Closed JessicaMeixner-NOAA closed 4 years ago
Dom is going to fix this in his PR #191 https://github.com/ufs-community/ufs-weather-model/pull/191 (fv3 PR 164 https://github.com/NOAA-EMC/fv3atm/pull/164). We plan to get it committed today.
On Mon, Aug 31, 2020 at 2:22 PM Jessica Meixner notifications@github.com wrote:
Description
'ccpp/framework' returns fatal: reference is not a tree when updating submodules for ufs-weather-model commit fd5c310 https://github.com/ufs-community/ufs-weather-model/commit/fd5c310f306c001be12877ecd99f0026b38a8923 To Reproduce:
What compilers/machines are you seeing this with? WCOSS-Dell (I assume all) Give explicit steps to reproduce the behavior. git clone https://github.com/ufs-community/ufs-weather-model cd ufs-weather-model git submodule update --init --recursive Output
$ git submodule update --init --recursive Submodule 'FMS' (https://github.com/NOAA-GFDL/FMS) registered for path 'FMS' Submodule 'FV3' (https://github.com/NOAA-EMC/fv3atm) registered for path 'FV3' Submodule 'NEMS' (https://github.com/NOAA-EMC/NEMS) registered for path 'NEMS' Submodule 'WW3' (https://github.com/NOAA-EMC/WW3) registered for path 'WW3' Submodule 'stochastic_physics' (https://github.com/noaa-psd/stochastic_physics) registered for path 'stochastic_physics' Cloning into 'FMS'... remote: Enumerating objects: 15444, done. remote: Total 15444 (delta 0), reused 0 (delta 0), pack-reused 15444 Receiving objects: 100% (15444/15444), 17.56 MiB | 16.04 MiB/s, done. Resolving deltas: 100% (10946/10946), done. Submodule path 'FMS': checked out 'f61416fef691d9ba39a40df1ce72aa574f54c390' Cloning into 'FV3'... remote: Enumerating objects: 11, done. remote: Counting objects: 100% (11/11), done. remote: Compressing objects: 100% (11/11), done. remote: Total 4149 (delta 0), reused 2 (delta 0), pack-reused 4138 Receiving objects: 100% (4149/4149), 7.58 MiB | 10.43 MiB/s, done. Resolving deltas: 100% (2956/2956), done. Submodule path 'FV3': checked out '0b2d3ec4ad172d718abdb05493e9fe6e5e9c272b' Submodule 'atmos_cubed_sphere' (https://github.com/NOAA-EMC/GFDL_atmos_cubed_sphere) registered for path 'atmos_cubed_sphere' Submodule 'ccpp/framework' (https://github.com/NCAR/ccpp-framework) registered for path 'ccpp/framework' Submodule 'ccpp/physics' (https://github.com/NCAR/ccpp-physics) registered for path 'ccpp/physics' Cloning into 'atmos_cubed_sphere'... remote: Enumerating objects: 2784, done. remote: Total 2784 (delta 0), reused 0 (delta 0), pack-reused 2784 Receiving objects: 100% (2784/2784), 2.88 MiB | 572.00 KiB/s, done. Resolving deltas: 100% (1864/1864), done. Submodule path 'FV3/atmos_cubed_sphere': checked out '8b59ebc039dafe1c20ed6dd21cb38ca564852b98' Cloning into 'ccpp/framework'... remote: Enumerating objects: 44, done. remote: Counting objects: 100% (44/44), done. remote: Compressing objects: 100% (33/33), done. remote: Total 5577 (delta 13), reused 27 (delta 11), pack-reused 5533 Receiving objects: 100% (5577/5577), 10.96 MiB | 13.79 MiB/s, done. Resolving deltas: 100% (3834/3834), done. fatal: reference is not a tree: f5d4cd2bf7752ebf1e4ed16dfdfae71dbfabfb76```
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Can not reproduce:
$ git clone https://github.com/ufs-community/ufs-weather-model
Cloning into 'ufs-weather-model'...
remote: Enumerating objects: 99, done.
remote: Counting objects: 100% (99/99), done.
remote: Compressing objects: 100% (94/94), done.
remote: Total 9959 (delta 26), reused 7 (delta 5), pack-reused 9860
Receiving objects: 100% (9959/9959), 54.23 MiB | 22.78 MiB/s, done.
Resolving deltas: 100% (7721/7721), done.
