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--- other:uvcdat:cdat_conda:index [2017/02/24 14:01]
jypeter Added section with the list of extra packages
+++ other:uvcdat:cdat_conda:index [2021/02/26 15:35]
jypeter Added link to 8.2.1
@@ Line 1: / Line 1: @@
-====== UV-CDAT conda-based versions installed by JYP ======
+====== CDAT versions installed by JYP ======
 <WRAP center round important 60%>
-This page describes the conda-based versions of UV-CDAT, 2.8.0 and later installed by JYP
+This page describes the **conda-based** versions of CDAT, ''2.8.0'' and later, installed by JYP
-For versions up to 2.1, check the [[.:installed|UV-CDAT versions installed by JYP]]
+Follow the [[other:python:starting#ultra_quick-start_on_the_lsce_servers|Ultra quick-start on the LSCE servers]] instructions for actually **using CDAT at LSCE**
-</WRAP>
-===== Useful links =====
-  * [[http://uvcdat.llnl.gov/|Official CDAT site]]
-  * [[https://github.com/UV-CDAT/uvcdat/wiki/|CDAT wiki]]
-  * [[https://github.com/UV-CDAT|CDAT @ github]]
-    * [[https://github.com/UV-CDAT/cdms|cdms]]
-    * [[https://github.com/UV-CDAT/cdtime|cdtime]]
-    * [[https://github.com/UV-CDAT/vcs|vcs]]
-    * [[https://github.com/UV-CDAT/cdutil|cdutil]]
-    * [[https://github.com/UV-CDAT/genutil|genutil]]
-===== 2.8.0 =====
-==== Installation with Anaconda2 ====
+For technical installation details, check [[..:conda_notes|Installing and maintaining CDAT with conda]]
-<WRAP center round alert 60%>
+For versions up to 2.1, check the (deprecated) [[..:installed|CDAT versions installed by JYP]] page
-[[#installation_with_miniconda2|Installing with Miniconda2]] rather than Anaconda2 will save disk space!
 </WRAP>
-<code># Keep a trace of what will be installed, with/without conda-forge
+===== Installed versions =====
-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
+Listed with the most recent version at the top
-conda create -n uvcdat-2.8.0 -c conda-forge -c uvcdat uvcdat=2.8.0</code>
-Lists of installed packages: {{ :other:uvcdat:uvcdat-2.8.0_install_dry_with-forge_160220.txt |with conda-forge}} or {{ :other:uvcdat:uvcdat-2.8.0_install_dry_no-forge_160220.txt |without conda-forge}}
+  * [[.::cdat_8_2_1|8.2.1]]
-Size of ''/home/share/unix_files/cdat/anaconda2'':
+  * [[.::cdat_8_1|8.1]]
-  * before installation: **2.1G**
-  * after installation: **4.6G**
-==== Installation with Miniconda2 ====
+  * [[.::cdat_8_0_py2|8.0]]
-Note: after installation, we use **//only// 2.7G** (details below), compared to the 4.6G of the Anaconda2 installation
+  * [[.:cdat_2_12|2.12]]
-<code># Keep a trace of what will be installed (with conda-forge)
+  * [[.:cdat_2_10|2.10]]
-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
+  * [[.:cdat_2_8_0|2.8.0]]
-conda create -n uvcdat-2.8.0 -c conda-forge -c uvcdat uvcdat=2.8.0</code>
-Lists of installed packages: {{ :other:uvcdat:uvcdat-2.8.0_install_dry_with-forge_160221.txt |List of installed packages}}
-<code>bash-4.1$ conda info --envs
+===== Useful links =====
-# 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
+  * [[http://uvcdat.llnl.gov/|Official CDAT site]]
-.7G    /home/share/unix_files/cdat/miniconda2
+  * [[https://github.com/UV-CDAT/uvcdat/wiki/|CDAT wiki]]
+  * [[https://github.com/UV-CDAT|CDAT @ github]]
-bash-4.1$ du -sh /home/share/unix_files/cdat/miniconda2/envs/*
+    * [[https://github.com/UV-CDAT/cdms|cdms]]
-.0G    /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0
+    * [[https://github.com/UV-CDAT/cdtime|cdtime]]
+    * [[https://github.com/UV-CDAT/vcs|vcs]]
-bash-4.1$ du -sh /home/share/unix_files/cdat/miniconda2/pkgs
+    * [[https://github.com/UV-CDAT/cdutil|cdutil]]
-.6G    /home/share/unix_files/cdat/miniconda2/pkgs
+    * [[https://github.com/UV-CDAT/genutil|genutil]]
-bash-4.1$ du -sh /home/share/unix_files/cdat/miniconda2/*
-.4M    /home/share/unix_files/cdat/miniconda2/bin
-.0K    /home/share/unix_files/cdat/miniconda2/conda-bld
-K    /home/share/unix_files/cdat/miniconda2/conda-meta
-.0G    /home/share/unix_files/cdat/miniconda2/envs
-K     /home/share/unix_files/cdat/miniconda2/etc
-.8M    /home/share/unix_files/cdat/miniconda2/include
-M     /home/share/unix_files/cdat/miniconda2/lib
-.0K    /home/share/unix_files/cdat/miniconda2/LICENSE.txt
-M    /home/share/unix_files/cdat/miniconda2/pkgs
-K     /home/share/unix_files/cdat/miniconda2/share
-.0K    /home/share/unix_files/cdat/miniconda2/ssl
-bash-4.1$ du -sh /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0/*
-M     /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0/bin
-.9M    /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0/conda-meta
