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Posted to user@spark.apache.org by Amit Behera <am...@gmail.com> on 2014/12/25 21:22:52 UTC
unable to do group by with 1st column
Hi Users,
I am reading a csv file and my data format is like :
key1,value1
key1,value2
key1,value1
key1,value3
key2,value1
key2,value5
key2,value5
key2,value4
key1,value4
key1,value4
key3,value1
key3,value1
key3,value2
required output :
key1:[value1,value2,value1,value3,value4,value4]
key2:[value1,value5,value5,value4]
key3:[value1,value1,value2]
How can I do it? Please help me to do.
Thanks
Amit
Re: unable to do group by with 1st column
Posted by Sean Owen <so...@cloudera.com>.
One value is at least 12 + 4 + 4 + 12 + 4 = 36 bytes if you factor in
object overhead, if my math is right. 60M of them is about 2.1GB for a
single key. I could imagine that blowing up an executor that's trying
to have one in memory and deserialize another. You won't want to use
groupByKey if the number of values is this big.
MapReduce doesn't quite operate this way. You would not have the
values in memory for a single key in general. That said, you don't
necessarily have to make Spark work this way either. There may be
other ways to do what you want that do not involve groupByKey but
rather reduceByKey or similar.
The error does not show a memory error per se, so it's not clear from
this why the executor is failing. If you search around you'll see
CancelledKeyException is a symptom of a couple things, some of which
are bugs that are recently fixed. Hard to know whether it matters but
you might use 1.2 to make sure.
You might also try the sort-based shuffle instead if you are doing
such a big shuffle?
On Sun, Dec 28, 2014 at 9:02 PM, Michael Albert <m_...@yahoo.com> wrote:
> Greetings!
>
> Thanks for the comment.
>
> I have tried several variants of this, as indicated.
>
> The code works on small sets, but fails on larger sets.
> However, I don't get memory errors.
> I see "java.nio.channels.CancelledKeyException" and things about "lost task"
> and then things like "Resubmitting state 1", and off it goes.
>
> I've already upped the memory (I think the last experiment had
> "--executor-memory 6G" and "--driver memory 6G".
>
> I'm experimenting with recoding this with map-reduce and so far seem to be
> having more success (with HADOOP_OPTS="-Xmx6g -Xmx5g")
>
> Again, each grouping should have no more than 6E7 values, and the data is
> (DataKey(Int,Int), Option[Float]), so that shouldn't need 5g?
>
> Anyway, thanks for the info.
>
> Best wishes,
> Mike
>
>
>
> ________________________________
> From: Sean Owen <so...@cloudera.com>
> To: Michael Albert <m_...@yahoo.com>
> Cc: user@spark.apache.org
> Sent: Friday, December 26, 2014 3:23 PM
> Subject: Re: unable to do group by with 1st column
>
> Here is a sketch of what you need to do off the top of my head and based on
> a guess of what your RDD is like:
> val in: RDD[(K,Seq[(C,V)])] = ...
> in.flatMap { case (key, colVals) =>
> colVals.map { case (col, val) =>
> (col, (key, val))
> }
> }.groupByKey
> So the problem with both input and output here is that all values for each
> key exist in memory at once. When transposed, each element contains 50M key
> value pairs.
> You probably should try to do what you're trying to do a slightly different
> way.
> Depends on what you mean by resubmitting but I imagine you need a cache() on
> an RDD you are reusing.
>
>
> On Dec 26, 2014 4:18 PM, "Michael Albert" <m_...@yahoo.com.invalid>
> wrote:
>
> Greetings!
>
> I'm trying to do something similar, and having a very bad time of it.
>
> What I start with is
>
> key1: (col1, val-1-1, col2: val-1-2, col3: val-1-3, col4: val-1-4...)
> key2: (col1: val-2-1, col2: val-2-2, col3: val-2-3, col4: val 2-4, ...)
> ....
>
> What I want (what I have been asked to produce :-)) is:
>
> col1: (key1: val-1-1, key2: val-2-1, key3, val-3-1, ...)
