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Change JRA55-do data directory #120

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aidanheerdegen opened this issue Nov 23, 2018 · 18 comments
Closed

Change JRA55-do data directory #120

aidanheerdegen opened this issue Nov 23, 2018 · 18 comments

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@aidanheerdegen
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The JRA55-do atmospheric dataset is currently used to force the ACCESS-OM2 models.

At the moment NCI users access this data in the ua8 directory where CMS (Paola) is downloading and updating the data.

JRA55-do is now an official dataset of input4MIPS, which is part of CMIP6. This means it is available under the qv56 project and centrally managed by NCI.

This is a good thing. It will reduce Paola's workload, be downloaded automatically, and most importantly will be versioned, which was something that we discussed at TWG and definitely wanted.

Anyone who wishes to use this dataset will have to join qv56, which means anyone who wishes to run the ACCESS-OM2 models at NCI will also have to join.

We will need to determine the file paths. The data is here:

/g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-3/

So for example:

$ cd /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-3/
$ ls atmos/3hr/rsds/gn/v20180412/rsds/
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_195801010130-195901010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_195901010130-196001010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_196001010130-196101010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_196101010130-196201010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_196201010130-196301010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_196301010130-196401010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_196401010130-196501010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_196501010130-196601010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_196601010130-196701010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_196701010130-196801010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_196801010130-196901010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_196901010130-197001010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_197001010130-197101010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_197101010130-197201010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_197201010130-197301010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_197301010130-197401010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_197401010130-197501010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_197501010130-197601010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_197601010130-197701010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_197701010130-197801010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_197801010130-197901010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_197901010130-198001010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_198001010130-198101010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_198101010130-198201010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_198201010130-198301010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_198301010130-198401010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_198401010130-198501010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_198501010130-198601010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_198601010130-198701010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_198701010130-198801010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_198801010130-198901010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_198901010130-199001010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_199001010130-199101010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_199101010130-199201010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_199201010130-199301010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_199301010130-199401010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_199401010130-199501010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_199501010130-199601010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_199601010130-199701010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_199701010130-199801010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_199801010130-199901010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_199901010130-200001010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_200001010130-200101010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_200101010130-200201010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_200201010130-200301010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_200301010130-200401010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_200401010130-200501010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_200501010130-200601010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_200601010130-200701010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_200701010130-200801010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_200801010130-200901010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_200901010130-201001010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_201001010130-201101010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_201101010130-201201010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_201201010130-201301010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_201301010130-201401010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_201401010130-201501010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_201501010130-201601010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_201601010130-201701010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_201701010130-201801010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_201801010130-201802020000.nc

This will need to be tested. I'll get around to it, but if someone else wants to put up their hands feel free and feedback to this issue so work is not duplicated.
@aekiss
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aekiss commented Aug 7, 2019

Should this be the JRA55-do path used for the default "vanilla" control directory repos?
That would require all users to join qv56 - are there any restrictions on membership of this group?

Also @nichannah - will YATM require modification to handle these filenames? Or should we just make a lot of symlinks with names in the format we want?

@aidanheerdegen
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aidanheerdegen commented Aug 7, 2019 •
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Should this be the JRA55-do path used for the default "vanilla" control directory repos?

Yes.

That would require all users to join qv56 - are there any restrictions on membership of this group?

Not that I know of.

Also @nichannah - will YATM require modification to handle these filenames? Or should we just make a lot of symlinks with names in the format we want?

I was in the middle of testing this when other things cropped up. As a work-around for supporting the frankly annoying filenames I did as you suggested and made a bunch of links:

