The following is a cookbook for compiling single-precision and double-precision GROMACS 3.3.3 in OSX 10.5 (specifically on a MacBook Pro, but most likely general to all things running 10.5) with OpenMPI 1.2.6. My hope is that this saves someone several hours of unnecessary work trying to overcome an otherwise unknown incompatibility between MPICH2 and GROMACS 3.3.3 in Leopard (10.5).

The content of this page is a result of an unsuccessful several hours of trying to build GROMACS-MPI versions with MPICH2 1.0.6 and 1.0.7. MPICH2 compiles just fine with standard options, including a successful testing of mpd and mpdtrace. GROMACS 3.3.3 compiles just fine with standard options for both single-precision and double-precision. Compiling GROMACS with MPI support yields an mdrun file that fails in the following manner:

[host:XXXX1] *** Process received signal ***

[host:XXXX1] Signal: Segmentation fault (11)

[host:XXXX1] Signal code: Address not mapped (1)

[host:XXXX1] Failing at address: 0xffffff94

[ 1] [0×00000000, 0xffffff94] (FP-)

[host:XXXX2] *** Process received signal ***

[host:XXXX2] Signal: Bus error (10)

[host:XXXX2] Signal code: (2)

[host:XXXX2] Failing at address: 0×2

[host:XXXX1] *** End of error message ***

[ 1] [0×00000000, 0×00000002] (FP-)

[marlin:XXXX2] *** End of error message ***

This problem, it has been discovered, is remedied by using OpenMPI 1.2.6. Not a proper diagnosis of the MPICH2/GROMACS problem, but my primary concern is getting MPI working in order to use both cores on my MacBook Pro to get calculations running, not fixing software bugs to get someone else’s calculations running (when there’s an easier fix, anyway).

Installation Procedure

You’ll need the following three files (relevant versions and links are subject to change!):

fftw-3.1.2, http://www.fftw.org/

According to the website:

FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST).

FFTW compiles double-precision libraries by default. You’ll need to build single-precision libraries for the single-precision GROMACS install.

gromacs-3.3.3, http://www.gromacs.org/

The newest version. Compilation of version 3.3.2 leads to various problems under OSX 10.5 (undiagnosed here, but certainly reproducible).

openmpi-1.2.6, http://www.open-mpi.org/

This is the MPICH2 replacement (meaning I’ve used MPICH2 for other programs). Again, I’m not playing favorites on a version-to-version level. On my MacBook Pro running OSX 10.5, OpenMPI does what I need, MPICH2 doesn’t.

GROMACS uses MPI to distribute processes between processors. If you don’t have GROMACS compiled with MPI, you don’t have multi-processor calculations (simple enough). That is to say, the Activity Monitor reads 100% for one processor and residual % for all other processes on the other chip (this was a point of confusion in a few discussions, in case someone wonders why I would bother bringing such a point up).

Associated Notes On Compilation

A few important notes to be aware of for the compilation.

XCode 3.0, http://developer.apple.com/tools/xcode/

If you’ve not installed XCode 3.0 yet, you should in order to get compilers and libraries installed on your machine. XCode is the official programmer’s toolbox under OSX and installs far more than you’ll need (but it never hurts). Note that this is a BIG download (1.1 GB) but is a far less taxing route to getting all of the necessary files installed on your machine than relying on (many, many) individual downloads.

Root Access

Running “make install” will install files into core directories that are inaccessible to typical OSX User accounts. Access to these directories (such as /usr/local and /usr/local/lib) is granted only to the root user in OSX, which is not activated by default (and a good thing, too). To turn on root access, go to:

Macintosh HD > Applications > Utilities > Directory Utility

In Directory Utility, go to

Edit > Enable Root User

At build time, you’ll want to be logged in as the root user (see below).

No Spaces In Folder Names

This goof also took some time to figure out. Regardless of where you start the program build processes from, you need to make sure your directory names have no spaces between words.

>& FILENAME.txt

>& FILENAME.txt is used to direct output to FILENAME.txt, providing a way to follow each step in the process for error checking and the like. For diagnosis purposes, the files from my build are provided here for the GROMACS work. Click on each name to open the log file.

Installation Process

How to follow the text below:

1. Step in the process (one per program, significant activity)

1a. Text that follows the numeric-alphabetical label is what needs to be typed in at the Terminal window prompt. Descriptive/explanatory text follows below each step.

The installation is assumed to be set up as follows: the GROMACS, OpenMPI, and FFTW .tar files (I suspect downloading will automatically unzip them) exist in a directory on your Desktop (say, INSTALL_DIRECTORY_NAME). Here’s the compilation procedure:

1. Open a Terminal (Macintosh HD > Applications > Utilities > Terminal). If you don’t have this application on your Dock, I recommend putting it there. You’ll certainly be getting some use out of it.

2. The Terminal window defaults to your User directory. First we change our user to root (for full access), then cd into the install directory.

2a. su

(put in root password at prompt)

at prompt, type:

2b. csh

2c. cd Desktop/INSTALL_DIRECTORY_NAME

3. untar the GROMACS, OpenMPI, and FFTW .tar downloads (again, I suspect they will have already been unzipped as part of the download). You’ll end up with three new directories in this folder.

3a. tar -xvf fftw-3.1.2.tar

3b. tar -xvf gromacs-3.3.3.tar

3c. tar -xvf openmpi-1.2.6.tar

4. Build FFTW

We’ll compile fftw-3.1.2 first. For the single-precision build, the steps are:

4a. cd fftw-3.1.2

4b. ./configure –enable-float –enable-threads >& configure_fftw_single.txt

4c. make >& make_fftw_single.txt

4d. make install >& make_install_fftw_single.txt

4e. make distclean >& make_distclean_fftw_single.txt

4f. cd ..