> col2: (key1: val-1-2, key2: val2-2, key3: val-3-2,...)
>
> So basically the transpose. The input is actually avro/parquet with each
> "key" in one record.
> In the output, the final step is to convert each column into a "matlab"
> file.
> Please don't ask me whether this is a good idea.
>
> I can get this to work for smallish data sets (e.g, a few hundred keys and a
> few hundred columns).
> However, if I crank up the number of keys to about 5e7, then this fails,
> even if I turn the number of columns that are actually used down to 10.
>
> The system seems to spend lots of time resubmitting parts of the first phase
> in which the data is read from the original records and shuffled and never
> quite finishes.
>
> I can't post the code, but I can give folks and idea of what I've tried.
>
> Try #1: Mapper emits data as (DataKey(col-as-int,key-as-int),
> value-as-Option[Any]),
> then create a ShuffledRDD using the col-as-int for partitioning and
> then "SetKeyOrdering" on the key-as-int. This is then fed to
> "mapPartitionWithIndex".
>
> Try #2: Emit (col-as-int, (key-as-int, value)) and groupBy, and have a final
> "map()" on each "col".
>
> Try #3: Emit (col-as-t, Collection[(key-as-int, value)]), then have a
> reduceByKey
> which takes the "union" of the collection (union for set, ++ for list) then
> have
> a final map() which attempts the final conversion.
>
> No matter what I do, it works for for "small" numbers of keys (hundreds),
> but
> when I crank it up, it seems to sit there resubmitting the shuffle phase.
>
> Happy holidays, all!
> -Mike
>
>
>
> ________________________________
> From: Amit Behera <am...@gmail.com>
> To: user@spark.incubator.apache.org
> Sent: Thursday, December 25, 2014 3:22 PM
> Subject: unable to do group by with 1st column
>
> Hi Users,
>
> I am reading a csv file and my data format is like :
>
> key1,value1
> key1,value2
> key1,value1
> key1,value3
> key2,value1
> key2,value5
> key2,value5
> key2,value4
> key1,value4
> key1,value4
> key3,value1
> key3,value1
> key3,value2
>
> required output :
>
> key1:[value1,value2,value1,value3,value4,value4]
> key2:[value1,value5,value5,value4]
> key3:[value1,value1,value2]
>
>
> How can I do it? Please help me to do.
>
> Thanks
> Amit
>
>
>
>
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Re: unable to do group by with 1st column
Posted by Michael Albert <m_...@yahoo.com.INVALID>.
Greetings!
Thanks for the comment.
I have tried several variants of this, as indicated.
The code works on small sets, but fails on larger sets.However, I don't get memory errors.I see "java.nio.channels.CancelledKeyException" and things about "lost task"and then things like "Resubmitting state 1", and off it goes.
I've already upped the memory (I think the last experiment had "--executor-memory 6G" and "--driver memory 6G".
I'm experimenting with recoding this with map-reduce and so far seem to be having more success (with HADOOP_OPTS="-Xmx6g -Xmx5g")
Again, each grouping should have no more than 6E7 values, and the data is (DataKey(Int,Int), Option[Float]), so that shouldn't need 5g?
Anyway, thanks for the info.
Best wishes,Mike
From: Sean Owen <so...@cloudera.com>
To: Michael Albert <m_...@yahoo.com>
Cc: user@spark.apache.org
Sent: Friday, December 26, 2014 3:23 PM
Subject: Re: unable to do group by with 1st column
Here is a sketch of what you need to do off the top of my head and based on a guess of what your RDD is like:val in: RDD[(K,Seq[(C,V)])] = ...in.flatMap { case (key, colVals) =>
colVals.map { case (col, val) =>
(col, (key, val))
}
}.groupByKeySo the problem with both input and output here is that all values for each key exist in memory at once. When transposed, each element contains 50M key value pairs. You probably should try to do what you're trying to do a slightly different way.Depends on what you mean by resubmitting but I imagine you need a cache() on an RDD you are reusing.
