20. November 2017 · Write a comment · Categories: Techie · Tags: , , , ,

Since the retirement of Google Reader, I had been itching for a RSS aggregator & feed reader for a while. While Vienna for OSX used to be a favorite when I had a desktop on close to 24-7, it could/would miss occasional posts once I started sleeping/powering down machines in their off-hours. I had been using Feedly for a year or two at this point, but was growing increasingly disenfranchised with their cloud-style model & push for pay-for services (accompanied with reduced free functionality).

Having surveyed some of the available open-source/self-hosting solutions, I finally settled on giving FreshRSS a try. Months ago, I attempted to set this up in a test jail on my FreeBSD sever to no avail, and abandoned the work until a couple weeks ago. About a month ago, I started experimenting with Linux (particularly Manjaro, an Arch derivative) as a potential desktop replacement.

With Arch running on a Raspberry Pi Zero W (to get more familiarized with the Arch/Manjaro ecosystem), I finally renewed my attempts to get this installed on a Linux platform (which had more documentation available). With substantially less problems, I was able to get it stably running & configured. Trialling it as a replacement for Feedly for a couple weeks, I was satisfied with its performance, even on the Pi Zero! Since I migrated my web hosting from Bluehost for this site and others to a VPS running FreeBSD, I now wanted to translate this self-hosted service from my private network to a production environment accessible from the Internet at large.

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Ever since I got my server started, it’s gone through various changes. It started on OpenSolaris, eventually got stable on FreeNAS, and finally matured into a more permanent FreeBSD.

With that, there has been some hardware changes, but moreso in the core guts of the machine. What hasn’t changed is the hard drives it has been running on. Unfortunately, they’re also running a tad long in the tooth. Dumping out the Power_On_Hours line from smartctl gives me a range of 30998–43674 hours (3.54–4.99 years). Yup. They’ve been powered on upwards of 5 years now.

Most of the drives are doing fine (Reallocated_Sector_Ct line is giving 0 for half the drives), but some of them are slowly accruing bad sectors (most are in the single digits, but I have two at 15 & 37, respectively). Unfortunately, these usually pop up overnight during the daily script FreeBSD runs from the smartmontools port, so by the morning, I’ve already gotten the email (example shown when you click through to the rest of the post) that the drive has been taken offline. Since these are all in a RAIDZ setup, a single drive loss is no big deal, but I do have to resolve the issue so the array does not remain degraded. After doing this over numerous incremental errors (out of a dozen read errors, I get maybe 1 or 2 reallocated sectors), I’ve semi-automated the process (although I need to write a better bash script to do this without intervention).

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I’ve been doing a horrible job of jotting things down here when I mean to, so I’m taking a stab at that again. I meant to jot down all my notes on getting GROMACS running with icc, OpenMP, and CUDA on my Mac Pro, but that’s been a few months since I did that now, and it’s drifted out of my head. So. Trying to take a new stab at this when I’m ‘hacking’ things (so to speak)…

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A few months ago, I finally got around to installing & learning NAMD for doing some molecular dynamics. Installation was (and has been) relatively easy. Leaning how to use it in the past was always a bit too much for me for some reason or another. However, at the encouragement1 of a new postdoc in one of the adjoining labs at work, I gave it another stab with much better results!

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In case you are a user of (free via MacPorts) PyMOL and haven’t heard the news, the upgrade to the latest Mac OS X release—Yosemite (10.10)—breaks the installation process. Which really sucks because you ideally need to reinstall the ports collection after upgrading (or fresh installing) to Yosemite. Thankfully, the port maintainer finally posted a temporary fix to get things working in the interim until the port can be properly updated. However, it may not be the most intuitive fix for everyone to employ.

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I mentioned that I was going to get around to talking about this stuffing I’ve made for years, so it’s about time I finally did so. It was passed down from a professor back at my doctoral institution. As part of it, you need to prep a pretty solid bird stock first, so let me detail that briefly.

You’ll need some dark-meat bird parts first, be it the neck (ideally) or thighs. Take three of them (mix & match as desired), put them in a pot or saucepan large enough to lay them flat, and fill the spaces & cover the turkey parts with onion, carrot, and celery (don’t need to chop it finely at all). Add a generous helping of sage, thyme, a bay leaf or two (if you have them), some peppercorns, and salt to your liking (I usually don’t bother), and then cover the whole mess with water. Cover it, bring it to a boil, then reduce it to a simmer for at least two hours (I let it simmer for three). Pull all the meat out (mind you, the meat will literally fall off of the thighs), and strain out the remaining parts by pouring the mix through cheesecloth. Once the vegetables have cooled enough to handle, mash them up a little (still in the cheesecloth) and then wring the last of the juices from the vegetables. So much more flavor hiding in there, so don’t neglect to do this step! Afterwards, feast on the delights of the amazing meat you’ve just prepared, and you have a batch of delicious stock!

Now, with that out of the way…onto the best part…the stuffing!

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Easter brought about another feast of food, as per usual. Any holiday that I can make a fancy meal for, I like to. Especially for company, but for myself if nothing else! Anyhoo. As with any bird-based meal that I prepare, I’ve got to make some stuffing. Fantastic stuff, this recipe.

I’ll be posting that in the near future, but I wanted to get working on some of the backlog of posts I’ve been meaning to do lately. With summer coming up soon, I’m slowly getting more & more of my evening time back, with the largest chunk coming back once I’m commuting via bicycle again! So without further ado, click on through for the deliciously smooth bacony-laced (although not bacon-laden…which is equally doable, clearly) mashed potatoes.

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