1. Installation¶

This section provides instructions on how to install NEMAT on your HPC system.

1.1. Prerequisites¶

Before installing NEMAT, ensure that you have the following prerequisites:

A SLURM-managed HPC system
GPUs available for computation (this is not a strict requirement, but it is not realistic (time-wise) to run NEMAT without GPUs)
GROMACS installed on the system (version 2024.2 was used in the development of NEMAT)

OPTIONAL:

GROMACS with multidir for parallelization of the transitions. Make sure that a gmx executable exists in addition to the gmx_mpi executable.

1.2. Installation Steps¶

1.2.1. Download NEMAT version (recommended)¶

Download the desired version (X.Y, i.e., 0.9) from the NEMAT GitHub:

wget https://github.com/QTC-IQAC/NEMAT/archive/refs/tags/vX.Y.tar.gz -O NEMAT-vX.Y.tar.gz

Then unpack with:

tar -xzf NEMAT-vX.Y.tar.gz

Then enter the nemat directory with

cd NEMAT-X.Y

For the LAST version (0.9):

wget https://github.com/QTC-IQAC/NEMAT/archive/refs/tags/v0.9.tar.gz -O NEMAT-v0.9.tar.gz
tar -xzf NEMAT-v0.9.tar.gz
cd NEMAT-0.9

First set up env:

bash bin/set_env.sh

If mamba is available, the environment will be created with mamba. If not, conda will be used. Make sure that any of these are loaded before running the setup script (module load mamba). Then, give execute permissions to the NEMAT executable

chmod +x $NMT_HOME/bin/nemat

If using nemat is not available, try updating the .bashrc file:

source ~/.bashrc

Verify the installation by activating the environment and then running:

nemat

This should display the NEMAT help message, confirming that the installation was successful.

1.2.2. Download NEMAT on the current state¶

Download NEMAT from GitHub using:

git clone https://github.com/QTC-IQAC/NEMAT.git

cd NEMAT