we had some old code using org.apache.parquet.hadoop.api.WriteSupport API to write Parquet formatted file, and we start to use Apache Spark to do the same thing.
Those two ways can successfully generate Parquet files with same input data, and the output data are almost identical. However, the output file size is quite different.
The one generated by WriteSupport is 2G-ish, whereas the one generated by Spark is 5.5G-ish. I compared the schema, they are same, is there any area I can further look into?
Btw, the WriteSupport has parquet-mr version 1.8.0; Spark one has 1.10.0.
Related
I'm using Apache Nifi 1.9.2 to load data from a relational database into Google Cloud Storage. The purpose is to write the outcome into Parquet files as it stores data in columnar way. To achieve this I make use of the ConvertAvroToParquet (default settings) processor in Nifi (followed by the PutGCSObject processor). The problem with these resulting files is that I cannot read Decimal typed columns when consuming the files in Spark 2.4.0 (scala 2.11.12): Parquet column cannot be converted ... Column: [ARHG3A], Expected: decimal(2,0), Found: BINARY
Links to parquet/avro example files:
https://drive.google.com/file/d/1PmaP1qanIZjKTAOnNehw3XKD6-JuDiwC/view?usp=sharing
https://drive.google.com/file/d/138BEZROzHKwmSo_Y-SNPMLNp0rj9ci7q/view?usp=sharing
As I know that Nifi works with the Avro format in between processors within the flowfile, I have also written the avro file (like it is just before the ConvertAvroToParquet processor) and this I can read in Spark.
It is also possible to not use logical types in Avro, but then I lose the column types in the end and all columns are Strings (not preferred).
I have also experimented with the PutParquet processor without success.
val arhg_parquet = spark.read.format("parquet").load("ARHG.parquet")
arhg_parquet.printSchema()
arhg_parquet.show(10,false)
printSchema() gives proper result, indicating ARHG3A is a decimal(2,0)
Executing the show(10,false) results in an ERROR: Parquet column cannot be converted in file file:///C:/ARHG.parquet. Column: [ARHG3A], Expected: decimal(2,0), Found: BINARY
To achieve this I make use of the ConvertAvroToParquet (default settings) processor in Nifi (followed by the PutGCSObject processor)
Try upgrading to NiFi 1.12.1, our latest release. Some improvements were made to handling decimals that might be applicable here. Also, you can use the Parquet reader and writer services to convert from Avro to Parquet now as of ~1.10.0. If that doesn't work, it may be a bug that should have a Jira ticket filed against it.
I have a job that reads csv files , converts it into data frames and writes in Parquet. I am using append mode while writing the data in Parquet. With this approach, in each write a separate Parquet file is getting generated. My questions are :
1) If every time I write the data to Parquet schema ,a new file gets
appended , will it impact read performance (as the data is now
distributed in varying length of partitioned Parquet files)
2) Is there a way to generate the Parquet partitions purely based on
the size of the data ?
3) Do we need to think to a custom partitioning strategy to implement
point 2?
I am using Spark 2.3
It will affect read performance if
spark.sql.parquet.mergeSchema=true.
In this case, Spark needs to visit each file and grab schema from
it.
In other cases, I believe it does not affect read performance much.
There is no way generate purely on data size. You may use
repartition or coalesce. Latter will created uneven output
files, but much performant.
Also, you have config spark.sql.files.maxRecordsPerFile or option
maxRecordsPerFile to prevent big size of files, but usually it is
not an issue.
Yes, I think Spark has not built in API to evenly distribute by data
size. There are Column
Statistics
and Size
Estimator may help with this.
I have a pipe delimited text file that is 360GB, compressed (gzip). The file is in an S3 bucket.
