RE: Spark will process _temporary folder on S3 is very slow and always cause failure
And one thing forget to mention, even I have this exception and the result
is not well format in my target folder (part of them are there, rest are
under different folder structure of _tempoary folder). In the webUI of
spark-shell, it is still be marked as successful step. I think this is a
bug?
Regards,
Shuai
From: Shuai Zheng [mailto:szheng.c...@gmail.com]
Sent: Friday, March 13, 2015 6:51 PM
To: user@spark.apache.org
Subject: Spark will process _temporary folder on S3 is very slow and always
cause failure
Hi All,
I try to run a sorting on a r3.2xlarge instance on AWS. I just try to run it
as a single node cluster for test. The data I use to sort is around 4GB and
sit on S3, output will also on S3.
I just connect spark-shell to the local cluster and run the code in the
script (because I just want a benchmark now).
My job is as simple as:
val parquetFile =
sqlContext.parquetFile("s3n://...,s3n://...,s3n://...,s3n://...,s3n://...,s3
n://...,s3n://...,")
parquetFile.registerTempTable("Test")
val sortedResult = sqlContext.sql("SELECT * FROM Test order by time").map {
row => { row.mkString("\t") } }
sortedResult.saveAsTextFile("s3n://myplace,");
The job takes around 6 mins to finish the sort when I am monitoring the
process. After I notice the process stop at:
15/03/13 22:38:27 INFO DAGScheduler: Job 2 finished: saveAsTextFile at
:31, took 581.304992 s
At that time, the spark actually just write all the data to the _temporary
folder first, after all sub-tasks finished, it will try to move all the
ready result from _temporary folder to the final location. This process
might be quick locally (because it will just be a cut/paste), but it looks
like very slow on my S3, it takes a few second to move one file (usually
there will be 200 partitions). And then it raise exceptions after it move
might be 40-50 files.
org.apache.http.NoHttpResponseException: The target server failed to respond
at
org.apache.http.impl.conn.DefaultResponseParser.parseHead(DefaultResponsePar
ser.java:101)
at
org.apache.http.impl.io.AbstractMessageParser.parse(AbstractMessageParser.ja
va:252)
at
org.apache.http.impl.AbstractHttpClientConnection.receiveResponseHeader(Abst
ractHttpClientConnection.java:281)
at
org.apache.http.impl.conn.DefaultClientConnection.receiveResponseHeader(Defa
ultClientConnection.java:247)
at
org.apache.http.impl.conn.AbstractClientConnAdapter.receiveResponseHeader(Ab
stractClientConnAdapter.java:219)
I try several times, but never get the full job finished. I am not sure
anything wrong here, but I use something very basic and I can see the job
has finished and all result on the S3 under temporary folder, but then it
raise the exception and fail.
Any special setting I should do here when deal with S3?
I don't know what is the issue here, I never see MapReduce has similar
issue. So it could not be S3's problem.
Regards,
Shuai
Re: Spark will process _temporary folder on S3 is very slow and always cause failure
If you use fileStream, there's an option to filter out files. In your case
you can easily create a filter to remove _temporary files. In that case,
you will have to move your codes inside foreachRDD of the dstream since the
application will become a streaming app.
Thanks
Best Regards
On Sat, Mar 14, 2015 at 4:26 AM, Shuai Zheng wrote:
> And one thing forget to mention, even I have this exception and the result
> is not well format in my target folder (part of them are there, rest are
> under different folder structure of _tempoary folder). In the webUI of
> spark-shell, it is still be marked as successful step. I think this is a
> bug?
>
>
>
> Regards,
>
>
>
> Shuai
>
>
>
> *From:* Shuai Zheng [mailto:szheng.c...@gmail.com]
> *Sent:* Friday, March 13, 2015 6:51 PM
> *To:* user@spark.apache.org
> *Subject:* Spark will process _temporary folder on S3 is very slow and
> always cause failure
>
>
>
> Hi All,
>
>
>
> I try to run a sorting on a r3.2xlarge instance on AWS. I just try to run
> it as a single node cluster for test. The data I use to sort is around 4GB
> and sit on S3, output will also on S3.
>
>
>
> I just connect spark-shell to the local cluster and run the code in the
> script (because I just want a benchmark now).
