other:python:starting
Differences
This shows you the differences between two versions of the page.
| Both sides previous revision Previous revision Next revision | Previous revision Next revision Both sides next revision | ||
|
other:python:starting [2017/03/09 15:33] jypeter Started the conda+cdat section |
other:python:starting [2019/04/25 07:19] jypeter [Working with Python] Added link to historic version of the page |
||
|---|---|---|---|
| Line 6: | Line 6: | ||
| </note> | </note> | ||
| + | Note: the former and **outdated** version (before the massive usage of //conda//) is still [[other:python:starting_170810|available for reference]] | ||
| ===== Where to start ===== | ===== Where to start ===== | ||
| In order to start working with Python, you need to have a //Python distribution// installed on your local computer or on the remote Linux server(s) you work on. A //distribution// provides a //Python interpreter//, and Python extensions (aka Python //modules// or //packages//). You may have several distributions installed on your computer and you need to know how to initialize them, and which one you are using at a given time (type ''which python'' on Linux to determine where the python executable is located) | In order to start working with Python, you need to have a //Python distribution// installed on your local computer or on the remote Linux server(s) you work on. A //distribution// provides a //Python interpreter//, and Python extensions (aka Python //modules// or //packages//). You may have several distributions installed on your computer and you need to know how to initialize them, and which one you are using at a given time (type ''which python'' on Linux to determine where the python executable is located) | ||
| - | If you are using a Linux computer or a Mac, you should already have a **default python** installed. The following example shows where the python interpreter is installed on the //asterix// LSCE server (if it's in ''/usr/bin'', it's the default python) and which version it is (example below: version //2.6.6// compiled in May 2015) | + | If you are using a Linux computer or a Mac, you should already have a **default python** installed. The following example shows where the python interpreter is installed on the //obelix// LSCE servers (if it's in ''/usr/bin'', it's the default python) and which version it is (example below: version //2.7.5// compiled in April 2019) |
| <code># Which is the current python (e.g. where is it located)? | <code># Which is the current python (e.g. where is it located)? | ||
| Line 18: | Line 19: | ||
| # Where is it coming from ('rpm' works on a RedHat-like Linux machine)? | # Where is it coming from ('rpm' works on a RedHat-like Linux machine)? | ||
| > rpm -qf /usr/bin/python | > rpm -qf /usr/bin/python | ||
| - | python-2.6.6-64.el6.x86_64 | + | python-2.7.5-77.el7_6.x86_64 |
| # You also get some information when you start the interpreter | # You also get some information when you start the interpreter | ||
| > python | > python | ||
| - | Python 2.6.6 (r266:84292, May 22 2015, 08:34:51) | + | Python 2.7.5 (default, Apr 9 2019, 14:30:50) |
| - | [GCC 4.4.7 20120313 (Red Hat 4.4.7-15)] on linux2 | + | [GCC 4.8.5 20150623 (Red Hat 4.8.5-36)] on linux2 |
| Type "help", "copyright", "credits" or "license" for more information. | Type "help", "copyright", "credits" or "license" for more information. | ||
| >>> | >>> | ||
| Line 30: | Line 31: | ||
| ===== Python distributions available for LSCE users ===== | ===== Python distributions available for LSCE users ===== | ||
| - | This section will help you choose a distribution in the big Python ecosystem (many distributions, python version 2.7.* or 3.*, ...). You should use a distribution that is already available near your data (e.g. do the computation on a server near your data, do not move/duplicate the data!) and try to identify who is maintaining it, if you need help or extra packages. | + | This section will help you choose a distribution in the big Python ecosystem (many distributions, python version 2.7.* or 3.*, ...). You should use a distribution that is already available near your data (e.g. do the computation on a server near your data, do not move/duplicate the data!) and try to identify who is maintaining it, if you need help or additional packages. |
| Only install a distribution yourself if you need it on your local computer, or if you need to install some modules that can't be installed by the contacts listed below. A python distribution can require several Gb of disk space, so do not install it in a backed up //home// directory! | Only install a distribution yourself if you need it on your local computer, or if you need to install some modules that can't be installed by the contacts listed below. A python distribution can require several Gb of disk space, so do not install it in a backed up //home// directory! | ||
| - | We suggest that you **use Python 2 rather than Python 3**. Or you can check the [[https://wiki.lsce.ipsl.fr/pmip3/doku.php/other:python:jyp_steps#python_27_vs_python_3|differences between both versions]] and try to write scripts that will work in both versions! 8-) | + | You can use either //Python 2// or //Python 3//. Most packages are now available in both versions, but you should make sure that the most important package/s you need is/are available in the selected version. Check the [[https://wiki.lsce.ipsl.fr/pmip3/doku.php/other:python:jyp_steps#python_27_vs_python_3|differences between both versions]] and try to write scripts that will work in both versions! 8-) |
