OM3 Runtime Output Files
Presenter: @chrisb13 (Chris Bull).
Date: 09/04/2026
Abstract
Today we're focusing on understanding model output when OM3 runs succesfully. We'll be looking at key OM3 output files and ending on how to interpret diagnostics on the MOM6 C-grid. Next week Helen will discover what to do when things go wrong.
We'll focus on a recent dev MC_25km_jra_iaf-1.0-beta-5165c0f8 OM3 experiment (/g/data/ol01/outputs/access-om3-25km/MC_25km_jra_iaf-1.0-beta-5165c0f8/).
Note
Providence of this run includes:
- Model build;
- Base configuration;
- Experiment (includes the Payu run log -- has a commit for each time the model cycled / had run time changes).
Further details about these simulations is available here.
Looking at the OM3 simulation folder /home/156/aek156/payu/MC_25km_jra_iaf we have:
[gadi-login-06: MC_25km_jra_iaf-1.0-beta-5165c0f8]$ ls /home/156/aek156/payu/MC_25km_jra_iaf
025km_jra_iaf_c.e156953262 025km_jra_iaf.o156963110 025km_jra_iaf_s.o157005692 input.nml postscript.sh.o156573831 postscript.sh.o156808786
025km_jra_iaf_c.e156963108 025km_jra_iaf.o156976044 025km_jra_iaf_s.o157015747 LICENSE postscript.sh.o156580484 postscript.sh.o156819850
025km_jra_iaf_c.e156976043 025km_jra_iaf.o156985131 025km_jra_iaf_s.o157180052 manifests postscript.sh.o156591178 postscript.sh.o156837563
025km_jra_iaf_c.e156985130 025km_jra_iaf.o156993836 025km_jra_iaf_s.o157180396 metadata.yaml postscript.sh.o156606425 postscript.sh.o156849829
025km_jra_iaf_c.e156993833 025km_jra_iaf.o157001496 025km_jra_iaf_s.o157180528 MOM_input postscript.sh.o156623297 postscript.sh.o156854528
025km_jra_iaf_c.e157001495 025km_jra_iaf.o157011761 025km_jra_iaf_s.o157185544 MOM_override postscript.sh.o156629387 postscript.sh.o156859814
025km_jra_iaf_c.e157011759 025km_jra_iaf_s.e156956754 025km_jra_iaf_s.o157186682 nuopc.runconfig postscript.sh.o156679792 postscript.sh.o156872003
025km_jra_iaf_c.o156953262 025km_jra_iaf_s.e156966829 025km_jra_iaf_s.o157186970 nuopc.runseq postscript.sh.o156683733 postscript.sh.o156886215
025km_jra_iaf_c.o156963108 025km_jra_iaf_s.e156979618 access-om3.err postscript.sh.o156435401 postscript.sh.o156688095 postscript.sh.o156915954
025km_jra_iaf_c.o156976043 025km_jra_iaf_s.e156988551 access-om3.out postscript.sh.o156456265 postscript.sh.o156696134 postscript.sh.o156931182
025km_jra_iaf_c.o156985130 025km_jra_iaf_s.e156998369 archive postscript.sh.o156463585 postscript.sh.o156703797 postscript.sh.o156956753
025km_jra_iaf_c.o156993833 025km_jra_iaf_s.e157005692 CITATION.cff postscript.sh.o156464418 postscript.sh.o156707261 postscript.sh.o156966827
025km_jra_iaf_c.o157001495 025km_jra_iaf_s.e157015747 config.yaml postscript.sh.o156464466 postscript.sh.o156712962 postscript.sh.o156979617
025km_jra_iaf_c.o157011759 025km_jra_iaf_s.e157180052 datm_in postscript.sh.o156464644 postscript.sh.o156717541 postscript.sh.o156988549
025km_jra_iaf.e156942635 025km_jra_iaf_s.e157180396 datm.streams.xml postscript.sh.o156473862 postscript.sh.o156722375 postscript.sh.o156998368
025km_jra_iaf.e156953263 025km_jra_iaf_s.e157180528 diagnostic_profiles postscript.sh.o156482340 postscript.sh.o156726486 postscript.sh.o157005691
025km_jra_iaf.e156963110 025km_jra_iaf_s.e157185544 diag_table postscript.sh.o156487555 postscript.sh.o156728454 postscript.sh.o157015746
025km_jra_iaf.e156976044 025km_jra_iaf_s.e157186682 docs postscript.sh.o156490910 postscript.sh.o156729873 postscript_synced.sh
025km_jra_iaf.e156985131 025km_jra_iaf_s.e157186970 drof_in postscript.sh.o156493354 postscript.sh.o156734274 postscript_synced.sh.o157623147
025km_jra_iaf.e156993836 025km_jra_iaf_s.o156956754 drof.streams.xml postscript.sh.o156496972 postscript.sh.o156742602 postscript_synced.sh.o157623806
