Life as a Physicist

How many of you use the 1960’s email reader, pine? This trusty old goat of a IMAP mail reader is everywhere. It is written by my home institution, University of Washington. I think (!?) the history is it was written as a test client to the original IMAP server - IMAP was built at UW. But somehow it became the default mail reader. If someone is using a text mail reader, they are using pine.

I hate it. The reason is that I can’t send embeded plots, hard to format things properly… Modern mail readers are much nicer from that point of view. People used to complain bitterly if I accidentally sent around a HTML formatted email message to a mailing list - “turn your Microsoft crap off!”. Now, I don’t get complaints any longer if I do it - what with everyone using modern Linux mail programs and also the mass injection of Mac’s. At any rate — I’m very happy to see this change.

I’m continually amazed by how many people use pine. Really. Modern GUI’s are so much more powerful for managing the 100’s of messages we get a day. But pine survives and, as far as I can tell, thrives. I don’t get it.

Of course, my opinion hasn’t stopped UW from moving forward. UW got a grant to rewrite it. The next version will be called Alpine. Actually, it is more an evolution of pine, but still.

Niiice.

After spending a month in the States visiting family, working at Fermilab, attending conferences (well, my wife, at least), we will arrive back in France on the 24th.

What better way to re-integrate ourselves into France than to be at the wrong end of a strike! Yes, our timing is impeccable. The SNCF is on strike again in the continuing battle between Sarkosy, the French president, and workers over benefits, working hours, etc.

The last time I was returning from the Unexpected conference I also got caught. That wasn’t too bad — I did make it back in the end, just late. But I was on my own. This time it will be the two of us, a boat load of luggage and Julia. Wish us luck!

Dealing with Julia full time takes a lot of time! I’m one of the reviewers for an ATLAS CSC note (along with most of the collaboration). The paper I’m reading is 50 pages long. Normally, that is a solid afternoon’s work for me. Not this time — took me more than 2 days to get it done. During the day I have a few hours during her nap and the evenings I was often too worn out for the careful work that a review requires. And when she is awake she would drop by to play with me every 15 minutes even when she was playing on her own.

I love the girl, but I’m looking forward to getting back together with my wife and arriving in France where we have a nou-nou that will take care of Julia during the day!

I complain about ROOT a lot. However, one thing I have to say is that when you report a bug it is only a matter of days before it gets fixed in their source code repository. Philippe Canal just did a whole bunch of work after I found a few bugs in the MakeProxy code that means it will now be possible to use weird variables like vector<vector<double> > without having to think (these are produced by the EventView tool in ATLAS). Nice!

BTW, MakeProxy is a step back in time. Remember PAW (ok, I know, some of you are still using it). One of the nice things about the FORTRAN macros back then was the auto-loading of ntuple columns. Only what you referenced in your FORTRAN code was loaded. That isn’t the case in ROOT — it has no good way to scan compiled C++ code to determine what is used. Philippe wrote an automatic proxy-generator that replaces each ntuple branch with a bit of code that first makes sure the data is read in before accessing it (I’m pretty sure Philippe was the progenitor of the idea). In the end this has the effect of doing the same thing — only what is needed is read. I’ve seen x10 speed-ups caused by this. The only it can’t do is look inside a custom compiled object — so this doesn’t buy you as much if you are running in that case.

Otherwise, I definitely recommend checking out TTree::MakeProxy.

Have you ever noticed that buzzing sound that comes from your computer speakers? Sounds like some sort of very evil bug? Happens when your cell phone is near your speakers?

I think it is caused by a GSM phone communicating data over the packet network (do Verizon phones do this as well??). The iPhone is a heavy user of the packet data network and so is a particularly bad offender.

Now, think about a video conference room. This is a room with a large table in the middle that everyone sits around, and there are numerous microphones distributed around its top. The microphones are, of course, hooked into the electronics via cables — which are perfect pick-up antennas for this GSM noise. Every self respecting physicist has a cell phone and many of them are smart phones - heavy users of the GSM packet network. This can be hell for those on the other end of a video conference. The buzzing is very loud and can drown out everybody’s conversation, prompting remote participants to yell “move your cell phones away!”

My Dad’s iPhone will cause the buzzing in computer speakers from 4 feet away. He has a very simple solution — just put it on a bit of tin foil. This effectively kills the induced sound. A metal table will do the same thing. Now, I’m sure not every single phone is designed the same way, but if this could eliminate those noisy video conference calls…

The Large Synoptic Survey Telescope (LSST) was given a 30 million dollar gift from a fund run by Charles Simonyi (20 million) and Bill Gates (10 million). The proposed telescope will scan the sky night-after-night providing time-lapse pictures at a scale and detail not previously available. It is a proven technique that has been used on a much smaller scale previously. This experiment looks to me, actually, a lot like a high energy physics detector, aimed at the sky (perhaps that is part of the reason I like it). And, perhaps, the fact that members of the UW physics department and astronomy department are involved in it.

This is old news, especially if you read other science blogs (I first saw mention of it on the 4th). But I wanted to post it for several reasons. First - this is great. I can’t tell you how happy I am to see private money like this flowing to science. I suppose it always has - especially for applied research. But the LSST is about as pure as it gets: there are no products coming out of this - this is a search for dark matter/dark energy. There are lots of ways to donate your private cash to research efforts. The one I’ve been aware of for the longest is to donate your computer time: Rosetta@Home, SETI@Home, LHC@Home, etc. But getting cash in isn’t easy - especially when you realize that $30 million is only part of the LSST’s budget (something around 170 million)!

