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update sql server rows, while reading the same table

I have a database in SQL Server 2012 and want to update a table in it.
My table has three columns, the first column is of type nchar(24). It is filled with billion of rows. The other two columns are from the same type, but they are null (empty) at this moment.
I need to read the data from the first column, with this information I do some calculations. The result of my calculations are two strings, this two strings are the data I want to insert into the two empty columns.
My question is what is the fastest way to read the information from the first column of the table and update the second and third column.
Read and update step by step? Read a few rows, do the calculation, update the rows while reading the next few rows?
As it comes to billion of rows, performance is the only important thing here.
Let me know if you need any more information!
EDIT 1:
My calculation can´t be expressed in SQL.
As the SQL server is on the local machine, the througput is nothing we have to be worried about. One calculation take about 0.02154 seconds, I have a total number of 2.809.475.760 rows this is about 280 GB of data.

Normally, DML is best performed in bigger batches. Depending on your indexing structure, a small batch size (maybe 1000?!) can already deliver the best results, or you might need bigger batch sizes (up to the point where you write all rows of the table in one statement).
Bulk updates can be performed by bulk-inserting information about the updates you want to make, and then updating all rows in the batch in one statement. Alternative strategies exist.
As you can't hold all rows to be updated in memory at the same time you probably need to look into MARS to be able to perform streaming reads while writing occasionally at the same time. Or, you can do it with two connections. Be careful to not deadlock across connections. SQL Server cannot detect that by principle. Only a timeout will resolve such a (distributed) deadlock. Making the reader run under snapshot isolation is a good strategy here. Snapshot isolation causes reader to not block or be blocked.

Linq is pretty efficient from my experiences. I wouldn't worry too much about optimizing your code yet. In fact that is typically something you should avoid is prematurely optimizing your code, just get it to work first then refactor as needed. As a side note, I once tested a stored procedure against a Linq query, and Linq won (to my amazement)

There is no simple how and a one-solution-fits all here.
If there are billions of rows, does performance matter? It doesn't seem to me that it has to be done within a second.
What is the expected throughput of the database and network. If your behind a POTS dial-in link the case is massively different when on 10Gb fiber.
The computations? How expensive are they? Just c=a+b or heavy processing of other text files.
Just a couple of questions raised in response. As such there is a lot more involved that we are not aware of to answer correctly.
Try a couple of things and measure it.
As a general rule: Writing to a database can be improved by batching instead of single updates.
Using a async pattern can free up some of the time for calculations instead of waiting.
EDIT in reply to comment
If calculations take 20ms biggest problem is IO. Multithreading won't bring you much.
Read the records in sequence using snapshot isolation so it's not hampered by write locks and update in batches. My guess is that the reader stays ahead of the writer without much trouble, reading in batches adds complexity without gaining much.
Find the sweet spot for the right batchsize by experimenting.

Best way to page through results in SqlCommand?

I have a database table that contains RTF documents. I need to extract these programmatically (I am aware I can use a cursor to step through the table - I need to do some data manipulation). I created a C# program that will do that, but the problem is that it can not load the whole table (about 2 million rows) into memory.
There is a MSDN page here.
That says there is basically two ways to loop through the data.
use the DataAdapter.Fill method to load page by page
run the query many times, iterating by using the primary key. Basically you run it once with a TOP 500 limit (or whatever) and PK > (last PK)
I have tried option 2, and it seems to work. But can I be sure I am pulling back all the data? When I do a SELECT COUNT (*) FROM Document it pulls back the same number of rows. Still, I'm nervous. Any tips for data validation?
Also which is faster? The data query is pretty slow - I optimized the query as much as possible, but there is a ton of data to transport over the WAN.

