Add build script and move build-related files to sorc dir #49

chan-hoo · 2024-02-13T13:32:08Z

Description

All build-related files and directories are moved to a new directory sorc to meet the NCO implementation standards.
Conda environment is built in the build script.
A build script is added:

cd land-DA_workflow/sorc
./app_build.sh

To load conda environment:

module use modulefiles
module load wflow_hera
conda activate land_da

To run a sample xml file:

cd parm
(modify the xml file as needed : ACCOUNT) 
rocotorun -w land_analysis_test.xml -d land_analysis_test.db

To generate a xml file from the yaml file using uwtools:

cd parm
(modify the yaml file) 
uw rocoto realize --input-file land_analysis.yaml --output-file land_analysis.xml
rocotorun -w land_analysis.xml -d land_analysis.db

Anticipated changes to regression tests:

Is baseline change expected ?

Subcomponents involved:

DA_update
vector2tile
ufs-land-driver
none

Linked PR's and Issues:

Testing (for CM's):

RDHPCS
- Hera
- Orion
- Jet
- Gaea
- Cheyenne
CI
- Completed
PW-Clouds
- AWS
- AZURE
- GCP

…into feature/nco_sorc

chan-hoo · 2024-02-23T14:15:26Z

@christinaholtNOAA, I integrated conda and uwtools into the build script. I copied the part from the build script of the UFS SRW App. I didn't have any errors in building the env, but I got the following error when I ran uw rocoto realize:

(land_da) [Chan-hoo.Jeon@hfe01 parm]$ uw rocoto realize --input-file land_analysis.yaml --output-file land_analysis.xml
[Errno 2] No such file or directory: '/scratch2/NCEPDEV/fv3-cam/Chan-hoo.Jeon/LAND-DA-WORKFLOW/land-DA_workflow/sorc/conda/envs/land_da/lib/python3.11/site-packages/uwtools/resources/rocoto.jsonschema'

When I checked the uwtools repo, I found that some files were not copied to the above path:
https://github.com/ufs-community/uwtools/tree/2.0.1/src/uwtools/resources

Can you let me know how to fix this issue?

jkbk2004 · 2024-02-23T16:09:35Z

@christinaholtNOAA, I integrated conda and uwtools into the build script. I copied the part from the build script of the UFS SRW App. I didn't have any errors in building the env, but I got the following error when I ran uw rocoto realize:
(land_da) [Chan-hoo.Jeon@hfe01 parm]$ uw rocoto realize --input-file land_analysis.yaml --output-file land_analysis.xml
[Errno 2] No such file or directory: '/scratch2/NCEPDEV/fv3-cam/Chan-hoo.Jeon/LAND-DA-WORKFLOW/land-DA_workflow/sorc/conda/envs/land_da/lib/python3.11/site-packages/uwtools/resources/rocoto.jsonschema'
When I checked the uwtools repo, I found that some files were not copied to the above path: https://github.com/ufs-community/uwtools/tree/2.0.1/src/uwtools/resources

Can you let me know how to fix this issue?

@WeirAE FYI: this might be an item to pick with next patch version.

jkbk2004 · 2024-02-25T17:43:24Z

@chan-hoo We need to use the weather model hash https://github.com/ufs-community/land-DA_workflow/blob/develop/CMakeLists.txt#L51.

chan-hoo · 2024-02-25T19:06:21Z

@jkbk2004, updated, but the ufsLand ctest still fails:

+ /apps/oneapi/mpi/2021.5.1/bin/mpiexec -n 1 /scratch2/NCEPDEV/fv3-cam/Chan-hoo.Jeon/ctest_landda/land-DA_workflow/sorc/build/bin/ufsLand.exe
MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found
 No such file or directory
Stopped

It is saying that some input files are missing, but I can't find which one is missing yet.
Any idea?

