Changed page weights

content/applications/user_software/compiling_an_openmp_application.md

 +++
 title = "Compiling an OpenMP Application"
 description = "How to compile an OpenMP-based application on HCC resources."
+weight=20
 +++
 
 Compiling an [OpenMP](https://computing.llnl.gov/tutorials/openMP)

content/applications/user_software/installing_perl_modules.md

 +++
 title = "Installing Perl modules"
 description = "How to install needed Perl modules under your account."
+weight=90
 +++
 
 If you need additional Perl modules, they can be installed into your

content/applications/user_software/using_anaconda_package_manager.md

++++
+title = "Using Anaconda Package Manager"
+description = "How to use the Anaconda Package Manager on HCC resources."
+weight=10
++++
+
+[Anaconda](https://www.anaconda.com/what-is-anaconda),
+from [Anaconda, Inc](https://www.anaconda.com)
+is a completely free enterprise-ready distribution for large-scale data
+processing, predictive analytics, and scientific computing. It includes
+over 195 of the most popular Python packages for science, math,
+engineering, and data analysis. **It also offers the ability to easily
+create custom _environments_ by mixing and matching different versions
+of Python and/or R and other packages into isolated environments that
+individual users are free to create.**  Anaconda includes the `conda`
+package and environment manager to make managing these environments
+straightforward.
+
+- [Using Anaconda](#using-anaconda)
+- [Installing Packages](#installing-packages)
+- [Adding Packages to an Existing Environment](#adding-packages-to-an-existing-environment)
+- [Using an Anaconda Environment in a Jupyter Notebook on Crane](#using-an-anaconda-environment-in-a-jupyter-notebook-on-crane)
+
+### Using Anaconda
+
+While the standard methods of installing packages via `pip`
+and `easy_install` work with Anaconda, the preferred method is using
+the `conda` command.  
+
+{{% notice info %}}
+Full documentation on using Conda is available
+at http://conda.pydata.org/docs/
+
+A [cheatsheet](/attachments/11635089.pdf) is also provided.
+{{% /notice %}}
+
+A few examples of the basic commands are provided here.  For a full
+explanation of all of Anaconda/Conda's capabilities, see the
+documentation linked above. 
+
+Anaconda is provided through the `anaconda` module on HCC machines.  To
+begin using it, load the Anaconda module.
+
+{{% panel theme="info" header="Load the Anaconda module to start using Conda" %}}
+{{< highlight bash >}}
+module load anaconda
+{{< /highlight >}}
+{{% /panel %}}
+
+To display general information about Conda/Anaconda, use the `info` subcommand.
+
+{{% panel theme="info" header="Display general information about Conda/Anaconda" %}}
+{{< highlight bash >}}
+conda info
+{{< /highlight >}}
+{{% /panel %}}
+
+Conda allows the easy creation of isolated, custom environments with
+packages and versions of your choosing.  To show all currently available
+environments, and which is active, use the `info `subcommand with the
+`-e` option.
+
+{{% panel theme="info" header="List available environments" %}}
+{{< highlight bash >}}
+conda info -e
+{{< /highlight >}}
+{{% /panel %}}
+
+The active environment will be marked with an asterisk (\*) character.
+
+The `list` command will show all packages installed
+in the currently active environment.
+
+{{% panel theme="info" header="List installed packages in current environment" %}}
+{{< highlight bash >}}
+conda list
+{{< /highlight >}}
+{{% /panel %}}
+
+### Installing Packages
+
+To find the names of packages, use the `search` subcommand.
+
+{{% panel theme="info" header="Search for packages" %}}
+{{< highlight bash >}}
+conda search numpy
+{{< /highlight >}}
+{{% /panel %}}
+
+If the package is available, this will also display available package
+versions and compatible Python versions the package may be installed
+under.
+
+The `create` command is used to create a new environment.  It requires
+at a minimum a name for the environment, and at least one package to
+install.  For example, suppose we wish to create a new environment, and
+need version 1.8 of NumPy.
+
+{{% panel theme="info" header="Create a new environment by providing a name and package specification" %}}
+{{< highlight bash >}}
+conda create -n mynumpy numpy=1.8 
+{{< /highlight >}}
+{{% /panel %}}
+
+This will create a new environment called 'mynumpy' and installed NumPy
+version 1.8, along with any required dependencies.  
+
+To use the environment, we must first *activate* it.
+
+{{% panel theme="info" header="Activate environment" %}}
+{{< highlight bash >}}
+source activate mynumpy
+{{< /highlight >}}
+{{% /panel %}}
+
+Our new environment is now active, and we can use it.  The shell prompt
