I have a Spark Streaming process, which inserts data into Cassandra.
Results of each computational process will depend on the previous insert, so what I need to do is find a way to efficiently keep in memory only the data of the previous insert. Also, that in memory structures will be updated with each insert..
I considered using accumulator variables, but I will need too many values -> more than 5-6000.. Queering them every time from Cassandra is definitely not providing good performance.
What do you think I should do?
Related
Recently I got a requirement to perform combination joins.
I have to perform around 30 to 36 joins in Spark.
It was consuming more time to build the execution plan. So I cached the execution plan in intermediate stages using df.localCheckpoint().
Is this a good way to do? Any thoughts, please share.
Yes, it is fine.
This is mostly discussed for iterative ML algorithms, but can be equally applied for a Spark App with many steps - e.g. joins.
Quoting from https://medium.com/#adrianchang/apache-spark-checkpointing-ebd2ec065371:
Spark programs take a huge performance hit when fault tolerance occurs
as the entire set of transformations to a DataFrame or RDD have to be
recomputed when fault tolerance occurs or for each additional
transformation that is applied on top of an RDD or DataFrame.
localCheckpoint() is not "reliable".
Caching is definitely a strategy to optimize your performance. In general, given that your data size and resource of your spark application remains unchanged, there are three points that need to be considered when you want to optimize your joining operation:
Data skewness: In most of the time, when I'm trying to find out the reason why the joining takes a lot of time, data skewness is always be one of the reasons. In fact, not only the joining operation, any transformation need a even data distribution so that you won't have a skewed partition that have lots of data and wait the single task in single partition. Make sure your data are well distributed.
Data broadcasting: When we do the joining operation, data shuffling is inevitable. In some case, we use a relatively small dataframe as a reference to filter the data in a very big dataframe. In this case, it's a very expensive operation to shuffle the dataframe. Instead, we can use the dataframe broadcasting to broadcast your small dataframe to every single node and prevent the costly shuffling.
Keep your joining data as lean as possible: like what I mentioned in point 2, data shuffling is inevitable when you do the joining operation. Therefore, please keep your dataframe as lean as possible, which means remove the rows / columns if it's unnecessary to reduce the size of data that need to be moved across the network during the data shuffling.
1.) I understand that "Spark's operators spills data to disk if it does not fit memory allowing it to run well on any sized data".
If this is true, why do we ever get OOM (Out of Memory) errors?
2.) Increasing the no. of executor cores increases parallelism. Would that also increase the chances of OOM, because the same memory is now divided into smaller parts for each core?
3.) Spark is much more susceptible to OOM because it performs operations in memory as compared to Hive, which repeatedly reads, writes into disk. Is that correct?
There is one angle that you need to consider there. You may get memory leaks if the data is not properly distributed. That means that you need to distribute your data evenly (if possible) on the Tasks so that you reduce shuffling as much as possible and make those Tasks to manage their own data. So if you need to perform a join, if data is distributed randomly, every Task (and therefore executor) will have to:
See what data they have
Send data to other executors (and tasks) to provide the same keys they need
Request the data that is needed by that task to the others
All that data exchange may cause network bottlenecks if you have a large dataset and also will make every Task to hold their data in memory plus whatever has been sent and temporary objects. All of those will blow up memory.
So to prevent that situation you can:
Load the data already repartitioned. By that I mean, if you are loading from a DB, try Spark stride as defined here. Please refer to the partitionColumn, lowerBound, upperBound attributes. That way you will create a number of partitions on the dataframe that will set the data on different tasks based on the criteria you need. If you are going to use a join of two dataframes, try similar approach on them so that partitions are similar (for not to say same) and that will prevent shuffling over network.
