I am trying to fetch data from Greenplum table using Apache NiFi - QueryDatabaseTableRecord. I am seeing GC overhead limit exceeded error and the NiFi webpage becomes unresponsive.
I have set the 'Fetch Size' property to 10000 but it seems the property is not being used in this case.
Other settings:
Database Type : Generic
Max Rows Per Flow File : 1000000
Output Batch Size : 2
jvm min/max memory allocation is 4g/8g
Is there an alternative to avoid the GC errors for this task ?
this is a clear case of the "Fetch Size" parameter not being used, see processor info on this.
Try to test the jdbc setFetchsize on its own to see if it works.
I'm trying to perform a simple join operation using Talend & Spark. The input data set is a few million records and the look up data set is around 100 records.(we might need to join with million records look up data too).
When trying to just read the input data and generate a flat file with the following memory settings, the job works fine and takes less amount of time to run. But, when trying to perform a join operation as explained above, the job gets stuck at 99.7%.
ExecutorMemory = 20g
Cores Per Executor = 4
Yarn resources allocation = Fixed
Num of executors = 100
spark.yarn.executor.memoryOverhead=6000 (On some preliminary research I found that this has to be 10% of the executor memory, but that didn't help too.)
After a while(30-40 minutes) the job prints a log saying - "Lost executor xx on abc.xyz.com". This is probably because it's put on wait for too long and the executor gets killed.
I'm trying to check if anyone has run into this issue where a Spark job gets stuck at 99.7% for a simple operation. Also, what are the recommended tuning properties to use in such a scenario.
My project is implement a interaction query for user to discover that data. Like we have a list of columns user can choose then user add to list and press view data. The current data store in Cassandra and we use Spark SQL to query from it.
The Data Flow is we have a raw log after be processed by Spark store into Cassandra. The data is time series with more than 20 columns and 4 metrics. Currently I tested because more than 20 dimensions into cluster keys so write to Cassandra is quite slow.
The idea here is load all data from Cassandra into Spark and cache it in memory. Provide a API to client and run query base on Spark Cache.
But I don't know how to keep that cached data persist. I am try to use spark-job-server they have feature call share object. But not sure it works.
We can provide a cluster with more than 40 CPU cores and 100 GB RAM. We estimate data to query is about 100 GB.
What I have already tried:
Try to store in Alluxio and load to Spark from that but the time to load is slow because when it load 4GB data Spark need to do 2 things first is read from Alluxio take more than 1 minutes and then store into disk (Spark Shuffle) cost more than 2 or 3 minutes. That mean is over the time we target under 1 minute. We tested 1 job in 8 CPU cores.
Try to store in MemSQL but kind of costly. 1 days it cost 2GB RAM. Not sure the speed is keeping good when we scale.
Try to use Cassandra but Cassandra does not support GROUP BY.
So, what I really want to know is my direction is right or not? What I can change to archive the goal (query like MySQL with a lot of group by, SUM, ORDER BY) return to client by a API.
If you explicitly call cache or persist on a DataFrame, it will be saved in memory (and/or disk, depending on the storage level you choose) until the context is shut down. This is also valid for sqlContext.cacheTable.
So, as you are using Spark JobServer, you can create a long running context (using REST or at server start-up) and use it for multiple queries on the same dataset, because it will be cached until the context or the JobServer service shuts down. However, using this approach, you should make sure you have a good amount of memory available for this context, otherwise Spark will save a large portion of the data on disk, and this would have some impact on performance.
Additionally, the Named Objects feature of JobServer is useful for sharing specific objects among jobs, but this is not needed if you register your data as a temp table (df.registerTempTable("name")) and cache it (sqlContext.cacheTable("name")), because you will be able to query your table from multiple jobs (using sqlContext.sql or sqlContext.table), as long as these jobs are executed on the same context.
I am working on a use case where I have to transfer data from RDBMS to HDFS. We have done the benchmarking of this case using sqoop and found out that we are able to transfer around 20GB data in 6-7 Mins.
Where as when I try the same with Spark SQL, the performance is very low(1 Gb of records is taking 4 min to transfer from netezza to hdfs). I am trying to do some tuning and increase its performance but its unlikely to tune it to the level of sqoop(around 3 Gb of data in 1 Min).
I agree to the fact that spark is primarily a processing engine but my main question is that both spark and sqoop are using JDBC driver internally so why there is so much difference in the performance(or may be I am missing something). I am posting my code here.
object helloWorld {
def main(args: Array[String]): Unit = {
val conf = new SparkConf().setAppName("Netezza_Connection").setMaster("local")
val sc= new SparkContext(conf)
val sqlContext = new org.apache.spark.sql.hive.HiveContext(sc)
sqlContext.read.format("jdbc").option("url","jdbc:netezza://hostname:port/dbname").option("dbtable","POC_TEST").option("user","user").option("password","password").option("driver","org.netezza.Driver").option("numPartitions","14").option("lowerBound","0").option("upperBound","13").option("partitionColumn", "id").option("fetchSize","100000").load().registerTempTable("POC")
val df2 =sqlContext.sql("select * from POC")
val partitioner= new org.apache.spark.HashPartitioner(14)
val rdd=df2.rdd.map(x=>(String.valueOf(x.get(1)),x)).partitionBy(partitioner).values
rdd.saveAsTextFile("hdfs://Hostname/test")
}
}
I have checked many other post but could not get a clear answer for the internal working and tuning of sqoop nor I got sqoop vs spark sql benchmarking .Kindly help in understanding this issue.
You are using the wrong tools for the job.
