This shows you the differences between two versions of the page.
Both sides previous revision Previous revision Next revision | Previous revision | ||
other:uvcdat:cdat_conda:cdat_2_8_0 [2017/03/10 14:37] jypeter Added the test data download section |
other:uvcdat:cdat_conda:cdat_2_8_0 [2017/08/31 12:04] jypeter [Packages that have no dependency problems] Added a note about PMIP read permission problem |
||
---|---|---|---|
Line 2: | Line 2: | ||
[ [[.:index|Back to all versions]] ] | [ [[.:index|Back to all versions]] ] | ||
+ | |||
+ | <WRAP center round tip 60%> | ||
+ | Follow the instructions about the [[other:python:starting#conda-based_versions_of_uv-cdat|conda-based versions of UV-CDAT initialization]] for actually using an installed version of ''2.8.0'' | ||
+ | </WRAP> | ||
+ | |||
+ | ===== What's New? ===== | ||
+ | |||
+ | * [[https://github.com/UV-CDAT/uvcdat/releases/tag/v2.8|2.8 announcement]] and features summary ([[https://github.com/UV-CDAT/uvcdat/releases|all versions]]) | ||
+ | * Full [[https://uv-cdat.llnl.gov/changelog.html#2.8|Change log]] | ||
+ | |||
===== Installation with Anaconda2 ===== | ===== Installation with Anaconda2 ===== | ||
<WRAP center round alert 60%> | <WRAP center round alert 60%> | ||
- | [[#installation_with_miniconda2|Installing with Miniconda2]] rather than Anaconda2 will save disk space! | + | [[#installation_with_miniconda2|Installing with Miniconda2]] rather than Anaconda2 is **much better** because it will save disk space! |
</WRAP> | </WRAP> | ||
Line 80: | Line 90: | ||
12K /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0/var | 12K /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0/var | ||
107M /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0/vistrails</code> | 107M /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0/vistrails</code> | ||
+ | |||
+ | ===== Downgrading conda ===== | ||
+ | |||
+ | Note: on June 1st 2017, we used the following step in order to **down**grade conda and be ready to install UV-CDAT 2.10 that required an older version of conda (strictly older than 4.3.13) than the one used for 2.8 | ||
+ | |||
+ | <code>bash-4.1$ conda install -n root "conda<4.3.13" | ||
+ | Fetching package metadata ......... | ||
+ | Solving package specifications: . | ||
+ | |||
+ | Package plan for installation in environment /home/share/unix_files/cdat/miniconda2: | ||
+ | |||
+ | The following packages will be DOWNGRADED due to dependency conflicts: | ||
+ | |||
+ | conda: 4.3.13-py27_0 --> 4.3.11-py27_0 | ||
+ | |||
+ | Proceed ([y]/n)? y | ||
+ | |||
+ | conda-4.3.11-p 100% |###############################################################| Time: 0:00:00 4.28 MB/s | ||
+ | |||
+ | bash-4.1$ conda info | ||
+ | Current conda install: | ||
+ | |||
+ | platform : linux-64 | ||
+ | conda version : 4.3.11 | ||
+ | conda is private : False | ||
+ | conda-env version : 4.3.11</code> | ||
===== Cloning uvcdat to add specific packages for LSCE ===== | ===== Cloning uvcdat to add specific packages for LSCE ===== | ||
+ | |||
+ | <WRAP center round tip 60%> | ||
+ | This section is about the creation of the **cdatm14** environment | ||
+ | |||
+ | Notes about [[https://wiki.lsce.ipsl.fr/pmip3/doku.php/other:python:starting#conda-based_versions_of_uv-cdat|actually using the cdatm14 conda-based python]] | ||
+ | </WRAP> | ||
+ | |||
Note: using hard links, cloning a full environment only adds an extra 100M of disk space | Note: using hard links, cloning a full environment only adds an extra 100M of disk space | ||
Line 148: | Line 191: | ||
* [[https://github.com/PCMDI/pcmdi_metrics|PCMDI metrics package]] (PMP) | * [[https://github.com/PCMDI/pcmdi_metrics|PCMDI metrics package]] (PMP) | ||
* ''conda install -n cdatm14 -c conda-forge -c pcmdi pcmdi_metrics'' | * ''conda install -n cdatm14 -c conda-forge -c pcmdi pcmdi_metrics'' | ||
+ | * Note: There was a [[https://github.com/PCMDI/pcmdi_metrics/issues/496|read permission problem on the files]] - <wrap em>Solved in 2.10</wrap> | ||
+ | * [[https://xlsxwriter.readthedocs.io/|XlsxWriter]]: a Python module for creating Excel XLSX files | ||
+ | * ''conda install -n cdatm14 xlsxwriter'' | ||
+ | * Note: <wrap hi>this is a dependency of ''dreqPy''</wrap> | ||
+ | * [[https://earthsystemcog.org/projects/wip/CMIP6DataRequest|dreqPy]]: CMIP6 Data Request Python API | ||
+ | * ''pip install dreqPy'' | ||
+ | * Update with: ''pip install %%--%%upgrade dreqPy'' | ||
+ | * Get version number with:\\ <code>$ drq -v | ||
