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UV-CDAT 2.10 installation notes

[ Back to all versions ]

Follow the instructions about the conda-based versions of UV-CDAT initialization for actually using an installed version of 2.10

What's New?

Installation with Miniconda2


We used the recommended downgraded version of conda that was available after installing UV-CDAT 2.8

DIsk space used before 2.10 installation (after running conda clean –all) 

 > du -sh /home/share/unix_files/cdat/miniconda2
6.5G	/home/share/unix_files/cdat/miniconda2

 > 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
272K	/home/share/unix_files/cdat/miniconda2/conda-meta
6.4G	/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
76K	/home/share/unix_files/cdat/miniconda2/pkgs
376K	/home/share/unix_files/cdat/miniconda2/share
364K	/home/share/unix_files/cdat/miniconda2/ssl

 >du -sh /home/share/unix_files/cdat/miniconda2/envs/*
2.8G	/home/share/unix_files/cdat/miniconda2/envs/cdatm14
1.7G	/home/share/unix_files/cdat/miniconda2/envs/keras
2.0G	/home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0

Actual installation 

bash-4.1$ conda create -n uvcdat-2.10 -c conda-forge -c uvcdat uvcdat=2.10

# Generate the list of installed packages
conda list -n uvcdat-2.10 > /home/scratch01/jypeter/uvcdat-2.10_list_170721.txt

List of installed packages: uvcdat-2.10_list_170721.txt

Disk space after 2.10 installation 

bash-4.1$ conda env list
cdatm14                  /home/share/unix_files/cdat/miniconda2/envs/cdatm14
keras                    /home/share/unix_files/cdat/miniconda2/envs/keras
uvcdat-2.10              /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.10
uvcdat-2.8.0             /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0
root                  *  /home/share/unix_files/cdat/miniconda2

 > du -sh /home/share/unix_files/cdat/miniconda2
11G	/home/share/unix_files/cdat/miniconda2

 > 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
272K	/home/share/unix_files/cdat/miniconda2/conda-meta
9.2G	/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
1.4G	/home/share/unix_files/cdat/miniconda2/pkgs
376K	/home/share/unix_files/cdat/miniconda2/share
364K	/home/share/unix_files/cdat/miniconda2/ssl

 > du -sh /home/share/unix_files/cdat/miniconda2/envs/*
2.8G	/home/share/unix_files/cdat/miniconda2/envs/cdatm14
1.7G	/home/share/unix_files/cdat/miniconda2/envs/keras
2.8G	/home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.10
2.0G	/home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0

Disk space after removing the keras environment that we don't need any more 

jypeter@asterix2 - ...cdat - 67 >du -sh /home/share/unix_files/cdat/miniconda2
9.0G	/home/share/unix_files/cdat/miniconda2
jypeter@asterix2 - ...cdat - 68 >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
272K	/home/share/unix_files/cdat/miniconda2/conda-meta
7.5G	/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
1.4G	/home/share/unix_files/cdat/miniconda2/pkgs
376K	/home/share/unix_files/cdat/miniconda2/share
364K	/home/share/unix_files/cdat/miniconda2/ssl
jypeter@asterix2 - ...cdat - 69 >du -sh /home/share/unix_files/cdat/miniconda2/envs/*
2.8G	/home/share/unix_files/cdat/miniconda2/envs/cdatm14
2.8G	/home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.10
2.0G	/home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0

Disk space used in a brand new directory hierarchy (cdat/miniconda2b, on the obelix servers) 

bash-4.2$ conda env list
uvcdat-2.10              /home/share/unix_files/cdat/miniconda2b/envs/uvcdat-2.10
root                  *  /home/share/unix_files/cdat/miniconda2b

bash-4.2$ du -sh /home/share/unix_files/cdat/miniconda2b
4.3G	/home/share/unix_files/cdat/miniconda2b

bash-4.2$ du -sh /home/share/unix_files/cdat/miniconda2b/*
4.4M	/home/share/unix_files/cdat/miniconda2b/bin
4.0K	/home/share/unix_files/cdat/miniconda2b/conda-bld
280K	/home/share/unix_files/cdat/miniconda2b/conda-meta
2.8G	/home/share/unix_files/cdat/miniconda2b/envs
20K	/home/share/unix_files/cdat/miniconda2b/etc
3.8M	/home/share/unix_files/cdat/miniconda2b/include
100M	/home/share/unix_files/cdat/miniconda2b/lib
8.0K	/home/share/unix_files/cdat/miniconda2b/LICENSE.txt
1.4G	/home/share/unix_files/cdat/miniconda2b/pkgs
16K	/home/share/unix_files/cdat/miniconda2b/share
376K	/home/share/unix_files/cdat/miniconda2b/ssl

