Wednesday, December 22, 2010

Python as an Alternative to Lisp or Java, Peter Norvig revisited

Because I'm a fan of Peter Norvig, and because I've recently been going through some of his articles about Lisp, I ran into an old entry of his from 1999 about Lisp and Java. In it, he links off to a study where a sample problem was provided in order to compare the efficiency of C++/Java programmers. Feel free to read his post Lisp as an Alternative to Java. How did Peter do 11 years ago?

I did not participate in the study, but after I saw it, I wrote my version in Lisp. It took me about 2 hours (compared to a range of 2 to 8.5 hours for the other Lisp programmers in the study, 3 to 25 for C/C++ and 4 to 63 for Java) and I ended up with 45 non-comment non-blank lines (compared with a range of 51 to 182 for Lisp, and 107 to 614 for the other languages). (That means that some Java programmer was spending 13 lines and 84 minutes to provide the functionality of each line of my Lisp program.)

While relaxing a bit while testing was going on for our code push today, I followed the same instructions, only in Python. I hadn't read his lisp code before (and reading it afterwards, there is a lot of Common-Lisp-isms that I don't really understand), nor had I read the specific problem before (though I solved a similar problem in the spring of 1999 during a local programming competition in undergrad in C++).

My first correct solution was done in an hour with 53 non-comment lines, but I could trim it to 37 lines if I was okay collapsing all lines that could be collapsed.

Looking around a bit while counting lines, I realized that if I added a utility function, I could remove some confusing stuff, while at the same time reducing line count. Spending another 10 minutes got me to 47 lines without comments or spaces, and 44 if I collapsed all lines that could be collapsed while limiting it to 78 columns wide.

My solution is available at this github gist. I didn't write this or this blog post to be "look at how good Python is", because obviously one's ability to program solutions to problems/puzzles/etc., is fundamentally related to your experience and ability to think in a given language. And, on the most part, I've been living and breathing Python for the past 10+ years, with the last 6 years programming 4-5 days a week in Python both professionally and personally. That said, I do think that similar conclusions can be drawn from this bit of the experiment as Peter made, primarily that Python is very effective, very expressive, and can cut out a lot of the bullshit that most Java programmers deal with on a regular basis.

UPDATE:
A commenter pointed out that I had a bug that was exposed running over the large input files and comparing with the large output file. I fell into the same ambiguity as was pointed out in the paper as the "hint" on page 12.

If you want to see more posts like this, you can buy my book, Redis in Action from Manning Publications today!

Friday, October 29, 2010

Being a student isn't easy, it requires actual work

Wandering about the internet this morning prior to doing some actual work, I happened upon a blog post by Seth Goodin about teaching, and how students should demand better instruction. Historically, I've generally agreed with and enjoyed Seth's blog (though lamenting being unable to comment there directly), but in this case, I think he's missing the point.

I can certainly appreciate the plight of college students everywhere, spending tens of thousands of dollars to go to school. I did the same thing for my college years, and even continued for another 5 1/2 years to go to grad school. Almost three years out of it, and I've still got loans, and probably will for a few years to come (9 1/2 years of postsecondary education isn't cheap in the states). However, I had the pleasure of being taught by amazing professors at both institutions that I attended, but even more importantly, attended school with interested and engaged students (I wasn't the only one doing homework on Friday nights). Sadly, this isn't always the case...

Everyone agrees that if you have a poor teacher/professor, your learning (and grades) will suffer... but there's a limit to which that is the instructor's fault. So often when I was both studying and teaching, I would hear complaints (and offered a few myself) about a poor instructor. Either they didn't care, didn't understand where their teaching fell on deaf ears, taught something unrelated to the course, ... However, when confronted with this type of instructor, a student is given an opportunity to engage themselves in learning. Classes come with books, and instructors are meant to help the student understand and integrate the knowledge and wisdom within those books. But prior to the internet, Wikipedia, or Khan Academy, students have managed to learn, despite poor instructors. How? They read and studied the books, consulting their fellow and elder students when they had questions. I know I was different in this regard, as when I found difficulty understanding my teacher during Trigonometry in high school, I read the book, studied, and understood it. When asked by other students how I managed to do well despite a confusing teacher, I pointed at the book. Only a few of them had taken the time to read the book beyond the problems, or when they did, would take the time to understand it.

