November 2005 Archives

In my previous post I mentioned that I love how the elements of story come together in J.K. Rowling's books and that I wanted to write a bit about why I love the story of the hero and the villian so much.  Although I wish I could say that these are original thoughts, sadly I cannot take credit for them.  They belong to a couple of authors which I have had the privilege to hear speak--Donald Miller and John Eldredge.  Donald Miller has written several books mostly on experiancing the character of God.  He gave a talk a year ago about how Romeo & Juliet was actually a metaphor about the relationship between God and the Church--it was a fantastic talk.  John Eldredge is famous for his book Wild at Heart.  I heard him speak several years ago and I'm probably not his biggest fan but I still think he had some good things to say.

Anyway, enough with the introductions and let me get on with the content of the post.  So, story.  I love the story of the struggle between good and evil and how good conquers all.  There's something about it that captivates me and sends chills down my spine.  I want to be like the hero's in the stories that unselfishly sacrifice themselves for their friends (and sometimes even their enemies) and simply because it is right.  The other story line that I always fall for hook, line and sinker is the story of romance.  It never fails, when the writer is trying to make me root for a particular relationship to happen I always do with my whole heart.  I like it when the hero gets the girl. 

As I watch these movies like Harry Potter and the Goblet of Fire or Smallville or any other number of flicks I can't help but ask myself: What is it about these rather prevalent storylines that can capture me so much so that it sends chills down my spine and can make me root from deep within for the hero to triumph?  I think it's God.  These stories tell a tale that resonant at exactly the frequencies our hearts, souls and minds are atuned too.  Christ's death was the ultimate act of sacrifice and heroism.  It captured us, it's what we are made for it's no wonder that stories that retell how good conquers all grabs me, how could it not?!?  And romance--romance is just the same.  It tells the story of Christ's relationship with the Church.  These stories resonate with us because they echo the tales of the ultimate hero who lives on today and whom we were made for.  His sacrifice has transformed us and we now daily participate in the romance of Christ and His bride.

As I read over this post I don't know that it has really captured what I feel but then again maybe what I am feeling is a very simple thing; but somehow I suspect whole chapters could be written on this very thing.  Those chapters will have to be by another man because I am afraid I am not the right one for the job.  Hope that everyone, if anyone, reading this had a fantastic Thanksgiving holiday and remember to give thanks for all things in our Lord Christ Jesus.

I saw Harry Potter and the Goblet of Fire tonight.  It was fabulous to say the least.  I definately think it is the best one yet.  I love how all the elements of story come together.  I was thinking alot why I love the story of the villian and the hero so much and I want to write about it but I am exahausted right now so it will have to wait till a bit later.  Maybe tomorrow I will update this post with my thoughts but I didn't want to go to sleep without saying anything at all.

I can't believe I only have one day left of supercomputing.  It's amazing how quickly time flies when you are having fun.  Today was fun.  We heard about the advances that were being made in the Biosciences from several professors.  After lunch we heard from two guys from disney explaining how they used computers to advanced the state of the art in the animation industry.  It was interesting to hear about the history of how Disney has used computers in their movies and what the future holds for them.  I also got a demo of the University of Chicago's SAGE software which was pretty cool.  SAGE is an application to tie a  whole bunch of monitors together and cauze them to act as a single desktop.  They also had and application that allowed you to view steroegraphic (3D) information without the 3D glasses that you normally need.  They had a pretty neat videoconferencing application running for the demo.

I know that I didn't write all that much today but it's been a long week and I'm kind of tired so this is all you get for now.

Today was filled with a lot of discussion about really cool technologies that have become something of buzz words like nano-technology and quantum computing.  I learned a lot today and this was probably my 2nd favorite day of the event next to the tutorial on parallel file systems.

I started the day out with a seminar on nanotech.  There was a technical discussion of a non-volatile memory that is likely to be available in the next couple of years.  It's a promising technology that will likely be about as fast as DRAM but have the potential to have much higher bit densities.  The speaker explained how the memory was based on nanowires and the difficulty is coming up with unique addressing for the wires.

