends. MC: start at WOA or from RYF spin up.
AH: For the model documentation paper there will be the standard 5 x IAF (JRA55) protocol for 1 degree and 0.25 degree. The MOM meeting discussed strategy for 0.1 degree. Andy Hogg thought the tenth was just too expensive to run this protocol and might have to run only one cycle of IAF, or maybe spin up with RYF and then run IAF from 85 onwards. Whatever was done would be repeated in a second quarter degree run to provide a point of comparison between the different resolutions.
RF: interested from 93 once the satellites go up.
JF: wanted to get up to speed. Looks over minutes when they come out, very useful. Mirko has been doing some runs. Will try and join in regularly. BoM will take up ACCESS-OM2 when up to speed. Will be OceanMaps version, used for forecasting.
AH: Andy running KDS50 for 0.25 deg for RYF spin up. Found KDS75 too unstable.
JF: Mirko is testing COSIMA models in back end. Mirko getting up to speed what we’ve done. Need the 75 level (COSIMA) grid. Will do some hindcast runs and compare with OceanMaps. Don’t have experience with sea ice model . Don’t know how it will affect forecasting. Need to look at the ice parameterisation. Also need to look at data assimilation. Will talk to Russ and Matt. At some point will be able to contribute back, will work from GitHub repo, using same codebase.
AK: run parameters and namelists on git repo are a long way out of date. JF: can we make sure these are updated. AK: Still in a state of flux. Still bedding down YATM configurations. Will do best.

ACCESS OM2/CM2 Code Harmonisation

AH: What is the other significant code difference in CM2 that Russ wanted to reimplement? RF: wave mixing scheme. Gets added into KPP. Comes via CVMix package. Two ways to implement. 1. 10m winds to come in via sbc. 2. Can empirically calculate them in MOM6. Russ has implemented this scheme under CM2.5 framework. Run for a while. Had to put in a limiter because it caused too much mixing. Dave reckoned it didn’t make difference. Haven’t looked at the most recent results. Running with CM2.5 coupled model.
RF: Also another scheme Russ wants to implement. Slightly different to ACCESS-CM2. Both schemes already in MOM6. One of them is in CVMix. That is what Dave has implemented in MOM5. Taken routine out of CVMix and plopped it into KPP module to give enhanced mixing. Also need 10m wind information to come in. Need changes in surface flux code. Russ has done this. Russ has implemented same thing, just change in the way winds get through. Not sure why ACCESS-CM2 didn’t see difference.
RF: Occasionally get massive mixing coefficients in KPP so put in a limiter.
RF: will put code changes into master branch. AH: when you have done this I can pull into CM2 and can test. RF: Griffies wants it in MOM5.
PD: followed along in slack channel. Not sure about all technical details. Big difference after 10 days between harmonised code and CM2 codebase. Has this been solved? How far along are we with this? Spinups will not have harmonised code if we don’t have a frozen version soon. ESM and CM2 groups want to know how close we are. We haven’t helped much to this point. How can I contribute.
PD: copied suite. Ran it. Thought was tracking down bug. PD: couldn’t find preprocessed source files. MW: do we run cpp? I get the right source code lines and don’t see .f90 files. No we don’t … which is why Peter couldn’t find them.
RF: why was red sea fix timing different? CM code has a fix? AH: might be because my fix uses relative time, not absolute model time. RF: timing fix should have absolute origin. AH: I’ll check.
AH: I don’t think there is that much more to go for the harmonisation
PD: when can I run harmonised MOM?
RF: when I can find some time to put in there. Now we have a way forward. Hopefully in a week or two.
PD: will put runs on ASAP. If harmonised code not ready, won’t be in spinups.
AH: will lease with Peter and tell him as soon as something is ready.
MW: if there are differences what do  they use? AH: they will use the MOM5 repo as far as I know.

Actions

New:

  • Edit tenth bathymetry to remove Cumberland Sound (RF)
  • Create calendar invites to TWG Meeting (AH)
  • Update model name list and other configurations on OceansAus repo (AK)
  • Check red sea fix timing is absolute, not relative (AH)

Existing:

  • Shared google doc on reproducibility strategy (AH)
  • Follow up with Andy Hogg regarding shared codebase (MW)
  • MW liase with AK about tenth model hangs (AK, MW)
  • Pull request for WOMBAT changes into MOM5 repo (MC, MW)
  • Compare out OASIS/CICE coupling code in ACCESS-CM2 and ACCESS-OM2 (RF)
  • After FMS moved to submodule, incorporate MPI-IO changes into FMS (MW)
  • Incorporate WOMBAT into CM2.5 decadal prediction codebase and publish to Github (RF)
  • Profile ACCESS-OM2-01 (MW)
  • Move FMS to submodule of MOM5 github repo (MW)
  • Make a proper plan for model release — discuss at COSIMA meeting. Ask students/researchers what they need to get started with a model (MW and TWG)
  • Blog post around issues with high core count jobs and mxm mtl (NH)
  • Look into OpenDAP/THREDDS for use with MOM on raijin (AH, NH)
  • Add RF ocean bathymetry code to OceansAus repo (RF)
  • Add MPI barrier before ice halo updates timer to check if slow timing issues are just ice load imbalances that appear as longer times due to synchronisation (NH).
  • Nudging code test case (RF)
  • Redo SSS restoring with patch smoothing (AH)
  • Get Ben/Andy to endorse provision of MAS to CoE (no-one assigned)
  • CICE and MATM need to output namelists for metadata crawling (AK)

COSIMA 2018 Workshop Details

The 2018 COSIMA workshop will be held on 7 & 8 May at the Australian Centre for China in the World on ANU Campus.

