Technical Working Group Meeting, August 2019

Minutes

Date: 14th August, 2019
Attendees:

  • Aidan Heerdegen (AH) CLEX ANU, Angus Gibson (AG) RSES ANU, Andrew Kiss (AK)  COSIMA ANU
  • Russ Fiedler (RF), Matt Chamberlain (MC) CSIRO Hobart
  • Rui Yang (RY) NCI
  • Marshall Ward (MW) GFDL
  • Nich Hannah (NH), Double Precision
  • James Munroe (JM), COSIMA

PIO work with CICE

NH: PIO code in CICE not as complete or thorough as netCDF code. Nothing to suggest it won’t work. Relies on NCAR PIO library, and a CESM utility library. Dependencies which are not part of CICE. Built PIO dependency on raijin, ran into CESM dependency. Can either remove dependency or remove code.
NH: Initially thought to use the MOM approach. Tile and collate. Russ’ comments encouraged to try PIO. Will be supported in future and will be supported in CICE6. Nothing working, but will soon test with 1 degree.
RF: Real bottleneck with high freq output. Worth a go. Attempt to put this into FMS by Hartnett. AH: Different to parallel netCDF? NH: PIO is wrapper around parallel netcdf. Written by NCAR to simplify parallel netcdf. Another layer. On GitHub, continuing to be maintained. RY: Wrapper that does work to match computing to IO domain. Not so useful for MOM5 as it has io_layout already.
MW: Harntnett motivated by FE3 (forecast model) rather than ocean. Not sure what project even involved in.
NH: Big test is handling interesting CICE layout, difference between cartesian grid and PE layout. MW: PIO will support explicit decomposition and other approaches.
NH: Parallel netCDF version on raijin only links with OpenMPI3.0. RY: New machine launched soon. OpenMPI 1.* will be dropped. No new software depending on 1. MW: OpenMPI 2 is not good. Should use 3.
NH: Probably have to test this with OpenMPI 3.0 RY: 3.1.3. Switch everything to that. Good test for new machine. AH: Working now? RY: My fault. Used unmatched openMPI library. Everything looks fine. OpenMPI 2/3/4 with Intel 19. All working. 1 deg & 0.25 deg working. Tenth not working. MW: I was able to run tenth with 3.1.2/3.1.3.
MW: One of the intel compilers broke MOM. A compiler bug with types in types.
AH: Should  start an issue for testing RY: Will email MW directly. RY: Not a MOM bug.
MW: Tried MOM-SIS tenth? Good test. RY: From earlier this year do have this working. This is testing for new machine, so ACCESS-OM2.

OMIP date restart protocol

RF: Talked to Griffies. GFDL take ensemble approach. Run for N years using true dates. At finish reset back to start date with correct calendar. Storing new stuff in different directory. End up with 5 sequences of 55 years. All dates are correct. No issues with leap years going wrong. Think this is the best way to go.
AK: Came to conclusion that this was right way to go, mostly due to leap year issue. Problem is, can we get the model to do that, but Maurice and Ryan had issues. Issue with CICE getting the correct date. CICE has a flag “use_restart_dates”. Suggested set this to false, and set the dates in access_restart.nml, but CICE is not picking up dates. Looks like libaccessom2 is not passing them on to CICE. Some confusion about exactly what they have done. Some instructions on Wiki for restarting, from restarting IAF from RYF at tenth, but doesn’t work for other people. NH: I’ll look at it. AK: Will send issue. NH: Didn’t realise it was happening. CICE date handling is not great.
AH: Downside with ensemble, difficult to get metrics across the whole time series. RF: Need extra meta-data added in. Maybe which cycle you’re in. An extra variable which gives the actual number of days since the start of the run. Down with post-processing. Might be able to concatenate files using extra meta-data. AH: Always have issues with missing leap years if it spans a century. But only daily is an issue. AK: Cookbook do something. MC: Pretend it is no leap? JM: Data looking at as time series? AH: Extra metadata, say offset day is a good idea. RF: Add buffer in netCDF file so don’t need copies. mppnccombine can add padding. usually done with nccreate, make sure the header has some space. hbuf?

Strategy for CICE updates for flexibly adding fields

RF: Way CICE drivers work, variables you want are either hard coded, or muck around with pre-processing to compile them in and out. Wondering if anyone looked at doing it on the fly. Using error codes coming back when setting up variables, so have flexible number of variables passed in and out. Would like this to pass total wind speed, to harmonise code. Also Hakase wants it for some BGC stuff. Phytoplankton through to the ice. So specify the variables, work out if they’re there or not.
NH: Would want the exe to handle configuration with different sets of coupling fields. Sometimes include total wind speed, sometimes not. RF: would know complete set, if not there skip it. Currently have to be hard wired in, or make another driver. NH: Way to do it, start with superset in namcouple, and code would exclude certain variables. RF: Maybe if variable not in namcouple, return an error code, but ignore error. NH: Shouldn’t be too hard to do. NH: OASIS does return error codes that could be used. Either abort or return error code. If aborting could change that. AH: Restart fields? NH: Should do behind the scenes.

Paths for JRA55-do forcing files. Some changes to support v1.4

AH: JRA55-do not part of Input4MIPs, part of CMIP6. Have to use the copy that is CMIP6. Encodes all the metadata in filename, consequently doesn’t currently work with YATM. Circumvented by creating symbolic links that worked with YATM. When I did this couldn’t reproduce. Not sure if this is actually an issue with the fields being different or not.
AH: Tried to use testing framework NH developed for this using jenkins. The historical test that tests against known checksums doesn’t seem to actually compare them. Not sure if that is intentional. Would like to use framework, as NH has done a great job with it.
MH: MOM6 has diag_mediator, supports CMOR name alongside internal model name. Porting to MOM5 is a big task, but idea is good and saved them a lot of work. Could create a thin wrapper to translate to CMOR name if that helps. AK: How integrate with YATM? MW: Don’t know. At FMS level, so only help with 1 model (MOM). AK: YATM access the JRA files. So libaccessom2 change. AH: Looked at YATM code. Generates filename form date. Input4MIPS has current year and next year, so would require code changes. Might just be easier to create a file with date->filename mapping? AH: Possible to do. Would need to add a token for year+1. Possible to do. Probably best to do it that way.
AK: Also need code changes with v1.4. Solid and liquid runoff are separate. What to do with solid runoff? Griffies either use iceberg model, or melt them and add them to runoff. Take account latent heat of fusion? Assuming solid runoff is at zero, which could be a problem. Put in a request to download v1.4. Scripts they have should automatically download it, but not. MW: Think GFDL only has v1.3.
MW: Fields go to end of 2017, is 2018 downloaded? Looking in wrong place? Looking in ua8. AK: Should look in qv56. AK: qv56 up to feb 2018. AH: If not automatically downloading, we should ask. What does the OMIP protocol say about end date? AK: JRA55 can find out about 2018. RF: It is specified, but would like latest for ongoing runs.

Testing FMS merge

AH: Putting FMS in as a sub-repo. Just needs testing. If it reproduces checksums for a month we’re sure it is ok? Is that sufficient?
NH: When Marshall upgraded FMS, went through every MOM test. Including 0.25. Can’t recall how strict we were. AH: Testing framework still there? NH: It is there. Because it never gets used, might be rotted a bit. Can give Jenkins URL of PR and it would do it. We should work together to get that working.

New NCI HPC hardware announcement

RY: System by end of the year. 2 phases, install new machine with Cascade Lake nodes. Short period gabi and raijin run simultaneously. After that skylake and broadwell will be merged with new machine and SandyBridge nodes removed. 100 GPU installed. 16 skylake k-80 nodes. PBS pro again. Storage and network infiniband. 200GB/s transfer speed. OS is CentOS 8. AH: Trying to figure out total core count for new machine. Do you know what core count will be? RY: Not clear on exact number. Can check with system guys if they know the exact number. If 32 cores/node, 150+K processors. AH: Will runtimes be extended for new machine. Find 5 hours too low for high core count jobs. Reduces flexibility. RY: Queue time limits are per project. Quite flexible. Contact NCI help. AH: Have asked for time limit changes in past, but usually time limited. RY: Have been asked by other users, not sure about the policy. Good time to ask and get a better policy for the new machine.