Later in the afternoon Stephan and I attended a session on how companies producing comodity items like toilet paper and cleaning supplies use HPC (high performance computing) to enable them to be more efficient in manufacturing and distribution of goods.  The speaker was from Proctor & Gamble; he had many examples of how P&G had used HPC to increase profit.  One of the more interesting examples he mentioned was that they had problems with pringles flying off the conveyor belts because they were trying to produce them too quickly and they also had the problem of seasoning not getting evenly distributed.  It's obvious that this would cause serious problems in the production of pringles.  P&G used HPC to model the aerodynamicity of the chips and devised a slightly better shape to facilitate the aerodynamics and also modified their conveyor system.  Who woulda guessed, HPC is even helping the manufacture of chips!

After the P&G example we heard from some researchers using HPC to improve our predictive capabilities with Tsunami's.  Their discussion was particularly interesting but I found the most interesting part of their discussion was the visualization software they used, GeoForce.

Finally the day ended with two presentations on quantum computing.  The first was by a company in New York that did cryptography.  They presented the basics of quantum cryptography, which was fascinating and then demonstrated an example system they had put togther.  One of the notable things about QC is that it is distance limited--the presenter thought the forseeable maximum distance would be around 250km, current technology only allows for about 100km.  The second presenter worked for a company that is at the cutting edge of quantum processor design.  He showed us a 16 qbit processor which was really neat to see, it's the cutting edge and only about half the size of your thumbnail.  According to the presenter this was 6 month old technology.  He thinks that as we discover the keys of quantum computing many ground breaking dsiscoveries will be made in nearly every one of the scienes, particularly physics.  After today, I am very excited about where we are heading with technology.

Day three was the first general session at SC05.  The day began with a keynote speech by Bill Gates about the future of HPC.  It was amazing how many people showed up to listen to the talk.  They filled up a caveranous conference room and two large overflow rooms.  After the talk I wondered around for a bit and had the opportunity to talk with a gentleman doing large-scale infiband installations.  It was very interesting talking to him and to see some of the applications of the technology that he had.  There was a really cool video conferencing app in hi-def.  We also got to take a look arond at some of the hardware that is installed here to support the massive network they have available.

After the Infiniband talk Stephan and I wondered around a bit and talked to some folks at Nasa.  One woman told us about her work on a project to enable faster sequencing of DNA.  It was very intresesting what she was doing and then she also showed us some work of one of her coworkers with carbon nanotubes.  I also had an opportunity to talk with another gentleman who had a simulation of airflow through a component in one of the engines that was having issues.  It was a cool simulation but the part that really struck me was the visualization tools that they were using.  The guy I was talking too had done all the visualizatoin so it was a great opportunity to get some suggestions as to some of the general methods we could visualize datasets.  He also had a wall of monitors and mentioned that they had written all the software to drive it themselves but that stanford had a package available called Chromium to do OpenGL rendering across multiple screens.

I forgot to mention the other day that we stopped by the scali booth and got a demo of the upcoming 5.0 release.  It's obvious that the system is not ready for prime time as they ran into several null pointer exceptions during the demo.  They completely revamped the GUI and it's a lot nicer than the old GUI.  It's easy to create views of different charts over time in the new system so if you have a general setup that you like to bring up regularly you can just save it to the desktop and with one click you have it back which is nice.  Unfortunately there were not any obvious changes to the system outside of the GUI.  They did mention that there were plans to make all information that was available via the GUI also available via command line tools. 

Day two of supercomputing began with another tutorial.  Today's was about the future of high performance computers.  It was an interesting tutorial but they had too much material to cover and for the sake of time a lot of slides were cut out which made it difficult to follow at times.

Some of the major points that I took away from the tutorial include:

• The curve describing cost per gigaflop has flattened since 2001
• Performance has continued to increase; however, at a much slower rate since the dot-com bubble
• As processors increase in speed the memory wall will become more of a problem, processors may overcome this problem in the future by placing several hundred megabytes of memory directly on the processor die.
• Non-volatile nano memory is likely to be available in the near future

The grand opening of the general conference was also today.  There were several booths we saw that were very interesting; but possibly the most interesting people we talked to was a company who was providing a product called Mitrion.  Mitrion provides a c like language to program FPGA's with.  The company claims at least that regular application programmers can easily take advantage of the benefits FPGA's have to offer without special knowledge of hardware or other things.  The programmer interacts with the FPGA via mitrion and then the mitrion code gets translated to VHDL code.  It is not tied to any particular FPGA vendor so the system is relatively portable.  This is a very interesting developmenti fwhat they claim is true.  I know that there are several people in our company who will be very interested in this.