You can download the latest draft of the COSIMA Workshop Program (updated 3rd May). The program includes instructions for uploading your talk, guidelines on how to contribute to our discussion and some preparatory homework for anyone attending the COSIMA Cookbook Tutorial.

Please contact Andy Hogg or Andrew Kiss if you have any queries.

Technical Working Group Meeting, April 2018

Minutes

Date: 10th April 2018
Attendees:

  • Marshall Ward (MW) (Chair), NCI
  • Aidan Heerdegen (AH) and Andrew Kiss (AK), CLEX ANU
  • Russ Fiedler (RF), Matt Chamberlain (MC), CSIRO Hobart
  • Peter Dobrohotoff (PD), CSIRO Aspendale

COSIMA Meeting

MW: Will we present something again? Same as last time, a list of achievements? Consensus was yes we should.
MW: Want to make time during the meeting to work together on collective problem? NH: Yes, definitely. Even for just a short time.

Common codebase

AH: Have rebased PDs MOM code on to latest MOM5 source. Wrapped all PDs changes that are incompatible in ifdef ACCESS_CM statements. This is available as branch cm2 on MOM5 GitHub repo. Created a pull request to allow code review (https://github.com/mom-ocean/MOM5/pull/214).

AH: PD has provided a rose suite (u-aw048) for testing. AH successfully copied (u-aw405) and ran this suite. Created another suite (u-aw445) to test that this reproduces first copy with no changes. It does. Created a third suite (u-aw497), changed git URL to point at cm2 branch, but initial compile failed to find the source. Eventually got it to recognise the updated source, now compile fails due to an absence of a main routine. Needs some modification.

PD: Best to make small incremental changes to a suite. In this case just change the fortran files and see if it works. Avoid changing how the compile is done, definitely avoid changing rose app conf. Was just trying to determine the compile flags use in UM fcm build from Met Office was not a trivial task.

MW: cylc is good, small and configurable. rose is difficult and opaque.

AH: Will get some help from others via the cm2-om2-harmonisation slack channel

AH: Next step is to do the same for CICE5 as has been done for MOM5.

NH: CSIRO is getting CICE from the UKMO. There are code changes under src, not just in the drivers.

AH: Does UKMO version of CICE5 have a special licence? Will we be able to host UKMO modifications to CICE5 on OceansAus repo? NH: CICE has a CICE licence

 MW: UKMO runs CICE as a NEMO/CICE5 executable, not linked through OASIS like us.

Models

PD: ACCESS-CM2 doesn’t reproduce over restarts. Would like to run CICE stand alone. Does CICE reproduce over restarts?

NH: cleanest way to test is in the coupling code, before any model sends anything to another model, checksum fields. That is the point you can compare the output of a model. In the case of restarts, can include in checksum what current model run time is.

MW: there are 2 restarts, individual models and oasis restarts. Have to make sure trigger the same number of time steps in models.

NH: OASIS restarts are not a problem. OASIS get tells you if it read out of a restart. Not reading out magically, still working using PUT and GET. GET is from a file instead of from a model.
After each GET and before each PUT, print out time, processor, checksum can see when the checksums diverge. Will be different before the PUT, can then identify the model. If you determine CICE was the culprit can then look at CICE only run.
PD: How to do checksum? NH: Just sum whole array. MW: use MPP_checksum? NH: not in CICE. Our CICE code will output checksums if required. NH has already done this for CICE.
MW: does OM2 reproduce? NH: I spent some time on this. Repro for a couple of coupling time steps, then diverges.
MW: PD has 1×2 days not same as 2×1. Have we done equivalent tests with OM2? NH: yes, not passing.
NH: MOM by itself might not do this anymore? MC: restarts ok. RF: if you had the redsea bug it wouldn’t reproduce. Old repro results null and void. Models also have coupling code that might cause repo issues.
MW: UM passes, would think GC3 reproduces.
MW: interesting OM2 does not reproduce. Easier platform to test.  ACCESS-om2 needs to reproduce. NH: looking at this. With MATM changes, needs to make sure it works to get others to use it.
MW: Does someone want to check MOM?  Restarts, processor layouts. AK: don’t change layouts often so wouldn’t know if it does currently reproduce with layout changes. NH: non repo with layoutt changes indicates bug. MW: maybe not bug, but definitely volatile behaviour, maybe in a collective.
MW: Did find a repo problem with MPP_sum. Ran MPP_sum and MPP_reprosum, and got difference in one bit. Even something that simple can cause issues. GFDL always matches with same test. Maybe something we can control with compiler flags.
PD: As voltages go down can get make random errors occur. MW: Bob found bug with tridiagonal solver due to voltage issue in Intel chip. Maybe something going on with flags?
RF: GFDL definitely use precise option. Atmospheric model crashes otherwise. MW: MetOffice also uses precise.
MW: Maybe all could look more carefully?
AH: Do we have a reproducibility checklist? Some strategy. Shared google doc?
NH: starting work on tenth degree performance. Anyone interested in doing some profiling? MW: Any Hogg pressuring to do this. Will do it this week, and send to NH. Hope to have a bunch of profiles for the meeting.
NH: MATM is now clean, 100 lines of code, uses CMake. Hoping to start using it. All goes through CICE. Nothing about coupling has changed.
NH: Want to use newest version of OASIS-mct (v3 not v2). Improvement in performance, can collect together MPI comms.