This series of steps configures (configure), builds (make), moves (install) and cleans up (distclean). The “>&” directs output to the .txt files for diagnosis (all of which you can leave off). To follow step progress, open a new Terminal window, get to the directory of interest and type:

4g. tail -f FILENAME_OF_INTEREST.txt

To build the double-precision version (FFTW default and what you’re better off building anyway)

4h. cd fftw-3.1.2

4i. ./configure –enable-threads >& configure_fftw_double.txt

4j. make >& make_fftw_double.txt

4k. make install >& install_fftw_double.txt

4l. make distclean >& distclean_fftw_double.txt

4m. cd ..

5. Build OpenMPI

This build could not be easier. This build will place the OpenMPI 1.2.6 executables into /usr/local/openmpi (in the interest of organization).

5a. cd openmpi-1.2.6

5b. ./configure –prefix=/usr/local/openmpi >& configure_openmpi.txt

5c. make >& make_openmpi.txt

5d. make install >& install_openmpi.txt

5e. make distclean >& distclean_openmpi.txt

5f. cd ..

6. Build GROMACS

The following four builds will yield all four possible combinations of GROMACS (single-precision and double-precision) and MPI (without and with). Do you need four builds of GROMACS? Definitely not. If you’re reading this page, you’re probably interested only in double-precision and MPI (the last of the four). The four builds listed below were performed for testing purposes only. I only ever use the double-precision MPI version when I’m doing my own work.

Note: Each build included the generation of links to executables that go into /usr/local/bin. Accordingly, all four versions are accessible from the Terminal window without having to specify directories (and each version has individually named files as defined in –program-suffix= ).

GROMACS Single-Precision

This will install a single-precision GROMACS build into /usr/local/gromacs333_single with no specific file suffix.

6a. cd gromacs-3.3.3

6b. ./configure –prefix=/usr/local/gromacs333_single >& gromacs_single_configure.txt

6c. make >& gromacs_single_make.txt

6d. make install >& gromacs_single_install.txt

6e. make links >& gromacs_single_links.txt

6f. make distclean >& gromacs_single_distclean.txt

6g. cd ..

GROMACS Single-Precision With OpenMPI

This will install a single-precision MPI-GROMACS build into /usr/local/gromacs333_single_mpi with the file suffix _mpi.

6h. cd gromacs-3.3.3

6i. ./configure –enable-mpi –program-suffix=_mpi –prefix=/usr/local/gromacs333_single_mpi
>& gromacs_single_mpi_configure.txt

6j. make >& gromacs_single_mpi_make.txt

6k. make install >& gromacs_single_mpi_install.txt

6l. make links >& gromacs_single_mpi_links.txt

6m. make distclean >& gromacs_single_mpi_distclean.txt

6n. cd ..

GROMACS Double-Precision

This will install a double-precision GROMACS build into /usr/local/gromacs333_double with the file suffix _d.

6o. cd gromacs-3.3.3

6p. ./configure –program-suffix=_d –prefix=/usr/local/gromacs333_double –enable-double
>& gromacs_double_configure.txt

6q. make >& gromacs_double_make.txt

6r. make install >& gromacs_double_install.txt

6s. make links >& gromacs_double_links.txt

6t. make distclean >& gromacs_double_distclean.txt

6u. cd ..

GROMACS Double-Precision With OpenMPI

This will install a double-precision MPI-GROMACS build into /usr/local/gromacs333_double_mpi with the file suffix _mpi_d.

6v. cd gromacs-3.3.3

6w. ./configure –enable-mpi –program-suffix=_mpi_d –prefix=/usr/local/gromacs333_double_mpi
–enable-double >& gromacs_double_mpi_configure.txt

6x. make >& gromacs_double_mpi_make.txt

6y. make install >& gromacs_double_mpi_install.txt

6z. make links >& gromacs_double_mpi_links.txt

6aa. make distclean >& gromacs_double_distclean_mpi.txt

6ab. cd ..

Running MPI-GROMACS Calculations (Non-specific)

Running MPI-GROMACS is straightforward, requiring only one additional step and a few changes to how you use grompp and mdrun.

a. mpd &

b. grompp_mpi_d … -np 2

-np 2 is added to tell grompp that two processors are being used. mdrun expects the same number of processors as was specified in grompp.

c. mpirun –np 2 /usr/local/gromacs333_double_mpi/bin/mdrun_mpi_d … -np 2

mpirun first calls the number of processors to use (-np 2) and then requires specification of the path to the mdrun executable (/usr/local/gromacs333_double_mpi). mdrun requires specifying the number of processors as well (-np 2) as per the specification in grompp.

And Finally…

Like all first draft cookbooks, this might be missing some important spices. If, by any chance, you found this page and have recommendations to improve speed, stability, organization, etc., please drop a line and I’ll keep track of modifications.

en.wikipedia.org/wiki/Single_precision
en.wikipedia.org/wiki/Double_precision
www.gromacs.org
www.apple.com/macosx/
en.wikipedia.org/wiki/Mac_OS_X_v10.5
www.apple.com/macbookpro/
www.open-mpi.org/
www.mcs.anl.gov/research/projects/mpich2/
www.gromacs.org/documentation/reference/online/mdrun.html
www-unix.mcs.anl.gov/mpi/
www.fftw.org
en.wikipedia.org/wiki/Activity_monitor
developer.apple.com/tools/xcode/
en.wikipedia.org/wiki/NetInfo_Manager
en.wikipedia.org/wiki/Terminal_(application)
en.wikipedia.org/wiki/Dock_(computing)
en.wikipedia.org/wiki/Tar_file
www.gromacs.org/documentation/reference/online/grompp.html

A repost of the original at the Syracuse Astronomical Society website.

