• Official CDAT site
• CDAT wiki
• CDAT @ github
  • cdms
  • cdtime
  • vcs
  • cdutil
  • genutil

# Keep a trace of what will be installed, with/without conda-forge
conda create --dry-run -n uvcdat-2.8.0 -c uvcdat uvcdat=2.8.0 > /home/scratch01/jypeter/uvcdat-2.8.0_install_dry_no-forge_160220.txt
conda create --dry-run -n uvcdat-2.8.0 -c conda-forge -c uvcdat uvcdat=2.8.0 > /home/scratch01/jypeter/uvcdat-2.8.0_install_dry_with-forge_160220.txt

# Do the actual installation
conda create -n uvcdat-2.8.0 -c conda-forge -c uvcdat uvcdat=2.8.0

Lists of installed packages: with conda-forge or without conda-forge

Size of /home/share/unix_files/cdat/anaconda2:

• before installation: 2.1G
• after installation: 4.6G

Note: after installation, we use only 2.7G (details below), compared to the 4.6G of the Anaconda2 installation

# Keep a trace of what will be installed (with conda-forge)
conda create --dry-run -n uvcdat-2.8.0 -c conda-forge -c uvcdat uvcdat=2.8.0 > /home/scratch01/jypeter/uvcdat-2.8.0_install_dry_with-forge_160220.txt

# Do the actual installation
conda create -n uvcdat-2.8.0 -c conda-forge -c uvcdat uvcdat=2.8.0

Lists of installed packages: List of installed packages

bash-4.1$ conda info --envs
# conda environments:
#
uvcdat-2.8.0             /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0
root                  *  /home/share/unix_files/cdat/miniconda2

bash-4.1$ du -sh /home/share/unix_files/cdat/miniconda2
2.7G    /home/share/unix_files/cdat/miniconda2

bash-4.1$ du -sh /home/share/unix_files/cdat/miniconda2/envs/*
2.0G    /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0

bash-4.1$ du -sh /home/share/unix_files/cdat/miniconda2/pkgs
2.6G    /home/share/unix_files/cdat/miniconda2/pkgs

bash-4.1$ du -sh /home/share/unix_files/cdat/miniconda2/*
4.4M    /home/share/unix_files/cdat/miniconda2/bin
4.0K    /home/share/unix_files/cdat/miniconda2/conda-bld
276K    /home/share/unix_files/cdat/miniconda2/conda-meta
2.0G    /home/share/unix_files/cdat/miniconda2/envs
20K     /home/share/unix_files/cdat/miniconda2/etc
3.8M    /home/share/unix_files/cdat/miniconda2/include
99M     /home/share/unix_files/cdat/miniconda2/lib
4.0K    /home/share/unix_files/cdat/miniconda2/LICENSE.txt
665M    /home/share/unix_files/cdat/miniconda2/pkgs
16K     /home/share/unix_files/cdat/miniconda2/share
8.0K    /home/share/unix_files/cdat/miniconda2/ssl

bash-4.1$ du -sh /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0/*
56M     /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0/bin
1.9M    /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0/conda-meta
48K     /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0/etc
420K    /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0/imports
67M     /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0/include
1.7G    /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0/lib
24K     /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0/man
3.1M    /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0/mkspecs
16M     /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0/mod
3.5M    /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0/plugins
57M     /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0/share
4.3M    /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0/ssl
2.7M    /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0/tests
12K     /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0/var
107M    /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0/vistrails

Note: using hard links, cloning a full environment only adds an extra 100M of disk space

bash-4.1$ du -sh /home/share/unix_files/cdat/miniconda2
2.7G    /home/share/unix_files/cdat/miniconda2

bash-4.1$ du -sh /home/share/unix_files/cdat/miniconda2/envs/*
2.0G    /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0

bash-4.1$ conda create -n cdatm14 --clone uvcdat-2.8.0
[...]

bash-4.1$ du -sh /home/share/unix_files/cdat/miniconda2
2.8G    /home/share/unix_files/cdat/miniconda2

bash-4.1$ du -sh /home/share/unix_files/cdat/miniconda2/envs/*
2.0G    /home/share/unix_files/cdat/miniconda2/envs/cdatm14
82M     /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0

After cloning, we are ready to install some extra packages that may be requested by LSCE users

