Overview

GROMACS is a high-performance molecular dynamics simulation package commonly used to study biological macromolecules such as proteins, lipids, and nucleic acids. It is widely used because of its computational efficiency and scalability across different computing environments.

This example demonstrates how to submit a GROMACS job in IEC by using MPI-based parallel execution.

Procedure

Preparing Input Data

1. Go to EonKube > HPC > File Explorer
2. Create a folder for the job data under the user's home directory, for example, gmx_data.
3. Upload or extract the required simulation files into the target folder.

Use commands similar to the following example:

wget -c https://ftp.gromacs.org/pub/benchmarks/water_GMX50_bare.tar.gz
tar xf water_GMX50_bare.tar.gz

Submitting the Job

1. Go to EonKube > Apps > Marketplace.
2. Open the GROMACS application page.
3. Click Submit.
4. Configure the required settings.
   • Basic Settings
     • Project: Select a Project from the drop-down menu.
     • Job Name: For example, gromacs-job
     • App Version: Select the version, such as 2024.1
     • MPI: Enable if MPI execution is required
   • Resource Configuration:
     Configure control node and compute node resources according to workload requirements.
     Example configuration:
     • Control Node
       • CPU: 1 Core
       • Memory: 2 GiBs.
       • GPU: 1 GPU
     • Compute Node
       • CPU: 4 Core.
       • Memory: 4 GiBs.
       • GPU: 1 GPU
       • Node: Select the required number of GPU-capable nodes, for example, 1 node.
   • Command Settings
     Enter the preprocessing and execution commands required by the workload.
     
     • If you are using an administrator account, add the --allow-run-as-root flag if required by the runtime environment.

       mpirun --allow-run-as-root ... ...

     • Preprocess the input files needed to run a molecular dynamics simulation.

       gmx_mpi grompp -f gmx_data/water-cut1.0_GMX50_bare/0096/pme.mdp -c gmx_data/water-cut1.0_GMX50_bare/0096/conf.gro -p gmx_data/water-cut1.0_GMX50_bare/0096/topol.top

     • Adjust $MPI_HOST and $NODE_NUM as needed for your environment.

       mpirun --host $MPI_HOST -np $NODE_NUM gmx_mpi mdrun -ntomp 3 -dlb yes -v -nsteps 1000 -gpu_id 0 -s topol.tpr

5. Click on Create to submit the job.

Monitoring the Job

1. Go to EonKube > HPC > Volcano Jobs.
2. Locate the GROMACS job.
3. Review the job status.
   Typical status values include:
   
   • Pending: Indicates that the process is still being prepared.
   • Running: Indicates that the computation is currently in progress.
   • Completed: Indicates that the GROMACS computation has finished.
4. Click ⋮ > View Logs to review execution detail. Check if there are information show like below.

   step 1000, remaining wall clock time:     0 s                                  Core t (s)   Wall t (s)        (%)             Time:      222.766       77.469      287.6                        (ns/day)    (hour/ns)              Performance:        2.233       10.749
       

Review Results

1. Go to EonKube > HPC > File Explorer.
2. Open the GROMACS job data folder.
3. Review the generated output files.

If visualization is required, deploy HPC Desktop and open the result files in a supported visualization tool such as PyMOL.