2008 Messier Marathon

Charles Messier (1730 - 1817). Click HERE for more info.

It is that time of year again! The opening of the observatory on April 4th will also be our official date for the 2008 Messier Marathon. While approaching the edge of the “ideal window” for the Marathon (which is between mid-March and very early April), the new Moon matches up with our ability to get near the Observatory soon after the beginning of Spring (when there’s usually snow still covering the scope pads). As our Society Meetings now coincide with Public Viewing sessions, this is an excellent opportunity for anyone interested to get a thorough “crash course” in astronomical objects and viewing equipment (a few of us will only attempt the Messier hunt with binoculars, while others will stay fixed to their telescopes for quality-over-quantity observing).

Courtesy Thierry Lombry, www.astrosurf.com/lombry Click on the image for a larger version.

I will save the discussion of the Marathon and its history for a few excellent websites on the subject. As for those planning to attend either Friday or Saturday night (Friday is the planned date, but check the website Friday afternoon for weather updates and the official call from the Board), be VERY sure to bring extra layers of clothing. After dark at the observatory, the temperatures can quickly drop to freezing and, without the Sun to help, you provide the heat to Darling Hill, not vice versa!

The February 21th MOST Lecture

For those that missed the MOST, I wanted to post a few notes and links mentioned by Prof. James Lloyd during his lecture on “Planets Orbiting Distant Stars.” These barely scratch the surface, put certainly provide some great reading and viewing.

Giordano Bruno

“It is then unnecessary to investigate whether there be beyond the heaven Space, Void or Time. For there is a single general space, a single vast immensity which we may freely call Void; in it are innumerable globes like this one on which we live and grow. This space we declare to be infinite, since neither reason, convenience, possibility, sense-perception nor nature assign to it a limit. In it are an infinity of worlds of the same kind as our own.” - Giordano Bruno, From De l’infinito universo et mondi (On the Infinite Universe and Worlds), 1584.

The proposal that ours is not the only (habitable?) planet in the universe is not at all recent, especially given that it’s been less than 20 years since the first discovery (HD 114762 b way back in 1989. I still have the clipping from the Post-Standard in my old Peterson Field Guide). One thing that has changed in the last +400 years is the way in which such new revelations are handled by society. Bruno burned at the stake for his then heretical views, a misunderstanding the Catholic church has since acknowledged regret for.

exoplanet.eu

At some point in the not too distant future, people will look upon the www.exoplanet.eu website and comment “They found yet another one. Ho hum.” In the meantime, this website, run by Jean Schneider of CNRS/LUTH (the French equivalent of our National Laboratory System) is the international place to go for updates on the total count of planets beyond our Solar System, including all kinds of information about the planetary properties and how they were discovered.

planetquest.jpl.nasa.gov

Our tax dollars at work, and including a free widget! The planetquest.jpl.nasa.gov site contains the up-to-the-minute tally of extrasolar planets, news articles (popular press) about those discoveries, and a download-able widget for Windows and OSX that provides the total count on your desktop.

Prof. Lloyd Quote Of The Night

“We know as much about the cores of extrasolar planets as we know about our own.”

Ye Olde Popular Press

In discussing the methods by which we discover extrasolar planets, Prof. Lloyd made reference to the phenomenon of gravitational lenses, one of the amazing aspects of the interaction of light and matter predicted by Albert Einstein before its reported observation by Arthur Eddington. I’ve heard it described as “The great reconciliation of Germany and England after World War I“, but recent studies indicate that Eddington’s measurements were within the error bars of not being credibly observable, although we know today with our increasingly sensitive equipment that the phenomenon is very real.

How often does science make the front page? The two clips are taken from the New York Times reporting the… peculiar revelations (that description sounds reasonably dated, yes?) of one Albert Einstein.

American Scientist Stamp Unveiling At The MOST

February 6th saw the official release by the US Postal Service of a panel of four stamps commemorating four American Scientists. For those keeping count, a set of four stamps came out in 2005 featuring Barbara McClintock, John von Neumann, Josiah Willard Gibbs (of Gibbs Free energy fame, of course) and the incomparable Richard Feynman. Included in the current set are Gerty Cori, Linus Pauling, John Bardeen, and the reason I mention the release, Edwin Hubble. Given just how far science has progressed us since the simpler times of Giordano Bruno’s Italy, it is still amazing that it wasn’t until the reporting of Hubble discoveries on January 1, 1925 that it became public knowledge that the Milky Way is not, in fact, the only galaxy in the universe. Less than 100 years ago, every galaxy we’ve now observed with the Hubble Space Telescope was believed to lie within the (still uncharacterized) bounds of our own galaxy. As a practicing scientist, I consider that a very humbling thought.

Click on the image for a larger version.

