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Transfers pipeline improvements #54

Merged
merged 47 commits into from
Apr 25, 2024
Merged

Transfers pipeline improvements #54

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a3f9096
add models
Joshdpaul Mar 27, 2024
cdf0976
allow multiple grid types to be listed in esgf holdings; fix MRI-ESM2…
Joshdpaul Mar 28, 2024
316d26a
handle missing grids / versions / files in ls routines; allows for al…
Joshdpaul Mar 29, 2024
329ea6d
draft notebook to explicitly select grids
Joshdpaul Mar 29, 2024
9ea6a3f
allow comparison of >2 grid types
Joshdpaul Mar 29, 2024
1028c28
remove E3SM-2-0 from the shopping list
Joshdpaul Mar 29, 2024
9c80c32
allow for multiple row returns in get_filenames() and add more descri…
Joshdpaul Apr 1, 2024
4b41a80
add "last resort" empty row
Joshdpaul Apr 2, 2024
f7e8374
add in all models for full test
Joshdpaul Apr 2, 2024
fb7d1b7
commit updated esgf holdings and script output file
Joshdpaul Apr 3, 2024
8b9e8a5
allow for multiple institutions per model
Joshdpaul Apr 4, 2024
b497ab2
refactor to allow institution lists in all instances of config.model_…
Joshdpaul Apr 4, 2024
88b217c
rm set() from row list chain
Joshdpaul Apr 4, 2024
72fa1f1
clean holdings run with no 502s, adds MPI-ESM1-2-LR ScenarioMIP (from…
Joshdpaul Apr 5, 2024
7732f82
rerun nb with new models
Joshdpaul Apr 5, 2024
502cf97
remove CESM2-WACCM from variant list, add doc, rerun nb and add E3SM …
Joshdpaul Apr 5, 2024
9151bf8
add "tee" instructions
Joshdpaul Apr 5, 2024
ade1705
add "E3SM-1-1"
Joshdpaul Apr 5, 2024
e3a0c4b
another clean run with E3SM-1-1 model added
Joshdpaul Apr 6, 2024
8bc0aa4
finish select grids nb, add grid lookup to config
Joshdpaul Apr 6, 2024
0ff5f6b
update manifest; revise generate_manifest.py to allow >1 grid type pe…
Joshdpaul Apr 6, 2024
9ef1833
update batch files with new models / grids
Joshdpaul Apr 6, 2024
1b7f1b8
fix typos
Joshdpaul Apr 11, 2024
5a36f66
rm CESM2-WACCM from lookup table
Joshdpaul Apr 11, 2024
08d5451
Add script for E3SM holdings
kyleredilla Apr 16, 2024
091dc30
format transfer utils script
kyleredilla Apr 17, 2024
63cded3
Improve retry logic of holdings audit script
kyleredilla Apr 18, 2024
3bca51d
add e3sm holdings table
kyleredilla Apr 18, 2024
e6ac736
update main holdings table
kyleredilla Apr 18, 2024
619443a
update holdings summary notebook
kyleredilla Apr 18, 2024
732cb34
add E3SM models to manifest script and update manifest table
kyleredilla Apr 18, 2024
2159645
decouple institution and models lookup in audit scripts
kyleredilla Apr 18, 2024
71fd94e
fix e3sm model list config
kyleredilla Apr 19, 2024
3cdd638
update holdings tables
kyleredilla Apr 19, 2024
be294a9
update holdings summary tables
kyleredilla Apr 22, 2024
d236328
use e3sm prefix in batch file generation, drop node arg
kyleredilla Apr 22, 2024
26386e4
update manifest and batch files with e3sm
kyleredilla Apr 22, 2024
1ec0dc5
skip e3sm in batch file generation
kyleredilla Apr 22, 2024
31f3676
update batch files
kyleredilla Apr 22, 2024
b13570f
update holdings table with SNAP holdings
kyleredilla Apr 23, 2024
bf44e71
add CESM2 back in to config
kyleredilla Apr 24, 2024
17337d6
update grid selection nb
kyleredilla Apr 24, 2024
0ffb099
update manifest and batch files after adding CESM2
kyleredilla Apr 24, 2024
a4e4c9d
update variatn selection notebook after improving holdings audit work…
kyleredilla Apr 24, 2024
297906c
remove unused esgf endpoint
kyleredilla Apr 24, 2024
3d56698
remove unused code in manifest script
kyleredilla Apr 25, 2024
c5f3c2b
change operation_ls back to original
Joshdpaul Apr 25, 2024
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10 changes: 5 additions & 5 deletions transfers/README.md
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Expand Up @@ -81,16 +81,16 @@ Email address to send failed slurm job notifications to.
export [email protected]
```

4. Use the `esgf_holdings.py` to create tables detailing availability of requested data combinations on a particular ESGF node. Requested data combinations used in this script are sourced from `config.py`. This script creates lists of the available filenames for all requested data. To list available data on the LLNL node, run it as a script like so:
4. Use the `esgf_holdings.py` to create tables detailing availability of requested data combinations on a particular ESGF node. Requested data combinations used in this script are sourced from `config.py`. This script creates lists of the available filenames for all requested data. The script will print statements about any empty folders encountered, and any HTTP errors encountered. To save these outputs for review, `tee` the output to a file. To list available data on the LLNL node, run it as a script like so:

