So in the attempt to upgrade my storage/file server with some new hardware, I unintentionally (albeit intentionally when I ordered the parts months earlier) broke the CompactFlash to PATA solution I was using to serve as a boot drive for the operating system (FreeNAS). Long since I last updated FreeNAS, it came to my attention that the project has evolved from FreeBSD 7 onto FreeBSD 9, and taken on the new name NAS4Free. Since I obviously needed to reinstall my operating system for the server on a new device, and FreeBSD 9 drastically updated the ZFS feature set present in this NAS distribution, it only made sense to drink the Koolaid and upgrade to NAS4Free. Unfortunately, in doing so, I have had to take in and utilize a lot more of FreeBSD’s native features to make this system workable to my own standards (despite NAS4Free claiming support).

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15. August 2012 · Write a comment · Categories: Grad Life · Tags:

My mind has been anywhere but one place lately. Being amidst the throes of finally finishing this PhD, I did not realize just how much extra crap came along with that. Instead of just finishing experiments, I’m doing that in addition to searching for post-doc opportunities and writing my thesis. Mark highly encouraged me to get as much (if not all) of the introduction done while I’m finishing up experiments. However, the frustration over just trying to get normal cDNA synthesis off of some RNA preps is driving me crazy right now, in addition to staving off the last few of my experiments (qPCR analysis of ~8 strains over 4 different genes).

Unfortunately, I could only wish that that was the extent of my mental spread. Here at home, I’m trying to deal with the craziness of Cori’s dog, who can be a real hellion when he wants to be. That is of an off-and-on nature, and more than anything just sours the mood I’m in if anything, because he seems to bipolarly swing between a sedated, relatively tolerable dog, and an insane brat with no regard for listening to anyone. Add that in with his tendency to overreact to any aggressive-like activity/motion/action, and I’m spending far more time concerning myself with what actions that I’m about to take than I probably should. However, he’s the sideshow to the disastrous ruin to my primary electronics at the moment.

At some point after moving into the new apartment, my Mac Pro started to have issues. It would spontaneously shutdown as if it was experiencing a thermal event (read: overheating), and the indicator lights on the mainboard indicated as much. The machine was far from being overheated, and other troubleshooting guides also dictated that this error can also be indicative of a failing power supply. Considering the power has been less than stellar in both this apartment and my last apartment, I figured it was finally time to get a line-conditioning UPS to help deal with power fluctuations. This appeared to have resolved the issue for a few weeks, but the problem has since returned. This evening, taking apart my Mac Pro once more to compressed air-blast out the heatsinks and power supply, I revisited booting it up again and watching the stability.

The system seemed stable enough. I was able to successfully rip another movie DVD to transcode it onto my file server, but I was watching the power supply temperatures in a paranoid fashion in the process. I typically keep an eye on this through the iStat Pro widget, but after reading some other forums on cooling issues in the pre-2009 Mac Pros, I fired up the full-blown iStat Menus to see the current draw in my system at the time. Upon closer inspection, I happened to notice a disturbing set of sensors: the CPU cores and the CPU heatsinks. The two CPU cores (this is a dual-processor system) were idling at approximately 65˚C, while their respective heatsinks were essentially at ambient (25˚C) temperature. Now, I know there is to be expected at least some difference between the two devices due to thermal transfer rates, but a difference of 40˚C (72˚F)?!? That’s just ridiculous! So, alas, it appears it is time for me to really gut my Mac Pro down to the motherboard, strip the heatsinks out, and reapply some thermal paste there. This won’t be an easy endeavor: I’m missing a tool necessary to unmount the heatsinks, and while I’m gutting everything open, it would apparently be in my best interests to reapply the thermal paste on the Northbridge chipset as well.

Oh. Did I mention I’m writing a thesis right now? Oh, yes, I did! And I need this machine for some of the structural renderings that I do, not to mention for designing figures in Adobe Illustrator. *facepalm*

To further complicate my electronics issues, I purchased upgrade components for my file server around 3-4 months ago and finally got to installing them about a week ago. Much to my dismay, I neglected to remember there was no PATA port on the motherboard. My entire FreeNAS operating system was on a CompactFlash card with an adapter running directly into the PATA port on the old motherboard. I no longer could use this after the upgrade, nor could I get it to boot from a CF->USB adapter. Apparently, the FreeNAS 7 project has since been renamed and updated to the NAS4Free project, with a full recoding of the OS off of FreeBSD 9.0, lending lots of new support to the project! Unfortunately, upgrading from FreeNAS 7 to NAS4Free was less than easily straightforward. But now that I had trashed being able boot my old FreeNAS 7 system, it seemed ironically convenient to make the upgrade now. So, for the past week, I’ve been trying to tweak that system into working again, so I can get back to backing up my lab documents on it and supplanting my evenings with the movies and television shows that I’ve transcoded from my discs to watch over the TV2 I have hooked up to the television. I’ll follow up with those issues a little more in the near future, as there is apparently little coverage of fixes for the bugs present in the NAS operating system so far.

So. To recap.

  • Busy trying to finish experiments.
  • Busy trying to troubleshoot early steps of final experiments.
  • Busy trying to write my introduction to my thesis.
  • Busy trying to figure out what the hell I’m interested in doing research on so I can properly scout for post-docs.
  • Need to start writing letters/emails to prospective post-doc mentors and get the interviews going.
  • Trying to keep my Mac Pro running, so I can use it to finish some of this lab experimentation/figure generation without incapacitating my poor little MacBook Pro.
  • Trying to get my file server going again so I can have some stress relief via some good ol’ cartoons when I get those moments of downtime.
  • Trying to learn more FreeBSD than I should have to in order to get NAS4Free running the way I need it to.
  • Trying to avoid getting chomped/bitten/otherwise maligned by the resident Eskimo doggie of the house when he’s well hydrated on Haterade.
  • Trying to lose some weight by biking to work, getting out and walking/running, and watching my diet.
  • Deciding what the fuck I still have to unpack, and what I should still leave packed, because I’ll likely have to move (again) for whatever post-doc position I take.

Honestly, I’d go bang my head on a wall somewhere if I knew I wouldn’t be wasting valuable time in doing so. I so so so SO can’t wait for this all to be over. And I do mean ALL of it…