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other:uvcdat:cdat_conda:cdat_8_0_py2 [2019/03/07 14:05]
jypeter [Environments summary] cdat-8.0_py2 and cdat-8.0_py2 removed from ciclad
other:uvcdat:cdat_conda:cdat_8_0_py2 [2021/02/26 21:11]
jypeter [Installing Miniconda3] Many updates
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 ==== Installing Miniconda3 ====  ==== Installing Miniconda3 ==== 
  
-We have installed a new version of Miniconda3 (steps below adapted from the [[other:​uvcdat:​conda_notes#​installing_miniconda|installing miniconda]] instructions)+  * You don't need to be (and **you should not be**) //root// when you install Miniconda3. You just need enough disk space where you have write access 
 +  * If you are installing ​Miniconda3 ​in a Linux environment on a [[other:​win10wsl|Windows 10 computer using Windows Subsystem for Linux (WSL)]], pay special attention to the instructions on the **WSL** lines 
 + 
 +The steps below are adapted from the older (but with lots of extra and possibly useful details) ​[[other:​uvcdat:​conda_notes#​installing_miniconda|installing miniconda]] instructions 
 + 
 +  * Get the [[https://​repo.anaconda.com/​miniconda/​Miniconda3-latest-Linux-x86_64.sh|Python 3.8 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, if you are using WSL) 
 +      * e.g. Linux at LSCE:\\ ''​cd /​home/​scratch01/<​your_login>''​ 
 +      * e.g. WSL, assuming that there is a ''​C:​\Scratch\<​your_login>''​ directory:​\\ ''​cd /​mnt/​c/​Scratch/<​your_login>''​ 
 +    * Use ''​wget''​ to download the installer:​\\ ''​wget https://​repo.anaconda.com/​miniconda/​Miniconda3-latest-Linux-x86_64.sh''​ (90 Mb, 26 Feb 2021)
  
-  * 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 
-      * Linux:''​cd /​home/​scratch01/​jypeter''​ 
-      * WSL: ''​cd /​mnt/​h/​Scratch/​jypeter/''​ (assuming that there is a ''​H:​\Scratch\jypeter''​ directory) 
-    * ''​wget https://​repo.continuum.io/​miniconda/​Miniconda3-latest-Linux-x86_64.sh''​ (67 Mo, 15 Feb 2019) 
   * Execute the installer   * Execute the installer
     * ''​bash Miniconda3-latest-Linux-x86_64.sh''​     * ''​bash Miniconda3-latest-Linux-x86_64.sh''​
       * Accept the license       * Accept the license
-      * 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: +      ​* Note: at the end of the installation (next step), **answer //no// to the following question**, so that the installer does not change your existing shell initialization files!\\ ''​Do you wish the installer to initialize Miniconda3 by running conda init? [yes|no]''​ => **NO** 
-        * Linux LSCE: ''/​home/​share/​unix_files/​cdat/​miniconda3''​ +      ​* Specify an explicit installation path **outside of your //home// directory**,​ with enough disk space (more than 3 Gb if you are going to install CDAT and some extra packages), preferably on a disk that is not backed up: 
-        * Linux ciclad: ''/​data/​jypmce/​cdat/​miniconda3''​ +        ​* Installations by //JYP//: 
-        * 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''​ +          ​* Linux at LSCE: ''/​home/​share/​unix_files/​cdat/​miniconda3'',​ or another subdirectory of ''/​home/​share/​unix_files/​cdat/​''​  
-        Resulting ​''​miniconda3''​ directory size is 302M\\ <​code>​ >du -sh miniconda3 +          * Linux on ciclad: ''/​data/​jypmce/​cdat/​miniconda3'',​ or another sub-directory of ''/​data/​jypmce/​cdat/​''​ 
-302M    ​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)\\ ​You need to accept the installation in the default location: ''/​home/​<​your_login>​/​miniconda3''​ 
- >​cd miniconda3 +      The resulting ​''​miniconda3''​ directory size is 342M\\ <​code>​ > du -sh miniconda3 
-/​home/​share/​unix_files/​cdat/​miniconda3 +342M    ​miniconda3 
- >​du -sh * + 
-6.3M    ​bin + > cd miniconda3 
-2.0M    compiler_compat + 
-524K    ​conda-meta + > du -sh * 
-4.0K    ​envs +20M     bin 
-28K     etc +0       ​compiler_compat 
-5.2M    ​include +4.0K    condabin 
-146M    lib +684K    ​conda-meta 
-8.0K    LICENSE.txt +0       envs 
-142M    ​pkgs +16K     etc 
-928K    ​share +5.5M    ​include 
-92K     ssl +4.0K    ​info 
-12K     x86_64-conda_cos6-linux-gnu</​code>​ +198M    lib 
-      Accept ​the automatic update of the //PATH// variable in ''​.bashrc''​ (note: the installer automatically creates a backup of ''​.bashrc''​). This will some extra lines at the end of ''​.bashrc''​ used by the //​old-style ​conda initialization//​ (we will later switch to the //​new-style//​). The added lines should look like+12K     LICENSE.txt 
-        * ''​# added by Miniconda3 installer''​\\ ''​export PATH="/home/share/unix_files/cdat/​miniconda3/​bin:​$PATH"''​ +114M    ​pkgs 
-        * ''#​ added by Miniconda4.xxx installer''​\\ ''​[some really fancy bash shell commands]''​ +604K    ​share 
-  Remove the installer: ''​rm Miniconda3-latest-Linux-x86_64.sh''​ +4.0K    shell 
-  * Open a new terminal (if you use bash) or open a new terminal and type ''​bash''​ +0       ssl 
-    * check if the python from the conda distribution has been correctly installed\\ ​<​code>​ > bash+0       x86_64-conda_cos6-linux-gnu</​code>​ 
 + 
 +  ​Initialize ​the newly installed ​conda environment
 +    bash shell: ​''​source <​installation_path>​/miniconda3/etc/profile.d/conda.sh''​ 
 +    tcsh shell: ''​source <​installation_path>/​miniconda3/​etc/​profile.d/conda.csh''​ 
 + 
 +  * Check if you can use the ''​conda'' ​command, and use it to initialize the //base// environment 
 +    * <​code>​$ which conda 
 +<​installation_path>/​miniconda3/​condabin/​conda
 $ which python $ which python
-/home/​share/​unix_files/​cdat/​miniconda3/​bin/​python +/usr/​bin/​python 
-which conda +$ conda activate 
-/​home/​share/​unix_files/​cdat/​miniconda3/​bin/​conda</​code>​ +(base) $ which python 
-    * Update ​and clean the new installation\\ <​code>​$ conda update --all +<​installation_path>​/​miniconda3/​bin/​python</​code>​ 
-$ du -sh /​home/​share/​unix_files/​cdat/​miniconda3 +  * Update the new installation 
-515M    /​home/​share/​unix_files/​cdat/​miniconda3 +    * <​code>​$ conda update --all
-$ conda clean --all +
-$ du -sh /​home/​share/​unix_files/​cdat/​miniconda3 +
-270M    /​home/​share/​unix_files/​cdat/​miniconda3 +
-$ conda list +
-# packages in environment at /​home/​share/​unix_files/​cdat/​miniconda3:​ +
-+
-# Name                    Version ​                  ​Build ​ Channel +
-[...] +
-python ​                   3.7.1                h0371630_3 +
-readline ​                 7.0                  h7b6447c_5 +
-requests ​                 2.20.0 ​                  ​py37_0+
 [...]</​code>​ [...]</​code>​
 +    * During the update, the ''​miniconda3''​ directory size goes from 432 Mb to 581 Mb. This directory will keep on growing, which is the reason why you should put it on a (preferably non backed up) disk where you have //enough// space
 +  * Remove the installer: ''​rm Miniconda3-latest-Linux-x86_64.sh''​
  