$ cd ufs-weather-model
$ git submodule update --init --recursive
Submodule 'FMS' (https://github.com/NOAA-GFDL/FMS) registered for path 'FMS'
Submodule 'FV3' (https://github.com/NOAA-EMC/fv3atm) registered for path 'FV3'
Submodule 'NEMS' (https://github.com/NOAA-EMC/NEMS) registered for path 'NEMS'
Submodule 'WW3' (https://github.com/NOAA-EMC/WW3) registered for path 'WW3'
Submodule 'stochastic_physics' (https://github.com/noaa-psd/stochastic_physics) registered for path 'stochastic_physics'
Cloning into '/gpfs/dell2/emc/modeling/noscrub/Dusan.Jovic/ufs/develop/ufs-weather-model/FMS'...
Cloning into '/gpfs/dell2/emc/modeling/noscrub/Dusan.Jovic/ufs/develop/ufs-weather-model/FV3'...
Cloning into '/gpfs/dell2/emc/modeling/noscrub/Dusan.Jovic/ufs/develop/ufs-weather-model/NEMS'...
Cloning into '/gpfs/dell2/emc/modeling/noscrub/Dusan.Jovic/ufs/develop/ufs-weather-model/WW3'...
Cloning into '/gpfs/dell2/emc/modeling/noscrub/Dusan.Jovic/ufs/develop/ufs-weather-model/stochastic_physics'...
Submodule path 'FMS': checked out 'f61416fef691d9ba39a40df1ce72aa574f54c390'
Submodule path 'FV3': checked out '0b2d3ec4ad172d718abdb05493e9fe6e5e9c272b'
Submodule 'atmos_cubed_sphere' (https://github.com/NOAA-EMC/GFDL_atmos_cubed_sphere) registered for path 'FV3/atmos_cubed_sphere'
Submodule 'ccpp/framework' (https://github.com/NCAR/ccpp-framework) registered for path 'FV3/ccpp/framework'
Submodule 'ccpp/physics' (https://github.com/NCAR/ccpp-physics) registered for path 'FV3/ccpp/physics'
Cloning into '/gpfs/dell2/emc/modeling/noscrub/Dusan.Jovic/ufs/develop/ufs-weather-model/FV3/atmos_cubed_sphere'...
Cloning into '/gpfs/dell2/emc/modeling/noscrub/Dusan.Jovic/ufs/develop/ufs-weather-model/FV3/ccpp/framework'...
Cloning into '/gpfs/dell2/emc/modeling/noscrub/Dusan.Jovic/ufs/develop/ufs-weather-model/FV3/ccpp/physics'...
Submodule path 'FV3/atmos_cubed_sphere': checked out '8b59ebc039dafe1c20ed6dd21cb38ca564852b98'
remote: Enumerating objects: 5, done.
remote: Counting objects: 100% (5/5), done.
remote: Compressing objects: 100% (2/2), done.
remote: Total 6 (delta 3), reused 5 (delta 3), pack-reused 1
Unpacking objects: 100% (6/6), done.
From https://github.com/NCAR/ccpp-framework
* branch f5d4cd2bf7752ebf1e4ed16dfdfae71dbfabfb76 -> FETCH_HEAD
Submodule path 'FV3/ccpp/framework': checked out 'f5d4cd2bf7752ebf1e4ed16dfdfae71dbfabfb76'
Submodule path 'FV3/ccpp/physics': checked out '4c17ff716a92d8ac0261d6cc2365bbd7a752b74a'
Submodule 'physics/rte-rrtmgp' (https://github.com/RobertPincus/rte-rrtmgp) registered for path 'FV3/ccpp/physics/physics/rte-rrtmgp'
Cloning into '/gpfs/dell2/emc/modeling/noscrub/Dusan.Jovic/ufs/develop/ufs-weather-model/FV3/ccpp/physics/physics/rte-rrtmgp'...
Submodule path 'FV3/ccpp/physics/physics/rte-rrtmgp': checked out '6ee0b62c1ac6204a89a4e922382b611c16dd5fa7'
Submodule path 'NEMS': checked out '5a781b5692d21e9881e53a404343dda753a44b05'
Submodule 'tests/produtil/NCEPLIBS-pyprodutil' (https://github.com/NOAA-EMC/NCEPLIBS-pyprodutil) registered for path 'NEMS/tests/produtil/NCEPLIBS-pyprodutil'
Cloning into '/gpfs/dell2/emc/modeling/noscrub/Dusan.Jovic/ufs/develop/ufs-weather-model/NEMS/tests/produtil/NCEPLIBS-pyprodutil'...
