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howto:python:start [2020/07/07 16:23]
ischeepers 		howto:python:start [2021/12/09 16:42] (current)
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 ====== Python ====== ====== Python ======
  
-There are a number of python versions installed on Lengau compiled with either gcc or the intel compiler, including python 2.7.11 to 2.7.15, python 3.5-3.7 and anaconda installs for python 2 and 3. +See the [[guide:python|Python User Guide]].
-Use this command to get a full list: +
-    module avail chpc/python +
- +
-All python modules should have mpi4py, numpy and scipy installed; however if matplotlib is required, please use anaconda (which also has the biggest range of 3rd-party python modules). The module chpc/python/3.5.2_gcc-6.2.0 also has a working matplotlib installation. +
- +
-To use tensorflow, the anaconda module for python3 is also recommended. +
- +
-==== User Package installation with Anaconda === +
-Modules for anaconda version 2 and 3 are installed on lengau.To load these modules, use the following command (either from the command-line in an interactive session, or in a script: +
-    module add chpc/python/anaconda/2 +
-or: +
-    module add chpc/python/anaconda/3-2019.10 +
- +
-Using virtualenv with anaconda is not recommended. +
-However, Anaconda does include a similar functionality, which allows users to create an anaconda virtual environment. +
- +
-The following instructions to set up your virtual environment. **YOU NEED ONLY DO THEM ONCE. Please replace USERNAME with your actual username wherever it occurs below.** +
- +
-1. log into lengau.chpc.ac.za +
- +
-2. ''ssh chpclic1'' +
-//Unlike the compute nodes, chpcviz1 and chpclic1 have a connection to the internet, which is needed here// +
- +
-3. Load the appropriate anaconda module  +
-    module load chpc/python/anaconda/3-2019.10 +
- +
-//you can substitute chpc/anaconda/2 if you want python 2// +
- +
-4. Do the  once-off initialisation for your shell:  +
- +
-    conda init bash +
-You might have to log out and back in at this point to enable the  +
-shell setup. +
- +
-5. Create a new conda environment: +
- +
- +
-    conda create --prefix /home/USERNAME/myenv python=3.6 anaconda +
- +
- +
- +
-// change python=3.6 to python=2.7 if you're using anaconda/2// +
- +
-6. Activate the environment +
- +
-    conda activate /home/USERNAME/myenv +
- +
-//You don't have to use "myenv", just replace it consistently with whatever name you prefer for your virtual environment. "myenv" will work, though.// +
- +
-7. You can now install whatever packages you need, that are not installed already for instance, for rpy2, type: +
- +
-   conda install rpy2 +
- +
-8. you can now type: +
-  conda deactivate /home/USERNAME/myenv +
-to exit the virtual environment. +
- +
- +
-Now, once you've done this, you can log out, and ready your job for submission from the login node. +
-**You must do the following in your job-submit script**: +
-Put it all near the top of your script, but after the #PBS directives: +
- +
-  module add chpc/python/anaconda/3-2019.10 +
- +
-  conda activate /home/USERNAME/myenv +
- +
-and at the end: +
-  conda deactivate /home/USERNAME/myenv +
- +
-Then submit your script as normal with qsub. +
- +
- +
-if you ever need to install new python packages, just repeat steps 1, 2, 3, 6, 7 and 8 from above. (omit 4 and 5). +
- +
- +
- +
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