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--- other:uvcdat:cdat_conda:cdat_8_2_1 [2021/03/01 11:08]
jypeter [Getting ready for a moving default CDAT] Updated for 8.2.1
+++ other:uvcdat:cdat_conda:cdat_8_2_1 [2021/03/05 20:41]
jypeter [Installing CDAT 8.2.1] started experimenting with nompi and strict options
@@ Line 72: / Line 72: @@
 M    /home/share/unix_files/cdat/miniconda3_21-02</code>
-We can also use ''conda env list'' and remove some obsolete versions with ''conda remove -n obsolete_name --all'' to get some space
+We can also use ''conda env list'' and remove some obsolete versions with ''conda remove -n obsolete_environment %%--%%all'', in order to free up some space
 === Python 2.7 version ===
-Python 2 is deprecated in CDAT, starting with CDAT 8.2.1. If you still need to use python 2.7, please use [[other:uvcdat:cdat_conda:cdat_8_1|CDAT 8.1]]
+<wrap hi>Python 2.x is deprecated in CDAT, starting with CDAT 8.2.1</wrap>.
+If you still need to use python 2.7, please use [[other:uvcdat:cdat_conda:cdat_8_1|CDAT 8.1]]
 === Python 3.8 version ===
 <WRAP center round important 60%>
-It's possible that, when using the tcsh shell and trying to use the ''conda create -n cdat-8.2.1_py3 lots_of_parameters_with_stars'' line, you will get the following error message:
+It's possible that, when using the //tcsh// shell and trying to use the ''conda create -n cdat-8.2.1_py3 lots_of_parameters_with_wildcards'' line, you will get the following error message:
 **conda: No match**
-This may be due to [[https://gitmemory.com/issue/conda/conda/9771/608209654|CSH install/search fail with '*' variable in an argument]]. In that case, just type ''bash'' and run the installation command in a //bash// shell
+Apparently the //tcsh// version of conda does not like wildcards too much ([[https://gitmemory.com/issue/conda/conda/9771/608209654|CSH install/search fail with '*' variable in an argument]])...
+In that case, just type ''bash'' and run the installation command in a //bash// shell
 </WRAP>
 The installation line below is based on information from the [[https://github.com/CDAT/cdat/wiki/install#for-linux-python|CDAT wiki page]]. See also [[https://github.com/CDAT/cdat/issues/2265|Some questions and notes about 8.2.1 installation]]
+<code>
+bash-4.2$ conda config --env --add channels conda-forge
+bash-4.2$ conda config --set channel_priority strict
+bash-4.2$ cat .condarc
+channels:
+  - conda-forge
+  - defaults
+$ conda config --describe channel_priority
+$ conda create -n cdat-8.2.1_nompi_py3 -c conda-forge -c cdat/label/v8.2.1 cdat "libnetcdf=*=nompi_*" "mesalib=18.3.1" "python=3"</code>
 <code>$ conda create -n cdat-8.2.1_py3 -c conda-forge -c cdat/label/v8.2.1 cdat "libnetcdf=*=mpi_openmpi_*" "mesalib=18.3.1" "python=3"</code>
-===== Cloning CDAT before adding specific packages for LSCE =====
+Resulting list of installed packages
+  * ''conda list -n cdat-8.2.1_py3 > cdat_8.2.1_installed_packages.txt''
+  * {{ :other:uvcdat:cdat_conda:cdat_8.2.1_installed_packages.txt |}}
+[[https://github.com/CDAT/cdat/issues/2265|Some extra installation notes]]
+===== Cloning the base CDAT environment before adding specific packages for LSCE =====
 <WRAP center round alert 60%>
@@ Line 109: / Line 128: @@
 Notes:
-  * Why //cloning//? The initial CDAT environment is strictly the one created at PCMDI and certified by PCMDI. Rather than making changes directly in there, we keep it as it is, clone it, and work on the clone
+  * Why //cloning//? The initial CDAT environment is strictly the one created at PCMDI and certified by PCMDI. Rather than making changes directly in there, we keep it as it is, clone it, and make changes in the cloned environment
-  * Carefully working on different python environments (possibly cloned) is safer in a multi-user environment
+  * Carefully working on different python environments (possibly cloned) is safer in a multi-user environment (i.e. you can have people use a specific environment, and make tests in another environment)
   * Cloning a full environment uses Linux hard links and  requires less disk space than making a real copy
@@ Line 123: / Line 142: @@
-===== Getting ready for a moving default CDAT =====
+===== Getting ready for a moving default CDAT environment =====
 <WRAP center round alert 60%>
@@ Line 134: / Line 153: @@
 This step could probably be listed at the **end**, especially in a multi-user environment!
