UV-CDAT conda-based versions installed by JYP

This page describes the conda-based versions of UV-CDAT, 2.8.0 and later installed by JYP For versions up to 2.1, check the UV-CDAT versions installed by JYP

Useful links

Official CDAT site

CDAT wiki

CDAT @ github

cdms

cdtime

vcs

cdutil

genutil

2.8.0

Installation with Anaconda2

Installing with Miniconda2 rather than Anaconda2 will save disk space!

# 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

Installation with Miniconda2

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

Cloning uvcdat to add specific packages for LSCE

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

Packages that have no dependency problems

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

Other packages

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

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