DZone
Thanks for visiting DZone today,
Edit Profile
  • Manage Email Subscriptions
  • How to Post to DZone
  • Article Submission Guidelines
Sign Out View Profile
  • Post an Article
  • Manage My Drafts
Over 2 million developers have joined DZone.
Log In / Join
Refcards Trend Reports
Events Video Library
Refcards
Trend Reports

Events

View Events Video Library

The Latest Data Topics

article thumbnail
When to Use MongoDB Rather than MySQL (or Other RDBMS): The Billing Example
NoSQL has been a hot topic a pretty long time (well, it's not only a buzz anymore). However, when should we really use it instead of an RDBMS?
March 3, 2014
by Moshe Kaplan
· 379,055 Views · 12 Likes
article thumbnail
Python CSV Files: Reading and Writing
Learn to parse CSV (Comma Separated Values) files with Python examples using the csv module's reader function and DictReader class.
March 3, 2014
by Mike Driscoll
· 375,824 Views · 6 Likes
article thumbnail
Getting Started with Mocking in Java using Mockito
We all write unit tests but the challenge we face at times is that the unit under test might be dependent on other components. And configuring other components for unit testing is definitely an overkill. Instead we can make use of Mocks in place of the other components and continue with the unit testing. To show how one can use mocks, I have a Data access layer(DAL), basically a class which provides an API for the application to access and modify the data in the data repository. I then unit test the DAL without actually the need to connect to the data repository. The data repository can be a local database or remote database or a file system or any place where we can store and retrieve the data. The use of a DAL class helps us in keeping the data mappers separate from the application code. Lets create a Java project using maven. mvn archetype:generate -DgroupId=info.sanaulla -DartifactId=MockitoDemo -DarchetypeArtifactId=maven-archetype-quickstart -DinteractiveMode=false The above creates a folder MockitoDemo and then creates the entire directory structure for source and test files. Consider the below model class for this example: package info.sanaulla.models; import java.util.List; /** * Model class for the book details. */ public class Book { private String isbn; private String title; private List authors; private String publication; private Integer yearOfPublication; private Integer numberOfPages; private String image; public Book(String isbn, String title, List authors, String publication, Integer yearOfPublication, Integer numberOfPages, String image){ this.isbn = isbn; this.title = title; this.authors = authors; this.publication = publication; this.yearOfPublication = yearOfPublication; this.numberOfPages = numberOfPages; this.image = image; } public String getIsbn() { return isbn; } public String getTitle() { return title; } public List getAuthors() { return authors; } public String getPublication() { return publication; } public Integer getYearOfPublication() { return yearOfPublication; } public Integer getNumberOfPages() { return numberOfPages; } public String getImage() { return image; } } The DAL class for operating on the Book model class is: package info.sanaulla.dal; import info.sanaulla.models.Book; import java.util.ArrayList; import java.util.Arrays; import java.util.Collections; import java.util.List; /** * API layer for persisting and retrieving the Book objects. */ public class BookDAL { private static BookDAL bookDAL = new BookDAL(); public List getAllBooks(){ return Collections.EMPTY_LIST; } public Book getBook(String isbn){ return null; } public String addBook(Book book){ return book.getIsbn(); } public String updateBook(Book book){ return book.getIsbn(); } public static BookDAL getInstance(){ return bookDAL; } } The DAL layer above currently has no functionality and we are going to unit test that piece of code (TDD). The DAL layer might communicate with a ORM Mapper or Database API which we are not concerned while designing the API. Test Driving the DAL Layer There are lot of frameworks for Unit testing and mocking in Java but for this example I would be picking JUnit for unit testing and Mockito for mocking. We would have to update the dependency in Maven’s pom.xml 4.0.0 info.sanaulla MockitoDemo jar 1.0-SNAPSHOT MockitoDemo http://maven.apache.org junit junit 4.10 test org.mockito mockito-all 1.9.5 test Now lets unit test the BookDAL. During the unit testing we will inject mock data into the BookDAL so that we can complete the testing of the API without depending on the data source. Initially we will have an empty test class: public class BookDALTest { public void setUp() throws Exception { } public void testGetAllBooks() throws Exception { } public void testGetBook() throws Exception { } public void testAddBook() throws Exception { } public void testUpdateBook() throws Exception { } } We will inject the mock BookDAL and mock data in the setUp() as shown below: public class BookDALTest { private static BookDAL mockedBookDAL; private static Book book1; private static Book book2; @BeforeClass public static void setUp(){ //Create mock object of BookDAL mockedBookDAL = mock(BookDAL.class); //Create few instances of Book class. book1 = new Book("8131721019","Compilers Principles", Arrays.asList("D. Jeffrey Ulman","Ravi Sethi", "Alfred V. Aho", "Monica S. Lam"), "Pearson Education Singapore Pte Ltd", 2008,1009,"BOOK_IMAGE"); book2 = new Book("9788183331630","Let Us C 13th Edition", Arrays.asList("Yashavant Kanetkar"),"BPB PUBLICATIONS", 2012,675,"BOOK_IMAGE"); //Stubbing the methods of mocked BookDAL with mocked data. when(mockedBookDAL.getAllBooks()).thenReturn(Arrays.asList(book1, book2)); when(mockedBookDAL.getBook("8131721019")).thenReturn(book1); when(mockedBookDAL.addBook(book1)).thenReturn(book1.getIsbn()); when(mockedBookDAL.updateBook(book1)).thenReturn(book1.getIsbn()); } public void testGetAllBooks() throws Exception {} public void testGetBook() throws Exception {} public void testAddBook() throws Exception {} public void testUpdateBook() throws Exception {} } In the above setUp() method I have: Created a mock object of BookDAL BookDAL mockedBookDAL = mock(BookDAL.class); Stubbed the API of BookDAL with mock data, such that when ever the API is invoked the mocked data is returned. //When getAllBooks() is invoked then return the given data and so on for the other methods. when(mockedBookDAL.getAllBooks()).thenReturn(Arrays.asList(book1, book2)); when(mockedBookDAL.getBook("8131721019")).thenReturn(book1); when(mockedBookDAL.addBook(book1)).thenReturn(book1.getIsbn()); when(mockedBookDAL.updateBook(book1)).thenReturn(book1.getIsbn()); Populating the rest of the tests we get: package info.sanaulla.dal; import info.sanaulla.models.Book; import org.junit.BeforeClass; import org.junit.Test; import static org.junit.Assert.*; import static org.mockito.Mockito.mock; import static org.mockito.Mockito.when; import java.util.Arrays; import java.util.List; public class BookDALTest { private static BookDAL mockedBookDAL; private static Book book1; private static Book book2; @BeforeClass public static void setUp(){ mockedBookDAL = mock(BookDAL.class); book1 = new Book("8131721019","Compilers Principles", Arrays.asList("D. Jeffrey Ulman","Ravi Sethi", "Alfred V. Aho", "Monica S. Lam"), "Pearson Education Singapore Pte Ltd", 2008,1009,"BOOK_IMAGE"); book2 = new Book("9788183331630","Let Us C 13th Edition", Arrays.asList("Yashavant Kanetkar"),"BPB PUBLICATIONS", 2012,675,"BOOK_IMAGE"); when(mockedBookDAL.getAllBooks()).thenReturn(Arrays.asList(book1, book2)); when(mockedBookDAL.getBook("8131721019")).thenReturn(book1); when(mockedBookDAL.addBook(book1)).thenReturn(book1.getIsbn()); when(mockedBookDAL.updateBook(book1)).thenReturn(book1.getIsbn()); } @Test public void testGetAllBooks() throws Exception { List allBooks = mockedBookDAL.getAllBooks(); assertEquals(2, allBooks.size()); Book myBook = allBooks.get(0); assertEquals("8131721019", myBook.getIsbn()); assertEquals("Compilers Principles", myBook.getTitle()); assertEquals(4, myBook.getAuthors().size()); assertEquals((Integer)2008, myBook.getYearOfPublication()); assertEquals((Integer) 1009, myBook.getNumberOfPages()); assertEquals("Pearson Education Singapore Pte Ltd", myBook.getPublication()); assertEquals("BOOK_IMAGE", myBook.getImage()); } @Test public void testGetBook(){ String isbn = "8131721019"; Book myBook = mockedBookDAL.getBook(isbn); assertNotNull(myBook); assertEquals(isbn, myBook.getIsbn()); assertEquals("Compilers Principles", myBook.getTitle()); assertEquals(4, myBook.getAuthors().size()); assertEquals("Pearson Education Singapore Pte Ltd", myBook.getPublication()); assertEquals((Integer)2008, myBook.getYearOfPublication()); assertEquals((Integer)1009, myBook.getNumberOfPages()); } @Test public void testAddBook(){ String isbn = mockedBookDAL.addBook(book1); assertNotNull(isbn); assertEquals(book1.getIsbn(), isbn); } @Test public void testUpdateBook(){ String isbn = mockedBookDAL.updateBook(book1); assertNotNull(isbn); assertEquals(book1.getIsbn(), isbn); } } One can run the test by using maven command: mvn test. The output is: ------------------------------------------------------- T E S T S ------------------------------------------------------- Running info.sanaulla.AppTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.029 sec Running info.sanaulla.dal.BookDALTest Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.209 sec Results : Tests run: 5, Failures: 0, Errors: 0, Skipped: 0 So we have been able to test the DAL class without actually configuring the data source by using mocks.
February 26, 2014
by Mohamed Sanaulla
· 233,571 Views · 18 Likes
article thumbnail
How to Estimate Memory Consumption
This story goes back at least a decade, when I was first approached by a PHB with a question “How big servers are we going to need to buy for our production deployment”. The new and shiny system we have been building was nine months from production rollout and apparently the company had promised to deliver the whole solution, including hardware. Oh boy, was I in trouble. With just a few years of experience down my belt, I could have pretty much just tossed a dice. Even though I am sure my complete lack of confidence was clearly visible, I still had to come up with the answer. Four hours of googling later I recall sitting there with the same question still hovering in front of my bedazzled face: “How to estimate the need for computing power?” In this post I start to open up the subject by giving you rough guidelines on how to estimate memory requirements for your brand new Java application. For the impatient ones – the answer will be to start with the memory equal to approximately 5 x [amount of memory consumed by Live Data] and start the fine-tuning from there. For the ones more curious about the logic behind, stay with me and I will walk you through the reasoning. First and foremost, I can only recommend to avoid answering a question phrased like this without detailed information being available. Your answer has to be based upon the performance requirements, so do not even start without clarifying those first. And I do not mean way-too-ambiguous “The system needs to support 700 concurrent users”, but a lot more specific ones about latency and throughput, taking into account the amount of data, usage patterns. One should also not forget about the budget also – we all can all dream about sub-millisecond latencies, but those without HFT banking backbone budgets – unfortunately it will only remain a dream. For now, lets assume you have those requirements in place. Next stop would be to create the load test scripts emulating user behaviour. If you are now able to launch those scripts concurrently you have built a foundation to the answer. As you might also have guessed, the next step involves our usual advice of measuring not guessing. But with a caveat. Live Data Size Namely, our quest for the optimal memory configuration requires capturing the Live Data Size. Having captured this, we have the baseline configuration in place for the fine-tuning. How does one define live data size? Charlie Hunt and Binu John in their “Java Performance” book have given it the following definition: Live data size is the heap size consumed by the set of long-lived objects required to run the application in its steady state. Equipped with the definition, we are ready to run your load tests against the application with the GC logging turned on (-XX:+PrintGCTimeStamps -Xloggc:/tmp/gc.log -XX:+PrintGCDetails) and visualize the logs (with the help of gcviewer for example) to determine the moment when the application has reached to the steady state. What you are after looks similar to the following: We can see the GC doing its job both with minor and Full GC runs in a familiar double-saw-toothed graphic. This particular application seems to have achieved a steady state already after the first full GC run on 21st second. In most cases however, it takes 10-20 Full GC runs to spot the change in trends. After four full GC runs we can estimate that the Live Data Size is equal to approximately 100MB. The aforementioned Java Performance book is now indicating that there is a strong correlation between the Live Data Size and the optimal memory configuration parameters in a typical Java EE application. The evidence from the field is also backing up their recommendations: Set the maximum heap size to 3-4 x [Live Data Size] So, for our application at hand, we should set the -Xmx to be in between 300m and 400m for the initial performance tests and take it from there. We have mixed feelings about other recommendations given in the book, recommending to set the maximum permanent generation size to 1.2-1.5 x [Live Data Size of the Permanent Generation] and the -XX:NewRatio being set to 1-1.5 x of the [Live Data Size]. We are currently gathering more data to determine whether the positive correlation exists, but until then I recommend to base your survival and eden configuration decisions on monitoring your allocation rate instead. Why should one bother you might now ask. Indeed, two reasons for not caring immediately surface: 8G memory chip is in sub $100 territory at the time of writing this article Virtualization, especially when using large providers such as Amazon AWS make adjusting the capacity easy Both of the reasons are partially valid and have definitely reduced the need for provisioning to be precise. But both of them are still putting you in the danger zone When tossing in huge amounts of memory “just in case” you are most likely going to significantly affect the latency – going into heaps above 8G it is darn easy to introduce Full GC pauses spanning over tens of seconds. When over-provisioning with the mindset of “lets tune it later”, the “later” part has a tendency of never arriving. I have faced numerous applications running on vastly over provisioned environments just because of this. For example the aforementioned application I discovered running on Amazon EC2 m1.xlarge instance was costing the company $4,200 per instance / year. Converting it to m1.small reduced the bill to just $520 for the instance. 