From a6a16e3db130087f92de2624953c2c9bfcceb93a Mon Sep 17 00:00:00 2001 From: Hsiang-He Lee <44912417+hsiangheleellnl@users.noreply.github.com> Date: Wed, 24 May 2023 14:02:45 -0700 Subject: [PATCH 1/3] Update README.md Update instruction for using ChemDyg via zppy --- README.md | 42 ++++++++++++++++++++++++++++++++++-------- 1 file changed, 34 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index c53d1f6..7494362 100644 --- a/README.md +++ b/README.md @@ -1,22 +1,48 @@ 2023/03/01 Hsiang-He Lee (lee1061@llnl.gov) +2023/05/24 updated -E3SM chemistry diagnostic package version1.0 (ChemDyg v1.0) is designed for E3SM chemistry development. There are total 11 types of plot and 3 types of table for model-to-model and model-to-observation comparison. +E3SM chemistry diagnostic package version 0.1.0 (ChemDyg v0.1.0) is designed for E3SM chemistry development. There are total 11 types of plot and 3 types of table for model-to-model and model-to-observation comparison. Index page and example figures: https://web.lcrc.anl.gov/public/e3sm/diagnostic_output/ac.lee1061/20220914.PAN.MZThet.v2.LR.bi-grid.amip.chemUCI_Linozv3/e3sm_chem_diags/plots/ ChemDyg is executed by zppy, which is a post-processing toolchain for E3SM written in Python (https://github.com/E3SM-Project/zppy). -*How to run ChemDyg via zppy script on chrysalis? -1. Setup environment ->source /gpfs/fs1/soft/chrysalis/manual/anaconda3/2020.11/etc/profile.d/conda.sh ->conda activate zppy_dev_chem +# How to run ChemDyg via zppy script on chrysalis? -2. Download zppy and ChemDyg on your working folder +*Clone repository -3. Modify .cfg run script and then ->zppy -c ChemDyg_example_script.cfg +```git clone git@github.com:E3SM-Project/zppy.git``` + +```cd zppy``` + +*Checkout branch +```git checkout golaz/plugins``` + +*Create environment + +```module load anaconda3/2020.11``` + +```conda env create --name zppy_dev_chem -f conda/dev.yml``` + +*Activate + +```source /gpfs/fs1/soft/chrysalis/manual/anaconda3/2020.11/etc/profile.d/conda.sh``` + +```conda activate zppy_dev_chem``` + +*Install chemdyg package + +```install -y -c e3sm/label/chemdyg_dev chemdyg``` + +*Install zppy in environment + +```python -m pip install .``` + +*Once this is done, you call is as + +```zppy -c ChemDyg_example_script.cfg``` ** Additional python script "DEBUG_chem_diags_timestep.py" is designed for debug purpose. The user gives the path of E3SM .h0 and .h1 outputs and other necessary information. The script will generate chem tendency table for each timestep. From efcc8d17a5f67b2afa57f9fe9b0762c2ad155051 Mon Sep 17 00:00:00 2001 From: Hsiang-He Lee <44912417+hsiangheleellnl@users.noreply.github.com> Date: Thu, 25 May 2023 15:11:22 -0700 Subject: [PATCH 2/3] Update README.md for the release version --- README.md | 50 +++++++------------------------------------------- 1 file changed, 7 insertions(+), 43 deletions(-) diff --git a/README.md b/README.md index 7494362..99db43e 100644 --- a/README.md +++ b/README.md @@ -1,52 +1,16 @@ -2023/03/01 -Hsiang-He Lee (lee1061@llnl.gov) -2023/05/24 updated - -E3SM chemistry diagnostic package version 0.1.0 (ChemDyg v0.1.0) is designed for E3SM chemistry development. There are total 11 types of plot and 3 types of table for model-to-model and model-to-observation comparison. +E3SM chemistry diagnostic package (ChemDyg) is designed for E3SM chemistry development. There are total 11 types of plot and 3 types of table for model-to-model and model-to-observation comparison. Index page and example figures: https://web.lcrc.anl.gov/public/e3sm/diagnostic_output/ac.lee1061/20220914.PAN.MZThet.v2.LR.bi-grid.amip.chemUCI_Linozv3/e3sm_chem_diags/plots/ ChemDyg is executed by zppy, which is a post-processing toolchain for E3SM written in Python (https://github.com/E3SM-Project/zppy). -# How to run ChemDyg via zppy script on chrysalis? - -*Clone repository - -```git clone git@github.com:E3SM-Project/zppy.git``` - -```cd zppy``` - -*Checkout branch -```git checkout golaz/plugins``` - -*Create environment - -```module load anaconda3/2020.11``` - -```conda env create --name zppy_dev_chem -f conda/dev.yml``` - -*Activate - -```source /gpfs/fs1/soft/chrysalis/manual/anaconda3/2020.11/etc/profile.d/conda.sh``` - -```conda activate zppy_dev_chem``` - -*Install chemdyg package - -```install -y -c e3sm/label/chemdyg_dev chemdyg``` - -*Install zppy in environment - -```python -m pip install .``` - -*Once this is done, you call is as - -```zppy -c ChemDyg_example_script.cfg``` - - -** Additional python script "DEBUG_chem_diags_timestep.py" is designed for debug purpose. The user gives the path of E3SM .h0 and .h1 outputs and other necessary information. The script will generate chem tendency table for each timestep. - +*How to run ChemDyg via zppy script on chrysalis (same as other zppy-supported machines)? +``` +source /lcrc/soft/climate/e3sm-unified/load_latest_e3sm_unified_chrysalis.sh +wget https://raw.githubusercontent.com/E3SM-Project/ChemDyg/main/ChemDyg_example_script.cfg +zppy -c ChemDyg_example_script.cfg +``` See [documentation](https://e3sm-project.github.io/zppy) for more details. ## License From 1d616fd0c00880c883022d2117f2fdceaf91d87c Mon Sep 17 00:00:00 2001 From: Hsiang-He Lee <44912417+hsiangheleellnl@users.noreply.github.com> Date: Thu, 25 May 2023 15:27:37 -0700 Subject: [PATCH 3/3] Provide E3SM-unified path in README.md --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 99db43e..e2f9ca9 100644 --- a/README.md +++ b/README.md @@ -5,13 +5,13 @@ https://web.lcrc.anl.gov/public/e3sm/diagnostic_output/ac.lee1061/20220914.PAN.M ChemDyg is executed by zppy, which is a post-processing toolchain for E3SM written in Python (https://github.com/E3SM-Project/zppy). -*How to run ChemDyg via zppy script on chrysalis (same as other zppy-supported machines)? +*How to run ChemDyg via zppy script on chrysalis? ``` source /lcrc/soft/climate/e3sm-unified/load_latest_e3sm_unified_chrysalis.sh wget https://raw.githubusercontent.com/E3SM-Project/ChemDyg/main/ChemDyg_example_script.cfg zppy -c ChemDyg_example_script.cfg ``` -See [documentation](https://e3sm-project.github.io/zppy) for more details. +**Note that the users need to change the'e3sm_unified' path on different zppy-supported machines (https://e3sm-project.github.io/zppy/_build/html/main/getting_started.html#activate-e3sm-unified-environment). ## License