Add v1 cryosphere and BGC data #64
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I still need to add the BGC data, but I added the cryo data. @chengzhuzhang @darincomeau -- let me know if anything needs to be changed for the v1 cryosphere data though. Preview results available here.
docs/source/v1/Cryosphere/index.rst
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| * 1850 PI Control | ||
| * 1850 PI control with ice shelf melt fluxes | ||
| * CORE-IAF control | ||
| * CORE-IAF with ice shelf melt fluxes | ||
| * 1850 PI control with ice shelf melt fluxes + 3DGM | ||
| * CORE-IAF with ice shelf melt fluxes + 3DGM | ||
| * 1850 PI control with ice shelf melt fluxes, bug fix run | ||
| * 1850 PI control with ice shelf melt fluxes + 3DGM, bug fix run |
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Should these have any additional explanation? I suppose we could use the full titles of the Confluence pages linked on https://e3sm.atlassian.net/wiki/spaces/ED/pages/4495441922/V1+Simulation+backfill+WIP, like "Low-Res, Pre-Industrial Control Run (60to30km B-cases) - A_WCYCL1850-DIB-ISMF; snowcapping"
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1850 piControl with standard snowcapping, constant GM (200 years)
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1850 piControl with ice shelf melt fluxes, constant GM (200 years)
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1850 piControl with ice shelf melt fluxes, variable GM (200 years)
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Ocean-Ice only (CORE-II atmosphere forced), constant GM, uniform iceberg spreading (100 years)
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Ocean-Ice only (CORE-II atmosphere forced), constant GM, data iceberg spreading (210 years)
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Ocean-Ice only (CORE-II atmosphere forced), variable GM, data iceberg spreading (210 years)
How's this? The wording is closer to how we described these simulations in the papers I listed below.
| Original run scripts are also not available in the `archive <https://github.com/E3SM-Project/e3sm_data_docs/tree/main/run_scripts/v1/original/>`_. A few methods to search for run scripts, in general: :: | ||
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| # Try looking directly | ||
| zstash ls --hpss=/home/projects/e3sm/www/Cryosphere/E3SMv1/<simulation_name>/ case_scripts/run_script_provenance/* | ||
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| # Try looking for provenance or run | ||
| zstash ls --hpss=/home/projects/e3sm/www/Cryosphere/E3SMv1/<simulation_name> > out.txt | ||
| grep -in provenance out.txt | ||
| grep -in run out.txt |
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I couldn't find original run scripts in the archives or on the Confluence pages. Do we have any record of those? I suppose they might not be much use since many of the machines used are out-of-service.
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The run scripts for the v1 Cryo campaign weren't intentionally stored anywhere, but I found a couple on NERSC, and can check on LCRC when it's back up later this week. I'm not sure they would be useful at all, but I can provide what we have if you want them for completeness.
| * *The DOE E3SM Coupled Model Version 1: Overview and Evaluation at Standard Resolution* `doi: 10.1029/2018MS001603 <https://doi.org/10.1029/2018MS001603>`_ | ||
| * *Description of historical and future projection simulations by the global coupled E3SMv1.0 model as used in CMIP6* `doi:10.5194/gmd-15-3941-2022 <https://doi.org/10.5194/gmd-15-3941-2022>`_ | ||
| * *Ensemble Spread Behavior in Coupled Climate Models: Insights From the Energy Exascale Earth System Model Version 1 Large Ensemble* `doi:10.1029/2023MS003653 <https://doi.org/10.1029/2023MS003653>`_ | ||
| * *The DOE E3SM Coupled Model Version 1: Description and Results at High Resolution* `doi:10.1029/2019MS001870 <https://doi.org/10.1029/2019MS001870>`_ |
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Are there any cryo-specific papers we'd want to add?