+ | dreqPy version 01.00.06 [Version 01.00.06]</code> | ||
+ | * [[https://cmor.llnl.gov/|CMOR]]: CMOR (//Climate Model Output Rewriter//) is used to produce CF-compliant netCDF files | ||
+ | * ''conda install -n cdatm14 -c conda-forge -c pcmdi -c uvcdat cmor'' | ||
+ | * Did not complete the installation yet, because it requested a downgrade of libnetcdf (see [[https://github.com/PCMDI/cmor/issues/138|github issue]]) | ||
+ | * Installation issue was solved in ''cmor-3.2.3'' | ||
+ | * [[https://github.com/pierre-rouanet/dtw|dtw]]: DTW (Dynamic Time Warping) python module | ||
+ | * ''pip install dtw'' | ||
+ | * Requested by Sentia Goursaud | ||
==== TODO ==== | ==== TODO ==== | ||
+ | //Add here packages that would be useful but have some problems that prevent their installation// | ||
- | * CMOR | + | * [[https://earthsystemcog.org/projects/esmpy/|ESMPy]]: ESMF Python Regridding Interface - <wrap hi>Works in [[.:cdat_2_10|2.10]]!</wrap> |
- | * ''conda install -n cdatm14 -c conda-forge -c pcmdi -c uvcdat cmor'' | + | * ''conda install -n cdatm14 -c conda-forge esmpy'' |
- | * Did not complete the installation yet, because it requested a downgrade of libnetcdf (see [[https://github.com/PCMDI/cmor/issues/138|github issue]]) | + | * Installation of esmpy ''7.0.0'' did not report errors, **but** esmpy seemed to have libraries based importation problems and has been removed |
+ | * ''conda -n cdatm14 remove esmpy'' | ||
+ | * [[http://www.gdal.org/|GDAL]]: Geospatial Data Abstraction Library - <wrap hi>Works in [[.:cdat_2_10|2.10]]!</wrap> | ||
+ | * Cannot be installed due to too many dependency problems, and because it requires the downgrade of geos and rpy2 | ||
==== Other packages ==== | ==== Other packages ==== | ||
Line 197: | Line 260: | ||
* trying to install ''rpy2'' will trigger the installation of ''R''! | * trying to install ''rpy2'' will trigger the installation of ''R''! | ||
* We force the **installation of only rpy2** in order to use the ''R'' already installed at LSCE | * We force the **installation of only rpy2** in order to use the ''R'' already installed at LSCE | ||
- | * ''conda install --force -n cdatm14 -c conda-forge -c uvcdat rpy2'' | + | * ''conda install %%--%%force -n cdatm14 -c conda-forge -c uvcdat rpy2'' |
===== Extra packages list ===== | ===== Extra packages list ===== | ||
Line 213: | Line 276: | ||
* [[https://github.com/conda-forge/basemap-data-hires-feedstock|basemap-data-hires]]: high resolution data for ''basemap'' | * [[https://github.com/conda-forge/basemap-data-hires-feedstock|basemap-data-hires]]: high resolution data for ''basemap'' | ||
* [[https://github.com/PCMDI/pcmdi_metrics|PCMDI metrics package]] (PMP): objectively compare results from climate models with observations using well-established statistical tests | * [[https://github.com/PCMDI/pcmdi_metrics|PCMDI metrics package]] (PMP): objectively compare results from climate models with observations using well-established statistical tests | ||
+ | * [[https://xlsxwriter.readthedocs.io/|XlsxWriter]]: a Python module for creating Excel XLSX files | ||
+ | * [[https://earthsystemcog.org/projects/wip/CMIP6DataRequest|dreqPy]]: CMIP6 Data Request Python API | ||
+ | * [[https://cmor.llnl.gov/|CMOR]]: CMOR (//Climate Model Output Rewriter//) is used to produce CF-compliant netCDF files | ||
+ | * [[https://github.com/pierre-rouanet/dtw|dtw]]: DTW (Dynamic Time Warping) python module | ||
* [[http://toblerity.org/shapely/project.html|shapely]]: a Python wrapper for GEOS for algebraic manipulation of geometry (manipulation and analysis of geometric objects in the Cartesian plane) | * [[http://toblerity.org/shapely/project.html|shapely]]: a Python wrapper for GEOS for algebraic manipulation of geometry (manipulation and analysis of geometric objects in the Cartesian plane) | ||
Line 226: | Line 293: | ||
===== Environments summary ===== | ===== Environments summary ===== | ||
- | After following the steps above, we get the following environments: | + | 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 |
- | * uvcdat-2.8.0 | + | |
- | * cdatm14 | + | ^ Environment\\ name ^ Server ^ ''conda list'' ^ |
+ | | uvcdat-2.8.0 | LSCE\\ ciclad | {{ :other:uvcdat:cdat_conda:conda_list_lsce_uvcdat-2.8.0_170310.txt |package list}} | | ||
+ | | cdatm14 | LSCE\\ ciclad | {{ :other:uvcdat:cdat_conda:conda_list_lsce_cdatm14_170310.txt|package list}} | | ||
/* standard page footer */ | /* standard page footer */ |