8-fold cost reduction will be visible from your operations budget if your deployments are large, trust me on this. Summary Unfortunately I still see way too many decisions made exactly like I was forced to do a decade ago. This leads to the under- and over planning of capacity, both of which can be equally poor choices, especially if you cannot enjoy the benefits of virtualization. I got lucky with mine, but you might not get away with your guestimate, so I can only recommend to actually plan ahead using the simple framework described in this post. If you enjoyed the content, I can only recommend to follow our performance tuning advice in Twitter.
February 25, 2014
by Nikita Salnikov-Tarnovski
· 11,976 Views
article thumbnail
Voron & Time Series Data: Getting Real Data Outputs
So far, we have just put the data in and out. And we have had a pretty good track record doing so. However, what do we do with the data now that we have it? As you can expect, we need to read it out. Usually by specific date ranges. The interesting thing is that we usually are not interested in just a single channel, we care about multiple channels. And for fun, those channel might be synchronized or not. An example of the first might be the current speed and the current engine temperature in a car. They are generally share the exact same timestamps. An example of out of sync is when you have a sensor on a rooftop measuring rainfall, and another sensor in the sewer measuring water flow rates. (Again, thanks to Dan for helping me with the domain). This is interesting, because it present quite a few interesting problems: We need to merge different streams into a unified view. We need to handle both matching and non matching sequences. We need to handle erroneous data, what happens when we have two reading for the same time for the same sensor? Yes, that shouldn’t happen, but it does. I solved this with the following API: public class RangeEntry { public DateTime Timestamp; public double?[] Values; } IEnumerable results = dts.ScanRanges(DateTime.MinValue, DateTime.MaxValue, new[] { "6febe146-e893-4f64-89f8-527f2dbaae9b", "707dcb42-c551-4f1a-9203-e4b0852516cf", "74d5bee8-9a7b-4d4e-bd85-5f92dfc22edb", "7ae29feb-6178-4930-bc38-a90adf99cfd3", }); This API gives me the results in the time order, with the same positions as the ids requested for the values. With nulls if there isn’t a value matching the value from that time in that particular sensor channel. The actual implementation relies on this method: IEnumerable ScanRange(DateTime start, DateTime end, string id) All this does it provide the entries all the entries in a particular date range, for a particular channel. Let us see how we implement multi channel scanning on top of this: private class PendingEnumerator { public IEnumerator Enumerator; public int Index; } private class PendingEnumerators { private readonly SortedDictionary> _values = new SortedDictionary>(); public void Enqueue(PendingEnumerator entry) { List list; var dateTime = entry.Enumerator.Current.Timestamp; if (_values.TryGetValue(dateTime, out list) == false) { _values.Add(dateTime, list = new List()); } list.Add(entry); } public bool IsEmpty { get { return _values.Count == 0; } } public List Dequeue() { if (_values.Count == 0) return new List(); var kvp = _values.First(); _values.Remove(kvp.Key); return kvp.Value; } } public IEnumerable ScanRanges(DateTime start, DateTime end, string[] ids) { if (ids == null || ids.Length == 0) yield break; var pending = new PendingEnumerators(); for (int i = 0; i < ids.Length; i++) { var enumerator = ScanRange(start, end, ids[i]).GetEnumerator(); if(enumerator.MoveNext() == false) continue; pending.Enqueue(new PendingEnumerator { Enumerator = enumerator, Index = i }); } var result = new RangeEntry { Values = new double?[ids.Length] }; while (pending.IsEmpty == false) { Array.Clear(result.Values,0,result.Values.Length); var entries = pending.Dequeue(); if (entries.Count == 0) break; foreach (var entry in entries) { var current = entry.Enumerator.Current; result.Timestamp = current.Timestamp; result.Values[entry.Index] = current.Value; if(entry.Enumerator.MoveNext()) pending.Enqueue(entry); } yield return result; } } We are getting a single entry from each channel into the pending enumerators. Then, we collate all the entries that share the same time into a single entry. We use the Index property to track the actual expected index of the entry in the output. And we handle duplicate times in the same channel by outputting multiple entries. Testing this on my 1.1 million records data set, we can get 185 thousands records back in 0.15 seconds.
February 25, 2014
by Oren Eini
· 5,451 Views
article thumbnail
The Risks Of Big-Bang Deployments And Techniques For Step-wise Deployment
If you ever need to persuade management why it might be better to deploy a larger change in multiple stages and push it to customers gradually, read on. A deployment of many changes is risky. We want therefore to deploy them in a way which minimizes the risk of harm to our customers and our companies. The deployment can be done either in an all-at-once (also known as big-bang) way or a gradual way. We will argue here for the more gradual (“stepwise”) approach. Big-bang or stepwise deployment? A big-bang deployment seems to be the natural thing to do: the full solution is developed and tested and then replaces the current system at once. However, it has two crucial flaws. First, it assumes that most defects can be discovered by testing. However, due to differences in test/prod environments, unknown dependencies, and the sheer scale of a typical larger system there always will be problems that are not discovered until production deployment or even until the application runs for a while in production (whichapplies even to airplanes). The more parts have been changed, the more of these production defects will happen at the same time. A gradual deployment makes it possible to discover and handle them one by one. Second, the more complex the deployment, the higher chance of human error(s), i.e. the deployment itself is a likely source of serious defects. Some of the drawbacks of a big-bang deployment in more detail: Complexity: A big-bang deployment requires coordination of many people and “moving parts” that depend on each other, providing a huge opportunity for human mistake (i.e. there will be mistakes). Lot of time: Such a deployment requires lot of time (typically also more than planed/expected) and thus lot of downtime when users cannot use the system. Hard troubleshooting: With a network of inter-dependent parts that changed all at the same time, while perhaps also changing the infrastructure (i.e. connections between them), it is extremely hard to pinpoint the source of defects, thus considerably increasing the time to detect and correct defects while also increasing the risk of people stepping on the toes of each other and “panic fixes” that either cause more problems than they remove or are not good enough (as the rollback that sped upKnight’s downfall). Rollback is likely either impossible or equally time-consuming and risky as the deployment itself, thus increasing the impact of defects and inviting even more human errors. Impact: Deploying everything to all users at the same time means that everybody will be impacted by a potential defect/error/mistake. Long freeze: All needs to be tested together after all development is finished, which requires a lot of time while the code is frozen and no more fixes and changes can get into production for weeks. Risk mitigation The goal of a good deployment plan is to mitigate the risk of the deployment and get it to an acceptable level. There are two aspects to risk: the probability of a defect and the impact of the defect. The following table shows how the possible measures affect them: Defect probability reduction Defect impact reduction testing stepwise deployment gradual migration of users to the new version (f.ex. 1 in 1000 or particular subsets) rollback mechanism => these also lead to much lower time to detect and fix defects Practices for stepwise deployment Enable stepwise deployment: Use parallel change and other Continuous Delivery techniques to make it possible to deploy updated components independently from each other and to switch on/off new features and to switch what versions of the components they depend on are currently used. (Parallel change – keeping the old and new code and being able to use one or the other – is crucial here. Also notice that parallel change applies also to data – you will need to evolve your data schema gradually and keep both old and new one at the same time in a period of time.) Enable rollback. The previous measure – stepwise deployment – makes it also easy(ier) to roll-back the changes by switching to a previous version of a dependency or by switching back to the old code. Migrate users gradually to the new version, i.e. expose the new version only to a small subset of the users initially and increase that subset until everybody uses it. This can be done f.ex. by deploying to only a subset of servers and sending a random/particular subset of users to the new servers but there are also ways if you have only a single machine. (See f.ex. my post Webapp Blue-Green Deployment Without Breaking Sessions/With Fallback With HAProxy.) Monitoring – make sure you are able to monitor flow of users through the system and detect any anomalies and errors early, long before angry calls from the business. Tools such as Logstash, Google Analytics (with custom events from JavaScript), client-side error logging via one of existing services or a custom solution are invaluable. About these ads
February 20, 2014
by Jakub Holý
· 22,330 Views
article thumbnail
Eclipse's BIRT: Scripted Data Set
This article presents the usage of sripted data set in the eclipse's BIRT.
February 18, 2014
by Kosta Stojanovski
· 38,924 Views · 1 Like
article thumbnail
Voron & Time Series: Working with Real Data
dan liebster has been kind enough to send me a real world time series database. the data has been sanitized to remove identifying issues, but this is actually real world data, so we can learn a lot more about this. this is what this looks like: the first thing that i did was take the code in this post , and try it out for size. i wrote the following: int i = 0; using (var parser = new textfieldparser(@"c:\users\ayende\downloads\timeseries.csv")) { parser.hasfieldsenclosedinquotes = true; parser.delimiters = new[] {","}; parser.readline();//ignore headers var startnew = stopwatch.startnew(); while (parser.endofdata == false) { var fields = parser.readfields(); debug.assert(fields != null); dts.add(fields[1], datetime.parseexact(fields[2], "o", cultureinfo.invariantculture), double.parse(fields[3])); i++; if (i == 25*1000) { break; } if (i%1000 == 0) console.write("\r{0,15:#,#} ", i); } console.writeline(); console.writeline(startnew.elapsed); } note that we are using a separate transaction per line , which means that we are really doing a lot of extra work. but this simulate very well incoming events coming one at a time. we were able to process 25,000 events in 8.3 seconds. at a rate of just over 3 events per millisecond . now, note that we have in here the notion of “channels”. from my investigation, it seems clear that some form of separation is actually very common in time series data. we are usually talking about sensors or some such, and we want to track data across different sensors over time. and there is little if any call for working over multiple sensors / channels at the same time. because of that, i made a relatively minor change in voron, that allows it to have an infinite number of separate trees. that means that i can use as many trees as you want, and we can model a channel as a tree in voron. i also changed things so we instead of doing a single transaction per line, we will do a transaction per 1000 lines. that dropped the time to insert 25,000 lines to 0.8 seconds. or a full order of magnitude faster. that done, i inserted the full data set, which is just over 1,096,384 records. that took 36 seconds. in the data set i have, there are 35 channels. i just tried, and reading all the entries in a channel with 35,411 events takes 0.01 seconds. that allows doing things like doing averages over time, comparing data, etc. you can see the code implementing this in the following link .
