Skip to content

Add v2.1 BGC data #56

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 4 commits into from
Mar 14, 2025
Merged

Add v2.1 BGC data #56

Show file tree
Hide file tree
Changes from 2 commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
94d30e2
Add v2.1 BGC data
forsyth2 Mar 12, 2025
b90af59
Generated table
forsyth2 Mar 12, 2025
4f488a0
Add original run scripts
forsyth2 Mar 12, 2025
30a568b
Address comments
forsyth2 Mar 14, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
17 changes: 17 additions & 0 deletions docs/source/v2.1/BGC/index.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,17 @@
E3SMv2.1 (BGC)
====================

The simulation campaign for E3SMv2.1 was performed with Low Resolution (LR) configuration

* **v2_1.LR** (lower resolution)

If you use data from this simulation campaign, please cite the following overview
manuscript:

* Note: Link will be provided upon publication

.. toctree::
:maxdepth: 2
:caption: Contents:

simulation_data/index
56 changes: 56 additions & 0 deletions docs/source/v2.1/BGC/simulation_data/index.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,56 @@
***************
Simulation Data
***************

The E3SMv2.1 simulation data is available on **ESGF** and **NERSC HPSS**.

The data is reformatted to conform to CMIP conventions and was submmited to the CMIP6 ESGF archive. (ESGF links are provided in the table below for published data).

Additionally, all native model output data has also been archived on **NERSC HPSS** using `zstash <https://e3sm-project.github.io/zstash>`_.

**If you have an account on NERSC**, you can retrieve the data locally or remotely using Globus.

To download simulation data locally on a NERSC machine: ::

zstash extract --hpss=<HPSS path below>

To download simulation data remotely using the zstash Globus interface: ::

zstash extract --hpss=globus://nersc/<HPSS path below>

or ::

zstash extract --hpss=globus://9cd89cfd-6d04-11e5-ba46-22000b92c6ec/<HPSS path below>

Note that the data management tool `zstash <https://github.com/E3SM-Project/zstash>`_ is available from the `E3SM-Unified <https://github.com/E3SM-Project/e3sm-unified>`_ conda environment. An example of retrieving all **eam.h0** (monthly atmosphere output files) between **years 0030 and 0049** for the v2_1.LR.piControl simulation at NERSC locally is demonstrated as below in two steps:

1. To activate E3SM-Unified environment by:
::

source /global/common/software/e3sm/anaconda_envs/load_latest_e3sm_unified_pm-cpu.sh

2. To retrieve files with zstash command:
::

zstash extract --hpss=/home/projects/e3sm/www/WaterCycle/E3SMv2_1/v2_1.LR.piControl "*.eam.h0.00[3-4]?-??.nc"


For more information, refer to `zstash usage <https://e3sm-project.github.io/zstash/_build/html/master/usage.html#extract>`_.


**If you do not have access to NERSC**, you can download simulation data directly through the NERSC HPSS
`web interface <https://portal.nersc.gov/archive/home/projects/e3sm/www/WaterCycle/E3SMv2_1>`_.
Note that this will be slow and inefficient since you'll have to download the tar files.

**v2_1.LR** simulations data has been archived on NERSC HPSS under: ::

/home/projects/e3sm/www/BGC/E3SMv2_1


Original run scripts can be found `here <https://github.com/E3SM-Project/e3sm_data_docs/tree/main/run_scripts/v2.1/original>`_.

