Adventures in Linux hosting: Getting Ubuntu onto my home Dell T30

My MacBook is between the new Dell T30 and my monitor. You can see the USB stick attached to the MacBook where I burned the ubuntu ISO

Thanks to the USPS for delivering on a Sunday. The new T30 arrived today at around 10AM. As I suspected, the contents are just the main box and a power cord. I went to Best Buy and picked up the cheapest USB2 keyboard and mouse I could find (there were probably some of these lying around the lab, but I bought new). I borrowed the HDMI cable we were using for the Apple TV, and hooked up to a monitor.

Cntrl-alt-delete reboots. Holding down F2 gives the Dell system management software.

Set up a USB stick for installation

I found the basic installation documentation kind of confusing. So I started with the steps in this tutorial: Create a bootable USB stick, on macOS.

  • Download Ubuntu Server 16.04.3 LTS from: https://www.ubuntu.com/download/server
  • Download Etcher. This is recommended for burning the image onto the USB stick. When Etcher is done, the MacBook complains about the inserted media not being readable. Just eject it.

Putting this stick in the USB port didn’t allow it to boot. But a clue comes from the last screenshot of the tutorial where the stick is shown as an EFI boot. Changed the Dell to look for UEFI boot. Now I get an installation option for Ubuntu when I reboot.

  • Used defaults except
    • to unmount before writing partitions.
    • automatically do security updates
  • Network failed until I plugged an ethernet cable into the back connected to the Airport Time Capsule.
  • Software selection
    • standard system utilities
    • OpenSSH server

After doing this and rebooting, I had to go back to the Dell system config to switch back to legacy boot instead of UEFI. But once I had done that, I get a boot into Ubuntu and I can ssh in using the local IP address.

Shut it down to move it to a better location in the living room instead of the dining room table. Now it’s running with no keyboard, mouse, or monitor and I can ssh into it from my MacBook.

Update: The Dell documentation talks about using their LifeCycle Controller to install an OS. But this doesn’t seem to come on the T30.

Adventures in Linux hosting: Development setup at home

One option to do my self-designed Linux education would be to do everything in VMWare. But while I’ve done that in the past, it hasn’t taught me what’s going on when we’ve had problems with our existing boxes where the IT people tell me that they had to do something with the kernel, or when I’ve had to reboot and watch the stream of warnings or worse on the local monitor before Ubuntu even loads.  I suspect that some of that has to do with a long-gone IT employee screwing up the initial installation, but I’d like to understand it better.

So, with computers being reasonably cheap, I decided it would be fun to set up a version of our websites on our home wifi network, not accessible to the outside world. Yesterday I ordered a Dell PowerEdge T30 Business Mini Tower Server System, and was pleasantly surprised that it had free shipping to arrive on Christmas Eve. The system comes with 8 Gb of RAM and a 1T HD. Eventually, I will probably upgrade both of those if I can (I think it’s possible with this model), but even with that base configuration it’s comparable to what we are currently using on our Macs. 

Debby has gone to visit family, leaving me to look after the cats in Texas. This will be an opportunity for a nerdy Xmas break! Off to read Ubuntu manuals…

Update:

The first question even before the thing arrives is about the appropriate installation. The Pentium G4400 dual core processor on the box I ordered is cheaper than the Xeon alternative. It seems that it falls under the Intel EM64T category of processors, even though the string “EM64T” doesn’t show up on the Intel page for that CPU.

Time for me to get more serious about Linux

My group started into bioinformatics thanks to former students Hai Zhu and Leonardo Marino-Ramirez, who set up the first LAMP webserver in the lab, a box they made that we called tofu.tamu.edu. Being Mac users, we thought that the Unix roots of OSX would be useful in the transition to doing informatics and web-based resources, so I purchased a G5 XServe  which started a series of machines we named based on protein quaternary structure. It was called dimer.tamu.edu. As the EcoliHub/PortEco/EcoliWiki projects got funded and we got some stimulus money to work on B. subtilis, we gradually added to our collection of machines. trimer and tetramer were intel XServes. hexamer was the last version of the Apple Intel Xserve shipped by Apple. Meanwhile pentamer and heptamer were linux boxes running Ubuntu. For the most part the heavy work was done on the Macs, and we even moved GONUTS to run on a mac mini after one of the Intel Xserves died.

