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other:uvcdat:cdat_conda:cdat_8_0_py2 [2018/11/08 18:01]
jypeter
other:uvcdat:cdat_conda:cdat_8_0_py2 [2019/03/13 14:54] (current)
jypeter
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 ==== Installing Miniconda3 ====  ==== Installing Miniconda3 ==== 
  
-We have installed a new version of Miniconda3, by following ​the existing ​[[other:​uvcdat:​conda_notes#​installing_miniconda|installing miniconda]] instructions+We have installed a new version of Miniconda3 ​(steps below adapted from the [[other:​uvcdat:​conda_notes#​installing_miniconda|installing miniconda]] instructions)
  
-  ​* Follow the [[https://​conda.io/​docs/​install/​quick.html|Quick install]] steps to install Miniconda +  * Get the [[https://​repo.continuum.io/​miniconda/​Miniconda3-latest-Linux-x86_64.sh|Python 3.7 Linux 64-bit (bash installer)]] (unless there is a [[https://​conda.io/​miniconda.html|more recent version?]]) 
-    ​* Get the [[https://​repo.continuum.io/​miniconda/​Miniconda3-latest-Linux-x86_64.sh|Python 3.7 Linux 64-bit (bash installer)]] (unless there is a [[https://​conda.io/​miniconda.html|more recent version?​]]) +    * Find some temporary space on Linux or Windows 
-      * ''​cd /​home/​scratch01/​jypeter''​ (some temporary storage space for the installer+      * Linux:''​cd /​home/​scratch01/​jypeter''​ 
-      * ''​wget https://​repo.continuum.io/​miniconda/​Miniconda3-latest-Linux-x86_64.sh''​ (60 Mo, 11 Nov 2018+      * WSL: ''​cd /​mnt/​h/​Scratch/​jypeter/​''​ (assuming that there is a ''​H:​\Scratch\jypeter''​ directory
-    * Execute the installer +    * ''​wget https://​repo.continuum.io/​miniconda/​Miniconda3-latest-Linux-x86_64.sh''​ (67 Mo, 15 Feb 2019
-      * ''​bash Miniconda3-latest-Linux-x86_64.sh''​ +  * Execute the installer 
-        * Accept the license +    * ''​bash Miniconda3-latest-Linux-x86_64.sh''​ 
-        * Specify an explicit installation path **outside of the home directory**,​ with enough disk space (more than 3G if you are going to install UV-CDAT and some extra packages), preferably on a disk that is not backed up: ''/​home/​share/​unix_files/​cdat/​miniconda3''​ +      * Accept the license 
-          * Resulting ''​miniconda3''​ directory size is 302M\\ <​code>​ >du -sh miniconda3+      * Specify an explicit installation path **outside of the home directory**,​ with enough disk space (more than 3G if you are going to install UV-CDAT and some extra packages), preferably on a disk that is not backed up
 +        * Linux LSCE: ''/​home/​share/​unix_files/​cdat/​miniconda3''​ 
 +        * Linux ciclad: ''/​data/​jypmce/​cdat/​miniconda3''​ 
 +        * WSL: installing to a directory that is not in ''/​home/''​ <wrap hi>does not work</​wrap>​ (e.g. ''/​mnt/​h/​CDAT/​miniconda3'',​assuming there is a ''​H:​\CDAT\''​ directory, does not work)\\ Need to accept the installation in the default location: ''/​home/​jypeter/​miniconda3''​ 
 +        ​* Resulting ''​miniconda3''​ directory size is 302M\\ <​code>​ >du -sh miniconda3
 302M    miniconda3 302M    miniconda3
  >​cd miniconda3  >​cd miniconda3
Line 45: Line 49:
 92K     ssl 92K     ssl
 12K     ​x86_64-conda_cos6-linux-gnu</​code>​ 12K     ​x86_64-conda_cos6-linux-gnu</​code>​
-        ​* Accept the automatic update of the //PATH// variable in ''​.bashrc''​ (note: the installer automatically creates a backup of ''​.bashrc''​) +      ​* Accept the automatic update of the //PATH// variable in ''​.bashrc''​ (note: the installer automatically creates a backup of ''​.bashrc''​). This will some extra lines at the end of ''​.bashrc''​ used by the //old-style conda initialization//​ (we will later switch to the //​new-style//​). The added lines should look like: 
