Installing and maintaining UV-CDAT with conda

Recent versions (2.8.0 and later?) of UV-CDAT are installed and maintained with conda. This page is about conda/Miniconda/Anaconda installation and related notes

Check the UV-CDAT conda-based versions installed by JYP page to see what is maintained by JYP

Miniconda

UV-CDAT requires a working version of Anaconda

Practicing with Miniconda

Follow the Quick install steps to install Miniconda

Get the Python 2.7 Linux 64-bit (bash installer)

cd /home/scratch01/jypeter

wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh (28 Mo, 16 Feb 2017)

Execute the installer

bash Miniconda2-latest-Linux-x86_64.sh

Accept the license

Specify an explicit installation path outside of the home directory, with enough disk space, preferably on a disk that is not backed up: /home/share/unix_files/cdat/miniconda2

Resulting miniconda2 directory size is 118M

jypeter@asterix3 - ...versions - 51 >du -sh miniconda2/
118M miniconda2/
jypeter@asterix3 - ...versions - 52 >cd miniconda2/
jypeter@asterix3 - ...miniconda2 - 54 >du -sh *
4.4M bin
268K conda-meta
4.0K envs
20K etc
3.8M include
99M lib
4.0K LICENSE.txt
23M pkgs
16K share
8.0K ssl

Accept the automatic update of the PATH variable in .bashrc (note: the installer automatically creates a backup of .bashrc)

# added by Miniconda2 4.3.11 installer
export PATH=“/home/share/unix_files/cdat/miniconda2/bin:$PATH”

Open a new terminal (if you use bash) or type bash and check if the python from the conda distribution has been correctly installed

bash-4.1$ which python
/home/share/unix_files/cdat/versions/miniconda2/bin/python
bash-4.1$ conda list
# packages in environment at /home/share/unix_files/cdat/versions/miniconda2:
#
cffi 1.9.1 py27_0
conda 4.3.11 py27_0
conda-env 2.6.0 0
cryptography 1.7.1 py27_0
[...]

Follow the 30-minute test drive steps

Removing Miniconda

Remove the installation directory: /home/share/unix_files/cdat/miniconda2

Remove the PATH update line from ~/.bash_profile

Remove the configuration files and directories from the home directory: ~/.condarc ~/.conda ~/.continuum

Anaconda

Installing Anaconda

Follow the Full installation steps to install Miniconda

Installation package Anaconda2-4.3.0-Linux-x86_64.sh is 462M (17 Feb 2017)

Size after initial installation : 2G

jypeter@asterix3 - ...anaconda2 - 93 >du -sh /home/share/unix_files/cdat/anaconda2
2.0G /home/share/unix_files/cdat/anaconda2
jypeter@asterix3 - ...anaconda2 - 94 >du -sh /home/share/unix_files/cdat/anaconda2/*
53M /home/share/unix_files/cdat/anaconda2/bin
3.3M /home/share/unix_files/cdat/anaconda2/conda-meta
564K /home/share/unix_files/cdat/anaconda2/doc
4.0K /home/share/unix_files/cdat/anaconda2/envs
80K /home/share/unix_files/cdat/anaconda2/etc
53M /home/share/unix_files/cdat/anaconda2/include
1.7G /home/share/unix_files/cdat/anaconda2/lib
244K /home/share/unix_files/cdat/anaconda2/libexec
8.0K /home/share/unix_files/cdat/anaconda2/LICENSE.txt
3.1M /home/share/unix_files/cdat/anaconda2/mkspecs
320K /home/share/unix_files/cdat/anaconda2/phrasebooks
186M /home/share/unix_files/cdat/anaconda2/pkgs
340K /home/share/unix_files/cdat/anaconda2/plugins
156K /home/share/unix_files/cdat/anaconda2/qml
4.0K /home/share/unix_files/cdat/anaconda2/sbin
1.3M /home/share/unix_files/cdat/anaconda2/share
8.0K /home/share/unix_files/cdat/anaconda2/ssl
12K /home/share/unix_files/cdat/anaconda2/translations
24K /home/share/unix_files/cdat/anaconda2/var

Size after conda update conda and conda update --all: 2.1G

List of installed packages : unix_files_cdat_anaconda2_170217.txt

Removing Anaconda

The steps are the same as for Removing Miniconda

Notes

Useful conda commands

There is also a summary available in the Conda cheat sheet

Getting help

conda --help, conda -h
same as conda command --help

Available environments

conda info --envs
same as conda env list

Creating an environment

conda create --name new_environment package1 package2 packageN
conda create -n new_environment package1 package2 packageN

Deleting an environment

conda remove --name crap_environment --all

Activating or going back to root

source activate existing_environment

source activate will activate the root environment

source deactivate

Installed packages

conda list

This will also list the packages installed with pip install package1 package2 packageN!!

Searching packages

conda search --full-name package_exact_name
conda search package_partial_name

Installing and removing packages
Add -n target_environment to act on another environment than the active one

conda install package1 package2 packageN

Add --channel channel_url_or_alias to install from a specific channel

If there is no URL, conda will use the value of channel_alias that defaults to https://conda.anaconda.org/

conda remove package1 package2 packageN

Updating conda (update the conda package, not the full Miniconda)

conda update conda

Misc

Available 'official' packages

Other packages

conda Full documentation

conda FAQ

Sharing (replicating) an environment

Centralized installation

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