# ESMF mesh and MOM6 domain masks are inconsistent **URL:** \ **Category:** Regional MOM6\ **Created:** [26 February 2025 02:17 UTC](https://forum.access-hive.org.au/t/esmf-mesh-and-mom6-domain-masks-are-inconsistent/4380 "2025-02-26T02:17:29Z")\ **Posts on this page:** 20\ **Page:** 2
**Author:** ![anton](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/anton/32/1836_2.png) [@anton](https://forum.access-hive.org.au/u/anton)\ **Post date:** [5 March 2025 23:46 UTC](https://forum.access-hive.org.au/t/esmf-mesh-and-mom6-domain-masks-are-inconsistent/4380/21 "2025-03-05T23:46:07Z")
> [@Paul.Gregory](#): > > ```auto > ValueError: OCN_modelio pio_root exceeds available PEs (max: 0) in nuopc.runconfig. > > ``` This check occurs before the model even runs - this is during payu setup. So I don’t see how it can be related to changing the masktable. Its a bit concerning is says the max availabe PEs is 0. What is `ocn_ntasks / ocn_nthreads / ocn_pestride / ocn_rootpe` in the PELAYOUT\_attributes section set to ? If you push your config to github ill have a look. ---
**Author:** ![Paul.Gregory](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/paul.gregory/32/2566_2.png) [@Paul.Gregory](https://forum.access-hive.org.au/u/Paul.Gregory)\ **Post date:** [24 March 2025 00:20 UTC](https://forum.access-hive.org.au/t/esmf-mesh-and-mom6-domain-masks-are-inconsistent/4380/22 "2025-03-24T00:20:13Z")
Ok just summarising my latest progress. Remember I had trouble running @Helen’s original configuration (140 x 249 Tasmanian domain at 0.05 resolution requesting 100 CPUs on a 10x10 layout) so I attempted to incrementally change @mmr 's original config (70x125 at 0.1 with 16 CPUs on a 4x4) I’ve been able to run @mmr0 's configuration for the following layouts: | Layout | Runtime | | --- | --- | | 4x4 | 09:48 | | 8x8 | 05:12 | | 10x10 | 04:07 | | 12x12 | 03:49 | All of these worked with no mask table in `MOM_layout` I then regenerated the 10x10 layout but using the higher resolution grid (i.e 140x249 (0.05 resolution). This first failed with : ```auto FATAL from PE 20: Discrepancy detected between ESMF mesh and internal MOM6 domain sizes. Check mask table. ``` So I added back the `MASKTABLE` entry in `MOM_layout` ```auto MASKTABLE = mask_table.2.10x10 ``` Ran again. This failed with ```auto FATAL from PE 3: ERROR: Difference between ESMF Mesh and MOM6 domain coords is greater than parameter EPS_OMESH. n, lonMesh(n), lon (n), diff_lon, EPS_OMESH= 1 147.2500000000000 145.1250000000000 0.21250D+01 0.10000D-03 ``` This implies the grids aren’t aligned. As an aside, I did a diff on the two directories: - The first created using Helen’s instructions - The second created by incrementally moving from Madi’s configuration into Helen’s. The diffs of consequence are: ```auto diff access-rom3-PG/datm_in access-rom3-MR-10by10-hires/datm_in 11,12c11,12 < model_maskfile = "./INPUT/access-rom3-ESMFmesh.nc" < model_meshfile = "./INPUT/access-rom3-ESMFmesh.nc" --- > model_maskfile = "./INPUT/access-rom3-nomask-ESMFmesh.nc" > model_meshfile = "./INPUT/access-rom3-nomask-ESMFmesh.nc" Only in access-rom3-MR-10by10-hires/: docs diff access-rom3-PG/drof_in access-rom3-MR-10by10-hires/drof_in 3,4c3,4 < model_maskfile = "./INPUT/access-rom3-ESMFmesh.nc" < model_meshfile = "./INPUT/access-rom3-ESMFmesh.nc" --- > model_maskfile = "./INPUT/access-rom3-nomask-ESMFmesh.nc" > model_meshfile = "./INPUT/access-rom3-nomask-ESMFmesh.nc" ``` i.e. Madi’s config uses the `nomask` mesh file. There are also differences in `MOM_input` regarding `OBC_SEGMENT` definitions ```auto diff access-rom3-PG/MOM_input access-rom3-MR-10by10-hires/MOM_input 109a110,133 > OBC_SEGMENT_001 = "J=0,I=0:N,FLATHER,ORLANSKI,NUDGED,ORLANSKI_TAN,NUDGED_TAN" ! > ! Documentation needs to be dynamic????? > OBC_SEGMENT_001_VELOCITY_NUDGING_TIMESCALES = 0.3, 360.0 ! [days] default = 0.0 > ! Timescales in days for nudging along a segment, for inflow, then outflow. > ! Setting both to zero should behave like SIMPLE obcs for the baroclinic > ! velocities. > OBC_SEGMENT_002 = "J=N,I=N:0,FLATHER,ORLANSKI,NUDGED,ORLANSKI_TAN,NUDGED_TAN" ! > ! Documentation needs to be dynamic????? > OBC_SEGMENT_002_VELOCITY_NUDGING_TIMESCALES = 0.3, 360.0 ! [days] default = 0.0 > ! Timescales in days for nudging along a segment, for inflow, then outflow. > ! Setting both to zero should behave like SIMPLE obcs for the baroclinic > ! velocities. > OBC_SEGMENT_003 = "I=0,J=N:0,FLATHER,ORLANSKI,NUDGED,ORLANSKI_TAN,NUDGED_TAN" ! > ! Documentation needs to be dynamic????? > OBC_SEGMENT_003_VELOCITY_NUDGING_TIMESCALES = 0.3, 360.0 ! [days] default = 0.0 > ! Timescales in days for nudging along a segment, for inflow, then outflow. > ! Setting both to zero should behave like SIMPLE obcs for the baroclinic > ! velocities. > OBC_SEGMENT_004 = "I=N,J=0:N,FLATHER,ORLANSKI,NUDGED,ORLANSKI_TAN,NUDGED_TAN" ! > ! Documentation needs to be dynamic????? > OBC_SEGMENT_004_VELOCITY_NUDGING_TIMESCALES = 0.3, 360.0 ! [days] default = 0.0 > ! Timescales in days for nudging along a segment, for inflow, then outflow. > ! Setting both to zero should behave like SIMPLE obcs for the baroclinic > ! velocities. 242a267,275 > OBC_SEGMENT_001_DATA = "U=file:forcing_obc_segment_001.nc(u),V=file:forcing_obc_segment_001.nc(v),SSH=file:forcing_obc_segment_001.nc(eta),TEMP=file:forcing_obc_segment_001.nc(temp),SALT=file:forcing_obc_segment_001.nc(salt)" ! > ! OBC segment docs > OBC_SEGMENT_002_DATA = "U=file:forcing_obc_segment_002.nc(u),V=file:forcing_obc_segment_002.nc(v),SSH=file:forcing_obc_segment_002.nc(eta),TEMP=file:forcing_obc_segment_002.nc(temp),SALT=file:forcing_obc_segment_002.nc(salt)" ! > ! OBC segment docs > OBC_SEGMENT_003_DATA = "U=file:forcing_obc_segment_003.nc(u),V=file:forcing_obc_segment_003.nc(v),SSH=file:forcing_obc_segment_003.nc(eta),TEMP=file:forcing_obc_segment_003.nc(temp),SALT=file:forcing_obc_segment_003.nc(salt)" ! > ! OBC segment docs > OBC_SEGMENT_004_DATA = "U=file:forcing_obc_segment_004.nc(u),V=file:forcing_obc_segment_004.nc(v),SSH=file:forcing_obc_segment_004.nc(eta),TEMP=file:forcing_obc_segment_004.nc(temp),SALT=file:forcing_obc_segment_004.nc(salt)" ! > ! OBC segment docs ``` i.e. Helen’s `MOM_layout` is missing all `OBC_SEGMENT` information (is this correct? Did I delete this accidentally?) Anyway - I’ll do a check on the lat/lon co-ordinates of the mesh files in Madi’s config and see if I can figure out the source of the error. To run Madi’s config at 0.05 resolution with 140x249, do I need to change the mask file to use the `nomask’ version? ---
**Author:** ![anton](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/anton/32/1836_2.png) [@anton](https://forum.access-hive.org.au/u/anton)\ **Post date:** [24 March 2025 05:41 UTC](https://forum.access-hive.org.au/t/esmf-mesh-and-mom6-domain-masks-are-inconsistent/4380/23 "2025-03-24T05:41:39Z")
> [@Paul.Gregory](#): > > To run Madi’s config at 0.05 resolution with 140x249, do I need to change the mask file to use the `nomask’ version? I believe both will run. I think both should give the same result. There are some cases the nomask version is needed for fields to be coupled conservatively. ---