February 7, 2014
by Oren Eini
· 4,090 Views
article thumbnail
Big Data Search, Part 6: Sorting Randomness
As it turns out, doing work on big data sets is quite hard. To start with, you need to get the data, and it is… well, big. So that takes a while. Instead, I decided to test my theory on the following scenario. Given 4 GB of random numbers, let us find how many times we have the number 1. Because I wanted to ensure a consistent answer, I wrote: public static IEnumerable RandomNumbers() { const long count = 1024 * 1024 * 1024L * 1; var random = new MyRand(); for (long i = 0; i < count; i++) { if (i % 1024 == 0) { yield return 1; continue; } var result = random.NextUInt(); while (result == 1) { result = random.NextUInt(); } yield return result; } } /// /// Based on Marsaglia, George. (2003). Xorshift RNGs. /// http://www.jstatsoft.org/v08/i14/paper /// public class MyRand { const uint Y = 842502087, Z = 3579807591, W = 273326509; uint _x, _y, _z, _w; public MyRand() { _y = Y; _z = Z; _w = W; _x = 1337; } public uint NextUInt() { uint t = _x ^ (_x << 11); _x = _y; _y = _z; _z = _w; return _w = (_w ^ (_w >> 19)) ^ (t ^ (t >> 8)); } } I am using a custom Rand function because it is significantly faster than System.Random. This generate 4GB of random numbers, at also ensure that we get exactly 1,048,576 instances of 1. Generating this in an empty loop takes about 30 seconds on my machine. For fun, I run the external sort routine in 32 bits mode, with a buffer of 256MB. It is currently processing things, but I expect it to take a while. Because the buffer is 256 in size, we flush it every 128 MB (while we still have half the buffer free to do more work). The interesting thing is that even though we generate random number, sorting then compressing the values resulted in about 60% compression rate. The problem is that for this particular case, I am not sure if that is a good thing. Because the values are random, we need to select a pretty high degree of compression just to get a good compression rate. And because of that, a significant amount of time is spent just compressing the data. I am pretty sure that for real world scenario, it would be better, but that is something that we’ll probably need to test. Not compressing the data in the random test is a huge help. Next, external sort is pretty dependent on the performance of… sort, of course. And sort isn’t that fast. In this scenario, we are sorting arrays of about 26 million items. And that takes time. Implementing parallel sort cut this down to less than a minute per batch of 26 million. That let us complete the entire process, but then it halts with the merge. The reason for that is that we push all the values into a heap, and there are 1 billion of them. Now, the heap never exceed 40 items, but those are still 1 billion * O(log 40) or about 5.4 billion comparisons that we have to do, and we do this sequentially, which takes time. I tried thinking about ways to parallel, but I am not sure how that can be done. We have 40 sorted files, and we want to merge all of them. Obviously we can sort each 10 files set in parallel, then sort the resulting 4, but the cost we have now is the actual sorting cost, not I/O. I am not sure how to approach this. For what is it worth, you can find the code for this here.
February 5, 2014
by Oren Eini
· 9,092 Views
article thumbnail
AES-256 Encryption with Java and JCEKS
Security has become a great topic of discussion in the last few years due to the recent releasing of documents from Edward Snowden and the explosion of hacking against online commerce stores like JC Penny, Sony andTarget. While this post will not give you all of the tools to help prevent the use of illegally sourced data, this post will provide a starting point for building a set of tools and tactics that will help prevent the use of data by other parties. This post will show how to adopt AES encryption for strings in a Java environment. It will talk about creating AES keys and storing AES keys in a JCEKS keystore format. A working example of the code in this blog is located athttps://github.com/mike-ensor/aes-256-encryption-utility It is recommended to read each section in order because each section builds off of the previous section, however, this you might want to just jump quickly jump to a particular section. Setup - Setup and create keys with keytool Encrypt - Encrypt messages using byte[] keys Decrypt - Decrypt messages using same IV and key from encryption Obtain Keys from Keystore - Obtain keys from keystore via an alias What is JCEKS? JCEKS stands for Java Cryptography Extension KeyStore and it is an alternative keystore format for the Java platform. Storing keys in a KeyStore can be a measure to prevent your encryption keys from being exposed. Java KeyStores securely contain individual certificates and keys that can be referenced by an alias for use in a Java program. Java KeyStores are often created using the "keytool" provided with the Java JDK. NOTE: It is strongly recommended to create a complex passcode for KeyStores to keep the contents secure. The KeyStore is a file that is considered to be public, but it is advisable to not give easy access to the file. Setup All encryption is governed by laws of each country and often have restrictions on the strength of the encryption. One example is that in the United States, all encryption over 128-bit is restricted if the data is traveling outside of the boarder. By default, the Java JCE implements a strength policy to comply with these rules. If a stronger encryption is preferred, and adheres to the laws of the country, then the JCE needs to have access to the stronger encryption policy. Very plainly put, if you are planning on using AES 256-bit encryption, you must install theUnlimited Strength Jurisdiction Policy Files. Without the policies in place, 256-bit encryption is not possible. Installation of JCE Unlimited Strength Policy This post is focusing on the keys rather than the installation and setup of the JCE. The installation is rather simple with explicit instructions found here (NOTE: this is for JDK7, if using a different JDK, search for the appropriate JCE policy files). Keystore Setup When using the KeyTool manipulating a keystore is simple. Keystores must be created with a link to a new key or during an import of an existing keystore. In order to create a new key and keystore simply type: keytool -genseckey -keystore aes-keystore.jck -storetype jceks -storepass mystorepass -keyalg AES -keysize 256 -alias jceksaes -keypass mykeypass Important Flags In the example above here are the explanations for the keytool's parameters: Keystore Parameters genseckey Generate SecretKey. This is the flag indicating the creation of a synchronous key which will become our AES key keystore Location of the keystore. If the keystore does not exist, the tool will create a new store. Paths can be relative or absolute but must be local storetype this is the type of store (JCE, PK12, JCEKS, etc). JCEKS is used to store symmetric keys (AES) not contained within a certificate. storepass password related to the keystore. Highly recommended to create a strong passphrase for the keystore Key Parameters keyalg algorithm used to create the key (AES/DES/etc) keysize size of the key (128, 192, 256, etc) alias alias given to the newly created key in which to reference when using the key keypass password protecting the use of the key Encrypt As it pertains to data in Java and at the most basic level, encryption is an algorithmic process used to programmatically obfuscate data through a reversible process where both parties have information pertaining to the data and how the algorithm is used. In Java encryption, this involves the use of a Cipher. A Cipher object in the JCE is a generic entry point into the encryption provider typically selected by the algorithm. This example uses the default Java provider but would also work with Bouncy Castle. Generating a Cipher object Obtaining an instance of Cipher is rather easy and the same process is required for both encryption and decryption. (NOTE: Encryption and Decryption require the same algorithm but do not require the same object instance) Cipher cipher = Cipher.getInstance("AES/CBC/PKCS5Padding"); Once we have an instance of the Cipher, we can encrypt and decrypt data according to the algorithm. Often the algorithm will require additional pieces of information in order to encrypt/decrypt data. In this example, we will need to pass the algorithm the bytes containing the key and an initial vector (explained below). Initialization In order to use the Cipher, we must first initialize the cipher. This step is necessary so we can provide additional information to the algorithm like the AES key and the Initial Vector (aka IV). cipher.init(Cipher.ENCRYPT_MODE, secretKeySpecification, initialVector); Parameters The SecretKeySpecification is an object containing a reference to the bytes forming the AES key. The AES key is nothing more than a specific sized byte array (256-bit for AES 256 or 32 bytes) that is generated by the keytool(see above). Alternative Parameteters There are multiple methods to create keys such as a hash including a salt, username and password (or similar). This method would utilize a SHA1 hash of the concatenated strings, convert to bytes and then truncate result to the desired size. This post will not show the generation of a key using this method or the use of a PBE key method using a password and salt. The password and/or salt usage for the keys is handled by the keytool using the inputs during the creation of new keys. Initialization Vector The AES algorithm also requires a second parameter called the Initialiation Vector. The IV is used in the process to randomize the encrypted message and prevent the key from easy guessing. The IV is considered a publicly shared piece of information, but again, it is not recommended to openly share the information (for example, it wouldn't be wise to post it on your company's website). When encrypting a message, it is not uncommon to prepend the message with the IV since the IV will be a set/known size based on the algorithm. NOTE: the AES algorithm will output the same result if using the same IV, key and message. It is recommended that the IV be randomly created each time an encryption takes place. With the newly initialized Cipher, encrypting a message is simple. Simply call: byte[] encryptedMessageInBytes = Cipher.doFinal((message.getBytes("UTF-8")); String base64EncodedEncryptedMsg = BaseEncoding.base64().encode(encryptedMessageInBytes); String base32EncodedEncryptedMsg = BaseEncoding.base32().encode(encryptedMessageInBytes); Encoding Results Byte arrays are difficult to visualize since they often do not form characters in any charset. The best recommendation to solve this is to represent the bytes in HEX (base-16), Double HEX (base-32) or Base64 format. If the message will be passed via a URL or POST parameter, be sure to use a web-safe Base64 encoding. Google Guava library provides a excellent BaseEncoding utility. NOTE: Remember to decode the encoded message before decrypting. Decrypt Decrypting a message is almost a reverse of the encryption process with a few exceptions. Decryption requires a known initialization vector as a parameter unlike the encryption process generating a random IV. Decryption When decrypting, obtain a cipher object with the same process as the encryption method. The Cipher object will need to utilize the exact same algorithm including the method and padding selections. Once the code has obtained a reference to a Cipher object, the next step is to initialize the cipher for decryption and pass in a reference to a key and the initialization vector. // key is the same byte[] key used in encryption SecretKeySpec secretKeySpecification = new SecretKeySpec(key, "AES"); cipher.init(Cipher.DECRYPT_MODE, secretKeySpecification, initialVector); NOTE: The key is stored in the keystore and obtained by the use of an alias. See below for details on obtaining keys from a keystore Once the