On Dec 26, 2014 4:18 PM, "Michael Albert" <m_...@yahoo.com.invalid> wrote:
Greetings!
I'm trying to do something similar, and having a very bad time of it.
What I start with is
key1: (col1, val-1-1, col2: val-1-2, col3: val-1-3, col4: val-1-4...)key2: (col1: val-2-1, col2: val-2-2, col3: val-2-3, col4: val 2-4, ...)....
What I want (what I have been asked to produce :-)) is:
col1: (key1: val-1-1, key2: val-2-1, key3, val-3-1, ...)col2: (key1: val-1-2, key2: val2-2, key3: val-3-2,...)
So basically the transpose. The input is actually avro/parquet with each "key" in one record. In the output, the final step is to convert each column into a "matlab" file.Please don't ask me whether this is a good idea.
I can get this to work for smallish data sets (e.g, a few hundred keys and a few hundred columns).However, if I crank up the number of keys to about 5e7, then this fails, even if I turn the number of columns that are actually used down to 10.
The system seems to spend lots of time resubmitting parts of the first phase in which the data is read from the original records and shuffled and never quite finishes.
I can't post the code, but I can give folks and idea of what I've tried.
Try #1: Mapper emits data as (DataKey(col-as-int,key-as-int), value-as-Option[Any]), then create a ShuffledRDD using the col-as-int for partitioning and then "SetKeyOrdering" on the key-as-int. This is then fed to "mapPartitionWithIndex".
Try #2: Emit (col-as-int, (key-as-int, value)) and groupBy, and have a final "map()" on each "col".
Try #3: Emit (col-as-t, Collection[(key-as-int, value)]), then have a reduceByKey which takes the "union" of the collection (union for set, ++ for list) then havea final map() which attempts the final conversion.
No matter what I do, it works for for "small" numbers of keys (hundreds), but when I crank it up, it seems to sit there resubmitting the shuffle phase.
Happy holidays, all!-Mike
From: Amit Behera <am...@gmail.com>
To: user@spark.incubator.apache.org
Sent: Thursday, December 25, 2014 3:22 PM
Subject: unable to do group by with 1st column
Hi Users,
I am reading a csv file and my data format is like :
key1,value1key1,value2
key1,value1
key1,value3
key2,value1
key2,value5
key2,value5
key2,value4key1,value4key1,value4
key3,value1
key3,value1
key3,value2
required output :
key1:[value1,value2,value1,value3,value4,value4]key2:[value1,value5,value5,value4]key3:[value1,value1,value2]
How can I do it? Please help me to do.
ThanksAmit
Re: unable to do group by with 1st column
Posted by Sean Owen <so...@cloudera.com>.
Here is a sketch of what you need to do off the top of my head and based on
a guess of what your RDD is like:
val in: RDD[(K,Seq[(C,V)])] = ...
in.flatMap { case (key, colVals) =>
colVals.map { case (col, val) =>
(col, (key, val))
}
}.groupByKey
So the problem with both input and output here is that all values for each
key exist in memory at once. When transposed, each element contains 50M key
value pairs.
You probably should try to do what you're trying to do a slightly different
way.
Depends on what you mean by resubmitting but I imagine you need a cache()
on an RDD you are reusing.
On Dec 26, 2014 4:18 PM, "Michael Albert" <m_...@yahoo.com.invalid>
wrote:
> Greetings!
>
> I'm trying to do something similar, and having a very bad time of it.
>
> What I start with is
>
> key1: (col1, val-1-1, col2: val-1-2, col3: val-1-3, col4: val-1-4...)
> key2: (col1: val-2-1, col2: val-2-2, col3: val-2-3, col4: val 2-4, ...)
> ....
>
> What I want (what I have been asked to produce :-)) is:
>
> col1: (key1: val-1-1, key2: val-2-1, key3, val-3-1, ...)
> col2: (key1: val-1-2, key2: val2-2, key3: val-3-2,...)
>
> So basically the transpose. The input is actually avro/parquet with each
> "key" in one record.
> In the output, the final step is to convert each column into a "matlab"
> file.