**Author:** ![Paul.Gregory](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/paul.gregory/32/2566_2.png) [@Paul.Gregory](https://forum.access-hive.org.au/u/Paul.Gregory)\ **Post date:** [25 March 2025 03:40 UTC](https://forum.access-hive.org.au/t/esmf-mesh-and-mom6-domain-masks-are-inconsistent/4380/24 "2025-03-25T03:40:14Z")
Ok I checked the dimensions of my `access-rom3-ESMFmesh.nc` and they were still the ‘low-res’ versions (i.e. 70 x 149). So I regenerated the ESMF mesh files and ran again. I now get the same error I had logged here : [ACCESS-ROM3 setup instructions - #55](https://forum.access-hive.org.au/t/access-rom3-setup-instructions/4107/55) ```auto FATAL from PE 86: ERROR: ESMF mesh and MOM6 domain masks are inconsistent! - MOM n, maskMesh(n), mask(n) = 306 1 0 FATAL from PE 82: ERROR: ESMF mesh and MOM6 domain masks are inconsistent! - MOM n, maskMesh(n), mask(n) = 81 1 0 Image PC Routine Line Source access-om3-MOM6 0000000002E3B304 mpp_mod_mp_mpp_er 72 mpp_util_mpi.inc access-om3-MOM6 0000000001E4F06F mom_error_handler 154 MOM_error_handler.F90 access-om3-MOM6 0000000001B83460 mom_cap_mod_mp_in 1246 mom_cap.F90 ``` So I’ve now generated the same error by building a config two seperate ways. I’ve checked my `ocean_mask.nc` and `access-rom3-ESMFmesh.nc` file and they are identical. Some questions: 1. Does anyone know which file `MOM6 domain mask` refers to the have above error message? 2. Does anyone have a config in git somewhere of the Tassie domain at 140x249 that will work out of the box? 3. @dougiesquire - do you want to catch up some time to run me through the masking process? Will ‘automasking’ potentially solve this? Thanks for reading ---
**Author:** ![dougiesquire](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/dougiesquire/32/16_2.png) [@dougiesquire](https://forum.access-hive.org.au/u/dougiesquire)\ **Post date:** [25 March 2025 03:54 UTC](https://forum.access-hive.org.au/t/esmf-mesh-and-mom6-domain-masks-are-inconsistent/4380/25 "2025-03-25T03:54:49Z")
@Paul.Gregory I think it is important to use the `nomask` version of the ESMF mesh in certain places. Could you please take a look at [this config](https://github.com/ACCESS-NRI/access-om3-configs/tree/dev-MC_1deg_jra_ryf) and check that you are using masked and unmasked versions in the same places. ---
**Author:** ![Paul.Gregory](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/paul.gregory/32/2566_2.png) [@Paul.Gregory](https://forum.access-hive.org.au/u/Paul.Gregory)\ **Post date:** [25 March 2025 05:30 UTC](https://forum.access-hive.org.au/t/esmf-mesh-and-mom6-domain-masks-are-inconsistent/4380/26 "2025-03-25T05:30:40Z")
Here is where ‘ESMFmesh.nc’ is used in my current config directory config.yaml: ```auto - /g/data/vk83/configurations/inputs/access-om3/share/meshes/share/2024.09.16/JRA55do-datm-ESMFmesh.nc - /g/data/vk83/configurations/inputs/access-om3/share/meshes/share/2024.09.16/JRA55do-drof-ESMFmesh.nc - /scratch/gb02/pag548/regional_mom6_configs/tassie-access-om2-forced/access-rom3-ESMFmesh.nc - /scratch/gb02/pag548/regional_mom6_configs/tassie-access-om2-forced/access-rom3-nomask-ESMFmesh.nc ``` datm\_in: ```auto model_maskfile = "./INPUT/access-rom3-nomask-ESMFmesh.nc" model_meshfile = "./INPUT/access-rom3-nomask-ESMFmesh.nc" ``` drof\_in: ```auto model_maskfile = "./INPUT/access-rom3-nomask-ESMFmesh.nc" model_meshfile = "./INPUT/access-rom3-nomask-ESMFmesh.nc" ``` nuopc.runconfig: ```auto mesh_atm = ./INPUT/access-om2-1deg-nomask-ESMFmesh.nc mesh_ice = ./INPUT/access-om2-1deg-ESMFmesh.nc mesh_mask = ./INPUT/access-rom3-ESMFmesh.nc mesh_ocn = ./INPUT/access-rom3-ESMFmesh.nc mesh_rof = ./INPUT/access-om2-1deg-nomask-ESMFmesh.nc ``` If I search for just ‘mask’ the following strings also match ```auto fd.yaml: - standard_name: Sg_icemask fd.yaml: - standard_name: Sg_icemask_coupled_fluxes fd.yaml: - standard_name: Si_imask fd.yaml: alias: ice_mask fd.yaml: description: sea-ice export - ice mask fd.yaml: - standard_name: So_omask fd.yaml: alias: ocean_mask fd.yaml: - standard_name: mask ice_in: maskhalo_bound = .true. ice_in: maskhalo_dyn = .true. ice_in: maskhalo_remap = .true. ice_in: f_tmask = .false. , f_umask = .false. ice_in: f_nmask = .false. , f_emask = .false. ``` I’ve checked this config against > **[GitHub - ACCESS-NRI/access-om3-configs at dev-MC\_1deg\_jra\_ryf](https://github.com/ACCESS-NRI/access-om3-configs/tree/dev-MC_1deg_jra_ryf)** > > dev-MC\_1deg\_jra\_ryf In the GitHub `.yaml` the JRA and access meshes are defined in a different order: ```auto - /g/data/vk83/configurations/inputs/access-om3/share/meshes/global.1deg/2024.01.25/access-om2-1deg-ESMFmesh.nc - /g/data/vk83/configurations/inputs/access-om3/share/meshes/global.1deg/2024.01.25/access-om2-1deg-nomask-ESMFmesh.nc - /g/data/vk83/configurations/inputs/access-om3/share/meshes/share/2024.09.16/JRA55do-datm-ESMFmesh.nc - /g/data/vk83/configurations/inputs/access-om3/share/meshes/share/2024.09.16/JRA55do-drof-ESMFmesh.nc ``` Those are the only differences I can spot? (Besides the presence of `rom3` meshes somewhere and `om2` meshes elsewhere. Should all mesh files in `nuopc.runconfig` use the regional `rom3` and not the global`om2` file ? ---
**Author:** ![helen](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/helen/32/2840_2.png) [@helen](https://forum.access-hive.org.au/u/helen)\ **Post date:** [27 March 2025 05:35 UTC](https://forum.access-hive.org.au/t/esmf-mesh-and-mom6-domain-masks-are-inconsistent/4380/27 "2025-03-27T05:35:21Z")
> [@Paul.Gregory](#): > > i.e. Helen’s `MOM_layout` is missing all `OBC_SEGMENT` information (is this correct? Did I delete this accidentally?) > [@Error outputting to non existent CICE file](https://forum.access-hive.org.au/t/error-outputting-to-non-existent-cice-file/4292/12): > > In the GitHub `.yaml` the JRA and access meshes are defined in a different order: Hi @Paul.Gregory, neither of these should be an issue. Different versions of the notebook put the boundary conditions in MOM\_override. ---
**Author:** ![helen](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/helen/32/2840_2.png) [@helen](https://forum.access-hive.org.au/u/helen)\ **Post date:** [27 March 2025 05:42 UTC](https://forum.access-hive.org.au/t/esmf-mesh-and-mom6-domain-masks-are-inconsistent/4380/28 "2025-03-27T05:42:32Z")
> [@Paul.Gregory](#): > > Should all mesh files in `nuopc.runconfig` use the regional `rom3` and not the global`om2` file ? No, we will need still need the global one for, e.g. the atmosphere ---
**Author:** ![anton](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/anton/32/1836_2.png) [@anton](https://forum.access-hive.org.au/u/anton)\ **Post date:** [27 March 2025 05:58 UTC](https://forum.access-hive.org.au/t/esmf-mesh-and-mom6-domain-masks-are-inconsistent/4380/29 "2025-03-27T05:58:40Z")
> [@Paul.Gregory](#): > > datm\_in: > > ```auto > model_maskfile = "./INPUT/access-rom3-nomask-ESMFmesh.nc" > model_meshfile = "./INPUT/access-rom3-nomask-ESMFmesh.nc" > > ``` > > drof\_in: > > ```auto > model_maskfile = "./INPUT/access-rom3-nomask-ESMFmesh.nc" > model_meshfile = "./INPUT/access-rom3-nomask-ESMFmesh.nc" > > ``` > > nuopc.runconfig: > > ```auto > mesh_atm = ./INPUT/access-om2-1deg-nomask-ESMFmesh.nc > mesh_ice = ./INPUT/access-om2-1deg-ESMFmesh.nc > mesh_mask = ./INPUT/access-rom3-ESMFmesh.nc > mesh_ocn = ./INPUT/access-rom3-ESMFmesh.nc > mesh_rof = ./INPUT/access-om2-1deg-nomask-ESMFmesh.nc > > ``` I am fairly confident all of these should be the `access-rom3` mesh You hopefully can delete the `mesh_ice` line . It looks