Syracuse Stamp Club Commemorative Hubble Cover

The first day of availability of the aforementioned “Scientific Panel” (certainly one that could have easily lost their audience without scratching the surface of their respective fields) was celebrated by the Syracuse Stamp Club with a Commemorative First Day Stamp Cover designed by Board of Director member and fellow Syracuse University alum Vincent Juchimek. After a delightful afternoon campus visit and First Day Stamp Cover education with his wife Dianne, Vincent graciously offered to make available a Hubble-centric stamp cover to SAS members (see the image below). I think they serve the important purposes of supporting the recognition of American Scientists (by buying the stamps from the US Post Office), demonstrating how two otherwise very different hobbies (I only ever pick up a magnifying glass when I’m trying to find a cluster in some dense pocket book to set the sights of my 25×100’s on) can overlap in a most productive way, and providing an artistic way to commemorate a national event in a most Syracuse-centric way. Thirty of these have been secured for the SAS that will be available to members for $3.00 each (which included the cover, the stamp, and the commemorative cancel). If you’re interested in obtaining one or more Hubble Stamp Covers, let me know as soon as possible and we’ll have them out as they come off the press!

Click on the image for a larger version.

Ice Pillars Attack Downtown Syracuse!

The SAS received a little bit of local recognition on the morning of February 29th with a news article in the Post-Standard about some remarkable pillars of lights the night before. I received a phone call from reporter Douglass Dowty asking for info about the strange lights observed downtown after he’d received information from the 911 Call Center about people reporting strange lights, flying discs, etc. After briefly peaking my head out the window (and running out quickly in socks to not miss what, given viewing conditions in Syracuse, could have been the last 5 seconds of “something wonderful“), I told him that the phenomenon looked like aurora, which I confirmed to myself by checking spaceweather.com to see if we were, in fact, in the middle of a major solar storm (which we reportedly were). After a bit more viewing from downtown, what I thought was aurora became decidedly more localized in nature. The phenomenon we all observed was “ice pillaring,” a specific example of “light pillaring,” a not-too-common phenomenon in itself that provides a different, but no less stunning, light show in the Night Sky.

I quickly threw together a picture of how ice pillars form (well, appear) that I’m including here (replete with local color).

Click on the image for a larger version.

After some posting on the article blog at syracuse.com, Douglass re-quoted me with my more likely explanation in the February 30th edition. Two of my best pictures of the pillars are provided below. The picture on top shows a slightly over-exposed view of North Syracuse (to make the pillars more prominent). The picture at bottom is exactly as my camera and I saw it, with very pronounced pillaring over St. Joseph’s Hospital. The pillars remind me a bit of the transporter signatures in the old Star Trek movies (very bright and very localized).

Click on either image for a larger version.

and finally…

Milky Way Gets Super-Sized (Sorry, I Can’t Resist)

Oh Henry! A Fast Break over the scientific newswire reports that the Milky Way has reportedly put on a bit of weight, but no one appears to be Snicker-ing. Like the rest of us, the Milky Way hasn’t gotten longer, only a little Chunky-er, or wider in the middle (and tailing off to either end). A group of astronomer Smarties at the University of Sydney didn’t need their 100 Grand scope, requiring only an analysis of small Mounds of data available on the internet to determine that the Milky Way is now 12,000 light years wide. Truly a low-cost, high-impact PayDay for Prof. Bryan Gaensler and co-workers, with some calling this the most important discovery in astronomy since the discovery of water on Mars.

Click on the image for more info.

We can only hope that the researchers performing the data analysis weren’t a group of Butterfingers. Stay tuned for S’More astronomy news.

If it weren’t bad enough that we’re less than 100 years past Hubble’s great announcement on the distance of other galaxies from our own, consider now how significant it is that we’re still uncovering the very largest-scale properties of our own galaxy.

Space is the place,
Damian Allis, Ph.D.
sas@somewhereville.com

Links Used Above (Subject To Web Changes)
www.astro.cornell.edu/people/facstaff-detail.php?pers_id=96
www.cornell.edu
www.most.org
seds.org/MESSIER/xtra/history/CMessier.html
en.wikipedia.org/wiki/Messier_marathon
en.wikipedia.org/wiki/Moon
www.astrosurf.com/lombry
seds.org/Messier/xtra/marathon/marathon.html
en.wikipedia.org/wiki/Sun
astrosun2.astro.cornell.edu/~jpl/
www.most.org
en.wikipedia.org/wiki/Giordano_Bruno
www.positiveatheism.org/hist/brunoiuw0.htm
en.wikipedia.org/wiki/HD_114762
www.syracuse.com
www.houghtonmifflinbooks.com/catalog/titledetail.cfm?titleNumber=681482
www.exoplanet.eu
www.obspm.fr/~schneider
www.cnrs.fr
en.wikipedia.org/wiki/Solar_system
planetquest.jpl.nasa.gov
www.microsoft.com
www.apple.com
en.wikipedia.org/wiki/Gravitational_lens
en.wikipedia.org/wiki/Albert_Einstein
en.wikipedia.org/wiki/Arthur_Eddington
en.wikipedia.org/wiki/World_War_I
www.nytimes.com
www.usps.gov
www.usps.com/communications/news/stamps/2004/sr04_076.htm
en.wikipedia.org/wiki/Barbara_McClintock
en.wikipedia.org/wiki/John_von_Neumann
en.wikipedia.org/wiki/Josiah_Willard_Gibbs
en.wikipedia.org/wiki/Richard_Feynman
en.wikipedia.org/wiki/Gerty_Cori
en.wikipedia.org/wiki/Linus_Pauling
en.wikipedia.org/wiki/John_Bardeen
en.wikipedia.org/wiki/Edwin_Hubble
www.aps.org/publications/capitolhillquarterly/200802/physicshistory.cfm
en.wikipedia.org/wiki/Milky_Way
hubblesite.org
en.wikipedia.org/wiki/First_day_cover
www.syracusestampclub.org
syracusestampclub.org/officers/officers.htm
www.syr.edu
www.syracuse.ny.us
www.linkedin.com/pub/2/543/B78
en.wikipedia.org/wiki/2010:_The_Year_We_Make_Contact
en.wikipedia.org/wiki/Aurora_%28astronomy%29
www.spaceweather.com
en.wikipedia.org/wiki/Light_pillar
blog.syracuse.com/news/2008/02/pillars_of_light_illuminate_sk.html
www.startrek.com
www.usyd.edu.au/news/84.html?newsstoryid=2163
en.wikipedia.org/wiki/Oh_Henry%21
en.wikipedia.org/wiki/Fast_Break_%28candy%29
www.usyd.edu.au/news/84.html?newsstoryid=2163
en.wikipedia.org/wiki/Milky_Way_%28candy%29
en.wikipedia.org/wiki/Snickers
en.wikipedia.org/wiki/Nestlé_Chunky
en.wikipedia.org/wiki/Smarties_%28Ce_De_Candy%29
www.usyd.edu.au
en.wikipedia.org/wiki/100_Grand
en.wikipedia.org/wiki/Mounds_%28candy%29
en.wikipedia.org/wiki/PayDay_%28confection%29
www.physics.usyd.edu.au/~bmg
apod.nasa.gov/apod/ap050401.html
en.wikipedia.org/wiki/Butterfinger
en.wikipedia.org/wiki/S%27more

