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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Poor Victoria has been attempting to slowly kick the bucket over the years. I already had to replace the power supply in the Mac Pro once before, and she’s been running solidly since. With the exception of my WiFi signal to the router upstairs in my landlord’s part of the house. If you follow me on Twitter, then you’ve likely seen at least one of my outbursts over the shitty connectivity I used to have with it (and in doing so, ruining the connectivity for the rest of my apartment unit).

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As I’ve mentioned previously, some of the command line tricks for batch processing PDB coordinates for electrostatics models throw some errors back at you, although they don’t implicitly prevent you from using APBS. They just make the surface models look a bit ugly, as you’ll have conflicting charges confined in an unnatural environment, yielding bizarre electrostatics representations (I’ll have to generate an image sometime).

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So, in a slight change of events, instead of the typical personal blog posts I’ve been doing lately, I feel a need to make a more technical one. Either for others’ benefit or for my own, in the event I happen to lose said notes on how to do this stuff. In any case, these are the summation of online searches, trial & error, and a bit of ingenuity in other random spots, all directed towards the generation, editing, and mapping of surface electrostatics maps on structural models of crystallized proteins. I’ll drop in cited links when I can, pending whether or not I can track some of them down again!

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