.. toctree::
:maxdepth: 2
:caption: Contents:

simulation_table
19 changes: 19 additions & 0 deletions docs/source/v2.1/BGC/simulation_data/simulation_table.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,19 @@
**********************************
v2.1 BGC simulation table
**********************************

+-------------------------------------------------------------------+-----------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------------------+
| Simulation | Data Size (TB) | ESGF Links | HPSS Path |
+===================================================================+=================+==================================================================================================================================================================================================================================================================================================================================================================================================================+==================================================================================+
| **LR > SPINUP** | | | |
+-------------------------------------------------------------------+-----------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------------------+
| CBGCv2.r05.chrysalis.I20TRGSWCNP | 3 | | /home/projects/e3sm/www/BGC/E3SMv2_1/CBGCv2.r05.chrysalis.I20TRGSWCNP |
+-------------------------------------------------------------------+-----------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------------------+
| **LR > HISTORICAL** | | | |
+-------------------------------------------------------------------+-----------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------------------+
| v2.LR.BGC-LNDATM.CONTRL | 11 | | /home/projects/e3sm/www/BGC/E3SMv2_1/v2.LR.BGC-LNDATM.CONTRL |
+-------------------------------------------------------------------+-----------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------------------+
| **LR > SSP** | | | |
+-------------------------------------------------------------------+-----------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------------------+
| v2.LR.BGC-LNDATM.SSP370 | 6 | | /home/projects/e3sm/www/BGC/E3SMv2_1/v2.LR.BGC-LNDATM.SSP370 |
+-------------------------------------------------------------------+-----------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------------------+
1 change: 1 addition & 0 deletions docs/source/v2.1/index.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,4 +5,5 @@ v2.1
:maxdepth: 2
:caption: Contents:

BGC/index
WaterCycle/index
1 change: 1 addition & 0 deletions run_scripts/v2.1/original/run.CBGCv2.r05.chrysalis.I20TRGSWCNP.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
# Placeholder for actual run script
1 change: 1 addition & 0 deletions run_scripts/v2.1/original/run.v2.LR.BGC-LNDATM.CONTRL.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
# Placeholder for actual run script
1 change: 1 addition & 0 deletions run_scripts/v2.1/original/run.v2.LR.BGC-LNDATM.SSP370.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
# Placeholder for actual run script
4 changes: 2 additions & 2 deletions utils/generate_html.bash
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
pr_num=52
pr_num=56

# Chrysalis
#destination_dir=/lcrc/group/e3sm/public_html/diagnostic_output/$USER/data_docs_${pr_num}
Expand All @@ -7,7 +7,7 @@ pr_num=52
destination_dir=/global/cfs/cdirs/e3sm/www/$USER/data_docs_${pr_num}
web_page="https://portal.nersc.gov/cfs/e3sm/$USER/data_docs_${pr_num}/html/"

#python generate_tables.py
python generate_tables.py
cd ../docs/ && make html
rm -rf ls ${destination_dir}
mv _build ${destination_dir}
Expand Down
5 changes: 4 additions & 1 deletion utils/generate_tables.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -178,6 +178,8 @@ def read_simulations(csv_file):
simulation_dict = {}
for i in range(len(header)):
label = header[i]
if len(row) != len(header):
raise RuntimeError(f"header has {len(header)} labels, but row has {len(row)} entries")
simulation_dict[label] = row[i].strip()
model_version_name = simulation_dict["model_version"]
group_name = simulation_dict["group"]
Expand Down Expand Up @@ -270,4 +272,5 @@ def construct_pages(csv_file: str, model_version: str, group_name: str, include_

