I run into this weird error all the time in Gaussian when doing optimization or frequency restarts. This is a big problem for me because a lot of times I run these on a large number of processors, but in a queue with a relatively short max wall time. Searching the web for this error yields one hit, and it’s in Chinese and not helpful even under Google translate.

Error originates: RdWrOT: IFlag = 2 Data mismatch
Search? I only get here. And the results aren’t exactly useful …

你给出的信息太少了,能不能多贴一点出来?

Anyway this almost always seems to be a problem with the collision of the previous and current route. Often I have to increase the number of optimization or SCF cycles because my systems are large and I do optimizations with diffuse functions, which tend to be pretty ill-behaved. Here’s the total head of the log:

******************************************
Gaussian 03: AM64L-G03RevE.01 11-Sep-2007
29-Mar-2009
******************************************
%chk=freq_min60.chk
%nprocshared=8
Will use up to 8 processors via shared memory.
%nproclinda=16
Will use up to 16 processors via Linda.
%mem=100MW
Default route: MaxDisk=200GB
----------------------------------------------------------------------
# freq=restart b3lyp/6-31+g(d) geom=allcheckpoint guess=read int=fmmna
toms=300 scf=tight
----------------------------------------------------------------------
1/10=4,30=1,35=1/3;
99//99;

GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
Berny optimization.
Restoring state from the checkpoint file "freq_min60.chk".
Title: min60
Route: # opt b3lyp/6-31+g(d) geom=allcheckpoint guess=read int=fmmnat
oms=300 optcyc=1000 scfcyc=1000
RdWrOT: IFlag = 2 Data mismatch
MaxStp (old) = 504 MaxStp (new) = 2
MaxJob (old) = 1 MaxJob (new) = 1
RdWrOT: Data mismatch on MaxStp/MaxJob
Error termination via Lnk1e in /apps/steele/g03-E.01/l103.exe at Sun Mar 29 01:19:04 2009.
Job cpu time: 0 days 0 hours 0 minutes 13.6 seconds.
File lengths (MBytes): RWF= 49 Int= 0 D2E= 0 Chk= 56 Scr= 1
Command exited with non-zero status 1


I’m posting this more so this error comes up in Google to Vdov so maybe, maybe someone can tell me about it (no one, including people who really know the software well, has been able to provide an acceptable explanation thus far). If the two routes are both optimizations, for instance, you can usually get around this error by eliminating the opt cycle specification in the new restarted route. But if you’re moving the guess and geometry to some new calculation, it’s nearly impossible to get around this. The solution is almost always to create a formatted checkpoint file (formchk) and convert back (unfchk), so the route disappears. You could also obviously do this by specifying the new geometry as a Z-matrix in the initial calculation, but I much prefer to read my initial guess from the checkpoint, so this is not a good option in many cases. Starting the calculation and then restarting from the new binary checkpoint file usually does the trick, as there are appear to be no collisions in the route cycles.

Anyway, cheers. Hopefully someone who knows something about this will let me know.

This is a method for generating data in gromacs programs which require the system to be composed of only those molecules or atoms on which statistics will be run.

Let’s say you have a system composed of N different species and you’ve got your xtc trajectory file from the run. Then let’s say you want to know about average cluster sizes of one of the species in the simulation. For some programs in gromacs (not g_clustsize, the one in question here) this is fairly easy because the software lets you specify, either through the program options itself or through an index file, what you’d like to consider. With others though, especially those with options for dealing with molecule statistics explicitly, that don’t allow you to do this for whatever reason. So, a workaround is necessary.

First, edit your input mdp file and topology with extreme prejudice, eliminating or commenting out references to anything you’re not interested in. For instance, in my files, I need to remove all water and ions. I call all these new files “fake” versions of the real files.

$ diff fake_fullmd.mdp fullmd.mdp
15,16c15,16
< xtc_grps = protein ; sol na+ cl-
< energygrps = protein ; sol na+ cl-
---
> xtc_grps = protein sol na+ cl-
> energygrps = protein sol na+ cl-


$ diff fake_topol.top topol.top
163a164,166
> SOL 9529
> NA+ 10
> CL- 10


Make sure you have an index file if you don’t already:

$ make_ndx -f conf.gro


Then dump the first frame of the real simulation. The program (trjconv) will ask you which parts of the frame you’d like to dump.

