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Installing Linux

Forenote: Glyph wrote me wondering how I managed to get things so messed up. He wrote

First, let me tell you how this whole mess is _supposed_ to go. You put in the install disk, it brings up a nice graphical display. It asks you for your target disk - which the installer *does* see. You can then use the full OS (pidgin, gimp, emacs, python, whatever you like) while the installation takes place in the background. There's a menu, which looks like a cell phone "bars" icon, and works more or less like the Airport menu, for setting up wireless. You definitely shouldn't have to type "dhclient3" on the command-line! I've probably installed ubuntu 30 times over the past 2 years, and modulo a few minor problems with nvidia cards giving me distorted resolutions, it has always worked that way.
I have no idea about the hard drive issue, but it sounds like your post- installation woes were likely caused by using the "server" installation CD instead of the "desktop" one.
Thinking backwards, that's almost certainly what happened. When I went to the Ubuntu page there was the option of "desktop" or "server" options. I wanted to install servers like Apache and MySQL. I figured a desktop machine is for people who want a web browser and some applications, while I wanted gcc, the unix command-line tools, etc. that I would use when developing servers. Plus, it says that the LTS server version gets a longer support - 5 years instead of 3 for the desktop. (I did not get the LTS version; I'm explaining how I decided to choose 'server' over 'desktop'.) I figured that was the case because the end-user applications change more frequently than the relatively stable development software.

Nothing on the Ubuntu page described the difference between desktop and server. That's changed. If you look at the page now you'll see that the "desktop" option shows a picture of a laptop, the "server" option shows some rack mounted machines, and there's links for each saying "learn more". This changed about 10 minutes ago because when I started writing this update it still had the old layout. Looking back through archive.org's history, it seems the lack of a "learn more" was an anomaly. Eg, you can see it exists in the snapshots from: 12 June 2007 and 10 Jan 2007. Archive.org lists nothing for since June and now. A-ha! At least for now you can see what used to be on the front page here, or here's a screenshot to show I wasn't being completely an ignoramus:

Grrrrrrrrr......!


Pipeline Pilot is a visual dataflow system with a domain focus in computational chemistry. Because of it's very strong marketing background and good technology, it's made a big noise on the small domain I work in. I happen to dislike dataflow systems and think its popularity is a measure of how generally unusable (in the HCI sense) chemistry software is. And again, marketing works.

Pipeline Pilot is a big scary monster to some of the other vendors. As a result, Knime, which is a dual-licensed free/commercial package from a university group, also with a chemistry focus, is itself getting some attention. A few people have asked me if I've looked at it, and I haven't. But I'm a consultant and perhaps it's something I should know about so people will give me money.

Which reminds me, I do more than consult for computational chemistry, so if you're looking for an experienced Python developer based in Göteborg, Sweden, email me. (After the fact: but obviously don't hire me as a system administrator :)

My primary machine is a Mac. I used to have a Thinkpad 600E (or some number like that) which worked out pretty well. I upgraded to a T23 but ended up with lots of programs getting Linux installed on it. My girlfriend at the time, a big Mac fan, helped convince me to get a Mac. I've not looked back sense.

Sometimes I need to go back. There is after all software that doesn't run on a Mac. One is Knime. It's written Java but there's some conflict between the AWT and the Eclipse SWT that means it doesn't work on my machine. When I visited friends in the US over Thanksgiving I pulled out my old T23 which I had stored in their garage. Perhaps I could use that to run the Linux version.

I tried to boot it but it didn't find the hard disk. Strange. Wonder if the disk went bad. I took it with my back from the US and since bad contacts are an easy problem to fix I did the first trick of pulling things apart and putting it back together again. Nope. Didn't work.

I made a install disk for Ubuntu Linux (Fiesty) to see what that would tell me. Went through the first few screens but couldn't find a disk. To be correct, it couldn't figure out which driver to use for the disk. My translation: disk is bad or hardware to the disk is bad. I figured the first case was more likely and went looking for a replacement. First step was to a local computer repair shop. He said (in Swedish as his English wasn't good), "yes, the disk is bad."

I went to a computer store on Hisingen (that's the island immediately across from downtown) and asked about getting a new hard disk. They didn't have any in stock that would work and suggested I go to another computer store somewhat nearby. He showed me where on the map but I had never been there, it wasn't easy to go to without a car, and it was about 5pm so the sun had set 1.5 hours earlier and I didn't want to hunt around in the darkness. I went home and looked up the place on the map so I could orient myself better.

It was also on Hisingen, but the bus that way goes only every 30 minutes so it was about a 15-20 minute walk from the Frihamn stop. Got there. It reminded me of a NAPA auto parts place, or of the really good hardware stores. The ones where you go to the desk and say "I want a 8-inch left-handed variable-speed smoke-shifter" and they'll get it for you from the stock room. They had a replacement drive, in 80 GB (the old was 50).

While I was there I opened the bag, plugged in the machine and ... no go. The machine still didn't see the disk. So it looks like I just wasted money for nothing. I checked - no return policy for this, even though I hadn't even left the store. I then checked with the repairs people, but they don't repair laptops, only desktops. They did give me the name of a place to go to, but I'm thinking the price is getting too much for exploratory research.

Subscribing to the sunken cost fallacy, can I spend some more money so the money I spent didn't go to waste? Well, I can buy an IDE enclosure so I can get my Mac to connect to the new drive over USB. Plus, the T23 might be see a USB drive. I bought it.

Started working on that today. (This is now day 3 of the attempt to install Knime.) Whaddaya know, the Ubuntu installer sees the USB disk and I can install onto it. And boot. It's dog slow because everything's going over USB2 and not the IDE bus, but usable. Problem is, there's only a console. I don't have a GUI and can't figure out how to get the wireless working so I can connect to my local base station.

