Gromacs Singularity Applications
This document shows how to run gromacs singularity application.
How To Run Gromacs Singularity Applications.
To start creating a workload, sign into the AAC web platform.
Select Application
Click on Applications. Search for Gromacs.
Select Container
Select the desired Gromacs version with desired container type as singularity.
Note: In this case, Gromacs 2022_3 version was seletced with container type as singularity.
New Workload
Click on New Workload button available on the top right corner.
Select Team
In case the user is assigned to more than one team, a pop window will required to select one of the customer teams to which the user is part of. If there is just one team assigned to the user, it will not be required.
Note: In this case, we have selected Team as AMD Internal.
Click Start new workload button.
Click Next button available on the top right corner.
Configure Runscript
Choose the desired benchmark type in Application configuration step.
Note: Uncomment the type of benchmark that needs to be run. Only "ONE" benchmark can be launched at a time. If more than one benchmark, say Adh_Dodec and Cellulose, is uncommented and launched, then the application fails.
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;
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;
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;
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 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.
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.
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.
The performance value in the STDERR tab is the performance of Gromacs singularity application.