 ==== Post-Miniconda3 installation ==== ==== Post-Miniconda3 installation ====
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     * ''​conda install -n cdatm17_py2 -c stefraynaud -c conda-forge spanlib''​     * ''​conda install -n cdatm17_py2 -c stefraynaud -c conda-forge spanlib''​
     * Test: ''​python -c 'from spanlib.analyzer import Analyzer'​ ''​     * Test: ''​python -c 'from spanlib.analyzer import Analyzer'​ ''​
 +  ​
 +  * [[https://​climaf.readthedocs.io/​en/​latest/​|CliMAF]]:​ a Climate Model Assessment Framework
 +    * [[other:​uvcdat:​cdat_conda:​climaf_install|Installation notes]]
  
 ==== TODO ==== ==== TODO ====
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   * [[http://​wrf-python.readthedocs.io/​en/​latest/​|wrf-python]]:​ A collection of diagnostic and interpolation routines for use with output from the Weather Research and Forecasting (WRF-ARW) Model   * [[http://​wrf-python.readthedocs.io/​en/​latest/​|wrf-python]]:​ A collection of diagnostic and interpolation routines for use with output from the Weather Research and Forecasting (WRF-ARW) Model
-    * ''​conda install -n cdatm15 ​-c conda-forge wrf-python''​+    * ''​conda install -n cdatxxx ​-c conda-forge wrf-python''​
    
   * [[https://​glances.readthedocs.io/​en/​stable/​index.html|glances]]:​ a cross-platform monitoring tool (similar to ''​top''​)   * [[https://​glances.readthedocs.io/​en/​stable/​index.html|glances]]:​ a cross-platform monitoring tool (similar to ''​top''​)
-    * ''​conda install -n cdatm15 ​-c conda-forge glances''​+    * ''​conda install -n cdatxxx ​-c conda-forge glances''​
     * [[https://​github.com/​nicolargo/​glances|glances@github]]     * [[https://​github.com/​nicolargo/​glances|glances@github]]
  
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   * [[https://​cmor.llnl.gov/​|CMOR]]   * [[https://​cmor.llnl.gov/​|CMOR]]
-    * Update with: ''​conda update -n cdatm15 ​-c conda-forge -c pcmdi -c uvcdat cmor''​+    * Update with: ''​conda update -n cdatxxx ​-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'​ ''​       * Get version number with: ''​python -c 'from cmor import *; print CMOR_VERSION_MAJOR,​ CMOR_VERSION_MINOR,​ CMOR_VERSION_PATCH'​ ''​
  
other/uvcdat/cdat_conda/cdat_8_0_py2.txt · Last modified: 2021/02/27 13:55 by jypeter