Submodule path 'NEMS/tests/produtil/NCEPLIBS-pyprodutil': checked out 'ca171b95095db4fcd0fc7b01c23d073d90becd99'
Submodule path 'WW3': checked out '19f3126c832b26ae4c5b27bca6c1dcc676755602'
Submodule path 'stochastic_physics': checked out '370d8e6b50aaa52977f992d1574e13b998e2e974'
$ git submodule status --recursive
f61416fef691d9ba39a40df1ce72aa574f54c390 FMS (2019.01.03)
0b2d3ec4ad172d718abdb05493e9fe6e5e9c272b FV3 (heads/develop)
8b59ebc039dafe1c20ed6dd21cb38ca564852b98 FV3/atmos_cubed_sphere (heads/dev/emc)
f5d4cd2bf7752ebf1e4ed16dfdfae71dbfabfb76 FV3/ccpp/framework (ccpp_transition_to_vlab_master_20190705-204-gf5d4cd2)
4c17ff716a92d8ac0261d6cc2365bbd7a752b74a FV3/ccpp/physics (ccpp_transition_to_vlab_master_20190705-746-g4c17ff7)
6ee0b62c1ac6204a89a4e922382b611c16dd5fa7 FV3/ccpp/physics/physics/rte-rrtmgp (1.2.1-15-g6ee0b62)
5a781b5692d21e9881e53a404343dda753a44b05 NEMS (heads/develop)
ca171b95095db4fcd0fc7b01c23d073d90becd99 NEMS/tests/produtil/NCEPLIBS-pyprodutil (heads/develop)
19f3126c832b26ae4c5b27bca6c1dcc676755602 WW3 (6.07.1-36-g19f3126c)
370d8e6b50aaa52977f992d1574e13b998e2e974 stochastic_physics (ufs-v1.0.0-68-g370d8e6)
@DusanJovic-NOAA What version of git are you using? On Dell I was using git version 1.8.3.1 and got the error I showed above (I checked out again to confirm), but on hera I am using git version 2.18.0 and get a similar output to what you show.
Thanks for the info @junwang-noaa, I guess this issue can be closed then.
@JessicaMeixner-NOAA
$ git --version
git version 2.14.3
$ which git
/usrx/local/dev/packages/git/2.14.3/bin/git
The submodule pointer is definitely wrong, it's pointing to some hash in @ClaraDraper-NOAA's fork.
How did it work for me then? Did git fetch 'f5d4cd2bf7752ebf1e4ed16dfdfae71dbfabfb76
' from Clara's fork? I do not see that.
I don't understand this at all either. Look here:
commit f5d4cd2bf7752ebf1e4ed16dfdfae71dbfabfb76 (HEAD)
Merge: 65f8ea1 209f1c9
Author: ClaraDraper-NOAA <Clara.Draper@noaa.gov>
Date: Mon Jul 20 21:44:25 2020 +0000
Merge commit '209f1c92d99b7d4cc63e0d41c652fcfd730bd9fa' into csd-cpf-sfcpert
commit 209f1c92d99b7d4cc63e0d41c652fcfd730bd9fa (origin/master, origin/HEAD, master)
Merge: b14e3e0 d71e0d5
Author: Dom Heinzeller <dom.heinzeller@icloud.com>
Date: Wed Jul 15 13:32:35 2020 -0600
Merge pull request #311 from climbfuji/add_degrees_to_radians_conversion
Add unit conversion from degrees to radians, address isssue #309
this was a recursive checkout on hera. If you go to NCAR ccpp-framework and look at the commits for branch "master", the latest is 209f1c92d99b7d4cc63e0d41c652fcfd730bd9fa. The commit f5d4cd2bf7752ebf1e4ed16dfdfae71dbfabfb76 is from a closed (!) PR that was never merged in Clara's fork, see here: https://github.com/NCAR/ccpp-framework/pull/316/commits.
Maybe, but just maybe, newer git versions are able to grab it, because they can find it in the closed PR history. Sounds odd to me, though.
Jessica, would you please check again if you still have problem on git submodule update? I can't repeat the issue on dell either.
worked with the latest develop branch today.
Description
'ccpp/framework' returns fatal: reference is not a tree when updating submodules for ufs-weather-model commit fd5c310f306c001be12877ecd99f0026b38a8923
To Reproduce:
What compilers/machines are you seeing this with? WCOSS-Dell (I assume all) Give explicit steps to reproduce the behavior. git clone https://github.com/ufs-community/ufs-weather-model cd ufs-weather-model git submodule update --init --recursive
Output