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- The DOE E3SM v1.2 Cryosphere Configuration: Description and Simulated Antarctic Ice-Shelf Basal Melting: https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2021MS002468
- Ice-shelf freshwater triggers for the Filchner–Ronne Ice Shelf melt tipping point in a global ocean–sea-ice model: https://tc.copernicus.org/articles/18/2917/2024/
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This page would be better reviewed with the preview link
forsyth2
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@chengzhuzhang I've addressed the comments for cryo. I'm working to add BGC. One question I have is how would we like the simulations to be labeled in the table? See comment below.
| ["20191107.BCRC_CNPCTC_SSP585_OIBGC.ne30_oECv3.compy"]="pub_archive_E3SM_1_1_ssp585-BCRC" | ||
| # CTC BCRD | ||
| ["20181217.BCRD_CNPCTC20TR_OIBGC.ne30_oECv3.edison"]="pub_archive_E3SM_1_1_hist-BCRD" | ||
| # These 2 map to the same pub archive: |
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There are 3 instances in https://e3sm.atlassian.net/wiki/spaces/ED/pages/4495441922/V1+Simulation+backfill+WIP where two simulation names map to the same publication archive (this appears to be because the run was split into two different runs to cover different years, perhaps running on different days or different machines).
I assumed we wanted the long-form names like BCRC_CNPECACNT_20TR.ne30_oECv3.edison and BCRC_CNPECACNT_20TR.ne30_oECv3.cori-knl, in which case it appears I'd have to symlink to the original directories rather than the publication archive. (I wanted to symlink to the publication archive because that would be less likely to be deleted than user-owned directories).
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@forsyth2 I'm wondering if it is possible to just use e.x.pub_archive_E3SM_1_1_piControl as simulation name and point directly to the pub archive path. As you mentioned, it is less likely to be removed and we don't need symlink in this case. The mapping between case name and pub_archive name could be explained in the data summary session:https://docs.e3sm.org/e3sm_data_docs/_build/html/v1/WaterCycle/index.html.
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@BunnyVon @chengzhuzhang I added the v1 BGC data. Can you please check if the new docs look good? Probably better to view from the preview link than reviewing the file changes here.
| E3SMv1 (BGC) | ||
| ==================== | ||
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| The `E3SM version 1 BGC simulation campaign <https://e3sm.org/research/bgc-and-energy/v1-bgc-and-energy/>`_ includes standard set of | ||
| Coupled Model Intercomparison Project Phase 6 (`CMIP6 <https://www.geosci-model-dev.net/9/1937/2016/>`_) | ||
| Diagnosis, Evaluation, and Characterization of Klima (DECK) simulations. | ||
| These E3SM simulations at standard resolution have been completed and the data is publicly available. | ||
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| Data Resolution: | ||
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| The standard resolution configuration of E3SM v1.0 BGC configuration has approximate horizontal resolution of | ||
| 1 deg latitude by 1 deg longitude in atmosphere (110 km grid spacing), | ||
| with ocean and sea ice grid of 60 km in the mid-latitudes and 30 km at the equator and poles, | ||
| and river transport at 55 km horizontal resolution. | ||
| This model configuration is described in | ||
| `“v1 1 deg CMIP” <https://e3sm.org/model/scientifically-validated-configurations/v1-configurations/v1-1-deg-cmip6/>`_ page | ||
| in `Scientifically Validated Configurations <https://e3sm.org/model/scientifically-validated-configurations/>`_. |
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Let me know if anything should be changed here.
docs/source/v1/BGC/index.rst
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| * *Description of historical and future projection simulations by the global coupled E3SMv1.0 model as used in CMIP6* `doi:10.5194/gmd-15-3941-2022 <https://doi.org/10.5194/gmd-15-3941-2022>`_ | ||
| * *Ensemble Spread Behavior in Coupled Climate Models: Insights From the Energy Exascale Earth System Model Version 1 Large Ensemble* `doi:10.1029/2023MS003653 <https://doi.org/10.1029/2023MS003653>`_ | ||
| * *The DOE E3SM Coupled Model Version 1: Description and Results at High Resolution* `doi:10.1029/2019MS001870 <https://doi.org/10.1029/2019MS001870>`_ | ||
| * (TODO: add BGC-specific papers) |
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Are there any BGC-specific papers to add?
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Please add this BGC-specific paper:https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2019ms001766
docs/source/v1/BGC/index.rst
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| Experiments: | ||
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| The datasets include the following experiments. Each case has a historical run and a ssp85 run. | ||
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| (TODO: add description to the top-level bullet points below) |
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Can you provide descriptions for each of the cases below?
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Description can be found in the BGC specific reference paper:https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2019ms001766
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| zstash extract --hpss=/home/projects/e3sm/www/BGC/E3SMv1/E3SM_1_1_piControl "*.cam.h0.00[3-4]?-??.nc" | ||
| # (TODO: run an actual zstash command to make sure it works as an example) |
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I will find an example zstash command to put here that works on this particular data set.