When you define partitions, try to make those values as evenly distributed among tasks as possible
The size of each partition should fit on memory. Although there could be spill to disk, that would slow down performance
If you don't have a column that make the data evenly distributed, try to create one that would have n number of different values, depending on the n number of tasks that you have
If you are reading from a csv, that would make it harder to create partitions, but still it's possible. You can either split the data (csv) on multiple files and create multiple dataframes (performing a union after they are loaded) or you can read that big csv and apply a repartition on the column you need. That will create shuffling as well, but it will be done once if you cache the dataframe already repartitioned
Reading from parquet it's possible that you may have multiple files but if they are not evenly distributed (because the previous process that generated didn't do it well) you may end up on OOM errors. To prevent that situation, you can load and apply repartition on the dataframe too
Or another trick valid for csv, parquet files, orc, etc. is to create a Hive table on top of that and run a query from Spark running a distribute by clause on the data, so that you can make Hive to redistribute, instead of Spark
To your question about Hive and Spark, I think you are right up to some point. Depending on the execute engine that Hive uses in your case (map/reduce, Tez, Hive on Spark, LLAP) you can have different behaviours. With map/reduce, as they are mostly disk operations, the chance to have a OOM is much lower than on Spark. Actually from Memory point of view, map/reduce is not that affected because of a skewed data distribution. But (IMHO) your goal should be to find always the best data distribution for the Spark job you are running and that will prevent that problem
Another consideration is if you are testing in a dev environment that doesn't have same data as in a prod environment. I suppose the data distribution should be similar although volumes may differ a lot (I am talking from experience ;)). In that case, when you assign Spark tuning parameters on the spark-submit command, they may be different in prod. So you need to invest some time on finding the best approach on dev and fine tune in prod
Huge majority of OOM in Spark are on the driver, not executors. This is usually a result of running .collect or similar actions on a dataset that won't fit in the driver memory.
Spark does a lot of work under the hood to parallelize the work, when using structured APIs (in contrast to RDDs) the chances of causing OOM on executor are really slim. Some combinations of cluster configuration and jobs can cause memory pressure that will impact performance and cause lots of garbage collection to happen so you need to address it, however spark should be able to handle low memory without explicit exception.
Not really - as above, Spark should be able to recover from memory issues when using structured APIs, however it may need intervention if you see garbage collection and performance impact.
I am recently working in spark and came across few queries which I still couldn't resolve.
Let's say i have a dataset of 100GB and my ram size of the cluster is
16 GB.
Now, I know in case of simply reading the file and saving it in the HDFS will work as Spark will do it for each partition. What will happen when I perform sorting or aggregation transformation on 100GB data? How will it process 100GB in memory since we need entire data in case of sorting?
I have gone through below link but this only tells us what spark do in case of persisting, what I am looking is Spark aggregations or sorting on dataset greater than ram size.
Spark RDD - is partition(s) always in RAM?
Any help is appreciated.
There are 2 things you might want to know.
Once Spark reaches the memory limit, it will start spilling data to
disk. Please check this Spark faq and also there are severals
question from SO talking about the same, for example, this one.
There is an algorihtm called external sort that allows you to sort datasets which do not fit in memory. Essentially, you divide the large dataset by chunks which actually fit in memory, sort each chunk and write each chunk to disk. Finally, merge every sorted chunk in order to get the whole dataset sorted. Spark supports external sorting as you can see here and here is the implementation.
Answering your question, you do not really need that your data fit in memory in order to sort it, as I explained to you before. Now, I would encourage you to think about an algorithm for data aggregation dividing the data by chunks, just like external sort does.
There are multiple things you need to consider. Because you have 16RAM and 100GB data set, it will be good idea to keep persistence in DISK. It maybe difficult as when aggregating if data set has high cardinality. If the cardinality is low you will be better of to do aggregate at each RDD before merging into whole dataset. Also remember to make sure that each partition in RDD is less than memory (default value 0.4*container_size)
In CouchDB and system designs like Incoop, there's a concept called "Incremental MapReduce" where results from previous executions of a MapReduce algorithm are saved and used to skip over sections of input data that haven't been changed.
