other:uvcdat:cdat_conda:cdat_8_0_py2
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other:uvcdat:cdat_conda:cdat_8_0_py2 [2018/11/13 17:21] jypeter Added details for activating conda |
other:uvcdat:cdat_conda:cdat_8_0_py2 [2019/03/01 16:12] jypeter |
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| ==== Installing Miniconda3 ==== | ==== 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 LSCE: ''/home/share/unix_files/cdat/miniconda3'' | ||
| + | * Linux ciclad: ''/data/jypmce/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 | ||
| 302M miniconda3 | 302M miniconda3 | ||
| >cd miniconda3 | >cd miniconda3 | ||
| Line 45: | Line 49: | ||
| 92K ssl | 92K ssl | ||
| 12K x86_64-conda_cos6-linux-gnu</code> | 12K 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''). 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: |
| - | * ''# 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'' | + | * ''# added by Miniconda4.xxx installer''\\ ''[some really fancy bash shell commands]'' |
| - | * check if the python from the conda distribution has been correctly installed\\ <code> > bash | + | * Remove the installer: ''rm Miniconda3-latest-Linux-x86_64.sh'' |
| + | * 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 | ||
| $ which python | $ which python | ||
| /home/share/unix_files/cdat/miniconda3/bin/python | /home/share/unix_files/cdat/miniconda3/bin/python | ||
| $ which conda | $ which conda | ||
| /home/share/unix_files/cdat/miniconda3/bin/conda</code> | /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 | $ du -sh /home/share/unix_files/cdat/miniconda3 | ||
| 515M /home/share/unix_files/cdat/miniconda3 | 515M /home/share/unix_files/cdat/miniconda3 | ||
| Line 71: | Line 77: | ||
| ==== Post-Miniconda3 installation ==== | ==== 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 | + | 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 (in order to avoid potentiel side effects) |
| === New style initialization === | === New style initialization === | ||
| Line 77: | Line 83: | ||
| Note: this is the **new** ''conda activate some_version'' style | 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 | + | 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. In both shell cases, if you are installing your own version of python, you need to use your own location of the initialization files in the ''source'' lines, and you can use another file name than ''conda3_jyp'' |
| <code>$ which python | <code>$ which python | ||
| Line 100: | Line 106: | ||
| # Jean-Yves Peterschmitt - LSCE - 11/2018 | # Jean-Yves Peterschmitt - LSCE - 11/2018 | ||
| - | . /home/share/unix_files/cdat/miniconda3/etc/profile.d/conda.sh | + | source /home/share/unix_files/cdat/miniconda3/etc/profile.d/conda.sh |
| # Use the alias below to easily determine where your python | # Use the alias below to easily determine where your python | ||
| Line 113: | Line 119: | ||
| $ source ~jypeter/.conda3_jyp.sh | $ source ~jypeter/.conda3_jyp.sh | ||
| - | $ conda activate cdatm | + | $ conda activate |
| - | (cdatm) $ which python | + | (base) $ which python |
| - | /home/share/unix_files/cdat/miniconda3/envs/cdatm/bin/python | + | /home/share/unix_files/cdat/miniconda3/bin/python |
| </code> | </code> | ||
| Line 147: | Line 153: | ||
| # interpreter is located | # interpreter is located | ||
| alias wp "which python" | alias wp "which python" | ||
| - | |||
| - | # Where are ALL the python interpreters in the search path | ||
| - | alias wpa "\which -a python" | ||
| # The end | # The end | ||
| Line 155: | Line 158: | ||
| >source ~jypeter/.conda3_jyp.csh | >source ~jypeter/.conda3_jyp.csh | ||
| - | >conda activate cdatm | + | >conda activate |
| + | |||
| + | (base) >which python | ||
| + | /home/share/unix_files/cdat/miniconda3/bin/python</code> | ||
| - | (cdatm) >which python | + | You probably don't want to type the //source// line each time you need to use your conda based python, so you can add a ''source ~jypeter/.conda3_jyp.sh'' line in your ''~/.bashrc'' file, and ''source ~jypeter/.conda3_jyp.csh'' line in your ''~/.cshrc'' file. Then, when you need a specific python environment, just type ''conda activate name_of_the_specific_environment'' |
| - | /home/share/unix_files/cdat/miniconda3/envs/cdatm/bin/python</code> | + | |
| === Old style initialization === | === Old style initialization === | ||
| + | |||
| + | <WRAP center round tip 60%> | ||
| + | The //old style// notes below are just for reference sake and you can skip them | ||
| + | </WRAP> | ||
| + | |||
| Note: this is the **old** ''source activate some_version'' style | Note: this is the **old** ''source activate some_version'' style | ||
| Line 205: | Line 215: | ||
| ==== Installing CDAT 8.0 ==== | ==== Installing CDAT 8.0 ==== | ||
| + | |||
| + | === Python 2.7 version === | ||
| <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 | ||
| Line 233: | Line 245: | ||
| 2.8G /home/share/unix_files/cdat/miniconda3/envs/cdat-8.0_py2</code> | 2.8G /home/share/unix_files/cdat/miniconda3/envs/cdat-8.0_py2</code> | ||
| + | === Python 3.6 version === | ||
| + | |||
| + | <code>$ conda create -n cdat-8.0_py3 -c cdat/label/v80 -c conda-forge -c cdat python=3.6 cdat</code> | ||
| ===== Cloning cdat to add specific packages for LSCE ===== | ===== Cloning cdat to add specific packages for LSCE ===== | ||
other/uvcdat/cdat_conda/cdat_8_0_py2.txt · Last modified: 2021/02/27 13:55 by jypeter
