Friday, January 31, 2014

Graduate School Finance 101

Dear Diary,

It has struck me recently that I am no longer an undergraduate.  I earn money for work.  But what is the money for?

I suppose I could go blow it on the slots, but the odds are not in my favor there...and if I start winning then I haven't solved my problems at all.  Now, let's pretend that I have a car (or any recreational activity...I don't) and could get out of here on the weekends to go camping and recharge my batteries.  I suppose money would go to that, but surely there'd be some left over (?).  Right now, the extras are placed securely inside my mattress (SHH!  Tell no one!), but what should I do?

Well, the folks on the internet tell me there are a few options that I'll discuss here.  Principally, one can invest money now for use later.  A novel concept! There seem to be mutual funds where stocks and bonds are bundled together.  Two types of companies can handle these for you: one is speculative and the other is indexed.  In the former, the company alleges that it can consistently find stocks that beat the average. The latter actually consistently outperforms the former by just matching the stock market day in and day out (there's also less hidden fees in this second option).

So, I went with the second option.  I put some money away in a Roth IRA which allows me to pay taxes on it now while I'm earning basically nothing.*  The other type of IRA makes you pay taxes when you withdraw (but you'll be earning more).  I also put a little into a regular mutual fund (why not?).

Oh, and I'm going to start looking for a leisure hobby.

*-An oxymoron considering the subject of the post.

Wednesday, January 29, 2014


Dear diary,

Most of us in the group were born while Pluto was in the house of Scorpio meaning that we will have to find ways to rebuild fundamental human connections.  This makes a lot of sense considering so many people play video games and can't interact except via texting.

Kieron has decided that we will try to put our heads together and collaborate on projects, so we're all supposed to catalog what we're doing and see if it can be combined with something else.  I emailed a template around and had the Computer Whiz make a soft linked folder on the group server so everyone had one place to put their stuff.  Bonus points if someone can link more than two projects together!

We'll see how this goes!  Especially considering Pluto is now entering Capricorn which means a time of much upheaval!

Monday, January 27, 2014

Email Signatures

Dear Diary,

Now that I'm finally communicating with people outside of the university, I feel the has come to add an email signature to my school emails.  I still have to introduce myself in emails, but it could be useful if someone wants to know more information.

I guess I could go with this one I get from a frequent collaborator:

Dalek Sek
Ph.D. wanna-be
Group of Davros
Holder of the Seventh Key to the Breeze-Bore Dimension
Ate Spaghetti Somehow for the First Time Last Night (It was Good)

What Department
Skaro University
Skaro, S&T 007

Tel: (123) 456-7890
Fax: (123) 456-7890


But that's a bit long for what I have...Maybe with the website around I'll pick something short:
The Doctor
Department of the Who, Gallifrey
And build it up through time (and relative dimension in space?!).

Saturday, January 25, 2014

You shall not covet (PRLs)

Dear Diary,

Physical Review Letters is upping the difficulty to get in once again.  The premiere physics journal previously set the bar higher and is now doing so again to make itself more prestigious.

That's bad news for all of us in the group.  Kieron has declared that we should shoot for more papers in this journal before we graduate.  You know what they say, Diary:  When the submission criteria get tougher, the graduate students stay longer.  Kieron's really good at these things (look at the track record!), but I can't help but be tremulous.

Especially so since I just got rejected from the journal for my old research, and I'm due for another rejection on a second paper, shortly.  The reviews have seemed really...well, I thought I'd said very clearly we were in the opposite limit from what they wanted to compare...and sometimes they come right out and say mean things.  I'll try to stay positive, though, and remember the reviewers are just trying to do their job.  PRLs are supposed to be hard to get.  Maybe I can pick up a few tips on a thick skin from Kieron.

Anyway, I guess there's no point in doing bad work to get into a worse journal (one must graduate!). But even if you do good work, it has to sell...I guess...It could be that some papers with good work just can't be shortened into three pages.  Maybe we'll be able to bust out a better paper in some other journal with all the free space for every detail we want...

...well...I'll get back to it...I guess...Maybe I can make progress on that calculation Kieron wanted me to do.

