{ "cells": [ { "cell_type": "markdown", "metadata": { "editable": true, "slideshow": { "slide_type": "" }, "tags": [] }, "source": [ "# Exploring the COSIMA Cookbook" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Statement of problem\n", "\n", "COSIMA is producing a lot of data and we need to be able to find it to analyse it. The data is contained in multiple locations. One of these locations is in the `outputs` directory in the `ik11` project. Contained within are subdirectories for each model resolution and within each of these directories are subdirectories for each model configuration" ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "access-cm2-025\taccess-om2-01\tmom6-eac\tmom6-om4-025 README\n", "access-om2\taccess-om2-025\tmom6-global-01\tmom6-panan\n" ] } ], "source": [ "!ls /g/data/ik11/outputs" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "01deg_jra55v13_iaf_4hourly\n", "01deg_jra55v13_ryf9091\n", "01deg_jra55v13_ryf9091_5Kv\n", "01deg_jra55v13_ryf9091_easterlies_down10\n", "01deg_jra55v13_ryf9091_easterlies_up10\n", "01deg_jra55v13_ryf9091_easterlies_up10_meridional\n", "01deg_jra55v13_ryf9091_easterlies_up10_noDSW\n", "01deg_jra55v13_ryf9091_easterlies_up10_zonal\n", "01deg_jra55v13_ryf9091_k_smag_iso3\n", "01deg_jra55v13_ryf9091_OFAM3visc\n", "01deg_jra55v13_ryf9091_qian_ctrl\n", "01deg_jra55v13_ryf9091_qian_wthmp\n", "01deg_jra55v13_ryf9091_qian_wthp\n", "01deg_jra55v13_ryf9091_qian_wtlp\n", "01deg_jra55v13_ryf9091_rerun_for_easterlies\n", "01deg_jra55v13_ryf9091_weddell_down2\n", "01deg_jra55v13_ryf9091_weddell_up1\n", "01deg_jra55v140_iaf\n", "01deg_jra55v140_iaf_cycle2\n", "01deg_jra55v140_iaf_cycle3\n", "01deg_jra55v140_iaf_cycle3_antarctic_tracers\n", "01deg_jra55v140_iaf_cycle3_HF\n", "01deg_jra55v140_iaf_cycle4\n", "01deg_jra55v140_iaf_cycle4_jra55v150_extension\n", "01deg_jra55v140_iaf_cycle4_MWpert\n", "01deg_jra55v140_iaf_cycle4_OLD\n", "01deg_jra55v140_iaf_cycle4_rerun_from_1980\n", "01deg_jra55v140_iaf_cycle4-test\n", "01deg_jra55v140_iaf_KvJ09\n", "01deg_jra55v150_iaf_cycle1\n", "basal_melt_outputs\n" ] } ], "source": [ "!ls /g/data/ik11/outputs/access-om2-01" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "All the data is contained in netCDF files, of which there are many. At the time of writing this, 48118 netCDF files in the above directories." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "**GOAL**: access data by specifying an experiment and a variable" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## COSIMA Cookbook solution" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "In order to achieve the above goal the COSIMA Cookbook provides tools to search directories looking for netCDF data files, read metadata from the files about the data they contain, and then save this data to an SQL database.\n", "\n", "The Cookbook also provides an API to query the database and retrieve data by experiment and variable name." ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [], "source": [ "import cosima_cookbook as cc" ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [], "source": [ "session = cc.database.create_session()" ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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172 | \n", "1deg_jra55_iaf_omip2spunup_cycle46 | \n", "Pat Wongpan | \n", "pat.wongpan@utas.edu.au | \n", "2023-01-20 | \n", "Continuation of omip2spunup up to 50 cycles (i... | \n", "None | \n", "None | \n", "/g/data/ik11/outputs/access-om2/1deg_jra55_iaf... | \n", "1014 | \n", "
173 | \n", "1deg_jra55_iaf_omip2spunup_cycle49 | \n", "Pat Wongpan | \n", "pat.wongpan@utas.edu.au | \n", "2023-01-20 | \n", "Continuation of omip2spunup up to 50 cycles (i... | \n", "None | \n", "None | \n", "/g/data/ik11/outputs/access-om2/1deg_jra55_iaf... | \n", "1014 | \n", "
