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| other:uvcdat:cdat_conda:cdat_8_0_py2 [2019/03/05 18:04] – Added the CLIMAF section jypeter | other:uvcdat:cdat_conda:cdat_8_0_py2 [2021/02/27 14:55] (current) – [Installing Miniconda3] jypeter |
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| ==== Installing Miniconda3 ==== | ==== Installing Miniconda3 ==== |
| |
| We have installed a new version of Miniconda3 (steps below adapted from the [[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 |
| | |
| | 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.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh|Python 3.8 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, if you are using WSL) |
| | * e.g. Linux at LSCE:\\ ''cd /home/scratch01/<your_login>'' |
| | * e.g. WSL, assuming that there is a ''C:\Scratch\<your_login>'' directory:\\ ''cd /mnt/c/Scratch/<your_login>'' |
| | * Use ''wget'' to download the installer:\\ ''wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh'' (90 Mb, 26 Feb 2021) |
| |
| * 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 | |
| * Linux:''cd /home/scratch01/jypeter'' | |
| * WSL: ''cd /mnt/h/Scratch/jypeter/'' (assuming that there is a ''H:\Scratch\jypeter'' directory) | |
| * ''wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh'' (67 Mo, 15 Feb 2019) | |
| * Execute the installer | * Execute the installer |
| * ''bash Miniconda3-latest-Linux-x86_64.sh'' | * ''bash Miniconda3-latest-Linux-x86_64.sh'' |
| * Accept the license | * Accept the license |
| * 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: | * 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** |
| * Linux LSCE: ''/home/share/unix_files/cdat/miniconda3'' | * 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: |
| * Linux ciclad: ''/data/jypmce/cdat/miniconda3'' | * Installations by //JYP//: |
| * 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'' | * Linux at LSCE: ''/home/share/unix_files/cdat/miniconda3'', or another subdirectory of ''/home/share/unix_files/cdat/'' |
| * Resulting ''miniconda3'' directory size is 302M\\ <code> >du -sh miniconda3 | * Linux on ciclad: ''/data/jypmce/cdat/miniconda3'', or another sub-directory of ''/data/jypmce/cdat/'' |
| 302M 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)\\ You need to accept the installation in the default location: ''/home/<your_login>/miniconda3'' |
| >cd miniconda3 | * The resulting ''miniconda3'' directory size is 342M\\ <code> > du -sh miniconda3 |
| /home/share/unix_files/cdat/miniconda3 | 342M miniconda3 |
| >du -sh * | |
| 6.3M bin | > cd miniconda3 |
| 2.0M compiler_compat | |
| 524K conda-meta | > du -sh * |
| 4.0K envs | 20M bin |
| 28K etc | 0 compiler_compat |
| 5.2M include | 4.0K condabin |
| 146M lib | 684K conda-meta |
| 8.0K LICENSE.txt | 0 envs |
| 142M pkgs | 16K etc |
| 928K share | 5.5M include |
| 92K ssl | 4.0K info |
| 12K x86_64-conda_cos6-linux-gnu</code> | 198M lib |
| * 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: | 12K LICENSE.txt |
| * ''# added by Miniconda3 installer''\\ ''export PATH="/home/share/unix_files/cdat/miniconda3/bin:$PATH"'' | 114M pkgs |
| * ''# added by Miniconda4.xxx installer''\\ ''[some really fancy bash shell commands]'' | 604K share |
| * Remove the installer: ''rm Miniconda3-latest-Linux-x86_64.sh'' | 4.0K shell |
| * Open a new terminal (if you use bash) or open a new terminal and type ''bash'' | 0 ssl |
| * check if the python from the conda distribution has been correctly installed\\ <code> > bash | 0 x86_64-conda_cos6-linux-gnu</code> |
| | |
| | * Initialize the newly installed conda environment: |
| | * bash shell: ''source <installation_path>/miniconda3/etc/profile.d/conda.sh'' |
| | * tcsh shell: ''source <installation_path>/miniconda3/etc/profile.d/conda.csh'' |
| | |
| | * Check if you can use the ''conda'' command, and use it to initialize the //base// environment |
| | * <code>$ 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 ==== |
| * ''conda install -n cdatm17_py2 -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' '' |
| | |
| | * [[https://climaf.readthedocs.io/en/latest/|CliMAF]]: a Climate Model Assessment Framework |
| | * [[other:uvcdat:cdat_conda:climaf_install|Installation notes]] |
| |
| ==== TODO ==== | ==== TODO ==== |
| |
| * [[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 | * [[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'' | * ''conda install -n cdatxxx -c conda-forge wrf-python'' |
| | |
| * [[https://glances.readthedocs.io/en/stable/index.html|glances]]: a cross-platform monitoring tool (similar to ''top'') | * [[https://glances.readthedocs.io/en/stable/index.html|glances]]: a cross-platform monitoring tool (similar to ''top'') |
| * ''conda install -n cdatm15 -c conda-forge glances'' | * ''conda install -n cdatxxx -c conda-forge glances'' |
| * [[https://github.com/nicolargo/glances|glances@github]] | * [[https://github.com/nicolargo/glances|glances@github]] |
| |
| |
| * [[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' '' |
| |
| * <code>cd climaf/testing | * <code>cd climaf/testing |
| ./test_install.sh</code> | ./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...</wrap> | * 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 | * LSCE: add to your .cshrc |
| * <code># Prerequisites for using CLIMAF | * <code># Prerequisites for using CLIMAF |
| </code> | </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 | * 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 ==== |
| |
| ^ Environment\\ name ^ Server ^ ''conda list'' ^ | ^ Environment\\ name ^ Server ^ ''conda list'' ^ |
| | cdat-8.0_py2 | LSCE\\ ciclad | | | | cdat-8.0_py2 | LSCE | | |
| | cdatm17_py2 | LSCE\\ ciclad | | | | cdatm17_py2 | LSCE | | |
| | cdat-nightly_py2 | LSCE\\ ciclad | | | | cdat-nightly_py2 | LSCE\\ ciclad | | |
| | cdatm-nightly_py2 | LSCE\\ ciclad | | | | cdatm-nightly_py2 | LSCE\\ ciclad | | |
