Tibanna Metrics isn't being gathered.

[klai5]

Hello!

I am using snakemake with tibanna. Is there something I have to enable/configure in order for metrics to be gathered? My postrun json metrics is empty:

"Metrics": {
            "max_mem_used_MB": "",
            "min_mem_available_MB": "",
            "total_mem_MB": "",
            "max_mem_utilization_percent": "",
            "max_cpu_utilization_percent": "",
            "max_disk_space_utilization_percent": "",
            "max_disk_space_used_GB": "",
            "max_ebs_read_bytes": ""
}

Thanks!

[SooLee]

@klai5 You shouldn't have to add any configuration to get the metrics, but if the instance runs for less than 5 minutes, the metrics data may not be collected. Was this the case? You can also check by running tibanna plot_metrics -j <job_id> and look at the html link generated.

[klai5]

Thanks for the fast response! No i was running picard's illuminabasecallstosam and it took ~25 minutes. I ran that command prior to checking the postrun json and it gave me "Metrics plot is already on S3 bucket." I checked the html/tsvs at the locations provided by the command and they were empty. The only thing logged was the start & end time. Do you know if you have to enable anything on the AWS side? Thanks again!

[SooLee]

@klai5 Is your region us-east-1? It looks like the metric collection may not work for the other regions.

[klai5]

I see. I am using us-west-2. Is there any way to make this work on other regions, or should I exclusively use us-east-1?

[SooLee]

I'm fixing it now.

[SooLee]

@klai5 It should work with 0.17.3. It requires redeployment. Thanks for reporting it and sorry about the problem!

tibanna deploy_core -n check_task_awsem [-g group] [-s suffix]

[SooLee]

@klai5 You should be able to get the metrics for the current job using tibanna plot_metrics -j <job_id> without redeployment.

[klai5]

Looks like it works! Thanks!