So I have a "large" number of "very large" ASCII files of numerical data (gigabytes altogether), and my program will need to process the entirety of it sequentially at least once.
Any advice on storing/loading the data? I've thought of converting the files to binary to make them smaller and for faster loading.
Should I load everything into memory all at once?
If not, is opening what's a good way of loading the data partially?
What are some Java-relevant efficiency tips?
You really haven't given us enough info to help you. Do you need to load each file in its entiretly in order to process it? Or can you process it line by line?
Loading an entire file at a time is likely to result in poor performance even for files that aren't terribly large. Your best bet is to define a buffer size that works for you and read/process the data a buffer at a time.
I've found Informatica to be an exceptionally useful data processing tool. The good news is that the more recent versions even allow Java transformations. If you're dealing with terabytes of data, it might be time to pony up for the best-of-breed ETL tools.
I'm assuming you want to do something with the results of the processing here, like store it somewhere.
You could convert to binary, but then you have 1+ something copies of the data, if you need to keep the original around.
It may be practical to build some kind of index on top of your original ascii data, so that if you need to go through the data again you can do it faster in subsequent times.
To answer your questions in order:
Should I load everything into memory all at once?
Not if don't have to. for some files, you may be able to, but if you're just processing sequentially, just do some kind of buffered read through the things one by one, storing whatever you need along the way.
If not, is opening what's a good way of loading the data partially?
BufferedReaders/etc is simplest, although you could look deeper into FileChannel/etc to use memorymapped I/O to go through windows of the data at a time.
What are some Java-relevant efficiency tips?
That really depends on what you're doing with the data itself!
Without any additional insight into what kind of processing is going on, here are some general thoughts from when I have done similar work.
Write a prototype of your application (maybe even "one to throw away") that performs some arbitrary operation on your data set. See how fast it goes. If the simplest, most naive thing you can think of is acceptably fast, no worries!
If the naive approach does not work, consider pre-processing the data so that subsequent runs will run in an acceptable length of time. You mention having to "jump around" in the data set quite a bit. Is there any way to pre-process that out? Or, one pre-processing step can be to generate even more data - index data - that provides byte-accurate location information about critical, necessary sections of your data set. Then, your main processing run can utilize this information to jump straight to the necessary data.
So, to summarize, my approach would be to try something simple right now and see what the performance looks like. Maybe it will be fine. Otherwise, look into processing the data in multiple steps, saving the most expensive operations for infrequent pre-processing.
Don't "load everything into memory". Just perform file accesses and let the operating system's disk page cache decide when you get to actually pull things directly out of memory.
I recommend strongly leveraging Regular Expressions and looking into the "new" IO nio package for faster input. Then it should go as quickly as you can realistically expect Gigabytes of data to go.
You might want to have a look at the entries in the Wide Finder Project (do a google search for "wide finder" java).
The Wide finder involves reading over lots of lines in log files, so look at the Java implementations and see what worked and didn't work there.
So then what if the processing requires jumping around in the data for multiple files and multiple buffers? Is constant opening and closing of binary files going to become expensive?
I'm a big fan of 'memory mapped i/o', aka 'direct byte buffers'. In Java they are called Mapped Byte Buffers are are part of java.nio. (Basically, this mechanism uses the OS's virtual memory paging system to 'map' your files and present them programmaticly as byte buffers. The OS will manage moving the bytes to/from disk and memory auto-magically and very quickly.
I suggest this approach because a) it works for me, and b) it will let you focus on your algorithm and let the JVM, OS and hardware deal with the performance optimization. All to frequently, they know what is best more so than us lowly programmers. ;)
How would you use MBBs in your context? Just create an MBB for each of your files and read them as you see fit. You will only need to store your results. .
BTW: How much data are you dealing with, in GB? If it is more than 3-4GB, then this won't work for you on a 32-bit machine as the MBB implementation is defendant on the addressable memory space by the platform architecture. A 64-bit machine & OS will take you to 1TB or 128TB of mappable data.
If you are thinking about performance, then know Kirk Pepperdine (a somewhat famous Java performance guru.) He is involved with a website, www.JavaPerformanceTuning.com, that has some more MBB details: NIO Performance Tips and other Java performance related things.
If at all possible, get the data into a database. Then you can leverage all the indexing, caching, memory pinning, and other functionality available to you there.
This depends a lot on the data in the file. Big mainframes have been doing sequential data processing for a long time but they don't normally use random access for the data. They just pull it in a line at a time and process that much before continuing.
For random access it is often best to build objects with caching wrappers which know where in the file the data they need to construct is. When needed they read that data in and construct themselves. This way when memory is tight you can just start killing stuff off without worrying too much about not being able to get it back later.
If you need to access the data more than once, load it into a database. Most databases have some sort of bulk loading utility. If the data can all fit in memory, and you don't need to keep it around or access it that often, you can probably write something simple in Perl or your favorite scripting language.