Cleaning doubles out of a massive word list - algorithm

I got a wordlist which is 56GB and I would like to remove doubles.
I've tried to approach this in java but I run out of space on my laptop after 2.5M words.
So I'm looking for an (online) program or algorithm which would allow me to remove all duplicates.
Thanks in advance,
Sir Troll
edit:
What I did in java was put it in a TreeSet so they would be ordered and removed of duplicated

I think the problem here is the huge amount of data. I would in a first step try to split the data into several files: e.g. make a file for every char like where you put words with the first character beeing 'a' into a.txt, first char equals 'b' into b.txt. ...
a.txt
b.txt
c.txt
-
afterwards i would try using default sorting algorithms and check whether they work with the size of the files. After sorting cleaning of doubles should be easy.
if the files remain to big you can also split using more than 1 char
e.g:
aa.txt
ab.txt
ac.txt
...

Frameworks like Mapreduce or Hadoop are perfect for such tasks. You'll need to write your own map and reduce functions. Although i'm sure this must've been done before. A quick search on stackoverflow gave this

I suggest you use a Bloom Filter for this.
For each word, check if it's already present in the filter, otherwise insert it (or, rather some good hash value of it).
It should be fairly efficient and you shouldn't need to provide it with more than a gigabyte or two for it to have practically no false negatives. I leave it to you to work out the math.

I do like the divide-and-conquer comments here, but I have to admit: If you're running into trouble with 2.5mio words, something's going wrong with your original approach. Even if we assume each word is unique within those 2.5mio (which basically rules out that what we're talking about is a text in a natural language) and assuming each word is on average 100 unicode characters long we're at 500MB for storing the unique strings plus some overhead for storing the set structure. Meaning: You should be doing really fine since those numbers are totally overestimated already. Maybe before installing Hadoop, you could try increasing your heap size?

Related

Perl processing a trillion records

Looking for some advice or insight on what I consider a simple method in PERL to compare text files to one another.
Lets assume you have 90,000 text files that are all structured similarly, say they have a common theme with a small amount of unique data in each.
My logic says to simply loop through the files (breaking into 1000 lines for simplicity), then loop through the # of files ... 90,000 - then loop through the 90,000 files again to compare to each other. This becomes a virtually endless loop of a bazillion lines or processes.
Now the mandatory step here is to "remove" any line that is found in any file except the file we are working on. The ultimate goal is to scrub all the files down to content that is unique across the entire collection, even if it means some files end up empty.
I am saying files, but this could be rows in a database, or elements in an array. (I`ve tried all.) The fastest solution so far has been to load all the files into mysql, then run
UPDATE table SET column=REPLACE(column, find, replace); Also tried Parallel::ForkManager when working with mysql.
The slowest approach actually led to exhausting my 32 GB of ram - that was loading all 90k files into an array. 90k files didnt work at all, smaller batches like 1000 works fine, but then doesnt compare to the other 89,000.
Server specs if helpful: Single Quad-Core E3-1240 4Cores x 3.4Ghz w/ HT 32GB DDR3 ECC RAM 1600MHz 1x256SSD
So how does an engineer solve this problem? I am just PERL hacker...
Tag every line with the filename (and maybe the line number) and sort all the lines using Sort::External. Then you can read the sorted records in order and write only a single unique line to the result files.
A Bloom filter is perfect for this, if you can handle arbitrarily small error.
To quote wikipedia: "A Bloom filter is a space-efficient probabilistic data structure that is used to test whether an element is a member of a set. False positive matches are possible, but false negatives are not; i.e. a query returns either 'possibly in set' or 'definitely not in set'."
In essence, you'll use k hashes to hash each row to k spots on a bit array. Each time you encounter a new row, you are guaranteed you haven't seen it if at least one of the k hashed indices has a '0' bit. You can read up on Bloom filters to see how to size the array and choose k to make false positives arbitrarily small.
Then you go through your files, and either delete rows where you get a positive match, or copy the negative match rows into a new file.
Sort the items using an external merge sort algorithm and remove the duplicates on the merge phase.
Actually, you can do that efficiently just calling the sort command with the -u flag. From Perl:
system "sort -u #files >output";
Your sort command may provide several adjustable parameters to improve its performance. For instance, the number of parallel processes or the amount of memory it can allocate.