New Repeat Year Spinup

We are currently undertaking a new spinup simulation using our highest resolution ocean-sea ice model: ACCESS-OM2-01. Our goal is to run at least 50 years of this simulation in the third quarter of 2019, using the  1990-91 Repeat Year Forcing strategy (that we call RYF9091). After the first month of the quarter, we have managed to complete 23 years of the simulation.

Early indications are that temperature and ice biases are reduced in the new simulation (compared with our previous RYF8485 spinup) but that many large scale circulation metrics, such as ACC transport) are largely unchanged.

Globally Averaged temperature from RYF9091 spinup.
ACC Transport from RYF9091 spinup

For those who are interested, this simulation is being stored in /g/data3/hh5/tmp/cosima/access-om2-01/01deg_jra55v13_ryf9091. Timeseries describing the simulation, periodically updated, can be found here, and additional diagnostics are available upon request.

COSIMA IV, ANU, 3-4 Sept 2019

Announcing that our 4th Annual COSIMA workshop will be held at ANU on Tuesday 3rd and Wednesday 4th September.

The workshop will feature our regular mix of talks and discussions, covering a mix of physical oceanography, sea ice, model development and technical advances. Our workshops are not restricted to ACCESS-OM2/MOM users – we welcome contributions from all who consider themselves part of the COSIMA community.

Registration is now closed, but you can join via Zoom – see below.

We will begin with morning tea at about 10am on the first morning (3 Sept), with the first talk at about 10:30.

Click here for the workshop program (updated 1st Sept).

Joining via Zoom
The workshop will be streamed via Zoom. When joining via zoom, please mute your mic and hide your video. Unfortunately we probably won’t have an ability to take questions from remote participants.

Connection details:

Join from a PC, Mac, iPad, iPhone or Android device: https://anu.zoom.us/j/8232211676

Join from a H.323/SIP room system:
Dial: +61 2 6222 7588
or SIP:7588@aarnet.edu.au
or H323:8232211676@182.255.112.21 (From Cisco)
or H323:182.255.112.21##8232211676 (From Huawei, LifeSize, Polycom)
or 162.255.36.11 or 162.255.37.11 (U.S.)

Meeting ID: 8232211676

 

The 3rd COSIMA workshop

ACCESS-OM2 at the CLEx Winter School

This week saw the ARC Centre of Excellence for Climate System Science hold its annual Winter School. This year’s edition is on modelling the climate system, hosted by the University of Melbourne. Yesterday was “Oceans Day” at the Winter School, and the highlight was an afternoon lab session based on ACCESS-OM2. Tasks included:

  • To run the ACCESS-OM2 model (about 65 of the 70 students managed to do this); and
  • To analyse some existing ACCESS-OM2 model output using the COSIMA cookbook (most students also completed this, with about a third of students producing great plots to show some new and intriguing results).

Progress was enabled by erstwhile helpers from CLEx’s CMS Team – Aidan, Claire Holger, Paola and Scott!

ACCESS-OM2 Workshop
Feverishly running ACCESS-OM2 at the 2019 CLEx Winter School.

ACCESS-OM2 Evaluation Paper

A community paper evaluating the performance of ACCESS-OM2 has been submitted to Geoscientific Model Development (GMD).  The paper has 30 authors from across the Australian community. GMD has an open review process, so you can track its progress.

This paper outlines the performance of ACCESS-OM2 at three different model resolutions, as indicated in the figure below.  It aims to spell out which versions of the model are suitable for different types of studies, and highlights the performance of the 0.1° resolution configuration (referred to as ACCESS-OM2-01). The paper shows that ACCESS-OM2 does a good job of representing many features of the ocean. Historical sea ice extent trends are well-represented, and the surface properties and transects in each ocean basin compare well with the observational record. The large scale overturning circulation, flow through the Indonesian archipelago and patterns of boundary currents are realistic, supporting the notion that this suite of models is competitive with similar models from other institutions. Areas for improvement include the relatively weak barotropic transport in the midlatitude gyres, particularly in the Pacific Ocean, the weaker than observed Drake Passage transport and the weak AMOC in the 1° configuration. For full details, feel free to browse the paper!

Kiss, A. E., Hogg, A. McC., Hannah, N., Boeira Dias, F., Brassington, G. B., Chamberlain, M. A., Chapman, C., Dobrohotoff, P., Domingues, C. M., Duran, E. R., England, M. H., Fiedler, R., Griffies, S. M., Heerdegen, A., Heil, P., Holmes, R. M., Klocker, A., Marsland, S. J., Morrison, A. K., Munroe, J., Oke, P. R., Nikurashin, M., Pilo, G. S., Richet, O., Savita, A., Spence, P., Stewart, K. D., Ward, M. L., Wu, F., and Zhang, X.: ACCESS-OM2: A Global Ocean-Sea Ice Model at Three Resolutions, Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2019-106, in review, 2019.

Technical Working Group Meeting, March 2019

Minutes

Date: 12th March, 2019
Attendees:

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

Updates

MW: Submitted parallel IO FMS patch. New automake made PR more complicated. FMS now buildable by automake. If we add new files/dependency build will fail. Not very auto. Works well. Some tuning with lustre. Just need a good io_layout with large contiguous chunks.

AH: Compression? MW: IO runtimes double with compression. Testing some of the newer algos and getting better numbers. AH: How does he get other compression into netCDF? MW: Custom libraries. Will make accessible when time comes. Have been using it. Good. MW: Haven’t heard back from GFDL yet. AH: will be needed for further high res models.

MW: RF big help with all the fill value stuff. RF: You put missing values in missing tiles. There is a mppnccombine bug which stuffs up. MW: Used netCDF fill value for restarts, MOM sets it to CMOR fill value.
automake goal is to make FMS into a library that can be centrally installed.
AH: Should just link against libFMS rather than have in the repo.
RF: part of decadal project is to update FMS. Wants to use it in AR4. MW: make it loadable module? AH: dynamic linking? AH: need access to compiled module files?
MW: Issues with GNU/Intel. Dale roberts wooing on this. Also module versions are an issue. Intel 18 can’t read 19 mod files for example. Don’t think there are any includes. If there are, should be fixed. RF: There is include mpi.f. Not sure how they include netcdf.
RF: Advanced with getting WOMBAT into CM2 harmonised MOM5. Fixed a few issues with redundant ifdefs. Hopefully sometime this week can finish. Pretty close by the end of the day.
MC: Might have an executable with WOMBAT compiled into it? RF: Yeah, just changed a few interfaces to get rid off ifdefs, changed to optional arguments for WOMBAT arguments.
MC: If Matear is there tomorrow, can try something.
AH: Now have a suite of models. Different resolutions, now with BGC as well. Great position to be in.

Technical Working Group Meeting, January 2019

Minutes

Date: 15th January, 2019
Attendees:

  • Marshall Ward (MW) (Chair) NCI
  • Aidan Heerdegen (AH) CLEX, Andrew Kiss (AK)  COSIMA, ANU
  • Russ Fiedler (RF) CSIRO Hobart
  • Nic Hannah (NH) Double Precision
  • Peter Dobrohotoff (PD), CSIRO Aspendale

MOM5 CM2 code harmonisation

PD: Stopping an 18 year run with harmonised code. Seems successful. Not losing summer Antarctic sea ice, which had been an issue. Dave Bi gave his approval.

PD: Looking at new bug fixes on GitHub. Didn’t appear to be in the CSIRO code.

RF: The fixes I added weren’t to do with harmonisation. Diagnostic for transport on density levels. PD: Won’t affect our model run? RF: Yes. PD: Maybe should keep the 18 year run going. RF: There is also a fix to a submeso scale smoothing that you’re probably not using. 99% likely you’re not using that. PD: Could check by looking at the namelist? RF: It’s smooth hblt, or something, but also a note in the code specifying the namelist that shouldn’t be used because of this error. PD: Could you send me the namelist value? RF: Should be in GitHub issue/pull-request. AH: I’ll put links from your commits on to the slack channel.

https://github.com/mom-ocean/MOM5/commit/11f06f989645b1b21aa990ade61440976451bbb6

https://github.com/mom-ocean/MOM5/commit/06a6d0afb55a1f188d0b58b89513d646d47f062f

AH: hblt_smooth

RF: If you applied the smoothing could smooth into rock. PD: Keep getting current going? Want to get an ENSO spectrum. RF: Shouldn’t make a difference, but will get noise due to changes in red sea fix. Statistics will be the same

AH: In the release candidate code we reproduced a red sea fix timing bug to make the comparison as clean as possible, using a namelist option. That has been stripped out before merging into the master branch. If you continue with this test run and it becomes your spin up run then you will not be able to do a clean comparison if you then change something else from the master branch version. Is this a test run or will it become a spin up?