-If there is already a ''cdatm_py3'' link, make sure that the new CDAT version is stable and working correctly before updating the ''cdatm_py3'' link
+If there is already a ''cdatm_py3'' link (pointing to an older environment), make sure that the new CDAT environment is stable and working correctly before updating the ''cdatm_py3'' link
 </WRAP>
-We create a **//cdatm_py3// symbolic link** in the ''envs'' directory, that has a //stable name// but can be moved to point to the latest default (and hopefully stable) CDAT. In that case, most users can just activate this //cdatm_py3// version and always get the latest stable version
+We create a **//cdatm_py3// symbolic link** in the ''envs'' directory, that has a //stable name// but can be moved to point to the latest default (and hopefully stable) CDAT environment. In that case, most users can just activate this //cdatm_py3// environment and always get the latest stable version.
 <code>$ cd /home/share/unix_files/cdat/miniconda3_21-02/envs
-$ ln -s cdatm19_py3 cdatm_py3</code>
+$ ln -s cdatm19_py3 cdatm_py3
-===== Customizing UV-CDAT for LSCE =====
+conda env list
+# conda environments:
+#
+base                  *  /home/share/unix_files/cdat/miniconda3_21-02
+cdat-8.2.1_py3           /home/share/unix_files/cdat/miniconda3_21-02/envs/cdat-8.2.1_py3
+cdatm19_py3              /home/share/unix_files/cdat/miniconda3_21-02/envs/cdatm19_py3
+cdatm_py3                /home/share/unix_files/cdat/miniconda3_21-02/envs/cdatm_py3
-==== Testing vcs ====
+$ ls -l /home/share/unix_files/cdat/miniconda3_21-02/envs/
+drwxr-xr-x [...] cdat-8.2.1_py3/
-Start python and paste the following lines
+drwxr-xr-x [...] cdatm19_py3/
+lrwxrwxrwx [...] cdatm_py3 -> cdatm19_py3/
-<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)...
+===== Customizing UV-CDAT for LSCE =====
-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
+==== A quick test of cdms2 and vcs ====
-<code>x.png('test_mesalib')
+You can use the quick test shown in [[https://github.com/CDAT/cdat/wiki/install#to-test-your-cdat-installation|To Test Your CDAT Installation]], and check if you get the expected png file
-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
+You can also check the [[other:uvcdat:cdat_conda:cdat_8_1#testing_vcs|Testing vcs]] section of the LSCE installation of CDAT 8.1
 ==== Downloading cdms2/vcs test data ====
-You should download the test data (174M of data...) and use it in the example scripts that you want to distribute, and scripts you write for reporting the errors you find (if any...)
+You should download the test data (174M of data...) and use it in the example scripts that you want to distribute, and scripts you write for reporting the errors you find (if any...). The downloaded data files will be available in: ''vcs.sample_data''
-<code>$ conda activate cdatm19_py2
+<code>$ conda activate cdatm19_py3
-(cdatm19_py2) $ python -c 'import vcs; vcs.download_sample_data_files(); print("\nFinished downloading sample data to " + vcs.sample_data)'
+(cdatm19_py3) $ python -c 'import vcs; vcs.download_sample_data_files(); print("\nFinished downloading sample data to " + vcs.sample_data)'
 [...]
-Finished downloading sample data to /home/share/unix_files/cdat/miniconda3/envs/cdatm19_py2/share/cdat/sample_data
+Finished downloading sample data to /home/share/unix_files/cdat/miniconda3_21-02/envs/cdatm19_py3/share/cdat/sample_data
-(cdatm19_py2) $ du -sh /home/share/unix_files/cdat/miniconda3/envs/cdatm19_py2/share/cdat/sample_data
+(cdatm19_py3) $ du -sh /home/share/unix_files/cdat/miniconda3_21-02/envs/cdatm19_py3/share/cdat/sample_data
-M    /home/share/unix_files/cdat/miniconda3/envs/cdatm19_py2/share/cdat/sample_data
+M    /home/share/unix_files/cdat/miniconda3_21-02/envs/cdatm19_py3/share/cdat/sample_data
-</code>
+$ python
+>>> import os, vcs
+>>> vcs.sample_data
+'/home/jypeter/miniconda3_21-02/envs/cdat-8.2.1_py3/share/cdat/sample_data'
+>>> os.listdir(vcs.sample_data)
+['BlueMarble.ppm', 'clt.nc', 'geo.1deg.ctl', 'geo.1deg.gmp', 'geo.1deg.grb', ...]</code>
 ==== Packages that have no dependency problems ====
-After cloning, we are ready to install some extra packages that may be requested by LSCE users
+After [[#cloning_the_base_cdat_environment_before_adding_specific_packages_for_lsce|cloning]], we are ready to install some extra packages that may be requested by LSCE users
   * We first try to install together as many packages as possible that don't require other channels than //conda-forge//, and that don't request a downgrade of what is already installed
@@ Line 185: / Line 212: @@
 <code># You can use the following to keep a trace of what will be installed
-#$ conda install --dry-run -n cdatm19_py2 -c conda-forge pillow pandas statsmodels seaborn scikit-image seawater gsw netcdf4 pyferret basemap-data-hires xlsxwriter cmocean rpy2 gdal windspharm  > somewhere/extra_packages.txt
+#$ conda install --dry-run -n cdatm19_py3 -c conda-forge pillow pandas statsmodels seaborn scikit-image seawater gsw netcdf4 pyferret basemap-data-hires xlsxwriter cmocean rpy2 gdal windspharm  > somewhere/extra_packages.txt