174 | \n", "1deg_jra55_iaf_omip2spunup_cycle48 | \n", "Pat Wongpan | \n", "pat.wongpan@utas.edu.au | \n", "2023-01-20 | \n", "Continuation of omip2spunup up to 50 cycles (i... | \n", "None | \n", "None | \n", "/g/data/ik11/outputs/access-om2/1deg_jra55_iaf... | \n", "1014 | \n", "
175 | \n", "1deg_jra55_iaf_omip2spunup_cycle47 | \n", "Pat Wongpan | \n", "pat.wongpan@utas.edu.au | \n", "2023-01-20 | \n", "Continuation of omip2spunup up to 50 cycles (i... | \n", "None | \n", "None | \n", "/g/data/ik11/outputs/access-om2/1deg_jra55_iaf... | \n", "1014 | \n", "
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54 | \n", "surface_salt | \n", "Practical Salinity | \n", "psu | \n", "1 daily | \n", "output243/ocean/ocean-2d-surface_salt-1-daily-... | \n", "time: mean | \n", "244 | \n", "1958-01-01 00:00:00 | \n", "2019-01-01 00:00:00 | \n", "
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Select a…" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "ee = explore.ExperimentExplorer(session=session, experiment='01deg_jra55v140_iaf')\n", "ee" ] }, { "cell_type": "code", "execution_count": 13, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
<xarray.DataArray 'surface_salt' (time: 1734, yt_ocean: 2700, xt_ocean: 3600)>\n", "dask.array<concatenate, shape=(1734, 2700, 3600), dtype=float32, chunksize=(1, 540, 720), chunktype=numpy.ndarray>\n", "Coordinates:\n", " * xt_ocean (xt_ocean) float64 -279.9 -279.8 -279.7 ... 79.75 79.85 79.95\n", " * yt_ocean (yt_ocean) float64 -81.11 -81.07 -81.02 ... 89.89 89.94 89.98\n", " * time (time) datetime64[ns] 1990-01-01T12:00:00 ... 1994-09-30T12:00:00\n", "Attributes: (12/13)\n", " long_name: Practical Salinity\n", " units: psu\n", " valid_range: [-10. 100.]\n", " cell_methods: time: mean\n", " time_avg_info: average_T1,average_T2,average_DT\n", " coordinates: geolon_t geolat_t\n", " ... ...\n", " ncfiles: ['/g/data/cj50/access-om2/raw-output/access-om2-01/01deg_...\n", " contact: Andrew Kiss\n", " email: andrew.kiss@anu.edu.au\n", " created: 2020-06-09\n", " description: 0.1 degree ACCESS-OM2 global model configuration under in...\n", " notes: Source code: https://github.com/COSIMA/access-om2 License...
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Experiment: | 025deg_jra55_iaf_omip2_cycle6 |
Description: | 0.25 degree ACCESS-OM2 global model configuration under interannual forcing. ACCESS-OM2-025 physics-only contribution to the CMIP6 Ocean Model Intercomparison Program project phase 2 (OMIP-2), as discussed by Tsujino et al. (2020, GMD, https://doi.org/10.5194/gmd-2019-363). The configuration is based on that described in Kiss et al. (2020), https://doi.org/10.5194/gmd-13-401-2020, but with many improvements. Initial conditions are WOA13v2 potential temperature and practical salinity. However, the WOA potential temperature field is converted to Conservative Temperature for the initical condition unlike earlier versions of ACCESS-OM2. The topography has also been updated (see https://github.com/COSIMA/access-om2/issues/158). Run with JRA55-do v1.4.0 interannually-varying forcing with all solid runoff converted to liquid runoff with no heat transfer. The OMIP-2 protocol consists of six consecutive cycles of the 61-year period starting on 1 Jan 1958 and finishing on 1 Jan 2019. To avoid issues with leap years and calendars, each cycle is run as a separate \"ensemble\" experiment - and thus each has the same time/calendar vector. The configuration files used for this simulation are on github in the repository https://github.com/rmholmes/025deg_jra55_iaf. Each cycle is under a different branch listed as omip_amoctopo_cycle[1-6]. |
Notes: | |
Contact: | Ryan Holmes <ryan.holmes@unsw.edu.au> |
Control repo: | |
No. files: | 2171 |
Created: | 2020-11-03 |
Practical Salinity (psu)