PD: Sometimes test runs become real runs, but I’ll say this is a test.

AH: If at any point you start a spin up you need to be on a commit on the master branch. Currently running from a commit on a pull request that no longer exists. There is no comparable commit on the MOM master branch repo because of removing the salinity time unfix option, and merging in RF’s bug fixes.

NH: Second that. Also important if we want to continue to be harmonised, this is a divergence and if we carry on with that we’re diverging immediately.

PD: Alright. Will leave this run going to test ENSO spectrum, but will start a new parallel run for safety. Don’t want to be in the position where the test run gets turned into a spin-up because of lack of time.

AH: Calendar time not compute time is your constraint? PD: Yes. AH: Definitely agree with that strategy. PD: Never have enough compute time, but always have that trade off.

AH: Will tag the code with CM2 version which can use to identify the code. PD: Should tag straight away and I will clone and let people know this is the correct code.

NH: Reproducibility is important, and the current MOM code does not reproduce. PD: On restarts. NH: Yes, so would be a shame to lose that by not using the merged code.

AH: Not only is it reproducible, but NH is running tests for this. NH: That’s right. Just a simple 2 day versus 2×1 day runs. To do that test presently turns off red sea fix. Now I can turn it back on? RF: It should now reproduce. AH: Turn it back on and check it reproduces? AH: This is reproducible between runs, not necessarily reproducible to before RF’s fix. PD: Which is reproducible on restarts and which isn’t? AH: Current harmonised code in the MOM5 master is reproducible between restarts, the code from the pull request that PD is currently running is potentially reproducible if you turn off the flag we introduced which emulated the incorrect behaviour of the old MOM5 CM2 code for testing purposes. PD: So the harmonised code in the pull request is different to the master branch? AH: Yes, in that the hack to emulate the incorrect timing behaviour of the red sea fix has been removed, and a couple of RF’s bug fixes added. PD: Going forward will there be a harmonised branch and a main branch? AH: No, there will be a tag identifying where you get your code from. If you need to pull in updates but don’t want all the updates in master, then you might start a new branch, and cherry pick those updates. At that point you might have a different branch, but not currently. In general better off not having a separate branch, as it just starts diverging again. I don’t know how you guys work and I’m guessing you don’t want code changes, but if, for example, you just wanted to add code changes that added diagnostics, you could add those in, and have something to compare against. PD: Just trying to figure out how it will work, if there are different branches, and if down the track we want to develop the harmonised code again. AH: Yes, and if you have some testing then you an add code and test to see if there are differences in the output, and so add code changes with confidence.

MW: Highlights that we have not been tagging MOM for some time. Maybe we need more regular tagging.

 

ESM code harmonisation

PD: In an ESM meeting on Friday Tilo said it was too late to include changed code for CMIP6.

AH: Whatever we did he wouldn’t put it in CMIP6? PD: Yes. AH: Invested too much time on spin ups? PD: Yes. AH: So no particular rush to do this. PD: I thought it was good to pass that on. AH: Good to know, thanks. MW: There ESM for CMIP6, but also in the CoE. Will they use what you’re working on? AH: Yes, but shame, as we’re not then using the same code as the CMIP6 submission. MW: I thought that was your interest in ESM. AH: Yes, not sure.

MOM5 Governance model

MW: Not sure how much we can do without Steve being present, or anyone from GFDL.

AH: Made some notes, hoped to get some feedback and others make changes, additions. MW did add some useful points about defining domain experts.

AH: The MOM5 repository and community is not welcoming to those outside the current clique of COSIMA. Pull requests languish for years without attention because it is no-one’s responsibility, no-one has a defined role. Even if some people put their hands up to monitor pull requests.

Have a contributing.md, to tell people how to contribute to the code. There are users outside this group who use it, see them on the MOM users mailing list, and can use that channel to advertise it.

MW: That was my experience as a grad student. Not sure who is charge of the code. Tried to contribute code and found it intimidating. Not a fan of overly prescriptive instructions on how pull requests must look, or how code must be written. That has made me less likely to report bugs. Would rather get bad contributions than no contributions. AH: Poor quality contributions require effort from us to work through them. MW: Yes, just want to make sure they know it is ok to screw-up. A lot of projects require a lot of environment information etc, which can be onerous for new users. Now tend to ignore those instructions and wait for devs to ask for it. Do think that governance model is good, but want to encourage contributions and emphasise it is the effort that matters rather than the quality of the contribution.

NH: I think I agree. Want to be more friendly to outsiders, also agree with MW, want to put as few roadblocks as possible. People have little incentive to contribute to the repository. The harder we make it, the less likely they are to contribute. With Pull Requests, in order to merge we need testing, but people aren’t going to do those tests. They test for themselves to satisfy their scientific goals and that’s it. Not sure how to reconcile that.

MW: Automated code coverage tests help. A lot of CI services panic too much when code coverage drops after a contribution. This can be useful if it then spurs contributors to improve units tests to improve that metric. AH: Currently have 0% code coverage, so it can’t get worse!

MW: Yes, one issue is we have no code coverage presently. But looking more broadly if we have some automated tests that can tell us what is broken that can help a lot. I know we have testing. AH: Only compilation testing.

AH: If we do this, it will be a burden, want to minimise this, hence the document defined some steps for assessing a PR:

  1. PR assigned to committer
  2. Committer checks PR conforms to guidelines
  3. PR passes CI checks
  4. Iterate until correct or time limit passes (say developer does not update PR as needed)
  5. Testing? Do we push that burden on to contributor to demonstrate bit repro? What about performance?
  6. Accept or reject (rejection is automatic if contributor does not meet expectations above and time limit is exceeded, so rejection at this point would be unusual, but might occur if the efficacy or efficiency of the code is questionable)

AH:

MW: James Munroe has experience contributing to dask, managed by experienced software engineers. He had to do a lot of testing, as well as style and engineering changes. They had someone asking him to make changes until it was deemed good enough. We could do this too, but it would require engagement from us. Also, are we overthinking this? We hardly get any pull requests.

AH: Yes, but some of this stuff is useful for us to do too. A lot of it is just good communication. It may sound onerous, but in many ways it makes it easier, so people aren’t trying to guess the right thing to do, e.g. with code style it may be as simple as pointing to a particularly well written section/module and say “seek to emulate this”

MW: GFDL is struggling with this right now. I sent them a beefy FMS patch and they did not how to handle it. They didn’t want it, but they didn’t want to just reject it. Might be worth figuring out how they are dealing with it. AH: They might copy what we end up doing. MW: Yes, they might end up copying this.

AH: First up, should we consider roles, e.g.

Contributors: Anyone who wants to contribute code

Committer: Anyone with commit access

Maintainers: Committers who check PRs, assign PRs to other committers and maybe do some other admin tasks.

Admins: Do we need another layer? Currently only Steve, Nic and I are Organisation Owners and Admins on the MOM5 repo. Need at least 2 admins at all times (run over by bus scenario).

Sponsoring institutions: Acknowledge role of institutions which provide time for code development?

BDFL: Steve? (Does he even want to be a Benevolent Dictator?)

 

AH: Do we want to do something like this? NH: Yes. It is a great idea. Write it down and we can use it ourselves, and our collaborators.

AH: Are we happy with the roles? NH: Yes, need to look more closely. Looks good. Keep it simple.

MW: Maintainers should be admins, at least for now. I wonder if Steve would prefer to not have a formal role, as he is transitioning out of the coding. AH: Would be want to be BDFL? MW: Would probably accept it, but maybe he doesn’t want to

AH: I think it is good to keep him there. At some point we will transition to MOM6 and it will no longer be my role to look after this. Others will move on too, so it would be good to have Steve still there in that eventuality.

MW: He could be a decider. AH: Yes, like having a Queen. Just have to host him in visits every now and then. MW: Head of State, but not the Head of Government.

AH: Ok, get rid of admin/maintainer distinction. Just make them Maintainers.