like you are using nomask and mask correctly, but they all should be the rom3 mesh files. The meshfiles used for the input files for the data atmosphere and data runoff are set in the `streams.xml` files (e.g [here](https://github.com/ACCESS-NRI/access-om3-configs/blob/495a82b01f5864a1b7db1b2f376beafa426735a9/datm.streams.xml#L17)). The data-model (CDEPS) then remaps the data from the input mesh, set in `streams.xml` to the `model_meshfile` set in `datm_in`. (I think … im not confident why there is a `model_meshfile` in `datm_in` and a `mesh_atm` in `nuopc.runconfig`) ---
**Author:** ![anton](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/anton/32/1836_2.png) [@anton](https://forum.access-hive.org.au/u/anton)\ **Post date:** [28 March 2025 00:24 UTC](https://forum.access-hive.org.au/t/esmf-mesh-and-mom6-domain-masks-are-inconsistent/4380/30 "2025-03-28T00:24:19Z")
> [@anton](#): > > You hopefully can delete the `mesh_ice` line . I remembered … don’t try this. CMEPS does some checks of this file even it it’s not being used. > ---
**Author:** ![helen](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/helen/32/2840_2.png) [@helen](https://forum.access-hive.org.au/u/helen)\ **Post date:** [3 April 2025 22:28 UTC](https://forum.access-hive.org.au/t/esmf-mesh-and-mom6-domain-masks-are-inconsistent/4380/31 "2025-04-03T22:28:01Z")
> [@Paul.Gregory](#): > > Does anyone have a config in git somewhere of the Tassie domain at 140x249 that will work out of the box? @Paul.Gregory I have put my latest working configuration [here](https://github.com/helenmacdonald/ACCESS-rOM3-tas) I put it together about a week ago using the latest version of the instructions. If you upload your latest configuration than I am happy to have a go at it to see if I can get it to work. Note that I have moved all these posts into a new thread to make it easier to find and follow for newcomers. ---
**Author:** ![Paul.Gregory](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/paul.gregory/32/2566_2.png) [@Paul.Gregory](https://forum.access-hive.org.au/u/Paul.Gregory)\ **Post date:** [4 April 2025 01:24 UTC](https://forum.access-hive.org.au/t/esmf-mesh-and-mom6-domain-masks-are-inconsistent/4380/32 "2025-04-04T01:24:16Z")
Hi Helen. I used your config and changed your paths in `config.yaml` from ```auto /scratch/tm70/hm6113/regional/accessom3/accessom3-test/etc. ``` to point to my regional meshes at ```auto /scratch/gb02/pag548/regional_mom6_configs/tassie-access-om2-forced ``` I now generate a different error. We have no longer have a mask-related issues, it’s a time-related issue with the boundary conditions.Some snippets. ```auto FATAL from PE 0: field u_segment_001 Array size mismatch in time_interp_external. Array "data" is too small. shape(data)= 121 1 75 FATAL from PE 20: time_interp_external 2: time 731215 (20030101.000000 is before range of list 734868-734872(20130101.00000 0 - 20130105.000000),file=INPUT/forcing_obc_segment_003.nc,field=u_segment_003 ``` Here are the time contents of my first `obc_segment` file: ```auto $ ncdump -v time forcing_obc_segment_001.nc netcdf forcing_obc_segment_001 { dimensions: time = UNLIMITED ; // (5 currently) double time(time) ; time:_FillValue = NaN ; time:calendar = "julian" ; time:units = "days since 2013-01-01 00:00:00" ; data: time = 0, 1, 2, 3, 4 ; } ``` I don’t have permissions to view `/scratch/tm70/hm6113/regional/accessom3/accessom3-test/` to compare against your input `obc_segment` files. ---