Strange thing is that I can only get a console interface. Where's X? When I installed there were a bunch of red lines in the output when it tried to connect over the network. Because wireless wasn't working, I had told it I would configure the network later. Perhaps had I had the network going it would have worked better? Or are all Ubuntu installs like this?

How do I install X? "xinit"? Nope. Though the error message gives me something about using apt to install a package. Tried that out. Red lines. Try "apt" and the various apt-programs. Figured out how to tell it to look at the CD-ROM for files. (Or it knew it already.) Messed around some, got some X client apps installed, but no X server. Do I need to connect to the network for the rest of this?

Finally gave up, unplugged my Airport Express (I have no router so can only plug one Ethernet cable in.) Nothing. Power-cycled the DSL modem. ifconfig says I've got some network traffic on eth0, but no DHCP. How do you tell Ubuntu/Linux to enable dhcp? Does the network even work? The install disk lets me configure for DHCP so rebooted with that. Yippee! It sees the network, and I can ssh out. But how do make that work with my install. Should I just reinstall from scratch given that I can see the network now? In retrospect I think the answer is "yes".

There's a program called "dhclient3". Wonder what that does. Run it. Interesting. Looks like .. yes .. I've got a DHCP connection. My "nslookup www" fails instead of timing out. I can see the outside world.

Worked with "apt" some more and figured out how to get the X server running. "startx" to get into it - and it exists. No window manager found. What does Ubuntu use? Gnome, right? Used apt to install various Gnome parts. Now I can get a system working .. but there's no window manager. I had installed metacity. How do I start it? Where's the terminal? Can't find that, but was able to make a desktop item that starts "/bin/bash" in a terminal. Only to get the message that gnome-terminal wasn't installed.

At this point I'm in the GUI, "Synaptic Packager Manager" and I install gnome-terminal. That's enough to get a window open where I can type "metacity". Terminal, web browser, and the ability to swap between windows. What more does anyone need?

For one, a slew of missing programs. A lot of Unix system utilities are missing. Go through Synaptic and toggle the ones that look important. There's an icon by some of them which I think means "part of the normal Ubuntu install". I clicked on that column so I would see them grouped together. After 5 minutes of near 100% CPU use I killed it and started again.

Toggled on the ones that I thought were useful, and chose ones like OpenOffice that have a lot of dependencies. Install. Time to go out salsa dancing. Came back.

In various bits of playing around I found the Network Manager and enabled eth0. Tried to enable my wireless but I've forgotten the password. I think I'll just reset it and let it be open. I still haven't figure out how to get Metacity as the initial window manager. And I installed yet more programs. I tried "wicd" as a perhaps easier way to deal with my wireless. It's got a tray control that might be something like what my Mac has. It worked enough to tell me the wireless was working, but then it failed, miserably, with a Python traceback saying it tried to send a Unicode string over DBUS. (Note to self; you've also said you're going to look into DBUS.) I couldn't get it working again.

In the meanwhile I downloaded Knime. All 170MB or so for the developer's version. This includes code from Eclipse, but it's huge. There's no reason such a program should take so much space, I think. Why, "when I was a kid I had ...." I remember Craig and I being astonished in 1990 when we took an operating system's course and found out that SunOS's kernel was over 1MB. On the other hand, it doesn't take all that long to download. I've got a 2MBit/sec connection here, for the same price as my old sub-1MBit/sec in Santa Fe.

I should reboot. In addition to getting the network (hopefully) working, I also installed a libc security update. I wonder if I'll get a GUI login. ... Or if it will boot. .... Well, that took a while. Text prompt, then startx, then .. oops, to the terminal to start metacity. Cool, the DNS is working. Go back to the package manager. A-ha! There's a "ubuntu-desktop" option (and a few others) which are virtual packages that load all of the dependencies. Looks like I'm missing a lot of files. *sigh*

While that's happening I did get Eclipse/Knime started. The first line in the README is .. "update the Knime installation."

Why am I writing this now? I'll skip the obvious Mac vs. Linux comparisons. The Ubuntu people are working on a really hard problem that Mac doesn't have because Apple controls the platform. A question is, should I be proud happy, excited or otherwise joyous that I managed to get all of this working? It was a lot to figure out on my own and there's many who wouldn't have gotten it, or would have given up, or would have (as I should have), just reinstalled and seen if that improved things.

In looking up some of the network problems I found several which had step-by-step walkthroughs of the installation process, and even one which had a video clip of a guy talking about the installation and suggestions for what to install afterwards. That's where I got the pointer to wicd. Yet it feels like the same problem I have when I buy a new computer. The field changes so much and I don't pay enough attention to it so that the knowledge gained doesn't really help for the next time.

There are people who like tracking hardware and OS information. I'm more at the application level, and do that myself with APIs and libraries and web interfaces. Which means I feel these last three days was almost a complete waste. I like being able to ignore things I don't care about. Linux feel more written for those who care about things I don't.

I hope the Knime investigation is worth it. There are a couple of other things I'm thinking to do with an extra Linux machine, so this isn't the only reason, just the driving one. But perhaps serendipity will strike with the others.

P.S. It's now the next day from when I wrote that. Everything's downloaded, installed (except some acp things that Synaptic said didn't install correctly and were removed; and Eclipse demanded interaction when looking for a mirror when I wanted to let it go overnight while I slept so I had to finish that off this morning) and working. I haven't yet checked to see if get a graphical login after reboot, or working window manager. What I've got is good enough. I'll say it again - working from a USB2-based drive is mind numbingly slow.


Andrew Dalke is an independent consultant focusing on software development for computational chemistry and biology. Need contract programming, help, or training? Contact me



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