MW: Sponsoring institutions is interesting. AH: It was to acknowledge that institutions that pay people like me might have a reasonable expectation that the people they pay to help maintain the code could have some say in the way it is run. RF: I don’t like that, it is a community code. MW: I agree with RF, but there is some reality. AH: More about expectations. If I leave my job, the CoE might have some expectation that my replacement would be able to become a committer/admin. MW: I worry about sponsoring institutions insisting on having some oversight. AH: I always thought CSIRO was a bit keener on the whole “official stamp of approval” thing, but if we don’t like it I’ll get rid of it. No worries.

AH: Ok. Lets codify the roles, and look into a contributing.md to sit at the top of the repo to tell people how to contribute code. This all started with wanting to have timely responses to Pull Requests. Who wants to be what?

MW: What is the

NH: Happy to be a maintainer, but COSIMA would have to pay for my time. AH:

MW: Don’t have an explicit list of users.

RF: How far back do you go with sponsoring institutions? Back to 2009?

MW: I would prefer not to involve them.

RF: Just leave it. Keep it simpler.

MW: When I say sponsor, I mean someone who can’t function without this code. Need a maintainer.

AH: It is literally my job, and happy to volunteer as a maintainer.

AH: Maintainers check PRs, and then assign them to people, we need others to be willing to have a PR assigned to them. MW: Happy to do it, but feel like others are more invested. AH: Doesn’t have to be just you. It is just having someone respond to a PR, check progress, feedback what is required to get it merged, close it if it doesn’t meet standards and the submitted doesn’t respond to queries to fix it.

MW: Yes we need that role, at the moment it is AH and NH. If you want to add me I’m happy to do it, just not sure where I will be in the near future.

AH: Ok how do people get these roles? Commit access is currently Steve, NH and AH. Do other people need it, or want it. How do we decide who should have it?

MW: Best to have one person responsible for commits/merges. AH: Steve recently merged a commit that needed to be reverted. MW: Which is what prompted this. AH: Yes, and he wouldn’t have felt the need to do it if he knew it was being handled.

AH: Do we need to do this now? Specify who is on “the committee”?

MW: Contributor is obvious. Pull committers from contributors. Pull maintainers from committers. If you don’t get enough commits, then a project just dies. AH: Don’t need to codify how someone becomes a committer? MW: No. We’re too small. Look on the issues, and PRs, represents very few people. AH: Ok, so no need right now.

MW: Quite premature to codify this.

AH: Need a `contributing.md`, how to contribute.

MW: Any role for governance is getting the word out. Find the user base. There are a lot of MOM users out there. Steve cited a thousand MOM users in 2010. Governance should be about where are these people, and then get the community. AH: You run the danger of “hey guys come and contribute” and not have processes in place. MW: A good problem to have. AH: What happens if you got 10 PRs tomorrow what would you do with them? MW: Deal with them one at a time. AH: But who would deal with it? We have existing PRs that people aren’t being dealt with, one has been there for a year. MW: Yeah, but it is a bit stupid. Changed an integer to an 8-byte. RF: I would have rejected it because it used a specific kind. Change was a good idea, but badly implemented. MW: Ok, let’s look at this and learn some lessons and produce a document.

MW: So lets look at this PR. What are we going to do about it? So who do we assign this to? I would assign to Russ as he has expressed a strong opinion. AH: Ok. MW: What would you say about this PR RF? RF: I would split into two, as they are unrelated. If you do submit these things, try and keep to individual issues. Specifically about this, first change is non-portable, which can easily be fixed. Would we do the fix, or would he do the fix? All it needs is a selected_integer_kind. MW: This is a portability issue. RF: Yes, anything from now on that gets contributed should be standard. MW: Lesson should be an evolving document about what we want. RF: Yes, standards compliant, independent commits. MW: Would you be ok with being assigned this? AH: Already done it. RF: Second part could be a real bug in remapping vectors. Maybe get back to him and ask if he can show a test case. AH: Ideally this would be associated with an Issue which explains the problem. AK: Really ideally would include a test case that fails and that subsequently passes with the fix in the PR. MW: I would argue against pedantry. GitHub treats Issues and PRs similarly, so while an Issue with a test would be ideal, shouldn’t be mandatory. If you would rather formalise then fine.

RF: Have to leave

Subsequent discussion:

AK: Who feels they have responsibility, so things don’t languish, and who has authority to say what is going to happen. NH: And who has time. MW: Good not to dump maintainer responsibilities on NH.

AH: If suggestion is prescriptive so as not to waste time wondering how to do things. Not mandatory, but good to give guidance.

MW: Current touchy point is assigning stuff to RF. Had a meeting and asked it was ok, but won’t scale. Let’s clean up the pull requests.

MW: I have different idea of purpose of Issues page to AH for payu. You see as dumping idea for ideas (AH: Yes), and I see it as something to keep as small as possible. Ok for a small group, but with a larger group it can balloon and lose track of good ideas. MW: Yes bad idea, or not enough time should be a criteria for closing an issue, without losing the idea. Would be great to get issues down to 1-2 pages, would reveal a lot of lessons.

AK: Paul’s PR is pretty substantial. A whole new file, ocean_basal_tracer. MW: But bungled the build script. Also made a timer that does nothing. This is a good issue with a terrible title. This is a good example.

MW: These projects work best when they’re community driven, that we agree to do it. AH: If you put up your hand to be assigned stuff, you will get assigned stuff. If they don’t, then people won’t. AK: If someone has that role you feel ok assigning to them.

MW: When we talk about governance, lets not worry about users, lets figure out how to assign issues, that is a great place to start. Not worry so much about how users should make PRs.

NH: I agree, but maybe still work on guidelines for contributors. There was a document called “How to contribute”, based on technical specifications. It was a markdown doc in the original website. AH: Maybe that exists somewhere. NH: It’ll be around somewhere, outlines how to do a PR and things like that. AH: Should definitely start with that.

MW: Make it a goal this week to deal with those two PRs. Assign me Paul’s if you want.

AH: Willing to be a maintainer? NH: Yes, I like being part of that community. Hard to know how to dedicate time to it sometimes. We need to do a certain amount of maintenance. Make think of it as pro-bono professional work. Matt England is keen on that sort of stuff, he might be willing to support it/sanction it/pay for it.

Agreed: Maintainers: Aidan, Nic, Marshall. Ask Steve if willing to have BDFL status.

COSIMA Models – ACCESS-OM2-01

AK: Modified topography to remove terraces (bug). Smoothed a seamount near Sverny Island, and eliminated very small cells near tripoles. 54KSU / model year. This is repeat year forcing. Time step is 720s. Did a test run with 900s and it crashed. 720s is a factor of 1800 (coupling time step). No factors in between.

AK: MOM was going unstable, generating 18 m/s velocities, CICE was the first thing to crash with ice remapping error. Was using ndtd (number of CICE time steps per MOM baroclinic timestep). When using ntdt=3, making CICE stable with vaguely unstable MOM. At one point in the run I added Rayleigh damping in Kara Strait as I had done in IAF run. MOM was going unstable in Kara Strait, moving ICE around too quickly, and CICE crashed. Once I stabilised MOM, could get away with ndtd=2, so now the model is CICE bound rather than MOM bound. AH: What is runtime? AK: 2 hours, so can do 2 months/submit. MW: What were the fails at the beginning? Related? AK: Showing out from a run-summarising tool. Just shows when runs failed. Not necessarily crashes, might have just stopped to change something. AH: So when you say MOM went unstable, not so unstable it crashed, but unphysical velocities? AK: Haven’t looked in detail, but imagine it would be grid scale alternation and that sort of thing. AH: Does that mean, in order to compatible with CICE, maybe we need to reduce some of MOM’s thresholds for warnings so they are better matched? AK: Yes. CICE has a CFL condition that is tighter than MOM. MW: They are solving different equations. AH: Not saying they should, or could be, exactly the same, but MOM is more permissive than CICE, but the crashes happen in CICE. So if you reduce the limits in MOM will diagnose the problem in the correct place, rather than indirectly through CICE crashing. A new user would then get the right information.

AK: Haven’t examined the fields. It is right on the limit of the barotropic CFL limit. Splitting factor of 80. The outputs show it is right on the limit. MW: Griffies would hate that. AH: Pretty routine to change that when timestep changes. AK: Had to go 100 for dt=900s for it to pass that check. Might be wise to up that number.

MW: This is tenth degree? Really dropped your CPU count. AK: This is a minimal config. Dropped from 6K to 2K, getting same throughput as larger model. MW: But with lower ndtd and higher timestep. AK: Yes. AH: timestep is like a superpower.

