====== UV-CDAT 2.12 installation notes ====== [ [[.:index|Back to all versions]] ] 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 ''2.12'' ===== What's New? ===== * [[https://github.com/UV-CDAT/uvcdat/releases/tag/v2.12|2.12 announcement]] and features summary ([[https://github.com/UV-CDAT/uvcdat/releases|all versions]]) * Full [[https://uvcdat.llnl.gov/changelog.html#2.12|Change log]] ===== Installation with Miniconda2 ===== Actual installation bash-4.1$ conda create -n uvcdat-2.12 -c conda-forge -c uvcdat uvcdat=2.12 # Generate the list of installed packages conda list -n uvcdat-2.12 > /home/scratch01/jypeter/uvcdat-2.12_list_170907.txt List of installed packages: {{:other:uvcdat:cdat_conda:uvcdat-2.12_list_170907.txt}} Disk space after 2.12 installation bash-4.1$ conda env list # conda environments: # cdatm /home/share/unix_files/cdat/miniconda2/envs/cdatm cdatm14 /home/share/unix_files/cdat/miniconda2/envs/cdatm14 cdatm15 /home/share/unix_files/cdat/miniconda2/envs/cdatm15 uvcdat-2.10 /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.10 uvcdat-2.12 /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.12 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 15G /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 13G /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 2.1G /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/* 0 /home/share/unix_files/cdat/miniconda2/envs/cdatm 2.8G /home/share/unix_files/cdat/miniconda2/envs/cdatm14 4.5G /home/share/unix_files/cdat/miniconda2/envs/cdatm15 630M /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.10 2.7G /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.12 2.0G /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.8.0 ===== Cloning uvcdat to add specific packages for LSCE ===== 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 cdatm16 conda-based python]] ==== Cloning ==== bash-4.1$ conda create -n cdatm16 --clone uvcdat-2.12 Source: /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.12 Destination: /home/share/unix_files/cdat/miniconda2/envs/cdatm16 [...] 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 4.5G /home/share/unix_files/cdat/miniconda2/envs/cdatm15 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 ==== Checking the permissions ==== 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: (cdatm16) bash-4.1$ find uvcdat-2.12 \! -perm /g+r,o+r -ls 24774102 4 -rw------- 3 jypeter lsce 670 Apr 4 20:35 uvcdat-2.12/lib/python2.7/site-packages/cdp/cdp_output.py 24774113 4 -rw------- 3 jypeter lsce 2436 Apr 4 20:35 uvcdat-2.12/lib/python2.7/site-packages/cdp/cdp_parameter.pyc 24774111 4 -rw------- 3 jypeter lsce 1821 Apr 4 20:35 uvcdat-2.12/lib/python2.7/site-packages/cdp/cdp_parser.py [...] 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 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 (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* ===== Getting ready for a moving default CDAT ===== 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''. ===== Customizing UV-CDAT for LSCE ===== ==== Downloading cdms2/vcs test data ==== 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 cdatm16 (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 (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 ==== Downgrading numpy ==== bash-4.1$ conda install -n cdatm16 -c conda-forge -c pcmdi -c uvcdat numpy=1.12 Fetching package metadata ............... Solving package specifications: . Package plan for installation in environment /home/share/unix_files/cdat/miniconda2/envs/cdatm16: The following NEW packages will be INSTALLED: blas: 1.1-openblas conda-forge openblas: 0.2.19-2 conda-forge The following packages will be UPDATED: 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)? ==== Packages that have no dependency problems ==== 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 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... 