>
>
>
> My job is as simple as:
>
> val parquetFile =
> sqlContext.parquetFile("s3n://...,s3n://...,s3n://...,s3n://...,s3n://...,s3n://...,s3n://...,")
>
> parquetFile.registerTempTable("Test")
>
> val sortedResult = sqlContext.sql("SELECT * FROM Test order by time").map
> { row => { row.mkString("\t") } }
>
> sortedResult.saveAsTextFile("s3n://myplace,");
>
>
>
> The job takes around 6 mins to finish the sort when I am monitoring the
> process. After I notice the process stop at:
>
>
>
> 15/03/13 22:38:27 INFO DAGScheduler: Job 2 finished: saveAsTextFile at
> :31, took 581.304992 s
>
>
>
> At that time, the spark actually just write all the data to the _temporary
> folder first, after all sub-tasks finished, it will try to move all the
> ready result from _temporary folder to the final location. This process
> might be quick locally (because it will just be a cut/paste), but it looks
> like very slow on my S3, it takes a few second to move one file (usually
> there will be 200 partitions). And then it raise exceptions after it move
> might be 40-50 files.
>
>
>
> org.apache.http.NoHttpResponseException: The target server failed to
> respond
>
> at
> org.apache.http.impl.conn.DefaultResponseParser.parseHead(DefaultResponseParser.java:101)
>
> at
> org.apache.http.impl.io.AbstractMessageParser.parse(AbstractMessageParser.java:252)
>
> at
> org.apache.http.impl.AbstractHttpClientConnection.receiveResponseHeader(AbstractHttpClientConnection.java:281)
>
> at
> org.apache.http.impl.conn.DefaultClientConnection.receiveResponseHeader(DefaultClientConnection.java:247)
>
> at
> org.apache.http.impl.conn.AbstractClientConnAdapter.receiveResponseHeader(AbstractClientConnAdapter.java:219)
>
>
>
>
>
> I try several times, but never get the full job finished. I am not sure
> anything wrong here, but I use something very basic and I can see the job
> has finished and all result on the S3 under temporary folder, but then it
> raise the exception and fail.
>
>
>
> Any special setting I should do here when deal with S3?
>
>
>
> I don’t know what is the issue here, I never see MapReduce has similar
> issue. So it could not be S3’s problem.
>
>
>
> Regards,
>
>
>
> Shuai
>
Re: Spark will process _temporary folder on S3 is very slow and always cause failure
I'm not super familiar w/ S3, but I think the issue is that you want to use
a different output committers with "object" stores, that don't have a
simple move operation. There have been a few other threads on S3 &
outputcommitters. I think the most relevant for you is most probably this
open JIRA:
https://issues.apache.org/jira/browse/SPARK-6352
On Fri, Mar 13, 2015 at 5:51 PM, Shuai Zheng wrote:
> Hi All,
>
>
>
> I try to run a sorting on a r3.2xlarge instance on AWS. I just try to run
> it as a single node cluster for test. The data I use to sort is around 4GB
> and sit on S3, output will also on S3.
>
>
>
> I just connect spark-shell to the local cluster and run the code in the
> script (because I just want a benchmark now).
>
>
>
> My job is as simple as:
>
> val parquetFile =
> sqlContext.parquetFile("s3n://...,s3n://...,s3n://...,s3n://...,s3n://...,s3n://...,s3n://...,")
>
> parquetFile.registerTempTable("Test")
>
> val sortedResult = sqlContext.sql("SELECT * FROM Test order by time").map
> { row => { row.mkString("\t") } }
>
> sortedResult.saveAsTextFile("s3n://myplace,");
>
>
>
> The job takes around 6 mins to finish the sort when I am monitoring the
> process. After I notice the process stop at:
>
>
>
> 15/03/13 22:38:27 INFO DAGScheduler: Job 2 finished: saveAsTextFile at
> :31, took 581.304992 s
>
>
>
> At that time, the spark actually just write all the data to the _temporary
> folder first, after all sub-tasks finished, it will try to move all the
> ready result from _temporary folder to the final location. This process
> might be quick locally (because it will just be a cut/paste), but it looks
> like very slow on my S3, it takes a few second to move one file (usually
> there will be 200 partitions). And then it raise exceptions after it move
> might be 40-50 files.
