other:uvcdat:cdat_conda:cdat_8_1
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other:uvcdat:cdat_conda:cdat_8_1 [2019/03/14 09:59] jypeter Added/updated cartopy |
other:uvcdat:cdat_conda:cdat_8_1 [2020/01/23 10:53] jypeter [What's New?] |
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| <WRAP center round tip 60%> | <WRAP center round tip 60%> | ||
| - | You have questions about Python? | + | If you have questions about Python, read: |
| - | + | * [[other:python:starting|Working with Python]] | |
| - | Read [[other:python:jyp_steps|JYP's recommended steps for learning python]]! | + | * [[other:python:jyp_steps|JYP's recommended steps for learning python]]! |
| </WRAP> | </WRAP> | ||
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| If you mostly want to use the CDAT 8.1 installed by JYP, just use the following steps and skip the next sections: | If you mostly want to use the CDAT 8.1 installed by JYP, just use the following steps and skip the next sections: | ||
| - | * Initialize conda: | + | * Initialize //conda// with: |
| ^ Server ^ tcsh ^ bash ^ | ^ Server ^ tcsh ^ bash ^ | ||
| Line 18: | Line 18: | ||
| | ciclad | ''source ~jypmce/.conda3_jyp.csh'' | ''source ~jypmce/.conda3_jyp.sh'' | | | ciclad | ''source ~jypmce/.conda3_jyp.csh'' | ''source ~jypmce/.conda3_jyp.sh'' | | ||
| - | * Activate the default environment: ''conda activate cdatm_py2'' | + | * Choose one of the [[#environments_summary|installed environments]] and activate it with: ''conda activate env_name'' |
| - | * Check the [[#environments_summary|Available environments]] for more options | + | * python 2.7.x: ''conda activate cdatm_py2'' |
| - | ===== What's New? ===== | + | * python 3.x: ''conda activate cdatm_py3'' (not available on ciclad, but could be installed) |
| + | ===== What's New in CDAT 8.1? ===== | ||
| * [[https://github.com/cdat/cdat/releases/tag/v8.1|8.1 announcement]] and features summary ([[https://github.com/UV-CDAT/uvcdat/releases|all versions]]) | * [[https://github.com/cdat/cdat/releases/tag/v8.1|8.1 announcement]] and features summary ([[https://github.com/UV-CDAT/uvcdat/releases|all versions]]) | ||
| * Full [[https://uvcdat.llnl.gov/changelog.html#8.1|Change log]] | * Full [[https://uvcdat.llnl.gov/changelog.html#8.1|Change log]] | ||
| + | |||
| + | Note: this particular CDAT installation at LSCE (and on other machines/servers) provides **many extra (non-CDAT) packages**. You can jump directly to the [[other:uvcdat:cdat_conda:cdat_8_1#extra_packages_list|Extra package list]] at the bottom of this page to see what is available | ||
| ===== Installation with Miniconda3 ===== | ===== Installation with Miniconda3 ===== | ||
| Line 113: | Line 116: | ||
| ===== Customizing UV-CDAT for LSCE ===== | ===== Customizing UV-CDAT for LSCE ===== | ||
| + | ==== Testing vcs ==== | ||
| + | Start python and paste the following lines | ||
| + | |||
| + | <code>import numpy as np, vcs | ||
| + | id100 = np.identity(100) | ||
| + | x = vcs.init() | ||
| + | x.plot(id100) | ||
| + | </code> | ||
| + | |||
| + | If you get the kind of errors described in [[https://github.com/CDAT/vcs/issues/393|x.plot crashes with OpenGL2 error]], the drivers on your server are probably not compatible with an interactive use of vcs... The workaround is to **install mesalib and work in //headless mode//** (e.g. without a display)... | ||
| + | |||
| + | Install //mesalib// with ''conda install -c cdat/label/v81 -c conda-forge mesalib vtk-cdat'' and try pasting again the few code lines above in python. If things work as expected, no canvas will be opened, but you'll be able to save the canvas to a file with | ||
| + | |||
| + | <code>x.png('test_mesalib') | ||
| + | x.pdf('test_mesalib')</code> | ||
| + | |||
| + | Note: using //mesalib// for headless mode work makes it possible to work without an X server, and with no DISPLAY variable defined | ||
| ==== Downloading cdms2/vcs test data ==== | ==== Downloading cdms2/vcs test data ==== | ||
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| * Get version number with:\\ <code>$ drq -v | * Get version number with:\\ <code>$ drq -v | ||
| dreqPy version 01.00.29 [Version 01.00.29]</code> | dreqPy version 01.00.29 [Version 01.00.29]</code> | ||
| + | |||
| + | * [[https://github.com/PBrockmann/ipython_ferretmagic|ipython_ferretmagic]]: IPython notebook extension for ferret | ||
| + | * ''conda activate cdatm18_py2''\\ ''pip install ferretmagic'' | ||
| The following packages have no dependency problems and were installed (or updated) //later// | The following packages have no dependency problems and were installed (or updated) //later// | ||
