merge in-place without external storage - c#

I want to merge two arrays with sorted values into one. Since both source arrays are stored as succeeding parts of a large array, I wonder, if you know a way to merge them into the large storage. Meaning inplace merge.
All methods I found, need some external storage. They often require sqrt(n) temp arrays. Is there an efficient way without it?
I m using C#. Other languages welcome also. Thanks in advance!

AFAIK, merging two (even sorted) arrays does not work inplace without considerably increasing the necessary number of comparisons and moves of elements. See: merge sort. However, blocked variants exist, which are able to sort a list of length n by utilizing a temporary arrays of lenght sqrt(n) - as you wrote - by still keeping the number of operations considerably low.. Its not bad - but its also not "nothing" and obviously the best you can get.
For practical situations and if you can afford it, you better use a temporary array to merge your lists.

If the values are stored as succeeding parts of a larger array, you just want to sort the array, then remove consecutive values which are equal.
void SortAndDedupe(Array<T> a)
{
// Do an efficient in-place sort
a.Sort();
// Now deduplicate
int lwm = 0; // low water mark
int hwm = 1; // High water mark
while(hwm < a.length)
{
// If the lwm and hwm elements are the same, it is a duplicate entry.
if(a[lwm] == a[hwm])
{
hwm++;
}else{
// Not a duplicate entry - move the lwm up
// and copy down the hwm element over the gap.
lwm++;
if(lwm < hwm){
a[lwm] = a[hwm];
}
hwm++;
}
}
// New length is lwm
// number of elements removed is (hwm-lwm-1)
}
Before you conclude that this will be too slow, implement it and profile it. That should take about ten minutes.
Edit: This can of course be improved by using a different sort rather than the built-in sort, e.g. Quicksort, Heapsort or Smoothsort, depending on which gives better performance in practice. Note that hardware architecture issues mean that the practical performance comparisons may very well be very different from the results of big O analysis.
Really you need to profile it with different sort algorithms on your actual hardware/OS platform.
Note: I am not attempting in this answer to give an academic answer, I am trying to give a practical one, on the assumption you are trying to solve a real problem.

Dont care about external storage. sqrt(n) or even larger should not harm your performance. You will just have to make sure, the storage is pooled. Especially for large data. Especially for merging them in loops. Otherwise, the GC will get stressed and eat up a considerable part of your CPU time / memory bandwidth.

Related

Is Dictionary.ContainsKey() any better than FirstOrDefault()?

I know, nothing one million of anything's gonna be performant. But I'm needing that piece o' knowledge right now.
I have a Dictionary and a string[]. The boolean in the dictionary is just to fill the space. Let's imagine that as an Inventory System just to make things easier.
In this inventory, I wanna check if I already had gotten one item. So what I'd do is:
if (dic.ContainsKey(item_id)) // That could be a TryGetValue() as well.
{
// Do some logic.
}
But would it be better to just have an array?
if (array.FirstOrDefault(a => a = item_id))
{
// Do magic.
}
I mean, which would perform better in that specific case?
I know, that's a silly question, but when you can have over one million (or over nine thousand, for the DBZ fans out there xD) checks, things can get pretty heavy, especially for mobile, VR and others with similar performance.
Plus, I just want my users to have the best experience with my Inventory (a.k.a. no lag), so I often take stuff like that in consideration.
There are two tradeoffs here space and time.
A Dictionary is a relatively heavy weight structure compared to an array.
The lookup time in a Dictionary (or a HashSet) if basically independant of the number of entries O(1), while with the array it increases linearly O(N).
So there is a certain number of items where the Dictionary (or HashSet) begins to be considerably faster. And 1 million is certainly above this threshold.

Pure Speed for Lookup Single Value Type c#?