I'm looking forward to tomorrow when we are supposed to get a tour of the network and there are a number of special sessions that I am excited for. 

Day one of Supercomputing down, five more to go.  I had a lot of fun today and learned a lot too.  I missed going to church today but beyond that had a great time.  Seattle is a neat town and, thanks to Ervin, we get to stay in a really nice hotel which is walking distance from the Convention Center.  It's amazing how much nicer it is to be a few blocks from the places you have to be versus having to drive in a foreign city.

Today was a tutorial session.  Both Stephan and I attended the "Parallel I/O in Practice" session. It was taught by Rob Latham, Rob Ross, and Rajeev Thakur from Argonne National Labs and Bill Loewe from Lawrence Livermore National Labs.  The first half of the day was spent mostly talking about parralellel file systems.  Three systems were discussed: IBM's GPFS (General Parallel File System), Argonne's PVFS2 (Paralllel Virtual File System), and Lustre which is the efforts of three DOE labs, Intel, HP, and cluster file systems inc. 

The major thing that I took away from the morning session is how much effect a dedicated MPI-IO library can have on the performance of a paralllel file system.  Both GPFS and PVFS2 have dedicated MPI-IO implementions, Lustre does not.  GPFS MPI-IO implemention is only available for AIX and PVFS2's is available on Linux.  Both GPFS (on an AIX system) and PVFS2 (on a linux system) exihibited good performance and excellent scalability; where as Lustre, due to the lack of an optimized MPI-IO library, lagged the other two significantly.  There was a quick table of do's and don'ts for parallel file systems which I thought might be useful:

1. PFS'es are not optimized for metadata, they are optimized for moving data around
1. ls and du on large directories significantly impacts performance on these filesystems.
2. Smaller directories work better.
2. Keep file create, close, and open to a minimum as they are slow operations.
1. Use one open and one close
2. Use shared files or at least a subset of tasks
3. Aggregate writes - PFS's are not databases they do better with large writes (64k blocks or larger is good)
1. Using collective I/O can make this possible.
2. Contiguous file formats are better than non-contigous ones.

In the afternoon session we discussed MPI-IO and the basics of the architecture.  Romio is the primary implementation available and was written by Argonne.  It is distributed with MPICH 2 and modern implementations do not require anything extra beyond including mpi.h.  MPI-IO mainly provides three functions for functionality: MPI_File_open, MPI_File_write, and MPI_File_read.  MPI-IO takes care of the things that POSIX doesn't allow such as collective access, etc.

Finally, we discussed two high level API's that sit atop a PFS and MPI-IO: PnetCDF and HDF5.  These are two portable file formats for storing data.  PnetCDF is based upon the netCDF and file format and is completely compatible.  HDF5 was the first parallel file format and the major difference between the two is that HDF5 provides a heirarchical system to programmer where as the data storage is flat in PnetCDF.

I don't see a lot of benefit in either of the high level file format API's for our system but using a Parallel Filesystem and MPI-IO could simplify our code, make it more robust and give us a significant speed improvement over our current method of using MPI scatter/gathers.  We would need to investigate whether or not Scali's MPI implementation includes Romio or if we would need to upgrade to MPICH 2.  Since Scali's version is based upon an older version of MPICH it might.  For the parallel file system we should probably use PVFS2 since it has MPI-IO optimizations for linux and we also know several people who have an intimate knowledge of the PVFS2 code base.

All in all I learned a lot today.  I'm looking forward to learning much more as the week goes on but if this was the only useful thing about the conference I would say it was definately worth the trip!  I'm already looking forward to getting back home and getting an opportunity to try out the new techniques we are learning.  Stay tuned for day two! 

I like books, I like them a lot.  I love how they help me to think clearer and the ideas they present.  I don't why but I've always loved books.  I just finished Beggars in Spain which is a scifi book by Nancy Kress.  It won the hugo award in 1992 and a friend of mine at work, Derek, told me about it.