-          * ''#​ added by Miniconda3 installer''​\\ ''​export PATH="/​home/​share/​unix_files/​cdat/​miniconda3/​bin:​$PATH"''​ +        * ''#​ added by Miniconda3 installer''​\\ ''​export PATH="/​home/​share/​unix_files/​cdat/​miniconda3/​bin:​$PATH"''​ 
-    * Open a new terminal (if you use bash) or open a new terminal and type ''​bash''​ +        * ''#​ added by Miniconda4.xxx installer''​\\ ''​[some really fancy bash shell commands]''​ 
-      * check if the python from the conda distribution has been correctly installed\\ <​code>​ > bash+  * Remove the installer: ''​rm Miniconda3-latest-Linux-x86_64.sh''​ 
 +  ​* Open a new terminal (if you use bash) or open a new terminal and type ''​bash''​ 
 +    * check if the python from the conda distribution has been correctly installed\\ <​code>​ > bash
 $ which python $ which python
 /​home/​share/​unix_files/​cdat/​miniconda3/​bin/​python /​home/​share/​unix_files/​cdat/​miniconda3/​bin/​python
 $ which conda $ which conda
 /​home/​share/​unix_files/​cdat/​miniconda3/​bin/​conda</​code>​ /​home/​share/​unix_files/​cdat/​miniconda3/​bin/​conda</​code>​
-      ​* Update and clean the new installation\\ <​code>​$ conda update --all+    ​* Update and clean the new installation\\ <​code>​$ conda update --all
 $ du -sh /​home/​share/​unix_files/​cdat/​miniconda3 $ du -sh /​home/​share/​unix_files/​cdat/​miniconda3
 515M    /​home/​share/​unix_files/​cdat/​miniconda3 515M    /​home/​share/​unix_files/​cdat/​miniconda3
Line 68: Line 74:
 requests ​                 2.20.0 ​                  ​py37_0 requests ​                 2.20.0 ​                  ​py37_0
 [...]</​code>​ [...]</​code>​
-  * Remove ​the miniconda3 initialization lines that were automatically added at the end of ''​.bashrc''​ and put them (and other useful commands) in a special initialization file (see ''​~jypeter/​.conda3_jyp.sh''​ below)that can be sourced only when we actually want to use conda and CDAT\\ ​<​code>​bash-4.2$ which python+ 
 +==== Post-Miniconda3 installation ==== 
 + 
 +The idea is to remove ​the miniconda3 initialization lines that were automatically added at the end of ''​.bashrc''​ and put them (and other useful commands) in a special initialization file, that can be sourced only when we actually want to use conda and CDAT (in order to avoid potentiel side effects) 
 + 
 +=== New style initialization === 
 + 
 +Note: this is the **new** ''​conda activate some_version''​ style 
 + 
 +See the ''​~jypeter/​.conda3_jyp.sh'' ​file below, ​and how to use it, **in a bash shell**. In a **tcsh shell**, see the ''​~jypeter/​.conda3_jyp.csh''​ further down. In both shell cases, if you are installing your own version of python, you need to use your own location of the initialization files in the ''​source''​ lines, ​and you can use another file name than ''​conda3_jyp''​ 
 + 
 +<​code>​$ which python
 /​usr/​bin/​python /​usr/​bin/​python
 +
 $ cat ~jypeter/​.conda3_jyp.sh $ cat ~jypeter/​.conda3_jyp.sh
-# Conda initialization by JYP+# Conda initialization by JYP, NEW style
 # #
 # Use this for working with conda and CDAT centrally managed by JYP # Use this for working with conda and CDAT centrally managed by JYP
 +#
 +# Execute this file in a BASH shell with
 +#     ​source path/​this_file
 +# Then get the list of available python distributions with
 +#     conda env list
 +# Then activate a specific distribution with
 +#     conda activate version_name
 # #
 # More details in: # More details in:
-#   ​https://​wiki.lsce.ipsl.fr/​pmip3/​doku.php/​other:​python:​starting#​conda-based_v ​                                   ersions_of_uv-cdat+#   ​https://​wiki.lsce.ipsl.fr/​pmip3/​doku.php/​other:​python:​starting#​conda-based_versions_of_uv-cdat
 #   ​https://​wiki.lsce.ipsl.fr/​pmip3/​doku.php/​other:​uvcdat:​conda_notes #   ​https://​wiki.lsce.ipsl.fr/​pmip3/​doku.php/​other:​uvcdat:​conda_notes
 # #
 # Jean-Yves Peterschmitt - LSCE - 11/2018 # Jean-Yves Peterschmitt - LSCE - 11/2018
  