I think the answer requires a lot more understanding of your true requirements. It's hard for me to imagine a recurring process or requirement where you have to regularly extract 2 million binary files to do some processing on them! If this is a one-time thing then alright, let's get 'er done!
Here are some initial thoughts:
Could you deploy your C# routine to SQL directly and execute everything via CLR?
Could you have run your C# app locally on the box and take advantage of shared memory protocol?
Do you have to process every single row? If, for instance, you're validating the structure of the RTF data has changes versus another file can you create hashes of each that can be compared?
If you must get all the data out, maybe try exporting it to local disk and the XCOPY'ing it to another location.
If want to get a chunk of rows at a time, create a table that just keeps a list of all ID's that have been processed. When grabbing of the next 500 rows just find rows that aren't in that table yet. Of course, update that table with the new ID's that you've exported.
If you must do all this it could have a serious effect on OLTP performance. Either throttle it to only run off hours or take a *.bak and process it on a separate box. Actually, if this is a one-time thing, restore it to the same box that's running the SQL and use the shared memory protocol.

Best way to store 10 - 100 million simulation outputs from .net (SQL vs. flat file)

I've been working on a project that is generating on the order of 10 - 100 million outputs from a simulation that I would like to store for future analyses. There are several nature levels of organization to the data e.g. Classrooms hold Students who take Tests which have a handful of different performance metrics.
It seems like my data is border line in terms of being able to fit in memory all at once (given the calculation of the simulations requires a fair amount of data in memory to do the calculation), but I don't have any immediate need for all of the data to be available to my program at once.
I am considering whether it would be better to be outputting the calculated values to a SQL database or a flat text file. I am looking for advice about which approach might be faster/easier to maintain (or if you have an alternate suggestion for storing the data I am open to that).
I don't need to be able to share the data with anyone else or worry about accessing the data years down the line. I just need a convenient way to avoid regenerating the simulations everytime I want to carry out a tweak to the analysis of the values.

I'd consider using a database - 100 million files is too many for a file system without some kind of classification scheme, while a database can easily handle this many rows. You could just serialize the output into a BLOB column so you don't have to map it. Also, consider that SQL Server has file stream access so this could be essentially a hybrid approach where SQL manages the files for you.

Offhand, it sounds like you would be better off saving the results of each simulation run into a flat file. It need not be a text file - it could be binary.
After one or more simulation runs, the files could be read and placed into a data warehouse for later analysis.

The back-of-the-envelope rate for loading the data from an RDBMS server into memory is roughly 10K records per second. If you have 100M records, and if you must use all data at some point, you are looking at roughly three hours to load the data. That is before you do any calculations!
Plain files can be orders of magnitude faster. You can get pretty fast with a text-based file; going binary would improve your speed some more at the expense of readability of your data file.

Take a look at MongoDB, which is around 30x-50x faster in performance than SQL Server 2008 apparently.
http://blog.michaelckennedy.net/2010/04/29/mongodb-vs-sql-server-2008-performance-showdown/

Finding Changes between 2 HUGE zone (text) files

I have access to the .com zone files. A zone file is a text file with a list of domain names and their nameservers. It follows a format such as:
mydomain NS ns.mynameserver.com.
mydomain NS ns2.mynameserver.com.
anotherdomain NS nameservers.com.
notinalphadomain NS ns.example.com.
notinalphadomain NS ns1.example.com.
notinalphadomain NS ns2.example.com.
As you can see, there can be multiple lines for each domain (when there are multiple nameservers), and the file is NOT in alpha order.
These files are about 7GB in size.
I'm trying to take the previous file and the new file, and compare them to find:
What domains have been Added
What domains have been Removed
What domains have had nameservers changed
Since 7GB is too much to load the entire file into memory, Obviously I need to read in a stream. The method I've currently thought up as the best way to do it is to make several passes over both files. One pass for each letter of the alphabet, loading all the domains in the first pass that start with 'a' for example.
Once I've got all the 'a' domains from the old and new file, I can do a pretty simple comparison in memory to find the changes.
The problem is, even reading char by char, and optimizing as much as I've been able to think of, each pass over the file takes about 200-300 seconds, with collecting all the domains for the current pass's letter. So, I figure in its current state I'm looking at about an hour to process the files, without even storing the changes in the database (which will take some more time). This is on a dual quad core xeon server, so throwing more horsepower at it isn't much of an option for me.
This timing may not be a dealbreaker, but I'm hoping someone has some bright ideas for how to speed things up... Admittedly I have not tried async IO yet, that's my next step.
Thanks in advance for any ideas!