Removing Duplicate Words Across Multiple and Large Dictionary Files

I have roughly ~600GB of dictionaries I've accumulated over the years, and I decided I want to clean them up and sort them
First of all, each file on average is very large, anywhere from 500MB to 9GB in size. A prerequisite for what I want to do is that I sort each dictionary. My end goal is to entirely remove duplicate words within and throughout all dictionary files.
The reason for this is that most of my dictionaries are sorted and organized by categories, but duplicates still often exist.
Load file
Read each line and put into data structure
Sort and remove any and all duplicate
Load next file and repeat
Once all files are individually unique, compare against eachother and remove duplicates
For Dictionaries D{1} to D{N}:
1) Sort D{1} through D{N} individually.
2) Check uniqueness of each word in D{i}
3) For each word in D{i}, check ALL words across D{i+1} to D{N}. Delete each word if unique in D{i} first.
I am considering using a sort of "hash" to improve this algorithm. Possibly by only checking the first one or two characters, since the list will be sorted (e.g. hash beginning line location for words starting with a, b, etc.).
4) Save and exit.
Example before (but far smaller):
Dictionary 1 Dictionary 2 Dictionary 3
]a 0u3TGNdB 2 KLOCK
all avisskriveri 4BZ32nKEMiqEaT7z
ast chorion 4BZ5
astn chowders bebotch
apiala chroma bebotch
apiales louts bebotch
avisskriveri lowlander chorion
avisskriverier namely PC-Based
avisskriverierne silking PC-Based
avisskriving underwater PC-Based
So it would see avisskriveri, chorion, bebotch and PC-Based are words that repeate both within and among each of the three dictionaries. So I see avisskriveri in D{1} first, so remove it in all other instances that I have seen it in. Then I see chorion in D{2} first, and remove that in all other instances first, and so forth. In D{3} bebotch and PC-Based are replicated, so I want to delete all but one entry of it (unless I've seen it before). Then save all files and close.
Example after:
Dictionary 1 Dictionary 2 Dictionary 3
]a 0u3TGNdB 2 KLOCK
all chorion 4BZ32nKEMiqEaT7z
ast chowders 4BZ5
astn chroma bebotch
apiala louts PC-Based
apiales lowlander
avisskriveri namely
avisskriverier silking
avisskriverierne underwater
avisskriving
Remember: I do NOT want to create any new dictionaries, only remove duplicates across all dictionaries.
Options:
"Hash" the amount of unique words for each file, allowing the program to estimate the computation time.
Specify a way give the location of the first word beginning with the desired first letter. So that the search may "jump" to a line and skip unecessary computational time.
Run on GPU for high performance parallel computing. (This is an issue because getting the data off of the GPU is tricky)
Goal: Reduce computational time and space consumption so that the method is affordable on a standard machine or server with limited abilities. Or device a method for running it remotely on a GPU cluster.
tl;dr - Sorting unique words across hundreds of files, where each file is 1-9GB in size.
Assuming the dictionaries are in alphabetical order and line by line, one word per line (as are most dictionaries), you could do something like this:
Open a file stream to each file.
Open a file stream to the compiled list file.
Read 1 entry from each file and put it onto a heap, priority queue, or other sorted data structure.
while you still have entries
find & remove the first entry, storing the word (it is not necessary to store the file)
read in the next entry from that file, if one exists
find & remove any duplicates of the stored entry
read in the next entry for each of those files, if one exists
write the stored word to your compiled list file
Close all of the streams
The efficiency of this is something like O(n*m*log(n)) and the space efficiency is O(n), where n is the number of files and m is the average number of entries.