An otherwise uneventful evening took a turn around 10:20 pm last night with a phone call from Douglass Dowty, crime and safety reporter for the Post-Standard in our fair city, Syracuse, NY. According to his message, people had been calling 911 about lights in the sky (always the kind of message that gets my undivided attention) and he wanted to check on whether or not were witnessing the Aurora Borealis. I jumped immediately outside in socks to take a look and caught what I thought was the aurora in full splendor. Having not done quite enough homework, I proceeded, with my Syracuse Astronomical Society hat on, to be quoted as saying the following:

“I’ve never seen it like this: pillars of orangish to greenish to yellow-blue light,” said Damian Allis, president of the Syracuse Astronomical Society.

The aurora borealis, or northern lights, caused the unusual display, Allis said.

…and then take many, many photos (click on any for a larger view).

Light pillars over St. Joseph’s Hospital.	Light pillars over Northern Syracuse (contrast-enhanced).
A photo of directly above (very contrast-enhanced)	Myself, Kirsten, Jupiter, and more pillars to the East.
A zoom-out of St. Joseph’s (two sets of pillars).	“Automobile Row,” or West Genesee Street.

…and I then began to take the harder look around. I realized, a bit later, that this wasn’t the aurora, but ice/light pillars. The two are similar in appearance but, with enough looking around for details, are differentiable. The light pillars are, of course, the dead giveaway (which jumped right out over St. Joseph’s). There’s quite a bit on ice/light pillars online, but I thought I’d take my own crack at an explanation (and figure).

So, the pillars are, in fact, a rather large-scale result of reflection in the atmosphere, with the city lights providing plenty of source. I qualified my report to Douglass in the comment section of the article on the syracuse.com website.

As the potential source of at least some of the heated discussion (although with the MONY tower reading “09″ degrees last night, heated might not be the best word), I wanted to correct/report/qualify a bit of the news story.

Was what we saw aurora or light pillars? When I first walked out on my roof, I suspected the phenomenon was the aurora. I suspected as such because (1) I didn’t see the “pillaring” of light (which was VERY prominent over St. Joseph’s Hospital), (2) spaceweather.com indicated that the aurora oval was over New York (this is the “band” of light we see on the ground due to all of the physics in the magnetosphere), and (3) the lights were prominent to the North and virtually invisible to the South (the lights basically ended at Jupiter to our East and Saturn to our West (the two brightest “stars” in the sky last night)), which is what you’d expect from an aurora show.

Anyone that looked in the direction of St. Joe’s saw very prominent pillars, which was the clincher (and, had I noticed those first before Douglass called (and he called because he’d gotten 911 reports. In case anyone was concerned, the aliens were not invading. If anything, light pillars look like transporter lights from Star Trek. If King Kong and the Jolly Green Giant are ever members of the Enterprise “Away Team,” their materializing on the surface might look remarkably like the giant pillars we saw last night)). While it’s possible that some component of last night was aurora-related, my money’s on our bearing witness to light pillars. Either way, I agree with lilschwib’s last comment, thank CornellLaxer for an eloquent and informative post, hope that dragbaby will forgive a scientist jumping the gun a little (my fuse is pretty short at 7:54 in the morning, too), and would like to throw my support to the “has nothing to do with global warming” contingent. Light pillars involve light, reflection, and ice crystals. They’ve very likely scared humans since the control of fire allowed us to venture out at night and I’m sure aliens on distant planets have had the same aurora/light pillar arguments on their comment boards (although they’re called “Pepsi” and “Coke,” respective, in the Vega system). In case anyone’s interested, we’ll be posting about it on the Syracuse Astronomical Society website (www.syracuse-astro.org) in early March.

cheers,
Damian Allis

Anyway, a wonderful break from the usual Thursday night.

www.linkedin.com/pub/2/543/B78
www.syracuse.com
en.wikipedia.org/wiki/Aurora_(astronomy)
www.syracuse-astro.org
en.wikipedia.org/wiki/Light_pillar
blog.syracuse.com/news/2008/02/pillars_of_light_illuminate_sk.html
www.sjhsyr.org/sjhhc/
www.spaceweather.com
en.wikipedia.org/wiki/Magnetosphere
www.startrek.com
en.wikipedia.org/wiki/King_Kong

A repost of the original at the Syracuse Astronomical Society website.