Preparing your data may help, both in terms of the best kind of code: the unwritten kind, and in terms of execution speed.
cat yesterday-com-zone | tr A-Z a-z | sort > prepared-yesterday
cat today-com-zone | tr A-Z a-z | sort > prepared-today
Now, your program does a very simple differences algorithm, and you might even be able to use diff:
diff prepared-today prepared-yesterday
Edit:
And an alternative solution that removes some extra processing, at the possible cost of diff execution time. This also assumes the use of GnuWin32 CoreUtils:
sort -f <today-com-zone >prepared-today
sort -f <yesterday-com-zone >prepared-yesterday
diff -i prepared-today prepared-yesterday
The output from that will be a list of additions, removals, and changes. Not necessarily 1 change record per zone (consider what happens when two domains alphabetically in order are removed). You might need to play with the options to diff to force it to not check for as many lines of context, to avoid great swaths of false-positive changes.
You may need to write your program after all to take the two sorted input files and just run them in lock-step, per-zone. When a new zone is found in TODAY file, that's a new zone. When a "new" zone is found in YESTERDAY file (but missing in today), that's a removal. When the "same" zone is found in both files, then compare the NS records. That's either no-change, or a change in nameservers.

The question has been already answered, but I'll provide a more detailed answer, with facts that are good for everyone to understand. I'll try to cover the existing solutions, and even how to distribute , with explanations of why things turned out as they did.
You have a 7 GB text file. Your disk lets us stream data at, let's be pessimistic, 20 MB/second. This can stream the whole thing in 350 seconds. That is under 6 minutes.
If we suppose that an average line is 70 characters, we have 100 million rows. If our disk spins at 6000 rpm, the average rotation takes 0.01 seconds, so grabbing a random piece of data off of disk can take anywhere from 0 to 0.01 seconds, and on average will take 0.005 seconds. This is called our seek time. If you know exactly where every record is, and seek to each line, it will take you 0.005 sec * 100,000,000 = 500,000 sec which is close to 6 days.
Lessons?
When working with data on disk you really want to avoid seeking. You want to stream data.
When possible, you don't want your data to be on disk.
Now the standard way to address this issue is to sort data. A standard mergesort works by taking a block, sorting it, taking another block, sorting it, and then merging them together to get a larger block. The merge operation streams data in, and writes a stream out, which is exactly the kind of access pattern that disks like. Now in theory with 100 million rows you'll need 27 passes with a mergesort. But in fact most of those passes easily fit in memory. Furthermore a clever implementation - which nsort seems to be - can compress intermediate data files to keep more passes in memory. This dataset should be highly structured and compressible, in which all of the intermediate data files should be able to fit in RAM. Therefore you entirely avoid disk except for reading and writing data.
This is the solution you wound up with.
OK, so that tells us how to solve this problem. What more can be said?
Quite a bit. Let's analyze what happened with the database suggestions. The standard database has a table and some indexes. An index is just a structured data set that tells you where your data is in your table. So you walk the index (potentially doing multiple seeks, though in practice all but the last tend to be in RAM), which then tells you where your data is in the table, which you then have to seek to again to get the data. So grabbing a piece of data out of a large table potentially means 2 disk seeks. Furthermore writing a piece of data to a table means writing the data to the table, and updating the index. Which means writing in several places. That means more disk seeks.
As I explained at the beginning, disk seeks are bad. You don't want to do this. It is a disaster.
But, you ask, don't database people know this stuff? Well of course they do. They design databases to do what users ask them to do, and they don't control users. But they also design them to do the right thing when they can figure out what that is. If you're working with a decent database (eg Oracle or PostgreSQL, but not MySQL), the database will have a pretty good idea when it is going to be worse to use an index than it is to do a mergesort, and will choose to do the right thing. But it can only do that if it has all of the context, which is why it is so important to push work into the database rather than coding up a simple loop.
Furthermore the database is good about not writing all over the place until it needs to. In particular the database writes to something called a WAL log (write access log - yeah, I know that the second log is redundant) and updates data in memory. When it gets around to it it writes changes in memory to disk. This batches up writes and causes it to need to seek less. However there is a limit to how much can be batched. Thus maintaining indexes is an inherently expensive operation. That is why standard advice for large data loads in databases is to drop all indexes, load the table, then recreate indexes.
But all this said, databases have limits. If you know the right way to solve a problem inside of a database, then I guarantee that using that solution without the overhead of the database is always going to be faster. The trick is that very few developers have the necessary knowledge to figure out the right solution. And even for those who do, it is much easier to have the database figure out how to do it reasonably well than it is to code up the perfect solution from scratch.
And the final bit. What if we have a cluster of machines available? The standard solution for that case (popularized by Google, which uses this heavily internally) is called MapReduce. What it is based on is the observation that merge sort, which is good for disk, is also really good for distributing work across multiple machines. Thus we really, really want to push work to a sort.
The trick that is used to do this is to do the work in 3 basic stages:
Take large body of data and emit a stream of key/value facts.
Sort facts, partition them them into key/values, and send off for further processing.
Have a reducer that takes a key/values set and does something with them.
If need be the reducer can send the data into another MapReduce, and you can string along any set of these operations.
From the point of view of a user, the nice thing about this paradigm is that all you have to do is write a simple mapper (takes a piece of data - eg a line, and emits 0 or more key/value pairs) and a reducer (takes a key/values set, does something with it) and the gory details can be pushed off to your MapReduce framework. You don't have to be aware of the fact that it is using a sort under the hood. And it can even take care of such things as what to do if one of your worker machines dies in the middle of your job. If you're interested in playing with this, http://hadoop.apache.org/mapreduce/ is a widely available framework that will work with many other languages. (Yes, it is written in Java, but it doesn't care what language the mapper and reducer are written in.)
In your case your mapper could start with a piece of data in the form (filename, block_start), open that file, start at that block, and emit for each line a key/value pair of the form domain: (filename, registrar). The reducer would then get for a single domain the 1 or 2 files it came from with full details. It then only emits the facts of interest. Adds are that it is in the new but not the old. Drops are that it is in the old but not the new. Registrar changes are that it is in both but the registrar changed.
Assuming that your file is readily available in compressed form (so it can easily be copied to multiple clients) this can let you process your dataset much more quickly than any single machine could do it.

