Importing NanoBlogger post "Vancouver, GROMACS, RasMol, iptables, and org-mode"

diff --git a/posts/Vancouver,_GROMACS,_RasMol,_iptables,_and_org-mode.mdwn b/posts/Vancouver,_GROMACS,_RasMol,_iptables,_and_org-mode.mdwn
new file mode 100644 (file)
index 0000000..dd9509d
--- /dev/null
+++ b/posts/Vancouver,_GROMACS,_RasMol,_iptables,_and_org-mode.mdwn
@@ -0,0 +1,81 @@
+[[!meta  title="Vancouver, GROMACS, RasMol, iptables, and org-mode"]]
+[[!meta  date="2008-08-28 04:17:33"]]
+I was off in the Vancouver area over the last two weeks visiting my
+fiancée's family, and I got out of the internet/blogging-zone for a
+while.  Now it's time to catch up some ;).
+
+Vancouver was wonderful, as always ;).  Flaky wind gave the advantage
+of maneuverability to the canoe navy, but the sunfish's mass held it in
+good stead.  Despite much sniping and tactical maneuvering, we all
+ended up in the ocean anyway… several times… that's either a win or a
+draw, but either way it was a good time :).
+
+Over the weekend I bought a pair of Logitech Quickcam for Notebooks
+(046d:08dd) so I could video-`skype` with my fiancée while we're apart
+for a bit.  Like a
+[bunch](http://backports.ubuntuforums.com/showthread.php?t=478890) of
+[other](http://forums.quickcamteam.net/archive/index.php/thread-22.html)
+[people](http://ubuntuforums.org/showthread.php?t=651375&page=3), I
+didn't realize that this version of “Logitech Quickcam for Notebooks”
+was not particularly well supported on Linux, since the *earlier*
+version of “Logitech Quickcam for Notebooks” is.  Since then I've been
+running around on my not-to-easy-to-get-source-for
+[EeePC](http://eeepc.assus.com/global/), wring to compile and install
+[Michel Xhaard's gspca drivers](http://mxhaard.free.fr/).
+
+`<rant>`
+
+Which is not difficult once you've removed the unionfs junk
+the EeePC comes with, cleared out a bunch of space, installed the
+necessary build tools, and generally manhandled your EeePC into
+something resembling a sane distributions basic installation.  Oh, and
+you'll need a nice external drive, since it's hard to compile a 400 MB
+kernel in the 150 MB of headroom I had left on my 2 GB Surf after I'd
+installed those, and emacs, and a few other fun toys :p.
+
+And after I had installed the drivers and had `xawtv` working fine
+with the camera, the problems weren't over, since `skype` pretty much
+pegs my CPU, which often causes the video to lock…  Sigh…
+
+`</rant>`
+
+Upon my return to work, Marisa expressed interest in the
+[GROMACS](http://www.gromacs.org/) Molecular Dynamics simulation
+software, so we installed in on our cluster and spent Monday learning
+the ropes.  Things seem to be going smoothly so far, although we're
+not sure if our nominally MPI-enabled `mdrun` is actually using more
+than one node, since I haven't found anyone using GROMACS over PBS via
+our [mpiexec](http://www.osc.edu/~pw/mpiexec/) (see (Kristina Wanous'
+note on
+[debianclusters](http://debianclusters.cs.uni.edu/index.php/MPICH:_Pick_Your_Paradigm)).
+We'll run some scaling benchmarks soon to convince ourselves that
+GROMACS is indeed using MPI.
+
+We also ran into some difficulty running the default Debian-packaged
+[RasMol](http://rasmol.org/) through a SSH tunneled X server.  No
+problem, says I, we'll use [Lionel Cons](http://cern.ch/lionel.cons)'
+[mxconns](http://cern.ch/mxconns/), which I had run across earlier
+while trying to set up a cluster-wide X port for running MPE.
+However, `rasmol` somehow manages to lock up so hard that it freezes
+the whole X server, right through `mxconns` and the SSH tunnel!  I
+didn't even think that was possible.  The current workaround is to run
+`rasmol` on your own machine ;).
+
+While discussing the cluster, Marisa pointed out the usefulness of
+`iptables` or some sort of firewall on the cluster.  I had just
+assumed it was already behind a conservative router.  Stupid
+assumption.  I spent most of Tuesday jumping between the Rasmol X-lock
+and figuring out how iptables works, and locking out my ssh connection
+a few times.  After an embarassing number of trips down to the cluster
+room to clear my bad rules, I believe I have things straightened out
+now.  Mostly following the [Linux Administration
+Handbook](http://www.pearsonhighered.com/educator/academic/product/0,3110,0131480049,00.html).
+
+Today I finally got back to work on testing my simulation, and broke
+down and installed [org-mode](http://orgmode.org/) for emacs.  I think
+I'm in love ;).  See, for example, [John
+Wiegley](http://newartisans.com/)'s 's blog on using [org-mode as a
+day
+planner](http://newartisans.com/blog_files/org.mode.day.planner.php).
+
+[[!tag  fun]]