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--- other:uvcdat:cdat_conda:cdat_8_1 [2019/03/12 14:52]
jypeter [Packages that have no dependency problems]
+++ other:uvcdat:cdat_conda:cdat_8_1 [2020/01/23 10:53]
jypeter [What's New?]
@@ Line 4: / Line 4: @@
 <WRAP center round tip 60%>
-Follow the instructions about the [[other:python:starting#conda-based_versions_of_uv-cdat|conda-based versions of UV-CDAT initialization]] for actually using an installed version of ''8.1''
+If you have questions about Python, read:
+  * [[other:python:starting|Working with Python]]
+  * [[other:python:jyp_steps|JYP's recommended steps for learning python]]!
 </WRAP>
-===== What's New? =====
+===== Using JYP version =====
+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// with:
+^  Server  ^  tcsh  ^  bash  ^
+|  LSCE  | ''source ~jypeter/.conda3_jyp.csh'' | ''source ~jypeter/.conda3_jyp.sh'' |
+|  ciclad  | ''source ~jypmce/.conda3_jyp.csh'' | ''source ~jypmce/.conda3_jyp.sh'' |
+  * Choose one of the [[#environments_summary|installed environments]] and activate it with: ''conda activate env_name''
+    * python 2.7.x: ''conda activate cdatm_py2''
+    * 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]])
   * 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 =====
@@ Line 100: / Line 116: @@
 ===== 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 ====
@@ Line 140: / Line 173: @@
       * Get version number with:\\ <code>$ drq -v
 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//
+  * [[https://cmor.llnl.gov/|CMOR]]: CMOR (//Climate Model Output Rewriter//) is used to produce CF-compliant netCDF files
+    * ''conda install -n cdatm18_py2 -c conda-forge cmor''
+    * Get version number with: ''python -c 'from cmor import *; print( (CMOR_VERSION_MAJOR, CMOR_VERSION_MINOR, CMOR_VERSION_PATCH) )' ''
+    * <wrap hi>Warning!</wrap> [[https://github.com/PCMDI/cmor/issues/449|CMOR currently requires Python 2.7]]
   * [[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
@@ Line 150: / Line 191: @@
     * ''conda install -n cdatm18_py2 -c stefraynaud -c conda-forge spanlib''
     * Test: ''python -c 'from spanlib.analyzer import Analyzer' ''
+  * [[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''
+  * [[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
     * [[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 ====
@@ Line 177: / Line 227: @@
 Some packages change more often than others, and can be easily updated the following way:
-  * [[https://cmor.llnl.gov/|CMOR]]
-    * Update with: ''conda update -n cdatm15 -c conda-forge -c pcmdi -c uvcdat cmor''
-      * Get version number with: ''python -c 'from cmor import *; print CMOR_VERSION_MAJOR, CMOR_VERSION_MINOR, CMOR_VERSION_PATCH' ''
   * [[https://earthsystemcog.org/projects/wip/CMIP6DataRequest|dreqPy]]
@@ Line 207: / Line 253: @@
   * [[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://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/PCMDI/pcmdi_metrics|PCMDI metrics package]] (PMP): objectively compare results from climate models with observations using well-established statistical tests
@@ Line 216: / Line 263: @@
   * [[https://github.com/pierre-rouanet/dtw|dtw]]: DTW (Dynamic Time Warping) python module
   * [[http://toblerity.org/shapely/project.html|shapely]]: a Python wrapper for GEOS for algebraic manipulation of geometry (manipulation and analysis of geometric objects in the Cartesian plane)
-  * [[http://scitools.org.uk/cartopy/|cartopy]]: a library providing cartographic tools for python
+  * [[http://scitools.org.uk/cartopy/|cartopy]]: a Python package designed for geospatial data processing in order to produce maps and other geospatial data analyses
   * [[https://rpy2.readthedocs.io/en/version_2.8.x/|rpy2]]: providing simple and robust access to R from within Python
   * [[http://matplotlib.org/cmocean/|cmocean]]: beautiful colormaps for oceanography
@@ Line 224: / Line 271: @@
   * [[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://joblib.readthedocs.io/en/latest/|joblib]]: running Python functions as pipeline jobs
+  * [[https://jiffyclub.github.io/palettable/|Palettable]]: Color palettes for Python
 ==== Removed packages ====
@@ Line 233: / Line 282: @@
 After following the steps above, we get the following environments. Use the ''conda env list'' command (same result as ''conda info %%--%%envs'') to get the up-to-date list of available environments.
-Use ''conda list -n env_name'' to get a detailed list of which packages/modules are installed
+Use ''conda list -n env_name'' to get a detailed list of which packages/modules are installed, or check the [[other:uvcdat:conda_notes#installation_history|conda Installation history]] section to get more details
-^  Environment\\ name  ^  Server  ^   Summary  ^  ''conda list''  ^
+^  Environment\\ name  ^  Server  ^   Summary  ^
-| 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 & Python 3.6 | |
+| cdatm-nightly_py2 |  LSCE\\ ciclad  | CDAT nightly & P 2.7 //JYP version// |
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