Note that you'll want to create a data type that pairs entries (strings) with file pointers/references, and sorts by string storing. You'll also need a data structure that allows you to peek before you pop.
If you have questions in implementation, ask me.
A more thorough analysis of the efficiency:
Space efficiency is pretty easy. You fill the data structure, and for every item you put on, you take one off, so it stays at O(n).
Computational efficiency is more complex. The looping itself is O(n*m), because you will consider each entry, and there are n*m entries. Some c percent of those will be valid, but that's a constant, so we don't care.
Next, adding and removing from a priority queue is log(n) both ways, so to find & remove is 2*log(n).
Because we add and remove each entry, we get n*m add and removes, so O(n*m*log(n)). I think it might actually be a theta in this case, but meh.
As far as I understand, there is no pattern to exploit in a clever way. So we want to do raw sorting.
Let us assume that no cluster farm is available (we could do other things then)
Then I would start with the easiest approach possible, the command line tool sort:
sort -u inp1 inp2 -o sorted
This will sort inp1 and inp2 together in output file sorted without duplicates (u = unique). Sort typically uses a customized mergesort algorithm, which can handle a limited amount of memory. So you should not run in memory problems.
You should have at least 600 gb (double the size) of free disk space.
You should test with only 2 input files how long it takes and what happens. My tests did not show any problems, but they had used different data and an afs server (which is rather slow, but is a better emulation as some HPC filesystem provider):
$ ll
2147483646 big1
2147483646 big2
$ time sort -u big1 big2 -o bigsorted
1009.674u 6.290s 28:01.63 60.4% 0+0k 0+0io 0pf+0w
$ ll
2147483646 big1
2147483646 big2
117440512 bigsorted
I'd start with something like:
#include <string>
#include <set>
int main()
{
typedef std::set<string> Words;
Words words;
std::string word;
while (std::cin >> word)
words.insert(word); // will only work if not seen before
for (Words::const_iterator i = words.begin(); i != words.end(); ++i)
std::cout << *i;
}
Then just:
cat file1 file2... | ./this_wonderful_program > greatest_dictionary.txt
Should be fine assuming the number of non-duplicate words fits in memory (likely on any modern PC, especially if you've 64 bits and > 4GB), this will probably be I/O bound anyway so no point fussing over unordered map vs (binary-tree) map etc.. You may want to convert to lower-case, strip spurious characters etc. before inserting to the map.
EDIT:
If the unique words don't fit in memory, or you're just stubbornly determined to sort each individual input then merge them, you can use the unix sort command on each file, then sort -m to efficiently merge the pre-sorted files. If you're not on UNIX/Linux, you can probably still find a port of sort (e.g. from Cygwin for Windows), your OS may have an equivalent program, or you could try compiling the sort source code. Note that this approach is a little different from tb-'s suggestion of asking one invocation of sort to sort everything (presumably in memory) - I'm not sure how well that would work, so best to try/compare.
On that that scale of 300GB+, you may want to consider using Hadoop or some other scalable store - otherwise, you will have to deal with memory issues through your own coding. You can try other, more direct methods (UNIX scripting, small C/C++ programs, etc...), but you will likely run out of memory unless you have a ton of duplicate words in your data.
Addendum
Just came across memcached which seems very close to what you are trying to accomplish: but you may have to tweak it not to throw away the oldest values. I don't have time to check right now, but you should do a search on Distributed Hash Tables.

