HPCC Operation During COVID-19 Crisis

Since the research computing infrastructure of the HPCC is designed to be accessed remotely, we are currently not expecting any major downtimes or restrictions for users due to the campus access restrictions caused by the COVID-19 pandemic. However, even this may change depending on the extent of the restrictions our university may have to implement. A few exceptions that are currently in effect for the HPCC facility are the following:

  • Our offices in 1208/1207 Genomics Building are closed. The HPCC staff will continue to work as usual but exclusively via remote access from home.
  • All in person contacts such as office visits or in-person training events are not possible during the current COVID-19 crisis. Alternatively, we will be offering remote training sessions via video conferencing using Zoom.

If users need to get in contact with us then please email your questions to support@hpcc.ucr.edu. For immediate help, users can also post questions on Slack (ucr-hpcc.slack.com). For latest news and updates, please also visit us on Twitter. With some delay, updates will also be posted on this website’s News and Alerts pages.

Unannounced exceptions

None currently observed.

For the most current information on short-term exceptions of the cluster please consult the HPCC Twitter site. Also see the Tweets window at the bottom of this and other pages of the HPCC website. Additional information and updates on exceptions may be posted here.

Scheduled exceptions and downtimes

None currently scheduled.

Standard Operating Procedures

SOP for unscheduled outages

When unforeseen issues arise they are categorized by severity:

  1. Green - Normal operation, no current issues
  2. Yellow - Minor issue[s], likely not observed by users (ie. jobs are not affected)
  3. Orange - Medium issue[s], likely observed by users but not fatal (ie. jobs may perform slower than usual)
  4. Red - Critical issue[s], major service or entire cluster is not functioning as expected (ie. jobs have terminated prematurely)

Email notifications are only sent to users if there is a Red critical issue.

SOP for scheduled shutdowns

The following outlines the timeline for advance email notifications on scheduled shutdowns of the HPCC cluster and other exceptions:

  1. Four weeks advance notice
  2. Followed by weekly reminders
  3. Final reminder the day before the outage

Team collaborations with Slack

Sign up and use Slack Team Collaboration app here: ucr-hpcc.slack

Past exceptions

22-Mar-2020: HPCC server room not accessible due to network outage on campus

Due to a campus-wide network outage at UCR, many HPCC services were not accessible between 8:00 AM and 1:00 PM. Currently, most HPCC services are accessible again. Note, running jobs on the cluster should not have been affected by this disruption. Updates about the current situations can be found here.

13-Mar-2020: Routine maintenance shutdown

We have scheduled an HPCC Cluster Maintenance Shutdown for Friday, March 13th. This will require a shutdown of ALL services: Slurm (queuing system), hosted websites, virtual environments/machines, storage systems, backup systems, and network services. We ask that you please make sure that you do not have any jobs running in the queue, and that you completely logout of the cluster (pigeon, pelican, parrot) before the shutdown.

08-Jan-2020: Storage outage

We had some issues with our storage systems this evening that may have caused disruptions in your work. These issues should be resolved. We’re continuing to monitor the situation to ensure everything is operational, and we apologize for any inconveniences this may have caused. Please let us know at support@hpcc.ucr.edu if you require any assistance regarding job status and recovery.

21-Nov-2019: Routine filesystem maintenance and diagnostics

We have scheduled an HPCC Cluster Maintenance Shutdown for this Thursday, November 21st. This will require a shutdown of ALL services: Slurm (queuing system), hosted websites, virtual environments/machines, storage systems, backup systems, and network services. We ask that you please make sure that you do not have any jobs running in the queue, and that you completely logout of the cluster (pigeon, pelican, parrot) before the shutdown.

23-Aug-2019: Routine maintenance shutdown

We have scheduled an HPCC Cluster Maintenance Shutdown for Friday, Aug 23, 2019. This will require a shutdown of ALL services: Slurm (queuing system), hosted websites, virtual environments/machines, storage systems, backup systems, and network services. We ask that you please make sure that you do not have any jobs running in the queue, and that you completely logout of the cluster (pigeon, pelican, globus) before the shutdown. Status: completed. For user changes related to this maintenance please see here.

01-Mar-2019: Routine Maintenance Shutdown

We have scheduled an HPCC Cluster Maintenance Shutdown for Friday, March 1st. This will require a shutdown of ALL services: Slurm (queuing system), hosted websites, virtual environments/machines, storage systems, backup systems, and network services. We ask that you please make sure that you do not have any jobs running in the queue, and that you completely logout of the cluster (pigeon, pelican, globus) before the shutdown. Status: successfully completed.

1:00 PM, 20-Dec-18: Outage due to AC failure

All systems were down for 3 hours due to a failure of the AC units in our server room. Electricians and AC technicians have repaired the units.

2:30 PM, 11-Jul-18: Storage Issues

For the past several weeks we have been observing slower storage access. In some cases the /bigdata storage was inaccessible for several minutes and caused some jobs to terminate prematurely. We have identified the issue and have taken steps to ensure that this problem does not reoccur.

6:00 PM, 02-Jul-18: Storage Issues

Storage issues on the afternoon of July 2, 2018 caused disruptions in some cluster services. The issues should be resolved, but we’re continuing to monitor the situation for any other developments.

12:00 AM, 31-Jan-18: routine maintenance shutdown

For routine maintenance and upgrades we have scheduled an HPCC (Biocluster) shutdown for 12:00AM, Jan-31-2018 to 12:00AM, Feb-01-2018. (complete)

12:00 AM, 05-Dec-17: NFS & SMB issues

NFS and SMB services have been suspended temporarily. This will cause many of our web services to not function properly. These include, but not limited to:

  • https://rstudio.bioinfo.ucr.edu & https://rstudio2.bioinfo.ucr.edu
  • https://galaxy.bioinfo.ucr.edu
  • https://dashboard.bioinfo.ucr.edu
  • https://biocluster.ucr.edu/~username (.html directories)
  • mysql://bioclusterdb.int.bioinfo.ucr.edu (databases)

Note, this issue was resolved soon after it occurred.

11:00 AM, 13-Aug-17: Cooling problem

Since Sat morning one of the HVAC units is not working properly. To avoid overheating, we have shut down most of the idle nodes (1:30PM, Sun). As soon as the HVAC unit is repaired we will power these nodes back on. Note, this issue was resolved on 17-Aug-17. UCR facility services has repaired the broken HVAC unit and serviced the second one.

12:00 AM, 16-Jun-17 to 17-Jun-17: maintenance shutdown

To sustain future growth, the power load in the HPCC server room needs to be optimized. For this we have scheduled an HPCC (Biocluster) shutdown in four weeks from now which will start at noon on June 16th and last until noon June 17th. This will require a shutdown of ALL services: Slurm (queuing system), hosted websites, virtual environments/machines, storage access, backup systems and network services. We ask that you please make sure that you do not have any jobs running in the queue, and that you completely logout of the cluster (pigeon, owl, penguin, pelican, globus) before the shutdown.

10:02 AM, 13-Apr-17: UPS failure

Our UPS unit went down some time last night causing a power failure on all systems. Jordan is bypassing the UPS to bring things back up in the next few hours. Nationwide Power will come in asap to repair the UPS. Note, this failure has not resulted in any overheating problems since the AC units are running on a different power cricuit.

11:22 AM, 13-Apr-17: Cluster back up running

Situation is resolved for now and things are working. We are currently discussing the situation with our electricians to avoid future instances.