Installing VASP

Authors: Sina G. Lewis , R. Peyton Cline , and Alexander Staat

Table of Contents

Pre-Installation

Regardless of the computer architecture, the first step of installing VASP is to retrieve the necessary files. VASP is not a free program and, therefore, requires a license to download and operate. We obtained our license through Materials Design, Inc. and need to download it from there, not the VASP portal. As of October 13, 2022, Sina G. Lewis is the contact for the login details.

After you have downloaded the files from the portal, do NOT unzip them yet. Peyton has experienced issues in the past when he unzips the files on his local machine. Instead, upload them to your project directory on the system where you intend to install VASP. I recommend having a folder in this directory called programs where you keep VASP and other programs like LAMMPS. The command to upload the files to this location on Summit or Alpine would then look like

    scp filename identikey@login.rc.colorado.edu:/projects/identikey/programs

Each installation of VASP should be contained within its own folder within your programs folder. The name of the folder should contain the version of VASP and preferably a few of the options that were used in the installation. For example, summit_vasp.6.3.1_O2_intel20 is the folder name for version 6.3.1 of VASP, installed on the cluster Summit, with the O2 optimization flag and version 20 of the Intel module.

The structure of VASP within the zip files changes frequently, so I recommend making a separate folder for each zip file within this summit_vasp.6.3.1_O2_intel20 folder. Typically, there are three zip files: one for the VASP installation, one for the LDA psuedopotentials, and one for the PBE pseudopotentials. Unzip the files within their own folder and then rearrange the output to your desired configuration. A good layout for a fully installed VASP is shown in the image below.

Folder layout example for a fully installed version of VASP

After organizing the files it’s time to start the installation process. Make sure you are on a compile node, NOT the login node. The following steps will likely throw an error if you are on a login node and it will slow down the whole system for everyone. Once you are on a compile node, load the modules needed for installation. The order matters for some of them because of dependencies, always load Intel first. You can check the available modules with module avail and the modules you have already loaded with module list. If you don’t see the module you want, try the command module spider or module spider string where string is a search keyword enclosed in quotes. The remaining steps may differ depending on where you are installing VASP. See the below sections.

Most of these installation instructions can be found on the wiki. As of VASP version 6 there is a testsuite to ensure the installation completed correctly. This testsuite should be run on the compile nodes after loading the correct modules.

Alpine Installation

Alpine is the most recent (Fall 2022) supercomputer. It is an institutionally funded supercomputer designed to replace Summit. To access Alpine, login via the following command

    ssh -X identikey@login.rc.colorado.edu

To access an Alpine compile node, submit a compile job by typing acompile --ntasks=4 on the terminal line. Note that there is no ssh needed, as was previously used on Summit. The specification --ntasks=4 is used because we later install VASP with 4 parallel processes. You can additionally request more than the default one hour of time by adding --time=03:00:00 if you wanted three hours for example. The whole process of installing VASP should take less than an hour, but the testsuite can take several hours to run, and the VASP documentation warns that running the testsuite on a different number of tasks may cause tests to fail.

Installing VASP requires us to load four modules: intel, mkl, impi, and hdf5. Intel is the compiler, mkl stands for math kernel library, impi is our intel message passing interface that is needed for parallel computing, and hdf5 is a special file format tailor-made for large files of numeric data like VASP outputs. The module load order matters due to module dependencies. Research computing recommends intel followed by impi and finally mkl.

Alpine currently has limited version choices for these modules. Nevertheless, it is best to specify the version so that you know concretely what you are using. As of November 2022 (and in March 2024), the command you would want to type is

    module load intel/2022.1.2 impi/2021.5.0 mkl/2022.0.2 hdf5/1.12.1

After loading these modules, we want to grab the correct makefile for our computer architecture from the arch folder that should have been unpacked from the VASP zip file. Because we are using intel, we will grab the makefile titled makefile.include.intel. Copy this file to the parent directory, where the rest of your VASP files should be, and rename it. This command would be

    cp makefile.include.intel ../makefile.include

Now, we need to edit a few lines in our new file makefile.include. Most importantly, because Alpine has AMD CPUs and not Intel CPUs we need to tell the compiler to use a different instruction set. This is done by finding the line that reads

    VASP_TARGET_CPU ?= -xHOST

and changing it to read

    VASP_TARGET_CPU ?= -march=core-avx2

Next, if we are using Intel Parallel Studio’s MKL, which we most likely are, we want to find the line FCL += -qmkl=sequential and remove the q so that it reads FCL += -mkl=sequential. During the make process, you will see warnings for -mkl=sequential being deprecated, the installation will still complete without issue.