$ trjconv -f traj.xtc -o fake_protein.gro -s b4md.tpr -n index.ndx -dump 0
...
Select group for output
Group 0 ( System) has 37968 elements
Group 1 ( Protein) has 1568 elements
Group 2 ( Protein-H) has 784 elements
...
Select a group:


Now generate the new input binary for your “fake” system.

$ grompp -f fake_fullmd.mdp -c fake_protein.gro -p fake_topol.top -o fake_b4md.tpr


Convert your trajectory, again selecting whichever part of the trajectory you’re interested in.

$ trjconv -f traj.xtc -o fake_protein.xtc -s b4md.tpr -n index.ndx
...
Select group for output
Group 0 ( System) has 37968 elements
Group 1 ( Protein) has 1568 elements
Group 2 ( Protein-H) has 784 elements
...
Select a group:


Now you’re ready to run your analysis! It won’t actually use the index file you specify here (since you’re only looking at molecules with the -mol option), though it requires it for some reason that eludes me.

$ g_clustsize -f fake_protein.xtc -s fake_b4md.tpr -mol -n index.ndx


And there you have it. Cluster statistics for an arbitrary subset of your system. Cheers.

NOTE: There actually are slightly more elegant ways of doing this, but this is perfectly sufficient for simple situations, like clustering of some molecule in some other explicit medium.

Who doesn’t like a good White Russian? Well Khalua is a damn expensive way to make your cream taste like sweet coffee. Thus I have concocted a simulacrum that would put a smile on The Dude’s face.

First you have to be in Rhode Island or it’s immediate vicinity because you need coffee syrup (it might be available elsewhere but I can’t vouch for it but it just happens to be half the ingredients for the state drink… coffeemilk) which is pictured to the left. Then it is cream and cheap vodka.

2 oz vodka
1 oz coffee syrup
light cream

Done!

UPDATE: If you search for “coffee syrup” you don’t get this but if you search for “eclipse syrup” you do… bravo

There is an interesting roundup at HubSpot of characteristics of Twitter users that correspond to more/less followers than the average number of followers. The one that caught my eye was followers by political affiliation. It corresponds to my earlier posts about politicians who use twitter and the observation that Republican politicians seem to twitter more often and more “authentically” than Democrats. Perhaps it is a reflection of the political makeup of the twitter community? I wouldn’t get too wild with pulling correlations from this data but it is interesting. (apparently #tcot is a tag for “top conservatives on twitter”

One of my favorite subjects and probably most briefly studied in college was Economics. It is one of the courses that I think everyone should take at least a little of or should read up on in their own time. That said I like to keep a couple Economics blogs in my RSS reader just to see the views Economists have on whatever is going on (not surprisingly they have a lot to say right now). I also like to get a few different perspectives so I usually read Paul Krugman in the Times, Marginal Revolution which is a couple different Economists, and Greg Mankiw’s blog. Krugman is a Nobel laureate in Economics, Tyler Cowen (Marginal Revolution) is a prof at George Mason and writes for the NYT, Alex Tabarrok (Marginal Revolution) is also a George Mason prof, and Greg Mankiw is a Harvard prof and author of the best selling intro Econ textbook.

So now the point of this is that Mankiw’s blog now has a great tie in done by the publisher of his textbook. The publisher went through his blog and made a “blog map” tying blog posts to specific citations in the textbook. Its pretty cool considering that the idea behind Mankiw’s blog is to keep students of Economics up to date with contemporary examples. Now I have no idea what the back end is like on the “blog map” but you can imagine how this could be seamlessly integrated in a very semantic way. For example tags on blog posts could auto update to the relevant citations on the map, certain phrases could trigger citation/tagging automatically, and on the textbook end you could imagine that sections be tagged in an electronic form as they are added in new additions thus updating citations throughout the blog map even with older posts. The awesome part is that you can really see the value added to the textbook. By linking it to the blog you basically get continuous additions by Mankiw making the value of his authorship continual rather than finite.

A while ago I wrote a post about government types on Twitter. What surprised me at the time was that Republicans seemed to outnumber Democrats on Twitter. A blogger from the UK, Mat Morrison, confirms my supposition with a nice map. He also brings up a point I hadn’t even considered. There is almost no cross-talk between the two parties (at least on Twitter). It really makes on wonder what contact Republicans and Democrats have online. Do congressmen text each other all the time? Email? Is participation in social media balkanizing or unifying? The one thing Mr. Morrison doesn’t address is the “authenticity” of congressional tweets. There is a HUGE difference between Hillary/Obama’s staffer written tweet directives and the personal tweeting of Rep. John Culberson, Tim Ryan, Thad McCotter, or Neil Abercrombie (who has a very odd twitter feed… and starts a lot of tweets with a “Hi everybody” or similar phrase).

