From: W. Trevor King Date: Thu, 28 Aug 2008 08:17:33 +0000 (+0000) Subject: Importing NanoBlogger post "Vancouver, GROMACS, RasMol, iptables, and org-mode" X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=802106f872fad490164367c7b9002de6ba45e995;p=blog.git 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 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/). + +`` + +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… + +`` + +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]]