Monthly Archives: October 2014

Taking memory dumps of Hadoop tasks

This post originally appeared in my older blog. I am carrying over a few of those posts which seem to be popular.


 

On the Hadoop users mailing list, I was recently working with a user on a recurring problem faced by users of Hadoop. The user’s tasks were running out of memory and he wanted to know why. The typical approach to debug this problem is to use a diagnostic tool like jmap, or hook up a profiler to the running task. However, for most Hadoop users, this is not feasible. In real applications, the tasks run on a cluster to which users do not have login access and they cannot debug the task as it runs. I was aware of an option that is provided by the JVM – -XX:+HeapDumpOnOutOfMemoryError that can be passed to the task’s Java command line. This option makes the JVM to take a dump when the task runs out of memory. However, the dump is saved by default to the current working directory of the task, which in Hadoop’s case is a temporary scratch space managed by the framework and it would become inaccessible once the task completes.

At this point, when we were pretty much giving up on options, Koji Noguchi, an ex-colleague of mine and a brilliant systems engineer and Hadoop debugger, responded with a way out. You can read about it here. The few lines mentioned feel almost like magic, so I thought I would write an explanation about how it is working, for people who are interested.

The requirement is to save the dump to a location which is accessible by the user running the task. Such a location, in Hadoop’s case, is … HDFS. So, what we want is to be able to save the dump to HDFS when the scenario happens.

To get there, the first observation is that the JVM offers hooks that can be passed to the task’s command line, for us to act on an OutOfMemory scenario. The options Koji used are:

These options instruct the JVM to take a dump on OutOfMemory, save it with a name of our choice, and importantly, run a custom script . It should be obvious now that the custom script can copy the generated dump to DFS, using regular DFS commands.

There are a couple of gaps to plug though – as the devil is in the details. How does the script (copy-dump.sh, in the example above) get to the cluster nodes ? For that, we use Hadoop’s feature – Distributed Cache. This feature allows arbitrary files to be packaged and distributed to cluster nodes where tasks require them – using HDFS as an intermediate store. The cached files are usually available to tasks via a Java API. However, since we need this outside the task’s context, we use a powerful option of the Distributed Cache – creating symlinks. This option not only makes the files available to the tasks via the API, but also creates a symbolic link of that file into the current working directory of the task. Hence, when we refer to the script in the task’s command line, we can refer to it relative to the current working directory of the task, i.e. ‘.’.

The specific options to set up all of the above are as follows:

The last detail in the whole solution is about how to save the dump on HDFS with a name that is unique. Because, realize that multiple tasks are running together at the same time, and more than one of them could run out of memory. Koji’s scripting brilliance for solving this problem was to use the following script:

The expression ${PWD//\//_} takes the current working directory of the task (from the environment), and replaces every occurrence of ‘/’ with an ‘_’. Nice !

So, using these options, features and diagnostics of Hadoop and the JVM, users can now get memory dumps of their tasks to locations that they can easily access and analyse. Thanks a lot to Koji for sharing this technique, and happy debugging !!!

 

 

facebooktwittergoogle_plusredditpinterestlinkedinmail

Using native Hadoop shell and UI on Amazon EMR

This post is carried over from my earlier blog site here. I am migrating posts that seem to have gathered most hits there.


Amazon’s Elastic MapReduce (EMR) is a popular Hadoop on the cloud service. Using EMR, users can provision a Hadoop cluster on Amazon AWS resources and run jobs on them. EMR defines an abstraction called the ‘jobflow’ to submit jobs to a provisioned cluster. A jobflow contains a set of ‘steps’. Each step runs a MapReduce job, a Hive script, a shell executable, and so on. Users can track the status of the jobs from the Amazon EMR console.

Users who have used a static Hadoop cluster are used to the Hadoop CLI for submitting jobs and also viewing the Hadoop JobTracker and NameNode user interfaces for tracking activity on the cluster. It is possible to use EMR in this mode, and is documented in the extensive EMR documentation. This blog collates the information for using these interfaces into one place for such a usage mode, along with some experience notes. The examples given here have been tested on OS X MountainLion. The details will vary for other operating systems, but should be similar.

When a cluster is provisioned, a node called the ‘master’ node is created on the EMR cluster, that runs the JobTracker and the NameNode. In short, the mechanism to access the Hadoop CLI is to ssh into the master node and use the installed Hadoop software. Likewise, for accessing the UI, an SSH tunnel needs to be set up to the web interfaces that also run on the master node.

Before we start

  • This blog assumes you already have signed up for an Amazon account.
  • Next, you need the Amazon EMR CLI. The CLI is a useful way to access Amazon EMR that provides a good balance between completeness of functionality and ease of use, compared to the Amazon EMR console.

