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--- other:uvcdat:cdat_conda:cdat_8_0_py2 [2018/11/08 17:01]
jypeter
+++ other:uvcdat:cdat_conda:cdat_8_0_py2 [2019/02/27 14:27]
jypeter
@@ Line 18: / Line 18: @@
 ==== Installing Miniconda3 ====
-We have installed a new version of Miniconda3, by following the existing [[other:uvcdat:conda_notes#installing_miniconda|installing miniconda]] instructions
+We have installed a new version of Miniconda3 (steps below adapted from the [[other:uvcdat:conda_notes#installing_miniconda|installing miniconda]] instructions)
-  * Follow the [[https://conda.io/docs/install/quick.html|Quick install]] steps to install Miniconda
+  * Get the [[https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh|Python 3.7 Linux 64-bit (bash installer)]] (unless there is a [[https://conda.io/miniconda.html|more recent version?]])
-    * Get the [[https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh|Python 3.7 Linux 64-bit (bash installer)]] (unless there is a [[https://conda.io/miniconda.html|more recent version?]])
+    * Find some temporary space on Linux or Windows
-      * ''cd /home/scratch01/jypeter'' (some temporary storage space for the installer)
+      * Linux:''cd /home/scratch01/jypeter''
-      * ''wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh'' (60 Mo, 11 Nov 2018)
+      * WSL: ''cd /mnt/h/Scratch/jypeter/'' (assuming that there is a ''H:\Scratch\jypeter'' directory)
-    * Execute the installer
+    * ''wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh'' (67 Mo, 15 Feb 2019)
-      * ''bash Miniconda3-latest-Linux-x86_64.sh''
+  * Execute the installer
-        * Accept the license
+    * ''bash Miniconda3-latest-Linux-x86_64.sh''
-        * Specify an explicit installation path **outside of the home directory**, with enough disk space (more than 3G if you are going to install UV-CDAT and some extra packages), preferably on a disk that is not backed up: ''/home/share/unix_files/cdat/miniconda3''
+      * Accept the license
-          * Resulting ''miniconda3'' directory size is 302M\\ <code> >du -sh miniconda3
+      * Specify an explicit installation path **outside of the home directory**, with enough disk space (more than 3G if you are going to install UV-CDAT and some extra packages), preferably on a disk that is not backed up:
+        * Linux: ''/home/share/unix_files/cdat/miniconda3''
+        * WSL: installing to a directory that is not in ''/home/'' <wrap hi>does not work</wrap> (e.g. ''/mnt/h/CDAT/miniconda3'',assuming there is a ''H:\CDAT\'' directory, does not work)\\ Need to accept the installation in the default location: ''/home/jypeter/miniconda3''
+        * Resulting ''miniconda3'' directory size is 302M\\ <code> >du -sh miniconda3
 M    miniconda3
  >cd miniconda3
@@ Line 45: / Line 49: @@
 K     ssl
 K     x86_64-conda_cos6-linux-gnu</code>
-        * Accept the automatic update of the //PATH// variable in ''.bashrc'' (note: the installer automatically creates a backup of ''.bashrc'')
+      * Accept the automatic update of the //PATH// variable in ''.bashrc'' (note: the installer automatically creates a backup of ''.bashrc'')
-          * ''# added by Miniconda3 installer''\\ ''export PATH="/home/share/unix_files/cdat/miniconda3/bin:$PATH"''
+        * ''# added by Miniconda3 installer''\\ ''export PATH="/home/share/unix_files/cdat/miniconda3/bin:$PATH"''
-    * Open a new terminal (if you use bash) or open a new terminal and type ''bash''
+  * Open a new terminal (if you use bash) or open a new terminal and type ''bash''
-      * check if the python from the conda distribution has been correctly installed\\ <code> > bash
+    * check if the python from the conda distribution has been correctly installed\\ <code> > bash
 $ which python
 /home/share/unix_files/cdat/miniconda3/bin/python
 $ which conda
 /home/share/unix_files/cdat/miniconda3/bin/conda</code>
-      * Update and clean the new installation\\ <code>$ conda update --all
+    * Update and clean the new installation\\ <code>$ conda update --all
 $ du -sh /home/share/unix_files/cdat/miniconda3
 M    /home/share/unix_files/cdat/miniconda3
@@ Line 68: / Line 72: @@
 requests                  2.20.0                   py37_0
 [...]</code>
-  * Remove the miniconda3 initialization lines that were automatically added at the end of ''.bashrc'' and put them (and other useful commands) in a special initialization file (see ''~jypeter/.conda3_jyp.sh'' below), that can be sourced only when we actually want to use conda and CDAT\\ <code>bash-4.2$ which python
+==== Post-Miniconda3 installation ====