Actions

New:

  • Poll TWG on list of achievements for Meeting presentation (MW)
  • Shared google doc on reproducibility strategy (AH)

Existing:

  • Follow up with Andy Hogg regarding shared codebase (MW)
  • MW liase with AK about tenth model hangs (AK, MW)
  • Pull request for WOMBAT changes into MOM5 repo (MC, MW)
  • Compare out OASIS/CICE coupling code in ACCESS-CM2 and ACCESS-OM2 (RF)
  • After FMS moved to submodule, incorporate MPI-IO changes into FMS (MW)
  • Incorporate WOMBAT into CM2.5 decadal prediction codebase and publish to Github (RF)
  • Profile ACCESS-OM2-01 (MW)
  • Move FMS to submodule of MOM5 github repo (MW)
  • Make a proper plan for model release — discuss at COSIMA meeting. Ask students/researchers what they need to get started with a model (MW and TWG)
  • Blog post around issues with high core count jobs and mxm mtl (NH)
  • Look into OpenDAP/THREDDS for use with MOM on raijin (AH, NH)
  • Add RF ocean bathymetry code to OceansAus repo (RF)
  • Add MPI barrier before ice halo updates timer to check if slow timing issues are just ice load imbalances that appear as longer times due to synchronisation (NH).
  • Nudging code test case (RF)
  • Redo SSS restoring with patch smoothing (AH)
  • Get Ben/Andy to endorse provision of MAS to CoE (no-one assigned)
  • CICE and MATM need to output namelists for metadata crawling (AK)

Sea-ice working group: Notes 20180228

MEETING NOTES COSIMA SEA-ICE WORKING GROUP MEETING: 

28 Feb 2018, 10:00 - 11:30am
Meeting held on Zoom.

Present: Andrew Kiss, Adele Morrison, (anyone else at ANU?), Andrew Hogg, Siobhan O'Farrell, Simon Marland,
         Fabio Diaz, xxx (1 other PhD student at CSIRO Aspendale), Will Hobbs, Petra Heil and from 11am Paul Spence.
Apologies: Nicolas Hannah, Matt E.

=======================================================
1) Recap of the AMOS presentation on COSIMA results so far.
ACCESS-OM2 suite (Andrew Kiss)
Based on MOM5, CICE5, OASIS3, Repeat year atm forcing.
Tripolar grid 1/10^o, 75 vertical resolution
Slow to run: 17hours/yr; 5559 PEs; dt = 450s   --> eddy resolving
Tripolar grid 1^o, 75 vertical resolution
              6mins/yr;  252 PEs; dt = 5400s   
------
Previous issue: 
Negative solution: Russ Fiedler fixed
         If salinity locally is less than 5 PSU, then salinity comes from the 
         surrounding.
------
Sea-ice thickness (1month average): Shows neat DKPs in Arctic.
=======================================================
2) Simon M: 
Fabio is working: Restoring 1^oC: NCEP/NCAR reanal rather than core runoff.
=======================================================
3) ACCESS-OM2 CICE config

Current CICE config in the coupled ocean/sea-ice mode:
4 ice layers plus snow
5 thickness categories
mushy ice TD
classic EVP Dynamics
melt poinds 
JRA55 - do V1.3 1984/85 repeat years forcing, 0.5625^o, 3 hourly
SSS restoring to WOA 2013 V2
1200 PUs for CICE + 4358PUS for MOM + 1 for Matm
--> No polynyas in 1/10^o even though JRA has good katabatics (Adele Land)
     --> look at LHF + net ice production
---
Ice volume in 1/10^o in Arctcic is too high: in access of 30Mio km^3
  Piomass comparison
--- 
Issues: 
* spin up
* compatible physical parameters in Mom & CICE   <-- not working
- TC using mushy ice TD but Bitz & Lipscome is xxx (? cannot read my notes)
- EVP or EAP? --> EVP seems to do ok producing DKPs  --> Use revised EVP.
=======================================================
4) What to use for validation? 
Simon M: Tamura's polynya ice prodution.
=======================================================
5) IcePack has been released (Petra)
Can it be ported to NCI?
=======================================================
6) Timing of COSIMA configs? 
Nick H. is still using/working on MOM5.
Hence MOM6 work is delayed. 
 But Los Alamos are doing MOM (?? which version) with CICE6.
=======================================================
7) Next steps: 
Start MOM6 with SIS2 for ease!!!
 1) Timing of advance and retreat   --> Siobhan OF: That is controlled by JRA forcing.
 2) Ice motion?  AVHRR data to compare  <-- Follow this one up.
=======================================================
8) Various:
* John Spence: 
Compare namelists with those used by others.
PH: Check with what the Arctic high-res folks use. 

* SOF: European updata: LIM2/3, Gelato (CERFACS and UKMet).
  --> Access: Where to couple ?  <-- new UKMet model: 2019 to do runs.
                                     --> C-grid (NEMO?)
=======================================================
=======================================================
Next meeting: 
At COSIMA workshop, Canberra, 08/09 May 2018
=======================================================

ACCESS-OM2 Update

Over the last few months, COSIMA folks have been working hard on releasing our ACCESS-OM2 suite of models. The current status is that we have now completed a 500 year spinup for 3 different cases using the JRA55-do (Tsujino et al., 2017, personal communication) forcing dataset. Some preliminary results can be seen in the figures below. We are also spinning up a CORE-NYF comparison case. For a more complete analysis have a look in the COSIMA Cookbook.

