other:uvcdat:cdat_conda:cdat_2_12
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other:uvcdat:cdat_conda:cdat_2_12 [2017/09/07 12:56] jypeter created (copy of 2.10 and first edits) |
other:uvcdat:cdat_conda:cdat_2_12 [2017/09/11 08:42] jypeter [Cloning uvcdat to add specific packages for LSCE] Added a perm check step |
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| <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 **cdatm16** 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 cdatm16 conda-based python]] |
| </WRAP> | </WRAP> | ||
| + | ==== Cloning ==== | ||
| - | Note: using hard links, cloning a full environment //only// adds an extra 500M of disk space | + | <code>bash-4.1$ conda create -n cdatm16 --clone uvcdat-2.12 |
| - | + | Source: /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.12 | |
| - | <code>bash-4.1$ du -sh /home/share/unix_files/cdat/miniconda2 | + | Destination: /home/share/unix_files/cdat/miniconda2/envs/cdatm16 |
| - | 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/* | 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 | 2.8G /home/share/unix_files/cdat/miniconda2/envs/cdatm14 | ||
| - | 2.8G /home/share/unix_files/cdat/miniconda2/envs/cdatm15 | + | 4.5G /home/share/unix_files/cdat/miniconda2/envs/cdatm15 |
| - | 573M /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.10 | + | 2.7G /home/share/unix_files/cdat/miniconda2/envs/cdatm16 |
| + | 630M /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.10 | ||
| + | 242M /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.12 | ||
| 2.0G /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0 | 2.0G /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0 | ||
| </code> | </code> | ||
| - | Disk space used after cloning, in <wrap em>in the new directory hierarchy</wrap> (''cdat/miniconda2b'', on the obelix servers) | + | ==== Checking the permissions ==== |
| - | <code>bash-4.2$ du -sh /home/share/unix_files/cdat/miniconda2b | + | The files of some packages may have been installed with incorrect access rights, and //may not be readable by everybody// (e.g. [[https://github.com/PCMDI/pcmdi_metrics/issues/496|pcmdi_metrics/issues/496]] or [[https://github.com/UV-CDAT/cdp/issues/21|cdp/issues/21]]). We have to check and correct this by hand: |
| - | 4.8G /home/share/unix_files/cdat/miniconda2b | + | |
| - | bash-4.2$ du -sh /home/share/unix_files/cdat/miniconda2b/* | + | <code>(cdatm16) bash-4.1$ find uvcdat-2.12 \! -perm /g+r,o+r -ls |
| - | 4.4M /home/share/unix_files/cdat/miniconda2b/bin | + | 24774102 4 -rw------- 3 jypeter lsce 670 Apr 4 20:35 uvcdat-2.12/lib/python2.7/site-packages/cdp/cdp_output.py |
| - | 4.0K /home/share/unix_files/cdat/miniconda2b/conda-bld | + | 24774113 4 -rw------- 3 jypeter lsce 2436 Apr 4 20:35 uvcdat-2.12/lib/python2.7/site-packages/cdp/cdp_parameter.pyc |
| - | 280K /home/share/unix_files/cdat/miniconda2b/conda-meta | + | 24774111 4 -rw------- 3 jypeter lsce 1821 Apr 4 20:35 uvcdat-2.12/lib/python2.7/site-packages/cdp/cdp_parser.py |
| - | 3.4G /home/share/unix_files/cdat/miniconda2b/envs | + | [...] |
| - | 20K /home/share/unix_files/cdat/miniconda2b/etc | + | 24774098 4 -rw------- 3 jypeter lsce 234 Apr 4 20:35 uvcdat-2.12/lib/python2.7/site-packages/cdp-1.0.3-py2.7.egg-info/PKG-INFO |
| - | 3.8M /home/share/unix_files/cdat/miniconda2b/include | + | 24774089 4 -rw------- 3 jypeter lsce 1 Apr 4 20:35 uvcdat-2.12/lib/python2.7/site-packages/cdp-1.0.3-py2.7.egg-info/not-zip-safe |
| - | 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/* | + | (cdatm16) bash-4.1$ chmod -R a+r cdatm16/lib/python2.7/site-packages/cdp* chmod -R a+r uvcdat-2.12/lib/python2.7/site-packages/cdp*</code> |
| - | 2.8G /home/share/unix_files/cdat/miniconda2b/envs/cdatm15 | + | |
| - | 574M /home/share/unix_files/cdat/miniconda2b/envs/uvcdat-2.10 | + | |
| - | </code> | + | |
| ===== Getting ready for a moving default CDAT ===== | ===== Getting ready for a moving default CDAT ===== | ||
| - | 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 | + | See the note about the [[https://wiki.lsce.ipsl.fr/pmip3/doku.php/other:uvcdat:cdat_conda:cdat_2_10#getting_ready_for_a_moving_default_cdat|cdatm]] link/version. At this point of installation, we are not yet ready to have //cdatm// point to ''2.12''. |
| - | + | ||
| - | <code>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 | + | |
| - | </code> | + | |
| ===== Customizing UV-CDAT for LSCE ===== | ===== Customizing UV-CDAT for LSCE ===== | ||
| Line 153: | Line 111: | ||
| 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...) | 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...) | ||
| - | <code>bash-4.1$ source activate cdatm15 | + | <code>bash-4.1$ source activate cdatm16 |
| (cdatm15) bash-4.1$ python -c 'import vcs; vcs.download_sample_data_files(); print "\nFinished downloading sample data to", vcs.sample_data' | (cdatm15) bash-4.1$ python -c 'import vcs; vcs.download_sample_data_files(); print "\nFinished downloading sample data to", vcs.sample_data' | ||
| Line 159: | Line 117: | ||
| Finished downloading sample data to /home/share/unix_files/cdat/miniconda2/envs/cdatm15/share/uvcdat/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 | + | (cdatm16) bash-4.1$ du -sh /home/share/unix_files/cdat/miniconda2/envs/cdatm16/share/uvcdat/sample_data |
| - | 174M /home/share/unix_files/cdat/miniconda2/envs/cdatm15/share/uvcdat/sample_data</code> | + | 174M /home/share/unix_files/cdat/miniconda2/envs/cdatm16/share/uvcdat/sample_data |
| + | </code> | ||
| Line 168: | Line 127: | ||
| <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 | + | bash-4.1$ conda install --dry-run -n cdatm16 -c conda-forge -c uvcdat -c pcmdi -c scitools -c vacumm pillow pandas statsmodels seaborn scikit-image seawater gsw netcdf4 pyferret basemap-data-hires pcmdi_metrics xlsxwriter cmor shapely cartopy iris rpy2 cmocean iris gdal vacumm > /home/scratch01/jypeter/lsce-cdatm16-extra_01_install_170907.txt |
| # Install... | # Install... | ||
other/uvcdat/cdat_conda/cdat_2_12.txt · Last modified: 2017/09/19 14:17 by jypeter
