=======================
VASP5 How-to
=======================

Last updated on 6-2-2023

This page includes the following items and is based on `VASP's official documentations <https://www.vasp.at/wiki/index.php/Installing_VASP.5.X.X>`_. 

- How to install VASP.5.4.4 on `csusb-hpc <https://csusb-hpc.nrp-nautilus.io>`_. 
- How to run VASP. 
- Some tips. 
  
.. note:: 

    ``VASP``, including VASP.5.4.4, is a licensed program. It can only be installed on the server whose owner has the program.

Installation
-------------

Intel oneAPI
~~~~~~~~~~~~~~~~

The VASP.5.4.4 installation requires some tools, 
and we use Intel's `oneAPI <https://www.intel.com/content/www/us/en/developer/tools/oneapi/overview.html#gs.odrq29>`_ to simplify the process. 
You may use the following command in the terminal to install oneAPI or load `the stack oneAPI <https://gitlab.nrp-nautilus.io/youngsu_kim/csusb-jupyter-stack/-/blob/main/stack-oneapi/Dockerfile>`_. 

.. code-block::

    wget -O- https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB | gpg --dearmor | sudo tee /usr/share/keyrings/oneapi-archive-keyring.gpg > /dev/null 
    echo "deb [signed-by=/usr/share/keyrings/oneapi-archive-keyring.gpg] https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list 
    sudo apt update 
    sudo apt install wget rsync
    sudo apt install intel-basekit intel-hpckit intel-oneapi-mkl intel-oneapi-mpi -y 

.. note:: 

    * Not all images have ``sudo``. 
    * When done with the installation run ``source /opt/intel/oneapi/setvars.sh`` load ``oneAPI``. 
    * If you want your server to run the above line at each start, you can achieve it by adding the command to your ``~/.bashrc`` file. This approach is reversible.
    * To install it into the user's directory without root privilege, refer to :doc:`Intel oneAPI Base+HPC <intel-oneAPI>`. 

VASP.5.4.4
~~~~~~~~~~~~

``VASP.5.4.4`` comes in a tarball file. 
Assuming that you have ``vasp.5.4.4.tar`` and a patch file (patch.5.4.4.16052018 in this example) in your home folder, run the following commands in the terminal to untar and apply the patch.

.. code-block::

    cd ~
    tar -xvf vasp.5.4.4.tar
    cp patch.5.4.4.16052018 ./vasp.5.4.4
    cd vasp.5.4.4
    patch -p0 < patch.5.4.4.16052018

Now, use the following lines to build ``vasp_std, vasp_gam, vasp_ncl``. You may replace ``all`` by ``std``, ``gam``, or ``ncl`` to build them separately.

.. code-block::

    source /opt/intel/oneapi/setvars.sh 
    cp arch/makefile.include.linux_intel ./makefile.include
    make all

Test the installation by running the following command.

.. code-block::

    time mpirun -n 1 ~/vasp.5.4.4/bin/vasp_std    

.. note:: 

    You may change the vasp.5.4.4 folder. Also, you may add the path to your path environment. 

Running VASP on JupyterHub
-------------------------------

When running VASP on JupyterHub, it may be useful to have a way to `share <https://pypi.org/project/jupyterlab-link-share/>`_ your workspace with your collaborators and `monitor <https://github.com/jupyter-server/jupyter-resource-usage>`_ system resources. 
The following command will add both packages. 

.. code-block::

    pip install --user jupyterlab-link-share jupyter-resource-usage

Error message(s)
-----------------

.. note:: 

    If you encouter ``forrtl: severe (174): SIGSEGV, segmentation fault occurred``, run the following command before you start vasp.

    .. code-block::

        ulimit -s unlimited