Sqoop will launch a slew of processes (on the datanodes) that will each make a connections to your database (see num-mapper) and they will each extract a part of the dataset. I don't think you can achieve kind of read parallelism with Spark.
Get the dataset with Sqoop and then process it with Spark.
you can try the following:-
Read data from netezza without any partitions and with increased fetch_size to a million.
sqlContext.read.format("jdbc").option("url","jdbc:netezza://hostname:port/dbname").option("dbtable","POC_TEST").option("user","user").option("password","password").option("driver","org.netezza.Driver").option("fetchSize","1000000").load().registerTempTable("POC")
repartition the data before writing it to final file.
val df3 = df2.repartition(10) //to reduce the shuffle
ORC formats are more optimized than TEXT. Write the final output to parquet/ORC.
df3.write.format("ORC").save("hdfs://Hostname/test")
#amitabh
Although marked as an answer, I disagree with it.
Once you give the predicate to partition the data while reading from the jdbc, spark will run separate tasks for each partition. In your case no of tasks should be 14 (u can confirm this using spark UI).
I notice that you are using local as master, which would provide only 1 core for executors. Hence there will be no parallelism. Which is what is happening in your case.
Now to get the same throughput as sqoop you need to make sure that these tasks are running in parallel. Theoretically this can be done either by:
1. Using 14 executors with 1 core each
2. Using 1 executor with 14 cores (other end of the spectrum)
Typically, I would go with 4-5 cores per executor. So I test the performance with 15/5= 3 executors (i added 1 to 14 to consider 1 core for the driver running in clustor mode).
Use: executor.cores, executor.instances in sparkConf.set to play with the configs.
If this does not significantly increase performance, the next thing would be to look at the executor memory.
Finally, I would tweak the application logic to look at mapRDD sizes, partition sizes and shuffle sizes.
I had the same problem because the piece of code you are using it's not working for partition.
sqlContext.read.format("jdbc").option("url","jdbc:netezza://hostname:port/dbname").option("dbtable","POC_TEST").option("user","user").option("password","password").option("driver","org.netezza.Driver").option("numPartitions","14").option("lowerBound","0").option("upperBound","13").option("partitionColumn", "id").option("fetchSize","100000").load().registerTempTable("POC")
You can check number of partitions created in you spark job by
df.rdd.partitions.length
you can use following code to connect db:
sqlContext.read.jdbc(url=db_url,
table=tableName,
columnName="ID",
lowerBound=1L,
upperBound=100000L,
numPartitions=numPartitions,
connectionProperties=connectionProperties)
To optimize your spark job following are the parameters:
1. # of partitions
2. --num-executors
3.--executor-cores
4. --executor-memory
5. --driver-memory
6. fetch-size
2,3,4 and 5 options are depends on you cluster configurations
you can monitor your spark job on spark ui.
Sqoop and Spark SQL both use JDBC connectivity to fetch the data from RDBMS engines but Sqoop has an edge here since it is specifically made to migrate the data between RDBMS and HDFS.
Every single option available in Sqoop has been fine-tuned to get the best performance while doing the data ingestions.
You can start with discussing the option -m which control the number of mappers.
This is what you need to do to fetch data in parallel from RDBMS. Can I do it in Spark SQL?
Of course yes but the developer would need to take care of "multithreading" that Sqoop has been taking care automatically.
The below solution helped me
var df=spark.read.format("jdbc").option("url","
"url").option("user","user").option("password","password").option("dbTable","dbTable").option("fetchSize","10000").load()
df.registerTempTable("tempTable")
var dfRepart=spark.sql("select * from tempTable distribute by primary_key") //this will repartition the data evenly
dfRepart.write.format("parquet").save("hdfs_location")
Apache Sqoop is retired now - https://attic.apache.org/projects/sqoop.html
Using Apache Spark is a good option. This link shows how Spark can be used instead of Sqoop - https://medium.com/zaloni-engineering/apache-spark-vs-sqoop-engineering-a-better-data-pipeline-ef2bcb32b745
Else one can choose any cloud services like Azure Data Factory or Amazon Redshift etc.
I am using HBaseStorage with -caching option in pig script as follows
HBaseStorage('countDetails:ansCount countDetails:divCount countDetails:unansCount countDetails:engCount countDetails:ineffCount countDetails:totalCount', '-caching 1000');
I can see this was reflecting in my job.xml
but I can see there is no time difference in it I am processing 10 million records and store data around 160mb in to HBase.
When I store the result in hdfs its taking 3 mins to process the same job takes 30mins to store into HBase.
I even tried by setting
SET hbase.client.scanner.caching 1000;
Please let me know how can I reduce the time.
Is there any alternative for HBaseStorage?
http://apmblog.compuware.com/2013/02/19/speeding-up-a-pighbase-mapreduce-job-by-a-factor-of-15/
the above blog says that I have to set hbase.client.scanner.caching in bootstrap scrip
I don't know how to do that
will it be enough If I set it in Hbase-conf.
Please help me out of this
hbase.client.scanner.caching points to number of rows that will be fetched when calling next on a scanner if it is not served from (local, client) memory.
Higher caching values will enable faster scanners but will eat up more memory and some calls of next may take longer and longer time when the cache is empty. Do not set this value such that the time between invocations is greater than the scanner timeout;
i.e. hbase.regionserver.lease.period This property is 1 min by default. Clients must
report in within this period else they are considered dead.
In my experience HBase doesn't perform very well with Pig. It you don't have requirement for random look-up then use only HDFS otherwie HBase MR job would be better option. Also, In Hadoop MR job, you can connect to Hbase(This option gave me the best performance).