jkbk2004 · 2024-02-25T19:57:32Z

(base) jongkim@Orion-login-2:/work/noaa/epic/jongkim/land-DA/merge/pr-49-v1/build$ ctest
Test project /work/noaa/epic/jongkim/land-DA/merge/pr-49-v1/build
    Start 1: test_vector2tile
1/7 Test #1: test_vector2tile .................   Passed   10.75 sec
    Start 2: test_create_ens
2/7 Test #2: test_create_ens ..................   Passed   10.08 sec
    Start 3: test_letkfoi_snowda
3/7 Test #3: test_letkfoi_snowda ..............   Passed   63.07 sec
    Start 4: test_apply_jediincr
4/7 Test #4: test_apply_jediincr ..............   Passed    5.44 sec
    Start 5: test_tile2vector
5/7 Test #5: test_tile2vector .................   Passed   15.15 sec
    Start 6: test_land_driver
6/7 Test #6: test_land_driver .................   Passed   11.11 sec
    Start 7: test_ufs_datm_land
7/7 Test #7: test_ufs_datm_land ...............   Passed  585.38 sec

100% tests passed, 0 tests failed out of 7

Total Test time (real) = 701.00 sec

jkbk2004 · 2024-02-25T19:59:31Z

@chan-hoo can you try to build one level up not inside sorc as ./app_build.sh -c=intel --conda=off --build --build-dir=/work/noaa/epic/jongkim/land-DA/merge/pr-49-v1/build ?

chan-hoo · 2024-02-25T20:56:55Z

@jkbk2004, It passed all ctests on Orion:

Test project /work/noaa/epic/chjeon/land_da_workflow/land-DA_workflow/sorc/build
    Start 1: test_vector2tile
1/7 Test #1: test_vector2tile .................   Passed    7.39 sec
    Start 2: test_create_ens
2/7 Test #2: test_create_ens ..................   Passed    9.92 sec
    Start 3: test_letkfoi_snowda
3/7 Test #3: test_letkfoi_snowda ..............   Passed   58.22 sec
    Start 4: test_apply_jediincr
4/7 Test #4: test_apply_jediincr ..............   Passed    5.22 sec
    Start 5: test_tile2vector
5/7 Test #5: test_tile2vector .................   Passed   11.95 sec
    Start 6: test_land_driver
6/7 Test #6: test_land_driver .................   Passed   11.14 sec
    Start 7: test_ufs_datm_land
7/7 Test #7: test_ufs_datm_land ...............   Passed  605.77 sec

100% tests passed, 0 tests failed out of 7

Total Test time (real) = 709.63 sec

I think the input files (/scratch2/NAGAPE/epic/UFS_Land-DA/inputs) are incomplete on Hera.
I'll open a new issue for this soon.
The following PR should be merged first:
ufs-community/land-DA#5

jkbk2004 · 2024-02-25T21:58:15Z

(base) [role.epic@Hera:/scratch1/NCEPDEV/nems/role.epic/testing/landda-2024/pr-49/build]# ctest
Test project /scratch1/NCEPDEV/nems/role.epic/testing/landda-2024/pr-49/build
    Start 1: test_vector2tile
1/7 Test #1: test_vector2tile .................   Passed    4.24 sec
    Start 2: test_create_ens
2/7 Test #2: test_create_ens ..................   Passed    5.66 sec
    Start 3: test_letkfoi_snowda
3/7 Test #3: test_letkfoi_snowda ..............   Passed   25.99 sec
    Start 4: test_apply_jediincr
4/7 Test #4: test_apply_jediincr ..............   Passed    1.84 sec
    Start 5: test_tile2vector
5/7 Test #5: test_tile2vector .................   Passed    1.90 sec
    Start 6: test_land_driver
6/7 Test #6: test_land_driver .................   Passed    7.52 sec
    Start 7: test_ufs_datm_land
7/7 Test #7: test_ufs_datm_land ...............   Passed   56.41 sec

