Running LAMMPS on Rescale

Overview

LAMMPS is an open source software with the focus on modelingModeling is the creation of a mathematical or conceptual rep... More of atomic systems, using classical Molecular Dynamics (MD). It is an acronym for Large-Scale Atomic/Molecular Massively Parallel Simulator. 

Solid-state material (metals and semiconductors) , soft material (polymers and biomolecules), and coarse-grained or mesoscopic systems can be modeled using LAMMPS. Many of its models have versions that provide accelerated performance on CPUs, GPUsGPUs (Graphics Processing Units) are specialized electronic ... More, and Intel Xeon Phis. The code is designed to be easy to modify or extend with new functionality.

Introductory Tutorial: Submitting LAMMPS Simulations to Rescale

The following example is a simulationSimulation is experimentation, testing scenarios, and making... More of a rhodopsin protein in a solvated lipid bilayer using Molecular Dynamics (MD) and CHARMM was applied as the force field. 

This tutorial will introduce you to submitting LAMMPS jobs into the Rescale platform. An input file is already created on the local computer and we will show you how to start a Rescale job, submit, and transfer the results back to your computer.

Configuring Your Job

Starting Up Rescale

To start up the Rescale platform:

• Go to the platform.rescale.com, log in using your account info. 
• From the main screen of the platform, click the +Create New Job button at the top left corner of your screen. Feel free to rename the job by clicking on the pencil icon next to the job name (“Untitled Job”) at the top of the page. Since Rescale’s platform saves all of your jobs , it is recommended that you name it something specific so that you will be able to find it again later.

This is the first step of submitting your job.

Input file

Now you can upload the input file from your local computer or if you already have it on the cloud, you can upload it using the cloud storagea simple and scalable way to store, access, and share data o... More.

• For this tutorial you will want to upload two files, first one is the data file containing all of the data describing the structure of rhodopsin protein and the second one is the LAMMPS script containing information about the simulation setting and force field commands
• Click Upload from the computer and select the file data.rhodo and in.rhodo from your computer.
  • If you cloned an example job, then click Use files from cloud storage and select the files you uploaded from the Desktop instanceAn Amazon Virtual Machine More

On completion, you will see your input file setup page look like that shown below:

Software Settings

Now we can configure our software package options on the Software Settings page. You can search for or directly select the tile for LAMMPS:

• Next, the Analysis options must be set.
• The drop down selector allows you to choose your preferred version of the software.
• The input file in this tutorial has been tested with LAMMPS (29Sep2021), so select that option.
• This is open source software, there is no need to select any type of license.
• Next you need to add the analysis execution command for your project. This command is specific for each software package and each input file being used. For this input file you will need to add the following:

mpirun lmp -in in.rhodo

The completed Software Setting should look like those in the images below:

Hardware Settings

Now we can select the type and number of cores to run on in the Hardware Settings page.

For a basic job, there are three hardware settings to edit: CoretypePre-configured and optimized architectures for different HPC... More, Number of Cores, and Walltime.

For this example, select 8 or more for the Number of Cores (1), 6 Hrs for the Walltime (2), and Emerald for the Corean individual processing unit within a multicore processor o... More Type. Rescale offers On-Demand Economy and On-Demand Priority  core type options. You can find more information on these options here.

There is no need to specify any Post Processing options for this tutorial. To continue to Review, click Next from the Post Processing screen.

After reviewing your selections, your case should now be ready for batch submission at this point.

Review

The Review step shows you a summary of your job prior to submission.

• Click the blue Submit button in the top right corner on any of the job configuration pages or in the middle of the Review page.
• Alternatively, instead of submitting the job, you can elect to Save the problem setup to be run at some later time.

Status

Now you can monitor the progress of your job from the Status tab:

• You can monitor the status of your job and get information about your clusterA computing cluster consists of a set of loosely or tightly ... More in real-time. Here you can see the live-tailing of the output “process_out.log
• Because this analysis is entirely run in the cloud, feel free to close your browser window or shut down your computer. You can check on the progress at any time by logging into Rescale and clicking on the Jobs tab. You will receive an email notifying you when the job is completed.
• A guide on Monitoring Status on Rescale can be found here
• Once the job has completed its run, you can Download all of the output files from the Results page. You can also launch a Desktop and attach this job to perform post-processing. 
• A guide on Managing your Job Results on Rescale is found here.

Configuring Your Desktop

Once the job is completed, follow these steps to view results on a Rescale Desktop:

Set up a Desktop session:

• Under the Workstations tab, select the Classic Desktop.
• From the main screen of the platform, click on the +Create New Desktop button at the top left corner of your screen. Feel free to rename the desktop by clicking on the pencil icon next to the desktop name (“Untitled Desktop”) at the top of the page. Since Rescale’s platform saves all of your desktops , it is recommended that you name it something specific so that you will be able to find it again later.
• In the next step, you can configure the software you need. 
• For the purpose of this tutorial ,VMD GUI is selected. under the Analysis option tab you can choose your preferred version which is considered 1.9.3 for the purpose of this tutorial.
• Under the jobs section , you can attach the specific job that you want to use on the Rescale desktop.
• For the hardware it is recommended to use the “Windows Servera server is a computer program that provides services to oth... More 2019 – Hardware Accelerated”, which is well suited for the purpose of this tutorial.
• Now you can select launch on the top right corner of the platform, and wait a couple of minutes for the desktop to connect.

Once the desktop is created, select the Connect button on the top right corner of the platform:

Now that we are connected to the system, we can launch the software by double clicking it and load our results. Any job that is attached to the desktop is accessible through a folder on the desktop. 

On the VMD top bar, select File and choose the New molecule. Find the Rhodopsin.lammpstrj file from the attached_job file and the rhodopsin protein in a solvated lipid bilayer will be shown on the screen. You can manipulate the graphics of the molecule by going to Graphics → Representations and change the Drawing Method to VDW.