-export PATH="/​home/​share/​unix_files/​cdat/​miniconda3/​bin:​$PATH"​+source ​/​home/​share/​unix_files/​cdat/​miniconda3/​etc/​profile.d/​conda.sh
  
 # Use the alias below to easily determine where your python # Use the alias below to easily determine where your python
Line 91: Line 116:
  
 # The end # The end
 +
 $ source ~jypeter/​.conda3_jyp.sh $ source ~jypeter/​.conda3_jyp.sh
 +
 +$ conda activate
 +(base) $ which python
 +/​home/​share/​unix_files/​cdat/​miniconda3/​bin/​python
 +
 +</​code>​
 +
 +**tcsh shell** usage example
 +
 +<​code>​ >which python
 +/​usr/​bin/​python
 +
 + >​cat ~jypeter/​.conda3_jyp.csh
 +# Conda initialization by JYP, NEW style
 +#
 +# Use this for working with conda and CDAT centrally managed by JYP
 +#
 +# Execute this file in a TCSH shell with
 +#     ​source path/​this_file
 +# Then get the list of available python distributions with
 +#     conda env list
 +# Then activate a specific distribution with
 +#     conda activate version_name
 +#
 +# More details in:
 +#   ​https://​wiki.lsce.ipsl.fr/​pmip3/​doku.php/​other:​python:​starting#​conda-based_versions_of_uv-cdat
 +#   ​https://​wiki.lsce.ipsl.fr/​pmip3/​doku.php/​other:​uvcdat:​conda_notes
 +#
 +# Jean-Yves Peterschmitt - LSCE - 11/2018
 +
 +source /​home/​share/​unix_files/​cdat/​miniconda3/​etc/​profile.d/​conda.csh
 +
 +# Use the alias below to easily determine where your python
 +# interpreter is located
 +alias wp "which python"​
 +
 +# The end
 +
 + >​source ​ ~jypeter/​.conda3_jyp.csh
 +
 + >​conda activate
 +
 +(base) >which python
 +/​home/​share/​unix_files/​cdat/​miniconda3/​bin/​python</​code>​
 +
 +You probably don't want to type the //source// line each time you need to use your conda based python, so you can add a ''​source ​ ~jypeter/​.conda3_jyp.sh''​ line in your ''​~/​.bashrc''​ file, and ''​source ​ ~jypeter/​.conda3_jyp.csh''​ line in your ''​~/​.cshrc''​ file. Then, when you need a specific python environment,​ just type ''​conda activate name_of_the_specific_environment''​
 +
 +=== Old style initialization ===
 +
 +<WRAP center round tip 60%>
 +The //old style// notes below are just for reference sake and you can skip them
 +</​WRAP>​
 +
 +
 +Note: this is the **old** ''​source activate some_version''​ style
 +
 +See the ''​~jypeter/​.conda3old_jyp.sh''​ file below, and how to use it, **in a bash shell**
 +
 +<​code>​bash-4.2$ which python
 +/​usr/​bin/​python
 +
 +$ cat .conda3old_jyp.sh
 +# Conda initialization by JYP, OLD style
 +#
 +# Use this for working with conda and CDAT centrally managed by JYP
 +#
 +# Execute this file in a BASH shell with
 +#     ​source path/​this_file
 +# Then get the list of available python distributions with
 +#     conda env list
 +# Then activate a specific distribution with
 +#     ​source activate version_name
 +#
 +# More details in:
 +#   ​https://​wiki.lsce.ipsl.fr/​pmip3/​doku.php/​other:​python:​starting#​conda-based_versions_of_uv-cdat
 +#   ​https://​wiki.lsce.ipsl.fr/​pmip3/​doku.php/​other:​uvcdat:​conda_notes
 +#
 +# Jean-Yves Peterschmitt - LSCE - 11/2018
 +
 +export PATH="/​home/​share/​unix_files/​cdat/​miniconda3/​bin:​$PATH"​
 +
 +# Use the alias below to easily determine where your python
 +# interpreter is located
 +alias wp="​which python"​
 +
 +# Where are ALL the python interpreters in the search path
 +alias wpa="​which -a python"​
 +
 +# The end
 +
 +$ source ~jypeter/​.conda3old_jyp.sh
 +
 $ wp $ wp
 /​home/​share/​unix_files/​cdat/​miniconda3/​bin/​python /​home/​share/​unix_files/​cdat/​miniconda3/​bin/​python
Line 98: Line 216:
 ==== Installing CDAT 8.0 ==== ==== Installing CDAT 8.0 ====
  