One of the things I liked about the XServe setup when we first got dimer was the way we could do server administration via the Server Admin and Workgroup Manager apps. But as the machines aged, and the older ones were not supported on newer OSX versions, Apple did something annoying: they made Server Admin incompatible with older OSX releases, even though it was pretty obvious that it was just a pretty front end to send unix commands and show the outputs in the GUI. So I gradually started learning how to do various system admin tasks via the terminal; there are some I’ve never figured out how to do completely without the GUI, though.

The rack mountable blade servers stopped supporting updates with Snow Leopard. We’ve kept the TAMU IT security people at bay by running MacPorts to replace obsolete packages, but it’s gotten to the point where time to give up on the Mac servers and migrate everything to Linux. My department prefers Ubuntu, so that’s the way I’m going to go.

In the long run I expect we will move from our own hardware to A&M server virtualization or maybe something like Amazon. But for now, I’m not comfortable with the capability and price for our own hosting, and there are issues with URLs and domains for moving some of our sites off campus.

Rain chains

We had rain chains installed as part of a recent remodel of the front of the house. It rained pretty hard last night and was still raining this morning. This video illustrates some problems with the installation.

It looks like the connection to the gutters isn’t actually feeding the flow onto the chain. This leads to a lot of splashing and erosion around the drain at the bottom.

 

Pichanha sous vide

We like to watch cooking competition shows and last week was the semifinals and finals of MasterChef Junior. In the semis, one of the young chefs made rib cap. The rib cap, aka deckle, comes from the area around ribeye or prime rib in the forequarter of a carcass, and is regarded by some as the best cut of all. When shopping at the Rosenthal meat center on Friday, I didn’t find rib cap, but I found sirloin cap, which is similar in being the cap part of a cut, but different in coming from much closer to the back end. When cooking beef sous vide, I like the way extended times allow cheaper cuts to retain flavor while being cooked medium rare. But I also had “cap” on the brain, so I picked one up. 1.83 lb at 4.69/lb.

Sirloin cap is also known as pichanha, which is prized in Brazil. There’s a Brazilian steakhouse in Philadelphia called Picanha (never been there, just saw it in the Google results). Picanha is often the thing that’s curled into a C shape and roasted on a spit in churrasco style cooking. When cooking that way, the fat is left on to render over the hot coals.

For my purposes, I trimmed a lot of fat off the cap, salted the meat, and did my usual 135F bath with a splash of soy and fish sauce. Started around 2:15 PM.

It’s not very creative, but I thought I’d make a chimichurri to go with this. Looking at recipes I didn’t realize that cilantro isn’t used in classic chimichurri; it’s based on parsley and oregano as the green herbs. So, parsley, garlic, salt, oregano, red pepper flakes, olive oil and red wine vinegar went into the food processor.

It was around 8:30 by the time we were ready to pull it out of the water bath. I vacillated on how to sear the thing. It’s not close to flat, and still had a layer of fat on the cap side, even after trimming a bunch of
fat. I ended up starting it in a cast iron pan, then putting it under a broiler, then finishing it back on the stovetop using tongs to hold different faces on the heat. Rendered a lot of fat. I think the broiler step wasn’t much of a help and holding the meat on the pan with the tongs was probably enough.

Served with roasted baby potatoes, chimichurri, and plantain chips.

This came out really well. The meat was pinker than it looks like in the photo, and it was tender and flavorful.

Food processor Chocolate-Cayenne cake

It’s Debby’s birthday, so I decided I should make a chocolate cake. This was a last minute decision, and I wanted to try something more conventional than the chocolate genois cakes I’ve done in the past. But, lacking a stand mixer, I also didn’t want to do the whole “cream butter and sugar” think either.

Nigella Lawson had a recipe in the NYT a year ago that involves throwing all the batter ingredients in a food processor and blitzing it all together. That sounded easy, but I was thinking I’d tweak it in a couple of ways. First, following the general principle of making muffins, I’d do the wet stuff and dry stuff separately and mix at the end.

Wet works:

  • 2 eggs
  • 1.5 sticks room temp butter
  • 0.75 c buttermilk/yogurt (sub for sour cream in the original). I had some buttermilk that needed to be used up.
  • 2 t vanilla extract
  • 1 c sugar. OK sugar is a dry ingredient, but I want it to dissolve.

Dry stuff. Sift together:

  • 1.5 c flour. I used 1 c cake flour and 0.5 c all purpose. Not sure if that mattered.
  • 0.33 c cocoa powder
  • 1 t baking powder
  • 0.5 t baking soda
  • 1 t kosher salt (not in the original)
  • 0.25 t cayenne pepper (not in original)
  • 0.25 t cinnamon (not in original)

Processed the wet stuff in the food processor. The butter didn’t really fully incorporate at this step, it looked like curdled eggs. But that was resolved by adding the dry stuff and processing until smooth. The consistency was thicker than I expected. It was reminiscent of soft-serve ice cream.