Plans in the coming weeks are to finalise spinups of our 0.25° case (ACCESS-OM2-025), and to begin running our flagship 0.1° simulation, ACCESS-OM2-01.

 

Technical Working Group Meeting, November 2017

Minutes

Date: 14th November 2017
Attendees:

  • Aidan Heerdegen (Chair), Andrew Kiss (ARCCSS ANU)
  • Fanghua Wu (National Climate Center, China Meteorological Administration, Visitor ANU)
  • James Munroe (Memorial University of Newfoundland, Visitor ANU)
  • Nicholas Hannah, Anthony (Double Precision)
  • Russ Fiedler and Matt Chamberlain (CSIRO Hobart)

COSIMA Models

  • Discussion around publicising 1/10th model spin up, in case interested parties would like diagnostics saved.
  • Bluelink are interested in full JRA55-do IAF style spin up, and would want 15-20 years of daily full 3D U,V,T,S and eta fields from that. What is required to construct ensembles/climatologies.
  • Nic looking into ACCESS-OM2-01 performance issues. Lots of time in ice coupling field halo updates. In serial so holding up ocean when it does this. Definite target for optimisation. Should use OASIS to fill the halos when it does the coupling step? Russ disagrees. OASIS shouldn’t know anything about what goes on in models. Gridding using block trains, a 1:1 mapping between grids. If you do this have a 1:many mapping. No longer have identical grids when put in halo information, might break optimisations. When Russ looked at 1/4 deg, hold up was due to synchro just before that. Not sure about 1/10th. Want a barrier just before calling clock before halo update. See if synchronisation issue, or actual time take with halo distribution. 5 halo distributions being done. Heaps more done in CICE itself. Nic: land imbalance between ice processors? Russ: yes my hunch. Load imbalances change a lot with resolution and processor layout. Nic: a problem doing halo updates without considering where field is used. Russ: agree. Velocities need updating, not sure about tracers.
  • Fanghua has been running the new tenth bathymetry with the MOM-SIS-KDS75 config. With JRA55 RYF forcing time step now 450s (from 150s initially). Runoff data now a problem with very low salinities in the arctic at about 7m depth, even with 150s timestep. Created new runoff data, spread more into the ocean but still have issues. Russ saw very high salinities in the Arctic (Laptev Sea). Might be brine rejection from forming sea ice from ice free start. Suggests decreasing salinity restoring timescale from current 60 days to 10 days or even 1 day, to get the model over the initialisation. Andrew suggested issue could be resolved with initial sea ice climatology. There were issues with these files and not been used for a long time. Recent poster to mom users google group has identified some of the problems.
  • Nic’s online runoff redistribution may help, as it is possible to specify maximum runoff per cell, which can help in these areas with very large runoff. Would require ACCESS-OM2-01 config.
  • Nic currently working on getting ACCESS-OM2-01 working with Russ’ new bathymetry. Had a couple of attempts. Getting close, various technical glitches with masks and so on.
  • Andy Hogg has MATM issue when running ACCESS-OM2-1deg for more than 4 years at a time. There is an error on netCDF open call, which comes from HDF layer. Nic ran valgrind, found a bunch of errors, and so recommends everyone update their MATM, but this did not fix the 5 year issue. Determined this was not a memory errors, but an HDF library error. Russ suggested using some HDF library calls to try and determine why the crash occurred. Also try different versions of the netcdf library.
  • Nic suggested we could change MATM to make few file open calls. Aidan has a new payu feature that allows multiple runs per PBS submission, so decided not a priority as MATM needs complete rewrite.
  • Regridding. Nic: need to choose which interpolation schemes to use for which fields. 2nd order cons for everything? Russ: Velocity should not be conservative. Momentum is not conserved. Patch for velocities, T and S. Will give smooth flux fields. Nic: 2nd order cons will be very smooth. Russ: do whatever is cheaper for T, S. U,V should be as smooth as possible. Patch should be 1st order cons, possible 1nd order.  AK: 1st order cons is piecewise constant (bad for wind stress curl). 2nd order is piecewise linear? So similar to bilinear. Need to go to patch for smoother. Russ: tried 2nd order cons, see problems at corners, nodes and edges with wind stress curl. Coarse to fine get artefacts. Patch should work. AK: half of the fields are fluxes. Those should be conservative (2nd order ideally). The remaining are not fluxes, don’t see strong argument for conservative. Is there an issue with different interpolation schemes from different fields? Will bulk formula at fine scale be an issue? Russ: will get jumps in some of the calculated fields. Quantities like T, S should be done with patch, end up with smooth fluxes. AK: Surface stress bulk formula, does it take atmosphere stability into account? Any drag coefficient? Russ: it does. Looks at a profile, figure out a profile. AK: Use SST and 10m T to determine stability? MC: Yes. Say warm atmosphere sitting over cold surface, that’s stable so air would slide over. Daytime, warm surface, near neutral stability so not so sensitive. Possible for temperature and humidity to have small effect on drag coefficient. AK: If we use different interpolation method for 10m winds/T, will it cause issues? Russ: Small jump in sensible heat maybe? Just go with patch or bilinear for all scalar quantities. Velocity go for patch. How will it take into account rotation in tripolar? Presume it is handled  well? AK: only an issue with velocity. Checked with current forcing fields and was ok. Will check new fields the same way.
  • AK: Final decision:
    • patch (the smoothest available) for u_10, v_10
    • 2nd order conservative for fluxes (rain, rdls, rsds, runoff_all and snow)
    • patch or bilinear for non-flux scalars (q_10, slp, t_10) suggest trying patch and only using bilinear if performance with patch is bad
  • Nic: what does MOM-SIS do? Aidan: Thought Steve said bicubic, used to use bilinear but wasn’t smooth enough. Smoother the better.
  • AK: Should WOA salinity restoring fields be smooth in the same way? Nic: What do we currently do? Nic: bilinear? Aidan did it. Russ: not a big issue if salinity restoring not too strong.