```
python esgf_holdings.py --node llnl
python esgf_holdings.py --node llnl --ncpus 24 | tee esgf_holdings_output.txt
```

To do the same for the variables we want at non-standard freqeuncies for future WRF runs, add the `--wrf` flag:

```
python esgf_holdings.py --node llnl --wrf
python esgf_holdings.py --node llnl --wrf --ncpus 24 | tee esgf_holdings_wrf_output.txt
```

These scripts will create `llnl_esgf_holdings.csv` and `llnl_esgf_holdings_wrf.csv`, which have been committed to version control.
Expand All @@ -112,13 +112,13 @@ These scripts will create `llnl_manifest.csv` and `llnl_manifest_wrf.csv`, which
6. Use the `generate_batch_files.py` script to generate batch files from the manifest to run the transfer in batches. Batch files will be saved to the `batch_files/` folder.

```
python generate_batch_files.py --node llnl
python generate_batch_files.py
```

To do the same for the variables we want at non-standard freqeuncies for future WRF runs, add the `--wrf` flag:

```
python generate_batch_files.py --node llnl --wrf
python generate_batch_files.py --wrf
```


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68 changes: 52 additions & 16 deletions transfers/batch_files/batch_llnl_Amon_clt.txt
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39 changes: 39 additions & 0 deletions transfers/batch_files/batch_llnl_Amon_uas.txt
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/css03_data/CMIP6/ScenarioMIP/CNRM-CERFACS/CNRM-CM6-1-HR/ssp245/r1i1p1f2/Amon/uas/gr/v20191202/uas_Amon_CNRM-CM6-1-HR_ssp245_r1i1p1f2_gr_201501-210012.nc /CMIP6/ScenarioMIP/CNRM-CERFACS/CNRM-CM6-1-HR/ssp245/r1i1p1f2/Amon/uas/gr/v20191202/uas_Amon_CNRM-CM6-1-HR_ssp245_r1i1p1f2_gr_201501-210012.nc
/css03_data/CMIP6/ScenarioMIP/CNRM-CERFACS/CNRM-CM6-1-HR/ssp370/r1i1p1f2/Amon/uas/gr/v20200127/uas_Amon_CNRM-CM6-1-HR_ssp370_r1i1p1f2_gr_201501-210012.nc /CMIP6/ScenarioMIP/CNRM-CERFACS/CNRM-CM6-1-HR/ssp370/r1i1p1f2/Amon/uas/gr/v20200127/uas_Amon_CNRM-CM6-1-HR_ssp370_r1i1p1f2_gr_201501-210012.nc
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/css03_data/CMIP6/ScenarioMIP/MIROC/MIROC6/ssp370/r1i1p1f1/Amon/uas/gn/v20190627/uas_Amon_MIROC6_ssp370_r1i1p1f1_gn_201501-210012.nc /CMIP6/ScenarioMIP/MIROC/MIROC6/ssp370/r1i1p1f1/Amon/uas/gn/v20190627/uas_Amon_MIROC6_ssp370_r1i1p1f1_gn_201501-210012.nc
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/css03_data/CMIP6/CMIP/MPI-M/MPI-ESM1-2-HR/historical/r1i1p1f1/Amon/uas/gn/v20190710/uas_Amon_MPI-ESM1-2-HR_historical_r1i1p1f1_gn_185001-185412.nc /CMIP6/CMIP/MPI-M/MPI-ESM1-2-HR/historical/r1i1p1f1/Amon/uas/gn/v20190710/uas_Amon_MPI-ESM1-2-HR_historical_r1i1p1f1_gn_185001-185412.nc
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