cipher has been provided the key, IV and initialized for decryption, the cipher is ready to perform the decryption. byte[] encryptedTextBytes = BaseEncoding.base64().decode(message); byte[] decryptedTextBytes = cipher.doFinal(encryptedTextBytes); String origMessage = new String(decryptedTextBytes); Strategies to keep IV The IV used to encrypt the message is important to decrypting the message therefore the question is raised, how do they stay together. One solution is to Base Encode (see above) the IV and prepend it to the encrypted and encoded message: Base64UrlSafe(myIv) + delimiter + Base64UrlSafe(encryptedMessage). Other possible solutions might be contextual such as including an attribute in an XML file with the IV and one for the alias to the key used. Obtain Key from Keystore The beginning of this post has shown how easy it is to create new AES-256 keys that reference an alias inside of a keystore database. The post then continues on how to encrypt and decrypt a message given a key, but has yet shown how to obtain a reference to the key in a keystore. Solution // for clarity, ignoring exceptions and failures InputStream keystoreStream = new FileInputStream(keystoreLocation); KeyStore keystore = KeyStore.getInstance("JCEKS"); keystore.load(keystoreStream, keystorePass.toCharArray()); if (!keystore.containsAlias(alias)) { thrownew RuntimeException("Alias for key not found"); } Key key = keystore.getKey(alias, keyPass.toCharArray()); Parameters keystoreLocation String - Location to local keystore file location keypass String - Password used when creating or modifying the keystore file with keytool (see above) alias String - Alias used when creating new key with keytool (see above) Conclusion This post has shown how to encrypt and decrypt string based messages using the AES-256 encryption algorithm. The keys to encrypt and decrypt these messages are held inside of a JCEKS formatted KeyStore database created using the JDK provided "keytool" utility. The examples in this post should be considered a solid start to encrypting/decrypting symmetric keys such as AES. This should not be considered the only line of defense when encrypting messages, for example key rotation. Key rotation is a method to mitigate risks in the event of a data breach. If an intruder obtains data and manages to hack a single key, the data contained in multiple files should have used several keys to encrypt the data thus bringing down risk of a total exposure loss. All of the examples in this blog post have been condensed into a simple tool allowing for the viewing of keys inside of a keystore, an operation that is not supported out of the box by the JDK keytool. Each aspect of the steps and topics outlined in this post are available at: https://github.com/mike-ensor/aes-256-encryption-utility. NOTE: The examples, sample code and any reference is to be used at the sole implementers risk and there is no implied warranty or liability, you assume all risks.
February 4, 2014
by Mike Ensor
· 102,518 Views · 2 Likes
article thumbnail
Export MS Visio Diagram to XML (VDX, VTX, VSX) Formats in C# & VB.NET
This technical tip shows how .NET developers can export Microsoft Visio diagram to XML inside their own applications using Aspose.Diagram for .NET. Aspose.Diagram for .NET lets you export diagrams to a variety of formats: image formats, HTML, SVG, SWF and XML formats: VDX defines an XML diagram. VTX defines an XML template. VSX defines an XML stencil. The Diagram class' constructors read a diagram and the Save method is used to save, or export, a diagram in a different file format. The code snippets in this article show how to use the Save method to save a Visio file to VDX, VTX and VSX. Exporting VSD to VDX VDX is a schema-based XML file format that lets you save diagrams in a format that products other than Microsoft Visio can read. It's a useful format for transferring diagrams between software applications and retaining editable data. To export a VSD diagram to VDX first create an instance of the Diagram class and call the Diagram class' Save method to write the Visio drawing file to VDX. Exporting from VSD to VSX VSX is an XML format for defining stencils, the basic objects from which a diagram is built up. When a Visio file is converted to VSX, only the stencils are exported. To export a VSD diagram to VSX first you need to create an instance of the Diagram class and then call the Diagram class' Save method to write the Visio drawing file to VSX. //The Sample code shows how to export VSD to VDX //[C# Sample] //Call the diagram constructor to load diagram from a VSD file Diagram diagram = new Diagram("D:\\Drawing1.vsd"); this.Response.Clear(); this.Response.ClearHeaders(); this.Response.ContentType = "application/vnd.ms-visio"; this.Response.AppendHeader("Content-Disposition", "attachment; filename=Diagram.vdx"); this.Response.Flush(); System.IO.Stream vdxStream = this.Response.OutputStream; //Save input VSD as VDX diagram.Save(vdxStream, SaveFileFormat.VDX); this.Response.End(); //[VB.NET Code Sample] 'Call the diagram constructor to load diagram from a VSD file Dim diagram As New Diagram("D:\Drawing1.vsd") Me.Response.Clear() Me.Response.ClearHeaders() Me.Response.ContentType = "application/vnd.ms-visio" Me.Response.AppendHeader("Content-Disposition", "attachment; filename=Diagram.vdx") Me.Response.Flush() Dim vdxStream As System.IO.Stream = Me.Response.OutputStream 'Save inpupt VSD as VDX diagram.Save(vdxStream, SaveFileFormat.VDX) Me.Response.End() //The Sample code shows how to export VSD to VSX format. [C# Code Sample] // Call the diagram constructor to load diagram from a VSD file Diagram diagram = new Diagram("D:\\Drawing1.vsd"); this.Response.Clear(); this.Response.ClearHeaders(); this.Response.ContentType = "application/vnd.ms-visio"; this.Response.AppendHeader("Content-Disposition", "attachment; filename=Diagram.vsx"); this.Response.Flush(); System.IO.Stream vsxStream = this.Response.OutputStream; //Save input VSD as VSX diagram.Save(vsxStream, SaveFileFormat.VSX); this.Response.End() //[VB.NET Code Sample] 'Call the diagram constructor to load diagram from a VSD file Dim diagram As New Diagram("D:\Drawing1.vsd") Me.Response.Clear() Me.Response.ClearHeaders() Me.Response.ContentType = "application/vnd.ms-visio" Me.Response.AppendHeader("Content-Disposition", "attachment; filename=Diagram.vsx") Me.Response.Flush() Dim vsxStream As System.IO.Stream = Me.Response.OutputStream 'Save input VSD as VSX diagram.Save(vsxStream, SaveFileFormat.VSX) Me.Response.End()
January 29, 2014
by David Zondray
· 14,629 Views
article thumbnail
Geek, dork, nerd and dweeb — the difference in a Venn diagram
Working in and around Silicon Valley and technology, I hear people throwing around the terms “geek”, “dork”, ”nerd” and “dweeb” constantly. They’re thrown around interchangeably, in fact, which is where the problem lies. They’re not the same and knowing that matters a great deal. In fact, using the wrong term gives credit where credit it isn’t due or unfairly labels someone’s better qualities. Venn diagram Finding a Venn diagram to explain the difference was a big moment. I suddenly see how I should interview for different roles and what to look for in partners and employees. I know what to seek and what to avoid. It was an epiphany. Starting from that point, I could see career paths for each and every one (OK, except one). It breaks out like this: Geek, Nerd, Dweeb and Dork in order of value to the organization Geek – Both smart and driven but able to talk about fun things — they’re your leaders and sales people Nerd - Centered in smarts and drive, tempered by some awkwardness — they sustain your company Dweeb – Smart and awkward but probably uncommitted — they won’t stay up all night to solve a problem Dork - Least fun of the bunch — Avoid these people because they waste your time and sap your will to live These may not be everyone’s definitions, but maybe it’s time to standardize in our labels lest we use the terms insensitively. For an interesting take on these categories, I found this on Democratic Underground. Geek: Someone who spends a lot of time and energy in a certain special but conventional area, like computer programming or trouble-shooting, but not necessarily computers or technology. You can apparently have chess geeks, guitar geeks, or cooking geeks. A geek is an outwardly normal person who can relate to others in general but who has taken the time to learn specific technical skills and would rather talk about their special obsession than anything else. They are generally not athletic and enjoy sedentary pursuits like video games, comic books, being on the internet, etc. They usually dress to suit their special interest, which can be flamboyant, such as wearing a tee-shirt describing their special obsession or a hat bearing a logo of their special pursuit. Geeks can be self-confident and proud of their traits. Nerd: Someone with a great interest in academic subjects like math and science and who is socially awkward and has trouble relating to others outside of their fields of academia. Their IQ often exceeds their weight. Science fiction such as The Matrix and Star Wars or LOTR are often their cup of tea, as are hobbies like astronomy or chemistry sets. Nerds usually dress conservatively and are more interested in the mind than their outward appearance, although as both men and women they tend to be tidy, clean-cut, and hygienic. Nerds generally are self-confident in the academic setting and take pride in their intellect and band together with other nerds although their social skills outside of their academic obsession are diminished. Dork: Someone who has special interests like a geek but whose interests and obsessions are less common and odd, such as having an oddball collection of some sort like old Three Stooges bubblegum cards or an uncommon skill like yodeling. Walking talking Star Trek encyclopedic knowledge and convention dress up obsessions can be considered dorky. They can act silly at times and not care what anyone thinks. Dorks are typically more noted for their quirky personality and tend to be loners. Hygiene can sometimes be an issue. Dorks can nonetheless be self-confident and proud of the way they are because they simply don’t care what others think. Dweeb: A person who tends to be regarded as physically wimpish, intellectually challenged, and socially awkward, with little self-confidence. Dweebs tend to be obsessed with unusual pursuits like dorks (tap dancing or ant farms) but are lacking in skill, knowledge, or ability. Dweebs tend to be loners like dorks but understand their shortcomings and lack pride. Hygiene can also be an issue. I’m not a dork, nor dweeb and I don’t see myself as a nerd…I’m clearly a geek :-). Thank you to the Great White Snark, where I found the Venn diagram.
January 27, 2014
by Christopher Taylor
· 21,403 Views
article thumbnail
Big Data Search, Part 5: Sorting Optimizations
I mentioned several times that the entire point of the exercise was to just see how this works, not to actually do anything production worthy. But it is interesting to see how we could do better here. In no particular order, I think that there are at least several things that we could do to significantly improve the time it takes to sort. Right now we defined 2 indexes on top of a 1GB file, and it took under 1 minute to complete. That gives us a runtime of about 10 days over a 15TB file. Well, one of the reason for this performance is that we execute this in a serial fashion, that is, one after another. But we have to completely isolated indexes, there is no reason why we can’t parallelize the work between them. For that matter, we are buffering in memory up to a certain point, then we sort, then we buffer some more, etc. That is pretty inefficient. We can push the actual sorting to a different thread, and continue parsing and adding to a buffer while we are adding to the buffer. We wrote to intermediary files, but we wrote to those using plain file I/O. But it is usually a lot more costly to write to disk than to compress and then write to disk. We are writing sorted data, so it is probably going to compress pretty well. Those are the things that pop to mind. Can you think of additional options?
January 27, 2014
by Oren Eini
· 7,893 Views
article thumbnail
Spring and Caching JMS Connections