>
>
>
> org.apache.http.NoHttpResponseException: The target server failed to
> respond
>
> at
> org.apache.http.impl.conn.DefaultResponseParser.parseHead(DefaultResponseParser.java:101)
>
> at
> org.apache.http.impl.io.AbstractMessageParser.parse(AbstractMessageParser.java:252)
>
> at
> org.apache.http.impl.AbstractHttpClientConnection.receiveResponseHeader(AbstractHttpClientConnection.java:281)
>
> at
> org.apache.http.impl.conn.DefaultClientConnection.receiveResponseHeader(DefaultClientConnection.java:247)
>
> at
> org.apache.http.impl.conn.AbstractClientConnAdapter.receiveResponseHeader(AbstractClientConnAdapter.java:219)
>
>
>
>
>
> I try several times, but never get the full job finished. I am not sure
> anything wrong here, but I use something very basic and I can see the job
> has finished and all result on the S3 under temporary folder, but then it
> raise the exception and fail.
>
>
>
> Any special setting I should do here when deal with S3?
>
>
>
> I don’t know what is the issue here, I never see MapReduce has similar
> issue. So it could not be S3’s problem.
>
>
>
> Regards,
>
>
>
> Shuai
>
Re: Spark will process _temporary folder on S3 is very slow and always cause failure
Actually, this is the more relevant JIRA (which is resolved):
https://issues.apache.org/jira/browse/SPARK-3595
6352 is about saveAsParquetFile, which is not in use here.
Here is a DirectOutputCommitter implementation:
https://gist.github.com/aarondav/c513916e72101bbe14ec
and it can be configured in Spark with:
sparkConf.set("spark.hadoop.mapred.output.committer.class",
classOf[DirectOutputCommitter].getName)
On Tue, Mar 17, 2015 at 8:05 AM, Imran Rashid wrote:
> I'm not super familiar w/ S3, but I think the issue is that you want to
> use a different output committers with "object" stores, that don't have a
> simple move operation. There have been a few other threads on S3 &
> outputcommitters. I think the most relevant for you is most probably this
> open JIRA:
>
> https://issues.apache.org/jira/browse/SPARK-6352
>
> On Fri, Mar 13, 2015 at 5:51 PM, Shuai Zheng
> wrote:
>
>> Hi All,
>>
>>
>>
>> I try to run a sorting on a r3.2xlarge instance on AWS. I just try to run
>> it as a single node cluster for test. The data I use to sort is around 4GB
>> and sit on S3, output will also on S3.
>>
>>
>>
>> I just connect spark-shell to the local cluster and run the code in the
>> script (because I just want a benchmark now).
>>
>>
>>
>> My job is as simple as:
>>
>> val parquetFile =
>> sqlContext.parquetFile("s3n://...,s3n://...,s3n://...,s3n://...,s3n://...,s3n://...,s3n://...,")
>>
>> parquetFile.registerTempTable("Test")
>>
>> val sortedResult = sqlContext.sql("SELECT * FROM Test order by time").map
>> { row => { row.mkString("\t") } }
>>
>> sortedResult.saveAsTextFile("s3n://myplace,");
>>
>>
>>
>> The job takes around 6 mins to finish the sort when I am monitoring the
>> process. After I notice the process stop at:
>>
>>
>>
>> 15/03/13 22:38:27 INFO DAGScheduler: Job 2 finished: saveAsTextFile at
>> :31, took 581.304992 s
>>
>>
>>
>> At that time, the spark actually just write all the data to the
>> _temporary folder first, after all sub-tasks finished, it will try to move
>> all the ready result from _temporary folder to the final location. This
>> process might be quick locally (because it will just be a cut/paste), but
>> it looks like very slow on my S3, it takes a few second to move one file
>> (usually there will be 200 partitions). And then it raise exceptions after
>> it move might be 40-50 files.
>>
>>
>>
>> org.apache.http.NoHttpResponseException: The target server failed to
>> respond
>>
>> at
>> org.apache.http.impl.conn.DefaultResponseParser.parseHead(DefaultResponseParser.java:101)
>>
>> at
>> org.apache.http.impl.io.AbstractMessageParser.parse(AbstractMessageParser.java:252)
>>
>> at
>> org.apache.http.impl.AbstractHttpClientConnection.receiveResponseHeader(AbstractHttpClientConnection.java:281)
>>
>> at
>> org.apache.http.impl.conn.DefaultClientConnection.receiveResponseHeader(DefaultClientConnection.java:247)
>>
>> at
>> org.apache.http.impl.conn.AbstractClientConnAdapter.receiveResponseHeader(AbstractClientConnAdapter.java:219)
>>
>>
>>
>>
>>
>> I try several times, but never get the full job finished. I am not sure
>> anything wrong here, but I use something very basic and I can see the job
>> has finished and all result on the S3 under temporary folder, but then it
>> raise the exception and fail.