Task follow ups

  • Should be using GFDL FMS code directly. Would work better to collaborate with GFDL. Use same code, submit bug reports easily.
  • Once we have FMS as submodule, use all pre/post processing code from GFDL. Make MOM5 leaner, easier to keep updated. Russ: what is the latest FMS version? Aidan: don’t know, and it is hard to tell. Russ: noticed there are new features, like new diagnostic output options, e.g. RMS on the fly, statistics. So things like diag_manager has been updated. Could be some other powerful tools.
  • Aidan: Currently huge step to upgrade. Small step, but could be really good. Not sure how Marshall did it, but not simple.
  • Nic has updated the access-om2 repo structure. Every single test case/experiment is in it’s own repo. Makes it easier for users to grab config without worrying about other configs and source code. OceansAus now has more experiment repos. Aidan: Andy has an issue with git clashes with multiple runs in a single repo. This will fix this.
  • Blog posts?

Actions

New:

  • Will have a December meeting. Tue 12th.
  • Determine if COSIMA intend to do IAF JRA55 spinup of tenth model (Aidan)
  • Send link to spinup diagnostics spreadsheet to Russ (Andrew Kiss)
  • Nic add MPI barrier before ice halo updates timer to check if slow timing issues are just ice load imbalances that appear as longer times due to synchronisation.
  • Test Andy’s 5 year config with different netcdf library versions to check MATM error is not a just a library issue (Aidan)
  • Check current sea surface salinity restoring smoothing (Aidan)

Existing:

  • Russ to add all his ocean bathymetry code to OceansAus repo.
  • Nic to help Peter get his MOM repo up to date with MOM5 master branch, and then merge changes
  • Look into OpenDAP/THREDDS for use with MOM on raijin (Aidan, Nic, Marshall)
  • Nic to present MATM code re-write proposal to TWG for feedback before sign-off. Will then be presented to Andy Hogg for approval.
  • Nic create a discussion document (on COSIMA?) to document current approaches and strategies for future
  • Move FMS to submodule of MOM5 github repo (Marshall). Liase with Nic on implementation?
  • Work up test cases to cover the nudging code (Justin, Mirko) and supply them to Nic.
  • Add new test cases to Jenkins test suite (Nic).
  • Start a new google doc about coupler issues and MATM (Marshall)
  • Ask Dale Roberts about effects of OpenMP for Roger (Marshall)
  • Make a proper plan for model release — discuss at COSIMA meeting. Ask students/researchers what they need to get started with a model (Marshall and TWG)
  • Blog post around issues with high core count jobs and mxm mtl (Nic)
  • Create document outlining options for configuration sharing (?)

COSIMA Cookbook

One of the goals of the COSIMA community is to create a common framework for evaluating and diagnosing model output. Our initial attempts to do this are encapsulated in the COSIMA Cookbook. The Cookbook aims to:

  • Create standard Jupyter Notebooks for diagnosing model simulations, or groups of simulations;
  • Documenting methods to efficiently interrogate large model datasets;
  • Document model sensitivity studies; and
  • Provide a gallery highlighting commonly used diagnostics.

The COSIMA Cookbook is publicly available on the OceansAus Github repository. We are also in the process of building documentation and the COSIMA gallery.

COSIMA 2 Workshop Report, May 2017.

The second meeting of the Consortium for Ocean Sea Ice Modelling in Australia (COSIMA) was held in Sydney on the 25-26 May 2017. There were 36 attendees (2 via video, 26 gave presentations) representing 9 different institutions. A full participant list and links to presentations is included at the end of this report. The workshop goals and agenda is here.

The consortium has 3 years remaining of 4 years funding from an ARC Linkage Project to build a model configuration which underpins a variety of applications. The consortium also aims to provide a lasting platform that engages and benefits all ocean-sea ice scientists and technicians in Australia. This report begins with an assessment of milestones achieved since the May 2016 meeting, followed by a list of the 2017 workshop highlights and discussion/action items to be undertaken in 2017/2018.