> Please don't ask me whether this is a good idea.
>
> I can get this to work for smallish data sets (e.g, a few hundred keys and
> a few hundred columns).
> However, if I crank up the number of keys to about 5e7, then this fails,
> even if I turn the number of columns that are actually used down to 10.
>
> The system seems to spend lots of time resubmitting parts of the first
> phase
> in which the data is read from the original records and shuffled and never
> quite finishes.
>
> I can't post the code, but I can give folks and idea of what I've tried.
>
> Try #1: Mapper emits data as (DataKey(col-as-int,key-as-int),
> value-as-Option[Any]),
> then create a ShuffledRDD using the col-as-int for partitioning and
> then "SetKeyOrdering" on the key-as-int. This is then fed to
> "mapPartitionWithIndex".
>
> Try #2: Emit (col-as-int, (key-as-int, value)) and groupBy, and have a
> final "map()" on each "col".
>
> Try #3: Emit (col-as-t, Collection[(key-as-int, value)]), then have a
> reduceByKey
> which takes the "union" of the collection (union for set, ++ for list)
> then have
> a final map() which attempts the final conversion.
>
> No matter what I do, it works for for "small" numbers of keys (hundreds),
> but
> when I crank it up, it seems to sit there resubmitting the shuffle phase.
>
> Happy holidays, all!
> -Mike
>
>
>
> ------------------------------
> *From:* Amit Behera <am...@gmail.com>
> *To:* user@spark.incubator.apache.org
> *Sent:* Thursday, December 25, 2014 3:22 PM
> *Subject:* unable to do group by with 1st column
>
> Hi Users,
>
> I am reading a csv file and my data format is like :
>
> key1,value1
> key1,value2
> key1,value1
> key1,value3
> key2,value1
> key2,value5
> key2,value5
> key2,value4
> key1,value4
> key1,value4
> key3,value1
> key3,value1
> key3,value2
>
> required output :
>
> key1:[value1,value2,value1,value3,value4,value4]
> key2:[value1,value5,value5,value4]
> key3:[value1,value1,value2]
>
>
> How can I do it? Please help me to do.
>
> Thanks
> Amit
>
>
>
Re: unable to do group by with 1st column
Posted by Michael Albert <m_...@yahoo.com.INVALID>.
Greetings!
I'm trying to do something similar, and having a very bad time of it.
What I start with is
key1: (col1, val-1-1, col2: val-1-2, col3: val-1-3, col4: val-1-4...)key2: (col1: val-2-1, col2: val-2-2, col3: val-2-3, col4: val 2-4, ...)....
What I want (what I have been asked to produce :-)) is:
col1: (key1: val-1-1, key2: val-2-1, key3, val-3-1, ...)col2: (key1: val-1-2, key2: val2-2, key3: val-3-2,...)
So basically the transpose. The input is actually avro/parquet with each "key" in one record. In the output, the final step is to convert each column into a "matlab" file.Please don't ask me whether this is a good idea.
I can get this to work for smallish data sets (e.g, a few hundred keys and a few hundred columns).However, if I crank up the number of keys to about 5e7, then this fails, even if I turn the number of columns that are actually used down to 10.
The system seems to spend lots of time resubmitting parts of the first phase in which the data is read from the original records and shuffled and never quite finishes.
I can't post the code, but I can give folks and idea of what I've tried.
Try #1: Mapper emits data as (DataKey(col-as-int,key-as-int), value-as-Option[Any]), then create a ShuffledRDD using the col-as-int for partitioning and then "SetKeyOrdering" on the key-as-int. This is then fed to "mapPartitionWithIndex".
Try #2: Emit (col-as-int, (key-as-int, value)) and groupBy, and have a final "map()" on each "col".
Try #3: Emit (col-as-t, Collection[(key-as-int, value)]), then have a reduceByKey which takes the "union" of the collection (union for set, ++ for list) then havea final map() which attempts the final conversion.
No matter what I do, it works for for "small" numbers of keys (hundreds), but when I crank it up, it seems to sit there resubmitting the shuffle phase.