Say I have 1 million rows divided into 20 partitions. If I run a simple MapReduce over this data, I could cache/store the result of reducing each separate partition, before they're combined and reduced again to produce the final result. If I only change data in the 19th partition then I only need to run the map & reduce steps on the changed section of the data, and then combine the new result with the saved reduce results from the unchanged partitions to get an updated result. Using this sort of catching I'd be able to skip almost 95% of the work for re-running a MapReduce job on this hypothetical dataset.
Is there any good way to apply this pattern to Spark? I know I could write my own tool for splitting up input data into partitions, checking if I've already processed those partitions before, loading them from a cache if I have, and then running the final reduce to join all the partitions together. However, I suspect that there's an easier way to approach this.
I've experimented with checkpointing in Spark Streaming, and that is able to store results between restarts, which is almost what I'm looking for, but I want to do this outside of a streaming job.
RDD caching/persisting/checkpointing almost looks like something I could build off of - it makes it easy to keep intermediate computations around and reference them later, but I think cached RDDs are always removed once the SparkContext is stopped, even if they're persisted to disk. So caching wouldn't work for storing results between restarts. Also, I'm not sure if/how checkpointed RDDs are supposed to be loaded when a new SparkContext is started... They seem to be stored under a UUID in the checkpoint directory that's specific to a single instance of the SparkContext.
Both use cases suggested by the article (incremental logs processing and incremental query processing) can be generally solved by Spark Streaming.
The idea is that you have incremental updates coming in using DStreams abstraction. Then, you can process new data, and join it with previous calculation either using time window based processing or using arbitrary stateful operations as part of Structured Stream Processing. Results of the calculation can be later dumped to some sort of external sink like database or file system, or they can be exposed as an SQL table.
If you're not building an online data processing system, regular Spark can be used as well. It's just a matter of how incremental updates get into the process, and how intermediate state is saved. For example, incremental updates can appear under some path on a distributed file system, while intermediate state containing previous computation joined with new data computation can be dumped, again, to the same file system.
I'm trying to benchmark a few approaches to putting an image processing algorithm into apache spark. For one step in this algorithm, a computation on a pixel in the image will depend on an unknown amount of surrounding data, so we can't partition the image with guaranteed sufficient overlap a priori.
One solution to that problem I need to benchmark is for a worker node to ask the master node for more data when it encounters a pixel with insufficient surrounding data. I'm not convinced this is the way to do things, but I need to benchmark it anyway because of reasons.
Unfortunately, after a bunch of googling and reading docs I can't find any way for a processingFunc called as part of sc.parallelize(partitions).map(processingFunc) to query the master node for more data from a different partition mid-computation.
Does a way for a worker node to ask the master for more data exist in spark, or will I need to hack something together that kind of goes around spark?
Master Node in Spark is for allocating the resources to a particular job and once the resources are allocated, the Driver ships the complete code with all its dependencies to the various executors.
The first step in every code is to load the data to the Spark cluster. You can read the data from any underlying data repository like Database, filesystem, webservices etc.
Once data is loaded it is wrapped into an RDD which is partitioned across the nodes in the cluster and further stored in the workers/ Executors Memory. Though you can control the number of partitions by leveraging various RDD API's but you should do it only when you have valid reasons to do so.
Now all operations are performed over RDD's using its various methods/ Operations exposed by RDD API. RDD keep tracks of partitions and partitioned data and depending upon the need or request it automatically query the appropriate partition.
In nutshell, you do not have to worry about the way data is partitioned by RDD or which partition stores which data and how they communicate with each other but if you do care, then you can write your own custom partitioner, instructing Spark of how to partition your data.
Secondly if your data cannot be partitioned then I do not think Spark would be an ideal choice because that will result in processing of everything in 1 single machine which itself is contrary to the idea of distributed computing.
Not sure what is exactly your use case but there are people who have been leveraging Spark for Image processing. see here for the comments from Databricks