 # Install...
-$ conda install -n cdatm19_py2 -c conda-forge pillow pandas statsmodels seaborn scikit-image seawater gsw netcdf4 pyferret ferret_datasets basemap-data-hires xlsxwriter cmocean rpy2 gdal windspharm
+$ conda install -n cdatm19_py3 -c conda-forge pillow pandas statsmodels seaborn scikit-image seawater gsw netcdf4 pyferret ferret_datasets basemap-data-hires xlsxwriter cmocean rpy2 gdal windspharm
 [...]
@@ Line 197: / Line 224: @@
 Packages installed with //pip//
   * [[https://earthsystemcog.org/projects/wip/CMIP6DataRequest|dreqPy]]: CMIP6 Data Request Python API
-    * ''conda activate cdatm19_py2''\\ ''pip install dreqPy''
+    * ''conda activate cdatm19_py3''\\ ''pip install dreqPy''
     * Update with: ''pip install %%--%%upgrade dreqPy''
       * Get version number with:\\ <code>$ drq -v
@@ Line 203: / Line 230: @@
   * [[https://github.com/PBrockmann/ipython_ferretmagic|ipython_ferretmagic]]: IPython notebook extension for ferret
-    * ''conda activate cdatm19_py2''\\ ''pip install ferretmagic''
+    * ''conda activate cdatm19_py3''\\ ''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 cdatm19_py2 -c conda-forge cmor''
+    * ''conda install -n cdatm19_py3 -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
-    * ''conda install -n cdatm19_py2 -c conda-forge -c vacumm vacumm''
+    * ''conda install -n cdatm19_py3 -c conda-forge -c vacumm vacumm''
     * <wrap hi>Warning!</wrap> [[https://github.com/VACUMM/vacumm/issues/15|standard install of vacumm does not work for Python3]]
   * [[https://github.com/stefraynaud/spanlib|spanlib]]: Spectral Analysis Library
-    * ''conda install -n cdatm19_py2 -c stefraynaud -c conda-forge spanlib''
+    * ''conda install -n cdatm19_py3 -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 cdatm19_py2 -c conda-forge cartopy''
+    * ''conda install -n cdatm19_py3 -c conda-forge cartopy''
   * [[https://joblib.readthedocs.io/en/latest/|joblib]]: running Python functions as pipeline jobs
-    * ''conda install -n cdatm19_py2 -c conda-forge joblib''
+    * ''conda install -n cdatm19_py3 -c conda-forge joblib''
   * [[https://climaf.readthedocs.io/en/latest/|CliMAF]]: a Climate Model Assessment Framework
@@ Line 230: / Line 257: @@
   * [[https://jiffyclub.github.io/palettable/|Palettable]]: Color palettes for Python
-    * ''conda install -n cdatm19_py2 -c conda-forge palettable''
+    * ''conda install -n cdatm19_py3 -c conda-forge palettable''
 ==== TODO ====
@@ Line 313: / Line 340: @@
 ^  Environment\\ name  ^  Server  ^   Summary  ^
-| cdat-8.2.1_py2 |  LSCE\\ ciclad  | CDAT 8.2.1 & Python 2.7 |
+| cdat-8.2.1_py3 |  LSCE\\ ciclad  | CDAT 8.2.1 & Python 2.7 |
 | cdat-8.2.1_py3 |  LSCE  | CDAT 8.2.1 & Python 3.6 |
-| cdatm19_py2\\ or //cdatm_py2// |  LSCE\\ ciclad  | CDAT 8.2.1 & P 2.7 //JYP version// |
+| cdatm19_py3\\ or //cdatm_py3// |  LSCE\\ ciclad  | CDAT 8.2.1 & P 2.7 //JYP version// |
 | cdatm19_py3\\ or //cdatm_py3// |  LSCE  | CDAT 8.2.1 & P 3.7 //JYP version// |
-| cdat-nightly_py2 |  LSCE\\ ciclad  | CDAT nightly & Python 2.7 |
-| cdatm-nightly_py2 |  LSCE\\ ciclad  | CDAT nightly & P 2.7 //JYP version// |
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