Assessment of  COSIMA Community Action Items from 2016 Workshop

  1. Need to create a website to outline COSIMA activities and developments. [We are in the process of acquiring the domain name cosima.org.au, and ANU will fund hosting and a web development team to put together a skeleton site.]
    • DONE (cosima.org.au).
  2. We will formalise a code of ethics for COSIMA users to abide by, based on the DRAKKAR agreement. [Spence]
    • DONE (http://cosima.org.au/index.php/about-2/ethics/) 
  3. We aim to register members on the website, and create a mailing list.
  4. We will need to formalise the use of technologies to share code configurations, analysis tools and data. It may be possible to have a data project code on NCI to help with this.
    • Substantial Progress: i) hh5 storage for COSIMA model data at nci; ii) cosima cook book github repository in use for data processing scripts; iii) git hub model code repositories in use for some configurations.
  5. We will release flagship configurations that are broadly supported by the community. The goal is to make the naming conventions consistent with the ACCESS community where possible, and to overlap with ACCESS developments where possible.  
    • Substantial Progress. New flagship configurations are under active developement: e.g. JRA-55 forcing of MOM-SIS and MOM-CICE configurations at multiple resolutions, including enhanced vertical resolution. Information regarding flagship simulations will be posted on website this quarter [Spence]. 
  6. COSIMA will hold an annual meeting in the last week of May, for two days. Venue will rotate around the partner institutions. The focus of the meeting will be on science applications of ocean models, but will also include a technical component.
    • DONE. Next meeting in first week of June, 2018, Canberra.
  7. We will aim to have more regular communications, including newsletters and video meetings.
    • Substantial Progress. Open COSIMA video conference meetings were held monthly. Linkage project CI meetings occurred quarterly. Regular Technical Working Group meeting were held. Meeting notes are often posted at cosima.org.au.
  8. We will establish working groups within the community, along with a working group chair. Proposed groups include
    • Sea Ice Modelling [Heil]
      • Limited activity from this group in 2016
    • Technical [Ward]
      • Best communicating group that holds regular meetings, posts notes, has active community and achieves results.
    • Linkage Project [Hogg]
      • Quarterly meetings are held to gage model development progress and funding usage.
  9. The major gap in the community was identified to be sea ice modelling and forecasting. We will all look for opportunities to attract visitors and expertise in this space.
    • Needs more work. 

Assessment of  ARC Linkage Project Action Items from 2016 Workshop

  1. There is a strong need to consider vertical resolution in future high resolution model developments (Stewart).
    • DONE. http://www.sciencedirect.com/science/article/pii/S1463500317300434
  2. Our MOM-CICE implementations using OASIS3-MCT coupling, but it is not clear that this solution will scale to 0.1° and beyond (Hannah)
    • Substantial Progress. Parallel OASIS-CICE now runs as fast as serial FMS-SIS with MOM5. Uncertainties remain regarding MOM6 coupling.
  3. Forced ocean-sea ice models should be transferring to the JRA-55 forcing set when possible (Marsland)
    • DONE. JRA-55 forced configurations are underway in multiple groups. Fabio Dias is running coarse resolution MOM5-OASIS-CICE simulations. The CoE Oceans Group is running MOM5-FMS-SIS and MOM5-OAIS-CICE simulations at multiple resolutions. A relative year forcing data set has been developed from JRA-55 (contact Kyle Stewart)
  4. There was general agreement that the Linkage Project should fund both the development and evaluation of new model configurations. This point implies that we should equally fund the technical and postdoctoral position, despite the partial funding of the program.
    • DONE. Hannah continues to excel at developing the model Linkage project model configurations. A scientist has been hired (starting Aug., 2017) to help develop and evaluate the model simulations.  
  5. In the first year we will look to upgrade current MOM5 implementations, focussing on the vertical grid and the incorporation of CICE.
    • Substantial Progress. A 1/10 degree 75 level ACCESS-OM2 configuration consisting of MOM5 and CICE5 is being developed. Several scalability and performance problems have been overcome and we are now completing a spin-up run. The work has also resulted in improvements to the lower resolution 1 and 1/4 degree configurations and ACCESS coupled models.
  6. In subsequent years we will look to adopt a MOM6 configuration.
    • Progress. Testing with MOM6 adaptive vertical coordinates is underway (Angus Gibson). Given that SIS2 is adopting much of the CICE5 code, uncertainties remain regarding the sea ice and coupling model to be used with MOM6.
  7. As configurations develop and have been properly evaluated, they will be distributed to the community.
    • Substantial Progress. The distribution platform is under development with substantial progress on the back-end. A COSIMA data repository on NCI exists, and currently houses several flagship simulations. A repository for python analysis code that accesses the data repository is in use (https://github.com/OceansAus/cosima-cookbook). Substantial progress has been made in adopting effective big data analysis techniques (James Munroe).

2017 Workshop_Highlights

  • Substantial progress in the development and analysis of coupled WOMBAT biogeochemistry simulations.
  • Exciting opportunities within the newly funded CSIRO Decadal Prediction team.
  • Our technical teams continue to excel at developing and optimising model configurations with effective collaborations. Hannah has made excellent progress in MOM-OASIS-CICE coupling. Ward provides a key conduit to understanding NCI optimisations. Heerdegen is supporting a multitude of operations. Fiedler continues to develop the new bathymetry.
  • The enhanced capabilities of CICE over SIS remain. CICE6 is being developed under a community framework. SIS2 has adopted some of the CICE code.
  • ACCESS is working towards the CMIP6 deadlines.
  • The blue link forecast models are now perceived to be limited more by the ocean model configuration than the data assimilation.
  • New model configurations (MOM5-OASIS-CICE, MOM5-FMS-SIS) using enhanced vertical resolution, JRA forcing (including an RYF forcing), and updated WOA initial conditions are underway.