NH: Great! Well done. AK: Thanks for your work. On the number of CPUs, it is good to run minimal configs, as they are inherently more load balanced. Each CPU is doing more work and a greater variety of work. A good reason this minimal config is more efficient. MW: Won’t it run slower if you reduced timestep? Doesn’t make it more efficient necessarily? NH: I think it does.

NH: How does this compare to MOM-SIS? We can’t really compare without running with the same grid? MW: Can usually use the MOM timing and add 15%. I went back and checked this numbers. AH: I think I was getting six months / submit with MOM-SIS at a nominal 7200 core layout, with dt=600s. The larger ACCESS-OM2 config has 6K cores in total, but only 4300 MOM cores.

PD: Have to go now. Bye.

NH: Are you going to try getting the bigger config running? AH: 6 months per submit is very interesting. Could do some decent 100 year runs. Could be worth looking at.

MW: According to the numbers I have been posting, could speed MOM up by a factor of 4 with more cores. CICE ice step is also scaling well. Don’t know if switched to sectrobin, or missing a coupling bottleneck. This model could scale well. Has anyone checked with sectrobin? NH: This is using it. MW: I am talking about much larger, I get improvement up to 12K CICE cores. AH: Load balancing not an issue? MW: Maybe, but I’m not seeing it with the function I am testing. Is this new? Or was this always the case and I’m not seeing what slows the model down? If it is new, maybe we should experiment with throwing more cores at CICE. Even with the low config, maybe you could ramp the CICE cores up to 600? NH: That one is MOM bound. AK: The IAF was using round robin, and dt=450s. MW: Right so, that is your difference right there. AK: Dropping ndtd to 2 makes it MOM bound.

NH: Let me know if there is anything I can do to improve the load balancing in larger config. Pretty sure there is larger config using sectrobin.

MW: I’ve seen consistent improvements in all CICE configs, including 1 deg. Doubling cpus in CICE and MOM individually in 1 degree saw improvement in both, but got errors when I tried to both. Gave up because 1 degree not so important. Will try again in tenth degree.

NH: Sounds like you’re discovering what the best config should be using some evidence based mechanism. The 1 degree config was pulling numbers out of hat that balanced ok with decent efficiency. Maybe want a small/medium/large config, but not for all resolutions. 1 degree maybe just want max throughput. Would be great to capture what you’ve discovered, and actually start to create those configurations.

MW: MOM numbers are clear. Time per step is very informative. Want numbers around 0.1s/step. Allows us to tackle this independent of time step. Surprised CICE is scaling. Reminds me of the last COSIMA talk which everyone said was wrong because I didn’t have enough ice. Will make a figure, which will show strong scaling numbers for CICE. Looks like it a strong scaling model.

AK: On CICE, there is a workshop in Hobart in late Feb. It is a CICE modelling workshop, and Elizabeth Hunke is visiting. AH: Are they up to CICE6? MW: Dealing with a fork. Los Alamos has a version no-one is allowed to see. NH: Worth looking at the CICE repo. Our CICE5 version contains all changes up to CICE6 tag, We’re as up to date as you can be on CICE5. AH: Have you back-ported stuff? NH: Yes, it wasn’t very hard. This is CICE6, but it has CICE5 in the repo. AH: They have a cice6 branch. MW: What is ice-pack? NH: They have split out the column physics to make it more portable. It is just code from CICE5 but repackaged. AH: Icepack is included in CICE6 as a submodule.

AH: Ruth has been having queuing issues, anyone else having problems? Might just be someone using broadwell heavily. Do you know if we have to use broadwell for minimal? NH: My runs used to crash. AK: My runs are ok normal. Running the same as Ruth. AH: Using less than 1GB/processor? NH: I put something in config.yaml so when running in normal it used the high memory nodes. Did you take that out? AK: Yes I removed that. NH: Who knows. So much has changed since then. Memory can spike.AK: Ruth should be able to run on normal without requesting extra memory. MW: What made you think it was a memory issue? NH: Crashed at a particular place on initialisation in MOM where I know there is a big jump in memory usage. I have made an issue about it. It is in FMS. As soon as I went to the high memory node and it went away. Doesn’t print out specific memory errors, but as soon I as I increased memory it ran fine. Good to go back if it has gone away. It is something that gets done on the MOM root PE on initialisation that increase memory usage a lot. AH: Shame we no longer have access to the PBS logs as there was a lot of information in there on this sort of thing.

MW: Intel 19 gives awesome error messages. Not only are tracebacks more readable, but they give 7 lines of code each side of the error. Now getting MPI trackbacks without even using mpi-debug. Can’t use openmpi/1.10 with Intel 19.

Parameter sweep runs

AH: To use extra time at the end of last quarter suggested we could do a parameter sweep, which would use up a lot of compute time in short order. It didn’t end up happening, but Andy Hogg thought it would be a good capability to develop in case we did want to deploy it. I understand AK has done this a lot? AK: Well sweeps of 2 parameters, yes.

AH: Not a big deal, using payu, maybe have a YaML file specifying parameters and how to sweep them, create a bunch of payu configs programmatically and run them. MW: Always wanted to add this a a feature in payu. Spin off 20 runs with one file. AH: Any particular ideas, or anyone want to do it, feel free, otherwise will go on my very long to-do list. NH: I couldn’t think of anything. I don’t know enough about the science. AH: Me too. I have no idea what parameters I would want to change, so that is where it stopped. The parameter search could mean you always have something to run if there is spare time and add it to the database. If you have a database of runs, you effectively have a parameter search if you change anything.

AK: Have a current grant to do a study on parameter sensitivity in CICE. This capability could be useful.

NH: I have written something which can divide your grid by an integer number, creates initial conditions and everything. Could be interesting to programatically create a bunch of configs and run them with something like this.

 

Technical Working Group Meeting, December 2018

Minutes

Date: 11th December 2018
Attendees:

  • Marshall Ward (MW) (Chair) NCI
  • Aidan Heerdegen (AH) and Andy M Hogg (AMH) CLEX, Andrew Kiss (AK)  COSIMA, ANU
  • Russ Fiedler (RF), Matt Chamberlain (MC) CSIRO Hobart
  • Nic Hannah (NH) Double Precision

COSIMA Models

Profiling

MW: Been profiling CICE, score-p profiling doesn’t work. Been timing by time step. Anomalously long time spent at step 72. AH: could it be atmosphere being updated. JRA55 is 3 hourly. Not sure timestep. MW: Seem to have lost my logs. Not sure best way to handle it.

CM2 Harmonisation update

AH: Peter has been testing release candidate. Russ supplied a diag_table which just outputs fields for first 2 time steps which is really good for seeing code issues. Russ found some bugs introduced by me. A couple of logic errors with preprocessor flags and omission of a couple of lines that got lost in translation. Confident latest update has squashed all the bugs. MW: Not old bugs? AH: Did find some old issues. Russ found a stuffed iceberg file. RF: Not related, but is something they were using for CMIP6. AH: Did find some old bugs, had to emulate the lack of reproducibility from a the readsea salinity fix timing bug to be able to closely reproduce CM2 output. Put a flag in to do the wrong thing to do the same as theirs, will remove before merging. MW: I thought reds fix had been changed to be faster but not reproducible. RF: That’s right, but not issue. This has to do with timing. Aidan fixed it, but not compatible with what they are using. AH: Just need something that reproduces CM2 output.

Narrator: The new way of doing salt fix will reproduce over time steps, but is not bit reproducible with the old algorithm. Don’t see that effect in these tests.

AH: Peter has a test suite which is old CM2, and a copy which uses updated MOM. He compiles the new code manually and runs the two suites side by side. Both use Russ’ diag_table. Just find out which fields don’t match. Most are the same, few different, seem to be affected by the same issue. Once we’re good for a few time steps then maybe look at them after a few months RF: Once chaos starts, hard to say. As long as nothing gross happening. Unless there is something further on with coupling. AH: Yes, look after a month and check it looks close. MW: Not trying to be bit reproducible? AH: Just want to fix my bugs. RF: Make sure you’re getting the same forcing fields. Can see out in the open ocean hardly any change. Just noise. This means we’re close. Saw the outline of where the forcing field is supposed to be. The bug in the forcing field data showed up, which indicated the issue. AH: Once we’ve confirmed fixed, will merge PR and then move on to ESM.