if __name__ == "__main__":
#construct_pages("simulations_v2.csv", "v2", "WaterCycle")
construct_pages("simulations_v2_1.csv", "v2.1", "WaterCycle")
#construct_pages("simulations_v2_1.csv", "v2.1", "WaterCycle")
construct_pages("simulations_v2_1.csv", "v2.1", "BGC")
23 changes: 13 additions & 10 deletions utils/simulations_v2_1.csv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,10 +1,13 @@
model_version, group, resolution, category, simulation_name, machine, checksum, experiment, ensemble_num, cmip_only, node,
v2.1, WaterCycle, LR, DECK, v2_1.LR.piControl, chrysalis, ebc5565e182e8b1cc887c185ca3eb144, piControl, 1, cmip_only, cels.anl,
v2.1, WaterCycle, LR, DECK, v2_1.LR.1pctCO2_0101, chrysalis, b7676ccc791941d1bdadde05c59d70b0, 1pctCO2, 1, cmip_only, cels.anl,
v2.1, WaterCycle, LR, DECK, v2_1.LR.abrupt-4xCO2_0101, chrysalis, fe50274534774678d55cb320412d1667, abrupt-4xCO2, 1, cmip_only, cels.anl,
v2.1, WaterCycle, LR, DECK, v2_1.LR.amip_0101, chrysalis, 832ca9c9db8b4988a109f8c5872b0fe7, amip, 1, cmip_only, cels.anl,
v2.1, WaterCycle, LR, Historical, v2_1.LR.historical_0101, chrysalis, 43efe5ba9216b535be21bd8474b15c22, historical, 1, cmip_only, cels.anl,
v2.1, WaterCycle, LR, Historical, v2_1.LR.historical_0151, chrysalis, , historical, 2, cmip_only, cels.anl,
v2.1, WaterCycle, LR, Historical, v2_1.LR.historical_0201, chrysalis, , historical, 3, cmip_only, cels.anl,
v2.1, WaterCycle, LR, Historical, v2_1.LR.historical_0251, chrysalis, , historical, 4, cmip_only, cels.anl,
v2.1, WaterCycle, LR, Historical, v2_1.LR.historical_0301, chrysalis, , historical, 5, cmip_only, cels.anl,
model_version, group, resolution, category, simulation_name, machine, checksum, experiment, ensemble_num, cmip_only, node,
v2.1, BGC, LR, SPINUP, CBGCv2.r05.chrysalis.I20TRGSWCNP, chrysalis, , , , , ,
Copy link
Collaborator Author

@forsyth2 forsyth2 Mar 12, 2025

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

  1. So, we still want this data grouped with v2.1 even though the cases are prefixed with v2 (not v2.1), and this simulation in particular seems to use a completely different naming convention?

v2.1, BGC, LR, HISTORICAL, v2.LR.BGC-LNDATM.CONTRL, chrysalis, , , , , ,
v2.1, BGC, LR, SSP, v2.LR.BGC-LNDATM.SSP370, chrysalis, , , , , ,
v2.1, WaterCycle, LR, DECK, v2_1.LR.piControl, chrysalis, ebc5565e182e8b1cc887c185ca3eb144, piControl, 1, cmip_only, cels.anl,
v2.1, WaterCycle, LR, DECK, v2_1.LR.1pctCO2_0101, chrysalis, b7676ccc791941d1bdadde05c59d70b0, 1pctCO2, 1, cmip_only, cels.anl,
v2.1, WaterCycle, LR, DECK, v2_1.LR.abrupt-4xCO2_0101, chrysalis, fe50274534774678d55cb320412d1667, abrupt-4xCO2, 1, cmip_only, cels.anl,
v2.1, WaterCycle, LR, DECK, v2_1.LR.amip_0101, chrysalis, 832ca9c9db8b4988a109f8c5872b0fe7, amip, 1, cmip_only, cels.anl,
v2.1, WaterCycle, LR, Historical, v2_1.LR.historical_0101, chrysalis, 43efe5ba9216b535be21bd8474b15c22, historical, 1, cmip_only, cels.anl,
v2.1, WaterCycle, LR, Historical, v2_1.LR.historical_0151, chrysalis, , historical, 2, cmip_only, cels.anl,
v2.1, WaterCycle, LR, Historical, v2_1.LR.historical_0201, chrysalis, , historical, 3, cmip_only, cels.anl,
v2.1, WaterCycle, LR, Historical, v2_1.LR.historical_0251, chrysalis, , historical, 4, cmip_only, cels.anl,
v2.1, WaterCycle, LR, Historical, v2_1.LR.historical_0301, chrysalis, , historical, 5, cmip_only, cels.anl,