# Keep a trace of what will be installed
bash-4.1$ conda install --dry-run -n cdatm14 -c conda-forge -c uvcdat -c vacumm pillow pandas statsmodels seaborn scikit-image seawater gsw netcdf4 pyferret vacumm > /home/scratch01/jypeter/lsce-extra_01_install_160223.txt

# Install...
bash-4.1$ conda install -n cdatm14 -c conda-forge -c uvcdat -c vacumm pillow pandas statsmodels seaborn scikit-image seawater gsw netcdf4 pyferret vacumm

# Check the disk space after installation
bash-4.1$ du -sh /home/share/unix_files/cdat/miniconda2
3.6G    /home/share/unix_files/cdat/miniconda2

bash-4.1$ du -sh /home/share/unix_files/cdat/miniconda2/envs/*
2.4G    /home/share/unix_files/cdat/miniconda2/envs/cdatm14
82M     /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0

# Check the disk space again after cleaning
bash-4.1$ conda clean all

bash-4.1$ du -sh /home/share/unix_files/cdat/miniconda2
2.9G    /home/share/unix_files/cdat/miniconda2

bash-4.1$ du -sh /home/share/unix_files/cdat/miniconda2/envs/*
2.4G    /home/share/unix_files/cdat/miniconda2/envs/cdatm14
82M     /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0

Lists of installed packages: lsce-extra_01_install_160223.txt

The following packages have no dependency problems and were installed later

• High resolution data for basemap
  • conda install -n cdatm14 -c conda-forge basemap-data-hires

• shapely request a downgrade of geos when installed from conda-forge (see github issue) but it will work when installed from the default repo
  • conda install -n cdatm14 shapely
  • We get a slightly older version (1.5.16-py27_0 instead of 1.5.17-np111py27_2)
  • Note: cartopy (below) requests the same downgrade of geos…
• cartopy requests a downgrade of geos and matplotlib (see github issue)
  • We install the requested dependencies and then we force the installation of cartopy
    

    (uvcdat-2.8.0) bash-4.1$ conda install -n cdatm14 -c conda-forge -c uvcdat libxslt lxml owslib pyepsg
    [...]
    The following NEW packages will be INSTALLED:
    
        libxslt: 1.1.29-3      conda-forge
        lxml:    3.7.2-py27_1  conda-forge
        owslib:  0.14.0-py27_0 conda-forge
        pyepsg:  0.3.1-py27_0  conda-forge
    [...]
    
    (uvcdat-2.8.0) bash-4.1$ conda install -n cdatm14 -c conda-forge cartopy
    [...]
    The following NEW packages will be INSTALLED:
    
        cartopy:    0.15.0-np111py27_0 conda-forge
    
    The following packages will be DOWNGRADED due to dependency conflicts:
    
        geos:       3.6.0-0            conda-forge --> 3.5.1-1           conda-forge
        matplotlib: 2.0.0-np111py27_2  conda-forge --> 1.5.3-np111py27_7 conda-forge
    
    Proceed ([y]/n)? n
    
    (uvcdat-2.8.0) bash-4.1$ conda install --force -n cdatm14 -c conda-forge cartopy
    [...]
    The following NEW packages will be INSTALLED:
    
        cartopy: 0.15.0-np111py27_0 conda-forge
    
    Proceed ([y]/n)? y

• trying to install rpy2 will trigger the installation of R!
  • We force the installation of only rpy2 in order to use the R already installed at LSCE
    • conda install –force -n cdatm14 -c conda-forge -c uvcdat rpy2

• pillow: the friendly PIL (Python Imaging Library) fork
• pandas: Python Data Analysis Library
• statsmodels: a Python module that allows users to explore data, estimate statistical models, and perform statistical tests
• seaborn: statistical data visualization
• scikit-image: image processing in Python
• seawater: Python re-write of the CSIRO seawater toolbox
• gsw: Python implementation of the Thermodynamic Equation Of Seawater
• netcdf4: a Python interface to the netCDF C library
• pyferret: Ferret encapsulated in Python
• vacumm: Validation, Analysis, Comparison - Utilities written in Python to validate and analyze Multi-Model outputs, and compare them to observations
• basemap-data-hires: high resolution data for basemap

• shapely: a Python wrapper for GEOS for algebraic manipulation of geometry (manipulation and analysis of geometric objects in the Cartesian plane)
• cartopy: a library providing cartographic tools for python
• rpy2: providing simple and robust access to R from within Python

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