-<​code>​conda create -n cdat-8.0_py2 -c cdat/​label/​v80 -c conda-forge -c cdat python=2.7 cdat+=== Python 2.7 version === 
 + 
 +<​code>​conda create -n cdat-8.0_py2 -c cdat/​label/​v80 -c conda-forge -c cdat python=2.7 cdat
 # Generate the list of installed packages # Generate the list of installed packages
-conda list -n cdat-8.0_py2 > /​home/​scratch01/​jypeter/​cdat-8.0_py2_list_181108.txt</​code>​+conda list -n cdat-8.0_py2 > /​home/​scratch01/​jypeter/​cdat-8.0_py2_list_181108.txt</​code>​
  
 List of installed packages: {{:​other:​uvcdat:​cdat_conda:​cdat-8.0_py2_list_181108.txt}} List of installed packages: {{:​other:​uvcdat:​cdat_conda:​cdat-8.0_py2_list_181108.txt}}
Line 125: Line 245:
 2.8G    /​home/​share/​unix_files/​cdat/​miniconda3/​envs/​cdat-8.0_py2</​code>​ 2.8G    /​home/​share/​unix_files/​cdat/​miniconda3/​envs/​cdat-8.0_py2</​code>​
  
 +=== Python 3.6 version ===
 +
 +<​code>​$ conda create -n cdat-8.0_py3 -c cdat/​label/​v80 -c conda-forge -c cdat python=3.6 cdat</​code>​
 +
 +==== Installing CDAT nightly ====
 +
 +Notes:
 +
 +  * This page is about CDAT 8.0, but we have added a short nightly section here as a convenient shortcut. This should probably be moved to a stand-alone nightly page later
 +  * [[https://​github.com/​CDAT/​cdat/​wiki/​Obtain-CDAT-nightly-packages|Official nightly page]]
 +
 +=== Python 2.7 version ===
 +
 +<​code>​$ conda create -n cdat-nightly_py2 -c cdat/​label/​nightly -c conda-forge -c cdat python=2.7 cdat</​code>​
 +
 +<wrap hi>Not tested!</​wrap>​ Can this be updated with ''​conda update -n cdat-nightly_py2 -c cdat/​label/​nightly -c conda-forge -c cdat --all''​ ???
 +
 +=== Python 3.6 version ===
 +
 +<​code>​$ conda create -n cdat-nightly_py3 -c cdat/​label/​nightly -c conda-forge -c cdat python=3.6 cdat</​code>​
  
 ===== Cloning cdat to add specific packages for LSCE ===== ===== Cloning cdat to add specific packages for LSCE =====
Line 137: Line 277:
 Note: using hard links, cloning a full environment //only// adds an extra 582M of disk space Note: using hard links, cloning a full environment //only// adds an extra 582M of disk space
  
-<​code>​$ du -sh /​home/​share/​unix_files/​cdat/​miniconda3/​envs/​* +<​code>​$ conda create -n cdatm17_py2 --clone cdat-8.0_py2
-2.8G    /​home/​share/​unix_files/​cdat/​miniconda3/​envs/​cdat-8.0_py2 +
-$ conda create -n cdatm17_py2 --clone cdat-8.0_py2+
 Source: ​     /​home/​share/​unix_files/​cdat/​miniconda3/​envs/​cdat-8.0_py2 Source: ​     /​home/​share/​unix_files/​cdat/​miniconda3/​envs/​cdat-8.0_py2
 Destination:​ /​home/​share/​unix_files/​cdat/​miniconda3/​envs/​cdatm17_py2 Destination:​ /​home/​share/​unix_files/​cdat/​miniconda3/​envs/​cdatm17_py2
Line 148: Line 286:
  
 $ du -sh /​home/​share/​unix_files/​cdat/​miniconda3/​envs/​* $ du -sh /​home/​share/​unix_files/​cdat/​miniconda3/​envs/​*
-2.8G    /​home/​share/​unix_files/​cdat/​miniconda3/​envs/​cdat-8.0_py2 +2.5G    /​home/​share/​unix_files/​cdat/​miniconda3/​envs/​cdat-8.0_py2 
-582M    /​home/​share/​unix_files/​cdat/​miniconda3/​envs/​cdatm17_py2+392M    /​home/​share/​unix_files/​cdat/​miniconda3/​envs/​cdatm17_py2 
 +839M    /​home/​share/​unix_files/​cdat/​miniconda3/​envs/​cdat-nightly_py2
  
