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| other:uvcdat:cdat_conda:cdat_2_12 [2017/09/07 14:56] – created (copy of 2.10 and first edits) jypeter | other:uvcdat:cdat_conda:cdat_2_12 [2017/09/19 16:17] (current) – What was changed here? Maybe the part about downgrading numpy? jypeter |
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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 | ===== Customizing UV-CDAT for LSCE ===== |
| |
| 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 | ==== Downloading cdms2/vcs test data ==== |
| |
| bash-4.2$ conda env list | 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...) |
| 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 | <code>bash-4.1$ source activate cdatm16 |
| |
| (cdatm) bash-4.2$ conda env list | (cdatm15) bash-4.1$ python -c 'import vcs; vcs.download_sample_data_files(); print "\nFinished downloading sample data to", vcs.sample_data' |
| cdatm * /home/share/unix_files/cdat/miniconda2b/envs/cdatm | [...] |
| cdatm15 /home/share/unix_files/cdat/miniconda2b/envs/cdatm15 | Finished downloading sample data to /home/share/unix_files/cdat/miniconda2/envs/cdatm15/share/uvcdat/sample_data |
| uvcdat-2.10 /home/share/unix_files/cdat/miniconda2b/envs/uvcdat-2.10 | |
| root /home/share/unix_files/cdat/miniconda2b | (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/cdatm16/share/uvcdat/sample_data |
| </code> | </code> |
| |
| ===== Customizing UV-CDAT for LSCE ===== | ==== Downgrading numpy ==== |
| |
| |
| ==== Downloading cdms2/vcs test data ==== | <code>bash-4.1$ conda install -n cdatm16 -c conda-forge -c pcmdi -c uvcdat numpy=1.12 |
| | Fetching package metadata ............... |
| | Solving package specifications: . |
| |
| 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...) | Package plan for installation in environment /home/share/unix_files/cdat/miniconda2/envs/cdatm16: |
| | |
| | The following NEW packages will be INSTALLED: |
| |
| <code>bash-4.1$ source activate cdatm15 | blas: 1.1-openblas conda-forge |
| | openblas: 0.2.19-2 conda-forge |
| |
| (cdatm15) bash-4.1$ python -c 'import vcs; vcs.download_sample_data_files(); print "\nFinished downloading sample data to", vcs.sample_data' | The following packages will be UPDATED: |
| [...] | |
| Finished downloading sample data to /home/share/unix_files/cdat/miniconda2/envs/cdatm15/share/uvcdat/sample_data | binaryio: 2.12-np113py27h8073811_0 uvcdat --> 2.12-np112py27h5813a3b_0 uvcdat |
| | cdms2: 2.12-np113py27_0 conda-forge --> 2.12-np112py27_0 conda-forge |
| | cdtime: 2.12-np113py27_2 conda-forge --> 2.12-np112py27_2 conda-forge |
| | cssgrid: 2.12-np113py27h3898552_0 uvcdat --> 2.12-np112py27hf1c8260_0 uvcdat |
| | dsgrid: 2.12-np113py27h9d524be_0 uvcdat --> 2.12-np112py27h822527b_0 uvcdat |
| | genutil: 2.12-np113py27_0 conda-forge --> 2.12-np112py27_0 conda-forge |
| | lmoments: 2.12-np113py27h5574120_0 uvcdat --> 2.12-np112py27h665d648_0 uvcdat |
| | matplotlib: 1.5.3-np113py27_8 conda-forge --> 2.0.0-np112py27_2 conda-forge |
| | natgrid: 2.12-np113py27h481ab8b_0 uvcdat --> 2.12-np112py27h569c149_0 uvcdat |
| | ort: 2.12-np113py27hd89025a_0 uvcdat --> 2.12-np112py27h964b06a_0 uvcdat |
| | regridpack: 2.12-np113py27hf1cacc0_0 uvcdat --> 2.12-np112py27h6a169cd_0 uvcdat |
| | scikit-learn: 0.19.0-np113py27_0 --> 0.19.0-py27_blas_openblas_201 conda-forge [blas_openblas] |
| | scipy: 0.19.1-np113py27_0 --> 0.19.1-py27_blas_openblas_202 conda-forge [blas_openblas] |
| | shgrid: 2.12-np113py27h2504d4d_0 uvcdat --> 2.12-np112py27h6f2dc27_0 uvcdat |
| | trends: 2.12-np113py27hedb240a_0 uvcdat --> 2.12-np112py27he3ac0c2_0 uvcdat |
| | uvcmetrics: 2.2.1-np113py27h151233a_0 uvcdat --> 2.2.1-np112py27_0 uvcdat |
| | zonalmeans: 2.12-np113py27h96f9f80_0 uvcdat --> 2.12-np112py27hbce4e2c_0 uvcdat |
| | |
| | The following packages will be SUPERCEDED by a higher-priority channel: |
| | |
| | numpy: 1.13.1-py27_0 --> 1.12.1-py27_blas_openblas_200 conda-forge [blas_openblas] |
| | |
| | Proceed ([y]/n)?</code> |
| |
| (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</code> | |
| |
| |
| |
| <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... |