**Author:** ![helen](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/helen/32/2840_2.png) [@helen](https://forum.access-hive.org.au/u/helen)\ **Post date:** [4 April 2025 01:51 UTC](https://forum.access-hive.org.au/t/esmf-mesh-and-mom6-domain-masks-are-inconsistent/4380/33 "2025-04-04T01:51:52Z")
Ahh, it looks like I have my dates as 2003 (which is not the 2013 in the instructions!) I have placed my files on gadi: ```auto /scratch/public/hm6113 ``` but these will be deleted soon so copy them across to a folder somewhere. To change the dates it is in nuopc.runconfig line 276: ```auto start_ymd = 20030101 ``` Change this to ```auto start_ymd = 20130101 ``` I’m not sure, but you may need to run ```auto payu setup ``` after making this change. ---
**Author:** ![Paul.Gregory](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/paul.gregory/32/2566_2.png) [@Paul.Gregory](https://forum.access-hive.org.au/u/Paul.Gregory)\ **Post date:** [7 April 2025 05:00 UTC](https://forum.access-hive.org.au/t/esmf-mesh-and-mom6-domain-masks-are-inconsistent/4380/34 "2025-04-07T05:00:45Z")
Hi Helen. I made the change to config.yaml ```auto $ grep start_ymd nuopc.runconfig restart_ymd = -999 start_ymd = 20130101 ``` But the error remains. I then repeated the run but linked to `/scratch/public/hm6113` in my config.yaml, so that all my inputs were: ```auto exe: access-om3-MOM6 input: - /g/data/vk83/configurations/inputs/access-om3/share/meshes/share/2024.09.16/JRA55do-datm-ESMFmesh.nc - /g/data/vk83/configurations/inputs/access-om3/share/meshes/share/2024.09.16/JRA55do-drof-ESMFmesh.nc - /g/data/vk83/configurations/inputs/access-om3/share/grids/global.1deg/2020.10.22/topog.nc - /g/data/vk83/configurations/inputs/access-om3/cice/grids/global.1deg/2024.05.14/grid.nc - /g/data/vk83/configurations/inputs/access-om3/mom/surface_salt_restoring/global.1deg/2020.05.30/salt_sfc_restore.nc - /g/data/vk83/configurations/inputs/access-om3/cice/grids/global.1deg/2024.05.14/kmt.nc - /g/data/vk83/configurations/inputs/access-om3/cice/initial_conditions/global.1deg/2023.07.28/iced.1900-01-01-10800.nc - /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0 - /scratch/public/hm6113/hgrid.nc - /scratch/public/hm6113/vcoord.nc - /scratch/public/hm6113/bathymetry.nc - /scratch/public/hm6113/init_tracers.nc - /scratch/public/hm6113/init_eta.nc - /scratch/public/hm6113/init_vel.nc - /scratch/public/hm6113/forcing_obc_segment_001.nc - /scratch/public/hm6113/forcing_obc_segment_002.nc - /scratch/public/hm6113/forcing_obc_segment_003.nc - /scratch/public/hm6113/forcing_obc_segment_004.nc - /scratch/public/hm6113/grid_spec.nc - /scratch/public/hm6113/ocean_mosaic.nc - /scratch/public/hm6113/access-rom3-ESMFmesh.nc - /scratch/public/hm6113/access-rom3-nomask-ESMFmesh.nc - /scratch/public/hm6113/land_mask.nc ``` The error remains. Ok, so this is strange. Remember now I’m running using your config at `git@github.com:helenmacdonald/ACCESS-rOM3-tas.git` Here is the `git diff` between what I’m running on disk, and what is in your repo for `config.yaml` and `nuopcy.runconfig` ```auto $ git diff origin/expt -- . diff --git a/config.yaml b/config.yaml index 33e3780..67f2b70 100644 --- a/config.yaml +++ b/config.yaml @@ -28,21 +28,21 @@ input: - /g/data/vk83/configurations/inputs/access-om3/cice/grids/global.1deg/2024.05.14/kmt.nc - /g/data/vk83/configurations/inputs/access-om3/cice/initial_conditions/global.1deg/2023.07.28/iced.1900-01-01-10800.nc - /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0 - - /scratch/tm70/hm6113/regional/accessom3/accessom3-test/hgrid.nc - - /scratch/tm70/hm6113/regional/accessom3/accessom3-test/vcoord.nc - - /scratch/tm70/hm6113/regional/accessom3/accessom3-test/bathymetry.nc - - /scratch/tm70/hm6113/regional/accessom3/accessom3-test/init_tracers.nc - - /scratch/tm70/hm6113/regional/accessom3/accessom3-test/init_eta.nc - - /scratch/tm70/hm6113/regional/accessom3/accessom3-test/init_vel.nc - - /scratch/tm70/hm6113/regional/accessom3/accessom3-test/forcing_obc_segment_001.nc - - /scratch/tm70/hm6113/regional/accessom3/accessom3-test/forcing_obc_segment_002.nc - - /scratch/tm70/hm6113/regional/accessom3/accessom3-test/forcing_obc_segment_003.nc - - /scratch/tm70/hm6113/regional/accessom3/accessom3-test/forcing_obc_segment_004.nc - - /scratch/tm70/hm6113/regional/accessom3/accessom3-test/grid_spec.nc - - /scratch/tm70/hm6113/regional/accessom3/accessom3-test/ocean_mosaic.nc - - /scratch/tm70/hm6113/regional/accessom3/accessom3-test/access-rom3-ESMFmesh.nc - - /scratch/tm70/hm6113/regional/accessom3/accessom3-test/access-rom3-nomask-ESMFmesh.nc - - /scratch/tm70/hm6113/regional/accessom3/accessom3-test/land_mask.nc + - /scratch/public/hm6113/hgrid.nc + - /scratch/public/hm6113/vcoord.nc + - /scratch/public/hm6113/bathymetry.nc + - /scratch/public/hm6113/init_tracers.nc + - /scratch/public/hm6113/init_eta.nc + - /scratch/public/hm6113/init_vel.nc + - /scratch/public/hm6113/forcing_obc_segment_001.nc + - /scratch/public/hm6113/forcing_obc_segment_002.nc + - /scratch/public/hm6113/forcing_obc_segment_003.nc + - /scratch/public/hm6113/forcing_obc_segment_004.nc + - /scratch/public/hm6113/grid_spec.nc + - /scratch/public/hm6113/ocean_mosaic.nc + - /scratch/public/hm6113/access-rom3-ESMFmesh.nc + - /scratch/public/hm6113/access-rom3-nomask-ESMFmesh.nc + - /scratch/public/hm6113/land_mask.nc collate: false runlog: true metadata: diff --git a/nuopc.runconfig b/nuopc.runconfig index cf5f7a8..0162674 100644 --- a/nuopc.runconfig +++ b/nuopc.runconfig @@ -273,7 +273,7 @@ CLOCK_attributes:: restart_ymd = -999 rof_cpl_dt = 99999 #not used start_tod = 0 - start_ymd = 20030101 + start_ymd = 20130101 stop_n = 2 stop_option = ndays stop_tod = 0 ``` Are we at the point where we think there is underlying configuration/environment issue? ---
**Author:** ![helen](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/helen/32/2840_2.png) [@helen](https://forum.access-hive.org.au/u/helen)\ **Post date:** [7 April 2025 05:32 UTC](https://forum.access-hive.org.au/t/esmf-mesh-and-mom6-domain-masks-are-inconsistent/4380/35 "2025-04-07T05:32:26Z")
Hi @Paul.Gregory, just checking - is “the error remains” referring to this error: `ESMF mesh and MOM6 domain masks are inconsistent!` or this one: `field u_segment_001 Array size mismatch in time_interp_external` ? > [@Paul.Gregory](#): > > Are we at the point where we think there is underlying configuration/environment issue? I am using payu1.1.6 upgraded from payu1.1.5 ---
**Author:** ![Paul.Gregory](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/paul.gregory/32/2566_2.png) [@Paul.Gregory](https://forum.access-hive.org.au/u/Paul.Gregory)\ **Post date:** [7 April 2025 06:21 UTC](https://forum.access-hive.org.au/t/esmf-mesh-and-mom6-domain-masks-are-inconsistent/4380/36 "2025-04-07T06:21:53Z")
Sorry. It’s still generating warnings and errors related to time dimensions, e.g. ```auto WARNING from PE 9: categorize_axes: Failed to identify x- and y- axes in the axis list (nx_segment_004, ny_segment_004, time) of a varia ble being read from INPUT/forcing_obc_segment_004.nc FATAL from PE 9: time_interp_external 2: time 734868 (20130101.000000 is after range of list 731215-731219(20030101.000000 - 20030105.00 0000),file=INPUT/forcing_obc_segment_001.nc,field=u_segment_001 ``` FYI I’m inquiring at NCI for help in MPI fortran debugging session. I have lots of serial fortran debugging experience (using gdb and ifort) so I’m thinking debugging this regional MOM6 configuration will be helpful tracking down these errors. Will also be good for my own MOM6 education. I’ll follow the spack-MOM6 compilation instructions again, and make sure I add debug flags. Then I’ll use this exe for my own config. But I’ll also try with payu 1.1.6 ---