As follow up to previous posts covering JMS, this post will delve into more depth on Spring's CachingConnectionFactory. Spring provides two implementations of the javax.jms.ConnectionFactory interface, namely, the SingleConnectionFactory and the CachingConnectionFactory. The SingleConnectionFactory returns as you might expect the same single connection upon all calls to the createConnection() method. This is fine for certain scenarios and applications but the CachingConnectionFactory provides a more performant and scalable solution. By default, a single session is cached so for a multi threaded application you would set the sessionCacheSize to be a more suitable number although this number wouldn't reflect the true number of sessions cached as this figure refers to the size of cache per session acknowledgement type eg AUTO_ACKNOWLEDGE, CLIENT_ACKNOWLEDGE, DUPS_OK_ACKNOWLEDGE and SESSION_TRANSACTED. By default, the CachingConnectionFactory will cache the Message Producers and Message Consumers for every session. As an aside the Message Consumers are cached using keys which include the JMS selector so the more fine grained the message filter the more Message Consumers there would be, and Message Consumers aren't closed until the session is closed and removed from the pool. An alternative is to use a Listener Container for consuming messages. Also to be noted is that on creating a CachingConnectionFactory instance, the reconnect on exception flag is set to be true. This should mean that the onException method on the default ExceptionListener class gets called which will reset the connections. You can also override the default exception listener with your own implementation. The below snippet of XML shows a simple configuration of a CachingConnectionFactory:
January 27, 2014
by Geraint Jones
· 52,770 Views · 1 Like
article thumbnail
Big Data Search, Part 4: The Index Format is Horrible
I have completed my own exercise, and while I wanted to try it with “few allocations” rule, it is interesting to see just how far out there the code is. This isn’t something that you can really use for anything except as a basis to see how badly you are doing. Let us start with the index format. It is just a CSV file with the value and the position in the original file. That means that any search we want to do on the file is actually a binary search, as discussed in the previous post. But doing a binary search like that is an absolute killer for performance. Let us consider our 15TB data set. In my tests, a 1GB file with 4.2 million rows produced roughly 80MB index. Assuming the same is true for the larger file, that gives us a 1.2 TB file. In my small index, we have to do 24 seeks to get to the right position in the file. And as you should know, disk seeks are expensive. They are in the order of 10ms or so. So the cost of actually searching the index is close to quarter of a second. Now, to be fair, there is going to be a lot of caching opportunities here, but probably not that many if we have a lot of queries to deal with ere. Of course, the fun thing about this is that even with a 1.2 TB file, we are still talking about less than 40 seeks (the beauty of O(logN) in action), but that is still pretty expensive. Even worse, this is what happens when we are running on a single query at a time. What do you think will happen if we are actually running this with multiple threads generating queries. Now we will have a lot of seeks (effective random) that would generate a big performance sink. This is especially true if we consider that any storage solution big enough to store the data is going to be composed of an aggregate of HDD disks. Sure, we get multiple spindles, so we get better performance overall, but still… Obviously, there are multiple solutions for this issue. B+Trees solve the problem by packing multiple keys into a single page, so instead of doing a O(log2N), you are usually doing O(log36N) or O(log100N). Consider those fan outs, we will have 6 – 8 seeks to do to get to our data. Much better than the 40 seeks required using plain binary search. It would actually be better than that in the common case, since the first few levels of the trees are likely to reside in memory (and probably in L1, if we are speaking about that). However, given that we are storing sorted strings here, one must give some attention to Sorted Strings Tables. The way those work, you have the sorted strings in the file, and the footer contains two important bits of information. The first is the bloom filter, which allows you to quickly rule out missing values, but the more important factor is that it also contains the positions of (by default) every 16th entry to the file. This means that in our 15 TB data file (with 64.5 billion entries), we will use about 15GB just to store pointers to the different locations in the index file (which will be about 1.2 TB). Note that the numbers actually are probably worse. Because SST (note that when talking about SST I am talking specifically about the leveldb implementation) utilize many forms of compression, it is actually that the file size will be smaller (although, since the “value” we use is just a byte position in the data file, we won’t benefit from compression there). Key compression is probably a lot more important here. However, note that this is a pretty poor way of doing things. Sure, the actual data format is better, in the sense that we don’t store as much, but in terms of the number of operations required? Not so much. We still need to do a binary search over the entire file. In particular, the leveldb implementation utilizes memory mapped files. What this ends up doing is rely on the OS to keep the midway points in the file in RAM, so we don’t have to do so much seeking. Without that, the cost of actually seeking every time would make SSTs impractical. In fact, you would pretty much have to introduce another layer on top of this, but at that point, you are basically doing trees, and a binary tree is a better friend here. This leads to an interesting question. SST is probably so popular inside Google because they deal with a lot of data, and the file format is very friendly to compression of various kinds. It is also a pretty simple format. That make it much nicer to work with. On the other hand, a B+Tree implementation is a lot more complex, and it would probably several orders of magnitude more complex if it had to try to do the same compression tricks that SSTs do. Another factor that is probably as important is that as I understand it, a lot of the time, SSTs are usually used for actual sequential access (map/reduce stuff) and not necessarily for the random reads that are done in leveldb. It is interesting to think about this in this fashion, at least, even if I don’t know what I’ll be doing with it.
January 24, 2014
by Oren Eini
· 12,132 Views
article thumbnail
Big Data Search, Part 3: Binary Search of Textual Data
The index I created for the exercise is just a text file, sorted by the indexed key. When doing a search by a human, that makes it very easy to work with. Much easier than trying to work with a binary file, it also helps debugging. However, it does make it running a binary search on the data a bit harder. Mostly because there isn’t a nice way to say “give me the #th line”. Instead, I wrote the following: public void SetPositionToLineAt(long position) { // now we need to go back until we either get to the start of the file // or find a \n character const int bufferSize = 128; _buffer.Capacity = Math.Max(bufferSize, _buffer.Capacity); var charCount = _encoding.GetMaxCharCount(bufferSize); if (charCount > _charBuf.Length) _charBuf = new char[Utils.NearestPowerOfTwo(charCount)]; while (true) { _input.Position = position - (position < bufferSize ? 0 : bufferSize); var read = ReadToBuffer(bufferSize); var buffer = _buffer.GetBuffer(); var chars = _encoding.GetChars(buffer, 0, read, _charBuf, 0); for (int i = chars - 1; i >= 0; i--) { if (_charBuf[i] == '\n') { _input.Position = position - (bufferSize - i) + 1; return; } } position -= bufferSize; if (position < 0) { _input.Position = 0; return; } } } This code starts at an arbitrary byte position, and go backward until it find the new line character ‘\n’. This give me the ability to go to a rough location and get the line oriented input. Once I have that, the rest is pretty easy. Here is the binary search: while (lo <= hi) { position = (lo + hi) / 2; _reader.SetPositionToLineAt(position); bool? result; do { result = _reader.ReadOneLine(); } while (result == null); // skip empty lines if (result == false) yield break; // couldn't find anything var entry = _reader.Current.Values[0]; match = Utils.CompareArraySegments(expectedIndexEntry, entry); if (match == 0) { break; } if (match > 0) lo = position + _reader.Current.Values.Sum(x => x.Count) + 1; else hi = position - 1; } if (match != 0) { // no match yield break; } The idea is that this positions us on the location of the index that has an entry with a value that is equal to what we are searched on. We then write the following to actually get the data from the actual data file: // we have a match, now we need to return all the matches _reader.SetPositionToLineAt(position); while(true) { bool? result; do { result = _reader.ReadOneLine(); } while (result == null); // skip empty lines if(result == false) yield break; // end of file var entry = _reader.Current.Values[0]; match = Utils.CompareArraySegments(expectedIndexEntry, entry); if (match != 0) yield break; // out of the valid range we need _buffer.SetLength(0); _data.Position = Utils.ToInt64(_reader.Current.Values[1]); while (true) { var b = _data.ReadByte(); if (b == -1) break; if (b == '\n') { break; } _buffer.WriteByte((byte)b); } yield return _encoding.GetString(_buffer.GetBuffer(), 0, (int)_buffer.Length); } As you can see, we are moving forward in the index file, reading one line at a time. Then we take the second value, the position of the relevant line in the data file, and read that. We continue to do so as long as the indexed value is the same. Pretty simple, all told. But it comes with its own set of problems. I’ll discuss that in my next post.
January 22, 2014
by Oren Eini
· 5,908 Views
article thumbnail
Big Data Search, Part 2: Setting Up
the interesting thing about this problem is that i was very careful in how i phrased things. i said what i wanted to happen, but didn’t specify what needs to be done. that was quite intentional. for that matter, the fact that i am posting about what is going to be our acceptance criteria is also intentional. the idea is to have a non trivial task, but something that should be very well understood and easy to research. it also means that the candidate needs to be able to write some non trivial code. and i can tell a lot about a dev from such a project. at the same time, this is a very self contained scenario. the idea is that this is something that you can do in a short amount of time. the reason that this is an interesting exercise is that this is actually at least two totally different but related problems. first, in a 15tb file, we obviously cannot rely on just scanning the entire file. that means that we have to have an index. and that means we have to build it. interestingly enough, an index being a sorted structure, that means that we have to solve the problem of sorting more data than can fit in main memory. the second problem is probably easier, since it is just an implementation of external sort, and there are plenty of algorithms around to handle that. note that i am not really interested in actual efficiencies for this particular scenario. i care about being able to see the code. see that it works, etc. my solution, for example, is a single threaded system that make no attempt at parallelism or i/o optimizations. it clocks at over 1 gb / minute and the memory consumption is at under 150mb. queries for a unique value return the result in 0.0004 seconds. queries that returned 153k results completed in about 2 seconds. when increasing the used memory to about 650mb, there isn’t really any difference in performance, which surprised me a bit. then again, the entire code is probably highly inefficient. but that is good enough for now. the process is kicked off with indexing: 1: var options = new directoryexternalstorageoptions("/path/to/index/files"); 2: var input = file.openread(@"/path/to/data/crimes_-_2001_to_present.csv"); 3: var sorter = new externalsorter(input, options, new int[] 4: { 5: 1,// case number 6: 4, // ichr 7: 8: }); 9: 10: sorter.sort(); i am actually using the chicago crime data for this. this is a 1gb file that i downloaded from the chicago city portal in csv format. this is what the data looks like: the externalsorter will read and parse the file, and start reading it into a buffer. when it gets to a certain size (about 64mb of source data, usually), it will sort the values in memory and output them into temporary files. those file looks like this: initially, i tried to do that with binary data, but it turns out that that was too complex to be easy, and writing this in a human readable format made it much easier to work with. the format is pretty simple, you have the value of the left, and on the right you have start position of the row for this value. we generate about 17 such temporary files for the 1gb file. one temporary file per each 64 mb of the original file. this lets us keep our actual memory consumption very low, but for larger data sets, we’ll probably want to actually do the sort every 1 gb or maybe more. our test machine has 16 gb of ram, so doing a sort and outputting a temporary file every 8 gb can be a good way to handle things. but that is beside the point. the end result is that we have multiple sorted files, but they aren’t sequential. in other words, in file #1 we have values 1,4,6,8 and in file #2 we have 1,2,6,7. we need to merge all of them together. luckily, this is easy enough to do. we basically have a heap that we feed entries from the files into. and that pretty much takes care of this. see merge sort if you want more details about this. the end result of merging all of those files is… another file, just like them, that contains all of the data sorted. then it is time to actually handle the other issue, actually searching the data. we can do that using simple binary search, with the caveat that because this is a text file, and there is no fixed size records or pages, it is actually a big hard to figure out where to start reading. in effect, what i am doing is to select an arbitrary byte position, then walk backward until i find a ‘\n’. once i found the new line character, i can read the full line, check the value, and decide where i need to look next. assuming that i actually found my value, i can now go to the byte position of the value in the original file and read the original line, giving it to the user. assuming an indexing rate of 1 gb / minute a 15 tb file would take about 10 days to index. but there are ways around that as well, but i’ll touch on them in my next post. what all of this did was bring home just how much we usually don’t have to worry about such things. but i consider this research well spent, we’ll be using this in the future.
