I am running my job with GROMACS and getting this
slurmstepd: error: *** JOB 4704121 ON gpu-001 CANCELLED AT 2022-09-25T14:20:15 DUE TO TIME LIMIT ***
Job banner turn to green as completed but files are empty
First, try at least one rerun.
If that also fails, this error means that there are input problems OR that the job is actually too large to process at the public server where you are working using the given inputs/parameters.
Check your inputs and tool form parameters for content and format problems using the guides and tutorials below. If you cannot solve the problem, you’ll need to share more information so we can help. This could include posting back: screenshots of the Dataset Information page (
icon), and stderr and stdout logs, and expanded input datasets in the history panel (captures the metadata and peek view). Or, share your entire history leaving the original job and your reruns/tests undeleted.
FAQs
- understanding-walltime-error-messages
- understanding-input-error-messages
- troubleshooting-errors – covers how to find the job/dataset information for any output not just red/errored & how to generate a shared history link
Tutorials
Got it what it means. I tried 4,5 times. job turns to green but empty files. yes Job is lengthy. I am going to run MD simulation and GROMACS is under the running process. What can be the alternative solutions for this issue?Suggestions are highly welcomed.
One of these
- Make the job smaller
- Try at a different public Galaxy server
- Set up your own private Galaxy server with sufficient resources