+The idea is to remove the miniconda3 initialization lines that were automatically added at the end of ''.bashrc'' and put them (and other useful commands) in a special initialization file, that can be sourced only when we actually want to use conda and CDAT
+=== New style initialization ===
+Note: this is the **new** ''conda activate some_version'' style
+See the ''~jypeter/.conda3_jyp.sh'' file below, and how to use it, **in a bash shell**. In a **tcsh shell**, see the ''~jypeter/.conda3_jyp.csh'' further down
+<code>$ which python
 /usr/bin/python
 $ cat ~jypeter/.conda3_jyp.sh
-# Conda initialization by JYP
+# Conda initialization by JYP, NEW style
 #
 # Use this for working with conda and CDAT centrally managed by JYP
+#
+# Execute this file in a BASH shell with
+#     source path/this_file
+# Then get the list of available python distributions with
+#     conda env list
+# Then activate a specific distribution with
+#     conda activate version_name
 #
 # More details in:
-#   https://wiki.lsce.ipsl.fr/pmip3/doku.php/other:python:starting#conda-based_v                                    ersions_of_uv-cdat
+#   https://wiki.lsce.ipsl.fr/pmip3/doku.php/other:python:starting#conda-based_versions_of_uv-cdat
 #   https://wiki.lsce.ipsl.fr/pmip3/doku.php/other:uvcdat:conda_notes
 #
 # Jean-Yves Peterschmitt - LSCE - 11/2018
-export PATH="/home/share/unix_files/cdat/miniconda3/bin:$PATH"
+. /home/share/unix_files/cdat/miniconda3/etc/profile.d/conda.sh
 # Use the alias below to easily determine where your python
@@ Line 91: / Line 114: @@
 # The end
 $ source ~jypeter/.conda3_jyp.sh
+$ conda activate cdatm
+(cdatm) $ which python
+/home/share/unix_files/cdat/miniconda3/envs/cdatm/bin/python
+</code>
+**tcsh shell** usage example
+<code> >which python
+/usr/bin/python
+ >cat ~jypeter/.conda3_jyp.csh
+# Conda initialization by JYP, NEW style
+#
+# Use this for working with conda and CDAT centrally managed by JYP
+#
+# Execute this file in a TCSH shell with
+#     source path/this_file
+# Then get the list of available python distributions with
+#     conda env list
+# Then activate a specific distribution with
+#     conda activate version_name
+#
+# More details in:
+#   https://wiki.lsce.ipsl.fr/pmip3/doku.php/other:python:starting#conda-based_versions_of_uv-cdat
+#   https://wiki.lsce.ipsl.fr/pmip3/doku.php/other:uvcdat:conda_notes
+#
+# Jean-Yves Peterschmitt - LSCE - 11/2018
+source /home/share/unix_files/cdat/miniconda3/etc/profile.d/conda.csh
+# Use the alias below to easily determine where your python
+# interpreter is located
+alias wp "which python"
+# Where are ALL the python interpreters in the search path
+alias wpa "\which -a python"
+# The end
+ >source  ~jypeter/.conda3_jyp.csh
+ >conda activate cdatm
+(cdatm) >which python
+/home/share/unix_files/cdat/miniconda3/envs/cdatm/bin/python</code>
+=== Old style initialization ===
+Note: this is the **old** ''source activate some_version'' style
+See the ''~jypeter/.conda3old_jyp.sh'' file below, and how to use it, **in a bash shell**
+<code>bash-4.2$ which python
+/usr/bin/python
+$ cat .conda3old_jyp.sh
+# Conda initialization by JYP, OLD style
+#
+# Use this for working with conda and CDAT centrally managed by JYP
+#
+# Execute this file in a BASH shell with
+#     source path/this_file
+# Then get the list of available python distributions with
+#     conda env list
+# Then activate a specific distribution with
+#     source activate version_name
+#
+# More details in:
+#   https://wiki.lsce.ipsl.fr/pmip3/doku.php/other:python:starting#conda-based_versions_of_uv-cdat
+#   https://wiki.lsce.ipsl.fr/pmip3/doku.php/other:uvcdat:conda_notes
+#
+# Jean-Yves Peterschmitt - LSCE - 11/2018
+export PATH="/home/share/unix_files/cdat/miniconda3/bin:$PATH"
+# Use the alias below to easily determine where your python
+# interpreter is located
+alias wp="which python"
+# Where are ALL the python interpreters in the search path
+alias wpa="which -a python"
+# The end
+$ source ~jypeter/.conda3old_jyp.sh
 $ wp
 /home/share/unix_files/cdat/miniconda3/bin/python
@@ Line 98: / Line 210: @@
 ==== Installing CDAT 8.0 ====
-<code>conda create -n cdat-8.0_py2 -c cdat/label/v80 -c conda-forge -c cdat python=2.7 cdat
+<code>$ conda create -n cdat-8.0_py2 -c cdat/label/v80 -c conda-forge -c cdat python=2.7 cdat
 # Generate the list of installed packages
-conda list -n cdat-8.0_py2 > /home/scratch01/jypeter/cdat-8.0_py2_list_181108.txt</code>
+$ conda list -n cdat-8.0_py2 > /home/scratch01/jypeter/cdat-8.0_py2_list_181108.txt</code>
 List of installed packages: {{:other:uvcdat:cdat_conda:cdat-8.0_py2_list_181108.txt}}

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