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other:uvcdat:cdat_conda:cdat_8_0_py2 [2018/11/08 09:47] jypeter |
other:uvcdat:cdat_conda:cdat_8_0_py2 [2018/11/08 16:10] jypeter |
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===== Installation with Miniconda3 ===== | ===== Installation with Miniconda3 ===== | ||
- | We have installed a new version of Miniconda3, based on the old [[other:uvcdat:conda_notes#installing_miniconda|installing miniconda]] instructions | + | ==== Installing Miniconda3 ==== |
+ | |||
+ | We have installed a new version of Miniconda3, by following the existing [[other:uvcdat:conda_notes#installing_miniconda|installing miniconda]] instructions | ||
* Follow the [[https://conda.io/docs/install/quick.html|Quick install]] steps to install Miniconda | * Follow the [[https://conda.io/docs/install/quick.html|Quick install]] steps to install Miniconda | ||
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requests 2.20.0 py37_0 | requests 2.20.0 py37_0 | ||
[...]</code> | [...]</code> | ||
- | * Remove the miniconda3 initialization lines 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 | + | * 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 |
+ | /usr/bin/python | ||
+ | $ cat ~jypeter/.conda3_jyp.sh | ||
+ | # Conda initialization by JYP | ||
+ | # | ||
+ | # Use this for working with conda and CDAT centrally managed by JYP | ||
+ | # | ||
+ | # 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:uvcdat:conda_notes | ||
+ | # | ||
+ | # Jean-Yves Peterschmitt - LSCE - 11/2018 | ||
- | Disk space used before 2.10 installation (after running ''conda clean --all'') | + | export PATH="/home/share/unix_files/cdat/miniconda3/bin:$PATH" |
- | <code> > du -sh /home/share/unix_files/cdat/miniconda2 | + | # Use the alias below to easily determine where your python |
- | 6.5G /home/share/unix_files/cdat/miniconda2 | + | # interpreter is located |
+ | alias wp="which python" | ||
- | > du -sh /home/share/unix_files/cdat/miniconda2/* | + | # Where are ALL the python interpreters in the search path |
- | 4.4M /home/share/unix_files/cdat/miniconda2/bin | + | alias wpa="which -a python" |
- | 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/* | + | # The end |
- | 2.8G /home/share/unix_files/cdat/miniconda2/envs/cdatm14 | + | $ source ~jypeter/.conda3_jyp.sh |
- | 1.7G /home/share/unix_files/cdat/miniconda2/envs/keras | + | $ wp |
- | 2.0G /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0</code> | + | /home/share/unix_files/cdat/miniconda3/bin/python |
- | + | </code> | |
- | Actual installation | + | |
- | <code>bash-4.1$ conda create -n uvcdat-2.10 -c conda-forge -c uvcdat uvcdat=2.10 | + | ==== 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 | ||
# Generate the list of installed packages | # Generate the list of installed packages | ||
- | conda list -n uvcdat-2.10 > /home/scratch01/jypeter/uvcdat-2.10_list_170721.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:uvcdat-2.10_list_170721.txt}} | + | List of installed packages: {{:other:uvcdat:cdat_conda:cdat-8.0_py2_list_181108.txt}} |
- | Disk space after 2.10 installation | + | Disk space after 8.0 installation |
- | <code>bash-4.1$ conda env list | + | <code>$ du -sh /home/share/unix_files/cdat/miniconda3 |
- | cdatm14 /home/share/unix_files/cdat/miniconda2/envs/cdatm14 | + | 4.3G /home/share/unix_files/cdat/miniconda3 |
- | keras /home/share/unix_files/cdat/miniconda2/envs/keras | + | $ du -sh /home/share/unix_files/cdat/miniconda3/* |
- | uvcdat-2.10 /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.10 | + | 15M /home/share/unix_files/cdat/miniconda3/bin |
- | uvcdat-2.8.0 /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0 | + | 2.4M /home/share/unix_files/cdat/miniconda3/compiler_compat |
- | root * /home/share/unix_files/cdat/miniconda2 | + | 4.0K /home/share/unix_files/cdat/miniconda3/conda-bld |
+ | 3.7M /home/share/unix_files/cdat/miniconda3/conda-meta | ||
+ | 2.8G /home/share/unix_files/cdat/miniconda3/envs | ||
+ | 28K /home/share/unix_files/cdat/miniconda3/etc | ||
+ | 4.9M /home/share/unix_files/cdat/miniconda3/include | ||
+ | 156M /home/share/unix_files/cdat/miniconda3/lib | ||
+ | 8.0K /home/share/unix_files/cdat/miniconda3/LICENSE.txt | ||
+ | 1.4G /home/share/unix_files/cdat/miniconda3/pkgs | ||
+ | 1.3M /home/share/unix_files/cdat/miniconda3/share | ||
+ | 24K /home/share/unix_files/cdat/miniconda3/ssl | ||
+ | 12K /home/share/unix_files/cdat/miniconda3/x86_64-conda_cos6-linux-gnu | ||
+ | $ du -sh /home/share/unix_files/cdat/miniconda3/envs/* | ||