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This file would be best reviewed by going to https://portal.nersc.gov/cfs/e3sm/forsyth/data_docs_64_try5/html/v1/BGC/simulation_data/simulation_table.html
@forsyth2 , BGCv1.1 production run was organized by @susburrows. She might be a better candidate for reviewing these files. |
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@forsyth2 The PR looks good. Some of the BGC files are cmorized and published to ESGF CMIP6 project, the ESGF column in utils/input/simulations_v1_bgc.csv and the code to generate ESGF links need to updated. I think you could address the comments and merge, I will need another PR to address removed and changed ESGF links, and can cover for v1 ESGF link in the new PR. |
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Sounds good, thanks. I also see there are now merge conflicts, which appear to be from the merging of #67. I will take care of those as well, and then merge this PR. Will try to work on that during Unified test runs this week. |
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@chengzhuzhang I've addressed your comments in the latest 2 commits. Preview pages:
One thing to note is that the new HPSS URLs seem to just download empty files, as compared to the working v3 links you introduced in #67. I'm not sure if I've set up something wrong of the HPSS URL should just be suppressed for this data.
Once I have next steps for the HPSS URL, I can go ahead and merge.
| header_cells, | ||
| f"../docs/source/{model_version}/{group_name}/simulation_data/simulation_table.rst", | ||
| [65, 15, 220, 120, 140] | ||
| [85, 15, 400, 140, 170] |
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Minor note: I noticed these numbers were reduced in #67:
[85, 15, 400, 140] => [65, 15, 220, 120, 140]. Typically, I only increase these numbers to fit longer simulation names, but it's not a huge deal since the script is run more-or-less independently per new data addition. In the future though, it would have been good for me to review PRs like #67. It appears my notification level for e3sm_data_docs was limited to only mentions. I've changed it to all activity now.
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I have to increase these numbers to fit the long urls...Sounds good, I will also tag you for future PRs.
I think it is a permission issue, if you could change group to e3sm, and also make chrmod 755 for the directories, that should work. |
@chengzhuzhang I'm not sure I have full control over the permissions. I can # Trying on a single directory:
# Try with the `@` that marks it as a symlink
chmod -R 755 20190225.GMPAS-DIB-IAF-ISMF.T62_oEC60to30v3wLI.cori-knl@
# *** hpss_FileSetAttributes: Invalid argument [-22: HPSS_EINVAL]
# /home/projects/e3sm/www/Cryosphere/E3SMv1/20190225.GMPAS-DIB-IAF-ISMF.T62_oEC60to30v3wLI.cori-knl@
# *** hpss_Chmod error -1 for `/home/projects/e3sm/www/Cryosphere/E3SMv1/20190225.GMPAS-DIB-IAF-ISMF.T62_oEC60to30v3wLI.cori-knl@'
# Try without
chmod -R 755 20190225.GMPAS-DIB-IAF-ISMF.T62_oEC60to30v3wLI.cori-knl
