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GROMACS

This article mainly introduces how to use the Bohrium platform to run GROMACS jobs.

Introduction​

GROMACS is an open source and free molecular dynamics simulation software that adheres to the LGPL v2.1 protocol and is often used for simulating biological and organic molecular systems such as proteins, phospholipids, nucleic acids, etc. The code for GROMACS is entirely written in C/C++and has been high-performance optimized for GPU, resulting in fast computation speed. For a more detailed introduction to GROMACS, please refer to itsofficial websiteordocument。Beginners can also refer to thedocumentto quickly get started with GROMACS.

How to run GROMACS jobs on Bohrium​

The job in this case will take 1 min 30 s

Step 1, prepare to input data​

First, you need to enable the New Nodes，In this case, the image is selected as ubuntu:20.04-py37。After connecting to the management node through Web Shell, the input file can be prepared.

The input files for GROMACS (including the coordinate file conf.gro, simulation parameter file prod.mdp, topology file topol.top, run script rungmx.sh, and lbg configuration file job.json) have been stored in the Bohrium_GROMACS_example folder. After entering the data disk using the cd /personal command, execute the following commands in sequence to download and unzip the input files:

wget https://bohrium-example.oss-cn-zhangjiakou.aliyuncs.com/Bohrium_GROMACS_example.zip
unzip Bohrium_GROMACS_example.zip
cd Bohrium_GROMACS_example

Step 2: Prepare the Configuration File​

The folder already contains the configuration file job.json. In the Files Management page , you can double-click the job.json file in the left file tree to edit and save it online. You can also edit it in the command line window:

vi job.json

Enter edit mode by typing i, and after making the modifications, press esc to exit edit mode. Then, type : to enter the command-line mode, and input wq to save and exit. The content of the configuration file is as follows:

Note: Replace the 0000 after "project_id": with your own project ID, which can be found on the "Project Management" page.

{
    "job_name": "bohrium-gmx-example",
    "command": "bash rungmx.sh > log",
    "log_file": "log",
    "backward_files": [],
    "project_id": 0000,
    "image_address": "registry.dp.tech/dptech/gromacs:2022.2",
    "machine_type": "c16_m62_1 * NVIDIA T4",
    "platform": "ali",
    "job_type": "container"
}

Step 3: Submit the job Submit the job using Bohrium CLI : Therefore, you first need to install the Bohrium CLI.​

bohr job submit -i job.json -p ./

Where:

  • -i specifies the configuration file of the job, which is job.json in this case
  • -p specifies the directory where the input files are located, Bohrium will package and upload the specified directory, unzip it on the computing node, and switch the working directory to that directory. In this case, it is ./

If you see the following output in the command line, it means the submission is successful. You can also see the JOB ID of the job, which can be used to track the progress of the job later.

Submit job succeed. 
JobId:  <JOB ID>
JobGroupId:  <JOB GROUP ID>

Check Job​

You can learn how to check the job status on the Bohrium platform in the Monitoring job Document.

Download Results​

You can learn how to download job results on the Bohrium platform in the Result Download Document.