I'm trying to do the following in hadoop map/reduce( written in java, linux kernel OS)
Text files 'rules-1' and 'rules-2' (total 3GB in size) contains some rules, each rule are separated by endline character, so the files can be read using readLine() function.
These files 'rules-1' and 'rules-2' needs to be imported as a whole from hdfs in every map function in my cluster i.e. these file are not splittable across different map function.
Input to the mapper's map function is a text file called 'record' (each line is terminated by endline character), so from the 'record' file we get the (key, value) pair. The file is splittable and can be given as input to different map function used in the whole map/reduce process.
What needs to be done is compare each value(i.e. lines from record file) with the rules inside 'rules-1' and 'rules-2'
Problem is, if I pull out each line of rules-1 and rules-2 files to a static arraylist only once, so that each mapper can share the same arraylint and try to compare elements in the arraylist with the each input value from the record file, I get a memory overflow error, since 3GB cannot be stored at a time in the arraylist.
Alternatively, if I import only few lines from the rules-1 and rules-2 files at a time and compare them to each value, map/reduce is taking a lot time to finish its job.
Could you guys provide me any other alternative ideas how can this be done without the memory overflow error? Will it help if I put those file-1 and file-2 inside a hdfs supporting database or something? I'm going out of ideas actually.Would really appreciate if some of you guys could provide me your valuable suggestions.
Iif you input files are small - you can load them into static variables and use rules as an input.
If above is not a case I can suggest the following ways:
a) To give rule-1 and rule-2 high replication factor close to the number of nodes you have. Then you can read from HDFS rule=1 and rule-2 for each record in the input relatively efficient - because it will be sequential read from the local datanode.
b) If you can consider some hash function which, when applied to the rule and to the input string will predict without false negatives that they can match - then you can emit this hash for rules, input record and resolve all possible matches in the reducer. It will be very similar to the way how a join is done using MR
c) I would consider some other optimization techniques like building search trees, or sorting since otherwise the problem looks computationally expensive and will took forever...
On this page find Real-World Cluster Configurations
it will cover file size configuration
You could use the param "mapred.child.java.opts" in conf/mapred-site.xml to increase the memory for your mappers. You might not be able to run as many map slots per server but with more servers in your cluster you could still parallelize your job.
Read the content text file from the MapReduce function and read the keyword text file from the mapper function (for reading your HDFS) and split using StringTokenizer value.toString reading from MapReduce and in your mapper function write HDFS read text file code it will read line-by-line so use two while loops here you compare. Whenever you want data send it to reducer.
Split the 3gb text file into several text files and apply that all text files as usual MapReduce your previous program.
For splitting text file I written Java program and you decide how many lines you want write in each text file.
Related
I’d like to be able to maintain a grouping of entities within a single PCollection element, but parallelize the fetching of those entities from Google Cloud Storage (GCS). i.e.PCollection<Iterable<String>> --> PCollection<Iterable<String>> where the starting PCollection is an Iterable of file paths and the resulting PCollection is Iterable of file contents. Alternatively, PCollection<String> --> PCollection<Iterable<String>> would also work and perhaps even be preferable, where the starting PCollection is a glob pattern, and the resulting PCollection is an iterable of file contents which matched the glob.
My use-case is that at a point in my pipeline I have as input PCollection<String>. Each element of the PCollection is a GCS glob pattern. It’s important that files which match the glob be grouped together because the content of the files–once all files in a group are read–need to be grouped downstream in the pipeline. I originally tried using FileIO.matchAll and a subsequently GroupByKey . However, the matchAll, window, and GroupByKey combination lacked any guarantee that all files matching the glob would be read and in the same window before performing the GroupByKey transform (though I may be misunderstanding Windowing). It’s possible to achieve the desired results if a large time span WindowFn is applied, but it’s still probabilistic rather than a guarantee that all files will be read before grouping. It’s also the main goal of my pipeline to maintain the lowest possible latency.
So my next, and currently operational, plan was to use an AsyncHttpClient to fan out fetching file contents via GCS HTTP API. I feel like this goes against the grain in Beam and is likely sub-optimal in terms of parallelization.
So I’ve started investigating SplittableDoFn . My current plan is to allow splitting such that each entity in the input Iterable (i.e. each matched file from the glob pattern) could be processed separately. I've been able to modify FileIO#MatchFn (defined here in the Java SDK) to provide mechanics for PCollection<String> -> PCollection<Iterable<String>> transform between input of GCS glob patterns and output of Iterable of matches for the glob.