Note: The EMR CLI is a Ruby application requiring Ruby 1.8.x. If you have installed Ruby 1.9 on your system, you have two options:

    • Use RVM, install Ruby 1.8.x. via RVM and switch the Ruby version. 
    • Alternatively, you can use a fork of the Amazon CLI that works with Ruby 1.9 called elastic-mapreduce-ruby.
  • Configure the EMR client by creating a credentials.json file. The file should be created in the home directory of your elastic-mapreduce client. A sample file’s contents is mentioned here:

  • In the example above, access_id and private_key are security credentials connected with your AWS account. The keypair is a resource associated to your Amazon EC2 service. The private key details of the keypair can be downloaded to a PEM file locally, whose path is specified in key-pair-file. You can refer to this link for details on how to get these various security parameters.

Launching a cluster

Once set up, we are now ready to launch an EMR cluster and access it to submit Hadoop jobs.

Typical deployments of a Hadoop cluster comprise of three types of nodes – the masters (JobTracker and NameNode), the slaves (TaskTrackers and DataNodes) and client nodes (typically called access nodes or gateways) from where users submit jobs. An EMR cluster too has three types of nodes – a single master node (that runs both the JobTracker and NameNode), core nodes (that run both TaskTrackers and DataNodes) and task nodes (that run only the TaskTrackers). As you can see, the categories of nodes are slightly different. But we could double up the master node in EMR to be a client node as well. Since the master node in an EMR cluster is used only by you, it is assumed it will have enough capacity to run the Hadoop CLI.

Start an EMR cluster with the CLI in this fashion:

The ‘elastic-mapreduce’ program will be in the home directory of the EMR client. The above command creates a cluster with 3 instances – 1 master and 2 slaves. The –alive flag ensures that the launched cluster stays alive until it is manually terminated by the user. This option is required to login into the master node and submit Hadoop jobs to the cluster directly. The output of this command will be a ‘jobflow’ ID – something that will look like j-FTW6FLQ1P2G0. Make a note of this ID, as we will use it in other commands below.

Note: You will be charged according to the EMR rates for your usage of the cluster, depending on the type and number of instances chosen.

You can also get more details about the launched cluster using the following command:

Of specific interest in the output of the above command will be the “State” attribute of the ExecutionStatusDetail node. You need to wait until the value of this attribute becomes “WAITING”. Once this state is reached, your cluster is ready for further action. Similarly, the “MasterPublicDnsName” attribute gives the DNS name of the machine running the Hadoop JobTacker and NameNode.

Browsing Hadoop web UI on the cluster

At this point, it will be useful to check out how the cluster looks like from the familiar JobTracker and NameNode web UI.

The JobTracker web server runs on port 9100 on the master node. In order to browse this UI, you can set up an SSH tunnel that will work as a SOCKS proxy server from your machine to the master node that dynamically forwards HTTP requests. The Amazon CLI provides a command to set up this proxy:

Note: This command helpfully prints out the SSH command that is invoked to set up the SOCKS proxy server. When facing problems with connectivity, I have been able to take this SSH command, modify it (for instance to add the -v option to ssh for enabling debug output) and run it directly for debugging / resolving issues.

After the socks proxy server is started, you can configure your browser’s or system’s proxy settings to use this SOCKS proxy for HTTP traffic. For Chrome, I did this by launching Settings > Change Proxy Settings > Select “SOCKS Proxy” > Enter the server address as 127.0.0.1 and the port as 8157.

socks-proxy

If things are fine here, you should be able to hit the URL http://<MasterPublicDnsName>:9100/ on the browser and see the JobTracker UI page and http://<MasterPublicDnsName>:9101/ for the NameNode UI.

The method described here routes all HTTP traffic from your browser through the tunnel. A better option would be to set up a rule that routes only traffic to the EMR clusters through the tunnel. Such a method is described in the EMR documentation, using the FoxyProxy Firefox browser plugin.

Submitting Jobs

The next step is to submit jobs to the EMR cluster using the Hadoop CLI. As described above, the master node doubles up as a Hadoop client node as well. So, we should SSH into the master node using the following command:

This command should drop you into the home directory of the ‘hadoop’ user on the master node. A quick listing of the home directory will show a full Hadoop installation, including bin and conf directories and all the jars that are part of the Hadoop distribution.

You can execute your Hadoop commands as usual from here. For e.g.

 

Using the UI that we set up in the previous step, you can also browse the job pages as usual.

Terminating the cluster

Once you are done with the usage, you must remember to terminate the cluster, as otherwise you will continue to accrue cost on an hourly basis irrespective of usage. The command to terminate is:

Note: Terminating the cluster will result in loss of data stored in the HDFS of the cluster. If you need to store data permanently, you can do so by providing Amazon S3 paths as output directories of your jobs.