Friday, January 24, 2014

Friday Magic

Dear Diary,

It's Friday.  That means the Friday magic will occur at either 5:30 or 8:30 pm local time.  I suppose I could stay and get perhaps these MKL Libraries to work...Hmm, I just realized that I was fixing MKL libraries on MLK day!  Yay!

Raphael just told me he had his most productive hour or so this week. He seems to have caught the magic wind.  I informed him that it's only good until Monday when the delirium for working so long wears off, you realize everything was wrong, and you fix it Tuesday night for good.

I think I'm heading home for crackers, cheese, and reading that paper that Kieron gave me.

Tuesday, January 21, 2014

At long last


I told you!  Working late on Tuesdays somehow fixes whatever breakthrough made you happy while working late on Fridays!  Today was just such a day:  a Tuesday!


I stayed late and started to redo some calculations that I'd done earlier since I'd run into a brick wall. The work-around paper that Kieron gave me was going to take a bit to digest, so why not double check some things first?  I went back, took Miles' data, and fit it.  I got his numbers spot on!  It's more amazing that Miles did this all by hand and was as accurate as a computer!

This is such a relief.  I had resorted to methods (even being non-sensical in front of Kieron!) to solve this problem that I would even agree were completely stupid.  It's the sort of crazy that makes you wonder if you're actually sitting in a padded room somewhere babbling incoherently; a feeling I frequently have while doing physics!

But, the battle isn't over.  I'll probably still do Kieron's suggested calculation, and  I suspect that these numbers only work in the low density limit.  The points we trained on were only quasi-uniform in the low density limit and we haven't really tested the fit on anything higher, but I have a sneaking suspicion that our numbers work best on only low densities.  I'd be happy to be wrong, though, since it means I don't have to rerun all the plots Lucas and Miles made!

One could ask why I couldn't get the numbers earlier.  I told Kieron that I was out of all my Luke-scuses at the end of last quarter, but I seem to remember that Lucas and I decided to put Miles' training sets into ours.  I also think we were weighting the data sets which would take us farther from the numbers.  Keep in mind, Diary, if I would have confirmed Miles' numbers at the beginning, we would not have serendipitously found the right answer in all the wrong ways.  If I'm wrong-wrong and have wasted all our time...well, then we're double sure!

I suppose I should look forward to some ribbing for dragging this out so.  Really, this has taken me too much time to see if Miles' numbers could be found from my fancy pants program.  Ok, sure, there was a fellowship, a test, a vacation, and lots of administrative things in the way, but I'd like to move this along.  I might even have something for the March Meeting!

Monday, January 20, 2014

Mucho Macho Pruebas!

Dear Diary,

The cluster has been humming with my calculations recently.  I'm preparing lots of data for Li.    I've spent a lot of time debugging how I was making all 2000 points for him and found one key error:  the number of spaces between four fingers is three (not four).  Basically, I set up my code to automatically generate the program files somewhat strangely.

Anyway, now I'm pumping out the correct data and will send it to Li as it comes out.  The cluster really makes it slick to calculate large data like this and I can't even imagine doing it on my personal machine.  I can basically run things overnight!

I have noticed that copying the scripts to set up all of the programs is really quick with Unix to boot. So, giving them more data shouldn't be a problem if it comes to that.

Now, Kieron asked us to run a "macho test" and I haven't quite looked into that yet.  Hopefully, I can see if something is located in previous papers, so I'll go take a peak now.

Friday, January 17, 2014

Cluster B(l)uster

Dear Diary,

Well, there's no easy way to say it...but I suppose you should know:  I broke the cluster.

For several weeks, those who use the computing cluster have complained that it's been abnormally slow.  In fact, I even received an email from another graduate student concerned that I might be using the resource improperly.  I denied it at the time, but it appears that I was complaining about myself for nearly a few months.

In retrospect, I should have known that something was wrong because the data was sometimes coming out strangely.

You see, you submit jobs to a temporary directory where it submits everything to the cluster machines.  If you need to copy back a lot of files from the temporary directory, then it gums up the system.   And I'm guilty here.  To fix it, my little script submission file now only has ">out" instead of ">(home directory)/out" to prevent it from copying everything back.  Further, I only needed two files out of the possibly thousands of files that are output.  So, I just added 'make clean' to the submission script and that gets rid of everything before it comes back to me.