Happy holidays, all!-Mike
From: Amit Behera <am...@gmail.com>
To: user@spark.incubator.apache.org
Sent: Thursday, December 25, 2014 3:22 PM
Subject: unable to do group by with 1st column
Hi Users,
I am reading a csv file and my data format is like :
key1,value1key1,value2
key1,value1
key1,value3
key2,value1
key2,value5
key2,value5
key2,value4key1,value4key1,value4
key3,value1
key3,value1
key3,value2
required output :
key1:[value1,value2,value1,value3,value4,value4]key2:[value1,value5,value5,value4]key3:[value1,value1,value2]
How can I do it? Please help me to do.
ThanksAmit
Re: unable to do group by with 1st column
Posted by Amit Behera <am...@gmail.com>.
Hi,
Thank you very much to all for your reply.
I am able to get it by groupByKey
Here is my code :
import au.com.bytecode.opencsv.CSVParser
val data = sc.textFile("/data/data.csv");
def pLines(lines:Iterator[String])={
val parser=new CSVParser()
lines.map(l=>{val vs=parser.parseLine(l)
(vs(0),vs(1).toInt)})
}
val result = data.mapPartitions(pLines).groupByKey.collect
Thanks
Amit
On Fri, Dec 26, 2014 at 2:18 PM, Sean Owen <so...@cloudera.com> wrote:
> This does not appear to be what the asker wanted as this makes one big
> string. groupByKey is correct after parsing to key value pairs.
> On Dec 26, 2014 3:55 AM, "Somnath Pandeya" <So...@infosys.com>
> wrote:
>
>> Hi ,
>>
>> You can try reducebyKey also ,
>>
>> Something like this
>>
>> JavaPairRDD<String, String> ones = lines
>>
>> .mapToPair(*new* *PairFunction<String,
>> String, String>()* {
>>
>> @Override
>>
>> *public* Tuple2<String, String>
>> call(String s) {
>>
>> String[] temp = s.split(",");
>>
>> *return* *new* Tuple2<String,
>> String>(temp[0], temp[1]);
>>
>> }
>>
>> });
>>
>>
>>
>> JavaPairRDD<String, String> *counts* = ones
>>
>> .reduceByKey(*new* *Function2<String, String,
>> String>()* {
>>
>> @Override
>>
>> *public* String call(String i1, String
>> i2) {
>>
>> *return* i1 + "," + i2;
>>
>> }
>>
>> });
>>
>>
>>
>> *From:* Tobias Pfeiffer [mailto:tgp@preferred.jp]
>> *Sent:* Friday, December 26, 2014 6:35 AM
>> *To:* Amit Behera
>> *Cc:* user@spark.incubator.apache.org
>> *Subject:* Re: unable to do group by with 1st column
>>
>>
>>
>> Hi,
>>
>>
>>
>> On Fri, Dec 26, 2014 at 5:22 AM, Amit Behera <am...@gmail.com>
>> wrote:
>>
>> How can I do it? Please help me to do.
>>
>>
>>
>> Have you considered using groupByKey?
>>
>> http://spark.apache.org/docs/latest/programming-guide.html#transformations
>>
>>
>>
>> Tobias
>>
>> **************** CAUTION - Disclaimer *****************
>> This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended solely
>> for the use of the addressee(s). If you are not the intended recipient, please
>> notify the sender by e-mail and delete the original message. Further, you are not
>> to copy, disclose, or distribute this e-mail or its contents to any other person and
>> any such actions are unlawful. This e-mail may contain viruses. Infosys has taken
>> every reasonable precaution to minimize this risk, but is not liable for any damage
>> you may sustain as a result of any virus in this e-mail. You should carry out your
>> own virus checks before opening the e-mail or attachment. Infosys reserves the
>> right to monitor and review the content of all messages sent to or from this e-mail
>> address. Messages sent to or from this e-mail address may be stored on the
>> Infosys e-mail system.
>> ***INFOSYS******** End of Disclaimer ********INFOSYS***
>>
>>
RE: unable to do group by with 1st column
Posted by Sean Owen <so...@cloudera.com>.
