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New Ceph Storage Hardware for iDigBio

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  • Thursday, September 20 2018 @ 08:56 am EDT
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Fun Stuff @ Work

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The Advanced Computing and Information Systems Lab where I work recently aquired new hardware to support the storage needs of iDigBio.We operate an open source Ceph cluster to provide object storage for media and datasets. iDigBio was too successful at mobilizing digital media about museum specimens... the original storage cluster is full!

The new hardware is racked and has received the base OS (Ubuntu 18.04 LTS). Ceph makes RAID obsolete, but to get the best utility out of the hardware we needed to flash each LSI controller with "IT" firmware. IT in this context means Initiator Target (also known as passthru). Ceph guides suggest IT/JBOD configuration in the storage controllers to maximize performance and to prevent crappy controller caches from interfering with Ceph's own redundancy.

Our servers from Supermicro include the LSI Logic / Symbios Logic SAS3008 PCI-Express Fusion-MPT SAS-3 adapter. Each host also contains 11 storage drives at 12TB each (plus an SSD for the boot drive), 16 cores of Xeon Sky Lake processor, a whopping 256 GB of RAM, and 10 gig ethernet plugged into the University of Florida Campus Research Network (CRN).

Here are pictures of myself and Nicholas Rejack doing the firmware updates:


Photo by Grace Hong


Photo by Grace Hong

The new cluster contains over 900TB raw, getting us close to a Petabyte.

I am now working through SaltStack and systemd configurations, working up to the point where we can actually begin migrating objects from the old cluster to the new cluster.

We are Hiring a Front-end Developer

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  • Wednesday, September 16 2015 @ 04:02 pm EDT
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My department at UF has a job opening for a Front-end Developer. This is the blurb that I sent to various tech-oriented mailing lists.

It appears that the initial posting duration is rather short (closes 30 Sep 2015).


OFFICIAL JOB POST:

  http://explore.jobs.ufl.edu/cw/en-us/job/493532/it-expert


The official information is at the above jobs link but I'm including more info below (from my own perspective) to hopefully answer most of the questions people might have about the position.

The position is located in Gainesville, Florida.


OVERVIEW:

Job Opportunity for a "front-end developer" (IT EXPERT) in the Advanced Computing and Information Systems (ACIS) Laboratory at the University of Florida to work on iDigBio, the National Resource for Advancing Digitization of Biodiversity Collections funded by the National Science Foundation.  Integrated Digitized Biocollections (iDigBio) enables data of millions of biological specimens to be used by the research community, government agencies, students, educators, and the general public.

Within the University of Florida, ACIS is housed under the Department of Electrical & Computer Engineering which is part of the College of Engineering. The ACIS Lab conducts fundamental and applied research on all aspects of systems that integrate computing and information processing. Current ACIS research falls under the broad categories of Cloud Computing, Cyberinfrastructure for e-science and e-health, Autonomic Computing, Computer Architecture, and Peer-to-peer Computing. 

ACIS is responsble for implementing the Cyberinfrastructure components of iDigBio.

More info:
  ACIS -   https://www.acis.ufl.edu/
  iDigBio -   https://www.idigbio.org/

Standing At Work

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  • Wednesday, January 21 2015 @ 08:42 am EST
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I have been standing pretty much full-time at work since 2011 and I am still quite happy using my Custom-Built Standing Workstation in my current job.

I do have my laptop on the lower desk surface in case I need to sit down, such as after a particularly hard morning running workout. However, I tend to only sit down at meetings and meals during the work day.





Today I was rocking my Skora shoes which are zero drop (no elevated heel) as are all of my shoes these days. I have no need for knee, hip, or back pain thank you very much.

Custom-Built Standing Workstation

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  • Friday, March 21 2014 @ 07:12 am EDT
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I have been standing at work since 2011. In January I started my new job and quickly felt the impact of sitting all day... sore back, stiff knees and ankles, basically feeling crippled. Whereas my last job had an adjustable desk surface and all I needed to do was add an LCD shelf, my current desk has a fixed-height surface.

I researched the standing workstation options that are available. Most of the "add-on" standing workstations or desks out there have the same fatal flaw... they put the monitors on the same surface as the keyboard. For proper vertical posture with the head level and the neck not bending down, the monitors need to be elevated so that the top of the screen is at eye level.

The Ergotron Workfit Sit-Stand is now priced under $400 and would be a really great option for a lot of people. There are also various IKEA furniture hacks that I considered. Instead, I decided to build my own out of scrap wood from my garage. I only spent money on spray paint and the LCD mounting arms.

The platform that I built is heavy and strong enough to allow a "c"-clamp style LCD mounting arm to attach. It is also robust enough to hold a conventional keyboard tray so I have also been able to fine-tune the position and angle of the keyboard and mouse.

If my legs, feet, or back get tired I still have a seated desk area and my laptop available.





I bought the dual-monitor LCD arms from Amazon for under $50. The only real issue with these is that they had a tendency to slide down the pole over time or as they are being adjusted. I fixed this with a quick hack of drilling in a self-tapping metal screw as pictured here:

New job - iDigBio Data Integration Expert

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  • Monday, March 17 2014 @ 06:28 am EDT
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In January I started my new position with the UF Advanced Computing and Information Systems Laboratory (ACIS) to work on the national Integrated Digitized Biocollections (iDigBio) project. This multi-institutional project is funded by the National Science Foundation to build a "National Resource for Digitization of Biological Collections" or as I sometimes describe it... "the big biological collection database in the sky". ACIS is responsible for designing and developing the middleware, supporting storage, and cloud infrastructure for the project.

I am now working For Science!



One of the things that I am enjoying so far is that I am able to take time for blade sharpening. Stephen Covey of "7 Habits" fame called this habit Sharpening the Saw.

I am also happy to get some exposure on a lot of new (to me) tech such as Elasticsearch, Reddis, Nodejs, Riak, OpenStack SWIFT, and Ceph.

Here is a short video about iDigBio:



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thatlinuxbox.com is the home of Dan Stoner's Personal Blog, Photos, and More (opinions, rants, techno-babble, and possibly a few useful tidbits of knowledge).

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