Charge 2 is requesting the correct number of computers and threads.  I had requested one computer and one thread, but a command for OpenMP (to parallelize the code and make it go faster) was set to request 8 threads.  So, my program was unhealthily bumping up against other's corrupting everyone's data and making it so that writing files out was not working.  This really made things messy.

The key here is to not look at the output files.  It says, simply, "nodes".  I had requested 1 node (aka computer) with ppn=8 (for 8 threads), but it reported 8 nodes...So, I should trust I filled out the fields correctly instead of looking at the output file...Summarily: nodes=1:ppn=8 (for 8 threads).

Now, none of this is particularly egregious...and I would have gotten away with it (if it weren't for you meddling kids!) but I was running so much data that little mistakes made a big difference.

I'm going to go and barricade myself over the weekend and lay low until this whole thing blows over...oh, and I'll run that data that I owe Li.  These fixes actually come at a good time because running jobs over the weekend is best (less use the cluster).

Wednesday, January 15, 2014

The Fellowship of the Grant

Dear Diary,

Whew.  I'm exhausted.  I just toted a tiny grant proposal all the way across middle winter.  I wasn't really equipped at first to handle this task and take the precious to the end, but I had a great band of comrades who helped me out.  The ability to fund oneself is important as one grant can rule them all and, in the physics, support it.

Sure, we bickered about how the essays should be written, what they should be written about, who to send reference letter requests to, and ultimately who gets the money if we win, but the real adventure is between friends.  At first, the essays seemed to dig too deep and too greedily.  Strangely enough, the more I attacked the essays in a short amount of time, the less effective I was.  So, it was important to space things out.*

I had enormous writer's block and had to rewrite everything approximately infinitely many times, but it led to a good place.  I am worried that if we wind up some of the essays any tighter, then they'll snap in half while the reviewers are reading them!

And if I win, the precious will be mine!  I'll be invisible to all external granting woes!  It can even go on my CV!

...oh, and there's the sweet physics I'll get to do too...

*-But maybe not three movies worth...

Monday, January 13, 2014

Get down with the sickness (Go home)

Dear Diary,

Everyone is sick.  Beware!  I don't need you getting sick!

I suppose, quite universally,* the sound medical advice is to go home, rest up, eat some soup, and wait until at least the fever passes.  But the physicist is a strange creature and the wrong sort of doctor to know these details.  No sickness can stop us from spreading it to everyone else.  Indeed, making everyone else sick will clear out the office and provide for some highly valued free thinking.  Further with the lack of regular exercise from the desk job-y nature, we don't have the crazy immune systems.

It's probably also a good competitive strategy to force an illness bug to mutate into a superbug that can't be tackled by viruses (which explains why everyone is taking cough medicine right now...and causing the bugs to adapt!).  This provides more work for our biologist brothers and sisters, and I think you might be able to send home a few pesky students by coating the bathroom door handles with germs.**  Less teaching!  Now if only we could get delays on grants through this somehow...

I guess I'm not the most effective messenger for the "Go Home" message because my ulterior motive is to get the office all to myself (Aha!  So staying healthy is also a competitive strategy!). But this is a double edged sword because if you're healthy, then you have to come in (you're healthy) and breathe in all errant sneeze particles and cough exhaust.  I'm not going to take a sick day just because all of you are sick.

The strangest part is that everyone who's sick got a flu shot. What does this mean?!***

It means: Go home if you're sick!****

*-even from mothers!

**-use soap!

***-Aha!  It means I don't have to bring cookies to group meeting if Kieron Skypes with us from the Prof. Kieron Infirmary!

****-Although, when I eventually get sick in a few days from breathing all the air, I'll probably refrain from staying reinfect everyone!

Cluster Q&A

Dear Diary,

Just recently, the resident computer cluster ran out of memory and quotas were reduced.  I recently sat down with one of the users who had an enormous amount of data sitting on the computer at the time.