Happy New Year Fellow Astrophiles! Let’s get right to it…

The Tradition Continues…

Four fearless drivers/SAS Board members and Herschel, the Observatory Director’s Canis Major, braved the Darling Hill drive New Year’s Day for the annual Observatory toast. The image at left shows Ray Dague, John McMahon, Mike Brady, and Dan O’Shea in their winter best. At right, well, I’ll let you figure out the musical chairs.

Click on an image for a larger view.

Bob Piekiel’s Baltimore Woods Winter Viewing

The year begins with a few scheduling points to help dust off your winter sky charts. Baltimore Woods (www.takeahike.org) is holding one viewing session a month in January (general viewing) and February (for the total lunar eclipse), the two months the SAS is almost guaranteed to not be able to make it up the driveway at the Darling Hill Observatory. The two viewing sessions are being hosted by Robert Piekiel, a noted astronomer, author of the e-book Celestron: The Early Years, and (if I have the right Bob Piekiel) banjoist. If you thought turning scope knobs was difficult at 30 Fahrenheit, imagine plucking metal strings!

From Baltimore Woods:

January 11:, “Star Party: Starlight on Snow,” 6 - 8 p.m., 4007 Bishop Hill Rd., Marcellus. Longer winter nights give us more time to enjoy the stars that light up our skies. Enjoy close-up views of these night-lights through the telescopes of astronomer Bob Piekiel. Large groups welcome. This is a great program for kids who are interested in astronomy. Dress for the weather. Members $2, families $5; non-members $5, families $15. Back-up date Jan. 12. Please call 673-1350 to register.February 20:, “Star Party: Lunar Eclipse,” 8:30 - 10:30 p.m., 4007 Bishop Hill Rd., Marcellus. Join astronomer Bob Piekiel to catch a glimpse of this rare astronomical event while you can. The next lunar eclipse in North America isn’t until 2010! Large groups welcome. This is a great program for kids who are interested in astronomy. Dress for the weather. Members $2, families $5; non-members; $15 family. Please call 673-1350 to register.

A Little About Baltimore Woods:

Baltimore Woods is located at 4007 Bishop Hill Rd., Marcellus, about 15 minutes from Syracuse. It is a private, not-for-profit nature center and environmental education organization committed to promoting environmental awareness, understanding, and responsible natural resource stewardship among all people, especially children.The 182-acre property contains stream, woodland, meadow and pond habitats, which are managed to attract birds and wildlife.There are more than six miles of trails for the public to enjoy, ranging from .15 miles long to more than a mile in length. Terrain on the various trails ranges from flat to hilly, and the hiking difficulty from easy to difficult, depending on the trail.Gardens on the property include Herb, Perennial, Wildflower and Weavers & Dyers, and there is an Arboretum Trail that showcases the trees of Baltimore Woods.There is no admission charge for parking or to enter Baltimore Woods, although donations are always welcome.The John Weeks Interpretive Center, containing restrooms, exhibits and meeting space, is open 9 a.m. to 4 p.m. weekdays and 10 a.m. to 4 p.m. Saturdays, and the entire property is open for hiking (and snowshoeing during the winter) from dawn to dusk.We ask that you please do not bring dogs to Baltimore Woods.You can get more information about programs, trails and volunteer opportunities available at Baltimore Woods by calling 673-1350 or visiting our web site at www.takeahike.org.

South Jersey Astronomy Club 2008 Star Party

I received this message a week ago from the South Jersey Astronomy Club, another optimisitc group of stargazers planning an early start to the viewing year (about the time of the year when one can stand being outside for an hour or more unphased). Yes, this does coincide with the opening of the Darling Hill Observatory weekend, so I post this for other interested parties (because, of course, YOU’LL be in Tully) or anyone that will be in the Juy’sey area that weekend. We don’t care which organization you’re looking up with that weekend, just be looking up!

From the South Jersey Astronomy Club:

Before you ring in the New Year…MARK YOUR CALENDAR NOW FOR THE 2008 SOUTH JERSEY SPRING STAR PARTY: April 4-6, 2008 ~ Belleplain State Forest, Cape May County, NJ.Save the date, and make plans now to attend the 2008 SOUTH JERSEY SPRING STAR PARTY! This “no frills” event will take place over the April 4-6, 2008 weekend at beautiful Belleplain State Forest in northern Cape May County, NJ. Bring your tent, supplies and telescope — weather permitting, the Star Party features some of the best dark-sky viewing conditions in the region!There’s camping on the five-acre observing field, and nearby you’ll find plenty of other camp sites, hot showers and other amenities. The area is famous for its ecology and natural beauty, and there are plenty of attractions to see during the day. Pre-register now and get 50% off the regular registration cost of the Star Party! Visit http://www.sjac.us and click on the SOUTH JERSEY STAR PARTY. Sign up now to reserve your space!WHAT: The 2008 South Jersey Spring Star PartyWHERE: Belleplain State Forest in northern Cape May County, NJWHEN: April 4-6, 2008 (Friday-Sunday)MORE INFO: http://www.sjac.us or contact Ray Maher, President of SJAC at rp2099@aol.com

The Tibbitts Takes

Yet another CNY astrophotographer (after our own Stu Forster) is willing to sacrifice life, limb, and equipment (!) in the interest of capturing images of the night’s sky. The following two images were taken by David Tibbitts, the first of the full Moon (anyone that’s tried to take a magnified photo of the Moon knows how easy it is to overexpose the image and completely ruin the view. This one came out quite well balanced), the second of Comet Holmes in exactly the same diffuse appearance I observed in my 7×50 binoculars. I hope to have many more messages include astrophotography from both David and Stu. They are certainly far more interesting than what I have to say about them.