025km_jra_iaf.e157001496 025km_jra_iaf_s.o156966829 drv_in postscript.sh.o156511423 postscript.sh.o156748735 postscript_synced.sh.o157626155
025km_jra_iaf.e157011761 025km_jra_iaf_s.o156979618 env.yaml postscript.sh.o156530694 postscript.sh.o156752864 README.md
025km_jra_iaf.o156942635 025km_jra_iaf_s.o156988551 fd.yaml postscript.sh.o156547767 postscript.sh.o156755583 testing
025km_jra_iaf.o156953263 025km_jra_iaf_s.o156998369 ice_in postscript.sh.o156564391 postscript.sh.o156782543 work
Key files (incomplete, edited for length):
config.yamlfile that defines the experiment options;025km_jra_iaf.o*standard output for each model cycle;025km_jra_iaf.e*standard output errors;postscript.sh.o*standard output for postprocessing script;access-om3.outom3 specific errors;access-om3.errom3 specific output;manifestspayu keeping track ofexe.yaml,input.yaml,restart.yaml;docs(available_diags.000000,MOM_parameter_doc.all,MOM_parameter_doc.debugging,MOM_parameter_doc.layout,MOM_parameter_doc.short);diag_table(symlinkdiag_table->diagnostic_profiles/diag_table_standard);archivewhere all the output goes once each experiment cycle is complete (symlinkarchive->/scratch/x77/aek156/access-om3/archive/MC_25km_jra_iaf-1.0-beta-5165c0f8);worktemporary working space for the model (where to look when it crashes -- symlinkwork->/scratch/x77/aek156/access-om3/work/MC_25km_jra_iaf-1.0-beta-5165c0f8);- model configuration files:
input.nml,metadata.yaml,MOM_input,MOM_override,nuopc.runconfig,nuopc.runseq,datm_in,datm.streams.xml,drof_in,drof.streams.xml,drv_in,env.yaml,fd.yaml,ice_in.
Looking at the archive output (/g/data/ol01/outputs/access-om3-25km/MC_25km_jra_iaf-1.0-beta-5165c0f8/) we have:
[gadi-login-04: MC_25km_jra_iaf-1.0-beta-5165c0f8]$ ls
datastore.csv git-runlog output009 output020 output031 output042 output053 restart006 restart017 restart028 restart039 restart050
datastore_invalid_assets_2025-12-11-14:49:23.csv metadata.yaml output010 output021 output032 output043 output054 restart007 restart018 restart029 restart040 restart051
datastore_invalid_assets_2025-12-12-10:15:36.csv output000 output011 output022 output033 output044 output055 restart008 restart019 restart030 restart041 restart052
datastore_invalid_assets_2025-12-15-14:14:40.csv output001 output012 output023 output034 output045 output056 restart009 restart020 restart031 restart042 restart053
datastore_invalid_assets_2025-12-16-05:19:19.csv output002 output013 output024 output035 output046 pbs_logs restart010 restart021 restart032 restart043 restart054
datastore_invalid_assets_2025-12-17-13:33:13.csv output003 output014 output025 output036 output047 restart000 restart011 restart022 restart033 restart044 restart055
datastore_invalid_assets_2025-12-18-11:17:27.csv output004 output015 output026 output037 output048 restart001 restart012 restart023 restart034 restart045 restart056
datastore_invalid_assets_2025-12-19-08:47:53.csv output005 output016 output027 output038 output049 restart002 restart013 restart024 restart035 restart046
datastore_invalid_assets_2026-01-08-14:43:25.csv output006 output017 output028 output039 output050 restart003 restart014 restart025 restart036 restart047
datastore.json output007 output018 output029 output040 output051 restart004 restart015 restart026 restart037 restart048
error_logs output008 output019 output030 output041 output052 restart005 restart016 restart027 restart038 restart049
Note:
- This is where the output is "archived" to;
- each
output0*is a cycle of output (yearly); - each
restart0*contains restart files; - file
datastore.jsonis an ESMdatastore.