+ | 2.8G /home/share/unix_files/cdat/miniconda3/envs/cdat-8.0_py2</code> | ||
- | > du -sh /home/share/unix_files/cdat/miniconda2 | ||
- | 11G /home/share/unix_files/cdat/miniconda2 | ||
- | > du -sh /home/share/unix_files/cdat/miniconda2/* | + | ===== Cloning cdat to add specific packages for LSCE ===== |
- | 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 | + | |
- | </code> | + | |
- | + | ||
- | Disk space after removing the keras environment that we don't need any more | + | |
- | + | ||
- | <code>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</code> | + | |
- | + | ||
- | Disk space used in <wrap em>a brand new directory hierarchy</wrap> (''cdat/miniconda2b'', on the obelix servers) | + | |
- | + | ||
- | <code>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 | + | |
- | </code> | + | |
- | + | ||
- | + | ||
- | ===== Cloning uvcdat to add specific packages for LSCE ===== | + | |
<WRAP center round tip 60%> | <WRAP center round tip 60%> | ||
- | This section is about the creation of the **cdatm15** environment | + | This section is about the creation of the **cdatm17** environment |
- | Notes about [[https://wiki.lsce.ipsl.fr/pmip3/doku.php/other:python:starting#conda-based_versions_of_uv-cdat|actually using the cdatm15 conda-based python]] | + | Notes about [[https://wiki.lsce.ipsl.fr/pmip3/doku.php/other:python:starting#conda-based_versions_of_uv-cdat|actually using the cdatm17 conda-based python]] |
</WRAP> | </WRAP> | ||
- | Note: using hard links, cloning a full environment //only// adds an extra 500M of disk space | + | Note: using hard links, cloning a full environment //only// adds an extra 582M of disk space |
- | <code>bash-4.1$ du -sh /home/share/unix_files/cdat/miniconda2 | + | <code>$ du -sh /home/share/unix_files/cdat/miniconda3/envs/* |
- | 9.0G /home/share/unix_files/cdat/miniconda2 | + | 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 | ||
+ | Destination: /home/share/unix_files/cdat/miniconda3/envs/cdatm17_py2 | ||
+ | Packages: 226 | ||
+ | Files: 3 | ||
- | 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 | + | $ du -sh /home/share/unix_files/cdat/miniconda3/envs/* |
- | 9.5G /home/share/unix_files/cdat/miniconda2 | + | 2.8G /home/share/unix_files/cdat/miniconda3/envs/cdat-8.0_py2 |
+ | 582M /home/share/unix_files/cdat/miniconda3/envs/cdatm17_py2 | ||
- | 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 | ||
- | </code> | ||
- | |||
- | Disk space used after cloning, 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 | ||
- | 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 | ||
</code> | </code> | ||
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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 | ||
- | <code>bash-4.2$ cd /home/share/unix_files/cdat/miniconda2b/envs | + | <code>$ cd /home/share/unix_files/cdat/miniconda3/envs |
- | + | $ conda env list | |
- | bash-4.2$ conda env list | + | base * /home/share/unix_files/cdat/miniconda3 |
- | cdatm15 /home/share/unix_files/cdat/miniconda2b/envs/cdatm15 | + | cdat-8.0_py2 /home/share/unix_files/cdat/miniconda3/envs/cdat-8.0_py2 |
- | uvcdat-2.10 /home/share/unix_files/cdat/miniconda2b/envs/uvcdat-2.10 | + | cdatm17_py2 /home/share/unix_files/cdat/miniconda3/envs/cdatm17_py2 |
- | root * /home/share/unix_files/cdat/miniconda2b | + | $ ln -s cdatm17_py2 cdatm |
- | + | $ conda env list | |
- | bash-4.2$ ln -s cdatm15 cdatm | + | base * /home/share/unix_files/cdat/miniconda3 |
- | + | cdat-8.0_py2 /home/share/unix_files/cdat/miniconda3/envs/cdat-8.0_py2 | |
- | bash-4.2$ conda env list | + | cdatm /home/share/unix_files/cdat/miniconda3/envs/cdatm |
- | cdatm /home/share/unix_files/cdat/miniconda2b/envs/cdatm | + | cdatm17_py2 /home/share/unix_files/cdat/miniconda3/envs/cdatm17_py2 |
- | cdatm15 /home/share/unix_files/cdat/miniconda2b/envs/cdatm15 | + | $ source activate cdatm |
- | 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) bash-4.2$ conda env list | ||
- | cdatm * /home/share/unix_files/cdat/miniconda2b/envs/cdatm | + | base /home/share/unix_files/cdat/miniconda3 |
- | cdatm15 /home/share/unix_files/cdat/miniconda2b/envs/cdatm15 | + | cdat-8.0_py2 /home/share/unix_files/cdat/miniconda3/envs/cdat-8.0_py2 |
- | uvcdat-2.10 /home/share/unix_files/cdat/miniconda2b/envs/uvcdat-2.10 | + | cdatm * /home/share/unix_files/cdat/miniconda3/envs/cdatm |
- | root /home/share/unix_files/cdat/miniconda2b | + | cdatm17_py2 /home/share/unix_files/cdat/miniconda3/envs/cdatm17_py2</code> |
- | </code> | + | |
===== Customizing UV-CDAT for LSCE ===== | ===== Customizing UV-CDAT for LSCE ===== |