This does not appear to be what the asker wanted as this makes one big
string. groupByKey is correct after parsing to key value pairs.
On Dec 26, 2014 3:55 AM, "Somnath Pandeya" <So...@infosys.com>
wrote:
> Hi ,
>
> You can try reducebyKey also ,
>
> Something like this
>
> JavaPairRDD<String, String> ones = lines
>
> .mapToPair(*new* *PairFunction<String, String,
> String>()* {
>
> @Override
>
> *public* Tuple2<String, String>
> call(String s) {
>
> String[] temp = s.split(",");
>
> *return* *new* Tuple2<String,
> String>(temp[0], temp[1]);
>
> }
>
> });
>
>
>
> JavaPairRDD<String, String> *counts* = ones
>
> .reduceByKey(*new* *Function2<String, String,
> String>()* {
>
> @Override
>
> *public* String call(String i1, String
> i2) {
>
> *return* i1 + "," + i2;
>
> }
>
> });
>
>
>
> *From:* Tobias Pfeiffer [mailto:tgp@preferred.jp]
> *Sent:* Friday, December 26, 2014 6:35 AM
> *To:* Amit Behera
> *Cc:* user@spark.incubator.apache.org
> *Subject:* Re: unable to do group by with 1st column
>
>
>
> Hi,
>
>
>
> On Fri, Dec 26, 2014 at 5:22 AM, Amit Behera <am...@gmail.com> wrote:
>
> How can I do it? Please help me to do.
>
>
>
> Have you considered using groupByKey?
>
> http://spark.apache.org/docs/latest/programming-guide.html#transformations
>
>
>
> Tobias
>
> **************** CAUTION - Disclaimer *****************
> This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended solely
> for the use of the addressee(s). If you are not the intended recipient, please
> notify the sender by e-mail and delete the original message. Further, you are not
> to copy, disclose, or distribute this e-mail or its contents to any other person and
> any such actions are unlawful. This e-mail may contain viruses. Infosys has taken
> every reasonable precaution to minimize this risk, but is not liable for any damage
> you may sustain as a result of any virus in this e-mail. You should carry out your
> own virus checks before opening the e-mail or attachment. Infosys reserves the
> right to monitor and review the content of all messages sent to or from this e-mail
> address. Messages sent to or from this e-mail address may be stored on the
> Infosys e-mail system.
> ***INFOSYS******** End of Disclaimer ********INFOSYS***
>
>
RE: unable to do group by with 1st column
Posted by Somnath Pandeya <So...@infosys.com>.
Hi ,
You can try reducebyKey also ,
Something like this
JavaPairRDD<String, String> ones = lines
.mapToPair(new PairFunction<String, String, String>() {
@Override
public Tuple2<String, String> call(String s) {
String[] temp = s.split(",");
return new Tuple2<String, String>(temp[0], temp[1]);
}
});
JavaPairRDD<String, String> counts = ones
.reduceByKey(new Function2<String, String, String>() {
@Override
public String call(String i1, String i2) {
return i1 + "," + i2;
}
});
From: Tobias Pfeiffer [mailto:tgp@preferred.jp]
Sent: Friday, December 26, 2014 6:35 AM
To: Amit Behera
Cc: user@spark.incubator.apache.org
Subject: Re: unable to do group by with 1st column
Hi,
On Fri, Dec 26, 2014 at 5:22 AM, Amit Behera <am...@gmail.com>> wrote:
How can I do it? Please help me to do.
Have you considered using groupByKey?
http://spark.apache.org/docs/latest/programming-guide.html#transformations
Tobias
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Re: unable to do group by with 1st column
Posted by Tobias Pfeiffer <tg...@preferred.jp>.
Hi,
On Fri, Dec 26, 2014 at 5:22 AM, Amit Behera <am...@gmail.com> wrote:
>
> How can I do it? Please help me to do.
>
Have you considered using groupByKey?
http://spark.apache.org/docs/latest/programming-guide.html#transformations
Tobias