.NET 4.5.1
I have a "bunch" of Int16 values that fit in a range from -4 to 32760. The numbers in the range are not consecutive, but they are ordered from -4 to 32760. In other words, the numbers from 16-302 are not in the "bunch", but numbers 303-400 are in there, number 2102 is not there, etc.
What is the all-out fastest way to determine if a particular value (eg 18400) is in the "bunch"? Right now it is in an Int16[] and the Linq Contains method is used to determine if a value is in the array, but if anyone can say why/how a different structure would deliver a single value faster I would appreciate it. Speed is the key for this lookup (the "bunch" is a static property on a static class).
Sample code that works
Int16[] someShorts = new[] { (short)4 ,(short) 5 , (short)6};
var isInIt = someShorts.Contains( (short)4 );
I am not sure if that is the most performant thing that can be done.
Thanks.
It sounds like you really want BitArray - just offset the value by 4 so you've got a range of [0, 32764] and you should be fine.
That will allocate an array which is effectively 4K in size (32764 / 8), with one bit per value in the array. It will handle finding the relevant element in the array, and applying bit masking. (I don't know whether it uses a byte[] internally or something else.)
This is a potentially less compact representation than storing ranges, but the only cost involved in getting/setting a bit will be computing an index (basically a shift), getting the relevant bit of memory to the CPU, and then bit masking. It takes 1/8th the size of a bool[], making your CPU cache usage more efficient.
Of course, if this is really a performance bottleneck for you, you should compare both this solution and a bool[] approach in your real application - microbenchmarks aren't nearly as important here as how your real app behaves.
Make one bool for each possible value:
var isPresentItems = new bool[32760-(-4)+1];
Set the corresponding element to true if the given item is present in the set. Lookup is easy:
var isPresent = isPresentItems[myIndex];
Can't be done any faster. The bools will fit into L1 or L2 cache.
I advise against using BitArray because it stores multiple values per byte. This means that each access is slower. Bit-arithmetic is required.
And if you want insane speed, don't make LINQ call a delegate once for each item. LINQ is not the first choice for performance-critical code. Many indirections that stall the CPU.
If you want to optimize for lookup time, pick a data structure with O(1) (constant-time) lookups. You have several choices since you only care about set membership, and not sorting or ordering.
A HashSet<Int16> will give this to you, as will a BitArray indexed on max - min + 1. The absolute fastest ad-hoc solution would probably be a simple array indexed on max - min + 1, as #usr suggests. Any of these should be plenty "fast enough". The HashSet<Int16> will probably use the most memory, as the size of the internal hash table is an implementation detail. BitArray would be the most space efficient out of these options.
If you only have a single lookup, then memory should not be a concern, and I suggest first going with a HashSet<Int16>. That solution is easy to reason about and deal with in a bug-free manner, as you don't have to worry about staying within array boundaries; you can simply check set.Contains(n). This is particularly useful if your value range might change in the future. You can fall back to one of the other solutions if you need to optimize further for speed or performance.
One option is to use the HashSet. To find if the value is in it, it is a O(1) operation
The code example:
HashSet<Int16> evenNumbers = new HashSet<Int16>();
for (Int16 i = 0; i < 20; i++)
{
evenNumbers.Add(i);
}
if (evenNumbers.Contains(0))
{
/////
}
Because the numbers are sorted, I would loop through the list one time and generate a list of Range objects that have a start and end number. That list would be much smaller than having a list or dictionary of thousands of numbers.
If your "bunch" of numbers can be identified as a series of intervals, I suggest you use Interval Trees. An interval tree allows dynamic insertion/deletions and also searching if a an interval intersects any interval in the tree is O(log(n)) where n is the number of intervals in the tree. In your case the number of intervals would be way less than the number of ints and the search is much faster.