Back when I was a TA in grad school, I made many mistakes (mostly in my first couple quarters). But by the final quarter of my teaching stint, I was doing 3 back-to-back sections for the same course, an hour each. The students who showed up and let even just a little bit of my enthusiasm rub off on them were engaged (if you are not excited about what you are teaching, students won't care, and students won't come). But what happened was that 5-10% of students never showed up for any of the discussion sections (except for reviews prior to exams). They would sometimes go to class (sometimes watching television or DVDs in the back rows), read their classmate's notes, hand in half-copied, half-bullshit homework, and expect to learn enough in one hour to be sufficient for an Algorithms/Data Structures midterm/final. Sometimes they managed to cram enough, but usually we would be overly generous and give them a D-.


I can appreciate what Seth is trying to say: expect more from your teachers/professors/instructors. But an amazing instructor can only go so far. Students must also be engaged and willing to participate in the process of learning, otherwise they are at least as much to blame for wasting their time and money as a poor instructor.

If you want to see more posts like this, you can buy my book, Redis in Action from Manning Publications today!

Sunday, October 10, 2010

YogaTable as a Database Server

As promised in my last update, YogaTable is no longer an embedded database. Included in the source is a new server component, which listens for requests on a configurable host and port, defaulting to localhost:8765 .

I have included a client for Python, which has everything necessary for basic and advanced YogaTable use. The protocol is basically JSON over HTTP GET/POST, which makes it straightforward for interacting with using just about any language. I am in the process of documenting what is necessary to write new clients, and will be writing a client for Javascript, as well as a more advanced Python client library. Some simple benchmarks with Apache Bench tell me that YogaTable can perform 60 single inserts/second, and around 2500 bulk inserts/second, but that's in mostly ideal conditions.

One of the features that I am most excited about is being able to script the modification of multiple rows in the database with Lisp. I've taken a merged version of Peter Norvig's lis.py and lispy.py, improved the performance, removed some unnecessary features (some of which were unnecessary for database updates), added some other features, and ... Well, let's just see what it looks like. The following is an example from the YogaTable's tests. It shows how you can transactionally update two rows in the database at the same time, and more specifically, how one could implement transferring money from one account to another.

First, let's set up our rows in the database.
d1 = {'value':decimal.Decimal('200.00')}
d2 = {'value':decimal.Decimal('0.00')}
ids = zip(*self.table.insert([d1, d2]))[0]
d1['_id'] = ids[0]
d2['_id'] = ids[1]

Now, let's set up our shared data, and prepare for the output of our test.
shared = {'transfer':decimal.Decimal('45.23')}
d1['value'] -= shared['transfer']
d2['value'] += shared['transfer']

Let's actually perform the conditional update...
out = self.table.update([
    {'_id':ids[0],
     '__ops':'''
        (load types)
        (define zero (decimal `0.00))
        (define balance (getv `doc `value zero))
        (define transfer (getv `shared `transfer zero))
        (if (>= balance transfer)
            (begin
                (setv `doc `value (- balance transfer))
                (setv `shared `transferred #t)))
        '''},
    {'_id':ids[1],
     '__ops':'''
        (load types)
        (define zero (decimal `0.00))
        (define balance (getv `doc `value zero))
        (define transfer (getv `shared `transfer zero))
        (if (getv `shared `transferred #f)
            (setv `doc `value (+ balance transfer)))
        (delv `shared `transferred)
        (delv `shared `transfer)
        '''}], shared=shared)

The Lisp in here may look a little strange, as some of it is nonstandard. The first few lines of the operations for the rows loads the 'types' module, which offers access to the Python decimal.Decimal datatype (among others), pulls some balance information, and determines how much money is supposed to be transfered. The last few lines in the first operation verifies that there is enough money in the account, then deducts the money, and sets the shared variable 'transferred' to True.

