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Follow the instructions about the conda-based versions of UV-CDAT initialization for actually using an installed version of 2.10
DIsk space used before 2.10 installation (after running conda clean –all
)
> du -sh /home/share/unix_files/cdat/miniconda2 6.5G /home/share/unix_files/cdat/miniconda2 > 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 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/* 2.8G /home/share/unix_files/cdat/miniconda2/envs/cdatm14 1.7G /home/share/unix_files/cdat/miniconda2/envs/keras 2.0G /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0
Actual installation
bash-4.1$ conda create -n uvcdat-2.10 -c conda-forge -c uvcdat uvcdat=2.10 # Generate the list of installed packages conda list -n uvcdat-2.10 > /home/scratch01/jypeter/uvcdat-2.10_list_170721.txt
List of installed packages: uvcdat-2.10_list_170721.txt
Disk space after 2.10 installation
bash-4.1$ conda env list cdatm14 /home/share/unix_files/cdat/miniconda2/envs/cdatm14 keras /home/share/unix_files/cdat/miniconda2/envs/keras uvcdat-2.10 /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.10 uvcdat-2.8.0 /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0 root * /home/share/unix_files/cdat/miniconda2 > du -sh /home/share/unix_files/cdat/miniconda2 11G /home/share/unix_files/cdat/miniconda2 > 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 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
Disk space after removing the keras environment that we don't need any more
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
Disk space used in a brand new directory hierarchy (cdat/miniconda2b
, on the obelix servers)
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
This section is about the creation of the cdatm15 environment
Notes about actually using the cdatm15 conda-based python
Note: using hard links, cloning a full environment only adds an extra 500M of disk space
bash-4.1$ du -sh /home/share/unix_files/cdat/miniconda2 9.0G /home/share/unix_files/cdat/miniconda2 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 9.5G /home/share/unix_files/cdat/miniconda2 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
Disk space used after cloning, in in the new directory hierarchy (cdat/miniconda2b
, on the obelix servers)
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
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
bash-4.2$ cd /home/share/unix_files/cdat/miniconda2b/envs bash-4.2$ conda env list cdatm15 /home/share/unix_files/cdat/miniconda2b/envs/cdatm15 uvcdat-2.10 /home/share/unix_files/cdat/miniconda2b/envs/uvcdat-2.10 root * /home/share/unix_files/cdat/miniconda2b bash-4.2$ ln -s cdatm15 cdatm bash-4.2$ conda env list cdatm /home/share/unix_files/cdat/miniconda2b/envs/cdatm cdatm15 /home/share/unix_files/cdat/miniconda2b/envs/cdatm15 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 * /home/share/unix_files/cdat/miniconda2b/envs/cdatm cdatm15 /home/share/unix_files/cdat/miniconda2b/envs/cdatm15 uvcdat-2.10 /home/share/unix_files/cdat/miniconda2b/envs/uvcdat-2.10 root /home/share/unix_files/cdat/miniconda2b
You should download the test data and use it in the example scripts that you want to distribute, and scripts you write for reporting the errors you find (if any…)
bash-4.1$ source activate cdatm15 (cdatm15) bash-4.1$ python -c 'import vcs; vcs.download_sample_data_files(); print "\nFinished downloading sample data to", vcs.sample_data' [...] Finished downloading sample data to /home/share/unix_files/cdat/miniconda2/envs/cdatm15/share/uvcdat/sample_data (cdatm15) bash-4.1$ du -sh /home/share/unix_files/cdat/miniconda2/envs/cdatm15/share/uvcdat/sample_data 174M /home/share/unix_files/cdat/miniconda2/envs/cdatm15/share/uvcdat/sample_data
After cloning, we are ready to install some extra packages that may be requested by LSCE users
# 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 # 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 [...] # Check the disk space after installation bash-4.1$ du -sh /home/share/unix_files/cdat/miniconda2 11G /home/share/unix_files/cdat/miniconda2 bash-4.1$ du -sh /home/share/unix_files/cdat/miniconda2/envs/* 0 /home/share/unix_files/cdat/miniconda2/envs/cdatm 2.8G /home/share/unix_files/cdat/miniconda2/envs/cdatm14 3.7G /home/share/unix_files/cdat/miniconda2/envs/cdatm15 574M /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.10 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
List of installed packages: lsce-extra_01_install_170808.txt
Disk space used after adding the extra packages, in in the new directory hierarchy (cdat/miniconda2b
, on the obelix servers)
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 5.4G /home/share/unix_files/cdat/miniconda2b
Packages installed with pip
pip install dreqPy
pip install --upgrade dreqPy
$ drq -v dreqPy version 01.00.06 [Version 01.00.06]
pip install dtw
The following packages have no dependency problems and were installed (or updated) later
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 [...] 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
conda install -n cdatm15 -c conda-forge cmocean
conda install -n cdatm15 -c conda-forge -c scitools iris
Add here packages that would be useful but have some problems that prevent their installation
conda install -n cdatm15 -c conda-forge fiona geopandas
pip install pysplit
basemap
dreqPy
After following the steps above, we get the following environments. Use the conda info –envs
command to get the up-to-date list of available environments
Environment name | Server | conda list |
---|---|---|
uvcdat-2.10 | LSCE | package list |
cdatm15 | LSCE | package list |
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