Across the Universe

I should write an update before May….Here it is:

I spent most of my waking hours during March working on my research. In particular, I reorganized my GADGET snapshot analysis code (GSnap), re-wrote the input/output routines in C++, and added quite a few features to the code. The code can now be used to perform all of the analysis tasks that were originally planned as well as several extra tasks that were not planned. In addition to my own development work, I have an undergraduate research assistant who will eventually add yet another feature to the code.

More details about my recent research progress can be found in the following research log entries:

Joblib gprof & research assistance
GSnap progress
GSnap previewer
GSnap previewer-optimized
Accretion-rate-vs-time
Nucelus-centered vs. cm-frame velocity dispersion
Volume rendering
Volume rendering 2-0
GSnap GUI
GSnap is usable

There’s also an nice little animation that was rendered using GSnap:

In late March, Melissa and I went to Virginia for Spring break. Since I don’t have to teach anymore, I was able to schedule the trip for later than usual. That allowed me to be in Virginia for my mom’s birthday. We spent eight days in Virginia. Unfortunately I didn’t get to enjoy it as much as I should have; I was sick for much of the time we were there. Melissa didn’t feel particularly good either.  She had been experiencing lower abdominal pain and back pain for months, but the pain got much worse while we were in Virginia. On the last day of our vacation, I took Melissa to the Urgent Care in Weyers Cave to get examined. The Urgent Care doctor couldn’t figure out what was wrong, so he ordered a CT scan at the ER. The CT scan allowed for a quick diagnosis of the problem. It’s nice to at least know what the problem is…

Upon returning to California, Melissa developed a horrible sore throat. She may have caught a pathogen while in the ER. The nurse practitioner at the local Minute Clinic said that it was just a sinus infection. She recovered in about 10 days.

I continued working on GSnap for a while after returning to CA, but then I found a nice place to pause and I finally began working on a new phase of my research project. On the 20th of April, I finally began using my allocated time on the Triton Resource (a supercomputer at the San Diego Supercomputer Center). So far I have only compiled the GADGET-2 code and performed a few short test simulations in an effort to identify a suitable set of code parameters for Triton.  There are certain parameters that effect the speed with which the code runs, but if these parameters are not properly set, the code will unexpectedly halt execution. I think I have found a suitable set of parameters, but I haven’t performed any further testing because I have had to work on something else.

The “something else” that I  mentioned above is the newest version of my computational astrophysics lectures.  I have been working on updating the notes, adding problems to the homework assignment, and presenting the lectures. So far I have presented the first two lectures, which are essentially a fast-paced survey of the essential astrophysics, N-body methods, ODE solvers, analytic fluid dynamics, and computational fluid dynamics needed to understand modern galaxy simulation codes. The next lecture will be on high performance computing.

On Monday of this week, I was notified that my application for the Dissertation Year Program Fellowship was accepted. I was awarded a fellowship for two quarters. This means that the university will pay me at a higher rate for the Fall and Winter quarters and I will now definitely be a 100% employee during the summers of 2012 and 2013. The fellowship also apparently pays for all of my fees during those quarters.  I’m hoping this means that I won’t have to pay the extra $200 to register each quarter and I won’t have to pay the new “technology” fee that UCR recently invented….but I doubt it does.

Earlier this week, while I was working on my home workstation, I got fed up with the slowness of the computer. The main problem was that many of the programs that are open regularly on my computer have become much more memory-hungry lately. It seems that the developers have stopped caring about maintaining small memory footprints. Thunderbird and Chromium are particularly bad in this sense. It’s now common for a single tab in the web browser to use more than 100 MB of system memory! It turns out that Firefox is now faster and less of a memory hog than Chrome and Chromium—quite a change! To combat the slowness, I first installed the new 3.3.3 Linux kernel. This noticeably sped things up, but When I tried to run a VirtualBox virtual machine, the computer still slowed to a craw because it ran out of RAM and had to resort to using virtual memory. So, I visited Newegg.com with the intention of ordering more RAM for my  four-year-old computer.  The RAM was cheap, so I checked the CPU prices. I found a very good price on a faster processor. The new memory and processor arrived yesterday afternoon and I installed them last night.  I increased my system’s memory capacity from 4.0 GB to 8.0 GB and increased the typical processor performance by about 60% for a grand total of only $188 (including tax and shipping). To top it off, the new processor is much more energy efficient than the old processor, so it will lower our electricity bill slightly.