+will change to indicate this as well (this can be disable if desired).
+
+### Adding Packages to an Existing Environment
+
+To install additional packages in an environment, use the `install`
+subcommand.  Suppose we want to install iPython in our 'mynumpy'
+environment.  While the environment is active, use `install `with no
+additional arguments.  
+
+{{% panel theme="info" header="Install a new package in the currently active environment" %}}
+{{< highlight bash >}}
+conda install ipython
+{{< /highlight >}}
+{{% /panel %}}
+
+If you aren't currently in the environment you wish to install the
+package in, add the `-n `option to specify the name.
+
+{{% panel theme="info" header="Install new packages in a specified environment" %}}
+{{< highlight bash >}}
+conda install -n mynumpy ipython
+{{< /highlight >}}
+{{% /panel %}}
+
+The `remove` subcommand to uninstall a package functions similarly.
+
+{{% panel theme="info" header="Remove package from currently active environment" %}}
+{{< highlight bash >}}
+conda remove ipython
+{{< /highlight >}}
+{{% /panel %}}
+
+{{% panel theme="info" header="Remove package from environment specified by name" %}}
+{{< highlight bash >}}
+conda remove -n mynumpy ipython
+{{< /highlight >}}
+{{% /panel %}}
+
+To exit an environment, we *deactivate* it.
+
+{{% panel theme="info" header="Exit current environment" %}}
+{{< highlight bash >}}
+source deactivate
+{{< /highlight >}}
+{{% /panel %}}
+
+Finally, to completely remove an environment, add the `--all `option
+to `remove`.
+
+{{% panel theme="info" header="Completely remove an environment" %}}
+{{< highlight bash >}}
+conda remove -n mynumpy --all
+{{< /highlight >}}
+{{% /panel %}}
+
+### Using an Anaconda Environment in a Jupyter Notebook on Crane
+
+It is not difficult to make an Anaconda environment available to a
+Jupyter Notebook. To do so, follow the steps below, replacing
+`myenv` with the name of the Python or R environment you wish to use:
+
+1.  Stop any running Jupyter Notebooks and ensure you are logged out of
+    the JupyterHub instance at https://crane.unl.edu
+    1.  If you are not logged out, please click the Control Panel button
+        located in the top right corner.
+    2.  Click the "Stop My Server" Button to terminate the Jupyter
+        server.
+    3.  Click the logout button in the top right corner.  
+          
+2.  Using the command-line environment, load the target conda
+    environment:
+    {{< highlight bash >}}source activate myenv{{< /highlight >}}
+
+3.  Install the Jupyter kernel and add the environment:
+
+    1.  For a **Python** conda environment, install the IPykernel
+        package, and then the kernel specification:
+
+        {{< highlight bash >}}
+        # Install ipykernel
+        conda install ipykernel
+
+        # Install the kernel specification
+        python -m ipykernel install --user --name "$CONDA_DEFAULT_ENV" --display-name "Python ($CONDA_DEFAULT_ENV)"
+        {{< /highlight >}}
+
+    2.  For an **R** conda environment, install the jupyter\_client and
+        IRkernel packages, and then the kernel specification:
+
+        {{< highlight bash >}}
+        # Install PNG support for R, the R kernel for Jupyter, and the Jupyter client
+        conda install r-png
+        conda install r-irkernel jupyter_client
+
+        # Install jupyter_client 5.2.3 from anaconda channel for bug workaround
+        conda install -c anaconda jupyter_client
+
+        # Install the kernel specification
+        R -e "IRkernel::installspec(name = '$CONDA_DEFAULT_ENV', displayname = 'R ($CONDA_DEFAULT_ENV)', user = TRUE)"
+        {{< /highlight >}}
+
+4.  Once you have the environment set up, deactivate it:
+    {{< highlight bash >}}source deactivate{{< /highlight >}}
+
+5.  To make your conda environments accessible from the worker nodes,
+    enter the following commands:
+
+    {{< highlight bash >}}
+    mkdir -p $WORK/.jupyter
+    mv ~/.local/share/jupyter/kernels $WORK/.jupyter
+    ln -s $WORK/.jupyter/kernels ~/.local/share/jupyter/kernels
+    {{< /highlight >}}
+
+{{% notice note %}}
+**Note**: Step 5 only needs to be done once. Any future created
+environments will automatically be accessible from SLURM notebooks
+once this is done.
+{{% /notice %}}
+
+6.  Login to JupyterHub at https://crane.unl.edu
+    and create a new notebook using the environment by selecting the
+    correct entry in the `New` dropdown menu in the top right
+    corner.  
+    {{< figure src="/images/24151931.png" height="400" class="img-border">}}
+

content/applications/user_software/using_singularity.md

 +++
 title = "Using Singularity and Docker Containers"
 description = "How to use the Singularity containerization software on HCC resources."
+weight=20
 +++
 
 ## What is Singularity