# *** hpss_FileSetAttributes: Permission denied [-1: HPSS_EPERM]
# /home/projects/e3sm/www/Cryosphere/E3SMv1/20190225.GMPAS-DIB-IAF-ISMF.T62_oEC60to30v3wLI.cori-knl
# *** hpss_Chmod error -1 for `/home/projects/e3sm/www/Cryosphere/E3SMv1/20190225.GMPAS-DIB-IAF-ISMF.T62_oEC60to30v3wLI.cori-knl'
# Try the other operation
chgrp e3sm 20190225.GMPAS-DIB-IAF-ISMF.T62_oEC60to30v3wLI.cori-knl@
# *** hpss_Chown: Invalid argument [-22: HPSS_EINVAL]
# /home/projects/e3sm/www/Cryosphere/E3SMv1/20190225.GMPAS-DIB-IAF-ISMF.T62_oEC60to30v3wLI.cori-knl@
chgrp e3sm 20190225.GMPAS-DIB-IAF-ISMF.T62_oEC60to30v3wLI.cori-knl
# *** hpss_Chown: Permission denied [-1: HPSS_EPERM]
# /home/projects/e3sm/www/Cryosphere/E3SMv1/20190225.GMPAS-DIB-IAF-ISMF.T62_oEC60to30v3wLI.cori-knl |
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Probably the permission needs to reset at this level /home/projects/e3sm/www/BGC/E3SMv1 ? |
hsi
A:/home/f/forsyth-> cd /home/projects/e3sm/www/BGC/E3SMv1
A:/home.../www/BGC/E3SMv1-> chmod -R 755 /home/projects/e3sm/www/BGC/E3SMv1
*** hpss_FileSetAttributes: Permission denied [-1: HPSS_EPERM]
/home/projects/e3sm/www/BGC/E3SMv1/E3SM_1_1_ECA_hist-BDRC
*** chmod: hpss_Chmod error -1 for `/home/projects/e3sm/www/BGC/E3SMv1/E3SM_1_1_ECA_hist-BDRC'
*** hpss_FileSetAttributes: Permission denied [-1: HPSS_EPERM]
/home/projects/e3sm/www/BGC/E3SMv1/E3SM_1_1_ECA_ssp585-BCRC
*** chmod: hpss_Chmod error -1 for `/home/projects/e3sm/www/BGC/E3SMv1/E3SM_1_1_ECA_ssp585-BCRC'
*** hpss_FileSetAttributes: Permission denied [-1: HPSS_EPERM]
/home/projects/e3sm/www/BGC/E3SMv1/E3SM_1_1_ssp585-BDRD
*** chmod: hpss_Chmod error -1 for `/home/projects/e3sm/www/BGC/E3SMv1/E3SM_1_1_ssp585-BDRD'
*** hpss_FileSetAttributes: Permission denied [-1: HPSS_EPERM]
/home/projects/e3sm/www/BGC/E3SMv1/E3SM_1_1_ECA_piControl-ext85yr
*** chmod: hpss_Chmod error -1 for `/home/projects/e3sm/www/BGC/E3SMv1/E3SM_1_1_ECA_piControl-ext85yr'
*** hpss_FileSetAttributes: Permission denied [-1: HPSS_EPERM]
/home/projects/e3sm/www/BGC/E3SMv1/E3SM_1_1_hist-BDRC
*** chmod: hpss_Chmod error -1 for `/home/projects/e3sm/www/BGC/E3SMv1/E3SM_1_1_hist-BDRC'
*** hpss_FileSetAttributes: Permission denied [-1: HPSS_EPERM]
/home/projects/e3sm/www/BGC/E3SMv1/E3SM_1_1_ssp585-BDRC
*** chmod: hpss_Chmod error -1 for `/home/projects/e3sm/www/BGC/E3SMv1/E3SM_1_1_ssp585-BDRC'
*** hpss_FileSetAttributes: Permission denied [-1: HPSS_EPERM]
/home/projects/e3sm/www/BGC/E3SMv1/E3SM_1_1_ECA_hist-BDRD
*** chmod: hpss_Chmod error -1 for `/home/projects/e3sm/www/BGC/E3SMv1/E3SM_1_1_ECA_hist-BDRD'
*** hpss_FileSetAttributes: Permission denied [-1: HPSS_EPERM]
/home/projects/e3sm/www/BGC/E3SMv1/E3SM_1_1_ECA_ssp585-BCRD
*** chmod: hpss_Chmod error -1 for `/home/projects/e3sm/www/BGC/E3SMv1/E3SM_1_1_ECA_ssp585-BCRD'
*** hpss_FileSetAttributes: Permission denied [-1: HPSS_EPERM]
/home/projects/e3sm/www/BGC/E3SMv1/E3SM_1_1_ECA_ssp585-BDRD
*** chmod: hpss_Chmod error -1 for `/home/projects/e3sm/www/BGC/E3SMv1/E3SM_1_1_ECA_ssp585-BDRD'
*** hpss_FileSetAttributes: Permission denied [-1: HPSS_EPERM]
/home/projects/e3sm/www/BGC/E3SMv1/E3SM_1_1_ECA_piControl
*** chmod: hpss_Chmod error -1 for `/home/projects/e3sm/www/BGC/E3SMv1/E3SM_1_1_ECA_piControl'
*** hpss_FileSetAttributes: Permission denied [-1: HPSS_EPERM]
/home/projects/e3sm/www/BGC/E3SMv1/E3SM_1_1_ECA_ssp585-BDRC
