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VASP

The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles.

VASP License

The VASP team allows only registered users who have purchased their own license to use the software and access is only given to the VASP release which is covered by the license of the respective research group. For those who are interested to use VASP on Negishi , please contact support to request access and provide your email address associated with your license for our verification. Once confirmed, the approved users will be given access to the vasp5 or/and vasp6 unix groups.

Prospective users can use the command below to check their unix groups on the system.

$ id $USER

If you are interested to purchase and get a VASP license, please visit VASP website for more information.

VASP 5 and VASP 6 Installations

Negishi provides VASP 5.4.4.pl2 and VASP 6.4.1 installations and modulefiles with our default environment compiler gcc/12.2.0 and mpi library openmpi/4.1.4. Note that only license-approved users can load the VASP modulefile as below.

You can use the VASP 5.4.4.pl2 module by:

$ module load vasp/5.4.4.pl2

You can use the VASP 6.4.1 module by:

$ module load vasp/6.4.1

Once a VASP module is loaded, you can choose one of the VASP executables to run your code: vasp_std, vasp_gam, and vasp_ncl.

The VASP pseudopotential files are not provided on Negishi, you may need to bring your own POTCAR files.

Build your own VASP 5 and VASP 6

If you would like to use your own VASP on Negishi, please follow the instructions for Installing VASP.6.X.X and Installing VASP.5.X.X.

In the following sections, we provide some instructions about how to install VASP 5 and VASP 6 as well as bash job submit script on Negishi:

VASP Job Submit Script

This shows an example of a job submission file for running VASP pre-built on Negishi:

#!/bin/bash

#SBATCH -A myqueuename  # Queue name(use 'slist' command to find queues' name)
#SBATCH --nodes=1       # Total # of nodes 
#SBATCH --ntasks=64     # Total # of MPI tasks
#SBATCH --time=1:00:00  # Total run time limit (hh:mm:ss)
#SBATCH -J myjobname    # Job name
#SBATCH -o myjob.o%j    # Name of stdout output file
#SBATCH -e myjob.e%j    # Name of stderr error file

# Manage processing environment, load compilers and applications.
module load vasp/5.4.4.pl2  # or module load vasp/6.4.1
module list

# Launch MPI code
mpirun -np $SLURM_NTASKS vasp_std

Build your own VASP 5

For VASP 5.X.X version, VASP provide several templates of makefile.include in the /arch folder, which contain information such as precompiler options, compiler options, and how to link libraries. You can pick up one based on your system and preferred features. Here we provide some examples about how to install the vasp.5.4.4.pl2.tgz version on Negishi with different module environments.

Step 1: Download

As a license holder, you can download the source code of VASP from the VASP Portal, we will not check your license in this case.

Copy the VASP resource file vasp.5.4.4.pl2.tgz to the desired location, and unzip the file tar zxvf vasp.5.4.4.pl2.tgz to obtain the folder /path/to/vasp-build-folder/vasp.5.4.4.pl2and reveal its content.

Step 2: Prepare makefile.include

We recommend to use GNU compilers parallelized using OpenMPI, combined with MKL for VASP compilation on Negishi.

We are using MKL library, which include BLAS, LAPACK, ScaLAPACK, and FFTW as suggested at VASP wiki, and we can modify makefile.include.linux_gnu from /arch folder:

$ cd /path/to/vasp-build-folder/vasp.5.4.4.pl2
cp arch/makefile.include.linux_gnu makefile.include

Here are the suggested changes for makefile.include, replace the lines between DEBUG=-O0 and OBJECTS= fftmpiw.o fftmpi_map.o fftw3d.o fft3dlib.o with

# Intel MKL (FFTW, BLAS, LAPACK, and scaLAPACK)
LLIBS     += -L${MKLROOT}/lib/intel64 -Wl,--no-as-needed -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_core -lmkl_scalapack_lp64 -lmkl_blacs_openmpi_lp64 -lgomp -lpthread -lm -ldl
INCS       = -I$(MKLROOT)/include/fftw
FFLAGS     += -march=znver3

# For gcc-10 and higher (comment out for older versions)
FFLAGS     += -fallow-argument-mismatch

Remove all the GPU stuff at the end of makefile.include file

Load the required modules:

module --force purge 
module load gcc/12.2.0 openmpi/4.1.4
module load intel-mkl/2019.9.304

Step 3: Make

Build VASP with command make all to install all three executables vasp_std, vasp_gam, and vasp_ncl or use make std to install only the vasp_std executable. Use make veryclean to remove the build folder if you would like to start over the installation process.

