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other:uvcdat:cdat_conda:cdat_8_0_py2 [2018/11/13 17:21]
jypeter Added details for activating conda
other:uvcdat:cdat_conda:cdat_8_0_py2 [2021/02/27 13:55] (current)
jypeter [Installing Miniconda3]
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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+  * You don't need to be (and **you should not be**) //root// when you install Miniconda3. You just need enough disk space where you have write access 
 +  * If you are installing ​Miniconda3 ​in a Linux environment on a [[other:win10wsl|Windows 10 computer using Windows Subsystem for Linux (WSL)]], pay special attention to the instructions ​on the **WSL** lines
  
-  * Follow ​the [[https://​conda.io/​docs/​install/​quick.html|Quick install]] steps to install Miniconda +The steps below are adapted from the older (but with lots of extra and possibly useful details) ​[[other:uvcdat:​conda_notes#​installing_miniconda|installing miniconda]] instructions 
-    * Get the [[https://​repo.continuum.io/​miniconda/​Miniconda3-latest-Linux-x86_64.sh|Python 3.Linux 64-bit (bash installer)]] (unless there is a [[https://​conda.io/​miniconda.html|more recent version?​]]) + 
-      * ''​cd /​home/​scratch01/​jypeter'' ​(some temporary storage space for the installer) +  * Get the [[https://​repo.anaconda.com/​miniconda/​Miniconda3-latest-Linux-x86_64.sh|Python 3.Linux 64-bit (bash installer)]] (unless there is a [[https://​conda.io/​miniconda.html|more recent version?]]
-      * ''​wget https://​repo.continuum.io/​miniconda/​Miniconda3-latest-Linux-x86_64.sh''​ (60 Mo11 Nov 2018+    * Find some temporary space on Linux (or Windows, if you are using WSL
-    * Execute the installer +      * e.g. Linux at LSCE:​\\ ​''​cd /​home/​scratch01/​<​your_login>​''​ 
-      * ''​bash Miniconda3-latest-Linux-x86_64.sh''​ +      * e.g. WSL, assuming that there is a ''​C:​\Scratch\<​your_login>''​ directory:​\\ ''​cd /​mnt/​c/​Scratch/<​your_login>''​ 
-        * Accept the license +    * Use ''​wget''​ to download the installer:​\\ ​''​wget https://​repo.anaconda.com/​miniconda/​Miniconda3-latest-Linux-x86_64.sh''​ (90 Mb26 Feb 2021
-        * 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''​ + 
-          * Resulting ​''​miniconda3''​ directory size is 302M\\ <​code>​ >du -sh miniconda3 +  ​* Execute the installer 
-302M    ​miniconda3 +    * ''​bash Miniconda3-latest-Linux-x86_64.sh''​ 
- >​cd miniconda3 +      * Accept the license 
-/​home/​share/​unix_files/​cdat/​miniconda3 +      * Note: at the end of the installation (next step), **answer //no// to the following question**, so that the installer does not change your existing shell initialization files!\\ ''​Do you wish the installer to initialize Miniconda3 by running conda init? [yes|no]''​ => **NO** 
- >​du -sh * +      ​* Specify an explicit installation path **outside of your //home// directory**,​ with enough disk space (more than 3 Gb if you are going to install CDAT and some extra packages), preferably on a disk that is not backed up
-6.3M    ​bin +        * Installations by //JYP//: 
-2.0M    compiler_compat +          * Linux at LSCE: ''/​home/​share/​unix_files/​cdat/​miniconda3'',​ or another subdirectory of ''/​home/​share/​unix_files/​cdat/​''​  
-524K    ​conda-meta +          * Linux on ciclad: ''/​data/​jypmce/​cdat/​miniconda3'',​ or another sub-directory of ''/​data/​jypmce/​cdat/''​ 
-4.0K    ​envs +        * 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)\\ You need to accept the installation in the default location: ''/​home/<​your_login>/​miniconda3''​ 
-28K     etc +      * The resulting ​''​miniconda3''​ directory size is 342M\\ <​code>​ > du -sh miniconda3 
-5.2M    ​include +342M    ​miniconda3 
-146M    lib + 
-8.0K    LICENSE.txt + > cd miniconda3 
-142M    ​pkgs + 
-928K    ​share + > du -sh * 
-92K     ssl +20M     bin 
-12K     x86_64-conda_cos6-linux-gnu</​code>​ +0       ​compiler_compat 
-        Accept the automatic update of the //PATH// variable in ''​.bashrc'' ​(note: the installer automatically creates a backup of ''​.bashrc''​) +4.0K    condabin 
-          * ''​# added by Miniconda3 installer''​\\ ''​export PATH="/home/share/unix_files/cdat/​miniconda3/​bin:​$PATH"​''​ +684K    ​conda-meta 
-    Open a new terminal (if you use bash) or open a new terminal and type ''​bash''​ +0       envs 
-      check if the python from the conda distribution has been correctly installed\\ ​<​code>​ > bash+16K     etc 
 +5.5M    ​include 
 +4.0K    ​info 
 +198M    lib 
 +12K     LICENSE.txt 
 +114M    ​pkgs 
 +604K    ​share 
 +4.0K    shell 
 +0       ssl 
 +0       x86_64-conda_cos6-linux-gnu</​code>​ 
 + 
 +  ​Initialize ​the newly installed conda environment:​ 
 +    * bash shell: ''​source <​installation_path>​/miniconda3/etc/profile.d/conda.sh''​ 
 +    tcsh shell: ​''​source <​installation_path>​/miniconda3/etc/profile.d/conda.csh''​ 
 + 
 +  ​Check if you can use the ''​conda'' ​command, and use it to initialize the //base// environment 
 +    * <​code>​$ which conda 
 +<​installation_path>/​miniconda3/​condabin/​conda
 $ which python $ which python
-/home/​share/​unix_files/​cdat/​miniconda3/​bin/​python +/usr/​bin/​python 
-which conda +$ conda activate 
-/​home/​share/​unix_files/​cdat/​miniconda3/​bin/​conda</​code>​ +(base) $ which python 
-      * Update ​and clean the new installation\\ <​code>​$ conda update --all +<​installation_path>​/​miniconda3/​bin/​python</​code>​ 
-$ du -sh /​home/​share/​unix_files/​cdat/​miniconda3 +  * Update the new installation 
-515M    /​home/​share/​unix_files/​cdat/​miniconda3 +    * <​code>​$ conda update --all
-$ conda clean --all +
-$ du -sh /​home/​share/​unix_files/​cdat/​miniconda3 +
-270M    /​home/​share/​unix_files/​cdat/​miniconda3 +
-$ conda list +
-# packages in environment at /​home/​share/​unix_files/​cdat/​miniconda3:​ +
-+
-# Name                    Version ​                  ​Build ​ Channel +
-[...] +
-python ​                   3.7.1                h0371630_3 +
-readline ​                 7.0                  h7b6447c_5 +
-requests ​                 2.20.0 ​                  ​py37_0+
 [...]</​code>​ [...]</​code>​
 +    * During the update, the ''​miniconda3''​ directory size goes from 432 Mb to 581 Mb. This directory will keep on growing, which is the reason why you should put it on a (preferably non backed up) disk where you have //enough// space
 +
 +  * Make sure we have the latest ''​conda''​ (just in case we did not get it with the //​update//​)\\ ''​conda update -n base -c defaults conda''​
 +
 +  * Remove the installer:​\\ ''​rm Miniconda3-latest-Linux-x86_64.sh''​
  