Cloning uvcdat to add specific packages for LSCE

This section is about the creation of the cdatm15 environment

Notes about actually using the cdatm15 conda-based python

Note: using hard links, cloning a full environment only adds an extra 500M of disk space 

bash-4.1$ du -sh /home/share/unix_files/cdat/miniconda2
9.0G	/home/share/unix_files/cdat/miniconda2

bash-4.1$ du -sh /home/share/unix_files/cdat/miniconda2/envs/*
2.8G	/home/share/unix_files/cdat/miniconda2/envs/cdatm14
2.8G	/home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.10
2.0G	/home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0

bash-4.1$ conda create -n cdatm15 --clone uvcdat-2.10 
Source:      /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.10
Destination: /home/share/unix_files/cdat/miniconda2/envs/cdatm15
[...]

bash-4.1$ du -sh /home/share/unix_files/cdat/miniconda2
9.5G	/home/share/unix_files/cdat/miniconda2

bash-4.1$ du -sh /home/share/unix_files/cdat/miniconda2/envs/*
2.8G	/home/share/unix_files/cdat/miniconda2/envs/cdatm14
2.8G	/home/share/unix_files/cdat/miniconda2/envs/cdatm15
573M	/home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.10
2.0G	/home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0

Disk space used after cloning, in in the new directory hierarchy (cdat/miniconda2b, on the obelix servers) 

bash-4.2$ du -sh /home/share/unix_files/cdat/miniconda2b
4.8G	/home/share/unix_files/cdat/miniconda2b

bash-4.2$ du -sh /home/share/unix_files/cdat/miniconda2b/*
4.4M	/home/share/unix_files/cdat/miniconda2b/bin
4.0K	/home/share/unix_files/cdat/miniconda2b/conda-bld
280K	/home/share/unix_files/cdat/miniconda2b/conda-meta
3.4G	/home/share/unix_files/cdat/miniconda2b/envs
20K	/home/share/unix_files/cdat/miniconda2b/etc
3.8M	/home/share/unix_files/cdat/miniconda2b/include
100M	/home/share/unix_files/cdat/miniconda2b/lib
8.0K	/home/share/unix_files/cdat/miniconda2b/LICENSE.txt
1.4G	/home/share/unix_files/cdat/miniconda2b/pkgs
16K	/home/share/unix_files/cdat/miniconda2b/share
376K	/home/share/unix_files/cdat/miniconda2b/ssl

bash-4.2$ du -sh /home/share/unix_files/cdat/miniconda2b/envs/*
2.8G	/home/share/unix_files/cdat/miniconda2b/envs/cdatm15
574M	/home/share/unix_files/cdat/miniconda2b/envs/uvcdat-2.10

Getting ready for a moving default CDAT

We create a cdatm symbolic link in the envs directory, that has a stable name but can be moved to point to the latest default CDAT. In that case, most users can just activate this cdatm version and always get the latest stable version 

bash-4.2$ cd /home/share/unix_files/cdat/miniconda2b/envs

bash-4.2$ conda env list
cdatm15                  /home/share/unix_files/cdat/miniconda2b/envs/cdatm15
uvcdat-2.10              /home/share/unix_files/cdat/miniconda2b/envs/uvcdat-2.10
root                  *  /home/share/unix_files/cdat/miniconda2b

bash-4.2$ ln -s cdatm15 cdatm

bash-4.2$ conda env list
cdatm                    /home/share/unix_files/cdat/miniconda2b/envs/cdatm
cdatm15                  /home/share/unix_files/cdat/miniconda2b/envs/cdatm15
uvcdat-2.10              /home/share/unix_files/cdat/miniconda2b/envs/uvcdat-2.10
root                  *  /home/share/unix_files/cdat/miniconda2b

bash-4.2$ source activate cdatm

(cdatm) bash-4.2$ conda env list
cdatm                 *  /home/share/unix_files/cdat/miniconda2b/envs/cdatm
cdatm15                  /home/share/unix_files/cdat/miniconda2b/envs/cdatm15
uvcdat-2.10              /home/share/unix_files/cdat/miniconda2b/envs/uvcdat-2.10
root                     /home/share/unix_files/cdat/miniconda2b

Downloading cdms2/vcs test data

You should download the test data and use it in the example scripts that you want to distribute, and scripts you write for reporting the errors you find (if any…) 

bash-4.1$ source activate cdatm15

(cdatm15) bash-4.1$ python -c 'import vcs; vcs.download_sample_data_files(); print "\nFinished downloading sample data to", vcs.sample_data'
[...]
Finished downloading sample data to /home/share/unix_files/cdat/miniconda2/envs/cdatm15/share/uvcdat/sample_data

(cdatm15) bash-4.1$ du -sh /home/share/unix_files/cdat/miniconda2/envs/cdatm15/share/uvcdat/sample_data
174M	/home/share/unix_files/cdat/miniconda2/envs/cdatm15/share/uvcdat/sample_data

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 cdatm15 -c conda-forge -c uvcdat -c pcmdi pillow pandas statsmodels seaborn scikit-image seawater gsw netcdf4 pyferret basemap-data-hires pcmdi_metrics xlsxwriter cmor shapely cartopy rpy2 > /home/scratch01/jypeter/lsce-extra_01_install_170808.txt

# Install...
bash-4.1$ conda install -n cdatm15 -c conda-forge -c uvcdat -c pcmdi pillow pandas statsmodels seaborn scikit-image seawater gsw netcdf4 pyferret basemap-data-hires pcmdi_metrics xlsxwriter cmor shapely cartopy rpy2
[...]