 </​code>​ </​code>​
 +
 +==== cdat nightly case ====
 +
 +''​conda create -n cdatm-nightly_py2 %%--%%clone cdat-nightly_py2''​
  
 ===== Getting ready for a moving default CDAT ===== ===== Getting ready for a moving default CDAT =====
 +
 +<note warning>​This step should probably be listed at the **end**, especially in a multi-user environment! If there is already a ''​cdatm''​ link, make sure that the new version is stable and working correctly before updating the ''​cdatm''​ link</​note>​
  
 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 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
Line 196: Line 341:
  
 After cloning, we are ready to install some extra packages that may be requested by LSCE users After cloning, we are ready to install some extra packages that may be requested by LSCE users
 +
 +  * We first try to install together as many packages as possible that don't require other channels than //​conda-forge//,​ and that don't request a downgrade of what is already installed
 +  * We then install individual extra packages with ''​conda install''​ or ''​pip install''​
  
 <​code>#​ Keep a trace of what will be installed <​code>#​ 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+$ conda install --dry-run -n cdatm17_py2 ​-c conda-forge pillow pandas statsmodels seaborn scikit-image seawater gsw netcdf4 pyferret basemap-data-hires xlsxwriter ​cmocean ​rpy2 gdal windspharm  ​> /​home/​scratch01/​jypeter/​lsce-extra_01_install_190304.txt
  
 # Install... # 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+$ conda install -n cdatm17_py2 ​-c conda-forge pillow pandas statsmodels seaborn scikit-image seawater gsw netcdf4 pyferret basemap-data-hires xlsxwriter ​cmocean ​rpy2 gdal windspharm
 [...] [...]
 +
 +# Install extra packages in the nightly version (if you need '​nightly'​)
 +$ conda install -n cdatm-nightly_py2 -c conda-forge pillow pandas statsmodels seaborn scikit-image seawater gsw netcdf4 pyferret basemap-data-hires xlsxwriter cmocean rpy2 gdal windspharm
  
 # Check the disk space after installation # Check the disk space after installation
-bash-4.1$ du -sh /​home/​share/​unix_files/​cdat/​miniconda2 +$ du -sh /​home/​share/​unix_files/​cdat/​miniconda3 
-11G /​home/​share/​unix_files/​cdat/​miniconda2+7.5G    ​/​home/​share/​unix_files/​cdat/​miniconda3
  
-bash-4.1$ du -sh /​home/​share/​unix_files/​cdat/​miniconda2/envs/* +$ du -sh /​home/​share/​unix_files/​cdat/​miniconda3/envs/* 
-0 /​home/​share/​unix_files/​cdat/​miniconda2/​envs/​cdatm +2.5G    ​/​home/​share/​unix_files/​cdat/​miniconda3/​envs/​cdat-8.0_py2 
-2.8G /​home/​share/​unix_files/​cdat/​miniconda2/envs/cdatm14 +1.2G    ​/​home/​share/​unix_files/​cdat/​miniconda3/envs/cdatm17_py2 
-3.7G /​home/​share/​unix_files/cdat/​miniconda2/​envs/​cdatm15 +938M    ​/​home/​share/​unix_files/​cdat/​miniconda3/envs/cdatm-nightly_py2 
-574M /​home/​share/​unix_files/​cdat/​miniconda2/​envs/​uvcdat-2.10 +450M    ​/​home/​share/​unix_files/​cdat/​miniconda3/envs/cdat-nightly_py2<​/code>
-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</​code>​ +
- +
-List of installed packages: {{ :​other:​uvcdat:​cdat_conda:​lsce-extra_01_install_170808.txt |}} +
- +
-Disk space used after adding the extra packages, in <wrap em>in the  new directory hierarchy</​wrap>​ (''​cdat/​miniconda2b'',​ on the obelix servers) +
- +
-<​code>​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 +List of installed packages: {{ :​other:​uvcdat:​cdat_conda:​lsce-extra_01_install_190304.txt |}}
-5.4G /​home/​share/​unix_files/​cdat/​miniconda2b</​code>​+
  