I need very big array length(size) in C#

public double[] result = new double[ ??? ];
I am storing results and total number of the results are bigger than the 2,147,483,647 which is max int32.
I tried biginteger, ulong etc. but all of them gave me errors.
How can I extend the size of the array that can store > 50,147,483,647 results (double) inside it?
Thanks...
An array of 2,147,483,648 doubles will occupy 16GB of memory. For some people, that's not a big deal. I've got servers that won't even bother to hit the page file if I allocate a few of those arrays. Doesn't mean it's a good idea.
When you are dealing with huge amounts of data like that you should be looking to minimize the memory impact of the process. There are several ways to go with this, depending on how you're working with the data.
Sparse Arrays
If your array is sparsely populated - lots of default/empty values with a small percentage of actually valid/useful data - then a sparse array can drastically reduce the memory requirements. You can write various implementations to optimize for different distribution profiles: random distribution, grouped values, arbitrary contiguous groups, etc.
Works fine for any type of contained data, including complex classes. Has some overheads, so can actually be worse than naked arrays when the fill percentage is high. And of course you're still going to be using memory to store your actual data.
Simple Flat File
Store the data on disk, create a read/write FileStream for the file, and enclose that in a wrapper that lets you access the file's contents as if it were an in-memory array. The simplest implementation of this will give you reasonable usefulness for sequential reads from the file. Random reads and writes can slow you down, but you can do some buffering in the background to help mitigate the speed issues.
This approach works for any type that has a static size, including structures that can be copied to/from a range of bytes in the file. Doesn't work for dynamically-sized data like strings.
Complex Flat File
If you need to handle dynamic-size records, sparse data, etc. then you might be able to design a file format that can handle it elegantly. Then again, a database is probably a better option at this point.
Memory Mapped File
Same as the other file options, but using a different mechanism to access the data. See System.IO.MemoryMappedFile for more information on how to use Memory Mapped Files from .NET.
Database Storage
Depending on the nature of the data, storing it in a database might work for you. For a large array of doubles this is unlikely to be a great option however. The overheads of reading/writing data in the database, plus the storage overheads - each row will at least need to have a row identity, probably a BIG_INT (8-byte integer) for a large recordset, doubling the size of the data right off the bat. Add in the overheads for indexing, row storage, etc. and you can very easily multiply the size of your data.
Databases are great for storing and manipulating complicated data. That's what they're for. If you have variable-width data - strings and the like - then a database is probably one of your best options. The flip-side is that they're generally not an optimal solution for working with large amounts of very simple data.
Whichever option you go with, you can create an IList<T>-compatible class that encapsulates your data. This lets you write code that doesn't have any need to know how the data is stored, only what it is.
BCL arrays cannot do that.
Someone wrote a chunked BigArray<T> class that can.
However, that will not magically create enough memory to store it.
You can't. Even with gcAllowVeryLargeObjects, the maximum size of any dimension in an array (of non-bytes) is 2,146,435,071
So you'll need to rethink your design, or use an alternative implementation such as a jagged array.
Another possible approach is to implement your own BigList. First note that List is implemented as an array. Also, you can set the initial size of the List in the constructor, so if you know it will be big, get a big chunk of memory up front.
Then
public class myBigList<T> : List<List<T>>
{
}
or, maybe more preferable, use a has-a approach:
public class myBigList<T>
{
List<List<T>> theList;
}
In doing this you will need to re-implement the indexer so you can use division and modulo to find the correct indexes into your backing store. Then you can use a BigInt as the index. In your custom indexer you will decompose the BigInt into two legal sized ints.
I ran into the same problem. I solved it using a list of list which mimics very well an array but can go well beyond the 2Gb limit. Ex List<List> It worked for an 250k x 250k of sbyte running on a 32Gb computer even if this elephant represent a 60Gb+ space:-)
C# arrays are limited in size to System.Int32.MaxValue.
For bigger than that, use List<T> (where T is whatever you want to hold).
More here: What is the Maximum Size that an Array can hold?