This is very similar to a Google interview question that goes something like "say you have a list on one-million 32-bit integers that you want to print in ascending order, and the machine you are working on only has 2 MB of RAM, how would you approach the problem?".
The answer (or rather, one valid answer) is to break the list up into manageable chunks, sort each chunk, and then apply a merge operation to generate the final sorted list.
So I wonder if a similar approach could work here. As in, starting with the first list, read as much data as you can efficiently work with in memory at once. Sort it, and then write the sorted chunk out to disk. Repeat this until you have processed the entire file, and then merge the chunks to construct a single sorted dataset (this step is optional...you could just do the final comparison using all the sorted chunks from file 1 and all the sorted chunks from file 2).
Repeat the above steps for the second file, and then open your two sorted datasets and read through them one line at a time. If the lines match then advance both to the next line. Otherwise record the difference in your result-set (or output file) and then advance whichever file has the lexicographically "smaller" value to the next line, and repeat.
Not sure how fast it would be, but it's almost certainly faster than doing 26 passes through each file (you've got 1 pass to build the chunks, 1 pass to merge the chunks, and 1 pass to compare the sorted datasets).
That, or use a database.

You should read each file once and save them into a database. Then you can perform whatever analysis you need using database queries. Databases are designed to quickly handle and process large amounts of data like this.
It will still be fairly slow to read all of the data into the database the first time, but you won't have to read the files more than once.

