Technical Working Group Meeting, April 2020


Date: 29th April, 2020
  • Aidan Heerdegen (AH) CLEX ANU
  • Andrew Kiss (AK) COSIMA ANU, Angus Gibson (AG) ANU
  • Russ Fiedler (RF), Matt Chamberlain (MC) CSIRO Hobart
  • Rui Yang (RY), Paul Leopardi (PL) NCI
  • Nic Hannah (NH) Double Precision
  • Marshall Ward (MW) GFDL

Apologies from Peter Dobrohotoff.

JRA55-do v1.4 support

AK: Staged rollout. NH tagged some branches, so existing master tagged 1.3.0, using old JRA55-do v 1.3.1 using NH new exes which also support 1.4
AK: Also working on a new feature branch for 1.4. Same exes configured to use JRA 1.4 version. Seems to run ok. Not looked at output. Will look at that today. Once satisfied that is ok will move into master, tag 1.4.
AK: Also looking at ak-dev branch with a wide variety of changes. Once this is ok will tag with a new ACCESS-OM2 version. Will be new standard for new experiments. Good to make an equivalent point across repos.
AH: COSIMA cookbook hackathon showed value of project boards. Might be a good idea next time something like this attempted. AK: Tried, but it didn’t go anywhere.
NH: Two freshwater fields coming from forcing, liquid and solid. Both go into the ICE model which accepts one new forcing field. Get added together, solid magically becomes liquid without heat changes, passed straight to Ocean. Ocean and Ice models have also been changed to accept liquid part of land/ice melt and heat part of land ice melt. Exist but just pass zeroes. Extra engineering not being used as yet. A harmonisation step which takes us close to CM2 as coupled model uses these fields.
RF: With my WOMBAT updates incorporated this new code, could get rid off ACCESS-CM preprocessor directives.
NH: In the future can put work into calculating those fields correctly in the ice model. Not a huge amount of work. Will then have river runoff, land ice runoff and land ice melt heat.
NH: New executables have another change, support different numbers of coupling fields. Land/ice coupling fields are optional. At runtime figures out what coupling fields used. Dependent on namcouple being consistent. Coded internally as a maximum set of coupling fields. You can take coupling fields out but not add new ones. Possibly useful for others. Not a fully flexible coupling framework.
NH: Working on ak-dev branch. Harmonising namcouple files. Have a lot of configuration fields, but a lot ignored. Could use same namcouple in all configs, but in practice might leave them looking a little different. They include the timestep in them, but ignored. Could set to zero? AH: Or a flag value that is obviously ignored?
NH: Only three variables used in namcouple. Rest ignored, bust must parse properly. Needs cruft to make it parse. Never liked namcouple. Completely inflexible, values must be changed in multiple places.
AK: On version Oasis3-mct2, have they improved it in new version?
NH: Can now bunch fields together, pass a single 3d field instead of many 2d fields. Should improve performance. RF: Not through namcouple at all. Just a function call.
MW: What does OASIS do now? NH: Just doing routing. Which is done by MCT anyway. Remapping done by ESMF. Coupler meant to do 3 things, config, remap and routing. Made libaccessom2 do as much as possible automatically. So OASIS does very little. Still using API, so would require effort to remove.
MW: Know about NUOPC? NCAR is using it. NH: Coupling API. If all use the same API then can go plug and play. MW: MOM6 has a NUOPC driver. NH: In the future would to look at OASIS4, but probably just chuck OASIS, use MCT to do the routing and ESMF to do remapping. MW: NCAR dropped MCT. NH: MCT is a small team. AK: Something that would suit ACCESS-CM. Any critical things that rely on OASIS? MW: At mercy of UM. Probably still use OASIS due to Europe. NH: Not using ESMF, so using OASIS a lot more than we are. Might never change because of that. AK: Even moving to v4 would require coordination with CM2. NH: Nicer and cleaner, but no clear benefit.

Updated ACCESS-OM2 model configs

AK: 3 different tags. 1.3.1, 1.4 in works. ak-dev new tag. 1.4 intended to be minimal other than change in JRA55-do version. ak-dev making more extensive changes. Ussing mppccombine-fast for tenth. Output compressed data and use fast collation. Not worthwhile for 1 deg. With 0.25 output uncompressed and use mppnccombine to do compression. Hopefully output will be a reasonable size.
AK: If outputting uncompressed restarts might get large. Might want to collate restarts. Wanted to verify which run is collated: just finished, or the previous run? AH: Yes it is the restarts which are not used in the next run.
AH: Because quarter degree is not compressed won’t get the inconsistent chunk sizes between different sized tiles. Ryan had the problem when he had a io_layout with very small chunk sizes which made his performance very bad. mppnccombine-fast might be faster, will definitely use less memory. Still got compression overhead but memory use much reduced. AK: Not such a big issue as tenth. AH: Paul Spence had some issues with the time to collate his outputs. Maybe because they were compressed. Would recommend using AK: Fast version will always be faster? AH: Yes, at least no slower, but definitely uses less memory and will be much faster with compressed output.
MW: No appetite for FMS with parallel-IO? AH: Compression? Without it won’t bother probably. RY: Did some tests on parallel IO compression tests. Can’t recall results. Interested to try again. Requires a bit more memory. gadi has optane as storage or as memory. Interesting to test. Probably can use that for parallel compression or even just serial compression. Thinking about, but haven’t started. AH: Please keep us updated.
NH: Anyone have thoughts on CICE? Planning on parallel IO on CICE. Are we going to need a compression step? RF: With daily would like compression. Post processing to do compression on smaller number of PEs would be fine. Improving IO is critical for Paul Sandrey and Pavel. NH: Might need a post processing step similar to MOM. RF: Yes. Getting parallel IO is the most important. Worry about compression later. NH: Did a run yesterday with parallel IO. Completed successfully. Output was garbage. Was expecting to do heaps of work and segfaults. Surprised at that. RF: Misaligned or complete garbage? NH: Default assumption as bad as can be. Just used parallel-IO output driver on CICE. AK and RF realised daily CICE output was a bottle neck on 0.1 performance. As model code existed, decided to get working. RY: Parallel IO need to set up mapping correctly between compute and IO domains. NH: Should be part of the current implementation. Mapping is a tricky part of CICE. AK: Values out of range, so maybe not just a mapping issue? NH: Completely broken, but not segfaulting. Just getting it building was one hurdle. Also had to call the right initialisation stuff within CICE. Had to rewrite some of it that was depending on another library from one of the NCAR models (CESM). CICE is used with  CESM and they had a dependency on another utility library. Changed some code to remove dependence. Relatively positive. Library under active development and well supported. AH: Did they develop just for their use case, and maybe doesn’t support round-robin? NH: Not sure. We do know never been used in any other model than CESM.
MW: Ed Hartnett (PIO) eager to get into FMS. Also lead maintainer of netCDF4.