The second operation checks to see if 'transferred' is True, and if so, adds the transferred balance to the second row. The two 'delv' lines in the second operation are merely there to remove the known shared variables so that if someone were to accidentally include a third row, then it wouldn't have access to this data.

And that's it. Money transfers in YogaTable. No need for 2-stage commits.


At this point, you are probably wondering where YogaTable is going as a piece of software. When Google first released AppEngine, one of the things that I was most intrigued by was it's Datastore. Some features I'd never seen before (indexes on all of the values in a list, in particular), and I wished that it was available outside of AppEngine. I'd been meaning to write an AppEngine Datastore-like backend for a long time, and some early versions of YogaTable were actually meant to allow for people to take the Google AppEngine SDK and plug my backend into it. It was meant as a way of scaling the SDK beyond trivial applications, and really, to allow for the full set of features and functionality offered by Appengine's Datastore to people who didn't want to run in Google's datacenters. That is not where YogaTable is going.

After having used MongoDB in production, I realized that the current software offerings for databases was missing something. Something that wasn't tied down to schemas like classic relational databases. Something that wasn't limited if you happened to *only* have a 32 bit machine. Something that could offer enough power for building a moderately-used web site (one million hits/day), but was flexible enough to not get in your way while you were developing it.

And thus, YogaTable was born. Aside from the design requirement of never performing table scans, and it's current lack of built-in replication/clustering, YogaTable today offers sufficient features to get almost any idea from concept to a million hits/day. And with the introduction of a Lisp interpreter, YogaTable is able to offer functionality that is otherwise very difficult in other systems (the simple multi-row update shown above requires a tricky 2-stage commit using AppEngine's Datastore).


There is still work to be done on YogaTable. Mostly, I need to document everything. From there, next steps include replication, clients in a few different languages, support for read-only replicas, automatic master/slave failover, clustering... But all in good time. Documentation first, features next.

I hope everyone stays interested, I know that I'm having fun.

Tuesday, September 14, 2010

YogaTable Part 2: An Embedded NoSQL Database

It's been far too long since my previous post about YogaTable, but in the process of writing tests, testing, and cleaning up some of my original code, I had discovered a few bugs with how some searches were being performed. Throw in some weekend work on Binary Space Partitions, and you have a recipe for a delayed post.

This version introduces an "embedded" interface to YogaTable.  Similar to how SQLite operates, you specify where you would like your tables to be stored, and you receive a Database instance: >>> import embedded; db = embedded.Database(path).  That Database instance has implicitly-defined tables, which can be accessed via db.table_name.insert/ update/ delete/ search/ add_index/ drop_index/... .

Why an embedded database?  Well, for starters, it's a good stepping stone from a storage engine to a full database server.  Once we have an embedded database (especially one with a straightforward interface like YogaTable has), a database serving daemon is just a protocol definition away.  And if you implement your embedded database correctly (like thread safety, etc.), then many of the hard parts relating to multiple clients and routing responses are already solved.

In order to handle index building for new indexes on old data, or index deletion for deleted indexes, and to handle threaded users of the embedded database, we chose to push the processing for each table off into it's own process via Python's convenient multiprocessing library.  Commands are forwarded to each of these processors via multiprocessing.Queue instances (one per table), with all responses for all tables coming back via a single queue.  Threads that make requests against a table don't all wait on the same queue, but each waits on it's own standard Queue.  Responses are routed to the appropriate caller via a special routing thread, which also handles cleanup for threads that have exited.  You can see how routing, process startup, etc., happens in embedded.py.

By pushing all processing into secondary processes, we are also able to leverage multiple processors (with multiple tables or databases) and multiple disks (with multiple databases), which should hopefully reduce latency and increase throughput for heavy users.  We do gain some latency with processes thanks to a serialization and deserialization step for each direction, but the convenience of not needing to write a multi-table load-balancer cannot be understated.  Remember, part of this project's purpose is to build on top of and re-use known-good components whenever we can, and letting the OS handle table-level processor and disk scheduling is the right thing to do.  To see how query processing occurs and how we balance queries with index creation and deletion, check out lib/processor.py.