$ ls -l /g/data/ua8/JRA55-do/input4MIPs/ | head
total 3452
lrwxrwxrwx  1 aph502 ua8 176 Apr 12 14:41 areacellg.nc -> /g/data1b/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-3/landIce/fx/areacellg/gn/v20180412/areacellg/areacellg_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn.nc
lrwxrwxrwx  1 aph502 ua8 174 Apr 12 14:41 areacello.nc -> /g/data1b/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-3/ocean/fx/areacello/gn/v20180412/areacello/areacello_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn.nc
lrwxrwxrwx  1 aph502 ua8 184 Apr 12 14:41 friver_1958.nc -> /g/data1b/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-3/ocean/day/friver/gn/v20180412/friver/friver_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_19580101-19590101.nc
lrwxrwxrwx  1 aph502 ua8 184 Apr 12 14:41 friver_1959.nc -> /g/data1b/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-3/ocean/day/friver/gn/v20180412/friver/friver_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_19590101-19600101.nc
lrwxrwxrwx  1 aph502 ua8 184 Apr 12 14:41 friver_1960.nc -> /g/data1b/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-3/ocean/day/friver/gn/v20180412/friver/friver_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_19600101-19610101.nc
lrwxrwxrwx  1 aph502 ua8 184 Apr 12 14:41 friver_1961.nc -> /g/data1b/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-3/ocean/day/friver/gn/v20180412/friver/friver_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_19610101-19620101.nc
lrwxrwxrwx  1 aph502 ua8 184 Apr 12 14:41 friver_1962.nc -> /g/data1b/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-3/ocean/day/friver/gn/v20180412/friver/friver_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_19620101-19630101.nc
lrwxrwxrwx  1 aph502 ua8 184 Apr 12 14:41 friver_1963.nc -> /g/data1b/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-3/ocean/day/friver/gn/v20180412/friver/friver_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_19630101-19640101.nc
lrwxrwxrwx  1 aph502 ua8 184 Apr 12 14:41 friver_1964.nc -> /g/data1b/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-3/ocean/day/friver/gn/v20180412/friver/friver_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_19640101-19650101.nc

It ain't pretty but it works. The current status is that it ran ok but did not reproduce results using the current JRA55-do dataset. This is problematic.

@aekiss
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aekiss commented Aug 8, 2019 •
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From Simon's email today it seems we should move to JRA55-do v1.4.0 but I can only find 1.3 in /g/data/qv56/replicas - can anyone suggest somewhere else to look? Or does it need to be downloaded?

@aidanheerdegen
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It will need to be downloaded, but there is a semi-automated process for that. I will consult with Paola.

@aekiss
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aekiss commented Aug 8, 2019

Thanks @aidanheerdegen

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aekiss commented Aug 9, 2019

I've lodged a help ticket at NCI to request download of 1.4.0.

@aekiss aekiss mentioned this issue Aug 12, 2019
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aekiss commented Aug 19, 2019

NCI has downloaded updates to JRA55-do here
/g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/
including 1.3.2 and 1.4.0

@aekiss
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aekiss commented Aug 19, 2019

The naming convention has changed for 1.4.0:

ls /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/ocean/day/tos/gn/v20190429/tos/
...
tos_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gn_20120101-20121231.nc
tos_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gn_20130101-20131231.nc
tos_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gn_20140101-20141231.nc
tos_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gn_20150101-20151231.nc
tos_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gn_20160101-20161231.nc
tos_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gn_20170101-20171231.nc
tos_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gn_20180101-20181231.nc
tos_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gn_20190101-20190105.nc

@aekiss
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aekiss commented Aug 19, 2019

Atmos data is more relevant:

ls /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/atmos/3hr/rsds/gr/v20190429/rsds/
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_195801010130-195812312230.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_195901010130-195912312230.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_196001010130-196012312230.nc
...
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_201801010130-201812312230.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_201901010130-201901052230.nc

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aekiss commented Aug 19, 2019

the time component of the filename is not the same for all files

cd /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/atmos
for d in */*/*/*/*; do ls -1 $d | head -n 1; done
prra_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_195801010130-195812312230.nc
prsn_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_195801010130-195812312230.nc
rlds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_195801010130-195812312230.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_195801010130-195812312230.nc
huss_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_195801010000-195812312100.nc
psl_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_195801010000-195812312100.nc
tas_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_195801010000-195812312100.nc
ts_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_195801010000-195812312100.nc
uas_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_195801010000-195812312100.nc
vas_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_195801010000-195812312100.nc
areacella_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr.nc
sftof_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr.nc