And that brings me to the second reason I have been wanting to post to this. The LSST is marked as one of Astrophysics top priorities. Numerous reviews of the field since have all put LSST at or near the top of the list. This is one of the experiments that would likely have benefited in the doubling of the science budget that was supposed to start this year but is likely now put off (for who knows how long). The LSST is high priority enough that eventually it will be funded - though if science funding in America continues to remain very tight who knows what other smaller experiments will suffer - in a similar way that science at NASA has suffered at the hands of the Mars program. Though, for me personally, this is very different - I don’t think of a manned mission to Mars as having much scientific value and I definitely think of the LSST has having scientific value.

Finally, I used to think of large private donors as being perfect for funding things that government won’t for political reasons. Cheap drugs because they are beholden to big-pharma, for example. Disease prevention in Africa because a government doesn’t think the continent is important enough (though I note that is finally starting to change). I have always thought that funding of pure research was the duty of a good government - it isn’t something that a company should be expected to shoulder and it is obviously important for the future of the country. So I find this a bit galling as well.

[Note: I wrote this post a long time ago; I'm not sure why it stayed in my drafts folder. But comments in response to this post on the java VM and Microsoft CLR made me realize I'd not posted it yet - though I thought I had!!]

I’ve been curious for a long time how much of a CPU hit do you take if you run your physics software in a Virtual Machine as opposed to the bare machine. I’m sure anyone who has used VM’s knows you take a hit — they always feel more sluggish. My impression is that for anything disk related they can be as much as 50% slower, but if it is just CPU it is just 5% or 10% slower. So, where does a real physics program stand in that?

To test this I and Todd, who works with our group back at UW, ran a few quick tests. We simulated about 20 ATLAS events. All of this was done on the same physical CPU. In all cases the ATLAS software was running on Scientific Linux 4 (basically a Red Hat clone). In no cases of the VM’s was any hardware vitalization going on.

** We also ran tests with VMWare, but I can’t find the email with the results now. However, I remember them being almost exactly the same as Virtual PC. The same hardware was used for all the tests.

So… running a VM will force you to buy 25% more machines to get the same work done. When you are running on a farm of 1000 CPUs that can be significant. On the other hand, using the approach that CoLinux does means you don’t loose nearly as much!

One reason we looked into this is that UW has a very large pool of Windows machines that sit in student Lab’s. Most of the time they are idle — so why not configure them to run simulation jobs during off hours? Of course, we can’t install Linux on them - so we thought about using VM’s instead. We did a pilot run with about 30 machines running the Virtual PC version, and produced about 40,000 events fairly quickly. It was very useful in allowing us to work with the machines we had.

Unfortunately, we had several BSODs installing CoLinux - but never one installing the VMWare or Virtual PC. And if one is running on Lab machines that are used by students one can not afford to have a BSOD: the lab manager will kick you off those machines so fast your head will spin! The other thing about colinux was that it was significantly more difficult to configure than any of the VM’s. However, just like the VM’s, once you got a disk up and running you could distribute that everywhere.

Sometimes it seems like our (USA, suburban) shopping life is spent in big-box shopping stores like Walgreens, etc. While I don’t mind them, I don’t like what they have done to the smaller stores that used to exist. Living in Marseille really drives the point home: to collect ingredients for a home cooked meal we will often visit a butcher, a vegetable market, a bakery, and perhaps, also, a pastry shop - though that last one is often the same as the bakery. In the US we might just go to someplace like Whole Foods or other big-box retailer.

As a result, when here in the US, I usually try to go to the local place first, and only after that doesn’t work to the big-box chain store. Just outside of Fermilab, for example, is a grocery store called Family Foods. It has been there as long as I can remember. A Walgreen’s has just opened up across the street from it. It is a sad fact that 2 of the three times I walked into Family Foods I had to then walk across the street to Walgreens.

Today, here in New Jersey, Paula and I had to get a document notarized so that I could travel out of the country alone with Julia. We started with the local Metuchen Savings bank - which looks like it is doing great business, but ended up walking over to the Chase bank to get it done. The Metuchen Savings bank had us waiting for about 15 minutes before we walked over to Chase. Chase, actually, had less business going on inside it so was able to serve us right away - so perhaps that is a counter argument.

And you can see this starting to happen in France as well. There are big-box super markets all around Marseille — just none that are in the downtown area. I’ve been to them once or twice - they are cheaper and always filled with people. I hope there is always space for the small local shops in this day and age of globalization (which, btw, I am very much in favor of).

The director of particle physics, Steve Kahn, at SLAC commenting on the budget cuts and the BaBar program:

As you all know, one of the consequences of the budget cut we face here at SLAC is the early conclusion of the B-factory run. Persis mentioned in her all-hands meeting that BaBar started operating in a different mode just before Christmas to make the most of the shortened run. The PEP-II accelerator team and BaBar physicists have put in a huge effort to adjust their program so rapidly to the changes imposed on us and it is testimony to their resourcefulness that this plan could be implemented so quickly.

Because they are turning off early a number of other science programs will go forward (the Tevatron, for example). What a pity!

Ok — I don’t usually do something like recommend software… but this was too good to pass up. For doing quick calculations on my computer I use Excel or some simple form of a calculator. While Excel is great - it is too heavy weight most of the time. And calculator apps - especially if I have to push buttons with the mouse - are slow and only good if I’m in Tablet mode.

I just discovered Calculatorium. It was first imagined as a side-bar gadget, something that will only run on Windows Vista. But you can download a stand-alone version as well now (they didn’t mention exactly where you can find that version to download ,however). But lets you define variables - “sz = 30*1024″ and then “sz/30″. Knows trig too. And a hole lot of other operations as described in the documentation - unfortunately, it looks like you have to download and install to see the documentation.