software:anaconda:caviness

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software:anaconda:caviness [2024-07-30 15:06] – [Recipes] anitasoftware:anaconda:caviness [2024-08-02 15:08] (current) – [Virtual Environment] thuachen
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 +====== Anaconda on Caviness ======
  
 +<code bash>
 +$ vpkg_versions anaconda
 +
 +Available versions in package (* = default version):
 +
 +[/opt/shared/valet/2.1/etc/anaconda.vpkg_yaml]
 +anaconda         Open Enterprise Python
 +* 5.2.0:python2  Anaconda Python2
 +  5.2.0:python3  Anaconda Python3
 +  2020.07        Anaconda Python3 (Python 2 deprecated)
 +  2022.05        Anaconda Python3 (Python 2 deprecated)
 +  2023.03        Anaconda Python3 (Python 2 deprecated)
 +  2024.02        Anaconda Python3 (Python 2 deprecated)
 +</code>
 +
 +See [[software:anaconda:caviness#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 Caviness 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 Python 3, specify a path in your home (''$HOME'') or workgroup (''$WORKDIR'') directory not in the system path for Anaconda, and also ignore the warnings to update ''conda'' as it is building your virtual environment.
 +
 +
 +See the example below which creates a virtual Anaconda environment based on Python 3 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 the ''devel'' partition to verify the new ''fenicsproject'' Anaconda environment is working properly. 
 +
 +<code>
 +[traine@login00 ~]$ vpkg_devrequire anaconda/2024.02
 +Adding package `anaconda/2024.02` to your environment
 +[traine@login00 ~]$ conda create -p ~/fenicsproject -c conda-forge fenics fenics-dijitso fenics-dolfin fenics-ffc fenics-fiat fenics-libdolfin fenics-ufl mshr
 +Solving environment: done
 +
 +## 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:
 +# > conda activate /home/1201/fenicsproject
 +#
 +# To deactivate an active environment, use:
 +# > conda deactivate
 +#
 +
 +[traine@login00 ~]$ workgroup -g it_css
 +[(it_css:traine)@login00 ~]$ salloc --partition=devel
 +salloc: Pending job allocation 28214017
 +salloc: job 28214017 queued and waiting for resources
 +salloc: job 28214017 has been allocated resources
 +salloc: Granted job allocation 28214017
 +salloc: Waiting for resource configuration
 +salloc: Nodes r00n56 are ready for job
 +[traine@r00n56 ~]$ vpkg_devrequire anaconda/2024.02
 +Adding package `anaconda/2024.02` to your environment
 +[traine@r00n56 ~]$ conda activate ~/fenicsproject
 +(/home/1201/fenicsproject) [traine@r00n56 ~]$ python3 -c "import mshr"
 +(/home/1201/fenicsproject) [traine@r00n56 ~]$ conda deactivate
 +[traine@r00n56 ~]$ exit
 +logout
 +salloc: Relinquishing job allocation 28214017
 +[(it_css:traine)@login00 ~]$
 +</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:jupyter-notebook|Building a Jupyter Notebook Python Virtual Environment]]
 +  * [[technical:recipes:keras-in-virtualenv|Keras Python Virtual Environment]]
 +  * Gurobi Python Virtual Environments
 +    * [[software:gurobi:caviness#serial-or-threaded-python-environment|Gurobi Python Threaded and Serial]]
 +    * [[software:gurobi:caviness#mpi-python-environment|Gurobi Python MPI]]
 +  * [[technical:recipes:emcee-in-virtualenv|Python Virtualenv: emcee and pyKLIP]]
 +  * [[technical:recipes:mpi4py-in-virtualenv|Building Python Virtual Environments with mpi4py]]
 +  * [[technical:recipes:tensorflow-in-virtualenv|Building a TensorFlow Python Virtual Environment]]
 +  * [[technical:recipes:openmm|Building an OpenMM Python Virtual Environment]]