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: {{ :other:uvcdat:cdat_conda: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// * [[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:\\ $ drq -v dreqPy version 01.00.06 [Version 01.00.06] * [[https://github.com/pierre-rouanet/dtw|dtw]]: DTW (Dynamic Time Warping) python module * ''pip install dtw'' * Requested by Sentia Goursaud The following packages have no dependency problems and were installed (or updated) //later// * [[http://www.earthsystemmodeling.org/esmf_releases/non_public/ESMF_7_0_0/esmpy_doc/html/index.html|ESMPy]]: ESMF Python Regridding Interface * We used the following to get a more up-to-date version of esmpy than the one bundled with 2.10 * 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 * [[http://matplotlib.org/cmocean/|cmocean]]: beautiful colormaps for oceanography * ''conda install -n cdatm15 -c conda-forge cmocean'' * [[http://scitools.org.uk/iris/index.html|iris]]: A Python library for Meteorology and Climatology * ''conda install -n cdatm15 -c conda-forge -c scitools iris'' * [[http://www.gdal.org/|OSGeo/GDAL]]: Geospatial Data Abstraction Library. GDAL is a translator library for raster and vector geospatial data formats * ''conda install -c conda-forge gdal'' * [[https://pcjericks.github.io/py-gdalogr-cookbook/|Python GDAL/OGR Cookbook]] ==== TODO ==== //Add here packages that would be useful but have some problems that prevent their installation// * [[http://www.ifremer.fr/vacumm/|vacumm]]: Validation, Analysis, Comparison - Utilities written in Python to validate and analyze Multi-Model outputs, and compare them to observations * As of August 08 2017, installing vacumm in 2.10 requires downgrading to 2.10 (see [[https://github.com/VACUMM/vacumm/issues/9|github issue]])! * Problem solved with **vacumm 3.4.1-1** on August 31st! Installation was OK with\\ ''conda install -n cdatm15 -c conda-forge -c vacumm vacumm'' * Install PySPLIT for Sentia\\ [[https://github.com/mscross/pysplit|PySPLIT]] A package for generating HYSPLIT air parcel trajectories trajectories, performing moisture uptake analyses, expediting HYSPLIT cluster analysis, and for visualizing trajectories, clusters, and along-trajectory meteorological data\\ Works with [[https://ready.arl.noaa.gov/HYSPLIT.php|HYSPLiT]] - ''conda install -n cdatm15 -c conda-forge fiona geopandas'' - ''pip install pysplit'' ==== Other packages ==== There is no warranty that the packages listed below will work correctly, because it was required to bypass the compatibility checks in order to install them... * NO such packages now! ==== Updating some packages ==== Some packages change more often than others, and can be easily updated the following way: * [[https://cmor.llnl.gov/|CMOR]] * Update with: ''conda update -n cdatm15 -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' '' * [[https://earthsystemcog.org/projects/wip/CMIP6DataRequest|dreqPy]] * Update with: ''pip install %%--%%upgrade dreqPy'' * Get version number with: ''drq -v'' ==== Cleaning up things ==== Some packages may have files that can only be read by the person who installed CDAT and the LSCE extensions (eg [[https://github.com/PCMDI/pcmdi_metrics/issues/496|pcmdi-metrics]] in 2.8.0 and [[https://github.com/UV-CDAT/cdp/issues/21|cdp]] in 2.10) We check if some of the installed files are missing read access for the //group// or //other//, and we manually change the permissions (cdatm15) bash-4.2$ find cdatm15 \! -perm /g+r,o+r -ls 50333969 4 -rw------- 2 jypeter lsce 234 Apr 4 20:35 cdatm15/lib/python2.7/site-packages/cdp-1.0.3-py2.7.egg-info/PKG-INFO 50333971 4 -rw------- 2 jypeter lsce 291 Apr 4 20:35 cdatm15/lib/python2.7/site-packages/cdp-1.0.3-py2.7.egg-info/SOURCES.txt 50333962 4 -rw------- 2 jypeter lsce 4 Apr 4 20:35 cdatm15/lib/python2.7/site-packages/cdp-1.0.3-py2.7.egg-info/top_level.txt 50333961 4 -rw------- 2 jypeter lsce 1 Apr 4 20:35 cdatm15/lib/python2.7/site-packages/cdp-1.0.3-py2.7.egg-info/dependency_links.txt 50333960 4 -rw------- 2 jypeter lsce 1 Apr 4 20:35 cdatm15/lib/python2.7/site-packages/cdp-1.0.3-py2.7.egg-info/not-zip-safe 50333987 8 -rw------- 2 jypeter lsce 5149 Apr 4 20:35 cdatm15/lib/python2.7/site-packages/cdp/cdp_viewer.pyc 50333986 8 -rw------- 2 jypeter lsce 4208 Apr 4 20:35 cdatm15/lib/python2.7/site-packages/cdp/cdp_metric.py 50333966 4 -rw------- 2 jypeter lsce 150 Apr 4 20:35 cdatm15/lib/python2.7/site-packages/cdp/__init__.pyc 50333968 4 -rw------- 2 jypeter lsce 201 Apr 4 20:35 cdatm15/lib/python2.7/site-packages/cdp/cdp_provenance.py 50333988 8 -rw------- 2 jypeter lsce 5365 Apr 4 20:35 cdatm15/lib/python2.7/site-packages/cdp/cdp_metric.pyc 50333982 4 -rw------- 2 jypeter lsce 1821 Apr 4 20:35 cdatm15/lib/python2.7/site-packages/cdp/cdp_parser.py 50333981 4 -rw------- 2 jypeter lsce 1773 Apr 4 20:35 cdatm15/lib/python2.7/site-packages/cdp/cdp_parameter.py 50333973 4 -rw------- 2 jypeter lsce 670 Apr 4 20:35 cdatm15/lib/python2.7/site-packages/cdp/cdp_output.py 50333980 4 -rw------- 2 jypeter lsce 1642 Apr 4 20:35 cdatm15/lib/python2.7/site-packages/cdp/cdp_output.pyc 50333979 4 -rw------- 2 jypeter lsce 1474 Apr 4 20:35 cdatm15/lib/python2.7/site-packages/cdp/_cache.pyc 50333967 4 -rw------- 2 jypeter lsce 187 Apr 4 20:35 cdatm15/lib/python2.7/site-packages/cdp/cdp_tool.py 50333989 0 -rw------- 2 jypeter lsce 0 Apr 4 20:35 cdatm15/lib/python2.7/site-packages/cdp/__init__.py 50333985 4 -rw------- 2 jypeter lsce 3843 Apr 4 20:35 cdatm15/lib/python2.7/site-packages/cdp/cdp_viewer.py 50333984 4 -rw------- 2 jypeter lsce 2436 Apr 4 20:35 cdatm15/lib/python2.7/site-packages/cdp/cdp_parameter.pyc 50333970 4 -rw------- 2 jypeter lsce 288 Apr 4 20:35 cdatm15/lib/python2.7/site-packages/cdp/cdp_io.py 50333974 4 -rw------- 2 jypeter lsce 692 Apr 4 20:35 cdatm15/lib/python2.7/site-packages/cdp/cdp_tool.pyc 50333978 4 -rw------- 2 jypeter lsce 878 Apr 4 20:35 cdatm15/lib/python2.7/site-packages/cdp/cdp_io.pyc 50333976 4 -rw------- 2 jypeter lsce 734 Apr 4 20:35 cdatm15/lib/python2.7/site-packages/cdp/_cache.py 50333983 4 -rw------- 2 jypeter lsce 2269 Apr 4 20:35 cdatm15/lib/python2.7/site-packages/cdp/cdp_parser.pyc 50333975 4 -rw------- 2 jypeter lsce 724 Apr 4 20:35 cdatm15/lib/python2.7/site-packages/cdp/cdp_provenance.pyc (cdatm15) bash-4.2$ chmod -R a+r cdatm15/lib/python2.7/site-packages/cdp* (cdatm15) bash-4.2$ find cdatm15 \! -perm /g+r,o+r -ls ===== Extra packages list ===== * [[https://python-pillow.org/|pillow]]: the friendly PIL (//Python Imaging Library//) fork * [[http://pandas.pydata.org/|pandas]]: Python Data Analysis Library * [[http://statsmodels.sourceforge.net/|statsmodels]]: a Python module that allows users to explore data, estimate statistical models, and perform statistical tests * [[https://seaborn.pydata.org/|seaborn]]: statistical data visualization * [[http://scikit-image.org/|scikit-image]]: image processing in Python * [[http://pythonhosted.org/seawater/|seawater]]: Python re-write of the CSIRO seawater toolbox * [[https://pypi.python.org/pypi/gsw/|gsw]]: Python implementation of the Thermodynamic Equation Of Seawater * [[http://unidata.github.io/netcdf4-python/|netcdf4]]: a Python interface to the netCDF C library * [[http://ferret.pmel.noaa.gov/Ferret/documentation/pyferret|pyferret]]: Ferret encapsulated in * [[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://xlsxwriter.readthedocs.io/|XlsxWriter]]: a Python module for creating Excel XLSX files * Note: this is a dependency of ''dreqPy'' * [[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://scitools.org.uk/cartopy/|cartopy]]: a library providing cartographic tools for python * [[https://rpy2.readthedocs.io/en/version_2.8.x/|rpy2]]: providing simple and robust access to R from within Python * [[http://matplotlib.org/cmocean/|cmocean]]: beautiful colormaps for oceanography * [[http://scitools.org.uk/iris/index.html|iris]]: A Python library for Meteorology and Climatology * [[http://www.gdal.org/|OSGeo/GDAL]]: Geospatial Data Abstraction Library. GDAL is a translator library for raster and vector geospatial data formats ==== Removed packages ==== * NO removed packages! ===== Environments summary ===== After following the steps above, we get the following environments. Use the ''conda info %%--%%envs'' or the ''conda env list'' 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}} | /* standard page footer */ \\ \\ \\ ---- [ [[pmip3:|PMIP3 Wiki Home]] ] - [ [[pmip3:wiki_help|Help!]] ] - [ [[wiki:syntax|Wiki syntax]] ]