| ==== LSCE distribution ==== | ==== LSCE distribution ==== | ||
| Line 43: | Line 44: | ||
| > module avail | > module avail | ||
| [...] | [...] | ||
| - | castem/12 ferret/6.9.5 hdf5/1.8.9 netcdf/4p python/2.7.5 sun-java/7.0.45 | + | 4ARTIC/3.6 grib_api/1.14 netcdf/3 python/2.7.5 |
| + | batch_env grib_api/1.14.0 netcdf/4 python/3.6 | ||
| + | [...] | ||
| + | glost/0.3.1 ncview/2.1.7 python/2.7 | ||
| [...] | [...] | ||
| - | > module load python/2.7.5 | + | > module load python/2.7 |
| > which python | > which python | ||
| - | /usr/local/install/python-2.7.5/bin/python | + | /usr/local/install/python-2.7/bin/python |
| > python | > python | ||
| - | Python 2.7.5 (default, Sep 18 2013, 15:47:43) | + | Python 2.7.15 |Anaconda, Inc.| (default, Oct 10 2018, 21:32:13) |
| - | [GCC 4.4.7 20120313 (Red Hat 4.4.7-3)] on linux2 | + | [GCC 7.3.0] on linux2 |
| Type "help", "copyright", "credits" or "license" for more information. | Type "help", "copyright", "credits" or "license" for more information. | ||
| >>> | >>> | ||
| Line 136: | Line 140: | ||
| <WRAP center round important 60%> | <WRAP center round important 60%> | ||
| - | The steps detailed in this section are for **UV-CDAT ''2.8.0'' and later** | + | \\ The steps detailed in this section are for [[other:uvcdat:cdat_conda:|UV-CDAT 2.8.0 and later]] |
| </WRAP> | </WRAP> | ||
| + | |||
| + | Note: if you need to maintain a **local** version on **your** machine, you can read [[other:uvcdat:conda_notes|Installing and maintaining UV-CDAT with conda]] and the [[other:uvcdat:cdat_conda:index#versions|versions specific notes]]. | ||
| == Configuring .bashrc == | == Configuring .bashrc == | ||
| Line 143: | Line 149: | ||
| You should **add** the following line at the end of your ''~/.bashrc'' configuration file (create the ''~/.bashrc'' file if it does not exist yet). This will basically make sure that your shell can find the ''conda'' executable it needs for initializing CDAT, and define a ''wp'' alias that you can use to find where the ''python'' executable is located | You should **add** the following line at the end of your ''~/.bashrc'' configuration file (create the ''~/.bashrc'' file if it does not exist yet). This will basically make sure that your shell can find the ''conda'' executable it needs for initializing CDAT, and define a ''wp'' alias that you can use to find where the ''python'' executable is located | ||
| - | | **LSCE** | ''source ~jypeter/.conda_jyp'' | | + | ^ Server ^ Line to add to ''.bashrc'' ^ |
| + | | **LSCE** | ''source ~jypeter/.conda_jyp.sh''\\ \\ Note:{{ :other:python:conda_jyp.txt |conda_jyp}} content | | ||
| + | | **ciclad** | ''source ~jypmce/.conda_jyp.sh'' | | ||
| - | Note: when you add the specified line to your ''bashrc'' file, you will then always get the python supplied by conda, instead of the system's python, when you use ''bash''. If you don't like this permanent behavior, just type ''source ~jyp_login_on_this_server/.conda_jyp'' in the bash shell where you want to use conda+CDAT, rather than adding it to the ''.bashrc'' file... | + | Note: when you add the specified line to your ''bashrc'' file, you will then always get the python supplied by conda, instead of the system's python, when you use ''bash''. If you don't like this permanent behavior, just type ''source ~jyp_login_on_this_server/.conda_jyp.sh'' in the bash shell where you want to use conda+CDAT, rather than adding it to the ''.bashrc'' file... |
| == Initializing UV-CDAT == | == Initializing UV-CDAT == | ||
| <WRAP center round tip 60%> | <WRAP center round tip 60%> | ||
| - | When you initialize UV-CDAT, it will be available only the **current** window/shell. In the other windows, you still get whatever your default python is. This should minimize potential side-effects | + | When you initialize UV-CDAT, it will be available only in the **current** window/shell. In the other windows, you still get whatever your default python is. This should minimize potential side-effects |
| </WRAP> | </WRAP> | ||
| Line 158: | Line 167: | ||
| * ''source activate conda_env_name'' | * ''source activate conda_env_name'' | ||
| * Use the table below to determine which environments are available on which server | * Use the table below to determine which environments are available on which server | ||
| - | - Use CDAT | + | - Use CDAT ! |
| - | ^ Server ^ UV-CDAT version ^ Environment name ^ | + | ^ UV-CDAT version ^ Server ^ Environment name\\ and activation line ^ Packages\\ (''conda list'') ^ |
| - | | **LSCE** | [[:other:uvcdat:cdat_conda:cdat_2_8_0|2.8.0]] | **cdatm14**\\ ''source activate cdatm14'' | | + | | [[:other:uvcdat:cdat_conda:cdat_2_8_0|2.8.0]] | **LSCE**\\ **ciclad** |**cdatm14** (''source activate cdatm14'') | {{ :other:uvcdat:cdat_conda:conda_list_lsce_cdatm14_170310.txt |cdatm14 installed packages}} | |
| + | | [[:other:uvcdat:cdat_conda:cdat_2_10|2.10]] | **LSCE** |**cdatm15** (''source activate cdatm15'') | {{ :other:uvcdat:cdat_conda:uvcdat-2.10_list_170721.txt |cdatm14 installed packages}} | | ||
| + | | **cdatm** will always point to the latest stable version |||| | ||
| + | | //latest stable version// | **LSCE** |**cdatm** (''source activate cdatm'') | ''conda list'' | | ||
| === Older versions of UV-CDAT === | === Older versions of UV-CDAT === | ||
other/python/starting.txt · Last modified: 2024/05/30 13:41 by jypeter