MW: Will the CM2 code remain in step with the MOM5 code? RF: CSIRO Aspendale not doing much code development at the moment. AH: Peter is pulling directly from his GitHub repo, but once it is harmonised they will pull directly from the MOM5 repo. They will want to have a tag and pull from the tag. RF: Yes they will want frozen versions. AH: Should have some automated tested, if we find a bug, should be able to updated CM2 code and confirm doesn’t change important answers.

AH: Short answer: Lots of progress. I made lots of bugs and Russ found them. Thanks Russ. NH: Yes thanks Russ.

Model reproducibility and payu bug

NH: working on documentation, wiki, tech report and model paper. Like to do more. Wiki doc easier as a brain dump. Made sure ACCESS-OM2 Jenkins tests are passing. Takes time something always seem to go wrong. Six tests passing and useful. Repro test working and now reproducing across restarts. Wasn’t working due to 1. payu bug, 2. red sea fix and 3. compiling with repro.
NH: Doing 2 runs with and without that payu bug on 1 and 0.25 degree. Doing 4 years as individual 1 year submits. Make sure bug not too serious. The way the coupling field restarts are done not good. Ocean has to write out a restart for cice (o2i.nc). Copy of restart file missing. Had in the past. Refactor with libaccessom2 and change of payu model driver didn’t carry this over. Means every first forcing fields that the ice model gets at the beginning of a new submit for the first coupling step are from the beginning of the run, not the previous run. Ice model is getting the wrong forcing for the first 3 hours.
MW: Has it been fixed? All runs affected? AK: Yes fixed now. Scope which runs affected. Only since YATM? NH: Yes. If your run uses YATM it will have this problem. Around the time the bug introduced. Restructured how config.yaml organised. Created libaccessom2 driver, and bug came in at that point. MW: Used to have oasis driver that did that. NH: Restart repro test existed but failing for other reasons, not being kept up to date. If that test was passing and then started failing, then would have been noticed. Doing a post mortem to see if there is anything significant on a 5 year run. Gut feeling, just in the ice. RF: Will just be the SST that it sees. If running a month at a time significant. Yearly not so important. Also depends what was in the initial coupling field. NH: Initial field correct, probably January. RF: Didn’t get updated for changes to landmasks? NH: Land has been eliminated so not necessary. NH: Any run which is a multiple of 1 year, problem is smaller. AH: Quarter and 1 degree aren’t that affected, tenth most affected. NH: Could do 1 month 1 degree runs. AH: Good idea. Don’t forget about runspersub option, could do 50 in a single submit. MW: payu restart flag now works as well. Could be useful for testing reproducibility. NH: This could be a problem in other cases as well. Existing restart is based on a specific time. May be correct for the specific model it was created for. RF: Should be matched to initial condition, with correct fields. MW: This is a cold start? NH: Needs to be created each time based on start time of your forcing. AH: Write code into model to read in IC and write back out to coupling fields? NH: Something like that might be good.
AK: Bunch of fields SST, SSS, SS velocity, SS slope, frazil ice formation energy. RF: SST and SSS only ones not zero in a cold start. AK: Replace by initial condition for entire experiment NH: There is a single file in the ACCESS-OM2 input directory that all experiments use. NH: Could diff that against what it should have been. MC: That is cold start bug, not so important. Warm start bug fixed? NH: yes fixed in latest version version 0.11.2. AK: People aren’t using that? MW: No, because it was broken. Now fixed. AH: Arguably should delete payu versions with the known warm start bug. Or back port the fix? MW: Don’t have framework to back port fix. AH: How many versions affected? NH: Put a warning message/assert in that stops and doesn’t let it load. MW: happy to delete old versions. Some people use a specific payu versions. Easy to put warnings in module files. Can also delete old ones. Not a huge problem.
AH: figure out which payu versions affected. Make a decision based on that. MW: Only those with libaccessom2. AH: Don’t delete straight away. Turn off modules first. See if there are people affected. AK: Could be people not using access-om2. AH: yes, but can use new versions. Need to make sure people not using buggy code. AK: Possibly move to new space. AH: yes, but might not be necessary. MW: May be impossible to back port fixes. Driver might not be functional. No problem doing backports, not sure how.
AH/MW: Might not need to back port, should:
  1. Confirm payu/0.11.2 working correctly
  2. Set as default version
  3. Determine which payu versions affected
  4. Turn off affected modules in modulefile and issue message about bug, what module to load and to email climate_help if users still has issues
  5. When complain assess individual cases
  6. If necessary move payu module to non-app path
  7. Delete old versions?
2 week time frame.
MW: People shouldn’t be encouraged not to specify module versions.
MW: Make sure 0.11.2 working correctly. Works for NH and AH. AK a good test for it as running. AK: Not running at the moment. Can we use old mppnccombine with payu/0.11.2. AH: Yes. MW: Use whichever you want. AH: works better for 1 deg in any case.
MW: added a restart directory feature. run 0 uses the restart and reset counters back to zero. AK: Had been copying stuff. MW: I’ve been symlinking and other hideous things. AK: Documents what you did better. AH: Used to have problems with drivers trying to delete symlinks when cleaning up restart directories.
AH: Will finish manifest this week. Chatted with Marshall and reimplementing it a bit differently. Will make NH’s job a lot easier. Run config has all the files, just need to clone and run. NH: awesome.
NH: Want any post-mortem or checking on tenth model for the payu bug? Could do some short 1 month runs. AK: Not sure what we would do with the information. Diagnosis without treatment. Interesting from an academic viewpoint. Planning to do a longer re-run with other changes and will be fixed in that. Interesting to see a couple of months and see scope of issue. Is it negligible? Maybe tell people AH: Choose a worse case: Southern summer? NH: Ok, might do that.

OpenMPI

MW: Been using OpenMPI/3.0.3. Working well. Speeds same as 1.10. uses ucx by default. Turn off all flags, except error aggregate if you want. Can try 3.1.3, had some issues. Likely the version on the next machine.
AH: Test on Jenkins with new OpenMPI? MW: Good idea
MW confirmed that using hyperthreading option in payu is harmless (might even be on by default).

COSIMA Models

Bathymetry

RF: Wanted to get rid of Ob river? 1150 looks good. Need an inlet to keep runoff in correct place. See GitHub issue. Plot shows 0.25 degree cell size is cut off.
AMH: Need to get rid off the Ob. Russ’ plot at 1150m looks good, maybe smooth out corners. RF: Have to look at index space, straight edges, no inlet, things like that. Depth is minimum depth, 10m, a lot more shallow in actuality. AK: Only real reason to keep it is to have the runoff in the right place. Had to smooth to stop model crashing. Main reason to keep is to make sure runoff is mapped correctly. AMH: Where is runoff coming from? Take it too far up and might get remapped to the wrong embayment. Why I like the minimal change. It is stable. AK: Yes since Russ’ fix that stops salinity drop below zero with ice formation. AH: If your map had water at depth zero, as opposed to land, then can follow the water along until it is > 0. Say this is water, use for remapping but not for model. AK: Need a separate file? AH: Not necessarily. Remapping using it’s own logic anyway. AK: Remapping takes no account for topography. NH: Could make the distance function smarter, use a directional weight, something like AH suggested, or take into account topography. AK: Go downslope.
RF: Other problem was Southhampton Island. Just taking out inlet was sufficient. AMH: Keep Island separated from mainland? RF: Yes. Hasn’t been causing problems? AK: No. AMH: Will leave cells smaller than 1150m. AK: Yes, but not too bad. Also an abrupt change in spacing. RF: Yes tripolar grid has discontinuity. AH: Cut of at 1150m, what was it before? AK: 880m. All crashes I had with ice remap error were less than 1100m. Those can be eliminated with closing channels. AMH: Worried about Southampton. AK: Never had issues there. Will be getting new constraints. Had to put damping on Kara Strait, and had issues with seamount off tip of Severny. AMH: Ok, keep it at 1150m and see.
AK: In quarter degree Baffin Island is attached to Canadian mainland. Tenth has much more open water. A lot of it extremely shallow (less than 100m), so unlikely important for sea water transport, but likely important for ice transport. AMH: And therefore fresh water transport. AH: Who will do this? RF: Planning to do it today or tomorrow. AMH: Awesome, thanks.