In other news, the planetarium director at JMU has invited me to give a seminar the next time I’m in Virginia and Gaby said that she will try to arrange a seminar or colloquium for me at The University of Hawaii while she is on sabbatical there in the fall. Melissa just bought tickets for us to see two of her favorite performers (Fiona Apple and Regina Spector) this summer. We have also begun making plans for our one-year wedding anniversary in Virginia in August. Ubuntu 12.04 LTS was released on Thursday. The new OS is a huge improvement over 11.10! My laptop is already running 12.04, but I don’t plan on upgrading my desktop from 10.04 LTS until I graduate.

A few hours ago, I found out that Svonne is employed again! I’m not sure if it’s full time or part time and it might be another commission-based job, but it’s good news in any case.

March has already arrived, so it’s time for another update…

I have made decent progress on my research lately.  There have been some snags, though.  The biggest issue is the fact that I no longer have a guaranteed amount of supercomputing time, so now I have to put effort into securing computing resources.  One of the 1.0 Terabyte hard drives on my  workstation at UCR is failing, so we will have to buy a replacement and perhaps buy an additional hard drive to allow me to store more data. On the positive side, a computer science major who was in my class over the summer contacted me last week about undergraduate research.  He was wondering if he could somehow become involved in my research project. I met with him on Tuesday and described a feature that should eventually be added to my analysis code. If everything goes well, he might become a co-author on one of my papers. In order to collaborate with another programmer, I had to comment my code more thoroughly so that it is more understandable. I also learned the basics of the Doxygen, automatic documentation generator and I uploaded the Git source repository to Bitbucket. In the process of commenting and organizing the code, I added some essential functionality. Now the code is almost ready to handle the most fundamental part of my analysis. A few days ago, Kyle gave me the IDL scripts that he uses to compute velocity dispersions from spectra.  That was one of the last tools that I needed in order to complete my project…Things are falling into place nicely!

As I mentioned in the previous entry, I was offered the opportunity to teach summer school again this year, but I had to decline the offer because I need to focus on research. I was presented with another teaching opportunity this week, but this time I accepted the offer because the time commitment was negligible in comparison.  I will be teaching elementary and middle school teachers some basic astronomy at the UCR Extension Center during the week of July 9-13. The teachers take the class for certification, re-certification or “enrichment” purposes. I presented one brief topic in astronomy last summer, but Gaby did most of the work.  Gaby will be in Africa during the summer school this year, so she recommneded me for the job.

Financially, things appear to finally be improving for the new Stickley Family  Our monthly expenses are now lower because the moving is finished and the rent and utilities are lower (although, there will soon be some car maintenance and repair expenses).  We were able to pay the credit cards off on time, so we didn’t have to pay interest;  we received a nice income tax refund a few days ago;  I’ve been tutoring weekly;  Melissa has been busier at work since the new spa director started promoting the spa. In addition to that, the Costco American Express Reward Card coupon came in the mail today ($225).  Looking forward, Gaby seems to be convinced that I will get the Dissertation Year Program Fellowship.  If that’s the case, my monthly income from UCR will increase for a while. I will be paid at 100% rather than 50% this summer….and the summer teaching gig should help give us another boost.

I have been playing with changing the default font on idius.net to a Computer Modern clone, but I haven’t tested it thoroughly. The font seems to look quite nice on the  CV page, but I’m undecided about its readability on the other pages.  Computer Modern is a fantastic font when presented in high resolution (i.e., printed material on paper or on the OLED display of a smart phone), but it can be slightly more difficult to read on a computer screen.

Tomorrow is Svonne’s birthday!

Melissa might have jury duty at some point next week.

I’m now a published scientist.  This morning I received an e-mail from The Astrophysical Journal informing me that my paper has been published.  It was actually published on Monday: http://iopscience.iop.org/0004-637X/747/1/33/

My research has been progressing rapidly lately. Two aspects of the project that I thought would be difficult have turned out to be trivial. On the other hand, one of the things I hoped would be easy has turned out to more difficult than I expected. I’ve written two research log entries so far this week:

http://www.idius.net/agn-spectrafilters-and-rgb-images/

http://www.idius.net/pyfits/

Some of the images in the first post are pretty cool.