**Author:** ![helen](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/helen/32/2840_2.png) [@helen](https://forum.access-hive.org.au/u/helen)\ **Post date:** [7 April 2025 06:51 UTC](https://forum.access-hive.org.au/t/esmf-mesh-and-mom6-domain-masks-are-inconsistent/4380/37 "2025-04-07T06:51:19Z")
> [@Paul.Gregory](#): > > It’s still generating warnings and errors related to time dimensions, e.g. In the meantime - I will redo my example so the time matches everyone else’s. ---
**Author:** ![anton](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/anton/32/1836_2.png) [@anton](https://forum.access-hive.org.au/u/anton)\ **Post date:** [9 May 2025 05:58 UTC](https://forum.access-hive.org.au/t/esmf-mesh-and-mom6-domain-masks-are-inconsistent/4380/38 "2025-05-09T05:58:43Z")
6 posts were split to a new topic: [Setting build options for OM3](https://forum.access-hive.org.au/t/setting-build-options-for-om3/4495) ---
**Author:** ![helen](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/helen/32/2840_2.png) [@helen](https://forum.access-hive.org.au/u/helen)\ **Post date:** [23 April 2025 06:26 UTC](https://forum.access-hive.org.au/t/esmf-mesh-and-mom6-domain-masks-are-inconsistent/4380/39 "2025-04-23T06:26:55Z")
@Paul.Gregory I haven’t tried recently, but I am expecting them to be the same. We wanted to have the global and regional models both on the symmetric executable but there are some restart reproducibility issues so we need to leave the `+mom_symmetric` step in for now. If you are using the most recent ACCESS-om3 version, you may need to follow the regional mom6 setup instructions from the start as there have been some changes in the global configurations that we base the regional configurations on (so the executable will not be compatible with the input files). ---
**Author:** ![helen](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/helen/32/2840_2.png) [@helen](https://forum.access-hive.org.au/u/helen)\ **Post date:** [29 April 2025 23:00 UTC](https://forum.access-hive.org.au/t/esmf-mesh-and-mom6-domain-masks-are-inconsistent/4380/41 "2025-04-29T23:00:39Z")
@Paul.Gregory, I now have a simulation with an error similar to yours. For me, it was caused by mixing and matching the input boundary condition (`forcing_obc_segment_00*.nc`) files and configuration files (`MOM_*`). There are different versions of the regional-mom6 package which has resulted in different versions of the boundary condition files floating around. The `forcing_obc_segment_00*.nc` files created in one version are incompatible with the `MOM_*` files created with a different version. Basically, there are differences in the order that the boundary conditions are specified and the direction they go in. This line: ```auto OBC_SEGMENT_001 = "J=N,I=N:0,FLATHER,ORLANSKI,NUDGED,ORLANSKI_TAN,NUDGED_TAN" !None ``` (and others like it for each of the 4 segments) tell the model which edge `forcing_obc_segment_001.nc` is on, and which direction the boundary is read in. It is different in different versions to reflect the differences in the netcdf files. Not too sure if this is what is causing your error – but it would be good to check that you are using the `MOM_*` files that were made with the same notebook as the input netcdf files. [Previous page](https://forum.access-hive.org.au/t/esmf-mesh-and-mom6-domain-masks-are-inconsistent/4380.md?page=1) [Next page](https://forum.access-hive.org.au/t/esmf-mesh-and-mom6-domain-masks-are-inconsistent/4380.md?page=3)