COSIMA Community Discussion/Action Items from 2017 Workshop

  1. Develop website into more of a community portal to flagship simulations. Provide model configuration and analysis with low barrier to entry for users. (Spence)
  2. Develop the COSIMA Cookbook portal  with a gallery of options (Munroe). Improve the community usage and contribution to the cookbook. Provide a visual gallery of code examples (ALL).
  3. Provide online chat capability for COSIMA model configurations. Look into using Slack teams. (Spence)
  4. Provide list of ongoing experiments, links to data available and diagnostics wanted, contacts for expts. (Spence)
  5. Consider separating models configs into Tier 1 (control flagships), 2 (perturbations from control), 3 (parameter sensitivities) to aid communication. (Spence)
  6. Provide discussion platform for new experiments. Wider discussion of methodologies and diagnostics.
  7. Provide platform for efficient explorations of parameter spaces (sea ice, neutral physics, bgc params, SSS restoring). How to share configurations? Tracking configs with git needs to be embraced by all! (Aidan, Hogg)
  8. Explore CICE efficiency, coupling a wave model to CICE, CICE6-MOM6 capabilities. Be aware of similar progress being made at NCAR. (Heil).
  9. Consider hiring admin support for the COSIMA website (England).

ARC Linkage Project Discussion/Action Items from 2017 Workshop

  1. A new 1/10 degree model bathymetry data set continues to be underdevelopment with substantial progress towards a final product expected with a few months (Russ Fiedler)
  2. Hannah continues to develop the MOM5-OASIS-CICE5 configurations. Expects to provide spinups at 3 model resolutions to the communitu (1, 1/4, 1/10). Discussion regarding the CICE settings (Heil), vertical resolution (Stewart), JRA forcing (Stewart) are needed. Does the model currently have a closed heat budget (Dias)?
  3. Excited to welcome Andrew Kiss as the scientist funded from this ARC Linkage grant. Hoping for a model evaluation paper before the next meeting.

 

Attendees

(Where available, talk files are linked from the presenter’s name.)

Andy Hogg (ANU)
Gary Brassington (BoM)
Nic Hannah (Breakaway Labs)
Dave Bi (CSIRO)
Matthew England (UNSW)
Adele Morrison (ANU)
Ryan Holmes (UNSW)
Jan Zika (UNSW)
Angus Gibson (ANU)
Andy Kiss (ANU)
Veronique Lago (UNSW)
Laurie Meviel(UNSW)
Kaitlin Alexander (UNSW)
David Webb (UNSW)
Peter Dobrotoff (CSIRO)
Leela Frankcombe (UNSW)
James Munroe (Memorial, Canada)
Joan Llort (Utas)
Arnold Sullivan (CSIRO)
Xuebin Zhang (CSIRO)
Terry Okane (CSIRO, Remote)
Peter Oke (CSIRO)
Paul Spence (UNSW)
Richard Matear (CSIRO)
Clothilde Langlais (CSIRO)
Stephen Griffies (GFDL, Remote)
Russel Fiedler (CSIRO)
Marshall Ward (NCI)
Matthew Chamberlain (CSIRO)
Fabio Dias (UTas)
Aidan Heerdegen (ANU)
Petra Heil (AAD & ACE CRC)
Siobhan O’Farrell (Remote, CSIRO)
Xiaobing Zhou (BoM)

Technical Working Group Meeting, May 2017

Minutes

Date: 16th May 2017
Attendees:

  • Marshall Ward (NCI, Chair)
  • Aidan Heerdegen and Andy Hogg (ARCCSS ANU)
  • Scott Wales (ARCCSS Melbourne Uni)
  • Nicholas Hannah (ARCCSS/Double Precision)
  • Russ Fiedler and Matt Chamberlain (CSIRO Hobart)
  • Justin Freeman (BoM)
  • Peter Dobrohotoff and Roger Bodman (CSIRO Aspendale)

Updates

  • Roger is having issues with N95 atmosphere. Marshall says it doesn’t scale past 256 cores. Roger would like to get RTM profiling working. Martin and Peter have got multiple threads working in AMIP. Has spoken to Scott Wales. Something odd happens in decomposition. Marshall will ask Dale Roberts about effects of OpenMP. Has chemistry has been enabled for OpenMP?

Liaison with COSIMA Management

  • Andy is here to get some feedback about our activities. Andy thinks TWG is doing a good job of communicating, a goal is to get more communication amongst COSIMA in general. Management team meets quarterly. No science talk or detail. Have to be better at merging/converging disparate code, TWG is crucial for this.
  • Andy wants a better framework for analysing and post-processing runs, and access others outputs. And we are currently doing some work in this space. The effort it is scattered, no one lead. Nic has done some work in past. Now using ipython notebooks to share analysis. James Munroe working on dashboards. Justin asked if COSIMA will deliver this? Andy: not explicitly funded but will benefit uptake. Need better ways to serve data.
  • Andy would like more engagement around COSIMA website. Blog our progress? Marshall: do you have sample topics? Is it legitimate to put updates on issues with library versions say? Andy: borderline, maybe just TWG for that example. Currently reply on members of TWG to propagate information back to users. Maybe more relevant would be update on scaling of code for example. Don’t want to limit people now. Encourage as much as possible and filter if required. Peter agreed: get useful information up there. Haven’t had anything over the last year. Suggestion to make minutes more report like? Nic thought blog posts are a nice idea, but need deeper insight to be useful and interesting.
  • Andy wants science side to publish results of runs, and point to data.
  • Andy also keen for COSIMA to have information about model versions. ACCESS doesn’t have a way of releasing versions and hosting code. ACCESS is somewhat hobbled with partner disputes. Would like ACCESS-OM releases on COSIMA. Marshall pointed out the TWG was set up to address this. Models were not ready at that stage. Marshall suggested we make a proper plan for a release — discuss at COSIMA meeting. Ask students/researchers what they need to get started with a model.
  • What are the expectations of TWG for the COSIMA Meeting? Andy: some already giving talks. Interact and discuss with others. Get to know each other and ambitions and look for synergies.
  • Andy will contact Paul to make sure TWG will have a slot to fill in others on progress.
  • Andy would like an email list for COSIMA announcements.