 Packages installed with //pip// Packages installed with //pip//
Line 244: Line 372:
     * Update with: ''​pip install %%--%%upgrade dreqPy''​     * Update with: ''​pip install %%--%%upgrade dreqPy''​
       * Get version number with:\\ <​code>​$ drq -v       * Get version number with:\\ <​code>​$ drq -v
-dreqPy version 01.00.06 [Version 01.00.06]</​code>​ +dreqPy version 01.00.29 [Version 01.00.29]</​code>​
-  * [[https://​github.com/​pierre-rouanet/​dtw|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// The following packages have no dependency problems and were installed (or updated) //later//
-  * [[http://​www.earthsystemmodeling.org/​esmf_releases/​non_public/​ESMF_7_0_0/​esmpy_doc/​html/​index.html|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 
-    * <​code>​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 +  * [[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 
-[...]+    * ''​conda install -n cdatm17_py2 ​-c conda-forge -c vacumm vacumm''​
  
-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</​code>​ 
-  * [[http://​matplotlib.org/​cmocean/​|cmocean]]:​ beautiful colormaps for oceanography 
-    * ''​conda install -n cdatm15 -c conda-forge cmocean''​ 
-  * [[http://​scitools.org.uk/​iris/​index.html|iris]]:​ A Python library for Meteorology and Climatology 
-    * ''​conda install -n cdatm15 -c conda-forge -c scitools iris''​ 
-  * [[http://​www.gdal.org/​|OSGeo/​GDAL]]:​ Geospatial Data Abstraction Library. GDAL is a translator library for raster and vector geospatial data formats 
-    * ''​conda install -c conda-forge gdal''​ 
-    * [[https://​pcjericks.github.io/​py-gdalogr-cookbook/​|Python GDAL/OGR Cookbook]] 
   * [[https://​github.com/​stefraynaud/​spanlib|spanlib]]:​ Spectral Analysis Library   * [[https://​github.com/​stefraynaud/​spanlib|spanlib]]:​ Spectral Analysis Library
-    * ''​conda install -n cdatm15 ​-c stefraynaud -c conda-forge spanlib''​+    * ''​conda install -n cdatm17_py2 ​-c stefraynaud -c conda-forge spanlib''​
     * Test: ''​python -c 'from spanlib.analyzer import Analyzer'​ ''​     * Test: ''​python -c 'from spanlib.analyzer import Analyzer'​ ''​
-  ​* [[http://​wrf-python.readthedocs.io/​en/​latest/​|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''​ +  * [[https://climaf.readthedocs.io/​en/​latest/|CliMAF]]: a Climate Model Assessment Framework 
-  * [[https://glances.readthedocs.io/​en/​stable/index.html|glances]]: a cross-platform monitoring tool (similar to ''​top''​) +    * [[other:uvcdat:cdat_conda:climaf_install|Installation notes]]
-    * ''​conda install -n cdatm15 -c conda-forge glances''​ +
-    * [[https://​github.com/​nicolargo/​glances|glances@github]] +
-  * [[https://​ajdawson.github.io/​windspharm/​latest/​|windspharm]]spherical harmonic wind analysis in Python +
-    * ''​conda install -n cdatm15 -c conda-forge windspharm''​ +
-    * [[https://​github.com/​ajdawson/​windspharm|windspharm@github]] +
  
 ==== TODO ==== ==== TODO ====
  
-//Add here packages that would be useful ​but have some problems that prevent their installation//​+//Add here packages that would be useful ​and have not been installed yet, or have some problems that prevent their installation//​
  
-  * [[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://scitools.org.uk/iris/index.html|iris]]: Python ​library for Meteorology ​and Climatology 
-    * As of August 08 2017, installing vacumm in 2.10 requires downgrading to 2.10 (see [[https://​github.com/​VACUMM/​vacumm/​issues/​9|github issue]])! +    * ''​conda install -n cdatxxx ​-c conda-forge ​iris''​
-    * <wrap hi>​Problem solved</​wrap>​ 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\\ ​[[https://github.com/mscross/pysplit|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 [[https://ready.arl.noaa.gov/HYSPLIT.php|HYSPLiT]] +  * [[http://wrf-python.readthedocs.io/en/latest/|wrf-python]]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 ​fiona geopandas''​ +    * ''​conda install -n cdatxxx -c conda-forge wrf-python''​ 
-    ​- ''​pip install pysplit''​+  
 +  * [[https://glances.readthedocs.io/en/​stable/​index.html|glances]]: a cross-platform monitoring tool (similar to ''​top''​) 
 +    ​''​conda install -n cdatxxx ​-c conda-forge ​glances''​ 
 +    ​* [[https://​github.com/​nicolargo/​glances|glances@github]]
  