Looking at output030, we have (trimmed for readability):
[gadi-login-06: output030]$ ls -1
access-om3.cice.1day.mean.1988-01.nc
access-om3.cice.1day.mean.1988-02.nc
access-om3.cice.1day.mean.1988-03.nc
access-om3.cice.static.nc
access-om3.err
access-om3.mom6.2d.tob.1day.mean.1988.nc
access-om3.mom6.2d.tos.1day.mean.1988.nc
access-om3.mom6.2d.tos.1mon.max.1988.nc
access-om3.mom6.2d.tos.1mon.min.1988.nc
access-om3.mom6.2d.umo_2d.1mon.mean.1988.nc
access-om3.mom6.2d.vmo_2d.1mon.mean.1988.nc
access-om3.mom6.2d.wfo.1mon.mean.1988.nc
access-om3.mom6.2d.zos.1mon.max.1988.nc
access-om3.mom6.2d.zos.1mon.mean.1988.nc
access-om3.mom6.2d.zos.1mon.min.1988.nc
access-om3.mom6.2d.zossq.1mon.mean.1988.nc
access-om3.mom6.3d.agessc.z.1mon.mean.1988.nc
access-om3.mom6.3d.diftrblo.1mon.mean.1988.nc
access-om3.mom6.3d.diftrelo.1mon.mean.1988.nc
access-om3.mom6.3d.e.1mon.mean.1988.nc
access-om3.mom6.3d.e.rho2.1mon.mean.1988.nc
access-om3.mom6.3d.GM_sfn_y.rho2.1mon.mean.1988.nc
access-om3.mom6.3d.uhGM.rho2.1mon.mean.1988.nc
access-om3.mom6.3d.umo.rho2.1mon.mean.1988.nc
access-om3.mom6.3d.uo.z.1mon.mean.1988.nc
access-om3.mom6.3d.vhGM.rho2.1mon.mean.1988.nc
access-om3.mom6.3d.vmo.rho2.1mon.mean.1988.nc
access-om3.mom6.3d.vo.z.1mon.mean.1988.nc
access-om3.mom6.geometry.nc
access-om3.mom6.scalar.1day.snap.1988.nc
access-om3.mom6.static.nc
access-om3.out
available_diags.000000
config.yaml
datm_in
datm.streams.xml
diag_table
drof_in
drof.streams.xml
drv_in
env.yaml
fd.yaml
ice_in
input.nml
log
logfile.000000.out
manifests
MOM_IC_1.nc
MOM_IC_2.nc
MOM_IC_3.nc
MOM_IC.nc
MOM_input
MOM_override
MOM_parameter_doc.all
MOM_parameter_doc.debugging
MOM_parameter_doc.layout
MOM_parameter_doc.short
nuopc.runconfig
nuopc.runseq
ocean.stats
ocean.stats.nc
Vertical_coordinate.nc
warnfile.000000.out
We'll focus on interpreting the diagnostic output.
Taking access-om3.mom6.3d.uo.z.1mon.mean.1988.nc as an example, this file consists of monthly time-mean zonal velocities for 1988. Looking at the structure of the file (edited for clarity):
[cyb561.gadi-login-06: output030]$ ncdump -c access-om3.mom6.3d.uo.z.1mon.mean.1988.nc | head -n100
netcdf access-om3.mom6.3d.uo.z.1mon.mean.1988 {
dimensions:
xq = 1441 ;
yh = 1152 ;
z_l = 75 ;
z_i = 76 ;
time = UNLIMITED ; // (12 currently)
nv = 2 ;
variables:
float uo(time, z_l, yh, xq) ;
uo:_FillValue = 1.e+20f ;
uo:missing_value = 1.e+20f ;
uo:units = "m s-1" ;
uo:long_name = "Sea Water X Velocity" ;
uo:cell_methods = "z_l:mean yh:mean xq:point time: mean" ;
uo:time_avg_info = "average_T1,average_T2,average_DT" ;
uo:standard_name = "sea_water_x_velocity" ;
uo:interp_method = "none" ;
double xq(xq) ;
xq:units = "degrees_east" ;
xq:long_name = "q point nominal longitude" ;
xq:axis = "X" ;
double yh(yh) ;
yh:units = "degrees_north" ;
yh:long_name = "h point nominal latitude" ;
yh:axis = "Y" ;
double z_l(z_l) ;
z_l:units = "meters" ;
z_l:long_name = "Depth at cell center" ;
z_l:axis = "Z" ;
z_l:positive = "down" ;
z_l:edges = "z_i" ;
double time(time) ;
time:units = "days since 1900-01-01 00:00:00" ;
time:long_name = "time" ;
time:axis = "T" ;
time:calendar_type = "GREGORIAN" ;
time:calendar = "gregorian" ;
time:bounds = "time_bnds" ;
We need to understand how MOM6's grid is defined.
Here are two different ways to visualise the C-grid that is used by MOM6.