This is my first time using Spark. I understand that you can partition a file in order to allow multiple worker nodes to operate on the data which results in huge performance gains. However, I'm trying to find an efficient way to turn my one 360GB file into a partitioned file. Is there a way to use multiple spark worker nodes to work on my one, compressed file in order to partition it? Unfortunately, I have no control over the fact that I'm just getting one huge file. I could uncompress the file myself and break it into many files (say 360 1GB files), but I'll just be using one machine to do that and it will be pretty slow. I need to run some expensive transformations on the data using Spark so I think partitioning the file is necessary. I'm using Spark inside of Amazon Glue so I know that it can scale to a large number of machines. Also, I'm using python (pyspark).
Thanks.
If i'm not mistaken, Spark uses Hadoop's TextInputFormat if you read a file using SparkContext.textFile. If a compression codec is set, the TextInputFormat determines if the file is splittable by checking if the code is an instance of SplittableCompressionCodec.
I believe GZIP is not splittable, Spark can only generate one partition to read the entire file.
What you could do is:
1. Add a repartition after SparkContext.textFile so you at least have more than one of your transformations process parts of the data.
2. Ask for multiple files instead of just a single GZIP file
3. Write an application that decompresses and splits the files into multiple output files before running your Spark application on it.
4. Write your own compression codec for GZIP (this is a little more complex).
Have a look at these links:
TextInputFormat
source code for TextInputFormat
GzipCodec
source code for GZIPCodec
These are in java, but i'm sure there are equivalent Python/Scala versions of them.
First I suggest you have to used ORC format with zlib compression so you get almost 70% compression and as per my research ORC is the most suitable file format for fastest data processing. So you have to load your file and simply write it into orc format with repartition.
df.repartition(500).write.option("compression","zlib").mode("overwrite").save("testoutput.parquet")
One potential solution could be to use Amazon's S3DistCp as a step on your EMR cluster to copy the 360GB file in the HDFS file system available on the cluster (this requires Hadoop to be deployed on the EMR).
A nice thing about S3DistCp is that you can change the codec of the output file, and transform the original gzip file into a format which will allow Spark to spawn multiple partitions for its RDD.
However I am not sure about how long it will take for S3DistCp to perform the operation (which is an Hadoop Map/Reduce over S3. It benefits from optimised S3 libraries when run from an EMR, but I am concerned that Hadoop will face the same limitations as Spark when generating the Map tasks).
I have a spark-submit job I wrote that reads an in directory of json docs, does some processing on them using data frames, and then writes to an out directory. For some reason, though, it creates individual avro, parquet or json files when I use df.save or df.write methods.
In fact, I even used the saveAsTable method and it did the same thing with parquet.gz files in the hive warehouse.
It seems to me that this is inefficient and negates the use of a container file format. Is this right? Or is this normal behavior and what I'm seeing just an abstraction in HDFS?
If I am right that this is bad, how do I write the data frame from many files into a single file?
As #zero323 told its normal behavior due to many workers(to support fault tolerance).
I would suggest you to write all the records in parquet or avro file which has avro generic record using something like this
dataframe.write().mode(SaveMode.Append).
format(FILE_FORMAT).partitionBy("parameter1", "parameter2").save(path);
but it wont write in to single file but it will group similar kind of Avro Generic records to one file(may be less number of medium sized) files
I'm coming from a Hadoop background, in hadoop if we have an input directory that contains lots of small files, each mapper task picks one file each time and operate on a single file (we can change this behaviour and have each mapper picks more than one file but that's not the default behaviour). I wonder to know how that works in Spark? Does each spark task picks files one by one or..?
Spark behaves the same way as Hadoop working with HDFS, as in fact Spark uses the same Hadoop InputFormats to read the data from HDFS.
But your statement is wrong. Hadoop will take files one by one only if each of your files is smaller than a block size or if all the files are text and compressed with non-splittable compression (like gzip-compressed CSV files).
So Spark would do the same, for each of the small input files it would create a separate "partition" and the first stage executed over your data would have the same amount of tasks as the amount of input files. This is why for small files it is recommended to use wholeTextFiles function as it would create much less partitions