Basically it's about the jeolousy that is bred in a society where there are genetically engineered humans who are clearly superior to the rest of the race.  One of the major genetic alterations is the ability to not sleep.  It turns out that these "Sleepless" are better in every regard, they are smarter, better socially adjusted, etc.  There are no negative side affects.  Kress disuccesses the idea of what it means to have community and what should be done with the unproductive members of society, the "beggars."  I think it's an interesting book because the technological ideas such as sleepless that she presents are interesting to me but I also belive she comes to an interesting conclusion about the social aspects of a society with clearly superior beings.  It is obvious that all men are not created equal in ALL regards--some are better looking, some are smarter, the list goes on and on but the important thing is that we are all created equal in the innate rights we are born with: liberty and freedom.  Kress challenges and explores these ideas which makes for a very intresting read.  If anyone out there likes to read definately add this one to your list.  If you don't like scifi I would still give it a chance because there is a lot of discussion of philosophy under the guise of scifi.

So the plans have begun for the 2nd annual pre-thanksgiving celebration for our frends here in Tucson.  It should be fun but the hardest part is trimming the guest list to something that is not too large.  The more that you think about it the more people you would like to come.  It should turn out really well though.  I'm looking forward to the turkey!

So just one last note, Byron wanted me to give him a shout out here.  Here it is, B!

This weekend was an eventful one.  It started with Friday night when Zak, Dave, and a few other people came over to play Kings with Charles and I--it was a lot of fun and there was lots of laughing.  I also got into an interesting converation about God with Erin.  She came from the standpoint that religion is a personal thing and the way that each man chooses to execute his faith is his own business. This seems to be a common belief in our society and it completely refuses to face the facts that either religion is only useful for psychological purposes or there really is an all powerful God out there who has a defined set of attributes and somebody is wrong.  Faith seems so weak if we refuse to say that there is no absolute truth assoicated with it.  It was fun to talk to her none-the-less.

On Saturday I had lunch with Aubry at Bison Witchs and that was very encouraging.  I love to hear what God is doing in people's lives.  And then Charles and I drove up to phoenix for our friend Jenny's wedding.  It was a really nice service and the reception was well done also.  It was cool because the focus was on God and they even used a bit of latin in the service (OK it wasn't spoken but it was on the little pamphlet's they passed out) which I am a sucker for.  After that we went to go catch up with Joey, one of my best friends.  He was at a bar with some friends from class.  There were a lot of scantily clad women and some that might as well as have been naked they were wearing so little.  I felt really sick there and like it was not a place that God wanted me.  I don't have a problem with bars in general but when you could almost confuse them as strip clubs that's ont a place that I think does anything for my christian walk.  Shortly after we arrived we went up to the balcony to hang out which I was greatfull for because it wasn't nearly as bad out there.  We were tlaknig with a guy from Norway named Andreas.  He was a computer science major and didn't seem like he had thought too much about religion.  He liked to talk about politics and was firmly against the war in Iraq.  It's very popular these days to argue that what President Bush did was such a terrible thing but I just can't understand.  Saddam Hussein was a terrible man by most standards--he persecuted his people and any opportunity he got he hurt the United States.  One argument that I've heard is that we aren't taking all the terrible dicators out of power so it was wrong take Saddam out of power.  That is one of the stupidest arguments I have ever heard.  Just  because we don't apply a good deed universally it does not mean that he good act was any less good for those it was applied too.  I agree that there are many atrosicities in this world but there are so many that we can fix and Iraq was one of them.  Ok, I guess that's enough politics for now.

We drove back to tucson on Sunday with very little sleep.  One encouraging thing to report though--no close calls on this trip! 

Tuesday nights are reserved for spending time with my roommates.  We usually go out and do something fun together.  Most of the time, my roommate Mike is not there because he has to work.  Tonight was nice because he had a bit of a break so he could hang out with us.  We got the chores we needed to taken care of, had a nice dinner, and then went to the dollar (well dollar-fifty theatre) and saw "The Exorcism of Emily Rose."  It wasn't a terrifing movie in the sense that it did not use loud music or excessively gruesome shots to send chills down the spines of it's viewers but it was terrifing because it could be real.  In fact, it was based on a true story.  The power of the supernatural is very scary and I thank God for the sacrifice he made for us on Calvary.  Watching the movie reminds me that I would like to write a book one day recording the superinatural events in the world of the time.  We live in a society so convinced that there is nothing supernatural, that there are no angels or demons, and that this world solely governed by the laws of nature that, I believe, it would be good for the believers to hear how God is moving through out the world.