January 21, 2014
by Oren Eini
· 3,484 Views
article thumbnail
Extending Guava Caches to Overflow to Disk
Caching allows you to significantly speed up applications with only little effort. Two great cache implementations for the Java platform are the Guava caches and Ehcache. While Ehcache is much richer in features (such as its Searchable API, the possibility of persisting caches to disk or overflowing to big memory), it also comes with quite an overhead compared to Guava. In a recent project, I found a need to overflow a comprehensive cache to disk but at the same time, I regularly needed to invalidate particular values of this cache. Because Ehcache's Searchable API is only accessible to in-memory caches, this put me in quite a dilemma. However, it was quite easy to extend a Guava cache to allow overflowing to disk in a structured manner. This allowed me both overflowing to disk and the required invalidation feature. In this article, I want to show how this can be achieved. I will implement this file persisting cache FilePersistingCache in form of a wrapper to an actual Guava Cache instance. This is of course not the most elegant solution (more elegant would to implement an actual Guava Cache with this behavior), but I will do for most cases. To begin with, I will define a protected method that creates the backing cache I mentioned before: private LoadingCache makeCache() { return customCacheBuild() .removalListener(new PersistingRemovalListener()) .build(new PersistedStateCacheLoader()); } protected CacheBuilder customCacheBuild(CacheBuilder cacheBuilder) { return CacheBuilder.newBuilder(); } The first method will be used internally to build the necessary cache. The second method is supposed to be overridden in order to implement any custom requirement to the cache as for example an expiration strategy. This could for example be a maximum value of entries or soft references. This cache will be used just as any other Guava cache. The key to the cache's functionality are the RemovalListener and the CacheLoader that are used for this cache. We will define these two implementation as inner classes of the FilePersistingCache: private class PersistingRemovalListener implements RemovalListener { @Override public void onRemoval(RemovalNotification notification) { if (notification.getCause() != RemovalCause.COLLECTED) { try { persistValue(notification.getKey(), notification.getValue()); } catch (IOException e) { LOGGER.error(String.format("Could not persist key-value: %s, %s", notification.getKey(), notification.getValue()), e); } } } } public class PersistedStateCacheLoader extends CacheLoader { @Override public V load(K key) { V value = null; try { value = findValueOnDisk(key); } catch (Exception e) { LOGGER.error(String.format("Error on finding disk value to key: %s", key), e); } if (value != null) { return value; } else { return makeValue(key); } } } As obvious from the code, these inner classes call methods of FilePersistingCache we did not yet define. This allows us to define custom serialization behavior by overriding this class. The removal listener will check the reasons for a cache entry being evicted. If the RemovalCause is COLLECTED, the cache entry was not manually removed by the user but it was removed as a consequence of the cache's eviction strategy. We will therefore only try to persist a cache entry if the user did not wish the entries removal. The CacheLoader will first attempt to restore an existent value from disk and create a new value only if such a value could not be restored. The missing methods are defined as follows: private V findValueOnDisk(K key) throws IOException { if (!isPersist(key)) return null; File persistenceFile = makePathToFile(persistenceDirectory, directoryFor(key)); (!persistenceFile.exists()) return null; FileInputStream fileInputStream = new FileInputStream(persistenceFile); try { FileLock fileLock = fileInputStream.getChannel().lock(); try { return readPersisted(key, fileInputStream); } finally { fileLock.release(); } } finally { fileInputStream.close(); } } private void persistValue(K key, V value) throws IOException { if (!isPersist(key)) return; File persistenceFile = makePathToFile(persistenceDirectory, directoryFor(key)); persistenceFile.createNewFile(); FileOutputStream fileOutputStream = new FileOutputStream(persistenceFile); try { FileLock fileLock = fileOutputStream.getChannel().lock(); try { persist(key, value, fileOutputStream); } finally { fileLock.release(); } } finally { fileOutputStream.close(); } } private File makePathToFile(@Nonnull File rootDir, List pathSegments) { File persistenceFile = rootDir; for (String pathSegment : pathSegments) { persistenceFile = new File(persistenceFile, pathSegment); } if (rootDir.equals(persistenceFile) || persistenceFile.isDirectory()) { throw new IllegalArgumentException(); } return persistenceFile; } protected abstract List directoryFor(K key); protected abstract void persist(K key, V value, OutputStream outputStream) throws IOException; protected abstract V readPersisted(K key, InputStream inputStream) throws IOException; protected abstract boolean isPersist(K key); The implemented methods take care of serializing and deserializing values while synchronizing file access and guaranteeing that streams are closed appropriately. The last four methods remain abstract and are up to the cache's user to implement. The directoryFor(K) method should identify a unique file name for each key. In the easiest case, the toString method of the key's K class is implemented in such a way. Additionally, I made the persist, readPersisted and isPersist methods abstract in order to allow for a custom serialization strategy such as using Kryo. In the easiest scenario, you would use the built in Java functionality which uses ObjectInputStream and ObjectOutputStream. For isPersist, you would return true, assuming that you would only use this implementation if you need serialization. I added this feature to support mixed caches where you can only serialize values to some keys. Be sure not to close the streams within the persist and readPersisted methods since the file system locks rely on the streams to be open. The above implementation will take care of closing the stream for you. Finally, I added some service methods to access the cache. Implementing Guava's Cache interface would of course be a more elegant solution: public V get(K key) { return underlyingCache.getUnchecked(key); } public void put(K key, V value) { underlyingCache.put(key, value); } public void remove(K key) { underlyingCache.invalidate(key); } protected Cache getUnderlyingCache() { return underlyingCache; } Of course, this solution can be further improved. If you use the cache in a concurrent scenario, be further aware that the RemovalListener is, other than most Guava cache method's executed asynchronously. As obvious from the code, I added file locks to avoid read/write conflicts on the file system. This asynchronicity does however imply that there is a small chance that a value entry gets recreated even though there is still a value in memory. If you need to avoid this, be sure to call the underlying cache's cleanUp method within the wrapper's get method. Finally, remember to clean up the file system when you expire your cache. Optimally, you will use a temporary folder of your system for storing your cache entries in order to avoid this problem at all. In the example code, the directory is represented by an instance field named persistenceDirectory which could for example be initialized in the constructor. Update: I wrote a clean implementation of what I described above which you can find on my Git Hub page and on Maven Central. Feel free to use it, if you need to store your cache objects on disk.
January 17, 2014
by Rafael Winterhalter
· 18,673 Views · 1 Like
article thumbnail
Understanding sun.misc.Unsafe
The biggest competitor to the Java virtual machine might be Microsoft's CLR that hosts languages such as C#. The CLR allows to write unsafe code as an entry gate for low level programming, something that is hard to achieve on the JVM. If you need such advanced functionality in Java, you might be forced to use the JNI which requires you to know some C and will quickly lead to code that is tightly coupled to a specific platform. With sun.misc.Unsafe, there is however another alternative to low-level programming on the Java plarform using a Java API, even though this alternative is discouraged. Nevertheless, several applications rely on sun.misc.Unsafe such for example objenesis and therewith all libraries that build on the latter such for example kryo which is again used in for example Twitter's Storm. Therefore, it is time to have a look, especially since the functionality of sun.misc.Unsafe is considered to become part of Java's public API in Java 9. Getting hold of an instance of sun.misc.Unsafe The sun.misc.Unsafe class is intended to be only used by core Java classes which is why its authors made its only constructor private and only added an equally private singleton instance. The public getter for this instances performs a security check in order to avoid its public use: public static Unsafe getUnsafe() { Class cc = sun.reflect.Reflection.getCallerClass(2); if (cc.getClassLoader() != null) throw new SecurityException("Unsafe"); return theUnsafe; } This method first looks up the calling Class from the current thread’s method stack. This lookup is implemented by another internal class named sun.reflection.Reflection which is basically browsing down the given number of call stack frames and then returns this method’s defining class. This security check is however likely to change in future version. When browsing the stack, the first found class (index 0) will obviously be the Reflection class itself, and the second (index 1) class will be the Unsafe class such that index 2 will hold your application class that was calling Unsafe#getUnsafe(). This looked-up class is then checked for its ClassLoader where a null reference is used to represent the bootstrap class loader on a HotSpot virtual machine. (This is documented in Class#getClassLoader() where it says that “some implementations may use null to represent the bootstrap class loader”.) Since no non-core Java class is normally ever loaded with this class loader, you will therefore never be able to call this method directly but receive a thrown SecurityException as an answer. (Technically, you could force the VM to load your application classes using the bootstrap class loader by adding it to the –Xbootclasspath, but this would require some setup outside of your application code which you might want to avoid.) Thus, the following test will succeed: @Test(expected = SecurityException.class) public void testSingletonGetter() throws Exception { Unsafe.getUnsafe(); } However, the security check is poorly designed and should be seen as a warning against the singleton anti-pattern. As long as the use of reflection is not prohibited (which is hard since it is so widely used in many frameworks), you can always get hold of an instance by inspecting the private members of the class. From the Unsafe class's source code, you can learn that the singleton instance is stored in a private static field called theUnsafe. This is at least true for the HotSpot virtual machine. Unfortunately for us, other virtual machine implementations sometimes use other names for this field. Android’s Unsafe class is for example storing its singleton instance in a field called THE_ONE. This makes it hard to provide a “compatible” way of receiving the instance. However, since we already left the save territory of compatibility by using the Unsafe class, we should not worry about this more than we should worry about using the class at all. For getting hold of the singleton instance, you simply read the singleton field's value: Field theUnsafe = Unsafe.class.getDeclaredField("theUnsafe"); theUnsafe.setAccessible(true); Unsafe unsafe = (Unsafe) theUnsafe.get(null); Alternatively, you can invoke the private