COSIMA Models

  • Nic: Was in Canberra week ago. Had tenth timestepping on <3000 cores. More than 3000 didn’t initialise. MCT couldn’t set up routing tables with more than 3000 cores. Would just hang. After discussions figured out some MPI switches and flags to get it working: mxm mtl makes it work better. Justin suggested this would make a good blog post. Marshall found MOM6 was failing at 3000 cores too. Went away with mxm mtl.
  • Andy: MOM-SIS tenth was also failing. About 30% fails. Russ has had similar. Nic now running on 6K cores in ocean.
  • Nic had discussions in Canberra around CICE halo updates. Made 12+ changes to CICE and MATM code. Made big improvements. For all three model resolutions (1,0.25,0.1) overhead of coupling is 1-2% compared to MOM solo. That is a tiny serial bit of interpolating forcing fields on to ocean. Like 20s/month for quarter degree.
  • Nic: quarter degree 1800s time step should be less than 75min/year. Andy: UNREAL!. 1 deg is also running super fast. 50 years/day. Did a new compile on MCT library to squeeze as much performance as possible.
  • Now have 3 new configs. 1 deg and 0.25 deg could be used. Focussing on tenth at the moment.
  • Andy: 70min MOM-SIS-025  + CORE, JRA55 adds 30%.
  • In old config, all models block waiting for MATM to read files. Now MATM has sent everything. Reduces difference between CORE and JRA55. Nic has not done longer runs as yet. No longer buffering multiple years of MATM output.
  • Agreed Andy should get these configs and do some longer runs.
  • Andy talking to NCAR about JRA55 forcing. CORE used NYF. JRA doesn’t have that. Others have used a single year. Our strategy is May-May forcing with a shock at the end of May. Candidate years are 84/85, 91/92, 03/04. Want to test this at 0.25 deg and 1deg. Should adopt just what Nic has done.
  • These are MOM-SIS as Andy wants a baseline. Doing MOM-SIS from CORE with WOA13. Repeat with JRA55 RYFs. Want to compare to ACCESS-OM config of Nic.
  • Nic and Andy to talk offline and try out a repeat year.
  • Although it is fast, the tenth is inefficient, as there is no ocean masking currently. This is the next priority. Probably beyond Nic’s current contract.
  • Nic can I use unmasked restarts? Russ: yes. Just need to combine them.

COSIMA Workshop

  •  Marshall: can we agree to transfer to CM2? To get on common version of CICE.
  • Andy: will the code we release in OM2 be different in ocean and/or ice? Can we manage it in one codebase? Marshall: should be possible. Set aside time to discuss this at meeting.
  • Discuss moving to common CICE repo for all.
  • Marshall: Justin need some info from us on OM config? Nic and Justin will liase.
  • Justin won’t be at the COSIMA Meeting, does he want us to cover anything? Justin: staying up to date with what we’re doing, will be engaging much more in future.

Updates on previous actions

  • Nic: has updated OceansAus repo to Peter’s CICE. Can Peter look at the code and check it.
  • Marshall: Justin need some info from us on OM config? Nic and Justin will liase.
  • Russ has been doing a lot of clicking for bathymetry. Aus and PNG done. Need help.

Actions

New:

  • Ask Dale Roberts about effects of OpenMP for Roger (Marshall)
  • Make a proper plan for model release — discuss at COSIMA meeting. Ask students/researchers what they need to get started with a model (Marshall and TWG)
  • Contact Paul Spence about TWG speaking slot at meeting (Andy)
  • Prepare slides for TWG presentation at COSIMA meeting, and present (Aidan and Marshall)
  • Email list for COSIMA announcements (Aidan)
  • Blog post around issues with high core count jobs and mxm mtl (Nic)
  • Do longer runs with Nic’s 1 deg and 0.25 deg ACCESS-OM2-JRA55 configs (Andy and Aidan)
  • Try repeat year forcing with Nic’s configurations (Nic and Andy)

Existing:

  • Nic to present MATM code re-write proposal to TWG for feedback before sign-off. Will then be presented to Andy Hogg for approval.
  • Nic create a discussion document (on COSIMA?) to document current approaches and strategies for future
  • Move FMS to submodule of MOM5 github repo (Marshall). Liase with Nic on implementation?
  • Test Nic’s access-om model config on OceansAus (All)
  • Work up test cases to cover the nudging code (Justin, Mirko) and supply them to Nic.
  • Add new test cases to Jenkins test suite (Nic).
  • Start a new google doc about coupler issues and MATM (Marshall)