In conclusion, tools like the elastic mapreduce CLI make it easy to not only provision a Hadoop cluster and run jobs on it, but also to provide the familiar look and feel of the Hadoop client and the Web UI.

 

facebooktwittergoogle_plusredditpinterestlinkedinmail

Comparing Apache Tez and Microsoft Dryad

This post is carried over from my earlier blog site here. I am migrating posts that seem to have gathered most hits there.


Hortonworks has been blogging about a framework called Tez, a general purpose data processing framework. Reading through the posts, I was reminded of a similar framework that had come from Microsoft Research a while back called Dryad. This blog post is an attempt at comparing them.

In order to structure the comparison, I am trying to express the points under the following topics: historical perspective, features, concepts, and architecture.

Historical Perspective

Both Tez and Dryad define distributed, data parallel computing frameworks that lay an emphasis on modelling data flow. A data processing ‘job’ in either is defined as a graph. The vertices of the graph represent computational processes, with the edges connecting them describing input they receive and output they send out from / to other computational vertices or data sources / sinks. Both systems attempt to provide an efficient execution environment for running these jobs, abstracting users away from needing to handle common distributed computing requirements such as communication, fault tolerance, etc.

At the time of its introduction, Dryad was possibly Microsoft’s view on how to build such a framework from ground up. In contrast to Hadoop, Dryad attempted even then to provide a framework that wasn’t restricted to just one model (MapReduce) of computation. Dryad was inspired by a variety of data processing systems including MPP databases, data parallel programs on GPUs, and MapReduce as well. It attempted to build a system that could express all these kinds of computation.

Tez was introduced as a generalisation of the MapReduce paradigm that had dominated Hadoop computation for several years. However, it seems to be inspired more by data flow frameworks like Dryad. It was enabled immensely by the separation of concerns brought to the Hadoop MapReduce layer in the form of Apache YARN, that separated cluster resource management from distributed job management, enabling more models than just MapReduce. A direct motivation for Tez was the Stinger initiative, launched to build a faster version of Apache Hive. Specifically, the idea was to enable expressing a HQL query as a single Tez job, rather than multiple MapReduce jobs, thereby avoiding the overhead of launching multiple jobs and also incurring the I/O overhead of having to store data between jobs on HDFS.

Features

Tez and Dryad share several features, such as:

  • The DAG model being the specification choice for a job
  • A flexible / pluggable system where the framework tries to give the user control of the computation, nature of input and output, etc.
  • Supporting multiple inputs and outputs for a vertex (that enable SQL like joins to be expressed, and various forms of data partitioning like the shuffle sort phase of Hadoop MapReduce)
  • An ability to modify the DAG at runtime based on feedback from executing part of the graph. The runtime modification is primarily used for improving the efficiency of execution in both systems. For e.g. in Dryad, this was used to introduce intermediate aggregator nodes (akin to the combiner concept in Hadoop MapReduce), while in Tez, this is being used as a way to optimise the number of reducers or when they would get launched.

Dryad was built from ground up without a supporting resource management or scheduling framework, and some of its ‘features’ are present in or shared by other layers of the Hadoop stack like YARN. In addition to those, Dryad allowed one specific optimisation through which processing nodes can execute concurrently, co-located and connected via  shared memory or pipes.

Tez on its hand, expands on learnings from the Hadoop MapReduce framework. For example, it expands on a feature available with MapReduce called JVM reuse, whereby ‘containers’ launched to run the vertex programs of Tez can be reused for multiple Tez tasks. It even allows sharing data between these tasks via an ‘Object Registry‘ without needing to have them run concurrently.

Concepts

Naturally, the core concepts of a Graph are common between the systems.

In Tez:

  • A vertex is defined by the input, output and processor associated with it.
  • The logical and physical manifestations of a graph are explicitly separated. Specifically, the inputs and outputs are of two types – a physical type and a logical type. The logical type describes the connection between a vertex pair as per the DAG definition, while the physical type will represent the connection between a vertex pair at runtime. The Tez framework automatically determines the number of physical instances of a vertex in a logical graph.
  • Edges are augmented with properties that relate to data movement (for e.g. multicast output between connected vertices), scheduling (co-schedule, or in sequence) and data source (persistence guarantees on the vertex’s output). Tez expects that by using a combination of these properties, one can replicate existing patterns of computation like MapReduce.
  • In addition to the graph concepts, there is also the concept of an ‘event’. Events are a means for the vertices and the framework to communicate amongst themselves. Events can be used to handle failures, learn about the runtime characteristics of the data or processing, or indicate the availability of data.