instructor. I do personally prefer this way since it works for example with Android while extracting the field does not: Constructor unsafeConstructor = Unsafe.class.getDeclaredConstructor(); unsafeConstructor.setAccessible(true); Unsafe unsafe = unsafeConstructor.newInstance(); The price you pay for this minor compatibility advantage is a minimal amount of heap space. The security checks performed when using reflection on fields or constructors are however similar. Create an Instance of a Class Without Calling a Constructor The first time I made use of the Unsafe class was for creating an instance of a class without calling any of the class's constructors. I needed to proxy an entire class which only had a rather noisy constructor but I only wanted to delegate all method invocations to a real instance which I did however not know at the time of construction. Creating a subclass was easy and if the class had been represented by an interface, creating a proxy would have been a straight-forward task. With the expensive constructor, I was however stuck. By using the Unsafe class, I was however able to work my way around it. Consider a class with an artificially expensive constructor: class ClassWithExpensiveConstructor { private final int value; private ClassWithExpensiveConstructor() { value = doExpensiveLookup(); } private int doExpensiveLookup() { try { Thread.sleep(2000); } catch (InterruptedException e) { e.printStackTrace(); } return 1; } public int getValue() { return value; } } Using the Unsafe, we can create an instance of ClassWithExpensiveConstructor (or any of its subclasses) without having to invoke the above constructor, simply by allocating an instance directly on the heap: @Test public void testObjectCreation() throws Exception { ClassWithExpensiveConstructor instance = (ClassWithExpensiveConstructor) unsafe.allocateInstance(ClassWithExpensiveConstructor.class); assertEquals(0, instance.getValue()); } Note that final field remained uninitialized by the constructor but is set with its type's default value. Other than that, the constructed instance behaves like a normal Java object. It will for example be garbage collected when it becomes unreachable. The Java run time itself creates objects without calling a constructor when for example creating objects for deserialization. Therefore, the ReflectionFactory offers even more access to individual object creation: @Test public void testReflectionFactory() throws Exception { @SuppressWarnings("unchecked") Constructor silentConstructor = ReflectionFactory.getReflectionFactory() .newConstructorForSerialization(ClassWithExpensiveConstructor.class, Object.class.getConstructor()); silentConstructor.setAccessible(true); assertEquals(10, silentConstructor.newInstance().getValue()); } Note that the ReflectionFactory class only requires a RuntimePermission called reflectionFactoryAccess for receiving its singleton instance and no reflection is therefore required here. The received instance of ReflectionFactory allows you to define any constructor to become a constructor for the given type. In the example above, I used the default constructor of java.lang.Object for this purpose. You can however use any constructor: class OtherClass { private final int value; private final int unknownValue; private OtherClass() { System.out.println("test"); this.value = 10; this.unknownValue = 20; } } @Test public void testStrangeReflectionFactory() throws Exception { @SuppressWarnings("unchecked") Constructor silentConstructor = ReflectionFactory.getReflectionFactory() .newConstructorForSerialization(ClassWithExpensiveConstructor.class, OtherClass.class.getDeclaredConstructor()); silentConstructor.setAccessible(true); ClassWithExpensiveConstructor instance = silentConstructor.newInstance(); assertEquals(10, instance.getValue()); assertEquals(ClassWithExpensiveConstructor.class, instance.getClass()); assertEquals(Object.class, instance.getClass().getSuperclass()); } Note that value was set in this constructor even though the constructor of a completely different class was invoked. Non-existing fields in the target class are however ignored as also obvious from the above example. Note that OtherClass does not become part of the constructed instances type hierarchy, the OtherClass's constructor is simply borrowed for the "serialized" type. Not mentioned in this blog entry are other methods such as Unsafe#defineClass, Unsafe#defineAnonymousClass or Unsafe#ensureClassInitialized. Similar functionality is however also defined in the public API's ClassLoader. Native Memory Allocation Did you ever want to allocate an array in Java that should have had more than Integer.MAX_VALUE entries? Probably not because this is not a common task, but if you once need this functionality, it is possible. You can create such an array by allocating native memory. Native memory allocation is used by for example direct byte buffers that are offered in Java's NIO packages. Other than heap memory, native memory is not part of the heap area and can be used non-exclusively for example for communicating with other processes. As a result, Java's heap space is in competition with the native space: the more memory you assign to the JVM, the less native memory is left. Let us look at an example for using native (off-heap) memory in Java with creating the mentioned oversized array: class DirectIntArray { private final static long INT_SIZE_IN_BYTES = 4; private final long startIndex; public DirectIntArray(long size) { startIndex = unsafe.allocateMemory(size * INT_SIZE_IN_BYTES); unsafe.setMemory(startIndex, size * INT_SIZE_IN_BYTES, (byte) 0); } } public void setValue(long index, int value) { unsafe.putInt(index(index), value); } public int getValue(long index) { return unsafe.getInt(index(index)); } private long index(long offset) { return startIndex + offset * INT_SIZE_IN_BYTES; } public void destroy() { unsafe.freeMemory(startIndex); } } @Test public void testDirectIntArray() throws Exception { long maximum = Integer.MAX_VALUE + 1L; DirectIntArray directIntArray = new DirectIntArray(maximum); directIntArray.setValue(0L, 10); directIntArray.setValue(maximum, 20); assertEquals(10, directIntArray.getValue(0L)); assertEquals(20, directIntArray.getValue(maximum)); directIntArray.destroy(); } First, make sure that your machine has sufficient memory for running this example! You need at least (2147483647 + 1) * 4 byte = 8192 MB of native memory for running the code. If you have worked with other programming languages as for example C, direct memory allocation is something you do every day. By calling Unsafe#allocateMemory(long), the virtual machine allocates the requested amount of native memory for you. After that, it will be your responsibility to handle this memory correctly. The amount of memory that is required for storing a specific value is dependent on the type's size. In the above example, I used an int type which represents a 32-bit integer. Consequently a single int value consumes 4 byte. For primitive types, size is well-documented. It is however more complex to compute the size of object types since they are dependent on the number of non-static fields that are declared anywhere in the type hierarchy. The most canonical way of computing an object's size is using the Instrumented class from Java's attach API which offers a dedicated method for this purpose called getObjectSize. I will however evaluate another (hacky) way of dealing with objects in the end of this section. Be aware that directly allocated memory is always native memory and therefore not garbage collected. You therefore have to free memory explicitly as demonstrated in the above example by a call to Unsafe#freeMemory(long). Otherwise you reserved some memory that can never be used for something else as long as the JVM instance is running what is a memory leak and a common problem in non-garbage collected languages. Alternatively, you can also directly reallocate memory at a certain address by calling Unsafe#reallocateMemory(long, long) where the second argument describes the new amount of bytes to be reserved by the JVM at the given address. Also, note that the directly allocated memory is not initialized with a certain value. In general, you will find garbage from old usages of this memory area such that you have to explicitly initialize your allocated memory if you require a default value. This is something that is normally done for you when you let the Java run time allocate the memory for you. In the above example, the entire area is overriden with zeros with help of the Unsafe#setMemory method. When using directly allocated memory, the JVM will neither do range checks for you. It is therefore possible to corrupt your memory as this example shows: @Test public void testMallaciousAllocation() throws Exception { long address = unsafe.allocateMemory(2L * 4); unsafe.setMemory(address, 8L, (byte) 0); assertEquals(0, unsafe.getInt(address)); assertEquals(0, unsafe.getInt(address + 4)); unsafe.putInt(address + 1, 0xffffffff); assertEquals(0xffffff00, unsafe.getInt(address)); assertEquals(0x000000ff, unsafe.getInt(address + 4)); } Note that we wrote a value into the space that was each partly reserved for the first and for the second number. This picture might clear things up. Be aware that the values in the memory run from the "right to the left" (but this might be machine dependent). The first row shows the initial state after writing zeros to the entire allocated native memory area. Then we override 4 byte with an offset of a single byte using 32 ones. The last row shows the result after this writing operation. Finally, we want to write an entire object into native memory. As mentioned above, this is a difficult task since we first need to compute the size of the object in order to know the amount of size we need to reserve. The Unsafe class does however not offer such functionality. At least not directly since we can at least use the Unsafe class to find the offset of an instance's field which is used by the JVM when itself allocates objects on the heap. This allows us to find the approximate size of an object: public long sizeOf(Class clazz) long maximumOffset = 0; do { for (Field f : clazz.getDeclaredFields()) { if (!Modifier.isStatic(f.getModifiers())) { maximumOffset = Math.max(maximumOffset, unsafe.objectFieldOffset(f)); } } } while ((clazz = clazz.getSuperclass()) != null); return maximumOffset + 8; } This might at first look cryptic, but there is no big secret behind this code. We simply iterate over all non-static fields that are declared in the class itself or in any of its super classes. We do not have to worry about interfaces since those cannot define fields and will therefore never alter an object's memory layout. Any of these fields has an offset which represents the first byte that is occupied by this field's value when the JVM stores an instance of this type in memory, relative to a first byte that is used for this object. We simply have to find the maximum offset in order to find the space that is required for all fields but the last field. Since a field will never occupy more than 64 bit (8 byte) for a long or double value or for an object reference when run on a 64 bit machine, we have at least found an upper bound for the space that is used to store an object. Therefore, we simply add these 8 byte to the maximum index and we will not run into danger of having reserved to little space. This idea is of course wasting some byte and a better algorithm should be used for production code. In this context, it is best to think of a class definition as a form of heterogeneous array. Note that the minimum field offset is not 0 but a positive value. The first few byte contain meta information. The graphic below visualizes this principle for an example object with an int and a long field where both fields have an offset. Note that we do not normally write meta information when writing a copy of an object into native memory so we could further reduce the amount of used native memoy. Also note that this memory layout might be highly dependent on an implementation of the Java virtual machine. With this overly careful estimate, we can now implement some stub methods for writing shallow copies of objects directly into native memory. Note that native memory does not really know the concept of an object. We are basically just setting a given amount of byte to values that reflect an object's current values. As long as we remember the memory layout for this type, these byte contain however enough information to reconstruct this object. public void place(Object o, long address) throws Exception { Class clazz = o.getClass(); do { for (Field f : clazz.getDeclaredFields()) { if (!Modifier.isStatic(f.getModifiers())) { long offset = unsafe.objectFieldOffset(f); if (f.getType() == long.class) { unsafe.putLong(address + offset, unsafe.getLong(o, offset)); } else if (f.getType() == int.class) { unsafe.putInt(address + offset, unsafe.getInt(o, offset)); } else { throw new UnsupportedOperationException(); } } } } while ((clazz = clazz.getSuperclass()) != null); } public Object read(Class clazz, long address) throws Exception { Object instance = unsafe.allocateInstance(clazz); do { for (Field f : clazz.getDeclaredFields()) { if (!Modifier.isStatic(f.getModifiers())) { long offset = unsafe.objectFieldOffset(f); if (f.getType() == long.class) { unsafe.putLong(instance, offset, unsafe.getLong(address + offset)); } else if (f.getType() == int.class) { unsafe.putLong(instance, offset, unsafe.getInt(address + offset)); } else { throw new UnsupportedOperationException(); } } } } while ((clazz = clazz.getSuperclass()) != null); return instance; } @Test public void testObjectAllocation() throws Exception { long containerSize = sizeOf(Container.class); long address = unsafe.allocateMemory(containerSize); Container c1 = new Container(10, 1000L); Container c2 = new Container(5, -10L); place(c1, address); place(c2, address + containerSize); Container newC1 = (Container) read(Container.class, address); Container newC2 = (Container) read(Container.class, address + containerSize); assertEquals(c1, newC1); assertEquals(c2, newC2); } Note that these stub methods for writing and reading objects in native memory only support int and long field values. Of course, Unsafe supports all primitive values and can even write values without hitting thread-local caches by using the volatile forms of the methods. The stubs were only used to keep the examples concise. Be aware that these "instances" would never get garbage collected since their memory was allocated directly. (But maybe this is what you want.) Also, be careful when precalculating size since an object's memory layout might be VM dependent and also alter if a 64-bit machine runs your code compared to a 32-bit machine. The offsets might even change between JVM restarts. For reading and writing primitives or object references, Unsafe provides the following type-dependent methods: getXXX(Object target, long offset): Will read a value of type XXX from target's address at the specified offset. putXXX(Object target, long offset, XXX value): Will place value at target's address at the specified offset. getXXXVolatile(Object target, long offset): Will read a value of type XXX from target's address at the specified offset and not hit any thread local caches. putXXXVolatile(Object target, long offset, XXX value): Will place value at target's address at the specified offset and not hit any thread local caches. putOrderedXXX(Object target, long offset, XXX value): Will place value at target's address at the specified offet and might not hit all thread local caches. putXXX(long address, XXX value): Will place the specified value of type XXX directly at the specified address. getXXX(long address): Will read a value of type XXX from the specified address. compareAndSwapXXX(Object target, long offset, long expectedValue, long value): Will atomicly read a value of type XXX from target's address at the specified offset and set the given value if the current value at this offset equals the expected value. Be aware that you are copying references when writing or reading object copies in native memory by using the getObject(Object, long) method family. You are therefore only creating shallow copies of instances when applying the above method. You could however always read object sizes and offsets recursively and create deep copies. Pay however attention for cyclic object references which would cause infinitive loops when applying this principle carelessly. Not mentioned here are existing utilities in the Unsafe class that allow manipulation of static field values sucht as staticFieldOffset and for handling array types. Finally, both methods named Unsafe#copyMemory allow to instruct a direct copy of memory, either relative to a specific object offset or at an absolute address as the following example shows: @Test public void testCopy() throws Exception { long address = unsafe.allocateMemory(4L); unsafe.putInt(address, 100); long otherAddress = unsafe.allocateMemory(4L); unsafe.copyMemory(address, otherAddress, 4L); assertEquals(100, unsafe.getInt(otherAddress)); } Throwing Checked Exceptions Without Declaration There are some other interesting methods to find in Unsafe. Did you ever want to throw a specific exception to be handled in a lower layer but you high layer interface type did not declare this checked exception? Unsafe#throwException allows to do so: @Test(expected = Exception.class) public void testThrowChecked() throws Exception { throwChecked(); } public void throwChecked() { unsafe.throwException(new Exception()); } Native Concurrency The park and unpark methods allow you to pause a thread for a certain amount of time and to resume it: @Test public void testPark() throws Exception { final boolean[] run = new boolean[1]; Thread thread = new Thread() { @Override public void run() { unsafe.park(true, 100000L); run[0] = true; } }; thread.start(); unsafe.unpark(thread); thread.join(100L); assertTrue(run[0]); } Also, monitors can be acquired directly by using Unsafe using monitorEnter(Object), monitorExit(Object) and tryMonitorEnter(Object). A file containing all the examples of this blog entry is available as a gist.
January 14, 2014
by Rafael Winterhalter
· 152,883 Views · 39 Likes
article thumbnail
JBoss 5 to 7 in 11 steps
Introduction Some time ago we decided to upgrade our application from JBoss 5 to 7 (technically 7.2). In this article I going to describe several things which we found problematic. At the end I also provided a short list of benefits we gained in retrospect. First some general information about our application. It was built using EJB 3.0 technology. We have 2 interfaces for communicating with other components – JMS and JAX-WS. We use JBoss AS 5 as our messaging broker which is started as a separate JVM process. This part of the system we were not allowed to change. Finally – we use JPA to store processing results to Oracle DB. Step #1 – Convince your Product Owner Although our application was rather small and built on JEE5 standard it took us 4 weeks to migrate it to JEE6 and JBoss 7. So you can't do it as a maintenance ticket – it's simply too big. There is always problem with providing Business Value of such migration for Product Owners as well as for key Stakeholders. There are several aspects which might help you convincing them. One of the biggest benefits is processing time. JBoss 7 is simply faster and has better caching (Infinispan over Ehcache). Another one is startup time (our server is ready to go in 5-6 seconds opposed to 1 minute in JBoss 5). Finally – development is much faster (EJB 3.1 is much better then 3.0). The last one might be translated to “time to market”. Having above arguments I'm pretty sure you'll convince them. Step #2 – Do some reading Here is a list on interesting links which are worth reading before the migration: JBoss 5 -> 7 migration guide: https://docs.jboss.org/author/display/AS7/How+do+I+migrate+my+application+from+AS5+or+AS6+to+AS7 JBoss 7 vs EAP libraries: https://access.redhat.com/site/articles/112673 JBoss EAP Faq: http://www.jboss.org/jbossas/faq Cache implementation benchmarks: http://sourceforge.net/p/nitrocache/blog/2012/05/performance-benchmark-nitrocache--ehcache--infinispan--jcs--cach4j/ JBoss 7 performence tuning: http://www.mastertheboss.com/jboss-performance/jboss-as-7-performance-tuning JBoss caching: http://www.mastertheboss.com/hibernate-howto/using-hibernate-second-level-cache-with-jboss-as-5-6-7 Step #3 – Off you go – change Maven dependencies JBoss 5 isn't packaged very well, so I suppose you many dependencies included in your classpath (either directly or by transitive dependencies). This is the first big change in JBoss 7. Now I strongly advice you to use this artifact in your dependency management section: org.jboss.as jboss-as-parent 7.2.0.Final pom import We also decided to stick only to JEE6 spec and configure all additional JBoss 7 options with proper XML files. If it sounds good for your project too, just add this dependency and you're done with this step: org.jboss.spec jboss-javaee-6.0 1.0.0.Final pom provided After cleaning up dependencies your code probably won't compile for a couple of days or even weeks. It takes time to clean this up. Step #4 – EJB 3.0 to 3.1 migration Dependency Injection is a heart of the application, so it is worth to start with it. Almost all of your code should work, but you'll have some problems with beans annotated with @Service (these are singletons with JBoss 5 EJB Extended API). You just need to replace them with @Singleton annotations and put @PostConstruct annotation on your init method. One last thing – remember to use proper concurrency strategy. We decided to use @ConcurrencyManagement(BEAN) and leave the implementation as is. Step #5 – Upgrade to JPA 2.0 If you used JPA 1.0 with Hibernate, I'm pretty sure you have a lot of non standard annotations defining caching or cascading. All of them might be successfully replaced with JPA 2.0 annotations and finally you might get rid of Hibernate from compile classpath and depend only on JPA 2.0. Here are several standard things to do: Get rid of Hibernate's Session.evict and switch to EntityManager.detach Get rid of Hibernate's @Cache annotation and replace it with @Cachable Fix Cascades (now delete orphan is a part of @XXXToYYY annotations) Remove Hibernate dependency and stick with JEE6 spec Step #6 – Fix Hibernate's sequencer Migrating Hibernate 3 to 4 is a bit tricky because of the way it uses sequences (fields annotated with @Id). Hibernate by default uses a pool of ids instead of incrementing sequence. An example will be more descriptive: Some_DB_Sequence.nextval -> 1 Hibernate 3: 1*50 = 50; IDs to be used = 50, 51, 52.…, 99 Some_DB_Sequence.nextval -> 2 Hibernate 3: 2*50 = 100; IDs to be used = 100, 101, 102.…, 149 In Hibernate 4.x there is a new sequence generator that uses new IDs that are 1:1 related to DB sequence. Typically it's disabled by default... but not in JBoss 7.1. So after migration, Hibernate tries to insert entities using IDs read from sequence (using new sequence generator) that were already used which causes constraint violation. The fastest solution is to switch Hibernate to the old method of sequence generation (described in example above), that requires following change in persistence.xml: Step #7 – Caching Infinispan is shipped with JBoss 7 and does not require much configuration. There is only one setting in persistence.xml which needs to be set and the others might be removed: Infinispan itself might require some extra configuration – just use standalone-full-ha.xml as guide. Step #8 – RMI with JBoss 5 If you're using a lot of RMI communicating with other JBoss 5 servers – I have bad information for you – JBoss 5 and 7 are totally different and this kind of comminication will not work. I strongly recommend to switch to some other technology like JAX-WS. In the retrospect we are very glad we decided to do it. Step #9 – JMS migration We thought it would be really hard to connect with JMS server based on JBoss 5. It turned out that you have 2 options and both work fine: Start HornetQ server on your own instance and create a bridge to JBoss 5 instance Use Generic JMS adapter: https://github.com/jms-ra/generic-jms-ra Step #10 – Fix EAR layout In JBoss 5 it does not matter where all jars are being placed. All EJBs are being started. It does not work with JBoss 7 anymore. All EJB which should start must be added as modules. Step #11 – JMX console Bad information – it's not present in JBoss 7. We liked it very much, but we had to switch to jvisualvm to invoke our JMX operations. There is a ticket in WildFly Jira opened for that: https://issues.jboss.org/browse/WFLY-1197. Unfortunately at moment of writing this article it is not resolved. Some thoughts in retrospect It is really time consuming task to migrate from JBoss 5 to 7. Although in my opinion it is worth it. Now we have better caching for cluster solutions (Infinispan), better DI (EJB 3.1) and better Web Services (CXF instead of JBoss WS). Processing time decreased by 25% without any code change. Development speed increased in my opinion (it is really hard to measure it) by 50% and we are much more productive (faster server restarts). Memory footprint lowered from 1GB to 512MB. Finally automatic application redeployment finally works! However there is always a price to pay – the migration took us 4 weeks (2 sprints). We didn't write any code for our business in that period. So make sure you prepare well for such migration and my last advice – invest some time to write good automatic functional tests (we use Arquillian for that). Once they're green again – you're almost crossing finishing line.
January 9, 2014
by Sebastian Laskawiec
· 47,088 Views
  • Previous
  • ...
  • 418
  • 419
  • 420
  • 421
  • 422
  • 423
  • 424
  • 425
  • 426
  • 427
  • ...
  • Next
  • RSS
  • X
  • Facebook

ABOUT US

  • About DZone
  • Support and feedback
  • Community research

ADVERTISE

  • Advertise with DZone

CONTRIBUTE ON DZONE

  • Article Submission Guidelines
  • Become a Contributor
  • Core Program
  • Visit the Writers' Zone

LEGAL

  • Terms of Service
  • Privacy Policy

CONTACT US

  • 3343 Perimeter Hill Drive
  • Suite 215
  • Nashville, TN 37211
  • [email protected]

Let's be friends:

  • RSS
  • X
  • Facebook
×