On the other hand, SQLite has well-known limitations with regards to multiple readers and/or writers.  As in: don't do it (without thinking really hard about it).  So we're not.  Each table processor is single threaded (aside from the effectively transparent communication threads), and has a query-driven event loop.  All requests are processed in-order as they come in to the processor.  When idle, the query processor picks up any outstanding index creation or deletion requests.  The next set of changes will include configuration options to allow for the balancing of request processing vs. indexing vs. cleanup.

If you aren't in the mood for yet another another embedded database, don't worry.  YogaTable is embedded-only just until my next post, whose update will include a RESTful interface for easy multi-language clients, runtime status information, and if I'm feeling frisky, a simple console for querying the database.


On a more personal note, I very much enjoyed building the processing and request routing pieces.  I'd wanted to build a request router for a Linda-like Tuple Space that I had implemented in the fall of 2005 (blog discussion:1 2 3), but that project never made it's way into the real world.  One of the reasons why it never made it's way off my hard drive was partly because of the multiprocessing package, which I saw as a better way of handling tasks for which Linda-like systems were designed.

Tuesday, August 31, 2010

Binary Space Partitions and You

One of the reasons that I do not have the next YogaTable post ready is because I've been spending time dealing with problems relating to geometry.  More specifically, I've had the need to break up some polygons of up to a million points into tiles along a unit grid.

Because of it's convenience, we've licensed GPC and are using it via the Polygon library in Python (GPC is free for non-commercial use, but since this is for work, we had to license it; Polygon is LGPL).  In particular, the Python library has a very simple method for generating tiles of the form we need: Polygon.Util.tile().  Sadly, it is not terribly efficient.  What do I mean?

Say that you wanted to pull one tile from a larger polygon region, using the Polygon library, you would just intersect your desired region with the larger polygon.  That's exactly what you want, and for GPC, is about as optimal as you can get (there are other libraries that offer computationally more efficient polygon intersections, but I've not found any that are as easy to use as GPC).  But what if you wanted tiles?  The algorithm used by Polygon.Util.tile() generates all of the tiles that you want, and performs intersections for each and every one of them.  I know what you are thinking: if the individual operation is optimal, why wouldn't applying the same operation over the larger space be optimal?  Repeated work.

Say we wanted to pull tiles 6a, 6b, and 6c out of the polygon below:
If we were to perform the intersections directly, then we have to trim to the right of column 5 three times, to the left of column 7 three times, and 6 partitions of column 6.  But what if we first performed a simple "trim to the right of column 5" followed by "trim to the left of column 7"?  Well, we would add 4 vertices to the polygon (which we would have needed to add anyways), but by trimming to the left first, we remove 8 vertexes that we never operate on again, as well as another vertex to the right. Over the sequence of operations, we reduce the number of vertexes we need to compute on, and aren't re-performing the same line intersections over and over.

In this simple example, we don't really gain much by partitioning our space, because the shape is so simple.  But by using a very simple algorithm that counts the number of points in each row and column to determine a good row/column to cut the space, we've seen huge returns in our programming investment.  In our case, relatively small polygons of 20-50k points have had their processing time drop from 30-45 seconds to 2-3 seconds.  Our moderately sized polygons of 150-300k points have gone from 15-25 minutes of computation time down to 15-25 seconds.  The killer polygon for us had just over a million points.  It had been running for over 6 hours before I rewrote the algorithm using a simple grid-based BSP algorithm.  We killed the process, and re-ran everything using the updated BSP version.  The entire process completed in under 30 minutes.

I have emailed the author of the Polygon library, so hopefully everyone will have a faster tile for free.  Those of you who can't wait, feel free to get the code from the gist here: http://gist.github.com/560298


ETA: added a link to the Binary Space Partitioning page at wikipedia.

Wednesday, August 18, 2010

Introducing YogaTable, the flexible NoSQL database

In my last post, I talked about building a new NoSQL database from scratch, and how I would describe the decisions I made during it's construction, as well as post code along the way.  This is the first of the series introducing YogaTable.  Strangely enough, the toughest part of all of it was coming up with a name.  At the current revision, insertion, updating, and deletion are all supported, and there are tests.  Querying is not yet in the repository, though I have written the query builder and tests.  Those subjects will be in the next post.


