software:anaconda:farber

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software:anaconda:farber [2020-02-03 18:23] – anitasoftware:anaconda:farber [2020-11-02 11:54] (current) – [Recipes] anita
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 +====== Anaconda on Farber ======
  
 +<code bash>
 +$ vpkg_versions anaconda
 +
 +Available versions in package (* = default version):
 +
 +[/opt/shared/valet/2.0.1/etc/anaconda.vpkg_json]
 +anaconda   Open Enterprise Python
 +* 2.5.0    Anaconda 2.5.0 (Python 2.x, 64-bit)
 +           + python2
 +  2.5.0    Anaconda 2.5.0 (Python 3.x, 64-bit)
 +           + python3
 +  5.0.1    Anaconda 5.0.1 (Python 2.7, 64-bit)
 +           + python2
 +  5.0.1    Anaconda 5.0.1 (Python 3.6, 64-bit)
 +           + python3
 +  5.2.0    Anaconda 5.2.0 (Python 2.7, 64-bit)
 +           + python2
 +  5.2.0    Anaconda 5.2.0 (Python 3.6, 64-bit)
 +           + python3
 +  python2  alias to anaconda/2.5.0:python2
 +  python3  alias to anaconda/2.5.0:python3
 +</code>
 +
 +See [[software:anaconda:farber#Recipes|Recipes]] for examples of building virtual environments for specific packages.
 +===== Virtual Environment ====
 +
 +If you are going to follow the instructions for creating an Anaconda virtual environment on Farber consider using a slight modification to the documentation provided by each software package and use VALET to load the proper version of Anaconda for Python 2 or Python3, also specify a path in your home directory not in the system path for Anaconda, and ignore the warnings to update ''conda'' while it is building your virtual environment.
 +
 +See the example below which creates a virtual Anaconda environment based on Python3 for FEniCS called ''fenicsproject'' in the ''traine'' home directory and installs all the fenics packages and mshr. Once the environment is created, then a simple interactive test is done on a compute node via ''qlogin'' to verify the new ''fenicsproject'' Anaconda environment is working properly. 
 +
 +<code>
 +[traine@farber ~]$ vpkg_devrequire anaconda/5.2.0:python3
 +Adding package `anaconda/5.2.0:python3` to your environment
 +[traine@farber ~]$ conda create -p ~/fenicsproject -c conda-forge fenics fenics-dijitso fenics-dolfin fenics-ffc fenics-fiat fenics-libdolfin fenics-ufl mshr
 +Solving environment: done
 +
 +
 +==> WARNING: A newer version of conda exists. <==
 +  current version: 4.5.11
 +  latest version: 4.8.1
 +
 +Please update conda by running
 +
 +    $ conda update -n base -c defaults conda
 +
 +
 +## Package Plan ##
 +
 +  environment location: /home/1201/fenicsproject
 +
 +  added / updated specs:
 +    - fenics
 +    - fenics-dijitso
 +    - fenics-dolfin
 +    - fenics-ffc
 +    - fenics-fiat
 +    - fenics-libdolfin
 +    - fenics-ufl
 +    - mshr
 +
 +
 +The following packages will be downloaded:
 +
 +...
 +...
 +...
 +Proceed ([y]/n)? y
 +
 +Preparing transaction: done
 +Verifying transaction: done
 +Executing transaction: done
 +...
 +...
 +...
 +#
 +# To activate this environment, use:
 +# > source activate /home/1201/fenicsproject
 +#
 +# To deactivate an active environment, use:
 +# > source deactivate
 +#
 +
 +[traine@farber ~]$ workgroup -g it_css
 +[(it_css:traine)@farber ~]$ qlogin
 +$ qlogin
 +Your job 3985323 ("QLOGIN") has been submitted
 +waiting for interactive job to be scheduled ...
 +Your interactive job 3985323 has been successfully scheduled.
 +Establishing /opt/shared/univa/local/qlogin_ssh session to host n038 ...
 +[(it_css:traine)@n038 ~]$ vpkg_devrequire anaconda/5.2.0:python3
 +Adding package `anaconda/5.2.0:python3` to your environment
 +[(it_css:traine)@n038 ~]$ source activate ~/fenicsproject
 +(/home/1201/fenicsproject) [(it_css:traine)@n038 ~]$ python3 -c "import mshr"
 +(/home/1201/fenicsproject) [(it_css:traine)@n038 ~]$ source deactivate
 +[(it_css:traine)@n038 ~]$ exit
 +exit
 +Connection to n038 closed.
 +/opt/shared/univa/local/qlogin_ssh exited with exit code 0
 +[(it_css:traine)@farber ~]$
 +</code>
 +
 +===== Recipes ====
 +
 +Examples documented as recipes to be used for specific installations including using a ''workgroup'' directory as well as creating VALET packages for these environments and job scripts setup for batch runs, but can also perhaps help others in solving similar installation dilemmas.
 +
 +  * [[technical:recipes:pyqt5-in-virtualenv|Building PyQt5 in a Python Virtual Environment]]
 +  * [[technical:recipes:keras-in-virtualenv|Keras Python Virtual Environment]]
 +  * [[technical:recipes:emcee-in-virtualenv|Python Virtualenv: emcee and pyKLIP]]
 +  * [[technical:recipes:mpi4py-in-virtualenv|Python Virtual Environments with mpi4py]]