100% tests passed, 0 tests failed out of 7

Total Test time (real) = 103.62 sec

chan-hoo · 2024-02-26T12:51:03Z

@jkbk2004, one test still fails on Hera on my end:

Test project /scratch2/NAGAPE/epic/Chan-hoo.Jeon/landda_ctest/land-DA_workflow/build
    Start 1: test_vector2tile
1/7 Test #1: test_vector2tile .................   Passed    0.98 sec
    Start 2: test_create_ens
2/7 Test #2: test_create_ens ..................   Passed    1.34 sec
    Start 3: test_letkfoi_snowda
3/7 Test #3: test_letkfoi_snowda ..............   Passed    4.98 sec
    Start 4: test_apply_jediincr
4/7 Test #4: test_apply_jediincr ..............   Passed    1.22 sec
    Start 5: test_tile2vector
5/7 Test #5: test_tile2vector .................   Passed    1.47 sec
    Start 6: test_land_driver
6/7 Test #6: test_land_driver .................***Failed    1.09 sec
    Start 7: test_ufs_datm_land
7/7 Test #7: test_ufs_datm_land ...............   Passed   45.88 sec

Since your test was completed successfully, I guess there may be a file permission issue on the input files on Hera.

chan-hoo · 2024-02-26T13:01:49Z

@jkbk2004, I found the following issue:

-rw-r--r-- 1 Rhaesung.Kim epic 7991744 Aug 17  2023 ufs-land_C96_static_fields.nc

Can you run chmod -R +x inputs on /scratch2/NAGAPE/epic/UFS_Land-DA/?

cd /scratch2/NAGAPE/epic/UFS_Land-DA
chmod -R +x inputs

jkbk2004 · 2024-02-26T14:01:33Z

@chan-hoo can you try to use /scratch1/NCEPDEV/nems/role.epic/testing/landda-2024/inputs ?

chan-hoo · 2024-02-26T14:12:59Z

@jkbk2004, the file in the new path doesn't have x permission either:

-rw-r--r-- 1 role.epic epic 7991744 Jan 25 21:04 ufs-land_C96_static_fields.nc

jkbk2004 · 2024-02-26T14:19:35Z

@jkbk2004, the file in the new path doesn't have x permission either:
-rw-r--r-- 1 role.epic epic 7991744 Jan 25 21:04 ufs-land_C96_static_fields.nc

try one more time

chan-hoo · 2024-02-26T14:25:02Z

@jkbk2004, the error was gone, but another error came out:

 workflow/../inputs/forcing/era5/datm/C96//C96_ERA5_forcing_2019-12-21.
 No such file or directory

Please add x to inputs and its sub-directories with -R:

cd /scratch1/NCEPDEV/nems/role.epic/testing/landda-2024/inputs
chmod -R +x inputs

jkbk2004 · 2024-02-26T14:27:43Z

forcing/era5/datm/C96/

Try one more time

chan-hoo · 2024-02-26T14:49:48Z

@jkbk2004, it works now!

Test project /scratch2/NAGAPE/epic/Chan-hoo.Jeon/show_p2/land-DA_workflow/sorc/build
    Start 1: test_vector2tile
1/7 Test #1: test_vector2tile .................   Passed    7.00 sec
    Start 2: test_create_ens
2/7 Test #2: test_create_ens ..................   Passed    4.81 sec
    Start 3: test_letkfoi_snowda
3/7 Test #3: test_letkfoi_snowda ..............   Passed   20.22 sec
    Start 4: test_apply_jediincr
4/7 Test #4: test_apply_jediincr ..............   Passed    1.64 sec
    Start 5: test_tile2vector
5/7 Test #5: test_tile2vector .................   Passed    1.77 sec
    Start 6: test_land_driver
6/7 Test #6: test_land_driver .................   Passed    7.79 sec
    Start 7: test_ufs_datm_land
7/7 Test #7: test_ufs_datm_land ...............   Passed   52.03 sec

100% tests passed, 0 tests failed out of 7

Thank you!

