Python-Sapelo2: Difference between revisions
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Also refer to [[Running Jobs on Sapelo2]] | Also refer to [[Running Jobs on Sapelo2]] | ||
There is | There is no default python command on the system. The OS comes with a default /usr/bin/python2 (v. 2.7.18) and a default /usr/bin/python3 (v. 3.6.8). Scripts that have the first line: | ||
<pre class="gscript"> | <pre class="gscript"> | ||
/usr/bin/python | /usr/bin/python | ||
Revision as of 12:24, 5 September 2023
Category
Programming
Program On
Sapelo2
Version
2.7.18, 3.7.4, 3.8.6, 3.9.6, 3.10.4
Author / Distributor
The Python Software Foundation
Description
Python is a programming language.
Running Program
Also refer to Running Jobs on Sapelo2
There is no default python command on the system. The OS comes with a default /usr/bin/python2 (v. 2.7.18) and a default /usr/bin/python3 (v. 3.6.8). Scripts that have the first line:
/usr/bin/python
will not work on Sapelo2 (with the Rocky 8 OS). We recommend that you change this line to
/usr/bin/env python
and load one of the Python modules before running the script.
We have a set of Python version installed on Sapelo2 via environment modules:
ml spider Python
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Python:
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Python is a programming language that lets you work more quickly and integrate your systems more effectively.
Versions:
Python/2.7.18-GCCcore-11.2.0-bare
Python/2.7.18-GCCcore-11.2.0
Python/2.7.18-GCCcore-11.3.0-bare
Python/2.7.18-GCCcore-11.3.0
Python/3.7.4-GCCcore-8.3.0
Python/3.8.6-GCCcore-10.2.0
Python/3.9.6-GCCcore-11.2.0-bare
Python/3.9.6-GCCcore-11.2.0
Python/3.10.4-GCCcore-11.3.0-bare
Python/3.10.4-GCCcore-11.3.0
Other possible modules matches:
Biopython Boost.Python GitPython IPython bx-python flatbuffers-python ...
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To find other possible module matches execute:
$ module -r spider '.*Python.*'
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For detailed information about a specific "Python" package (including how to load the modules) use the module's full name.
Note that names that have a trailing (E) are extensions provided by other modules.
For example:
$ module spider Python/3.10.4-GCCcore-11.3.0
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About Python packages
Some common third-party Python packages are installed individually as separate modules on the cluster.
numpy, scipy, pandas
The numpy, scipy, pandas, mpi4py, mpmath, and deap packages are installed in SciPy-bundle module:
ml spider SciPy-bundle
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SciPy-bundle:
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Description:
Bundle of Python packages for scientific software
Versions:
SciPy-bundle/2021.10-foss-2021b-Python-2.7.18
SciPy-bundle/2021.10-foss-2021b
SciPy-bundle/2021.10-foss-2022a-Python-2.7.18
SciPy-bundle/2022.05-foss-2022a
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For detailed information about a specific "SciPy-bundle" package (including how to load the modules) use the module's full name.
Note that names that have a trailing (E) are extensions provided by other modules.
For example:
$ module spider SciPy-bundle/2022.05-foss-2022a
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Note that, when you load SciPy-bundle module, a specific version of Python that the package is built for will be loaded at first. This means that you don't have to load the Python module separately from loading SciPy-bundle module. For example:
```Note```:
- Python/3.9.6-GCCcore-11.2.0 will be automatically loaded when SciPy-bundle/2021.10-foss-2021b is loaded.
- Python/3.10.4-GCCcore-11.3.0 will be automatically loaded when SciPy-bundle/2022.05-foss-2022a is loaded.
- Python/2.7.18-GCCcore-11.2.0 will be automatically loaded when SciPy-bundle/2021.10-foss-2021b-Python-2.7.18 is loaded.
- Python/2.7.18-GCCcore-11.3.0 will be automatically loaded when SciPy-bundle/2021.10-foss-2022a-Python-2.7.18 is loaded.
matplotlib
The matplotlib package is installed in matplotlib module.
ml spider matplotlib
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matplotlib:
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Description:
matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python
scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.
Versions:
matplotlib/2.2.5-foss-2021b-Python-2.7.18
matplotlib/2.2.5-foss-2022a-Python-2.7.18
matplotlib/3.4.3-foss-2021b
matplotlib/3.5.2-foss-2021b
matplotlib/3.5.2-foss-2022a
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For detailed information about a specific "matplotlib" package (including how to load the modules) use the module's full name.
Note that names that have a trailing (E) are extensions provided by other modules.
For example:
$ module spider matplotlib/3.5.2-foss-2022a
----------------------------------------------------------------------------------
Same as SciPy-bundle, when you load matplotlib module, a specific version of Python that matplotlib is built for will be loaded at first, which means you don't have to load the Python module separately from loading matplotlib module. For example:
- Python/3.9.6-GCCcore-11.2.0 will be automatically loaded when you load matplotlib/3.4.3-foss-2021b or matplotlib/3.5.2-foss-2021b.
- Python/3.10.4-GCCcore-11.3.0 will be automatically loaded when you load matplotlib/3.5.2-foss-2022a.
- Python/2.7.18-GCCcore-11.2.0 will be automatically loaded when you load matplotlib/2.2.5-foss-2021b-Python-2.7.18.
- Python/2.7.18-GCCcore-11.3.0 will be automatically loaded when you load matplotlib/2.2.5-foss-2022a-Python-2.7.18.
Biopython
The Biopython package is installed in Biopython module.
ml spider biopython
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Biopython:
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Description:
Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries
and applications which address the needs of current and future work in bioinformatics.
Versions:
Biopython/1.79-foss-2021b
Biopython/1.79-foss-2022a
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For detailed information about a specific "Biopython" package (including how to load the modules) use the module's full name.
Note that names that have a trailing (E) are extensions provided by other modules.
For example:
$ module spider Biopython/1.79-foss-2022a
----------------------------------------------------------------------------------
Same as above SciPy-bundle and matplotlib, when you load Biopython module, a specific version of Python that the package is built for will be loaded at first. You don't have to load the Python module separately from loading Biopython module. For ecample:
- Python/3.9.6-GCCcore-11.2.0 will be automatically loaded when Biopython/1.79-foss-2021b is loaded.
- Python/3.10.4-GCCcore-11.3.0 will be automatically loaded when Biopython/1.79-foss-2022a is loaded.
Examples
Example of using Python3
To use Python 3.9.6, you can use the following in the first line of your Python code:
#!/apps/eb/Python/3.9.6-GCCcore-11.2.0/bin/python3
Or use the following line in the first line of your Python code:
#!/usr/bin/env python
an then you run your program as:
module load Python/3.9.6-GCCcore-11.2.0 python myProgram.py
Example of using Python2
To use Python 2.7.18, you can use the following in the first line of your Python code:
#!/apps/eb/Python/2.7.18-GCCcore-11.2.0/bin/python
Or use the following line in the first line of your Python code:
#!/usr/bin/env python
an then you run your program as:
module load Python/2.7.18-GCCcore-11.2.0 python myProgram.py
Documentation
Please see http://www.python.org/
Installation
EasyBuild recipes
System
64-bit Linux