The challenge I’ve encountered is: how do I go about grouping/gathering the split invocations back into a single output value in my DoFn? I’ve tried using stateful processing and using a BagState to collect file contents along the way, but I realized part way along that the ProcessElement method of a splittable DoFn may only accept ProcessContext and Restriction tuples, and no other args therefore no StateId args referring to a StateSpec (throws an invalid argument error at runtime).
I noticed in the FilePatternWatcher example in the official SDF proposal doc that a custom tracker was created wherein FilePath Objects kept in a set and presumably added to the set via tryClaim. This seems as though it could work for my use-case, but I don’t see/understand how to go about implementing a #SplitRestriction method using a custom RestrictionTracker.
I would be very appreciative if anyone were able to offer advice. I have no preference for any particular solution, only that I want to achieve the ability to maintain a grouping of entities within a single PCollection element, but parallelize the fetching of those entities from Google Cloud Storage (GCS).
Would joining the output PCollections help you?
PCollectionList
.of(collectionOne)
.and(collectionTwo)
.and(collectionThree)
...
.apply(Flatten.pCollections())
I have some large files in a local binary format, which contains many 3D (or 4D) arrays as a series of 2D chunks. The order of the chunks in the files is random (could have chunk 17 of variable A, followed by chunk 6 of variable B, etc.). I don't have control over the file generation, I'm just using the results. Fortunately the files contain a table of contents, so I know where all the chunks are without having to read the entire file.
I have a simple interface to lazily load this data into dask, and re-construct the chunks as Array objects. This works fine - I can slice and dice the array, do calculations on them, and when I finally compute() the final result the chunks get loaded from file appropriately.
However, the order that the chunks are loaded is not optimal for these files. If I understand correctly, for tasks where there is no difference of cost (in terms of # of dependencies?), the local threaded scheduler will use the task keynames as a tie-breaker. This seems to cause the chunks to be loaded in their logical order within the Array. Unfortunately my files do not follow the logical order, so this results in many seeks through the data (e.g. seek halfway through the file to get chunk (0,0,0) of variable A, then go back near the beginning to get chunk (0,0,1) of variable A, etc.). What I would like to do is somehow control the order that these chunks get read, so they follow the order in the file.
I found a kludge that works for simple cases, by creating a callback function on the start_state. It scans through the tasks in the 'ready' state, looking for any references to these data chunks, then re-orders those tasks based on the order of the data on disk. Using this kludge, I was able to speed up my processing by a factor of 3. I'm guessing the OS is doing some kind of read-ahead when the file is being read sequentially, and the chunks are small enough that several get picked up in a single disk read. This kludge is sufficient for my current usage, however, it's ugly and brittle. It will probably work against dask's optimization algorithm for complex calculations. Is there a better way in dask to control which tasks win in a tie-breaker, in particular for loading chunks from disk? I.e., is there a way to tell dask, "all things being equal, here's the relative order I'd like you to process this group of chunks?"
Your assessment is correct. As of 2018-06-16 there is not currently any way to add in a final tie breaker. In the distributed scheduler (which works fine on a single machine) you can provide explicit priorities with the priority= keyword, but these take precedence over all other considerations.
I'm trying to retrieve the alignment score of two sequences compared using emboss in biopython. The only way that I know is to retrieve it from an output text file produced by emboss. The problem is that there will be hundreds of these files to iterate over. Is there an easier/cleaner method to retrieve the alignment score, without resorting to that? This is the main part of the code that I'm using.
From Bio.Emboss.Applications import StretcherCommandline
needle_cline = StretcherCommandline(asequence=,bsequence=,gapopen=,gapextend=,outfile=)
stdout, stderr = needle_cline()
I had the same problem and after some time spent on searching for a neat solution I popped up a white flag.
However, to speed up significantly the processing of output files I did the following things:
1) I used re python module for handling regular expressions to extract all data needed.
2) I created a ramdisk space for the output files. The use of a ramdisk here allowed for processing and exchanging all the data in RAM memory (much faster than writing and reading the output files from a hard drive, not to mention it saves your hdd in case of processing massive number of alignments).
I don't know if there is one specifically for your command.