Fast data structure for small sets

I'm in need for a data structure that can handle small sets (10-20 strings, at most 50, of varying length) very fast. False positives is ok, but false negatives are not.
The last requirement makes bloom filters seem like a good fit, but I'm not sure about their speed, any other recommendations?
Edit: The set only needs to support insert + membership test.
How about an array of strings that you use a for-loop over checking membership with String.Equals?
For sets this small, fancy data structures may incur too much overhead, and big-oh does not apply. Have you tried doing the simplest possible thing and measuring that?
(If false positives are ok, you might also keep e.g. an array of 1024 bools, where you compute a poor 'hash' of strings by looking at just the first two characters' lowest 5 bits to give you a 10-bit index into the boolean array. Seems like this would be just a few instructions long.)
Depending on what operations you wish to perform against the set, the fastest will likely be a HashSet<string>. See HashSet for more.
ADDITION
Asking Mr. Google, here's an article written by a gentlemen that wrote a Bloom Filter function in C#. However, he's still using (multiple) hashcodes to populate the filter. I would expect that on small data sets it will be slower than a HashSet.
If the set of strings to check for membership is much larger than the set of valid strings then a Trie might give you better performance than a HashSet. The speed of a lookup in a hashset is dependent on the run time of the hashing algorithm which is usually O(k) where k is the length of the string. This is true whether the string is in the hashset or not.
With a Trie, lookup is still O(k), but if the string is not in the Trie, it will terminate the lookup as soon as a single character doesn't match. So best-case, a lookup for an invalid string is O(1).
Why not use a Radix Tree? It's a specialized set data structure based on the trie that is used to store a set of strings.
Check out the System.Collections.Specialized Namespace on MSDN.
Especially the HybridDictionary and the StringDictionary.
I know they're not sets, but you can use null values for each key. (Java does the same with out-of-the box Sets and still is "fast".
If HashSet is too slow for you, you can use classic LZ compressor's technique: fixed size array of hash codes where each entry points to linked list of strings.
In case you know domain of your data just construct ideal hash function and use it.
If it's not your case you can use string.GetHashCode() of something like Murmur hash
and use hash(str) % array.Length as array's index.
I suppose array size of 256-512 entries in good enough for your data structure with 50 strings.
The main benefit of bloom filters over hash tables is that their size depends on the number of objects in the database and the permitted probability for false positives, but not on the size of the objects themselves. Since your database is so small I doubt its size is your main concern.
HashSets are theoretically the best data structure for your requirement, but since the database is so small, an O(log (n)) structure like a SortedDictionary is often preferable, or maybe even just linear search (as mentioned). I recall stories where switching from hash-based collections to tree-based ones drastically increased performance for small sets.
The best way is to switch between them and compare the performance of each.

What is the fastest way to count the unique elements in a list of billion elements?