-K     /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0/etc
-K    /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0/imports
-M     /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0/include
-.7G    /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0/lib
-K     /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0/man
-.1M    /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0/mkspecs
-M     /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0/mod
-.5M    /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0/plugins
-M     /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0/share
-.3M    /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0/ssl
-.7M    /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0/tests
-K     /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0/var
-M    /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0/vistrails</code>
-==== Cloning uvcdat to add specific packages for LSCE ====
-Note: using hard links, cloning a full environment only adds an extra 100M of disk space
-<code>bash-4.1$ du -sh /home/share/unix_files/cdat/miniconda2
-.7G    /home/share/unix_files/cdat/miniconda2
-bash-4.1$ du -sh /home/share/unix_files/cdat/miniconda2/envs/*
-.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
-.8G    /home/share/unix_files/cdat/miniconda2
-bash-4.1$ du -sh /home/share/unix_files/cdat/miniconda2/envs/*
-.0G    /home/share/unix_files/cdat/miniconda2/envs/cdatm14
-M     /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0</code>
-=== Packages that have no dependency problems ===
-After cloning, we are ready to install some extra packages that may be requested by LSCE users
-<code># 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
-.6G    /home/share/unix_files/cdat/miniconda2
-bash-4.1$ du -sh /home/share/unix_files/cdat/miniconda2/envs/*
-.4G    /home/share/unix_files/cdat/miniconda2/envs/cdatm14
-M     /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
-.9G    /home/share/unix_files/cdat/miniconda2
-bash-4.1$ du -sh /home/share/unix_files/cdat/miniconda2/envs/*
-.4G    /home/share/unix_files/cdat/miniconda2/envs/cdatm14
-M     /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0</code>
-Lists of installed packages: {{ :other:uvcdat:lsce-extra_01_install_160223.txt |}}
-=== Other packages ===
-<note warning>There is no warranty that the packages listed below will work correctly, when it was required to bypass the compatibility checks in order to install them...</note>
-  * ''shapely'' request a downgrade of ''geos'' when installed from //conda-forge// (see [[https://github.com/Toblerity/Shapely/issues/472|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 [[https://github.com/SciTools/cartopy/issues/853#issuecomment-282023158|github issue]])
-    * We install the requested dependencies and then we **force** the installation of ''cartopy''\\ <code>(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</code>
-  * 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 ===
-  * [[https://python-pillow.org/|pillow]]: the friendly PIL (//Python Imaging Library//) fork
-  * [[http://pandas.pydata.org/|pandas]]: Python Data Analysis Library
-  * [[http://statsmodels.sourceforge.net/|statsmodels]]: a Python module that allows users to explore data, estimate statistical models, and perform statistical tests
-  * [[https://seaborn.pydata.org/|seaborn]]: statistical data visualization
-  * [[http://scikit-image.org/|scikit-image]]: image processing in Python
-  * [[http://pythonhosted.org/seawater/|seawater]]: Python re-write of the CSIRO seawater toolbox
-  * [[https://pypi.python.org/pypi/gsw/|gsw]]: Python implementation of the Thermodynamic Equation Of Seawater
-  * [[http://unidata.github.io/netcdf4-python/|netcdf4]]: a Python interface to the netCDF C library
-  * [[http://ferret.pmel.noaa.gov/Ferret/documentation/pyferret|pyferret]]: Ferret encapsulated in Python
-  * [[http://www.ifremer.fr/vacumm/|vacumm]]: Validation, Analysis, Comparison - Utilities written in Python to validate and analyze Multi-Model outputs, and compare them to observations
-  * [[http://toblerity.org/shapely/project.html|shapely]]: a Python wrapper for GEOS for algebraic manipulation of geometry (manipulation and analysis of geometric objects in the Cartesian plane)
-  * [[http://scitools.org.uk/cartopy/|cartopy]]: a library providing cartographic tools for python
-  * [[https://rpy2.readthedocs.io/en/version_2.8.x/|rpy2]]: providing simple and robust access to R from within Python
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