| Line 171: | Line 194: | ||
| * [[http://scitools.org.uk/cartopy/|cartopy]]: a Python package designed for geospatial data processing in order to produce maps and other geospatial data analyses | * [[http://scitools.org.uk/cartopy/|cartopy]]: a Python package designed for geospatial data processing in order to produce maps and other geospatial data analyses | ||
| * ''conda install -n cdatm18_py2 -c conda-forge cartopy'' | * ''conda install -n cdatm18_py2 -c conda-forge cartopy'' | ||
| + | |||
| + | * [[https://joblib.readthedocs.io/en/latest/|joblib]]: running Python functions as pipeline jobs | ||
| + | * ''conda install -n cdatm18_py2 -c conda-forge joblib'' | ||
| * [[https://climaf.readthedocs.io/en/latest/|CliMAF]]: a Climate Model Assessment Framework | * [[https://climaf.readthedocs.io/en/latest/|CliMAF]]: a Climate Model Assessment Framework | ||
| * [[other:uvcdat:cdat_conda:climaf_install|Installation notes]] | * [[other:uvcdat:cdat_conda:climaf_install|Installation notes]] | ||
| + | |||
| + | * [[https://jiffyclub.github.io/palettable/|Palettable]]: Color palettes for Python | ||
| + | * ''conda install -n cdatm18_py2 -c conda-forge palettable'' | ||
| ==== TODO ==== | ==== TODO ==== | ||
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| * [[http://www.ifremer.fr/vacumm/|vacumm]]: Validation, Analysis, Comparison - Utilities written in Python to validate and analyze Multi-Model outputs, and compare them to observations | * [[http://www.ifremer.fr/vacumm/|vacumm]]: Validation, Analysis, Comparison - Utilities written in Python to validate and analyze Multi-Model outputs, and compare them to observations | ||
| * [[http://unidata.github.io/netcdf4-python/|netcdf4]]: a Python interface to the netCDF C library | * [[http://unidata.github.io/netcdf4-python/|netcdf4]]: a Python interface to the netCDF C library | ||
| - | * [[http://ferret.pmel.noaa.gov/Ferret/documentation/pyferret|pyferret]]: Ferret encapsulated in | + | * [[http://ferret.pmel.noaa.gov/Ferret/documentation/pyferret|pyferret]]: Ferret encapsulated in Python |
| + | * [[https://github.com/PBrockmann/ipython_ferretmagic|ipython_ferretmagic]]: IPython notebook extension for ferret | ||
| * [[https://github.com/conda-forge/basemap-data-hires-feedstock|basemap-data-hires]]: high resolution data for ''basemap'' | * [[https://github.com/conda-forge/basemap-data-hires-feedstock|basemap-data-hires]]: high resolution data for ''basemap'' | ||
| * [[https://github.com/PCMDI/pcmdi_metrics|PCMDI metrics package]] (PMP): objectively compare results from climate models with observations using well-established statistical tests | * [[https://github.com/PCMDI/pcmdi_metrics|PCMDI metrics package]] (PMP): objectively compare results from climate models with observations using well-established statistical tests | ||
| Line 241: | Line 271: | ||
| * [[https://ajdawson.github.io/windspharm/latest/|windspharm]]: spherical harmonic wind analysis in Python | * [[https://ajdawson.github.io/windspharm/latest/|windspharm]]: spherical harmonic wind analysis in Python | ||
| * [[https://climaf.readthedocs.io/en/latest/|CliMAF]]: a Climate Model Assessment Framework | * [[https://climaf.readthedocs.io/en/latest/|CliMAF]]: a Climate Model Assessment Framework | ||
| + | * [[https://joblib.readthedocs.io/en/latest/|joblib]]: running Python functions as pipeline jobs | ||
| + | * [[https://jiffyclub.github.io/palettable/|Palettable]]: Color palettes for Python | ||
| ==== Removed packages ==== | ==== Removed packages ==== | ||
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| | cdat-8.1_py2 | LSCE\\ ciclad | CDAT 8.1 & Python 2.7 | | | cdat-8.1_py2 | LSCE\\ ciclad | CDAT 8.1 & Python 2.7 | | ||
| | cdat-8.1_py3 | LSCE | CDAT 8.1 & Python 3.6 | | | cdat-8.1_py3 | LSCE | CDAT 8.1 & Python 3.6 | | ||
| - | | cdatm18_py2 | LSCE\\ ciclad | CDAT 8.1 & P 2.7 //JYP version// | | + | | cdatm18_py2\\ or //cdatm_py2// | LSCE\\ ciclad | CDAT 8.1 & P 2.7 //JYP version// | |
| - | | cdatm18_py3 | LSCE | CDAT 8.1 & P 3.7 //JYP version// | | + | | cdatm18_py3\\ or //cdatm_py3// | LSCE | CDAT 8.1 & P 3.7 //JYP version// | |
| | cdat-nightly_py2 | LSCE\\ ciclad | CDAT nightly & Python 2.7 | | | cdat-nightly_py2 | LSCE\\ ciclad | CDAT nightly & Python 2.7 | | ||
| | cdatm-nightly_py2 | LSCE\\ ciclad | CDAT nightly & P 2.7 //JYP version// | | | cdatm-nightly_py2 | LSCE\\ ciclad | CDAT nightly & P 2.7 //JYP version// | | ||
other/uvcdat/cdat_conda/cdat_8_1.txt · Last modified: 2021/03/26 09:10 by jypeter