DrWho: So, what did it feel like to have your name on the list of people who would be over the new, reduced quota?
V: Uh, well, nothing much really.
DrWho: You must have been impressed with yourself.
V: I guess...really it's my fault for keeping so much data on the login computers.  We have a whole separate server for things like that.
DrWho: Did you lose any data?
V: No. In truth, I hadn't run anything for a month or so.  Did you?
DrWho: Yes, I was running some things the night before, so I must have put the server over on it's gross quota before they reduced everything.
V: Oh, oops. Bummer. Hopefully it wasn't important...
DrWho: No, of course not.  I do have to somewhat annoyingly truncate my enormous calculations with the reduced quota...What advice would you have for incoming graduate students so they don't overuse their resources?
V: Why not just ask for a bit more quota space?  Wait, this isn't going on your dumb bl-
DrWho: -and we'll have to keep it there for now.  Thanks for the interview and tuning in!

Friday, January 10, 2014

Double-Double Blindness!

Dear Diary,

Kieron enjoyed things that are double blind so much, that I thought I'd give him another one:

A double-double blind test!

Miles and I and trying to fit a particularly pesky correlation funcational.  Miles went very high tech and programmed infinite DMRG.  One wonders how it finished!

Meanwhile, I've been lazing around all winter break and writing a fellowship (more on that later).  So lazy!  I found the paper but haven't even looked at what Kieron wanted me to look at (a way to find one of the coefficients exactly), and my Bethe Ansatz calculation is only started (and I'll probably need to review because I started it before the break).

Needless to say, Miles got done first but the results weren't a nail in the coffin.  I put together an summary document that shows why, but I'm not sending it to Kieron right away.  I want to see if I can do a calculation or two before my individual meeting and provide the way forward!  It wouldn't be completely useful to him right now anyway...he's reviewing my fellowship stuff, a paper I gave him, and teaching a class! If I was unsure about what to do and wasn't busy, then I'd show it to him, but since I haven't done what he asked, I'll see if I can put together a complete story by the time individual meetings roll around.

But here's the catch, diary!  I'm not going to let Miles send me the data he has...I have to calculate it on my own and hope it matches (the first blind!)!  Then, Kieron won't have seen what we have done at all (the second blind!) until I can get a firmer result!

Physics is totally blind!

Tuesday, January 7, 2014

Old Computer, New Computer, Red Computer, Blue Computer

Deary Diary,

Kieron wants me to upgrade my circa 2005 laptop.  I'm reluctant.  I've been able to keep this thing together through blue screens, lost work, and hours of inane debugging with Arch Linux.


The joke is, my current computer is almost as good as all the new ones if it just had double the hard disk space and twice the processing speed.*  Processor speeds have sort of maxed out because their cooling abilities can't handle the extra heat generated by a faster processor.  That's where spintronic/quantum computing applications might one day help.  Oh, and my current laptop weighs 12 pounds.

So, you have me on the heaviness thing.

Unfortunately, I'm not an undergraduate, so I might not be able to deduct this off my taxes, but I'm ready to go from Eric Clapton to Eddie van Halen and accept that the computing world got itself into a big hurry.  While I might someday regret choosing the fast computing life and leaving the safety and comfort of yesterday's small town computing palace, Kieron is adamant and I have no leverage.

After an exhausting search, I've decided to get another laptop.  Getting a desktop would be like playing the cello in a marching band for what I need it for: conferences and the weekly group meetings. My strategy is to go small and go light.  The lightest options as of writing this blog** are the Macbook Air and the Ultrabook series.

I originally was going to get some stupid cheap, old laptop and install Linux on it (which you can do really easily on either class of laptops, apparently).  But it seems like it's not cheap enough to justify the headache--and I need it to work without spending all my time on it.  Further, I get a university education discount with Apple at least because I work for one.  Another reason is that the first*** year graduate students keep egging me to (Kieron, skip to the next paragraph!) play online video games with them.  Haha!  Jokes on them, I just wind up getting my spawn points camped and feeding the other team, n00bs/lol/lmao/l337!