Optimal storage of data structure for fast lookup and persistence

Scenario
I have the following methods:
public void AddItemSecurity(int itemId, int[] userIds)
public int[] GetValidItemIds(int userId)
Initially I'm thinking storage on the form:
itemId -> userId, userId, userId
and
userId -> itemId, itemId, itemId
AddItemSecurity is based on how I get data from a third party API, GetValidItemIds is how I want to use it at runtime.
There are potentially 2000 users and 10 million items.
Item id's are on the form: 2007123456, 2010001234 (10 digits where first four represent the year).
AddItemSecurity does not have to perform super fast, but GetValidIds needs to be subsecond. Also, if there is an update on an existing itemId I need to remove that itemId for users no longer in the list.
I'm trying to think about how I should store this in an optimal fashion. Preferably on disk (with caching), but I want the code maintainable and clean.
If the item id's had started at 0, I thought about creating a byte array the length of MaxItemId / 8 for each user, and set a true/false bit if the item was present or not. That would limit the array length to little over 1mb per user and give fast lookups as well as an easy way to update the list per user. By persisting this as Memory Mapped Files with the .Net 4 framework I think I would get decent caching as well (if the machine has enough RAM) without implementing caching logic myself. Parsing the id, stripping out the year, and store an array per year could be a solution.
The ItemId -> UserId[] list can be serialized directly to disk and read/write with a normal FileStream in order to persist the list and diff it when there are changes.
Each time a new user is added all the lists have to updated as well, but this can be done nightly.
Question
Should I continue to try out this approach, or are there other paths which should be explored as well? I'm thinking SQL server will not perform fast enough, and it would give an overhead (at least if it's hosted on a different server), but my assumptions might be wrong. Any thought or insights on the matter is appreciated. And I want to try to solve it without adding too much hardware :)
[Update 2010-03-31]
I have now tested with SQL server 2008 under the following conditions.
Table with two columns (userid,itemid) both are Int
Clustered index on the two columns
Added ~800.000 items for 180 users - Total of 144 million rows
Allocated 4gb ram for SQL server
Dual Core 2.66ghz laptop
SSD disk
Use a SqlDataReader to read all itemid's into a List
Loop over all users
If I run one thread it averages on 0.2 seconds. When I add a second thread it goes up to 0.4 seconds, which is still ok. From there on the results are decreasing. Adding a third thread brings alot of the queries up to 2 seonds. A forth thread, up to 4 seconds, a fifth spikes some of the queries up to 50 seconds.
The CPU is roofing while this is going on, even on one thread. My test app takes some due to the speedy loop, and sql the rest.
Which leads me to the conclusion that it won't scale very well. At least not on my tested hardware. Are there ways to optimize the database, say storing an array of int's per user instead of one record per item. But this makes it harder to remove items.
[Update 2010-03-31 #2]
I did a quick test with the same data putting it as bits in memory mapped files. It performs much better. Six threads yields access times between 0.02s and 0.06s. Purely memory bound. The mapped files were mapped by one process, and accessed by six others simultaneously. And as the sql base took 4gb, the files on disk took 23mb.

After much testing I ended up using Memory Mapped Files, marking them with the sparse bit (NTFS), using code from NTFS Sparse Files with C#.
Wikipedia has an explanation of what a sparse file is.
The benefits of using a sparse file is that I don't have to care about what range my id's are in. If I only write id's between 2006000000 and 2010999999, the file will only allocate 625,000 bytes from offset 250,750,000 in the file. All space up to that offset is unallocated in the file system. Each id is stored as a set bit in the file. Sort of treated as an bit array. And if the id sequence suddenly changes, then it will allocate in another part of the file.
In order to retrieve which id's are set, I can perform a OS call to get the allocated parts of the sparse file, and then I check each bit in those sequences. Also checking if a particular id is set is very fast. If it falls outside the allocated blocks, then it's not there, if it falls within, it's merely one byte read and a bit mask check to see if the correct bit is set.
So for the particular scenario where you have many id's which you want to check on with as much speed as possible, this is the most optimal way I've found so far.
And the good part is that the memory mapped files can be shared with Java as well (which turned out to be something needed). Java also has support for memory mapped files on Windows, and implementing the read/write logic is fairly trivial.

I really think you should try a nice database before you make your decision. Something like this will be a challenge to maintain in the long run. Your user-base is actually quite small. SQL Server should be able to handle what you need without any problems.

2000 users isn't too bad but with 10 mil related items you really should consider putting this into a database. DBs do all the storage, persistence, indexing, caching etc. that you need and they perform very well.
They also allow for better scalability into the future. If you suddenly need to deal with two million users and billions of settings having a good db in place will make scaling a non-issue.