 ==== Other packages ==== ==== Other packages ====
Line 305: Line 411:
  
   * [[https://​cmor.llnl.gov/​|CMOR]]   * [[https://​cmor.llnl.gov/​|CMOR]]
-    * Update with: ''​conda update -n cdatm15 ​-c conda-forge -c pcmdi -c uvcdat cmor''​+    * Update with: ''​conda update -n cdatxxx ​-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'​ ''​       * Get version number with: ''​python -c 'from cmor import *; print CMOR_VERSION_MAJOR,​ CMOR_VERSION_MINOR,​ CMOR_VERSION_PATCH'​ ''​
  
Line 311: Line 417:
     * Update with: ''​pip install %%--%%upgrade dreqPy''​     * Update with: ''​pip install %%--%%upgrade dreqPy''​
       * Get version number with: ''​drq -v''​       * Get version number with: ''​drq -v''​
 +
 +==== Installing CLIMAF ====
 +
 +The [[https://​climaf.readthedocs.io/​|CLIMAF]] installation is a special case, because we may want to use it with the Python installed for CDAT, but it is not installed using conda
 +
 +We follow the steps for the [[https://​climaf.readthedocs.io/​en/​latest/​installing.html#​installing-climaf-if-you-are-not-at-cnrm-on-ciclad-or-climserv|installation of a non-standard server]]
 +
 +  * Go to the appropriate installation directory (we choose the directory where we have also installed miniconda3):​
 +    * LSCE: ''​cd /​home/​share/​unix_files/​cdat''​
 +    * ciclad: ''/​data/​jypmce/​cdat/''​
 +  * ''​git clone https://​github.com/​senesis/​climaf climaf''​
 +  * Add CLIMAF to the PYTHONPATH environment variable
 +    * LSCE & tcsh: ''​setenv PYTHONPATH ${PYTHONPATH}:/​home/​share/​unix_files/​cdat/​climaf''​
 +    * LSCE & bash: ''​export PYTHONPATH=${PYTHONPATH}:/​home/​share/​unix_files/​cdat/​climaf''​
 +    * ciclad: same as above, using ''/​data/​jypmce/​cdat/​climaf''​
 +  * Test the installation
 +    * make sure the [[https://​climaf.readthedocs.io/​en/​latest/​requirements.html#​requirements|Requirements]] are available:
 +      * LSCE: ''​module load netcdf/4 nco cdo ncl ncview''​
 +      * ciclad: ''​module load netcdf4 nco cdo ncl/​6.3.0''​
 +      * optional: start an X server
 +      * <​code>​cd climaf/​testing
 +./​test_install.sh</​code>​
 +  * Once the tests are OK, add the required //module load// and environment variables definitions to the ''​.basrc''​ and ''​.cshrc''​ files. <wrap hi>Note: maybe these lines should go to the ''​.profile''​ and ''​.login''​ files...(check [[https://​www.gnu.org/​software/​bash/​manual/​html_node/​Bash-Startup-Files.html|Bash Startup Files]])</​wrap> ​
 +    * LSCE: add to your .cshrc
 +      * <​code>#​ Prerequisites for using CLIMAF
 +module load netcdf/4 nco cdo ncl ncview
 +
 +# CLIMAF environment variables
 +setenv CLIMAF /​home/​share/​unix_files/​cdat/​climaf
 +setenv PYTHONPATH "​${PYTHONPATH}:​${CLIMAF}"​
 +#setenv PYTHONPATH $CLIMAF
 +setenv PATH "​${PATH}:​${CLIMAF}/​bin"​
 +setenv CLIMAF_CACHE "/​home/​scratch01/​${USER}/​climaf_cache"​
 +setenv TMPDIR $CLIMAF_CACHE
 +setenv CLIMAF_LOG_DIR $CLIMAF_CACHE
 +
 +#conda activate cdatm-nightly_py2</​code>​
 +    * ciclad: add to your .bashrc
 +      * <​code>#​ Prerequisites for using CLIMAF when not using the 
 +# default '​module load climaf'​
 +module load netcdf4 nco cdo ncl/6.3.0
 +
 +# CLIMAF environment variables
 +export CLIMAF=/​data/​jypmce/​cdat/​climaf
 +#export PYTHONPATH=$PYTHONPATH:​$CLIMAF
 +export PYTHONPATH=$CLIMAF
 +export PATH=$PATH:​$CLIMAF/​bin
 +export CLIMAF_CACHE=/​data/​jypmce/​climaf_cache
 +export TMPDIR=$CLIMAF_CACHE
 +export CLIMAF_LOG_DIR=$CLIMAF_CACHE
 +
 +#conda activate cdatm-nightly_py2
 +</​code>​
 +  * Open a new shell and <wrap em>run the tests again</​wrap>​. If there is an error that was not there, check what you have added to the shell init files
 +  * [[other:​uvcdat:​cdat_conda:​climaf_test|Test CLIMAF on ciclad]]
  
