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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Because not all of you know me behind the walled garden that is Facebook, I am leaving this post I made last night here for everyone else. As I state further down, I have no interest in the dialogue it generates, personally: I disabled notifications to the post, and I refuse to go back and look at what transpired because of it (I was too emotionally distraught to be bothered with figuring out how to lock the post from commenting at the time).

In similar fashion, I am disabling comments on this post. But I leave it here for any others to see, as I am not comfortable with the idea of making it public on Facebook, because I see what happens with posts that go viral there. I absolutely what none of that.

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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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Sometimes you just have to hover around in a holding pattern until you figure out what you’re doing. Keep the day-to-day operations running, right?

It’s just a problem when you’re stuck in a holding pattern, and the day-to-day eats up most of your resources. You keep running out of steam, and lose the energy to negotiate the bigger stuff.

How the hell does one get a proper recharge in to deal with that stuff? Every time I get a decent mental decompression, something else just eats up all the time right afterwards. Or I don’t even get that much of a mental break, because I’m already worrying about more stuff. Uffda.

I think I’m just lost in a loop of worrying about self presentation more than self preservation. Why must this be so difficult to stay focused on?

…and on that note, I’m going to go hide from reality in the youth of my Nintendo DS & some 2007-era game.

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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