usegalaxy.org job length

Question: usegalaxy.org job length

4.3 years ago by

lynny • 20

United States

lynny • 20 wrote:

Greetings,

I used the join command at usegalaxy.org and would like to know how long the job ran:

Tool: Join
Name:	Join on data 1 and data 2
Created:	Fri Jul 25 11:47:19 2014 (UTC)
Filesize:	52.7 MB
Dbkey:	hg19
Format:	interval
Galaxy Tool Version:	1.0.0
Tool Version:
Tool Standard Output:	stdout
Tool Standard Error:	stderr
Tool Exit Code:	0
API ID:	bbd44e69cb8906b5718132ea354f613b

The links to stdout and stderr are to blank pages.

Can I access a log that tells me how long the job ran?

Thank you,

Lynn

utility galaxy • 928 views

ADD COMMENT • link •

modified 4.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.3 years ago by lynny • 20

I wanted to know the run time for some jobs too, but as far as I've been able to figure out, there is no way to tell how long a job ran from the user end of things on galaxy (if anyone else has found otherwise, please correct me!).

ADD REPLY • link written 4.3 years ago by Suzanne Gomes • 120

4.3 years ago by

Martin Čech ♦♦ 4.9k

United States

Martin Čech ♦♦ 4.9k wrote:

This feature currently does not exist. I believe we have the information in the database but it is not accessible through the UI.

It is one of the priorities for coming releases.

ADD COMMENT • link written 4.3 years ago by Martin Čech ♦♦ 4.9k

4.3 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Certain tools now have an option included to report the mapping time (example: Bowtie2 (correction from Tophat2 - that will be coming soon!)). This is found in the full parameter settings, near the end. Please keep in mind that this does not include queue time. The public server is often busy - but how busy is the important bit.

Execute the job and see, it will vary, expectedly. Then permit the job to run to completion without stopping/restarting, or you will lose your original place in the queue, extending wait time.
http://wiki.galaxyproject.org/Support#Dataset_status_and_how_jobs_execute

Queue time is dependent on these major factors: the type of job you run (compute intensive jobs, often found in tool groups staring with an "NGS", go to our busiest queue - due to the jobs often executing for the longest time period), how many other users are also using the public Main instance (http://usegalaxy.org) or other Galaxy - if not using a local/dloud, and how many jobs are queued to execute prior to this one in any of your histories (prioritize if work is urgent). This wait time is difficult to predict, of course, but our team (and extended team) has been discussing methods, and our new configuration at TACC this past year offers more potential.

This all said, Main can very often be quite speedy. When you happen across such a window, it is a very good time to launch a workflow.

Hopefully this helps you both, Jen, Galaxy team

ADD COMMENT • link modified 4.3 years ago • written 4.3 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Jennifer,

Thank you for the response.

We are very grateful for public galaxy and are simply interested in a benchmark of the join command.

We would like to see the total time elapsed and the time used to execute the command.

Warmly, Lynn

ADD REPLY • link modified 4.3 years ago • written 4.3 years ago by lynny • 20

Hello Lynn, Adding run time for all tools is a priority in the upcoming releases. However, keep in mind that run-time on our cluster/database configuration may differ from yours, and that this particular command is sensitive to the size and composition of the inputs. If this benchmarking is intended for anything other than use on the public Main instance, you might want to run this on the cloud or local Galaxy it will be executed on (in bulk?), with your actual data (samples - small and large), to get a truer sense of timing. Best, Jen, Galaxy team

ADD REPLY • link written 4.3 years ago by Jennifer Hillman Jackson ♦ 25k

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