For Primer3CommandLine, there is Primer3. Make your life much easier with something like:
from Bio.Emboss import Primer3
inputFile = "./wherever/your/outputfileis.out"
with open(inputFile) as fileHandle:
record = Primer3.parse(fileHandle)
# XXX check is len>0
primers = record.next().primers
numPrimers = len(primers)
# you should have access to each primer, using a for loop
# to check how to access the data you care about. For example:
I would also check http://biopython.org/wiki/SeqIO#Sequence_Input
New user of hadoop and mapreduce, i would like to create a mapreduce job to do some measure on images. this why i would like to know if i can passe an image as input to mapreduce?if yes? any kind of example
thanks
No.. you cannot pass an image directly to a MapReduce job as it uses specific types of datatypes optimized for network serialization. I am not an image processing expert but I would recommend to have a look at HIPI framework. It allows image processing on top of MapReduce framework in a convenient manner.
Or if you really want to do it the native Hadoop way, you could do this by first converting the image file into a Hadoop Sequence file and then using the SequenceFileInputFormat to process the file.
Yes, you can totally do this.
With the limited information provided, I can only give you a very general answer.
Either way, you'll need to:
1) You will need to write a custom InputFormat that instead of taking chunks of files in HDFS locations (like TextInputFormat and SequenceFileInputFormat do), it actually passes to each map task the Image's HDFS path name. Reading the image from that won't be too hard.
If you plan to have a Reduce phase in which Images are passed around through the framework, you'll need to:
2) You will need to make an "ImageWritable" class that implements Writable (or WritableComparable if you're keying on the image). In your write() method, you'll need to serialize your image to a byte array. When you do this, what I would do is first write to the output an int/long which is the size of the array you're going to write. Lastly, you'll want to write the array as bytes.
In your read() method, you'll read an int/long first (which will describe the payload of the image), create an byte array of this size, and then read the bytes fully into your byte array up to the length of your int/long that you captured.
I'm not entirely sure what you're doing, but that's how I'd go about it.
I had an pre-interview task, which I have completed and the solution works, however I was marked down and did not get an interview due to having used a TADODataset. I basically imported a CSV file which populated the dataset, the data had to be processed in a specific way, so I used Filtering and Sorting of the dataset to make sure that the data was ordered in the way I wanted it and then I did the logic processing in a while loop. The feedback that was received said that this was bad as it would be very slow for large files.
My main question here is if using an in memory dataset is slow for processing large files, what would have been better way to access the information from the csv file. Should I have used String Lists or something like that?
It really depends on how "big" and the available resources(in this case RAM) for the task.
"The feedback that was received said that this was bad as it would be very slow for large files."
CSV files are usually used for moving data around(in most cases that I've encountered files are ~1MB+ up to ~10MB, but that's not to say that others would not dump more data in CSV format) without worrying too much(if at all) about import/export since it is extremely simplistic.
Suppose you have a 80MB CSV file, now that's a file you want to process in chunks, otherwise(depending on your processing) you can eat hundreds of MB of RAM, in this case what I would do is:
while dataToProcess do begin
// step1
read <X> lines from file, where <X> is the max number of lines
you read in one go, if there are less lines(i.e. you're down to 50 lines and X is 100)
to process, then you read those
// step2
process information
// step3
generate output, database inserts, etc.
end;
In the above case, you're not loading 80MB of data into RAM, but only a few hundred KB, and the rest you use for processing, i.e. linked lists, dynamic insert queries(batch insert), etc.
"...however I was marked down and did not get an interview due to having used a TADODataset."
I'm not surprised, they were probably looking to see if you're capable of creating algorithm(s) and provide simple solutions on the spot, but without using "ready-made" solutions.
They were probably thinking of seeing you use dynamic arrays and creating one(or more) sorting algorithm(s).
"Should I have used String Lists or something like that?"
The response might have been the same, again, I think they wanted to see how you "work".
The interviewer was quite right.
The correct, scalable and fastest solution on any medium file upwards is to use an 'external sort'.
An 'External Sort' is a 2 stage process, the first stage being to split each file into manageable and sorted smaller files. The second stage is to merge these files back into a single sorted file which can then be processed line by line.
It is extremely efficient on any CSV file with over say 200,000 lines. The amount of memory the process runs in can be controlled and thus dangers of running out of memory can be eliminated.
I have implemented many such sort processes and in Delphi would recommend a combination of TStringList, TList and TQueue classes.
Good Luck