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by Andrew Dalke.
Original Post: Installing Linux
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Feed Description: Writings from the software side of bioinformatics and chemical informatics, with a heaping of Python thrown in for good measure.
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.
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.
Strage 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.
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