In Dryad:

  • Inputs and outputs are considered vertices just like processing vertices.
  • Dryad represents the logical representation of the DAG as a set of ‘stages’. However, this does not seem to be a first class concept to specify the DAG at definition time. Specifically, Dryad expects the specific number of instances of  a vertex at runtime to be defined at definition time.
  • A lot of operators are defined which help to build a graph. For instance:
    • Cloning: is an operation by which a given Vertex is replicated. Such a cloning operation is used to define a physical manifestation of a graph.
    • Composition: is used to define types of data movement patterns (akin to the edge property in Tez)  like round robin data transfer, scatter-gather etc.
    • Merge: is used for defining operations like fork/join etc.
    • Encapsulation: is a way of collapsing a graph into a single vertex, which makes it execute on a single node – used to express concurrent, co-located execution.
  • It appears the idea behind the operators is again to try and define patterns of computation like MapReduce.
  • A ‘channel’ is an abstraction of how data is transferred along an edge. There is support for different types of channels like File, Shared Memory, Pipes etc. This is similar to the physical Input/Output types in Tez.

Architecture

Tez is a YARN application. A Tez job is coordinated by the Tez Application Master (AM). It is comprised of Tez tasks. Each task encapsulates a processor (vertex) of the DAG and all inputs and outputs connected to it. A Tez task is launched within a YARN container. However, in the interest of providing good performance, a single YARN container could be reused for multiple Tez tasks. This is managed by a ‘TezTask’ host. The host also manages a store of objects that can be shared between Tez tasks that run within the host.

The Tez Application Master has a Vertex Manager plugin (that can be customised by the developer) for every type of Vertex. In addition, the AM also maintains a Vertex State Machine. As the state of the DAG changes, the Vertex Manager is invoked by the Application Master, who can then act on the State machine to customise the graph execution.

Another point to note is that Tez relies on YARN’s resource manager and scheduler for initial assignment of containers, etc. However, it has the ability to make the scheduling a two level activity. For example, Tez does come with scheduling capabilities, which it uses for features like container reuse.

Dryad’s architecture includes components that do resource management as well as the job management. A Dryad job is coordinated by a component called the Job Manager. Tasks of a job are executed on cluster machines by a Daemon process. Communication with the tasks from the job manager happens through the Daemon, which acts like a proxy. In Dryad, the scheduling decisions are local to an instance of the Dryad Job Manager – i.e. it is decentralised.

The logical plan for a Dryad DAG results in each vertex being placed in a ‘Stage’. The stages are managed by a ‘Stage manager’ component that is part of the job manager, similar to the Vertex Manager in Tez. The Stage manager is used to detect state transitions and implement optimisations like Hadoop’s speculative execution.

Conclusion

Dryad was discontinued by Microsoft in late 2011. Microsoft has since been contributing to Hadoop. Given the similarities between the two systems, a question is about how Tez’s prospects are going to be different from Dryad. A few points that seem to favour Tez, IMO:

  • Tez rides on years of learning from Hadoop MapReduce and other systems including Dryad. Microsoft recently posted that it contributes to Tez. The expectation then would be that the insights and learnings from systems (including what did not work) will help build a better system.
  • The separation of concerns brought about by YARN potentially helps Tez to focus on problems specific to the graph processing model, while delegating resource management and scheduling decisions to another layer – at least partially.
  • The API for Graph construction in Tez appears a lot simpler and intuitive to understand than the corresponding one in Dryad. Hence, it seems easier to adopt the model from a programmer perspective.
  • Given Tez was launched with a specific initiative of making Hive faster, there is a goal it is working towards, and there seems to already be evidence that Tez is enabling improvements in Hive as shown here.

Personally, I feel it would be good to have Tez succeed and several people who have invested in Hive will be able to see huge improvements in performance from their existing applications.

Acknowledgements

Most of the information for this post has come from the publicly available knowledge in blog posts and published paper. If there is any omission or mis-representation, please do let me know !

An initial draft of this post was reviewed by a few committers at Hortonworks: Siddharth Seth, Bikas Saha, Hitesh Shah and Vinod Kumar Vavilapalli. I am thankful to them for their feedback. While I have incorporated some of it, I felt some others are best explained from their end, possibly as comments. I will notify them once the blog is published.

Specifically calling out two points:

  • Both Sid and Hitesh have called out that there are going to be additional changes to the architecture and features in Tez that will soon be published. As this blog was being written, a new post came out from Hortonworks mentioning a new concept called Tez Sessions. So, be sure to watch out for Hortonworks blogs on Tez for more information.
  • Bikas provided feedback about Tez’s motivation being closer not just to systems like Dryad, but also other data flow systems like Hyracks and Nephele. It may be a good academic exercise to see these other systems as well from a perspective of learning.
facebooktwittergoogle_plusredditpinterestlinkedinmail