Step 4: Test

You can open an Interactive session to test the installed VASP with GNU/openMPI compilation, you may bring your own VASP test files:

$ cd /path/to/vasp-test-folder/
module --force purge 
module load gcc/12.2.0 openmpi/4.1.4 intel-mkl/2019.9.304
module list
mpirun /path/to/vasp-build-folder/vasp.5.4.4.pl2/bin/vasp_std

Step 5: submit a bash job

To submit a bash job with your own compiled VASP on Negishi, here is an example about how to set up your environment and launch MPI code.

#!/bin/bash

#SBATCH -A myqueuename  # Queue name(use 'slist' command to find queues' name)
#SBATCH --nodes=1       # Total # of nodes 
#SBATCH --ntasks=64     # Total # of MPI tasks
#SBATCH --time=1:00:00  # Total run time limit (hh:mm:ss)
#SBATCH -J myjobname    # Job name
#SBATCH -o myjob.o%j    # Name of stdout output file
#SBATCH -e myjob.e%j    # Name of stderr error file

# Manage processing environment,load compilers and applications.
module purge
module load gcc/12.2.0 openmpi/4.1.4 intel-mkl/2019.9.304
module list
export PATH=/path/to/vasp-build-folder/vasp.x.x.x/bin:$PATH

# Launch MPI code
mpirun -np $SLURM_NTASKS vasp_std

Build your own VASP 6

For VASP 6.X.X version, VASP provide several templates of makefile.include, which contain information such as precompiler options, compiler options, and how to link libraries. You can pick up one based on your system and preferred features . Here we provide some examples about how to install vasp 6.4.1 on Negishi with different module environments.

Step 1: Download

As a license holder, you can download the source code of VASP from the VASP Portal, we will not check your license in this case.

Copy the VASP resource file vasp.6.4.1.tgz to the desired location, and unzip the file tar zxvf vasp.6.4.1.tgz to obtain the folder /path/to/vasp-build-folder/vasp.6.4.1 and reveal its content.

Step 2: Prepare makefile.include

We recommend to use GNU compilers parallelized using OpenMPI + OpenMP, combined with MKL for VASP build on Negishi.

We are using MKL library, which include BLAS, LAPACK, ScaLAPACK, and FFTW as suggested at VASP wiki. We can modify makefile.include.gnu_ompi_mkl_omp from /arch folder to fit for system setup:

$ cd /path/to/vasp-build-folder/vasp.6.4.1
$ cp makefile.include.gnu_ompi_mkl_omp makefile.include

Here are the suggested changes for makefile.include:

  • change VASP_TARGET_CPU ?= -march=native to

    VASP_TARGET_CPU ?= -march=znver3

  • remove MKLROOT ?= /path/to/your/mkl/installation

  • change LLIBS_MKL = to

    LLIBS  +=

  • comment out or remove all the lines after INCS = -I$(MKLROOT)/include/fftw

Then, load the required modules:

$ module purge 
$ module load gcc/12.2.0  openmpi/4.1.4
$ module load intel-mkl/2019.9.304

Step 3: Make

Open makefile, make sure the first line is VERSIONS = std gam ncl.

Build VASP with command make all to install all three executables vasp_std, vasp_gam, and vasp_ncl or use make std to install only the vasp_std executable. Use make veryclean to remove the build folder if you would like to start over the installation process.

Step 4: Test

You can open an Interactive session to test the installed VASP 6. Here is an example of testing above installed VASP 6.4.1 with GNU compilers and OpenMPI:

$ cd /path/to/vasp-build-folder/vasp.6.4.1/testsuite
$ module purge 
$ module load gcc/12.2.0 openmpi/4.1.4 intel-mkl/2019.9.304
$ ./runtest

Step 5: Submit a bash job

To submit a bash job with your own compiled VASP on Negishi, here is an example about how to set up your environment and launch MPI code.

#!/bin/bash

#SBATCH -A myqueuename  # Queue name(use 'slist' command to find queues' name)
#SBATCH --nodes=1       # Total # of nodes 
#SBATCH --ntasks=64     # Total # of MPI tasks
#SBATCH --time=1:00:00  # Total run time limit (hh:mm:ss)
#SBATCH -J myjobname    # Job name
#SBATCH -o myjob.o%j    # Name of stdout output file
#SBATCH -e myjob.e%j    # Name of stderr error file

# Manage processing environment,load compilers and applications.
module purge
module load gcc/12.2.0 openmpi/4.1.4 intel-mkl/2019.9.304
module list
export PATH=/path/to/vasp-build-folder/vasp.x.x.x/bin:$PATH

# Launch MPI code
mpirun -np $SLURM_NTASKS vasp_std
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