Yesterday I was offered the opportunity to teach during the first summer session again because my reviews were positive last year. Unfortunately, I had to decline the offer because it would slow my research progress and it wouldn’t even pay more than my regular summer research salary. I’m not often in a situation where I have to turn down a job offer. It’s quite a different situation than last year; I didn’t even ask to teach this year, the university asked me. I’ll take that as a compliment and try to remain humble. Hopefully they’ll find another qualified graduate student who would like the opportunity to teach a course.

The security deposit refund from the old apartment complex arrived in the mail yesterday.  It came just in time because I need to pay my credit card bill and pay for car maintenance. My brake pads have worn down to almost nothing and they make a grinding, scraping sound as I come to a complete stop.

Since Melissa and I moved to the new apartment, we have been sleeping much better!  As I mentioned in my previous post, it is much quieter here. We have not quite finished putting everything away and decorating, but most of the work is finished. One evening, shortly after writing my previous blog entry, I built a bench for my bonsai (image below).  The bench is near our front window. As I write this, I can see the blooming azalea bonsai outside of the window.  The front of the house has southern exposure, which is perfect for the trees; they will get more light here than they did at the old apartment! It’s also much easier to monitor their progress because I walk by them several times each day. When they were on the balcony at the old apartment, I didn’t see them nearly as often.

Photo of the new bonsia bench -- taken with my Samsung Galaxy Nexus

Moving the heavy boxes of books and heavy furniture reminded me of how weak I have become once again. As a result, I’ve begun exercising again. I’ve also become more productive with my research. I’ve been reading a lot more than I was before.  About 11 days ago, I successfully ran the Sunrise code on a snapshot. After a few more days of struggling, I found sets of parameters that allowed me to run the code without it freezing (never converging to a solution) .  I have now overcome most of the major hurdles involved in performing my project. I just have to learn a few more things, figure out a few more non-trivial details, and then work on generating and analyzing a large amount of data.

I posted my first paper to arxiv.org: http://arxiv.org/abs/1201.4600 about two weeks ago. Soon after it appeared on  arxiv.org, T.J. Cox sent me an e-mail complimenting me on the paper and notifying me that the MakeGalaxy code is now available on Bitbucket. Patrik Jonsson (the author of the Sunrise code) e-mailed Gaby and notified us of a paper that we weren’t aware of and invited us to join the Sunrise mailing list. Yesterday, I recieved an e-mail from a professor in Australia who complimented me on the paper, asked me a question, and let me know about one of his recent papers. I had no idea that people would take time to send me e-mail about the paper…that’s pretty cool.

Financially, the security deposit for the new apartment—combined with the moving expenses—has drained my account. I also have to pay a $48 “technology fee” to UCR for some reason, but I’ll wait until next month. Fortunately, I received a letter in the mail informing me that I will get back most of my security deposit from the old apartment complex! Also, my Costco American Express card reward should arrive this month, and I’ve begun tutoring again. My regular monthly expenses have also decreased considerably, so things shouldn’t be too bad once the credit card bills are paid this month.  I’ve also reduced my long-term car maintenance expenses slightly because I bought ramps so that I can change my oil myself. That should save me almost $100 this year and potentially $150 next year; every little bit helps.

About two weeks ago, I had the electricity turned on at the new apartment and I set up a new Charter Cable Internet account so there wouldn’t be a gap in Internet service between moving out of the old apartment and moving into the new one. After spending several days cleaning the dust out of the new apartment, I began moving some of my books and book cases out of the old apartment.  I rented a U-Haul truck on Thursday (1/12/2012). Melissa and I moved the bulk of our stuff  into the new apartment and the storage unit. I spent the next few days thoroughly cleaning the old apartment and moving the remainder of our belongings.  Everything was finished by yesterday afternoon! Now we have to unpack and organize things. I should find out how much of my security deposit will be returned within 20 days.