Which one is suitable datastructure for file comparison?

Two files, each of size in terabytes. A file comparison tool compares i-th line of file1 with
i-th line of file2. if they are same it prints. which datastructure is suitable.
B-tree
Linked list
Hash tables
None of them
It can be done using Longest Commons Subsequence, check this out...
Depends how much memory you have and how fast it needs to go - though this really feels like an exam question rather than a true question. I'd go as far as to say that any of the above answers could be 'correct' depending on what exactly the machine specs were.
First, you'd need to make sure that both lists are sorted (this could be done using a merge sort). Then you compare the two files, line by line.

How to sort (million/billion/...) integers?

Sometimes interviewers ask how to sort million/billion 32-bit integers (e.g. here and here). I guess they expect the candidates to compare O(NLog(N)) sort with radix sort. For million integers O(NLog(N)) sort is probably better but for billion they are probably the same. Does it make sense ?
If you get a question like this, they are not looking for the answer. What they are trying to do is see how you think through a problem. Do you jump right in, or do you ask questions about the project requirements?
One question you had better ask is, "How optimal of solution does the problem require?" Maybe a bubble sort of records stored in a file is good enough, but you have to ask. Ask questions about what if the input changes to 64 bit numbers, should the sort process be easily updated? Ask how long does the programmer have to develop the program.
Those types of questions show me that the candidate is wise enough to see there is more to the problem than just sorting numbers.
I expect they're looking for you to expand on the difference between internal sorting and external sorting. Apparently people don't read Knuth nowadays
As aaaa bbbb said, it depends on the situation. You would ask questions about the project requirements. For example, if they want to count the ages of the employees, you probably use the Counting sort, I can sort the data in the memory. But when the data are totally random, you probably use the external sorting. For example, you can divide the data of the source file into the different files, every file has a unique range(File1 is from 0-1m, File2 is from 1m+1 - 2m , ect ), then you sort every single file, and lastly merge them into a new file.
Use bit map. You need some 500 Mb to represent whole 32-bit integer range. For every integer in given array just set coresponding bit. Then simply scan your bit map from left to right and get your integer array sorted.
It depends on the data structure they're stored in. Radix sort beats N-log-N sort on fairly small problem sizes if the input is in a linked list, because it doesn't need to allocate any scratch memory, and if you can afford to allocate a scratch buffer the size of the input at the beginning of the sort, the same is true for arrays. It's really only the wrong choice (for integer keys) when you have very limited additional storage space and your input is in an array.
I would expect the crossover point to be well below a million regardless.

Log combing algorithm

We get these ~50GB data files consisting of 16 byte codes, and I want to find any code that occurs 1/2% of the time or more. Is there any way I can do that in a single pass over the data?
Edit: There are tons of codes - it's possible that every code is different.
EPILOGUE: I've selected Darius Bacon as best answer, because I think the best algorithm is a modification of the majority element he linked to. The majority algorithm should be modifiable to only use a tiny amount of memory - like 201 codes to get 1/2% I think. Basically you just walk the stream counting up to 201 distinct codes. As soon as you find 201 distinct codes, you drop one of each code (deduct 1 from the counters, forgetting anything that becomes 0). At the end, you have dropped at most N/201 times, so any code occurring more times than that must still be around.
But it's a two pass algorithm, not one. You need a second pass to tally the counts of the candidates. It's actually easy to see that any solution to this problem must use at least 2 passes (the first batch of elements you load could all be different and one of those codes could end up being exactly 1/2%)
Thanks for the help!
Metwally et al., Efficient Computation of Frequent and Top-k Elements in Data Streams (2005). There were some other relevant papers I read for my work at Yahoo that I can't find now; but this looks like a good start.
Edit: Ah, see this Brian Hayes article. It sketches an exact algorithm due to Demaine et al., with references. It does it in one pass with very little memory, yielding a set of items including the frequent ones you're looking for, if they exist. Getting the exact counts takes a (now-tractable) second pass.
this will depend on the distribution of the codes. if there are a small enough number of distinct codes you can build a http://en.wikipedia.org/wiki/Frequency_distribution in core with a map. otherwise you probably will have to build a http://en.wikipedia.org/wiki/Histogram and then make multiple passes over the data examining frequencies of codes in each bucket.
Sort chunks of the file in memory, as if you were performing and external sort. Rather than writing out all of the sorted codes in each chunk, however, you can just write each distinct code and the number of occurrences in that chunk. Finally, merge these summary records to find the number of occurrences of each code.
This process scales to any size data, and it only makes one pass over the input data. Multiple merge passes may be required, depending on how many summary files you want to open at once.
Sorting the file allows you to count the number of occurrences of each code using a fixed amount of memory, regardless of the input size.
You also know the total number of codes (either by dividing the input size by a fixed code size, or by counting the number of variable length codes during the sorting pass in a more general problem).
So, you know the proportion of the input associated with each code.
This is basically the pipeline sort * | uniq -c
If every code appears just once, that's no problem; you just need to be able to count them.
That depends on how many different codes exist, and how much memory you have available.
My first idea would be to build a hash table of counters, with the codes as keys. Loop through the entire file, increasing the counter of the respective code, and counting the overall number. Finally, filter all keys with counters that exceed (* overall-counter 1/200).
If the files consist solely of 16-byte codes, and you know how large each file is, you can calculate the number of codes in each file. Then you can find the 0.5% threshold and follow any of the other suggestions to count the occurrences of each code, recording each one whose frequency crosses the threshold.
Do the contents of each file represent a single data set, or is there an arbitrary cutoff between files? In the latter case, and assuming a fairly constant distribution of codes over time, you can make your life simpler by splitting each file into smaller, more manageable chunks. As a bonus, you'll get preliminary results faster and can pipeline then into the next process earlier.

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