Changes to Galaxy-qld

Galaxy-qld is getting popular, with over 900 registered users. The server is crunching the data 24/7. Demand for computing resources is rising rapidly, and at times Galaxy-qld runs at full capacity, without any spare compute resources. User activity goes up around noon (Brisbane time) and remains high until late evening. We maxed out the available resources, both in storage and CPUs, and introduced changes to the server to improve performance. Since today, the registered users can run up to 12 concurrent jobs, including four concurrent jobs required 5 CPUs (most aligners, some tools from Cufflinks and GATK2 packages).

Performance of the server also can be improved by better user practice. If submitted jobs are queued for long time, check @GVL_QLD updates on Twitter. The updates are accessible to anyone through the link. There is no need to have an account on Twitter to see the feed.

Do not delete and resubmit the queued jobs. The submitted jobs will be completed eventually, usually overnight. It is ok to submit other jobs, if you have queued jobs.

Not all jobs are identical. All assembly jobs run on 16 CPUs and need a whole worker node. These jobs tend to stay in the queue for a long time. Simple jobs such as filtering, FastQC or FASTQ Groomer use a single CPU and sneak into any available slot. Most aligners use five CPUs and also tend to queue for some time.

Advertisements

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s