The new place is small and the plumbing and wiring leave a lot to be desired. The bathroom sink supplies a mere trickle of cold water—comparable to a water pistol. Our small heat pump shares the same circuit as half of the outlets in the apartment, so it’s quite easy to accidentally trip the breaker. On the other hand,  it is relatively quiet here!  There’s no loud dog barking endlessly next door, the train is not as loud, there is no roar of freeway traffic 24/7, there are no gamers playing FPS video games, and there is no crazy pothead downstairs laughing maniacally at all hours of the day and night—polluting our apartment with smoke. I’ve been resting better without the noise.  Saving several hundred dollars per month on rent is also a major benefit. I may actually be able to earn enough from tutoring to pay my half of the rent…..for the next few months anyway.

Side notes:

I put my three containers of Irish moss (pearlwort or sagina subulata) in the yard last night temporarily until I could figure out what to do with them.  A dog apparently got in the yard during the night or early morning and tore one of the trays apart. So now I know that it’s not safe to put my bonsai in the back yard. The fence apparently does nothing to protect the yard from dogs. I may plant some little bits of the Irish moss in the yard to see if it survives…

My assigned parking spot is directly beside the dumpster.  This seems like a recipe for trouble.

Among the chaos of moving, I managed to apply for UCR’s Dissertation Year Program (DYP) Fellowship. The fellowship is merit-based and more than one person in the Physics Department will receive it this year, so I have a decent chance of success.

Wikipedia and a few other websites will go dark tomorrow in protest of the horrible SOPA and PIPA legislation.

Three long-awaited events occurred today.  In chronological order:

I ordered the Samsung Galaxy Nexus!

Background: I’ve had my current cell phone since the summer of 2008–before I moved to CA. I have been waiting to get an Android phone for a while now, but I’ve been very selective.  This summer, I decided to get the next Google flagship phone with Android 4.0.  The Galaxy Nexus is that phone and it was officially released to the American public yesterday.  Since I waited so long to get a new phone, I had a $100 discount in addition to the regular discounts for buying online and starting a new two-year contract.

My paper has been accepted for publication!

Background: I started writing this paper (which will be part of my PhD thesis) in January.  There were many interruptions along the way.  When it was finally finished and submitted, it took several weeks for the editor to find a reviewer for the paper.  Once the reviewer was found, it took approximately  one month to receive his report.  It took me a while to respond to the comments, edit the paper, and resubmit.  Then nearly one week passed before I received notice that my article had been accepted for publication (in The Astrophysical Journal).

Melissa and I have signed a lease for a new apartment!

Background:  We have needed to reduce our expenses and get away from our current neighbors for over a year.  We should be able to save slightly more than $200 per month compared with the current apartment, so the financial stress will be lowered somewhat. We have also moved to #72 on the waiting list for the UCR student family housing.  In September, we were at >100 on the list.  At this rate, we won’t have to live in the new apartment long before moving into the student housing.  The new apartment is a large studio in an old house in downtown Riverside. Photos of the house are shown below.

The front:

The back:

The first page of the paper:

The phone:

It has been over a month since my last entry and a lot has happened, so I’ll have to summarize quite a bit and omit some things:

I have spent most of my time working on research.  I’m trying to catch up to my self-imposed schedule. I’m almost back on schedule now and I should be completely back on track by the end of February.

Shortly after my previous entry, I successfully compiled the P-GADGET-2 simulation code with several different sets of makefile options.  The code has quite a few conditional compilation options so that the simulations can be customized at compile time.  I’ve also tested a lot of different parameter file options; once the code is compiled, there are still many options that are adjustable at run-time.  I compiled a program called IFrIT with a GADGET-2 snapshot reading plugin so that I could visualize the simulations that I’m working with and easily rotate and zoom to explore the systems that I’ve modeled.

To see a video of a merger simulation that I ran and find out more details, refer to these three research log entries:

http://www.idius.net/first-simulations/

http://www.idius.net/quadratic-spline-interpolation/

http://www.idius.net/and-now-a-two-point-cubic-spline/

I’ve also been working on a C++ code that can read, analyze, manipulate, and save GADGET-2 snapshots.  In order to use the code more efficiently, I spent a few days learning to use the Qt framework for creating cross-platform GUI applications.  Now I can use the program from the command line, call it from a script, or interactively use the program with the GUI that I designed. Using the GUI allows me to explore individual snapshots more quickly, while the command line interface allows me to automate my analysis.