Transferred to a 9″ ringform, buttered, floured, and with a circle of parchment on the bottom. I had buttered it to make sure the joints were sealed, but that wasn’t an issue with this batter.

Baked in a 350 F oven for about 50 minutes. I had set a timer for 35 based on the original recipe, which is for 2 8″ pans. Kept it going until a toothpick came out clean.

The cake had a distinct dome shape. If/when I do this again, I’ll try some of the tips from this site, starting with lowering the temperature and backing longer. The cake cooled while we went shopping and made dinner (Pan-fried Dover Sole in lemon butter with roasted baby potatoes and green beans) and watched the season premiere of series 10 of Doctor Who.

With the video on pause, and Debby feeding the cats, I brushed some framboise on to the cake and dusted it with powdered sugar. We weren’t in the mood for frosting. Served with some lactose free Breyers vanilla ice cream and some raspberries.

I think it was pretty successful. The chocolate flavor was strong from the cocoa powder and the cayenne and cinnamon added some nice warmth to the flavor. The texture was light, tender and cakey. On general principles, more liquor might have made it even better.

If the tips to make it flat work, this could be a nice base for a fancier presentation.

Sous vide black bean ribs

I had purchased some pork spareribs intending to try one of the previous rib recipes I’ve posted here, finishing them on a gas grill instead of in the broiler. But I procrastinated getting them marinated, and it’s been a rainy day here in College Station, so I decided to try a sous vide version of braised or steamed black bean ribs. I’ve made something like this in the microwave before, but the unattended timing of sous vide seemed like it would be worth trying.

Anova has done a sous vide version. I used their 167F temperature but improvised the rest based on what I’ve done before and what we have around on a day when we need to shop for groceries.

  • Ribs – cutting these into the desired shorter chunks was a pain (not having a bandsaw), so I only did some of them
  • Splash of soy
  • A handful of minced fermented black beans
  • minced ginger
  • Splash of fish sauce
  • Splash of dry sherry
  • Spoonful of chiu chow chili oil

Bag the whole thing and throw it in at about 1:15 PM on Sunday. Took them out and thickened the cooking liquid a little with corn starch, then served with rice.

It was pretty good, but a bit on the bland side. When I do this with chicken, I brown before braising. Neither recipe I looked at does that, but maybe it would have helped. Longer pre-cook marination, as recommended, might also have been good.

MacBook Pro connection confusion

Migrating from my old MacBook Air to my new 2016 Macbook Pro has involved some confusion about adapters and accessories. Overall, I like my new Macbook, but there have been a number of annoying things. The biggest is still Apple’s decision to kill the MagSafe power connector. More minor annoyances:

  • Out of the box, the brick used to come with a 3 prong extension in addition to the stubby 2 prong power connection. Now it’s extra.  The longer cable on the brick end is really valuable when you have a bunch of people (e.g. at a conference or students in a class, or even at an airport waiting area) sharing a wall plug or power strip. Fortunately, I can recycle a bunch of these from my old power bricks that don’t work anymore for the new MacBook.
  • If you buy the power brick you now have to buy a separate USB-C charge cable.  As far as I can tell, this should work with a generic USB-C cable. What was annoying here was buying a power supply at an Apple Store and not having the Apple employee ask if I needed the cable.
  • The original Thunderbolt was a superset of MiniDisplayPort, and Thunderbolt 1 and 2 used miniDisplayPort connectors.  There is a Thunderbolt 3/USB-C to Thunderbolt 2 adaptor, but although Thunderbolt 2 is a superset of MiniDisplayPort, the adaptor works for Thunderbolt connections but not for miniDisplayPort-based adaptors. In other words, plugging a Thunderbolt Display (discontinued in 2016, but some of us still have various versions) in works. What doesn’t work is MacBook-Thunderbolt adaptor-miniDisplayPort to VGA or HDMI adaptor-monitor.
  • If you want to sync an iPhone or an iPad to your MacBook Pro, you will need either a USB-C to lightning cable or a USB-C to USB-A adaptor. This means that if you buy a brand new MacBook Pro and a brand new iPad, you can’t connect them right out of the box. The USB-C to Lightning will allow you to use the MacBook power brick to charge an iPhone or iPad with or without the MacBook in the middle, so that could reduce the number of things.