chan-hoo · 2024-02-26T18:24:07Z

@jkbk2004, ctest was completed successfully on Orion:

Test project /work/noaa/epic/chjeon/show_p2/land-DA_workflow/sorc/build
    Start 1: test_vector2tile
1/7 Test #1: test_vector2tile .................   Passed    8.19 sec
    Start 2: test_create_ens
2/7 Test #2: test_create_ens ..................   Passed    8.72 sec
    Start 3: test_letkfoi_snowda
3/7 Test #3: test_letkfoi_snowda ..............   Passed   60.03 sec
    Start 4: test_apply_jediincr
4/7 Test #4: test_apply_jediincr ..............   Passed    4.42 sec
    Start 5: test_tile2vector
5/7 Test #5: test_tile2vector .................   Passed   12.46 sec
    Start 6: test_land_driver
6/7 Test #6: test_land_driver .................   Passed    8.24 sec
    Start 7: test_ufs_datm_land
 7/7 Test #7: test_ufs_datm_land ...............   Passed  438.21 sec

100% tests passed, 0 tests failed out of 7

chan-hoo added 30 commits January 29, 2024 17:48

move build-related dirs/files to sorc

79657e8

update cmakelists for ufs-weather-model

787442e

move test to sorc

350fe8a

remove unnecessary envir

611442f

add detect_platform

0284633

update app build script

4d7f6d3

rename module files

2eac800

fix issues on app_build.sh

e7d00b8

update path in scripts

26a5c8a

cp lib/lib64 to homedir

82eb7ca

change branch of land-DA

e97bcc5

add export execdir to script

a1bb9af

update docs

5508ab2

fix typo

d5a441c

Merge branch 'develop' of https://github.com/chan-hoo/land-DA_workflow …

c5a277c

…into feature/nco_sorc

replace with submodule

16dd597

update gitignore

767b5b6

update submodules

4777437

change hash ufs-weather-model

f82b7e4

change hash of ufs-land-driver-emc-dev

5bab48f

point to feature branch of DA_update

3fb0692

remove extrn from app_build.sh

7508100

update test jenkins

be637fe

rename tile2tile to tile2tile_converter.fd

72b2368

rename submodule to meet NCO standards

0917092

update hash of ufsLand

116aad2

update build script

3e30681

clean up build script

663e80e

remove unnecessary line

607d3e9

update build script

6329976

add conda=only and update uwtools ver

a9f1030

chan-hoo added 3 commits February 23, 2024 14:59

fix typo in rocoto yaml file

4655220

add temporary fix for missing files in uwtools

f714486

fix typo

31af448

chan-hoo added 2 commits February 24, 2024 15:40

fix part of ctest

ab5745b

another fix for ctest

2ce805d

update hash of weather model

fa639e5

chan-hoo added 2 commits February 26, 2024 16:34

update hashes

3dbbd5d

fix hash of weather model

bd9aacf

jkbk2004 approved these changes Feb 26, 2024

View reviewed changes

chan-hoo merged commit 61bff0d into ufs-community:develop Feb 27, 2024
1 check passed

chan-hoo deleted the feature/nco_sorc branch February 28, 2024 15:08

gspetro-NOAA mentioned this pull request Mar 5, 2024

Update documentation with wflow changes from February 2024 PRs #71

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Add build script and move build-related files to sorc dir #49

Add build script and move build-related files to sorc dir #49

chan-hoo commented Feb 13, 2024 •

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Add build script and move build-related files to sorc dir #49

Add build script and move build-related files to sorc dir #49

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chan-hoo commented Feb 13, 2024 • edited Loading

Description

Anticipated changes to regression tests:

Subcomponents involved:

Linked PR's and Issues:

Testing (for CM's):

chan-hoo commented Feb 23, 2024

jkbk2004 commented Feb 23, 2024

jkbk2004 commented Feb 25, 2024

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chan-hoo commented Feb 13, 2024 •

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