How to Install (Linux)

Preparation for Installation

This software is installed using an installer. Please download them from the respective links below.

  • Main Program

  • Our modified calculation engines (Quantum ESPRESSO / LAMMPS)

  • Additional GNN force field model files (Required only if using FAIR-Chem or SevenNet)

Installation

In a terminal, change the current working directory to where the installer is located. After granting execute permission, first run the Advance/NeuralMD installer.

$ chmod +x install_neural_linux.bin install_nanolabo_tool_linux.bin
$ sudo ./install_neuralmd_linux.bin

Note

Root privileges are required to install the License Manager (Sentinel-LDK-RTE).

It can also be run by a standard user if the installation of Sentinel-LDK-RTE is not required (e.g., it is already installed).

Note

The installer can also run in the console mode (no GUI is displayed, even only the CUI completes the operation). If the installer does not enter console mode at runtime in environment without a GUI, execute as follows.

$ ./install_neuralmd_linux.bin -i console

When the language selection screen appears, select the language to be used during installation (not the language used in the software itself).

Follow the on-screen instructions to set up the installation.

Note

It cannot be installed to a location without write permission. Please specify a location with write permission (e.g. /home/username/AdvanceSoft/NeuralMD) as the installation location or run the installer as a user with write permission.

  • If you are using the software as a client with a floating license, select No for ‘Install Sentinel-LDK-RTE?’ (this confirmation prompt will not be displayed if run by a standard user).

    If the license server is on a different network segment, enter the license server’s IP address or hostname on the next screen. Even if you do not specify it here, you can configure the license server’s IP address or hostname later. For details, refer to Floating license.

    ../_images/install_license_server_l.en.png

After the setup is complete, a summary screen will appear.

../_images/install_summary_l.en.png

Clicking Finish on the last screen will complete the Advance/NeuralMD installation.

Then run the Advance/NanoLabo Tool installer.

$ ./install_nanolabo_tool_linux.bin

Follow the on-screen instructions to set up the installation.

../_images/install_tool_l.en.png

After the installation, click Finish on the last screen to complete the installation of the Advance/NanoLabo Tool.

If using FAIR-Chem or SevenNet, please also install Advance/NanoLabo GNNP in the same way.

For information on how to use the calculation engines (Quantum ESPRESSO and LAMMPS) included with the Advance/NanoLabo Tool, please refer to Calculation Engines included in Nanolabo Tool.

Since the dynamic library in mpi/lib is required when running NeuralMD, execute the following to set up the environment variable LD_LIBRARY_PATH.

Example of installing in the default location
export LD_LIBRARY_PATH=/opt/AdvanceSoft/NeuralMD/mpi/lib:$LD_LIBRARY_PATH

In addition, the environment variable PATH and that of OPAL_PREFIX for Open MPI must be set, execute the followings.

Example of installing in the default location
export PATH=/opt/AdvanceSoft/NeuralMD/mpi/bin:$PATH
export OPAL_PREFIX=/opt/AdvanceSoft/NeuralMD/mpi

Note

The MPI executable files and libraries are included in both the NeuralMD main unit installer and the NanoLabo Tool installer.

The former is located in the mpi and the latter in the exec.LINUX/mpi directory in the installation location.

The contents are the same, so you only need to set one of them in the environment variable.

It is also helpful to set the path to the NeuralMD executable in the environment variable PATH.

Example of installing in the default location
export PATH=/opt/AdvanceSoft/NeuralMD/bin:$PATH

License Configuration

Follow the procedure in License Setup and Update to configure the license.

Update/Upgrade

  • When upgrading from the trial version to the full version, there is no need to perform a new installation. Refer to License Update to update only the license.

  • When updating to a new version, it is possible to perform an overwrite install. However, uninstalling the previous version or changing the installation location beforehand is recommended.

  • When updating to a new major version of NeuralMD, a license update is required. Please update the license by referring to License Update.

Uninstallation

Launch the Change NeuralMD Installation in the _NeuralMD_installation directory in the installation location in the terminal.

$ AdvanceSoft/NeuralMD/_NeuralMD_installation/Change\ NeuralMD\ Installation

Follow the on-screen instructions to uninstall the software.

After uninstalling Advance/NeuralMD, uninstall Advance/NanoLabo Tool in the same manner.

Note

Installation log files may remain after uninstallation. Also, if you are using a FlexNet license, the license file will remain undeleted. In such cases, please delete them manually.

Note

To uninstall Sentinel-LDK-RTE later, execute dunst contained in the Sentinel-LDK-RTE installer.