 ==== Post-Miniconda3 installation ==== ==== 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+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 === === New style initialization ===
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 Note: this is the **new** ''​conda activate some_version''​ style 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+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 <​code>​$ which python
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 # Jean-Yves Peterschmitt - LSCE - 11/2018 # Jean-Yves Peterschmitt - LSCE - 11/2018
  
-/​home/​share/​unix_files/​cdat/​miniconda3/​etc/​profile.d/​conda.sh+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
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 $ source ~jypeter/​.conda3_jyp.sh $ source ~jypeter/​.conda3_jyp.sh
  
-$ conda activate ​cdatm +$ conda activate 
-(cdatm) $ which python +(base) $ which python 
-/​home/​share/​unix_files/​cdat/​miniconda3/envs/cdatm/bin/python+/​home/​share/​unix_files/​cdat/​miniconda3/​bin/​python
  
 </​code>​ </​code>​
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 # interpreter is located # interpreter is located
 alias wp "which python"​ alias wp "which python"​
- 
-# Where are ALL the python interpreters in the search path 
-alias wpa "​\which -a python"​ 
  
 # The end # The end
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  >​source ​ ~jypeter/​.conda3_jyp.csh  >​source ​ ~jypeter/​.conda3_jyp.csh
  
- >​conda activate ​cdatm+ >​conda activate
  
-(cdatm) >which python +(base) >which python 
-/​home/​share/​unix_files/​cdat/​miniconda3/envs/cdatm/​bin/​python</​code>​+/​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 === === 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 Note: this is the **old** ''​source activate some_version''​ style
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 ==== Installing CDAT 8.0 ==== ==== Installing CDAT 8.0 ====
 +
 +=== 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 <​code>​$ conda create -n cdat-8.0_py2 -c cdat/​label/​v80 -c conda-forge -c cdat python=2.7 cdat
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 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 =====
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 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
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 $ 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
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 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 352: Line 378:
     * 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 413: Line 417:
  
   * [[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'​ ''​
  
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     * 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 ====
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 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 478: Line 511:
   * [[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 494: Line 525:
  
 ^  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 ​ | |
  
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other/uvcdat/cdat_conda/cdat_8_0_py2.1542129699.txt.gz · Last modified: 2018/11/13 17:21 by jypeter