Click on either image for a larger view.

An Odd Use Of An Observatory Scope

During the closest approach of Mars in August of 2003 the SAS hosted a very well-attended viewing party (that started at 8 p.m. and went well beyond 2 a.m. I remember little except the phenomenal cold I suffered for two weeks after). As the night began to approach morning, I used my last time at the observatory scope to attempt a photo of Mars at high magnification. In my ignorance, I left the flash on during my first attempt, yielding the image shown below. I’ve still not diagnosed it completely, but do recognize (a) the small orange ball is Mars with the polar ice cap barely visible at about 12 o’clock and a bit of equatorial color splotches visible, (b) what I think is my left eye through the view window (haven’t we all seen those floaters when we look just right at a light source?). And this is why I don’t do astrophotography anymore…

Click on the image for a larger view.

Best Views Of The Year At Bad Astronomy

Phil Plait isn’t a bad astronomer at all. With a doctorate in the field and one very well received book to his name (the aptly titled “Bad Astronomy: Misconceptions and Misuses Revealed, from Astrology to the Moon Landing ‘Hoax’“), one would argue that he knows “bad astronomy” when he sees it. His website, badastronomy.com, is full of his own writings on astronomical misconceptions, flat-out astronomical falsehoods in movies and TV (did anyone else wonder how the shuttle “banked” in Armageddon?), and a very popular (among scientific sites, anyway) blog. One of his most popular posts of the year highlighted ten of the best celestial eye candy of 2007. Instead of reposting all of his selections, I recommend spending a few minutes reading through his descriptions and, of course, following the links to more information (a good scientist, he never forgets his references. In the case of the web, that means links back to the sources). The site’s certainly enlightening enough to consider a deeper perusal.

In Dr. Plait’s own words…

Science doesn’t take away from the beauty of nature. It enhances it, multiplies it.There are so many incredible astronomical photographs released every year that picking ten as the most beautiful is a substantial task. But it becomes easier when you consider the science behind the image as well. Does this image tell us more than that one? Was the scientific result drawn from an image surprising, or did it firm up a previously considered hypothesis?Still, there’s something to be said for a simple, drop dead gorgeous picture.

Click the image to go to badastronomy.com.

I will, however, post the video that made the Top 10 to whet your appetite for one of the far more profound applications of youtube. This movie is a transit of our own Moon as seen from the two satellites that make up the Solar Terrestrial Relations Observatory, or STEREO. When we view such events on Earth, we call them eclipses, a coincidental (depending on who you talk to, of course) result of the Moon and Sun appearing to be the same size from our terrestrial vantage point.

2007 WD5 Rendezvous With Mars (or Not)

This will either be a very interesting event or, well, it won’t. According to NASA calculations, asteroid 2007 WD5 now (as of this post) has a 4% chance of impacting the Martian surface on January 30 at10:56 UT. While a 4% chance is pretty low by most standards, this represents a major possibility by astronomical standards, although nothing will likely come of it as NASA and other agencies make more observations and refine the likely path of the asteroid as it crosses Mars’ orbit. Then again, an impact crater would make an excellent addition to the February Message… Keep track of astronomy websites towards the end of the month for more information. If an impact will happen, you’ll be sure Astronomy Magazine and Sky and Telescope will be covering it as front-page material.

Black, White, and Red Acetate All Over

The good Dr. Forster sent the following animated GIF file from someone “speaking truth to precipitation” about the usual viewing session of your typical amateur astronomer. Proof that the quality of the presentation does not always detract from the message.

Click to go to the animated GIF.

Passage Of The Tully Lighting Ordinance

Member of the SAS Board and I are pleased to report on the successful efforts of our own John McMahon on the passage of a new Tully Lighting Ordinance (Local Law #7 - 2007). Whereas many astronomers talk-the-talk about light pollution and the diminution of our viewable celestial objects, Dr. McMahon has a long history of walking-the-walk (or running-the-run, as it were) as part of his work with SELENE-NY, his efforts on the Tully Town Board, and even as closing thoughts in the past few of his presentations I’ve had the pleasure of attending. Control of lighting, more efficient lighting, appropriately installed lighting is good for night viewing, it’s good for energy conservation, it’s even good for differentiating night and day.

A snippet from a draft copy:

“These regulations are intended to reduce problems created by improperly designed and installed outdoor lighting, and to enhance the natural beauty of the night sky and preserve the rural nature of our community. The objective is to reduce or eliminate problems of glare, minimize light trespass on adjoining properties and reduce energy consumption by establishing regulations that limit the types of acceptable outdoor lighting fixtures and their illumination levels. By regulating outdoor lighting, community character and aesthetics will be enhanced and excessive lighting that can become a distraction of [sic] traveling public and an annoyance to occupants of neighboring properties caused by improper lighting can be avoided.”

Jack Troeger’s Dark Sky Initiative Website

To continue the lighting and dark sky theme and finish this month’s message, I’m including the contents of an email I received from Jack Troeger, the owner/webmaster/vocal proponent/the “dark knight of the night” at darkskyinitiative.org. I specifically note the first few lines of the opening page of his site:

“Light Pollution wastes $5 Million nightly,magnifying global climate change!”