Profiling

AMH: getting different numbers between IAF and RYF due to AK needing more ice time steps in IAF case. He can’t run with ndtd=2, so load imbalanced to cice. ntdt=2 with minimal. AK: Time difference is due to value of ndtd. Ruth still getting bad departure points with minimal. Reduces ocean time step for a single submit. I reduced ndtd instead. AMH: This has caused a load imbalance. Not the same as our optimisation that NH targeted. NH used ndtd=2 in optimisation. AK using 50% more time.
MW: What optimisation? AMH: When NH looking at load balancing. AK using 50% more time steps, and taking 50% more time.
NH: Now have a rebalanced tenth minimal with ndtd=3. With the bathymetry changes might not need it. AH: Hold off on that until AK can tell if we need it. AK: May still on occasion need to reduce time step every 5 or 10 years, preferable to ndtd=3. IAF variability means can’t guarantee it will work with every year.
MW: OASIS timing issue. Struggling to define main loop time. Looking at 1 deg, outputting time of every time step. Not literally useful due to overhead. AH: Give you scaling? MW: Not sure.
MW: timing between 170-200ms per step. Step 32 get a big number. 36s in one, 72s in the other. Is it just waiting? Doing IO? Maybe some sort of OASIS thing happening to bootstrap. Get infrequent huge time steps. Run again and don’t get them. Going to remove the largest timestep. Anyone know what is causing this?
NH: What are you profiling? MW: Just the coupling step. Reporting the coupling code.
MW: Does it do a lot of IO on that first coupling step? NH: Yes it does on the first step. What about CICE diagnostics? Are they printing to ice_diag.d. Should be consistent. If it goes away?
RF: CICE does IO through one PE, so does a global collective. MW: Could be IO and MPI collective issues. Not sure if this is legitimate timing or not?
NH: Not sure what the bigger picture is, but find targeting specific routines to look at load imbalance. NH: definitely look into CICE diagnostics.
MW: Timing so inconsistent. AH: Run a bunch of use the minimum. Turn off all diagnostics. AH: For the paper MOM scales well. Need to say something about CICE scaling. Doesn’t need to be the final word. MOM gives some leeway and these are the best configurations …
NH: Happy to help. Can do more fine grained stuff. Do some counting. MW: like score-p but it dies with CICE.

Grid scale noise

 RF: Chris Chapman problem with submeso scale stuff (see issue). There is a smoothing feature in submeso but says it doesn’t reproduce. Think I found a bug. Does smoothing of mixed layer. Possible to put mixed layer into rock with smoothing, doesn’t seem to be any check. Might get some others to look at it. If they agree we might be able to fix it and reduce the checkerboard. AK: This in MOM6? Also in MOM5? RF: There is a namelist parameter, says not to use because not repro, but because buggy. No reason it shouldn’t reproduce.
MW: Is this filtering a numerical mode? AK: KPP purely numerical, so adjacent columns can decouple. RF: Will point out code and see if people agree. AK: Get fixed and could be good to put in for next tenth degree run.

Technical Working Group Meeting, November 2018

Minutes

Date: 13th November 2018
Attendees:

  • Marshall Ward (MW) (Chair) NCI
  • Aidan Heerdegen (AH) CLEX, and Andrew Kiss (AK) COSIMA, ANU
  • Russ Fiedler (RF), Matt Chamberlain (MC) CSIRO Hobart
  • Nic Hannah (NH) Double Precision

Payu update

MW: payu is now python3 compatible. Can be run from a .local install. No longer uses modules. Tagged 0.11.1. AH: will also install into conda environment on raijin. NH: sounds great. Have used in conda python27 environment. Good to have python3.

MW: Want to get this to a position where I can leave it to others to support. Might get GFDL interested in it. Have time to wrap up a lot of things.

AK: How rigid is the 3 digit output in archives? MW: Only a print statement. Should work with higher numbers. AH: Won’t list nicely. MW: Had meant to add a format option.

MW: Try out the new payu, want to make it the new one.

TWG Organisation

AH: Peter Dobrohotoff sends his apologies, cannot make meeting.

AH: Do we need to decide on a new chairman? MW: Happy to resign straight away. MW: Considering going to GFDL in February to bootstrap remote working. AH: Nic did you want to take over? NH: No, convinced it’s not a good idea. AH: Sort something out next meeting. Last one of the year?

OM2/CM2 MOM5 Harmonisation

AH: Peter Dobrohotoff sends his apologies, cannot make meeting.

AH: Shame, as PD tested harmonised MOM5 but used incorrect namelist options. Losing some momentum as would like to have that checked off so we could start harmonised ESM.

MC: Wrong namelist options? RF: Didn’t have correct namelist options to include my new mixing scheme.

AH: They were also concerned about background mixing, in case that as having an effect. Could point them to the relevant PR/Issue on GitHub with all the plots and documentation showing it was working correctly.This is a valuable resource and a good way of working.

AH: Richard Matear contacted me and wanted to know status of ESM harmonisation and what he could do to help it progress.

ESM MOM5 Harmonisation

ESM is using an version of MOM5 updated to the beginning of the year with WOMBAT added by MC. It was decided to not continue with ESM harmonisation until CM2 bedded down, as it requires some of the code changes from the CM2 harmonisation.

MW: Is cylc suite used for testing using the MOM repo compilation? AH: I believe Peter is currently turning off the automatic compilation in the suite and using the repo compilation script on the command line to create the MOM executable. MW: I think improving/streamlining and harmonising the cylc suite is as important as harmonising the code. AH: I would have liked a test suite that incorporates this, but this is the way Peter has been comfortable working. Can’t progress ESM until have the all clear that CM2 is working correctly.

MW: Richard & Matt are using the ESM model? Not using GFDL stack? MC: GFDL in decadal project. This harmonisation will get WOMBAT in the MOM5 master branch, which has long been a goal. Decadal project not using UM. Research effort there is data assimilation and reanalysis that they’re running, rather than updating the model. Won’t hear much from them. When AH gets the WOMBAT code in, please contact us. Have experience using payu runs at 0.25 deg. Will fix you up with files and help when it comes to testing. AH: I will mostly be relying on others to run stuff. MC: Not running under payu currently. Out of the loop at the moment. Did run one of Kial’s runs. I need help running with payu. AH: Yes we can do that together. Holger is trying to get payu to run with ESM, making slow progress. MW: Who is supporting the ESM? Surprised Richard will contact AH. AH: Someone told him it was part of this code harmonisation. MC: Richard’s interest is WOMBAT in MOM5. AH: ESM will be the CLEX coupled model. MW: Who will be responsible for ESM? AH: Tilo is doing a CMIP6 submission with ESM. CLEX will be wanting to use all of Tilo’s runs to spin off their own experiments. At that point CLEX CMS will support the model with payu on NCI HPC systems. MC: Tilo is doing the work of the equivalent of the entire CM2 team to get ESM working. We support Tilo somewhat, and there are others who are no longer formally part of the team but contribute. Richard has interests in this space also. AH: Tilo can benefit from work we’re doing. Scott found a 10% improvement in UM speed. MC: Speed/efficiency not a priority right now. Focus on land model, forcing etc. Not #1 priority. AH: If they’re open to that input, they can still get the benefit even if it isn’t their focus.

MC: Have to go to another meeting.

AH: Do we need to move the meeting? MW: Happy to move to another day if it works for people. AH: Doodle poll? RF: Next year MW: Ok, do something next year.

Minimal 0.1 MOM

AH: Working really well. Would like to get it to run a little faster so she could get 2 months per submit. Which would improve her throughput a lot. Does NH have any ideas to speed it up? Seems like MOM model has 10 minutes of spare time. Is it CICE bound? NH: That might be the initialisation time. AH: Don’t MOM timings take into account initialisation? NH: Not until recently. Marshall fixed it. MW: Clocks weren’t showing MPI initialisation time, just MOM initialisation time. AH: Could be 10 minutes? MW: I would be surprised. Would guess 5 mins, less than 10. Big model, spends a lot of time on field exchange.