Now, I've seen Windows 8.  I've watched commercials for Windows 8 (which, let's face it aren't particularly good), and reviews for Windows 8.  I'm not saying Windows 8 is bad (even though everyone else seems to)...I'm just saying that Windows 8 isn't Unix based and since I'm using more open source software and Unix type things, it makes more sense to not get Windows 8 right now.  Further, there's this Open Office thingy that has a Word equivalent...and the buttons are all like it's 1999 instead of whatever they are nowadays!  Yay!  I'm using LaTeX now exclusively, though, so...

In short, I wound up ruling out the ultrabook because they're more expensive than the Macbook air in general and have hardware issues that seem petrifying if I'm going to keep this thing for another 8 years.  Lots of Youtube videos helped guide that decision.

You see, Youtube isn't just a huge waste of time!

So, take a bite out of the Apple.  Why buy a Windows machine to just overwrite it with Linux?  Why not instead get an Apple operating system, not play any games, and eventually need to upgrade after 2 years because the next generation of software updates will (uncannily) slow your system down to something unusable until you finally A) buy a new Apple computer (Apple hopes) or B) give yourself a headache installing Linux.****

Pick your poison.

And the poison I pick is the Apple because at least you (incoherent Snow White pun:) get the seven dwarves. I'll upgrade to Linux as soon as Kieron starts bugging me about the age of my computer again to steal a few more years of usable life out of it. The price...well, it's worth the lost weight when I carry this around (~2.5 pounds, a 480% improvement).

But which monopolistic-ally priced Apple device should I purchase?  I see with a cheapish external hard drive, the 128 Gb device should suit my needs--and look!  I already got a 1TB external drive because I was convinced my current laptop would crash by now and needed backups!  And for the guys and gals who play video games, it appears it will handle those too.  I could even get a monitor and see things comfortably instead of on the 11 inch screen I picked.

I made sure to look at it in the store before buying and had it shipped to the campus store to get it quicker.  I can't wait to see Kieron's reaction when I roll up to group meeting with it!  Well...maybe the biggest reaction will be the lack of sighs and grunts from the whole group when the computer works.

Now what to do with this old computer...and we'll figure that out in another post.

*-and a better graphics card, resolution, faster USB/HDMI ports, battery life, internet speed, the ability for a USB clicker for a presentation to be plugged in and not have the laser pointer button make the screen toggle between full size and otherwise, and a working F11 key.  You know, the trivial stuff.

**-[Editor's note: This information is already out of date]

***-Now second years!

****-Oh, and upgrading Linux versions generally makes the whole thing crash, so I heard. Therefore, the Linux fix might not be so fixy!

Monday, January 6, 2014

You're as cold as ice!

Dear Diary!

Lots of my astronomy brothers and sisters got stuck in transit to the American Astronomical Society meeting because the weather is as Cold as Ice!  One such anonymous removed-acquaintance has had their flight delayed 3 times!

What's weird is that the American Astrological Society has no explanation for this either!  Mercury is not in retrograde!  As an optical illusion, the planets occasionally travel the opposite direction along the ecliptic, and when Mercury does this, communication is inhibited as are travel plans!

Something else must be afoot...On Burke Blog Plus, we're having a ruthless discussion about the need or not need for travel insurance. But you only get access if you're cool enough (former, current students or the chillest of bros...those as Cold as Ice!) and beg Kieron for an invitation!

Wednesday, January 1, 2014

New Year, Same Old Desk (part 2/2)


Well, isn't this embarrassing.  The computer up there wouldn't let me sign in (apparently it's not connected to the modeling facility even though that doesn't make sense), and it's sweltering in that room on the weekend when the fans aren't on.

I guess I'm staying put.  I'll have to stand up to the meeting manager* the next time he asks for something.

Happy new year.

*-wait, isn't that me?

New Year, Old Desk

Dear Diary,

Today the group manager stormed into my office and told me to switch desks back to where I was in the summer.  John left and so this is how it's gonna be now.  New year, new* desk!

I made sure to get the information on the website switched so that everyone knows where to find me. I also moved John to the swanky alumni section of the website.  The only real drawback of switching offices is that the new year has come, so my old wall calendar is only but a recyclable.

No longer will the patrons of the printer stumble into my office and see that the white board is a huge dada-esk comment on graduate work: it's been wiped clean!  Yay!