 ==== Cleaning up things ==== ==== Cleaning up things ====
Line 317: Line 478:
  
 We check if some of the installed files are missing read access for the //group// or //other//, and we manually change the permissions We check if some of the installed files are missing read access for the //group// or //other//, and we manually change the permissions
-<​code>​(cdatm15) bash-4.2$ ​find cdatm15 \! -perm /g+r,o+r -ls +<​code> ​>find /home/share/unix_files/cdat/miniconda3/envs \! -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 +# Everything OK!</​code>​
-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</​code>​+
  
  
Line 370: Line 505:
   * [[https://​rpy2.readthedocs.io/​en/​version_2.8.x/​|rpy2]]:​ providing simple and robust access to R from within Python   * [[https://​rpy2.readthedocs.io/​en/​version_2.8.x/​|rpy2]]:​ providing simple and robust access to R from within Python
   * [[http://​matplotlib.org/​cmocean/​|cmocean]]:​ beautiful colormaps for oceanography   * [[http://​matplotlib.org/​cmocean/​|cmocean]]:​ beautiful colormaps for oceanography
-  * [[http://​scitools.org.uk/​iris/​index.html|iris]]:​ A Python library for Meteorology and Climatology 
   * [[http://​www.gdal.org/​|OSGeo/​GDAL]]:​ Geospatial Data Abstraction Library. GDAL is a translator library for raster and vector geospatial data formats   * [[http://​www.gdal.org/​|OSGeo/​GDAL]]:​ Geospatial Data Abstraction Library. GDAL is a translator library for raster and vector geospatial data formats
 +    * [[https://​pcjericks.github.io/​py-gdalogr-cookbook/​|Python GDAL/OGR Cookbook]]
   * [[https://​github.com/​stefraynaud/​spanlib|spanlib]]:​ Spectral Analysis Library   * [[https://​github.com/​stefraynaud/​spanlib|spanlib]]:​ Spectral Analysis Library
-  * [[http://​wrf-python.readthedocs.io/​en/​latest/​|wrf-python]]:​ A collection of diagnostic and interpolation routines for use with output from the Weather Research and Forecasting (WRF-ARW) Model 
-  * [[https://​glances.readthedocs.io/​en/​stable/​index.html|glances]]:​ a cross-platform monitoring tool (similar to ''​top''​) 
   * [[https://​ajdawson.github.io/​windspharm/​latest/​|windspharm]]:​ spherical harmonic wind analysis in Python   * [[https://​ajdawson.github.io/​windspharm/​latest/​|windspharm]]:​ spherical harmonic wind analysis in Python
  
Line 386: Line 519:
  
 ^  Environment\\ name  ^  Server ​ ^  ''​conda list'' ​ ^ ^  Environment\\ name  ^  Server ​ ^  ''​conda list'' ​ ^
- ​uvcdat-2.10  ​|  LSCE  |  ​{{  ​|package list}} ​ | +cdat-8.0_py2 |  LSCE  | | 
- ​cdatm15  ​|  LSCE  |  ​{{ ​|package list}} ​ |+| cdatm17_py2 |  LSCE | 
 +cdat-nightly_py2 ​|  LSCE\\ ciclad ​ | | 
 +| cdatm-nightly_py2 |  LSCE\\ ciclad ​ | |
  
 /* standard page footer */ /* standard page footer */
other/uvcdat/cdat_conda/cdat_8_0_py2.1541696475.txt.gz · Last modified: 2018/11/08 18:01 by jypeter