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Run GROMACS Docker Application

This guide shows how to run the GROMACS Docker 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 docker.

Note

In this example we use Gromacs 2022_3 with docker.

Select version

New workload

Click New Workload at the top right.

New workload button

Select team

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

Selected team

Next button

Configure run script

In the Application Configuration step, choose the benchmark type you want.

Select benchmark

Note

Uncomment only one benchmark at a time. If you uncomment more than one (e.g. Adh_Dodec and Cellulose), the application will fail.

Benchmark type 1 : Adh_Dodec

Uncomment the Adh_Dodec benchmark command for MI210 from the run script to execute the Adh_Dodec benchmark.

nstlist=180; ntomp=16; cd /benchmarks/adh_dodec; tar -xvf adh_dodec.tar.gz;

Select Adh_Dodec

Benchmark type 2: Cellulose

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

nstlist=320; ntomp=16; cd /benchmarks/cellulose_nve; tar -xvf cellulose_nve.tar.gz;

Uncomment Cellulose

Benchmark type 3: STMV

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

nstlist=400; ntomp=8; cd /benchmarks/stmv; tar -xvf stmv.tar.gz;

Uncomment STMV

Select resources

Set Maximum allowed runtime (e.g. 1 hour), enable telemetry if needed, and set the number of GPUs (e.g. 8). You cannot change runtime after launch. Click Next.

Select resource next

Select GPUs

Select compute

Select the cluster and queue for your team (e.g. AAC Plano, AAC Plano RHEL, CirraScale). In this example 1CN128C8G2H_2IB_MI210_SLES15 (Pre-emptible) is selected. Click Next.

Queue next button

Review workload submission

Review the workload details. Use Change in any section to edit, then click Run Workload.

Run workload button App input change button

App config change button

Container change button

Queue change button

Run workload

Note

Payment information may differ depending on your team.

After you submit, monitor the workload on the Workloads page. States: Created, Sent, Pending, Running, Completed, Failed, Cancelled.

Monitor workload

When the run finishes, the status is Completed. Use the STDOUT and STDERR tabs to view logs; the Performance tab shows telemetry. You can view SysLog, Stdout, Stderr, and Download log files from the Workload Information screen.

Job information

The GROMACS performance value appears in the STDERR tab.

STDERR logs