Running Inside a Docker Container

Docker lets you encapsulate the solver and all dependencies inside a container, ensuring consistency and portability across different systems.

Example 1: Binding a Specific Directory

If your input files (like .prm, .pqr or .pdb) are stored in a known directory, you can bind that directory into the container like this:

sudo docker run -v /your/local/files:/App -w /App <image_name>:latest mpirun -np 4 ngpb --prmfile options.prm
  • Replace /your/local/files with the absolute path to your input files.
  • Replace <image_name> with the name of your Docker image, e.g., nextgenpb.

Example 2: Using the Current Working Directory

If you’re already in the directory where your input files are located, just run:

sudo docker run -v "$(pwd)":/App -w /App <image_name>:latest mpirun -np 4 ngpb --prmfile options.prm

Docker does not have access to your files by default—you must explicitly bind the directory using -v.

Running with Apptainer / Singularity

For high-performance computing clusters or environments where Docker is unavailable, Apptainer (formerly known as Singularity) is the preferred alternative.

Example 1: Binding a Specific Directory 

apptainer exec --pwd /App --bind /your/local/files:/App /path/to/NextGenPB_ompi4.sif mpirun -np 4 ngpb --prmfile options.prm

Example 2: Using the Current Working Directory 

apptainer exec --pwd /App --bind "$(pwd)":/App /path/to/NextGenPB_ompi4.sif mpirun -np 4 ngpb --prmfile options.prm
  • The .sif file is your Apptainer container image, e.g., NextGenPB_ompi4.sif.
  • Replace /path/to/NextGenPB_ompi4.sif with the full path to your .sif file.

As with Docker, always bind the necessary directories to make your input files accessible inside the container.

Alternative Input Method: –potfile

The –potfile flag can be used in place of –prmfile if you’ve already preprocessed your parameters:

--potfile <file.pot> – can be used instead of --prmfile <file.prm>

Example:

mpirun -np 4 ngpb --potfile options.prm --pqrfile molecule.pqr

⬅️ Return to the Installation Guide if you haven’t installed the solver yet.

➡️ Go to input files to learn everything about .prm, .pot, .pqr, and other input formats.