The first design decision I have made with this system is that I will not be building a durable data store; that is, one that offers write-or-fail semantics given modern hardware, handling of system crashes, etc.  It's a hard problem.  Systems which make use of more lazy approaches to durability (like mmap in the case of MongoDB) *will* fail at some point due to the laziness, even ignoring bad disks.  Fixing this issue with replication is great, but it requires more hardware, and in the case of sane underlying systems (real hardware, and/or good virtualization solutions like vmware, xen, etc.), doing it right the first time allows us to not have to band-aid over it with replication.  I will instead use an existing system that does it's absolute best to be durable and transactional by design.

I have also decided that I will not be building a B-Tree indexing system from scratch.  Like the durable data store issue just mentioned, B-Trees are terribly difficult to get right.  So to reduce the amount of time it will take to go from no code to fully-working system, I'm just not going to write a new one.  I will instead use a system that already includes support for B-Tree indexes.

Those of you who know me will already guess that YogaTable will be written in Python, primarily because I know Python better than I know any other language, and secondarily because Python includes all of the tools necessary to build YogaTable out of the box on a modern machine.  In fact, Python includes two transactional data stores with B-Tree indexes as part of the standard library: bsddb.btree and sqlite3.

Because I am not without a sense of irony, and because I have had bsddb.btree bite me with data corruption in the past (when not using the transactional semantics that are not documented in the standard library), I'm going to use Python's interface to SQLite 3, which has been included with the core Python distribution since 2.5 .  As such, YogaTable will be "NoSQL" for the external interface to the database, rather than the actual underlying data store.  Also, because of this choice, it will be fairly straightforward for someone to replace SQLite with another SQL database to offer functionality that I might not have gotten around to adding quite yet (like read-only slaves via MySQL, etc).  Once YogaTable is feature complete (according to my earlier requirements and desires), it is my intent to use this in a small-medium scale production environment for my own projects, fixing bugs as they crop up (or as others report them).

I'm sure someone is going to think and/or point out how backwards it is to use a SQL database to store data for a NoSQL database.  And that's reasonable.  But this world is filled with unsolved difficult programming problems.  I could spend literally months rewriting either the durable data store or the B-Tree index.  On the other hand, I have the utmost respect for those who have already built said systems, and have happily used them in dozens of projects.  Two secrets to software and systems engineering: pick your battles, and stand on the shoulders of giants.  I'm going to do both, at the price of a little SQL.


Now that we have a place to store data and indexes, we've got to decide how it's going to be laid out.  For the sake of simplicity with regards to backup, etc., and because I know a little something about how SQLite 3 works, I'm going to lean towards simplicity.  Each table, information about it's indexes, and the indexes themselves will be stored in a single sqlite3 database file.  This file will have three tables; the data table, the index metadata table, and a single table that includes the index data.  Each table will have various B-Tree indexes over them to ensure that our access patterns are fast.  The general 3-table layout and the db abstraction guts are available in lib/om.py.  Also, as a "new to me" bug, I learned that Python's sqlite3 library doesn't handle list/tuple arguments for 'IN' queries, requiring some str(tuple(data)) shenanigans.

For the index table, we will be prefixing the index data with an index id, which will ensure that we are searching the proper subset of index rows when we search.  Now, we could have placed each index in a separate file, then use SQLite's 'ATTACH DATABASE' command, but then we would have had to query all index tables/databases whenever we perform an update/delete, and that's a pain in the ass (never mind a performance killer whenever we have more than one or two indexes).  We do miss being able to determine the size of each index individually, but that wasn't one of our requirements (though we could keep track of this manually).  For details about how we generate index rows, check out lib/pack.py.

To offer greater flexibility, etc., we will not be storing any Python-centric data in our database.  Data will be stored as JSON, and will be automatically converted to/from JSON by sqlite3 adapters/converters.  Also, for the sake of everyone's sanity, we've included support for dates, datetimes, times, and decimals.  Documentation is forthcoming for future non-Python users to easily convert to/from these formats.  For the impatient, check out lib/adapt.py.