The lovely and talented jgronberg who is a sometimes vdov reader and good friend has sent out his yearly and very exclusive email album review. With his gracious permission we are posting it here (mostly to shame ourselves for the lack of posting or any end of the year lists this year). Consider yourselves lucky…

Time to look back, if just for a moment. ‘08 is probably a year that many want to leave far, far behind, but at least there was some decent music. For the 4th year running, here’s some albums I liked that you may want to check out.

Following college it has been increasingly difficult to present a solid list of compelling albums. With the slim trickle of new music reaching my ears when compared to the bountiful days of WBOR and Bowdoin College, I have a much smaller list of music to choose from. I know a lot of my friends find themselves in a similar situation. So- hopefully this provides a few new items for you. Here it is: my non-hipster approved list, starting, as usual, with number 10.

(10) Fleet Foxes- s/t (June 2008)
Alright, Ryan. Fine. I like it. I listened to it a bunch over the Holidays and it was good. My parents even remarked “this is great Christmas music!”. You win, you always do. Goulet.

(9) Cut Copy- In Ghost Colours (April 2008)
Disco’s back, baby! Or is it 80s pop-synth-electronica? Whatever it is, it’s fun. Though- I sometimes get odd looks if I crank this album while driving around town in my Miata with the top down. Can’t quite explain that one.

(8) Airborne Toxic Event - s/t (August 2008)
Maybe they don’t have the most developed sound- in fact, you might even liken it to that poppy-happy crap that swills out of most of the major labels. Then again, its catchy and I like it. I can’t fault that all too much. Perhaps my tastes are drifting more toward the mainstream at this point. Being further from the vast wealth of new music that is college radio, my exposure to new work has fallen off– though KEXP provides a steady stream of awesome indie music. Airborne Toxic Event has expanded their EP from 2007 quite nicely with a well-rounded album that offers fast paced songs like “Wishing Well” and more gallant, “epic” sounding songs like “Sometime Around Midnight”. All together the album hits a number of points, albeit with slightly emo lyrics, and provides an enjoyable listening experience.

(7) TV on the Radio- Dear Science (September 2008)
TV on the Radio (TOTR?) sound like a refined, professional version of The Mathematicians- especially in “Dancing Choose”. I cannot complain about such a resemblance. The more palatable sound perhaps means I would be able to get more than a small group of close friends to listen to the group- such has not been the case with The Mathematicians. I applaud those who see the genius in Dewey Decimal and Pete Pythgoras, and perhaps an album like Dear Science can be the gateway drug to more cultish favorites.

(6) Cold War Kids- Loyalty to Loyalty (September 2008)
Some records are “headphone albums” or “scream-out-loud-in-the-car albums”. Loyalty to Loyalty is most definitely a vinyl album. It is best enjoyed on a nice set of turntables with giant speakers attached, encouraging you to sit close by and drink in the intricacies of the music. CWK is still on my list of must-sees- I missed one show in Boston (for which I even had tickets!), but I won’t let such a tragedy happen again.

(5) Vampire Weekend- s/t (January 2008)
Again, more mainstream-ish. They seem to be getting popular awfully quick. I hope a second album follows that is just as good. I may have burned out on this one simply because I listened to it so often over the summer; that’s a sign of a great album in my book, though. I like cohesive albums, and this seems to lack the strong theme(s) that many of the other compilations on this list have, but each song is so strong on its own that I can let such a foible pass.

(4) Bon Iver - For Emma, Forever Ago (February 2008)
I want to be relaxing in a leather chair in front of a fireplace, looking outside at the falling snow, with a glass of scotch in my hand as I listen to this album. It is supremely relaxing, and evokes a distinct calm winter night vibe that is simply perfect. Okay- fine- their name is “Good Winter” but still… you could call them Bob’s Oyster Sandwich Team, and I’d still get the same feeling. I missed their show in Boston this year, which came at a perfect time to reflect on cold evenings, but I am not sure if I missed much- this really seems like an album for at home in the living room.