*** chmod: hpss_Chmod error -1 for `/home/projects/e3sm/www/BGC/E3SMv1/E3SM_1_1_ECA_ssp585-BDRC'
*** hpss_FileSetAttributes: Permission denied [-1: HPSS_EPERM]
/home/projects/e3sm/www/BGC/E3SMv1/E3SM_1_1_piControl
*** chmod: hpss_Chmod error -1 for `/home/projects/e3sm/www/BGC/E3SMv1/E3SM_1_1_piControl'
*** hpss_FileSetAttributes: Permission denied [-1: HPSS_EPERM]
/home/projects/e3sm/www/BGC/E3SMv1/E3SM_1_1_ECA_hist-BCRD
*** chmod: hpss_Chmod error -1 for `/home/projects/e3sm/www/BGC/E3SMv1/E3SM_1_1_ECA_hist-BCRD'
*** hpss_FileSetAttributes: Permission denied [-1: HPSS_EPERM]
/home/projects/e3sm/www/BGC/E3SMv1/E3SM_1_1_hist-BCRD
*** chmod: hpss_Chmod error -1 for `/home/projects/e3sm/www/BGC/E3SMv1/E3SM_1_1_hist-BCRD'
*** hpss_FileSetAttributes: Permission denied [-1: HPSS_EPERM]
/home/projects/e3sm/www/BGC/E3SMv1/E3SM_1_1_hist-BDRD
*** chmod: hpss_Chmod error -1 for `/home/projects/e3sm/www/BGC/E3SMv1/E3SM_1_1_hist-BDRD'
*** hpss_FileSetAttributes: Permission denied [-1: HPSS_EPERM]
/home/projects/e3sm/www/BGC/E3SMv1/E3SM_1_1_piControl-ext85yr
*** chmod: hpss_Chmod error -1 for `/home/projects/e3sm/www/BGC/E3SMv1/E3SM_1_1_piControl-ext85yr'
*** hpss_FileSetAttributes: Permission denied [-1: HPSS_EPERM]
/home/projects/e3sm/www/BGC/E3SMv1/E3SM_1_1_ECA_hist-BCRC
*** chmod: hpss_Chmod error -1 for `/home/projects/e3sm/www/BGC/E3SMv1/E3SM_1_1_ECA_hist-BCRC'
*** hpss_FileSetAttributes: Permission denied [-1: HPSS_EPERM]
/home/projects/e3sm/www/BGC/E3SMv1/E3SM_1_1_hist-BCRC
*** chmod: hpss_Chmod error -1 for `/home/projects/e3sm/www/BGC/E3SMv1/E3SM_1_1_hist-BCRC'
*** hpss_FileSetAttributes: Permission denied [-1: HPSS_EPERM]
/home/projects/e3sm/www/BGC/E3SMv1/E3SM_1_1_ssp585-BCRC
*** chmod: hpss_Chmod error -1 for `/home/projects/e3sm/www/BGC/E3SMv1/E3SM_1_1_ssp585-BCRC'
*** hpss_FileSetAttributes: Permission denied [-1: HPSS_EPERM]
/home/projects/e3sm/www/BGC/E3SMv1/E3SM_1_1_ssp585-BCRD
*** chmod: hpss_Chmod error -1 for `/home/projects/e3sm/www/BGC/E3SMv1/E3SM_1_1_ssp585-BCRD' |
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I think the links worked now! |
Oh interesting, yes both BGC and Cryo seem to be working now. So, I suppose for future reference, it's just the top-level subdirectories ( A few notes: hsi
cd /home/projects/e3sm/www/BGC/E3SMv1
ls -l
# /home/projects/e3sm/www/BGC/E3SMv1:
# lrwxrwxrwx 1 forsyth forsyth 79 Sep 26 15:10 E3SM_1_1_ECA_hist-BCRC@ -> /home/projects/e3sm/www/publication-archives/pub_archive_E3SM_1_1_ECA_hist-BCRC
# ...
# Note 1: We can see the group is still forsyth, not e3sm for the simulation subdirectories
# Note 2: We can see the directory permissions are lrwxrwxrwx
# That might be too permissive, but it looks to me like that's just the directories themselves:
ls -l /home/projects/e3sm/www/publication-archives/pub_archive_E3SM_1_1_ECA_hist-BCRC
# /home/projects/e3sm/www/publication-archives/pub_archive_E3SM_1_1_ECA_hist-BCRC:
# -rw-r--r-- 1 tonyb tonyb 274855383040 Aug 23 2024 000000.tar
# ...
# The files in the symlinked dir have original permissions.In any case, the links work, so I will go ahed and merge. |
Resolve #63 by adding cryosphere and BGC data