As a final edit, we want to compile VASP with the flag -DVASP_HDF5 in the CPP_OPTIONS, includes INCS, and linking LLIBS instructions. There is a section near the bottom of the makefile.include that you can simply uncomment for this. The environment variable for HDF5 in the makefile disagrees with the CURC environment variable. The appropriate line looks like

    HDF5_ROOT ?= $(CURC_HDF5_ROOT)

In the future if the makefile is having difficulty linking to CURC modules, you can compare your environment variables with theirs on the compile node using set and then replace $(ENV_ROOT) with the appropriate variable name.

We are now good to install VASP. We want to run the command

    make DEPS=1 -j4 all

to install all versions of VASP with 4 parallel processes and DEPS=1 ensures the installation doesn’t crash because of dependency issues while installing in parallel. VASP can also be installed with standard-only (std), gamma-point only (gam), or non-collinear only (ncl).

The VASP wiki instructions end by adding the executables to your VASP with

export PATH=$PATH:/path/to/vasp.x.x.x/bin

but it is also sufficient to just define the variable

VASP_DIR=/path/to/vasp.x.x.x/bin/vasp_std

in your sbatch file (if you want to point to the standard version of VASP).

Finish everything off by running the testsuite.

make test

Uninstalling VASP

When you go to delete VASP, you might find that you don’t have the correct permissions to delete the LDA/PBE files. The quick work around is to use chmod -R 766 on the file(s) you wish to delete. For example, if you wish to only delete the files within the folder LDA, you would type chmod -R 766 LDA in the parent directory. The option -R makes chmod recursive and it will act on all the files in the folder LDA. The specific combination 766 for chmod provides read, write, and execute permissions for the user and read and write permissions for the group and others. See the wikipedia page for more information.

Once you delete the LDA/PBE files you should be able to just normally delete the other files in your VASP install folder. That’s all you need to do!

Summit Installation

Summit is the supercomputer that we used to use, but was largely phased out by CU in August 2022. Although it currently can be used, the scratch space is no longer supported and is unstable. These instructions for installing VASP on Summit are kept for posterity.

To access Summit, login using the following command

    ssh -X identikey@login.rc.colorado.edu

and then access a compile node using ssh compile.

Installing VASP requires us to load three modules: intel, mkl, and impi. Intel is the compiler, mkl stands for math kernel library, and impi is our intel message passing interface that is needed for parallel computing. Remember that the order modules are loaded matters because of possible dependencies. I spoke with someone at research computing who recommended intel followed by impi and finally mkl. Peyton has said in the past that it didn’t seem to matter if you installed impi before mkl or after. In my first installation of VASP, I used

    module load intel/20.2 mkl/20.2 impi/19.8

to load the intel compiler version 20.2, the math kernel library (mkl) version 20.2, and the intel message passing interface (impi)–needed for parallel computing–version 19.8 in that order.

As a final step, we need to edit a few lines in our new file makefile.include. If we are using Intel Parallel Studio’s MKL, which we most likely are, we want to find the line FCL += -qmkl=sequential and remove the q so that it reads FCL += -mkl=sequential. While we are here, we can go ahead and comment out the next line that starts MKLROOT. Finally, in the line #LLIBS += -L$(WANNIER90_ROOT)/lib -lwannier, we want to remove the /lib part. These last two steps are only important for a Wannier installation, but are fine to do in a general installation.

We are now good to install VASP. We want to run the command

    make DEPS=1 -j4 all

to install all versions of VASP with 4 parallel processes and DEPS=1 ensures the installation doesn’t crash because of dependency issues while installing in parallel. VASP can also be installed with standard-only, gamma-point only, or non-collinear only.