(3) Ra Ra Riot - The Rhumb Line (August 2008)
Somehow, an album for which I cannot particularly remember specific songs has made it to #3 this year. I am a loss of what to say. However, as I thought about the album in comparison to each of the others on the list, it kept climbing. There is just something about it that really works. It’s not pop crap, its not erudite indie drivel, and its certainly not emo crooning. Its just a great album. FWIW- they are the highest ranked “band I have not seen live” from any year (discounting last year because, as I mentioned in that email, the non- #1 albums really weren’t that great in the grand scheme of things).

(2) Amanda Palmer - Who Killed Amanda Palmer? (September 2008)
Some people call her narcissistic for her obsessions with talking about herself. I find it entertaining that Amanda Palmer details so many things in her life to her audience- it makes her one of the most accessible artists I have encountered. Whether it is watching her sing Rhianna’s Umbrella on some street in Belfast with a broken foot, or auctioning off band gear as a intermission at her concerts, or writing her own twitter updates, she connects with the crowd. The songs on Who Killed Amanda Palmer work toward this goal of sharing by being deeply personal. The rhythms are pretty catchy, and her powerful voice shines through as always. I was also impressed with the input of Ben Folds in producing and arranging the album. Well done! To top it all off, the opening track on this album rocks, and a killer opening track will always win me over. PS- the Dresden Dolls album this year, No Virginia, is quite good too- I just did not want to flood the list with Palmer entries (and the opening track of the Dolls album is rather weak).

(1) The Hold Steady - Stay Positive (July 2008)
When I first heard the Stay Posi’ songs at the Paradise last spring, the band clearly had not practiced them much in front of a crowd- I was worried. After hearing the full album, though, I was totally sold. It’s damn good. Really damn good. THS’s sound has matured from earlier iterations. Not the “that cheese smells terrible” sort of matured, but the “Craig Finn can carry a tune!” matured. If Craig can continue this upward trajectory, he may even win Jessi over one day. The Hold Steady managed to impress me while playing at the Orpheum in Boston- possibly the most horrid venue in the world for such a band- it was clearly designed for midgets with binoculars and highly sensitive hearing. Oh- and if it is still up, check out this video. Muppets doing THS. woot.

Now, the massive post scriptum, my historical top 10s, starting with 2005.

2005
10. The 88 - Over and Over
9. Absolute Music volume 47, Swedish edition
8. The Mathematicians - Level One
7. Maggie, Pearce and EJ - Morgon, Mittag, Nacht
6. Death Cab for Cutie - Plans
5. Roman Candles - Bang! Bang! Bang!
4. Why? - Elephant Eyelash
3. Broken Social Scene - s/t
2. The Decemberists - Picaresque
1. Clap Your Hands Say Yeah! - s/t

2006
10. Beirut - Gulag Orkestar
9. Killers - Sam’s Town
8. Yeah Yeah Yeahs - Show Your Bones
7. Wolf Parade - Apologies to the Queen Mary
6. Architecture in Helsinki - In Case We Die
5. Electric President - s/t
4. Dresden Dolls - Yes, Virginia
3. The Decemberists - Crane Wife
2. The Mathematicians - Level Two
1. The Hold Steady - Boys and Girls in America

2007
10. Feist - The Reminder
9. Radiohead - In Rainbows
8. Spoon - Ga Ga Ga Ga
7. Modest Mouse - We Were Dead Before the Ship Even Sank
6. Beirut - Flying Club Cup
5. The New Pornographers - Challengers
4. Tally Hall - Marvin’s Marvelous Mechanical Museum
3. Pela - Anytown Graffiti
2. Okkervil River - The Stage Names
1. The National - Boxer

1) Listen to them try to sell you various products they’re working on

2) Actually sign up for any of those products

3) Invite people over who need to reinstall N > 2 computers

4) Have absolutely nothing else to do

Merry day after Christmas. Cheers.

Since I have been home in Indy and driving around in my brother’s car which doesn’t play nice with iPhone tunes I have been listening to a bunch of satellite radio while cruising around. This coincides to hearing the Killers about once an hour. I just wanted to point out they seem to have a massive structural misconception in “Human.” Merry Christmas kids…

PS: The classic “NORAD tracks Santa” can be seen here: NORAD Santa Tracker (note that Iran is on the bad list… but the ISS was over Iran when Santa hit up that crew)

I’ve been giving a lot of thought to how crappy my home network has become. Of course this has gotten me to think about what my ideal home network would look like. So, for all of you out there, let’s do a little thought experiment. Say you have the money to put together your “perfect” home network. What would it look like? What major components would it use? What services would it run? How would it be organized?