AH: Not compiled with AVX2. Will that help? MW: Did AVX and AVX2 test. Could see the difference, wasn’t large enough to bother making non-compatible binaries. NH: Slack me the path and I can take a look. Haven’t spent a lot of time trying to optimise it. MW: Can sometimes improve time by changing layout. GFDL tried very long tiles that means halo updates are only north/south. NH: She might have an older config. I switched to Sandybridge for efficiency. MW: I think you can get 7-8% speed up going from AVX to AVX2. AH: I advised Ruth to use broadwell due to memory requirements making for better throughput. AH: I suggested she have higher diag_steps, but RF pointed out global scalars mean she is doing daily global MPI calls. RF said doesn’t necessarily have to be this way? Could it be changed in FMS? RF: Yeah, all the diagnostic code. In many cases time average can be commuted with area average. Every timestep doing a MPP sum or MPP global sum, can do local sums on local process and call MPP sum when you need to. Could rewrite the MOM code to do cumulative average and do an instantaneous output. Sort of fudge an average. MW: Wouldn’t make much difference to speed. RF: Depends how much those global sums are hurting you if any, but it might be a single global sum acts as a synchronisation point and doesn’t really matter. MW: I told NCI MOM didn’t do collectives because they were so fast they didn’t show up in profile. So unlikely to help a lot. RF: MOM collectives are very simple. If not doing bitwise stuff, just taking a collective of one number. MW: Caveat, only tested at 0.25 deg, so can’t know for sure it is the same at 0.1 deg. Should do it because it will eventually start to bite. Could do a profile?

AH: AK only does 2 months/submit, so maybe we would all be better running a minimal config? MW: doesn’t bode well for exascale. AH: So many constraints with PBS etc. AK: Optimised for model+machine+queue constraints not for the model on its own. NH: Could just bump all the cpus by 10%? AH: You’ve got a nice sweet spot there, first try AVX2 and see if we can get the speed up we need.

MW: Vectorisation can help. AH: Would bigger tiles help? MW: So much time moving in and out of L1 cache that it doesn’t make much difference. AH: Broadwell got bigger caches? MW: Bigger L3 but 12 more cores. NH: Is she using 600s timestep without crashing? AH: Had an ice remap crash after a couple of years. AK: Unclear if that will happen again. Doing RYF, and I found once the crashes started happening they kept happening. RF: Using latest bathymetry? AK: Yes. RF: Any difference? AK: No idea. NH: I think it  is generally more stable.

MW: Can play with barotropic halo. Barotropic solver has halo of 10 so it can do it’s work every 10 steps. Might be able to get some speed up by playing with that. AH: Put path to Ruth’s control directory on TWG slack channel.

NCRIS ACCESS meeting

NCRIS is doing a scoping study to see if it is feasible for a team of 15-20 people to support ACCESS modelling in Australia, which would be used for submission for funding from NCRIS. The meeting was to get feedback to help write the submission.

Some discussion of the experience of the meeting.

Calendar issues

RF: MOM uses Proleptic Gregorian calendar type, but does not use the correct calendar attribute when outputting the file. It sets it as Gregorian instead. So, when using days since 01/01/0001 there is a jump in October 1582 depending on which calendar is used. Get a 2 day offset for IAF files because of this incorrect calendar attribute. Found python netCDF interface uses udunits calendars and has problems. Had to force it to proleptic gregorian to read dates correctly. Big issue when dealing with daily data. Output files need to be fixed. Could change the calendar attribute to Proleptic Gregorian or change units to be days since a year after 1582. MW: GFDL use since 1900? RF: Yes, as this is what Ferret uses.

AH: Had a lot of date issues using python. Uses date library from numpy as there is limited date range available due to nanosecond resolution. We often have to do date offsets anyway, so probably don’t see this issue as much. Should we put proleptic gregorian into MOM? MW: Shouldn’t we change the start date? RF: That is the easiest thing. There is a lot of broken software that doesn’t treat these calendars correctly. MW: should tell GFDL about this RF: Looked at the code and made some changes, but not uploaded. AK: Is MOM using the correct dates? As with coupling to CICE etc? RF: Works ok internally. AH: Arguably a bug if they’re using proleptic and not using correct attribute. RF: Yes. CMIP6 accounts for this. Checks for dates before 1582 and requires using proleptic gregorian. Future runs should have an offset of some later date.

RF: Getting huge number of messages from restoring files starting at year 0000. Restoring files on a time modulo axis and created from Ferret, which automatically treats any file with a start year of zero or one as modulo. However year zero does not exist and is incorrect. Just need to change that attribute in the restoring files, won’t make any difference to operation but save a huge number of warning messages. MW: I get 482,000 lines of errors. I would be very happy if this is fixed. MW: Someone should change those fields. RF: I don’t have access. MW: Should go and edit the public forcing fields. What specific files? AH: If you’re talking about the ACCESS-OM2 configs, NH has the most ability to change them. MW: salt_sfc_restore? RF: Yes, and temperature, chlorophyll. Anything seasonal, a restoring. MW: Anything that says “months since 0000”? AH: Yes change to 0001. RF: Anything that uses that date (zero years) can be changed. AK: Anything that isn’t JRA that isn’t multiyear? RF: Maybe runoff? Do we use the JRA runoff? The problem really is the stuff MOM reads directly, like sponges. NH: I am happy to look into this. I might be the only one with access, hope not. Have been thinking about this for a while. Changed the OASIS code as well to ensure DEBUG_LEVEL zero does not output anything. Was outputting thousands of lines. Also an Andy Hogg GitHun issue and this was the next one on my list. MW: So far I can only find salt restore and ssw shortwave. RF: Shouldn’t be using that. Should be using GFDL formulation which reads in chl.nc.

AK: Some files in those ACCESS-OM2 input tarballs that aren’t used. Should they be removed? NH: Posted on slack about this? AK: Yes, but not sure they aren’t used by someone. NH: Bit messy how this is done. Should really just have a bunch of files and grab what they need. Would save a lot space. Currently versioning sets of files rather than individual files.

mppnccombine-fast

AK: Some issues on GitHub. RF: Been discussing this with AH and Scott Wales. An attribute needs to be removed. AH: Biggest issue is regional outputs having incorrect dimensioning. Which has been fixed. Also fixed the unlimited dimension getting squashed. Also another issue with passing too many files on the command line due to an MPI issue. Requires a change to payu as globbing is now done internally so any glob needs to be quoted. It’s on my list of tasks.

MW: Original tool used a pattern? AH: Didn’t implement that in mppnccombine-fast, maybe we should? MW: Stopped doing that in payu to support some coupled FMS codes where tiles didn’t start at zero, but could go back to the old way. AH: Does using the pattern work with masked configs when tiles are missing? I can’t recall. MW: Not sure.

ACCESS-OM2 disk usage

AH: AK and I went through some of the 0.1 deg output directories and found we could get significant space savings in the ice diagnostics AK: Ice outputs are not compressed, daily data is in individual files half of which is grid data. Can get a 8 fold decrease in size. Out of 20TB of total data can save 12TB of space. AH: Want to make a post processing script to run this automatically. AK: Yes, also delete all the zero length log files AH: This was to clean up for archiving. MW: payu should do this, maybe not looking in the right places. NH: FORTRAN has an option when closing a file to delete if empty, so looking into that. Also some CICE logs just have one line at the top with exactly the same text. AH: Yes we found those, matched the same number of bytes and deleting them. MW: If payu isn’t deleting zero length files not sweeping through submodes. AH: A lot tidier after cleaning. AK: Yes an hour well spent.

COSIMA Update

Over the last day we have completed initial spinup runs of the ACCESS-OM2 model.
The model has been run at 3 different resolutions, as listed below:

ACCESS-OM2 = [MOM5.1 + CICE5.1 + OASIS3-MCT + YATM + JRA55v13-do]

ACCESS-OM2:

  • 1° resolution, 50 levels
  • 252 cores
  • 48 yrs/day – 160 SU/yr
  • 5 InterAnnual Forcing (IAF) cycles complete
  • Numerous Repeat Year Forcing (RYF) cases

ACCESS-OM2-025:

  • 0.25° resolution, 50 (KDS) levels
  • 1824 cores
  • 16 yrs/day – 2800 SU/yr
  • 5 IAF cycles complete
  • Additional IAF and RYF cases run

ACCESS-OM2-01:

  • 0.1° resolution, 75 (KDS) levels
  • 5744 cores
  • 2.2 yrs/day – 63 kSU/yr (provided dt=600 sec)
  • Minimal config with 2064 cores, ~1 yr/day
  • 40-year RYF spinup with variable parameters, tweaks, date fixes during spinup.
  • Single IAF run from 1985 to 2017

For a full recount of today’s COSIMA meeting presentation, see the COSIMA Update slides.