From 32f36cadf24444c59c2ff416d05203e3b18e3c81 Mon Sep 17 00:00:00 2001 From: Geert Jan Bex Date: Wed, 20 Nov 2019 13:29:04 +0100 Subject: [PATCH 1/4] Make R and Python conda installation instructions consistent --- source/software/r_package_management.rst | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/source/software/r_package_management.rst b/source/software/r_package_management.rst index 889e91a4d..34d8fa441 100644 --- a/source/software/r_package_management.rst +++ b/source/software/r_package_management.rst @@ -33,6 +33,12 @@ 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 ``$VSC_HOME`` + would be exceeded soon. + Optionally, you can add the path to the Miniconda installation to the PATH environment variable in your ``.bashrc`` file. This is convenient, but may lead to conflicts when working with the module system, so make sure From e37328ca062336b9399f1ea167ac7e3a6ae776a9 Mon Sep 17 00:00:00 2001 From: Geert Jan Bex Date: Wed, 20 Nov 2019 13:36:20 +0100 Subject: [PATCH 2/4] Add note on miniconda3 installation and .bashrc --- source/software/python_package_management.rst | 6 ++++++ source/software/r_package_management.rst | 6 ++++++ 2 files changed, 12 insertions(+) diff --git a/source/software/python_package_management.rst b/source/software/python_package_management.rst index 98a94fe36..0a09b2e5d 100644 --- a/source/software/python_package_management.rst +++ b/source/software/python_package_management.rst @@ -71,6 +71,12 @@ Once downloaded, run the installation script:: since environments tend to be large, and your quota in ``$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 index 34d8fa441..3722794ca 100644 --- a/source/software/r_package_management.rst +++ b/source/software/r_package_management.rst @@ -39,6 +39,12 @@ Once downloaded, run the installation script:: since environments tend to be large, and your quota in ``$VSC_HOME`` would be exceeded soon. +.. warning:: + + The installation script will offer to modify your ``.bashrc`` file. + You will not be able to log in on NX nodes when you allow the + installer to do so. + Optionally, you can add the path to the Miniconda installation to the PATH environment variable in your ``.bashrc`` file. This is convenient, but may lead to conflicts when working with the module system, so make sure From 528d06057181fa435bffb7c7eef50793f45929bd Mon Sep 17 00:00:00 2001 From: Geert Jan Bex Date: Wed, 20 Nov 2019 13:41:04 +0100 Subject: [PATCH 3/4] Add remark on miniconda3 installtion and .bashrc --- source/leuven/running_jupyter_notebooks.rst | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/source/leuven/running_jupyter_notebooks.rst b/source/leuven/running_jupyter_notebooks.rst index b5c9dd9e5..22787c9b3 100644 --- a/source/leuven/running_jupyter_notebooks.rst +++ b/source/leuven/running_jupyter_notebooks.rst @@ -19,10 +19,16 @@ Prerequisites The most convenient way to install Jupyter, and any other Python packages you require is using conda. In case you're not familiar with conda, please check out the information on :ref:`managing Python packages using conda -`. In this how-to, we will assume that the conda -environment's name that has Jupyter installed is `science`. We will also -assume that the `$VSC_DATA/miniconda3/bin` directory is in your ``PATH`` -variable. +`. + +.. 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 From aa946d43a7de4b9bf047bdb5d44f5c3405ec2127 Mon Sep 17 00:00:00 2001 From: Geert Jan Bex Date: Wed, 20 Nov 2019 13:49:15 +0100 Subject: [PATCH 4/4] Add remark on miniconda3 installer problems --- source/access/nx_start_guide.rst | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/source/access/nx_start_guide.rst b/source/access/nx_start_guide.rst index 897bf8545..857ad1d73 100644 --- 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 `. 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 ------------------