VASP5 How-to

Last updated on 6-2-2023

This page includes the following items and is based on VASP’s official documentations.

  • How to install VASP.5.4.4 on csusb-hpc.

  • 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 to simplify the process. You may use the following command in the terminal to install oneAPI or load the stack oneAPI.

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 Intel oneAPI Base+HPC.

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.

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.

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

Test the installation by running the following command.

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 your workspace with your collaborators and monitor system resources. The following command will add both packages.

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.

ulimit -s unlimited