" } }, "3621805552304dd4af01a074e5354b8e": { "model_module": "@jupyter-widgets/controls", "model_module_version": "1.5.0", "model_name": "DropdownModel", "state": { "_options_labels": [ "01deg_jra55_iaf_cycle3_melt", "01deg_jra55_SAMextr_0203_from9091", "01deg_jra55_SAMextr_1011_from9091", "01deg_jra55_SAMextr_9192_from9091", "01deg_jra55_SAMextr_9899_from9091", "01deg_jra55v13_iaf", "01deg_jra55v13_iaf_4hourly", "01deg_jra55v13_ryf9091", "01deg_jra55v13_ryf9091_5Kv", "01deg_jra55v13_ryf9091_easterlies_down10", "01deg_jra55v13_ryf9091_easterlies_up10", "01deg_jra55v13_ryf9091_easterlies_up10_meridional", "01deg_jra55v13_ryf9091_easterlies_up10_noDSW", "01deg_jra55v13_ryf9091_easterlies_up10_zonal", "01deg_jra55v13_ryf9091_k_smag_iso3", "01deg_jra55v13_ryf9091_OFAM3visc", "01deg_jra55v13_ryf9091_qian_ctrl", "01deg_jra55v13_ryf9091_qian_wthmp", "01deg_jra55v13_ryf9091_qian_wthp", "01deg_jra55v13_ryf9091_qian_wtlp", "01deg_jra55v13_ryf9091_rerun_for_easterlies", "01deg_jra55v13_ryf9091_weddell_down1", "01deg_jra55v13_ryf9091_weddell_down2", "01deg_jra55v13_ryf9091_weddell_up1", "01deg_jra55v140_iaf", "01deg_jra55v140_iaf_cycle2", "01deg_jra55v140_iaf_cycle3", "01deg_jra55v140_iaf_cycle3_antarctic_tracers", "01deg_jra55v140_iaf_cycle3_HF", "01deg_jra55v140_iaf_cycle4", "01deg_jra55v140_iaf_cycle4_jra55v150_extension", "01deg_jra55v140_iaf_cycle4_MWpert", "01deg_jra55v140_iaf_KvJ09", "01deg_jra55v150_iaf_cycle1", "01deg_jra55v150_iaf_cycle1_old", "025deg_jra55_iaf_omip2_cycle1", "025deg_jra55_iaf_omip2_cycle2", "025deg_jra55_iaf_omip2_cycle3", "025deg_jra55_iaf_omip2_cycle4", "025deg_jra55_iaf_omip2_cycle5", "025deg_jra55_iaf_omip2_cycle6", "025deg_jra55_iaf_omip2_cycle6_14to17", "025deg_jra55_iaf_omip2_cycle6_78to08", "025deg_jra55_iaf_omip2_cycle6_ext", "025deg_jra55_iaf_omip_straits_topo2_cycle1", "025deg_jra55_iaf_omip_straits_topo3_cycle1", "025deg_jra55_iaf_omip_straits_topo4_cycle1", "025deg_jra55_iaf_omip_straits_topo5_cycle1", "025deg_jra55_iaf_omip_straits_topo_cycle1", "025deg_jra55_ryf9091_bgc", "025deg_jra55_ryf9091_gadi", "025deg_jra55_ryf9091_gadi_noGM", "025deg_jra55_ryf9091_gadi_norediGM", "025deg_jra55_ryf9091_GMhi", "025deg_jra55v13_iaf_gmredi6", "025deg_jra55v13_ryf8485_RCP45", "025deg_jra55v13_ryf8485_spinup", "025deg_jra55v13_ryf9091_gmredi6", "025deg_jra55v13_SAMx_0203_from_ryf9091_yr160_gmredi6", "025deg_jra55v13_SAMx_1011_from_ryf9091_yr160_gmredi6", "025deg_jra55v13_SAMx_9192_from_ryf9091_yr160_gmredi6", "025deg_jra55v13_SAMx_9899_from_ryf9091_yr160_gmredi6", "1deg_iamip2_CMCC-ESM2ssp126", "1deg_iamip2_CMCC-ESM2ssp585", "1deg_iamip2_con", "1deg_iamip2_EC-Earth3ssp126", "1deg_iamip2_EC-Earth3ssp585", "1deg_iamip2_exc", "1deg_iamip2_his", "1deg_jra55_iaf_omip2_cycle1", "1deg_jra55_iaf_omip2_cycle2", "1deg_jra55_iaf_omip2_cycle3", "1deg_jra55_iaf_omip2_cycle4", "1deg_jra55_iaf_omip2_cycle5", "1deg_jra55_iaf_omip2_cycle6", "1deg_jra55_iaf_omip2_cycle6_bgcinit", "1deg_jra55_iaf_omip2dEdd_cycle1", 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<xarray.DataArray 'surface_salt' (time: 1734, yt_ocean: 2700, xt_ocean: 3600)>\ndask.array<concatenate, shape=(1734, 2700, 3600), dtype=float32, chunksize=(1, 540, 720), chunktype=numpy.ndarray>\nCoordinates:\n * xt_ocean (xt_ocean) float64 -279.9 -279.8 -279.7 ... 79.75 79.85 79.95\n * yt_ocean (yt_ocean) float64 -81.11 -81.07 -81.02 ... 89.89 89.94 89.98\n * time (time) datetime64[ns] 1990-01-01T12:00:00 ... 1994-09-30T12:00:00\nAttributes: (12/13)\n long_name: Practical Salinity\n units: psu\n valid_range: [-10. 100.]\n cell_methods: time: mean\n time_avg_info: average_T1,average_T2,average_DT\n coordinates: geolon_t geolat_t\n ... ...\n ncfiles: ['/g/data/cj50/access-om2/raw-output/access-om2-01/01deg_...\n contact: Andrew Kiss\n email: andrew.kiss@anu.edu.au\n created: 2020-06-09\n description: 0.1 degree ACCESS-OM2 global model configuration under in...\n notes: Source code: https://github.com/COSIMA/access-om2 License...