Stay tuned for the next post where I will be discussing the sql query generator, and automatic background index construction.

ETA: updated links to reflect some moved files.

Monday, August 9, 2010

Building a New NoSQL Database from Scratch

Over the course of the last few months, I've been writing a new NoSQL database.  Most readers will laugh and say one of a few different things.  Maybe something like, "NoSQL is a fad", "there are already so many NoSQL options, creating a new one is pointless", or even "unless you bring something new to the table, your adventure is going nowhere".  To sum up my response: yes, it is offering something new.

Every existing SQL/NoSQL solution has tradeoffs.  From the MyISAM storage backend for MySQL (no ACID compliance), to Postgres 8.4 and prior's lack of replication tools (I know I am looking forward to Postgres 9), to secondary index setup/creation in Cassandra, to MongoDB's use of memory-mapped files without transaction log, ... each database trades different advantages for other disadvantages.  For the existing nontrivial noSQL solutions that I have examined (Cassandra, MongoDB, CouchDB, S3, Voldemort, SimpleDB, etc.), I have found that many of my required features are just not available.  In the rare case where my required features were available (Google's AppEngine datastore), it's not available where I need it (Amazon AWS, Slicehost, etc.).

What do I require?

  • scales reasonably on small systems (MongoDB fails here)
  • document/row store (S3 and Voldemort fail here)
  • secondary indexes (SimpleDB fails here)
  • the ability to add/remove indexes during runtime (Cassandra fails here)
  • no surprise queries (aka no table scans, MongoDB, Cassandra, and CouchDB fail here)
  • no corruption on system restart (AWS and other cloud hosting providers sometimes lose your instance for a bit, MongoDB fails here)

Additional points for:

  • no schema (MongoDB, CouchDB, SimpleDB, ...)
  • multiple values per column (MongoDB and AppEngine's list columns)
  • sub-documents (like MongoDB's {'sub-doc':{'attr1':'val1', ...},} )
  • the ability to perform queries against a secondary index while it is being built
  • 10k+ rows inserted/second on modest hardware (MongoDB, ...)
  • replication / sharding / clustering (MongoDB Replica Sets would be optimal)

Astute observers will note that MongoDB offers all of these things, except for scaling well on small systems, and 'no surprise queries'.  To clarify what I mean by both of these; when you are using a 32 bit platform (small Amazon AWS hosts, some smaller VPS machines on other hosts), you are limited to 2 gigs of data and indexes with MongoDB.  This is because they use memory-mapped files as an interface to on-disk files, which limits you to the architecture address space.  As such, MongoDB really only makes sense for relatively small systems, or when you have a 64 bit system.  Further, if you forget to explain your queries in advance (like during ad-hoc queries), to ensure that you are using an index, you can end up scanning your multi-gig database for a simple count query.  On other databases (PostgreSQL and MySQL in the SQL world being the two I am most familiar with), a table scan will slow down other queries, but it won't destroy overall performance.  With MongoDB, that table scan will destroy write throughput for any other operation.  I have run into this myself.

To solve the table scan issue, we need to require an index for every query we perform (this is what Google's AppEngine datastore does).  This somewhat limits ad-hoc queries, but with the ability to add/remove secondary indexes during runtime, and with the ability to make queries against indexes while they are being built (and drop the index during it's creation), we can start an index creation, and immediately perform our query.  If there isn't enough data, we can wait and perform the query again.  Yes, the index building operation does perform a table scan to create the index, but it can be designed to balance itself with incoming queries so that performance doesn't suffer greatly.


Over the course of the coming weeks, I will be documenting the process of building this new NoSQL database from the ground up.  Yes, I said weeks.  Part of the design and implementation will include the use of a readily-available, fast, durable data store (which bypasses many of the nasty implementation details), wrapped with an interface to offer all of the requirements and the first five pluses I list above.  I do have a design for replication/sharding/clustering, but it's the only part of the system I've not built yet.  We'll see how it goes.  I will be posting source on Github as I discuss the design of the system, offering code as the nitty-gritty details of the higher-level design I will describe.