I had wanted to learn to create GUI applications for about ten years, so I was very excited when I learned to do it!  It’s surprisingly easy with Qt. Here are some screenshots of the current (basic) version of my “GSnap” code running in Unity, GNOME 2, KDE, and Windows 7 (I don’t have access to a Mac, so I can’t show what it looks like in Mac OS).

I received the referee’s comments regarding my first paper a few weeks ago and yesterday I finally finished making edits and replying to all of the referee’s comments.  The paper was resubmitted last night.  Hopefully it will be accepted for publication soon!

Melissa and I have been budgeting pretty successfully.  We’re putting a fixed amount of our monthly income into our joint saving account and we have reduced our living expenses.  In addition to that, I started tutoring again in November, so I’ve had some supplemental income lately. The tutoring job has been pretty interesting; A local periodontist who is also a clinical assistant professor at The University of Redlands contacted the physics department at UCR seeking a tutor for his son. His son had a ‘B’ in AP physics, and he needed a tutor in order to get straight ‘A’s.  He is the only 11th grader at his school taking AP physics and he hasn’t learned much trigonometry or calculus yet, but he’s doing pretty well. I replied to the e-mail and got the job.  He paid me $75 per hour for my inconvenience; now his son now has a low ‘A’ in AP physics going into the final exam. It was nice to do some teaching again!

In addition to the extra tutoring income, my mom gave us a small wedding present and she sent two care packages with some food, which helped us save on groceries!

Yesterday Melissa and I checked out a studio apartment that she found through Craigslist the day before. It’s a large studio, which means that it’s smaller than our current apartment, but it’s significantly cheaper and it is in a house rather than an apartment complex, so we will have a yard and fewer close neighbors to deal with. We will save about $230 per month on rent compared with the cost of continuing to live in our current apartment, but some of that will be offset because I’ll be getting renter’s insurance.  The house is within walking distance of the Mission Inn, which means that Melissa can walk to work and we can save slightly on gasoline. I’ll need to either take the bus to UCR (the bus is free for UCR students) or buy a parking sticker and drive. Since the studio is smaller, we will have to put some things into storage until we are able to move into the UCR student family housing. Fortunately, we already have a storage unit that should work.

Melissa’s Verizon Wireless contract ended at the beginning fo December, so she was able to get a new phone at a discounted price.  She now has a Motorola Droid X2.  I’ll have to wait until next year for my next phone  (the Samsung Galaxy Nexus) to become available.

Today Melissa and I have been married for one month and one week.  Melissa is now officially Melissa Stickley on all of her important documents except for her passport.

Since writing my last blog entry, I have finished writing the first draft of my paper and started working on my actual thesis project! I submitted the paper to the Astrophysical Journal yesterday!  In addition to research-related things, I’ve been reading an introductory particle physics book, the Landau and Lifshitz series on theoretical physics, and an interesting history of science book called “The Age of Entanglement”.

Last Wednesday Melissa and I visited my auto insurance agent.  I updated the marital status on my policy, which reduced my annual insurance premium by approximately $300. That helps a bit, but the overall financial outlook for the rest of the year is not very bright.  I spend more than 50% of my income on rent alone. With the exception of February, I have had a net negative income each month this year.  Next month Melissa and I will begin following a strict budget to try to get back on track or at least stabilize the situation.  We are also looking for a more affordable apartment.  Earlier this year, I applied for a rent reduction, which would have saved me about $200 per month. Unfortunately I was ultimately ineligible because I’m a student (I’m not sure why graduate students are ineligible for financial assistance, while wife beating, smoking, drinking, child abusing non-students get special treatment!). The university has special family housing for graduate students, but there is a long waiting list (over 100 people were ahead of us in the waiting list, as of a few weeks ago).  It would be nice to be able to live there, though. The little houses are nicer than our current apartment, the neighbors would HAVE to be better than what we have now, and the rent is approximately HALF of what I’m currently paying.  I’m hoping to at least have a decent tax return next year and a sizable reward on my Costco American Express card. I’m also hoping to be a 100% research assistant during the summer months rather than 45% employee or whatever I am at the moment. I may also try getting out of the student employee union.  I can’t really afford for UAW to deduct from my monthly income.

In short, I need to finish this thesis project and move on as soon as possible!