My problem is not usual. Let's imagine few billions of strings. Strings are usually less then 15 characters. In this list I need to find out the number of the unique elements.
First of all, what object should I use? You shouldn't forget if I add a new element I have to check if it is already existing in the list. It is not a problem in the beginning, but after few millions of words it can really slow down the process.
That's why I thought that Hashtable would be the ideal for this task because checking the list is ideally only log(1). Unfortunately a single object in .net can be only 2GB.
Next step will be to implement a custom hashtable which contains a list of 2GB hashtables.
I am wondering maybe some of you know a better solution.
(Computer has extremely high specification.)
I would skip the data structures exercise and just use an SQL database. Why write another custom data structure that you have to analyze and debug, just use a database. They are really good at answering queries like this.
I'd consider a Trie or a Directed acyclic word graph which should be more space-efficient than a hash table. Testing for membership of a string would be O(len) where len is the length of the input string, which is probably the same as a string hashing function.
This can be solved in worst-case O(n) time using radix sort with counting sort as a stable sort for each character position. This is theoretically better than using a hash table (O(n) expected but not guaranteed) or mergesort (O(n log n)). Using a trie would also result in a worst-case O(n)-time solution (constant-time lookup over n keys, since all strings have a bounded length that's a small constant), so this is comparable. I'm not sure how they compare in practice. Radix sort is also fairly easy to implement and there are plenty of existing implementations.
If all strings are d characters or shorter, and the number of distinct characters is k, then radix sort takes O(d (n + k)) time to sort n keys. After sorting, you can traverse the sorted list in O(n) time and increment a counter every time you get to a new string. This would be the number of distinct strings. Since d is ~15 and k is relatively small compared to n (a billion), the running time is not too bad.
This uses O(dn) space though (to hold each string), so it's less space-efficient than tries.
If the items are strings, which are comparable... then I would suggest abandoning the idea of a Hashtable and going with something more like a Binary Search Tree. There are several implementations out there in C# (none that come built into the Framework). Be sure to get one that is balanced, like a Red Black Tree or an AVL Tree.
The advantage is that each object in the tree is relatively small (only contains it's object, and a link to its parent and two leaves), so you can have a whole slew of them.
Also, because it's sorted, the retrieval and insertion time are both O log(n).
Since you specify that a single object cannot contain all of the strings, I would presume that you have the strings on disk or some other external memory. In that case I would probably go with sorting. From a sorted list it is simple to extract the unique elements. Merge sorting is popular for external sorts, and needs only an amount of extra space equal to what you have. Start by dividing the input into pieces that fit into memory, sort those and then start merging.
With a few billion strings, if even a few percent are unique, the chances of a hash collision are pretty high (.NET hash codes are 32-bit int, yielding roughly 4 billion unique hash values. If you have as few as 100 million unique strings, the risk of hash collision may be unacceptably high). Statistics isn't my strongest point, but some google research turns up that the probability of a collision for a perfectly distributed 32-bit hash is (N - 1) / 2^32, where N is the number of unique things that are hashed.
You run a MUCH lower probability of a hash collision using an algorithm that uses significantly more bits, such as SHA-1.
Assuming an adequate hash algorithm, one simple approach close to what you have already tried would be to create an array of hash tables. Divide possible hash values into enough numeric ranges so that any given block will not exceed the 2GB limit per object. Select the correct hash table based on the value of the hash, then search in that hash table. For example, you might create 256 hash tables and use (HashValue)%256 to get a hash table number from 0..255. Use that same algorithm when assigning a string to a bucket, and when checking/retrieving it.
divide and conquer - partition data by first 2 letters (say)
dictionary of xx=>dictionary of string=> count
I would use a database, any database would do.
Probably the fastest because modern databases are optimized for speed and memory usage.
You need only one column with index, and then you can count the number of records.
+1 for the SQL/Db solutions, keeps things simple --will allow you to focus on the real task at hand.
But just for academic purposes, I will like to add my 2 cents.
-1 for hashtables. (I cannot vote down yet). Because they are implemented using buckets, the storage cost can be huge in many practical implementation. Plus I agree with Eric J, the chances of collisions will undermine the time efficiency advantages.
Lee, the construction of a trie or DAWG will take up space as well as some extra time (initialization latency). If that is not an issue (that will be the case when you may need to perform search like operations on the set of strings in the future as well and you have ample memory available), tries can be a good choice.
Space will be the problem with Radix sort or similar implementations (as mentioned by KirarinSnow) because the dataset is huge.
The below is my solution for a one time duplicate counting with limits on how much space can be used.
If we have the storage available for holding 1 billion elements in my memory, we can go for sorting them in place by heap-sort in Θ(n log n) time and then by simply traversing the collection once in O(n) time and doing this:
if (a[i] == a[i+1])
dupCount++;
If we do not have that much memory available, we can divide the input file on disk into smaller files (till the size becomes small enough to hold the collection in memory); then sort each such small file by using the above technique; then merge them together. This requires many passes on the main input file.
I will like to keep away from quick-sort because the dataset is huge. If I could squeeze in some memory for the second case, I would better use it to reduce the number of passes rather than waste it in merge-sort/quick-sort (actually, it depends heavily on the type of input we have at hand).
Edit: SQl/DB solutions are good only when you need to store this data for a long duration.
Have you tried a Hash-map (Dictionary in .Net)?
Dictionary<String, byte> would only take up 5 bytes per entry on x86 (4 for the pointer to the string pool, 1 for the byte), which is about 400M elements. If there are many duplicates, they should be able to fit. Implementation-wise, it might be verrryy slow (or not work), since you also need to store all those strings in memory.
If the strings are very similar, you could also write your own Trie implementation.
Otherwise, you best bets would be to sort the data in-place on disk (after which counting unique elements is trivial), or use a lower-level, more memory-tight language like C++.
A Dictionary<> is internally organized as a list of lists. You won't get close to the (2GB/8)^2 limit on a 64-bit machine.
I agree with the other posters regarding a database solution, but further to that, a reasonably-intelligent use of triggers, and a potentially-cute indexing scheme (i.e. a numerical representation of the strings) would be the fastest approach, IMHO.
If What you need is a close approximation of the unique counts then look for HyperLogLog Algorithm. It is used to get a close estimation of the cardinality of large datasets like the one you are referring to. Google BigQuery, Reddit use that for similar purposes. Many modern databases have implemented this. It is pretty fast and can work with minimal memory.

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