This has been a pretty fun little experiment for me, and I’ve come up with configurations anywhere from relative modesty to incredible setups which would cost tens if not hunders of thousands of dollars and include substantial modifications to wiring and home configuration (network closet anyone?)

Maybe some of you have some ideas. Cheers.

It sometimes amazes me how a lot of people are much happier to ask stupid questions than to just do the basic work themselves, maybe even learning something in the process. In the Gromacs community, the past couple weeks have been a great time for some nice examples of this. Version 4 came out, which *substantially* improves the scalability of parallelized molecular simulations, due to a move from the previously standard particle decomposition method to the much more general domain decomposition (DD) method. The DD method has been popular in continuum physics and in other fields for quite some time, but this is the first real application to discrete work it has seen.

So, of course, people need to know how to do parallel simulations with this code. In all major package managers 4.0.2 hasn’t made it through any appropriate channels, so people have to build it themselves. Unlike most major scientific packages, building Gromacs is absurdly simple. Things are quite beautiful actually.

Anyway, my point isn’t to extol the virtues of Gromacs but rather to suggest that if something doesn’t work, do the initial work to figure out the problem and exhaust at least the most obvious problems with the software before throwing your hands up in the air. Problem with MPI? Test it first! Anyone working with MPI should at the very least be able to look up how to write a basic MPI application.

An example:

#include "stdio.h"
#include "mpi.h"

int
main(argc, argv)
int   argc;
char  *argv[];
{
  int  rank, size, length;

  char name[MPI_MAX_PROCESSOR_NAME];

  MPI_Init(&argc, &argv);
  MPI_Comm_rank(MPI_COMM_WORLD, &rank);
  MPI_Comm_size(MPI_COMM_WORLD, &size);
  MPI_Get_processor_name(name, &length);

  printf ("process %d of %d on %s\n", rank, size, name);

  MPI_Finalize();

  return 0;
}

If you’re on a modern Debian or Ubuntu build with OpenMPI installed (pretty much the standard MPI implementation you should be using), then build.

$ mpicc.openmpi -o hello hello.c
$ mpirun.openmpi -np 4 hello
process 1 of 4 on enskog
process 2 of 4 on enskog
process 3 of 4 on enskog
process 0 of 4 on enskog

I do love my MPI. And Gromacs does dynamic load balancing now … so freaking fast.

Cheers.

Ah it’s time to go on a bit of a rant here. I learned a number of important travel tips while I was trying to get back to the states from Italy. They are:

• Flying random airlines localized to a specific country is usually a very bad idea
• … Especially when those airlines are localized to a country where strikes are often completely random in nature.
• Never, ever, when traveling internationally, book multiple trips on the same day.

Now some specifics:

I arrive, after a really fantastic trip in Italy, to the major Rome international airport (FCO). My flight was to London on Alitalia, where I was to pick up a seperate set of flights back to Indianapolis. The UK government paid for my trip to and from London whereas my trip to Italy was for personal business, so these two trips were booked separately.

Accordingly to Alitalia, my flight was “confirmed” and my ticket was “valid”. Ha! Well it turns out that Alitalia was randomly striking at the time, but only sort of striking, as some pilots would show up to fly the planes and others would not. This seemed to be completely par for the course there, which didn’t make much sense to me. Turns out people had been waiting there for a flight to London for over 3 days. None of their flights had left due to this strike. And of course all other flights to London were way overbooked because Alitalia hadn’t had a flight there in nearly a week. But, of course, according to the airline, the tickets were still “valid”, they just didn’t have pilots to fly the planes.

As the time came where it became obvious that I wasn’t going to make my connections in London, I started to freak out a bit, since it seemed no one was going anywhere from Rome and I was never going to be able to get home. I forfeited my flights from London to Indianapolis and was stuck in Rome because of this crappy airline. So, I had to wake up my parents at 2 am on the west coast to book me new flights back to Indianapolis through Frankfurt and DC. What was a nearly free 2 week stay in Europe had just become much more expensive.

Obviously I couldn’t show up for my flights in London, so those tickets were just flat gone. Would Alitalia at the very least give me my money back? Of course not, they claimed my tickets were still “valid”. Good lord. Screw you people.

When I arrived in Rome and told the people I was staying with that I was flying out on Alitalia, they openly laughed at me and said “good luck getting home”. Ugh.

Never fly Alitalia.

Cheers.