- The first way shows both the horizontal and vertical staggering. Note that the tracers, velocities and vorticity points are horizontally and vertically staggered:
Image from the pycomodo project.
- The second grid visualisation, focuses on the horizontal, and uses the the notation that is used in the MOM6 documentation:
Image from the MOM6 RTD.
We can find complete information about the MOM6 grid in this file access-om3.mom6.static.nc. This is very important when you want to do offline model diagnostics accurately (e.g. fluxes across sections, calculate gradients, integrals etc).
The file has a lot of useful information, so we'll look at it in chunks.
[gadi-login-06: output030]$ ncdump -c access-om3.mom6.static.nc | head -n220
netcdf access-om3.mom6.static {
dimensions:
xh = 1440 ;
yh = 1152 ;
time = UNLIMITED ; // (1 currently)
xq = 1441 ;
yq = 1153 ;
variables:
double xh(xh) ;
xh:units = "degrees_east" ;
xh:long_name = "h point nominal longitude" ;
xh:axis = "X" ;
double yh(yh) ;
yh:units = "degrees_north" ;
yh:long_name = "h point nominal latitude" ;
yh:axis = "Y" ;
double xq(xq) ;
xq:units = "degrees_east" ;
xq:long_name = "q point nominal longitude" ;
xq:axis = "X" ;
double yq(yq) ;
yq:units = "degrees_north" ;
yq:long_name = "q point nominal latitude" ;
yq:axis = "Y" ;
Think of the above as "indices" for the Tracer and velocity points. Once, we have these we can then define latitude (geolat_*) and longitude (geolon_*) anywhere on the C-grid...
double geolat_c(yq, xq) ;
geolat_c:_FillValue = 1.e+20 ;
geolat_c:missing_value = 1.e+20 ;
geolat_c:units = "degrees_north" ;
geolat_c:long_name = "Latitude of corner (Bu) points" ;
geolat_c:cell_methods = "time: point" ;
geolat_c:interp_method = "none" ;
double geolat(yh, xh) ;
geolat:_FillValue = 1.e+20 ;
geolat:missing_value = 1.e+20 ;
geolat:units = "degrees_north" ;
geolat:long_name = "Latitude of tracer (T) points" ;
geolat:cell_methods = "time: point" ;
double geolat_u(yh, xq) ;
geolat_u:_FillValue = 1.e+20 ;
geolat_u:missing_value = 1.e+20 ;
geolat_u:units = "degrees_north" ;
geolat_u:long_name = "Latitude of zonal velocity (Cu) points" ;
geolat_u:cell_methods = "time: point" ;
geolat_u:interp_method = "none" ;
double geolat_v(yq, xh) ;
geolat_v:_FillValue = 1.e+20 ;
geolat_v:missing_value = 1.e+20 ;
geolat_v:units = "degrees_north" ;
geolat_v:long_name = "Latitude of meridional velocity (Cv) points" ;
geolat_v:cell_methods = "time: point" ;
geolat_v:interp_method = "none" ;
double geolon_c(yq, xq) ;
geolon_c:_FillValue = 1.e+20 ;
geolon_c:missing_value = 1.e+20 ;
geolon_c:units = "degrees_east" ;
geolon_c:long_name = "Longitude of corner (Bu) points" ;
geolon_c:cell_methods = "time: point" ;
geolon_c:interp_method = "none" ;
double geolon(yh, xh) ;
geolon:_FillValue = 1.e+20 ;
geolon:missing_value = 1.e+20 ;
geolon:units = "degrees_east" ;
geolon:long_name = "Longitude of tracer (T) points" ;
geolon:cell_methods = "time: point" ;
double geolon_u(yh, xq) ;
geolon_u:_FillValue = 1.e+20 ;
geolon_u:missing_value = 1.e+20 ;
geolon_u:units = "degrees_east" ;
geolon_u:long_name = "Longitude of zonal velocity (Cu) points" ;
geolon_u:cell_methods = "time: point" ;
geolon_u:interp_method = "none" ;
double geolon_v(yq, xh) ;
geolon_v:_FillValue = 1.e+20 ;
geolon_v:missing_value = 1.e+20 ;
geolon_v:units = "degrees_east" ;
geolon_v:long_name = "Longitude of meridional velocity (Cv) points" ;
geolon_v:cell_methods = "time: point" ;
