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UV-CDAT 2.10 installation notes

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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

Customizing UV-CDAT for LSCE

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

List of installed packages: lsce-extra_01_install_170808.txt

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 (or updated) 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
  • cmocean: beautiful colormaps for oceanography
    • conda install -n cdatm15 -c conda-forge cmocean
  • iris: A Python library for Meteorology and Climatology
    • conda install -n cdatm15 -c conda-forge -c scitools iris
  • OSGeo/GDAL: Geospatial Data Abstraction Library. GDAL is a translator library for raster and vector geospatial data formats
  • spanlib: Spectral Analysis Library
    • conda install -n cdatm15 -c stefraynaud -c conda-forge spanlib
    • Test: python -c 'from spanlib.analyzer import Analyzer'
  • wrf-python: A collection of diagnostic and interpolation routines for use with output from the Weather Research and Forecasting (WRF-ARW) Model
    • conda install -n cdatm15 -c conda-forge wrf-python
  • glances: a cross-platform monitoring tool (similar to top)
  • windspharm: spherical harmonic wind analysis in Python

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)!
    • Problem solved with vacumm 3.4.1-1 on August 31st! Installation was OK with
      conda install -n cdatm15 -c conda-forge -c vacumm vacumm
  • Install PySPLIT for Sentia
    PySPLIT A package for generating HYSPLIT air parcel trajectories trajectories, performing moisture uptake analyses, expediting HYSPLIT cluster analysis, and for visualizing trajectories, clusters, and along-trajectory meteorological data
    Works with HYSPLiT
    1. conda install -n cdatm15 -c conda-forge fiona geopandas
    2. pip install pysplit

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…
  • NO such packages now!

Updating some packages

Some packages change more often than others, and can be easily updated the following way:

    • Update with: conda update -n cdatm15 -c conda-forge -c pcmdi -c uvcdat cmor
      • Get version number with: python -c 'from cmor import *; print CMOR_VERSION_MAJOR, CMOR_VERSION_MINOR, CMOR_VERSION_PATCH'
    • Update with: pip install --upgrade dreqPy
      • Get version number with: drq -v

Cleaning up things

Some packages may have files that can only be read by the person who installed CDAT and the LSCE extensions (eg pcmdi-metrics in 2.8.0 and cdp in 2.10)

We check if some of the installed files are missing read access for the group or other, and we manually change the permissions

(cdatm15) bash-4.2$ find cdatm15 \! -perm /g+r,o+r -ls
50333969    4 -rw-------   2 jypeter  lsce          234 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp-1.0.3-py2.7.egg-info/PKG-INFO
50333971    4 -rw-------   2 jypeter  lsce          291 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp-1.0.3-py2.7.egg-info/SOURCES.txt
50333962    4 -rw-------   2 jypeter  lsce            4 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp-1.0.3-py2.7.egg-info/top_level.txt
50333961    4 -rw-------   2 jypeter  lsce            1 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp-1.0.3-py2.7.egg-info/dependency_links.txt
50333960    4 -rw-------   2 jypeter  lsce            1 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp-1.0.3-py2.7.egg-info/not-zip-safe
50333987    8 -rw-------   2 jypeter  lsce         5149 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp/cdp_viewer.pyc
50333986    8 -rw-------   2 jypeter  lsce         4208 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp/cdp_metric.py
50333966    4 -rw-------   2 jypeter  lsce          150 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp/__init__.pyc
50333968    4 -rw-------   2 jypeter  lsce          201 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp/cdp_provenance.py
50333988    8 -rw-------   2 jypeter  lsce         5365 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp/cdp_metric.pyc
50333982    4 -rw-------   2 jypeter  lsce         1821 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp/cdp_parser.py
50333981    4 -rw-------   2 jypeter  lsce         1773 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp/cdp_parameter.py
50333973    4 -rw-------   2 jypeter  lsce          670 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp/cdp_output.py
50333980    4 -rw-------   2 jypeter  lsce         1642 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp/cdp_output.pyc
50333979    4 -rw-------   2 jypeter  lsce         1474 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp/_cache.pyc
50333967    4 -rw-------   2 jypeter  lsce          187 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp/cdp_tool.py
50333989    0 -rw-------   2 jypeter  lsce            0 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp/__init__.py
50333985    4 -rw-------   2 jypeter  lsce         3843 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp/cdp_viewer.py
50333984    4 -rw-------   2 jypeter  lsce         2436 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp/cdp_parameter.pyc
50333970    4 -rw-------   2 jypeter  lsce          288 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp/cdp_io.py
50333974    4 -rw-------   2 jypeter  lsce          692 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp/cdp_tool.pyc
50333978    4 -rw-------   2 jypeter  lsce          878 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp/cdp_io.pyc
50333976    4 -rw-------   2 jypeter  lsce          734 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp/_cache.py
50333983    4 -rw-------   2 jypeter  lsce         2269 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp/cdp_parser.pyc
50333975    4 -rw-------   2 jypeter  lsce          724 Apr  4 20:35 cdatm15/lib/python2.7/site-packages/cdp/cdp_provenance.pyc
(cdatm15) bash-4.2$ chmod -R a+r cdatm15/lib/python2.7/site-packages/cdp*
(cdatm15) bash-4.2$ find cdatm15 \! -perm /g+r,o+r -ls

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
  • vacumm: Validation, Analysis, Comparison - Utilities written in Python to validate and analyze Multi-Model outputs, and compare them to observations
  • 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
  • cmocean: beautiful colormaps for oceanography
  • iris: A Python library for Meteorology and Climatology
  • OSGeo/GDAL: Geospatial Data Abstraction Library. GDAL is a translator library for raster and vector geospatial data formats
  • spanlib: Spectral Analysis Library
  • wrf-python: A collection of diagnostic and interpolation routines for use with output from the Weather Research and Forecasting (WRF-ARW) Model
  • glances: a cross-platform monitoring tool (similar to top)
  • windspharm: spherical harmonic wind analysis in Python

Removed packages

  • NO removed packages!

Environments summary

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

Environment
name
Server conda list
uvcdat-2.10 LSCE package list
cdatm15 LSCE package list





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other/uvcdat/cdat_conda/cdat_2_10.txt · Last modified: 2018/10/03 11:56 by jypeter