Skip to content

Run GROMACS Singularity Application

This guide shows how to run the GROMACS Singularity application. Sign in to AAC if you have not already.

Select application

Click Applications and search for Gromacs.

Search GROMACS

Select container

Select the GROMACS version with container type singularity.

Note

In this example we use Gromacs 2022_3 with singularity.

Select Singularity

New workload

Click New Workload at the top right.

New button

Select team

If you have more than one team, select one in the pop-up and click Launch. Click Next.

Selected team

Select input next

Configure run script

In the Application configuration step, choose the benchmark type. Uncomment only one benchmark at a time.

Select benchmark

Benchmark type 1 : Adh_Dodec

Uncomment the Adh_Dodec benchmark command from the run script to execute the Adh_Dodec benchmark.

nstlist=150; ntomp=8; BENCHMARK=/benchmarks/adh_dodec/adh_dodec.tar.gz;

Select Adh_Dodec benchmark in run script

Benchmark type 2 : Cellulose

Uncomment the Cellulose benchmark command from the run script to execute the Cellulose benchmark.

nstlist=200; ntomp=8; BENCHMARK=/benchmarks/cellulose_nve/cellulose_nve.tar.gz;

Uncomment Cellulose benchmark in run script

Benchmark type 3 : STMV

Uncomment the STMV benchmark command from the run script to execute the STMV benchmark.

nstlist=400; ntomp=8;BENCHMARK=/benchmarks/stmv/stmv.tar.gz;

Uncomment STMV benchmark in run script

Select resources

In the following image, the maximum allowed runtime is selected as '1 hour' by default with telemetry enabled. The number of GPU's are selected as '8'.

Note: The time for which workload is allowed to run should be specified in the Maximum allowed runtime field. By default 1 hour will be selected.

If maximum allowed run time is 1 hour, it implies, workload will run for 1 hour and then it will be automatically stopped after 1 hour as it will not be allowed to exceed Maximum allowed runtime.

Based on the time required for workload, user should change the Maximum allowed runtime. Once workload is launched, user cannot change the total workload time. It has to be configured in the current step.

Click on Next button available on the top right corner.

Select resource next button

Select benchmark type

Select compute

Select the cluster and desired queue to run the job.

The availables queues are AAC Plano, AAC Plano RHEL and CirraScale.

In this case 1CN128C8G2H_2IB_MI210_RHEL8 (Pre-emptible) was selected. Click on Next button available on the top right corner.

Queue next button

Review workload submission

Review Workload Submission. Review the information that has entered for this workload. If any change is needed, it can be changed by clicking Change button in the appropriate sections to make revisions.

GROMACS review run workload

GROMACS change button

GROMACS app config

Resources change button

Queue change button

GROMACS run workload button

Note: Please note that the payment information might be different from the above image because you might be added to a different team.

After submitting a workload, user can monitor how the workload is performing by checking the Workload Status on the Workloads page and the Workload Information page. Each workload goes through several different states after it is submitted.

Created – The workload has been created in the system.

Sent – The workload has been sent to the queue that you selected in the workload submission process.

Pending – The workload is in a waiting state in the queue.

Running – The workload has started running in the selected queue.

Completed – The workload has successfully finished processing.

Failed – A problem has occurred which has prevented the workload from completing successfully.

Cancelled – The workload has been canceled by the user and stopped running.

Monitor workload

Once the application execution is successful then the status gets changed into Completed. The user can check the STDOUT and STDERR logs by clicking on respective tabs. The Performace tab shows the telemetry collected. View Log Click on the links shown on the Workload Information screen to view the job log, stdout log and stderr log:

View SysLog - Information about the workload throughout the entire process.

View Stdout - Standard output that presents the output of a workload and sometimes includes the results of the workload.

View Stderr - Standard Error that helps you understand why you may have encountered certain issues during the process.

Download log files - Download all information about the Log, STDOUT and STDERR log files.

GROMACS parameter tab

The performance value in the STDERR tab is the performance of Gromacs singularity application.

GROMACS STDERR output with performance