# Check the disk space after installation
bash-4.1$ du -sh /home/share/unix_files/cdat/miniconda2
11G	/home/share/unix_files/cdat/miniconda2

bash-4.1$ du -sh /home/share/unix_files/cdat/miniconda2/envs/*
0	/home/share/unix_files/cdat/miniconda2/envs/cdatm
2.8G	/home/share/unix_files/cdat/miniconda2/envs/cdatm14
3.7G	/home/share/unix_files/cdat/miniconda2/envs/cdatm15
574M	/home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.10
2.0G	/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
9.9G	/home/share/unix_files/cdat/miniconda2

Lists of installed packages: lsce-extra_01_install_170808.txt </code>

Disk space used after adding the extra packages, in in the new directory hierarchy (cdat/miniconda2b, on the obelix servers) 

bash-4.2$ du -sh /home/share/unix_files/cdat/miniconda2b 
6.4G	/home/share/unix_files/cdat/miniconda2b

bash-4.2$ du -sh /home/share/unix_files/cdat/miniconda2b/envs/*
0	/home/share/unix_files/cdat/miniconda2b/envs/cdatm
3.8G	/home/share/unix_files/cdat/miniconda2b/envs/cdatm15
630M	/home/share/unix_files/cdat/miniconda2b/envs/uvcdat-2.10

# Check the disk space again after cleaning
bash-4.2$ conda clean --all

bash-4.2$ du -sh /home/share/unix_files/cdat/miniconda2b
5.4G	/home/share/unix_files/cdat/miniconda2b

Packages installed with pip

  • dreqPy: CMIP6 Data Request Python API
    • pip install dreqPy
    • Update with: pip install --upgrade dreqPy
      • Get version number with:
        $ drq -v
dreqPy version 01.00.06 [Version 01.00.06]
  • dtw: DTW (Dynamic Time Warping) python module
    • pip install dtw
    • Requested by Sentia Goursaud

The following packages have no dependency problems and were installed later

  • ESMPy: ESMF Python Regridding Interface
    • We used the following to get a more up-to-date version of esmpy than the one bundled with 2.10
    • bash-4.1$ conda list | grep -i esm
esmf                      7.0.0                         6    conda-forge
esmpy                     7.0.0                    py27_1    conda-forge

bash-4.1$ conda install -n cdatm15 -c nesii/channel/dev-esmf -c conda-forge esmpy=7.1.0.dev32
[...]

bash-4.1$ conda list | grep -i esm
esmf                      7.1.0.dev32                   1    nesii/channel/dev-esmf
esmpy                     7.1.0.dev32              py27_1    nesii/channel/dev-esmf

TODO

Add here packages that would be useful but have some problems that prevent their installation

  • vacumm: Validation, Analysis, Comparison - Utilities written in Python to validate and analyze Multi-Model outputs, and compare them to observations
    • As of August 08 2017, installing vacumm in 2.10 requires downgrading to 2.10 (see github issue)!

Other packages

There is no warranty that the packages listed below will work correctly, because it was required to bypass the compatibility checks in order to install them…
  • 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

Extra packages list

  • 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
  • basemap-data-hires: high resolution data for basemap
  • PCMDI metrics package (PMP): objectively compare results from climate models with observations using well-established statistical tests
  • XlsxWriter: a Python module for creating Excel XLSX files
    • Note: this is a dependency of dreqPy
  • dreqPy: CMIP6 Data Request Python API
  • CMOR: CMOR (Climate Model Output Rewriter) is used to produce CF-compliant netCDF files
  • dtw: DTW (Dynamic Time Warping) python module
  • 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

Removed packages

  • wget: pure python download utility
    • Used conda install -n cdatm14 -c daler wget=3.2 in order to get version 3.2, the same as the one on Pypi
    • REMOVED because it did not work correctly in the script where it was needed: it emulated wget with ftp and failed in our case after downloading the first file

Environments summary

After following the steps above, we get the following environments. Use the conda info –envs command to get the up-to-date list of available environments

Environment
name 		Server conda list
uvcdat-2.8.0 LSCE
ciclad 		package list
cdatm14 LSCE
ciclad 		package list




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other/uvcdat/cdat_conda/cdat_2_10.1502294381.txt.gz · Last modified: 2017/08/09 17:59 by jypeter
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