other:uvcdat:cdat_conda:cdat_8_0_py2
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other:uvcdat:cdat_conda:cdat_8_0_py2 [2019/03/04 17:23] jypeter |
other:uvcdat:cdat_conda:cdat_8_0_py2 [2021/02/26 16:03] jypeter Updated the Miniconda3 install instructions |
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| ==== Installing Miniconda3 ==== | ==== Installing Miniconda3 ==== | ||
| + | |||
| + | * You don't need to be //root// when you install Miniconda3 (actually **you should not be //root//**) | ||
| + | * 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 | ||
| We have installed a new version of Miniconda3 (steps below adapted from the [[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) | ||
| - | * 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.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 | + | * Find some temporary space on Linux (or Windows, if you are using WSL) |
| - | * Linux:''cd /home/scratch01/jypeter'' | + | * e.g. Linux at LSCE:\\ ''cd /home/scratch01/<your_login>'' |
| - | * WSL: ''cd /mnt/h/Scratch/jypeter/'' (assuming that there is a ''H:\Scratch\jypeter'' directory) | + | * e.g. WSL, assuming that there is a ''C:\Scratch\<your_login>'' directory:\\ ''cd /mnt/c/Scratch/<your_login>'' |
| - | * ''wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh'' (67 Mo, 15 Feb 2019) | + | * Use ''wget'' to download the installer:\\ ''wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh'' (90 Mb, 26 Feb 2021) |
| * Execute the installer | * Execute the installer | ||
| * ''bash Miniconda3-latest-Linux-x86_64.sh'' | * ''bash Miniconda3-latest-Linux-x86_64.sh'' | ||
| Line 382: | Line 385: | ||
| * ''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 ==== | ||
| Line 391: | Line 397: | ||
| * [[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]] | ||
| Line 408: | Line 414: | ||
| * [[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 414: | Line 420: | ||
| * 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 461: | Line 522: | ||
| ^ 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 | | | ||
other/uvcdat/cdat_conda/cdat_8_0_py2.txt · Last modified: 2021/02/27 13:55 by jypeter