>>
>>
>>
>> Any special setting I should do here when deal with S3?
>>
>>
>>
>> I don’t know what is the issue here, I never see MapReduce has similar
>> issue. So it could not be S3’s problem.
>>
>>
>>
>> Regards,
>>
>>
>>
>> Shuai
>>
>
>
RE: Spark will process _temporary folder on S3 is very slow and always cause failure
Thanks!
Let me update the status.
I have copied the DirectOutputCommitter to my local. And set:
Conf.set("spark.hadoop.mapred.output.committer.class",
"org..DirectOutputCommitter")
It works perfectly.
Thanks everyone J
Regards,
Shuai
From: Aaron Davidson [mailto:ilike...@gmail.com]
Sent: Tuesday, March 17, 2015 3:06 PM
To: Imran Rashid
Cc: Shuai Zheng; user@spark.apache.org
Subject: Re: Spark will process _temporary folder on S3 is very slow and always
cause failure
Actually, this is the more relevant JIRA (which is resolved):
https://issues.apache.org/jira/browse/SPARK-3595
6352 is about saveAsParquetFile, which is not in use here.
Here is a DirectOutputCommitter implementation:
https://gist.github.com/aarondav/c513916e72101bbe14ec
and it can be configured in Spark with:
sparkConf.set("spark.hadoop.mapred.output.committer.class",
classOf[DirectOutputCommitter].getName)
On Tue, Mar 17, 2015 at 8:05 AM, Imran Rashid wrote:
I'm not super familiar w/ S3, but I think the issue is that you want to use a
different output committers with "object" stores, that don't have a simple move
operation. There have been a few other threads on S3 & outputcommitters. I
think the most relevant for you is most probably this open JIRA:
https://issues.apache.org/jira/browse/SPARK-6352
On Fri, Mar 13, 2015 at 5:51 PM, Shuai Zheng wrote:
Hi All,
I try to run a sorting on a r3.2xlarge instance on AWS. I just try to run it as
a single node cluster for test. The data I use to sort is around 4GB and sit on
S3, output will also on S3.
I just connect spark-shell to the local cluster and run the code in the script
(because I just want a benchmark now).
My job is as simple as:
val parquetFile =
sqlContext.parquetFile("s3n://...,s3n://...,s3n://...,s3n://...,s3n://...,s3n://...,s3n://...,")
parquetFile.registerTempTable("Test")
val sortedResult = sqlContext.sql("SELECT * FROM Test order by time").map { row
=> { row.mkString("\t") } }
sortedResult.saveAsTextFile("s3n://myplace,");
The job takes around 6 mins to finish the sort when I am monitoring the
process. After I notice the process stop at:
15/03/13 22:38:27 INFO DAGScheduler: Job 2 finished: saveAsTextFile at
:31, took 581.304992 s
At that time, the spark actually just write all the data to the _temporary
folder first, after all sub-tasks finished, it will try to move all the ready
result from _temporary folder to the final location. This process might be
quick locally (because it will just be a cut/paste), but it looks like very
slow on my S3, it takes a few second to move one file (usually there will be
200 partitions). And then it raise exceptions after it move might be 40-50
files.
org.apache.http.NoHttpResponseException: The target server failed to respond
at
org.apache.http.impl.conn.DefaultResponseParser.parseHead(DefaultResponseParser.java:101)
at
org.apache.http.impl.io.AbstractMessageParser.parse(AbstractMessageParser.java:252)
at
org.apache.http.impl.AbstractHttpClientConnection.receiveResponseHeader(AbstractHttpClientConnection.java:281)
at
org.apache.http.impl.conn.DefaultClientConnection.receiveResponseHeader(DefaultClientConnection.java:247)
at
org.apache.http.impl.conn.AbstractClientConnAdapter.receiveResponseHeader(AbstractClientConnAdapter.java:219)
I try several times, but never get the full job finished. I am not sure
anything wrong here, but I use something very basic and I can see the job has
finished and all result on the S3 under temporary folder, but then it raise the
exception and fail.
Any special setting I should do here when deal with S3?
I don’t know what is the issue here, I never see MapReduce has similar issue.
So it could not be S3’s problem.
Regards,
Shuai