Energy, and ways to move ourselves out from the inefficient use of it in modern society, has finally become a major issue in government and media due to the state of the world. It is also a very direct way to address the light pollution issue to people that might otherwise not see the significance of freezing outside all night behind binoculars in the age of the Hubble Telescope. Do check out his site and offer your support!

From Jack Troeger:

I am a charter Member-at-Large of the Astronomical League, a 64 year old lifelong amateur astronomer (stargeezer), and retired high school earth science (astronomy / geology / meteorology) teacher. I do not believe we astronomers should flee like cockroaches to the dark corners of the country whenever the lights are turned on. We have a right to starlight, and we must fight harder to protect it and rescue it. Once upon a time I believed we could rescue and restore dark skies using the currently applied strategies, but they have not been effective. After careful review and analysis, I am now convinced we must press forward with all possible dispatch creating and initiating new and more effective tactics. I’ve begun posting periodic reflections and refractions (R & R) on my website as well as rewritten links. You won’t always agree with my scribblings (I hope), but perhaps they will stir some astronomical stew and motivate all of us to press forward… If we do nothing new or different immediately, the Milky Way will soon be extinct.Please share my new website with your group, post it on your organization’s website, and respond to my sincere, unconventional efforts.Thank you. Sunny Days and Milky Way Nights,Jack TroegerDark Sky InitiativeAmes, Iowa 50010troegerj@raccoon.com www.darkskyinitiative.org

Our friends in the South Jersey Astronomy Club also have a webpage devoted to light pollution and I would hope ANY astronomy club has a page about the same to spread the message.And that’s the story for the new year. Do stay tuned for more information on mid-winter/early spring viewing sessions and, of course, don’t forget about the Space Science Series meeting in February. Hope to see you.

Space is the place,
Damian Allis, Ph.D.
sas@somewhereville.com

Links Used Above (Subject To Web Changes)

astrosun2.astro.cornell.edu/~jpl/
www.cornell.edu
www.most.org
en.wikipedia.org/wiki/Canis_Major
en.wikipedia.org/wiki/William_Herschel
www.takeahike.org
www.astromart.com/articles/article.asp?article_id=167
www.takeahike.org
www.marcellusny.com
www.syracuse.ny.us
www.sjac.us
www.tullyny.org
en.wikipedia.org/wiki/Moon
en.wikipedia.org/wiki/Comet_Holmes
en.wikipedia.org/wiki/Mars
www.badastronomy.com/info/whois.html
www.badastronomy.com/book/index.html
www.badastronomy.com
www.badastronomy.com/bad/movies/armpitageddon.html
www.badastronomy.com/bablog/2007/12/13/top-ten-astronomy-pictures-of-2007
stereo.gsfc.nasa.gov
neo.jpl.nasa.gov/news/news153.html
en.wikipedia.org/wiki/2007_WD5
www.astronomy.com
www.skyandtelescope.com
home.earthlink.net/~urbanimager/cartoon.htm
webserver.lemoyne.edu/~mcmahon/mcmahon.html
selene-ny.org
www.darkskyinitiative.org
hubblesite.org
members.aol.com/sjastroc/sjaclht.html

Christmas came one day late.

A special issue of the International Journal of High Speed Electronics and Systems dedicated to a previous symposium on terahertz spectroscopy and imaging applications has made its way into hardcover in the form of a Selected Topics in Electronics and Systems volume (Vol. 46). The original article was blogged on this site in post #50, including the abstract and a couple of figures from the article. The book reproduces all images in greyscale, although the cover image includes an HMX molecule in pixelated technicolor. In the interest of readability (had I known…), I’m posting the images here as a single pdf (3.0 MB).

Click here or on the image above to download the image pdf.

According to amazon.com:

The inherent advantages and potential payoffs of the terahertz (THz) regime for military and security applications serve as an important driver for interest in new THz-related science and technology. In particular, the very rapid growth in more recent years is arguably most closely linked to the potential payoffs of THz sensing and imaging (THz-S&I).

This book presents some of the leading fundamental research efforts towards the realization of practical THz-S&I capabilities for military and security applications. Relevant subjects include theoretical prediction and/or measurement of THz spectroscopic phenomenon in solid-state materials such as high explosives (e.g. HMX, PETN, RDX, TNT, etc.), carbon-fiber composites, biological agents (e.g. DNA, RNA, proteins, amino acids) and organic-semiconductor nanostructures. Individual papers also address the effective utilization of state-of-the-art THz-frequency technology in military and security relevant scenarios such as standoff S&I, screening of packages and personnel, and perimeter defense. Technical papers introduce novel devices and/or concepts that enhance THz source and detector performance, enabling completely new types of sensor functionality at THz frequency (e.g. detection at nanoscale/molecular levels), and defining new and innovative sensing modalities (e.g. remote personnel identification) for defense and security. Therefore, the collective research presented here represents a valuable source of information on the evolving field of THz-S&I for military and security applications.

Get your copy HERE. In the right discourse community, it makes a great gift.

www.worldscinet.com/ijhses/ijhses.shtml
en.wikipedia.org/wiki/Terahertz_radiation
www.worldscibooks.com/series/stes_series.shtml
www.worldscibooks.com/engineering/6608.html
www.somewhereville.com/?p=50
en.wikipedia.org/wiki/HMX
www.amazon.com
www.amazon.com/Terahertz-Technology-Military-Applications-Electronics/dp/9812771794/…