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aekiss commented Aug 19, 2019 •
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for comparison, here's 1.3.0 1.3.1:

cd /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-3/atmos/
for d in */*/*/*/*; do ls -1 $d | head -n 1; done
prra_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_195801010130-195901010000.nc
prsn_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_195801010130-195901010000.nc
rlds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_195801010130-195901010000.nc
rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_195801010130-195901010000.nc
huss_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_195801010000-195812312230.nc
psl_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_195801010000-195812312230.nc
tas_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_195801010000-195812312230.nc
ts_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_195801010000-195812312230.nc
uas_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_195801010000-195812312230.nc
vas_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-3_gn_195801010000-195812312230.nc

@aekiss aekiss mentioned this issue Aug 19, 2019
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aekiss commented Aug 19, 2019

I think it will cover all cases to have a new key year+1. How does this look? COSIMA/libaccessom2#26

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aekiss commented Aug 19, 2019

the month and time part of the filename can be specified in forcing.json which I expect (but haven't checked) will be the same for all files of a given field in a given version of JRA55-do, except perhaps for 2019 which is of course incomplete

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aekiss commented Aug 26, 2019

make_remap_weights.py and make_remap_weights.sh specify /g/data1/ua8/JRA55-do/ so I guess these should also be updated.

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aekiss commented Aug 26, 2019

scratch that thought - they're RYF files

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aekiss commented Dec 10, 2019 •
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I've tested PR COSIMA/libaccessom2#26 with these runs

  1. https://github.com/COSIMA/1deg_jra55_iaf/tree/1deg_jra55_iaf_control - using /g/data/ua8/JRA55-do/v1-3 and latest master https://github.com/COSIMA/libaccessom2/tree/2cc76e2
  2. https://github.com/COSIMA/1deg_jra55_iaf/tree/1deg_jra55_iaf_test_yearp1 - using /g/data/ua8/JRA55-do/v1-3 and the PR additional key year+1 to support input4MIPS -- #25 libaccessom2#26 commit https://github.com/COSIMA/libaccessom2/tree/13315f5
  3. https://github.com/COSIMA/1deg_jra55_iaf/tree/1deg_jra55_iaf_test_yearp1_qv56 - same as test 3 but using /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-3
  4. https://github.com/COSIMA/1deg_jra55_iaf/tree/1deg_jra55_iaf_test_yearp1_qv56_2 - same as test 3 but with forcing path specified via config.yaml
  5. https://github.com/COSIMA/1deg_jra55_iaf/tree/1deg_jra55_iaf_test_yearp1_qv56_2_hybrid - same as test 4 but using /g/data/ua8/JRA55-do/v1-3 for temperature and humidity

using these scripts

Runs 1 and 2 are identical, as expected.
Run 3 and 4 are identical, but differ from 1 and 2.
Run 5 is identical to runs 1 and 2.

@aidanheerdegen also noted above that /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-3 gives different results from /g/data/ua8/JRA55-do/v1-3.

This is because the near-surface temperature and humidity (tas and huss) are slightly different (as confirmed in run 5). Paola says qv56 is a slightly newer version (source_version = "1.3.1" in .nc attributes) than ua8 (version = "v1.3"), which explains it.

I've also confirmed that the month and time part of the filename is identical for all years (except the final incomplete year) in each variable we use in /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-3, so the pattern used in forcing.json won't miss any v1.3 files (I haven't checked this for version 1.4 yet).
I've also checked nothing (except the final incomplete year) is missed for v1.4.0 with forcing.json and config.yaml in https://github.com/COSIMA/1deg_jra55_iaf/tree/1deg_jra55v1p4p0_iaf_test_gadi (check script: https://github.com/aekiss/notebooks/blob/master/check-MRI-JRA55-do-1-4-0.ipynb).

So in summary I'm confident that PR COSIMA/libaccessom2#26 is ready to use.

@aekiss aekiss mentioned this issue Dec 10, 2019
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aekiss commented Dec 10, 2019 •
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Remaining things to do in all IAF JRA55-do 1.3 configs:

  • update all executables in config.yaml to use updated libaccessom2
  • use this forcing.json and the atmosphere inputs in this config.yaml

These have been done in COSIMA/1deg_jra55_iaf@283e0bc but not at the other resolutions.

This was referenced Dec 16, 2019
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aekiss commented Dec 16, 2019

Closing. Both items above have now been done in the gadi-transition branch of all RYF and IAF configs (not including the minimal 0.1 deg configs).

@aekiss aekiss closed this as completed Dec 16, 2019
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