Status of WOMBAT in ACCESS-OM2

RF: Compiled. Next is testing. Up to current ACCESS-OM2 code changes. Had issues with submodules. AK: Previously libaccessom2 dependencies brought in through CMake, now moved to submodules. If you have an existing repo will have initialise submodules to pull in latest from GitHub.
RF: Made some changes to installation procedures. Can go between BGC version or standard ACCESS-OM. Want it to be different for BGC version. Changes to install scripts and hashexe etc. AH: Good that it is up to date, could have been an messy merge otherwise. RF: Will run tests today or tomorrow.


AH: See this PR? Seemed a bit odd to me. First idea was to ask them to split the PR into science changes and config changes. RF: Looked like a lot of it was config changes. MW: Adding the GEOS5 stuff, which they shouldn’t. Code changes are challenging. Introduced a generic tracer, not sure what they’re doing with it. AH: Strategy? Ask them to wrap science stuff in preprocessor flags? MW: First step is to get config stuff out. Asked GFDL about it. GEOS are switching from MOM5 to MOM6. This must be associated with that effort to validate their runs. Maybe just giving back what it took to get it work. Maybe just makes his build process easier. AH: They have a specific requirement to use the same FMS library. Seems odd, as MOM5 and MOM6 are not likely to share FMS versions in the future. MW: Thorny topic, as it is not clear how FMS compatible MOM6 will be in the future. AH: Using FMS for less and less. MW: The PR needs to be cleaned up. AH: Also put in a CMake build system. MW: They need to explain more.
AK: Has conflicts, so can’t be merged at the moment. AH: Only going to get more conflicted. Which is why I was thinking they could split it up. I have a CMake build system in another branch, but never finished. if we can use theirs cool. I’ll engage with them.


AH: Been experimenting with graceful error recovery with payu. Can specify a script which can decide if the error is something you can just resubmit after. Mostly of interest to the production guys.
PL: Scalability testing with land masks, manifests, and payu setup. Supposed to be simpler but taking some time to get used to it. AH: Manifests are relatively new so some of the use cases have not been as well tested. MW: Are not all using manifests? AH: They are, but can be used in different ways. Tracking always works, but options to reproduce inputs and runs. Suggested PL could use reproduce to start a run. It was confounded by some restarts being missing, so not quite sure if it works as we would like. This is a very desirable feature, as it makes it very simple to fork off new runs from existing ones as well as making sure the files are consistent. PL: Working now. Next step is to change core counts and look for scalability numbers. AH: When I was doing scalability stuff for MOM-SIS I use input directory categories to isolate processor changes. Not quite doing that same thing anymore, but you can do something similar, but you won’t want use the reproduce flag if you are changing any of the input files.
AK: Just MOM scaling or CICE as well? PL: Just looking at MOM to begin with to see dependency and wait times. AK: CICE run time is critically dependent on daily outputs. Revelance to scaling data to production output. MW: Make sure your clock can tell them apart. In principle can distinguish compute from IO. AH: Daily output always part of production? AK: Ice modellers want very high temporal output. Ice is very dynamic. Even daily output not enough to resolve  some features. Maybe wait for PIO for CICE scaling tests? AH: I thought scaling tests always turned off IO? Can’t properly test scaling with daily output, as it dominates runtime.
NH: Would be nice to look at performance with and without PIO. PL: Will also look at CICE. Start with ocean model. AK: Were you (MW) running models coupled for paper scaling numbers? MW: Coupled. Not sure what IO was set to. Subtracted it and don’t recall it was large. Don’t recall a bottle neck, so might have had it turned off. RF: Wouldn’t be running with daily IO. Monthly IO doesn’t show up. MW: sounds likely.
AK: For IAF had a lot of daily CICE output. Not complete set of fields.
MW: Starting to run performance tests at GFDL and want to use payu. Has it changed much? Manifest stuff hasn’t made a big difference? Will have to get slurm working. Filesystem will be a nightmare. You moved PBS stuff into a component? AH: No, you did that. Not huge differences. Will be great to have slurm support.