hpcleuven · gjbex · Nov 20, 2019 · Nov 20, 2019 · Nov 20, 2019 · Nov 20, 2019
diff --git a/source/access/nx_start_guide.rst b/source/access/nx_start_guide.rst
@@ -93,7 +93,7 @@ step-by-step or to the :download:`document containing graphical
 instructions <nx_start_guide/nx_config_guide.pdf>`.
 
 How to start using NX on Genius?
-----------------------------------
+--------------------------------
 
 #. Once your desktop is open, you can use all available GUI designed
    software that is listed within the Applications menu. Software is
@@ -117,6 +117,16 @@ How to start using NX on Genius?
    information how to **connect the local HDD** to the NX session for
    easier transfer of data between the cluster and your local computer.
 
+
+Troubleshooting
+---------------
+
+In some circumstances, you may not be able to log in using NX, in particular,
+if you allowed the ``miniconda3`` installation script to modify you ``.bashrc``,
+your login will fail.  You will have to remove the definition of the ``conda``
+function from your ``.bashrc``.
+
+
 Attached documents
 ------------------
 

diff --git a/source/leuven/running_jupyter_notebooks.rst b/source/leuven/running_jupyter_notebooks.rst
@@ -19,10 +19,16 @@ Prerequisites
 The most convenient way to install Jupyter, and any other Python packages
 you require is using conda.  In case you're not familiar with conda, please
 check out the information on :ref:`managing Python packages using conda
-<conda for Python>`.  In this how-to, we will assume that the conda
-environment's name that has Jupyter installed is `science`.  We will also
-assume that the `$VSC_DATA/miniconda3/bin` directory is in your ``PATH``
-variable.
+<conda for Python>`.
+
+.. warning::
+
+   Pay attention to the warning `not` to let the installation script modify
+   your ``.bashrc`` file.
+
+In this how-to, we will assume that the conda environment's name that has
+Jupyter installed is ``science``.  We will also assume that the
+``$VSC_DATA/miniconda3/bin`` directory is in your ``PATH`` variable.
 
 
 Using a notebook on an NX node

diff --git a/source/software/python_package_management.rst b/source/software/python_package_management.rst
@@ -71,6 +71,12 @@ Once downloaded, run the installation script::
    since environments tend to be large, and your quota in ``$VSC_HOME``
    would be exceeded soon.
 
+.. warning::
+
+   The installation script will offer to modify your ``.bashrc`` file.
+   You will not be able to log in on NX nodes when you allow the
+   installer to do so.
+
 Optionally, you can add the path to the Miniconda installation to the
 ``PATH`` environment variable in your ``.bashrc`` file. This is convenient, but
 may lead to conflicts when working with the module system, so make sure

diff --git a/source/software/r_package_management.rst b/source/software/r_package_management.rst
@@ -33,6 +33,18 @@ Once downloaded, run the installation script::
 
    $ bash Miniconda3-latest-Linux-x86_64.sh -b -p $VSC_DATA/miniconda3
 
+.. warning::
+
+   It is important to use ``$VSC_DATA`` to store your conda installation
+   since environments tend to be large, and your quota in ``$VSC_HOME``
+   would be exceeded soon.
+
+.. warning::
+
+   The installation script will offer to modify your ``.bashrc`` file.
+   You will not be able to log in on NX nodes when you allow the
+   installer to do so.
+
 Optionally, you can add the path to the Miniconda installation to the
 PATH environment variable in your ``.bashrc`` file. This is convenient, but
 may lead to conflicts when working with the module system, so make sure