geolon_v:interp_method = "none" ;
The areacello variables (e.g. calculating fluxes through a face):
double areacello(yh, xh) ;
areacello:_FillValue = 1.e+20 ;
areacello:missing_value = 1.e+20 ;
areacello:units = "m2" ;
areacello:long_name = "Ocean Grid-Cell Area" ;
areacello:cell_methods = "area:sum yh:sum xh:sum time: point" ;
areacello:standard_name = "cell_area" ;
double areacello_cu(yh, xq) ;
areacello_cu:_FillValue = 1.e+20 ;
areacello_cu:missing_value = 1.e+20 ;
areacello_cu:units = "m2" ;
areacello_cu:long_name = "Ocean Grid-Cell Area" ;
areacello_cu:cell_methods = "area:sum yh:sum xq:sum time: point" ;
areacello_cu:standard_name = "cell_area" ;
double areacello_cv(yq, xh) ;
areacello_cv:_FillValue = 1.e+20 ;
areacello_cv:missing_value = 1.e+20 ;
areacello_cv:units = "m2" ;
areacello_cv:long_name = "Ocean Grid-Cell Area" ;
areacello_cv:cell_methods = "area:sum yq:sum xh:sum time: point" ;
areacello_cv:standard_name = "cell_area" ;
double areacello_bu(yq, xq) ;
areacello_bu:_FillValue = 1.e+20 ;
areacello_bu:missing_value = 1.e+20 ;
areacello_bu:units = "m2" ;
areacello_bu:long_name = "Ocean Grid-Cell Area" ;
areacello_bu:cell_methods = "area:sum yq:sum xq:sum time: point" ;
areacello_bu:standard_name = "cell_area" ;
The dx* and dy* variables (e.g. calculating fluxes through a section, calculating gradients, integrals etc):
double dxt(yh, xh) ;
dxt:_FillValue = 1.e+20 ;
dxt:missing_value = 1.e+20 ;
dxt:units = "m" ;
dxt:long_name = "Delta(x) at thickness/tracer points (meter)" ;
dxt:cell_methods = "time: point" ;
dxt:interp_method = "none" ;
double dyt(yh, xh) ;
dyt:_FillValue = 1.e+20 ;
dyt:missing_value = 1.e+20 ;
dyt:units = "m" ;
dyt:long_name = "Delta(y) at thickness/tracer points (meter)" ;
dyt:cell_methods = "time: point" ;
dyt:interp_method = "none" ;
double dxCu(yh, xq) ;
dxCu:_FillValue = 1.e+20 ;
dxCu:missing_value = 1.e+20 ;
dxCu:units = "m" ;
dxCu:long_name = "Delta(x) at u points (meter)" ;
dxCu:cell_methods = "time: point" ;
dxCu:interp_method = "none" ;
double dyCu(yh, xq) ;
dyCu:_FillValue = 1.e+20 ;
dyCu:missing_value = 1.e+20 ;
dyCu:units = "m" ;
dyCu:long_name = "Delta(y) at u points (meter)" ;
dyCu:cell_methods = "time: point" ;
dyCu:interp_method = "none" ;
double dxCv(yq, xh) ;
dxCv:_FillValue = 1.e+20 ;
dxCv:missing_value = 1.e+20 ;
dxCv:units = "m" ;
dxCv:long_name = "Delta(x) at v points (meter)" ;
dxCv:cell_methods = "time: point" ;
dxCv:interp_method = "none" ;
double dyCv(yq, xh) ;
dyCv:_FillValue = 1.e+20 ;
dyCv:missing_value = 1.e+20 ;
dyCv:units = "m" ;
dyCv:long_name = "Delta(y) at v points (meter)" ;
dyCv:cell_methods = "time: point" ;
dyCv:interp_method = "none" ;
double dyCuo(yh, xq) ;
dyCuo:_FillValue = 1.e+20 ;
dyCuo:missing_value = 1.e+20 ;
dyCuo:units = "m" ;
dyCuo:long_name = "Open meridional grid spacing at u points (meter)" ;
dyCuo:cell_methods = "time: point" ;
dyCuo:interp_method = "none" ;
double dxCvo(yq, xh) ;
dxCvo:_FillValue = 1.e+20 ;
dxCvo:missing_value = 1.e+20 ;
dxCvo:units = "m" ;
dxCvo:long_name = "Open zonal grid spacing at v points (meter)" ;
dxCvo:cell_methods = "time: point" ;
dxCvo:interp_method = "none" ;
double deptho(yh, xh) ;
deptho:_FillValue = 1.e+20 ;
deptho:missing_value = 1.e+20 ;
deptho:units = "m" ;
deptho:long_name = "Sea Floor Depth" ;
deptho:cell_methods = "area:mean yh:mean xh:mean time: point" ;
deptho:cell_measures = "area: areacello" ;
deptho:standard_name = "sea_floor_depth_below_geoid" ;
Further information: