Difference between revisions of "Python"
(Remove link to obsolete personal modules page) |
|||
| (7 intermediate revisions by 3 users not shown) | |||
| Line 20: | Line 20: | ||
Python is a programming language that lets you work more quickly and integrate your systems more effectively. You can learn to use Python and see almost immediate gains in productivity and lower maintenance costs. Python version 3 is the current implementation of Python while python2 is a legacy version no longer supported after 2020-01-01. | Python is a programming language that lets you work more quickly and integrate your systems more effectively. You can learn to use Python and see almost immediate gains in productivity and lower maintenance costs. Python version 3 is the current implementation of Python while python2 is a legacy version no longer supported after 2020-01-01. | ||
| − | |||
| − | |||
| − | |||
==Environment Modules== | ==Environment Modules== | ||
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | ||
| Line 40: | Line 37: | ||
You can request installation of additional modules by {{Fileabug}}. | You can request installation of additional modules by {{Fileabug}}. | ||
| − | See also: [ | + | See also: [[Managing Python environments and Jupyter kernels]] |
===Matplotlib backend=== | ===Matplotlib backend=== | ||
| − | If you are trying to use matplotlib and get an error similar to | + | If you are trying to use matplotlib and get an error similar to either of the following: |
| − | + | *<pre>ImportError: No module named _tkinter</pre> | |
| − | + | *<pre>This application failed to start because no Qt platform plugin could be initialized.</pre> | |
| − | + | then you should try the following before importing pyplot from matplotlib: | |
| − | |||
| − | then you should try the following: | ||
import matplotlib | import matplotlib | ||
matplotlib.use('Agg') | matplotlib.use('Agg') | ||
| − | |||
| − | |||
| − | |||
===Output Buffering=== | ===Output Buffering=== | ||
If your job starts, but doesn't appear to produce output from 'print' statements in the job log for a long time, but you want to see that output immediately then turn off output buffering. You can either add a <code>flush=True</code> argument to the print calls you are interested in or run the script with | If your job starts, but doesn't appear to produce output from 'print' statements in the job log for a long time, but you want to see that output immediately then turn off output buffering. You can either add a <code>flush=True</code> argument to the print calls you are interested in or run the script with | ||
srun --unbuffered python SCRIPT.py | srun --unbuffered python SCRIPT.py | ||
| + | }} | ||
| − | |||
==Available modules== | ==Available modules== | ||
| − | To see all installed modules names load the environment module and run <code> | + | * To see all installed modules names load the environment module and run <code>pip list</code> or <code>python -c "help('modules')"</code> command before submitting a request for a new module installation. |
| + | * To install their own packages, users can load any module that has python within and run <code>pip install "package"</code>. | ||
| + | * Users can define an install path by running: <code>pip install --install-option="--prefix=/some/path/" package_name</code>. | ||
| + | |||
| + | Below is a list of modules and versions installed in the default python version. | ||
| + | <div class="mw-collapsible mw-collapsed" style="width:70%; padding: 5px; border: 1px solid gray;"> | ||
| + | ''Expand this section to view list of available modules.'' | ||
| + | <div class="mw-collapsible-content" style="padding: 5px;"> | ||
{{:Python_Modules}} | {{:Python_Modules}} | ||
| + | </div> | ||
| + | </div> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}} | See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}} | ||
| Line 79: | Line 80: | ||
{{#if: {{#var: installation}}|==Installation== | {{#if: {{#var: installation}}|==Installation== | ||
See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}} | See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}} | ||
| + | __NOTOC__ | ||
Latest revision as of 19:42, 3 February 2023
Description
Python is a programming language that lets you work more quickly and integrate your systems more effectively. You can learn to use Python and see almost immediate gains in productivity and lower maintenance costs. Python version 3 is the current implementation of Python while python2 is a legacy version no longer supported after 2020-01-01.
Environment Modules
Run module spider python to find out what environment modules are available for this application.
System Variables
- HPC_PYTHON_DIR - installation directory
- HPC_PYTHON_BIN - executable directory
- HPC_PYTHON_LIB - library directory
and modifies PYTHONPATH and PYTHONHOME, so you could use them in your scripts.
Additional Information
- After the appropriate environment module is loaded - type "python" at the command line to open an interactive session.
- To run a python script type
python scriptname.py. If the correct "shebang" line is used at the top of the script E.g.
#!/usr/bin/env python
then the script can be run directly as scriptname.py if it's in the executable path or as ./scriptname.py if it's in the current directory. The same rules apply to using a python script in a batch job script.
You can request installation of additional modules by submitting a request ticket in the Support System. The support request tickets can be used for requesting software installation, finding a solution to a particular problem, or just asking a question.
See also: Managing Python environments and Jupyter kernels
Matplotlib backend
If you are trying to use matplotlib and get an error similar to either of the following:
ImportError: No module named _tkinter
This application failed to start because no Qt platform plugin could be initialized.
then you should try the following before importing pyplot from matplotlib:
import matplotlib
matplotlib.use('Agg')
Output Buffering
If your job starts, but doesn't appear to produce output from 'print' statements in the job log for a long time, but you want to see that output immediately then turn off output buffering. You can either add a flush=True argument to the print calls you are interested in or run the script with
srun --unbuffered python SCRIPT.py
Available modules
- To see all installed modules names load the environment module and run
pip listorpython -c "help('modules')"command before submitting a request for a new module installation. - To install their own packages, users can load any module that has python within and run
pip install "package". - Users can define an install path by running:
pip install --install-option="--prefix=/some/path/" package_name.
Below is a list of modules and versions installed in the default python version.
Expand this section to view list of available modules.
Automatically generated list of python modules installed with the Python Package Manager (pip) under the default python version. File PYTHON_MODULES is missing.
| Name | Version |
|---|