Re: Job config before read fields
Hi Shahab, Sorry about the late reply, a personal matter came up and it took most of my time. Thank you for your replies. The solution I chose was to temporarily transfer the metadata along with the data and then restore it on the reduce nodes. This works from a functional perspective as long as there are no performance requirements and it will have to do for now. The permanent solution will likely involve tweaking hadoop, but that is a different kettle of fish. On Sun, Sep 1, 2013 at 12:48 AM, Shahab Yunus shahab.yu...@gmail.comwrote: Personally, I don't know a way to access job configuration parameters in custom implementation of Writables ( at least not an elegant and appropriate one. Of course hacks of various kinds be done.) Maybe experts can chime in? One idea that I thought about was to use MapWritable (if you have not explored it already.) You can encode the 'custom metadata' for you 'data' as one byte symbols and move your data in the M/R flow as a map. Then while deserialization you will have the type (or your 'custom metadata') in the key part of the map and the value would be you actual data. This aligns with the efficient approach that is used natively in Hadoop for Strings/Text i.e. compact metadata (though I agree that you are not taking advantage of the other aspect of non-dependence between metadata and the data it defines.) Take a look at that: Page 96 of the Definitive Guide: http://books.google.com/books?id=Nff49D7vnJcCpg=PA96lpg=PA96dq=mapwritable+in+hadoopsource=blots=IiixYu7vXusig=4V6H7cY-MrNT7Rzs3WlODsDOoP4hl=ensa=Xei=aX4iUp2YGoaosASs_YCACQsqi=2ved=0CFUQ6AEwBA#v=onepageq=mapwritable%20in%20hadoopf=false and then this: http://www.chrisstucchio.com/blog/2011/mapwritable_sometimes_a_performance_hog.html and add your own custom types here (note that you are restricted by size of byte): http://hadoop.sourcearchive.com/documentation/0.20.2plus-pdfsg1-1/AbstractMapWritable_8java-source.html Regards, Shahab On Sat, Aug 31, 2013 at 5:38 AM, Adrian CAPDEFIER chivas314...@gmail.comwrote: Thank you for your help Shahab. I guess I wasn't being too clear. My logic is that I use a custom type as key and in order to deserialize it on the compute nodes, I need an extra piece of information (also a custom type). To use an analogy, a Text is serialized by writing the length of the string as a number and then the bytes that compose the actual string. When it is deserialized, the number informs the reader when to stop reading the string. This number is varies from string to string and it is compact so it makes sense to serialize it with the string. My use case is similar to it. I have a complex type (let's call this data), and in order to deserialize it, I need another complex type (let's call this second type metadata). The metadata is not closely tied to the data (i.e. if the data value changes, the metadata does not) and the metadata size is quite large. I ruled out a couple of options, but please let me know if you think I did so for the wrong reasons: 1. I could serialize each data value with it's own metadata value, but since the data value count is in the +tens of millions and the metadata value distinct count can be up to one hundred, it would waste resources in the system. 2. I could serialize the metadata and then the data as a collection property of the metadata. This would be an elegant solution code-wise, but then all the data would have to be read and kept in memory as a massive object before any reduce operations can happen. I wasn't able to find any info on this online so this is just a guess from peeking at the hadoop code. My solution was to serialize the data with a hash of the metadata and separately serialize the metadata and its hash in the job configuration (as key/value pairs). For this to work, I would need to be able to deserialize the metadata on the reduce node before the data is deserialized in the readFields() method. I think that for that to happen I need to hook into the code somewhere where a context or job configuration is used (before readFields()), but I'm stumped as to where that is. Cheers, Adi On Sat, Aug 31, 2013 at 3:42 AM, Shahab Yunus shahab.yu...@gmail.comwrote: What I meant was that you might have to split or redesign your logic or your usecase (which we don't know about)? Regards, Shahab On Fri, Aug 30, 2013 at 10:31 PM, Adrian CAPDEFIER chivas314...@gmail.com wrote: But how would the comparator have access to the job config? On Sat, Aug 31, 2013 at 2:38 AM, Shahab Yunus shahab.yu...@gmail.comwrote: I think you have to override/extend the Comparator to achieve that, something like what is done in Secondary Sort? Regards, Shahab On Fri, Aug 30, 2013 at 9:01 PM, Adrian CAPDEFIER chivas314...@gmail.com wrote: Howdy, I apologise for the lack of code in this message, but the code is fairly convoluted and it would obscure my problem. That
Re: Job config before read fields
Thank you for your help Shahab. I guess I wasn't being too clear. My logic is that I use a custom type as key and in order to deserialize it on the compute nodes, I need an extra piece of information (also a custom type). To use an analogy, a Text is serialized by writing the length of the string as a number and then the bytes that compose the actual string. When it is deserialized, the number informs the reader when to stop reading the string. This number is varies from string to string and it is compact so it makes sense to serialize it with the string. My use case is similar to it. I have a complex type (let's call this data), and in order to deserialize it, I need another complex type (let's call this second type metadata). The metadata is not closely tied to the data (i.e. if the data value changes, the metadata does not) and the metadata size is quite large. I ruled out a couple of options, but please let me know if you think I did so for the wrong reasons: 1. I could serialize each data value with it's own metadata value, but since the data value count is in the +tens of millions and the metadata value distinct count can be up to one hundred, it would waste resources in the system. 2. I could serialize the metadata and then the data as a collection property of the metadata. This would be an elegant solution code-wise, but then all the data would have to be read and kept in memory as a massive object before any reduce operations can happen. I wasn't able to find any info on this online so this is just a guess from peeking at the hadoop code. My solution was to serialize the data with a hash of the metadata and separately serialize the metadata and its hash in the job configuration (as key/value pairs). For this to work, I would need to be able to deserialize the metadata on the reduce node before the data is deserialized in the readFields() method. I think that for that to happen I need to hook into the code somewhere where a context or job configuration is used (before readFields()), but I'm stumped as to where that is. Cheers, Adi On Sat, Aug 31, 2013 at 3:42 AM, Shahab Yunus shahab.yu...@gmail.comwrote: What I meant was that you might have to split or redesign your logic or your usecase (which we don't know about)? Regards, Shahab On Fri, Aug 30, 2013 at 10:31 PM, Adrian CAPDEFIER chivas314...@gmail.com wrote: But how would the comparator have access to the job config? On Sat, Aug 31, 2013 at 2:38 AM, Shahab Yunus shahab.yu...@gmail.comwrote: I think you have to override/extend the Comparator to achieve that, something like what is done in Secondary Sort? Regards, Shahab On Fri, Aug 30, 2013 at 9:01 PM, Adrian CAPDEFIER chivas314...@gmail.com wrote: Howdy, I apologise for the lack of code in this message, but the code is fairly convoluted and it would obscure my problem. That being said, I can put together some sample code if really needed. I am trying to pass some metadata between the map reduce steps. This metadata is read and generated in the map step and stored in the job config. It also needs to be recreated on the reduce node before the key/ value fields can be read in the readFields function. I had assumed that I would be able to override the Reducer.setup() function and that would be it, but apparently the readFields function is called before the Reducer.setup() function. My question is what is any (the best) place on the reduce node where I can access the job configuration/ context before the readFields function is called? This is the stack trace: at org.apache.hadoop.io.WritableComparator.compare(WritableComparator.java:103) at org.apache.hadoop.mapred.MapTask$MapOutputBuffer.compare(MapTask.java:) at org.apache.hadoop.util.QuickSort.sortInternal(QuickSort.java:70) at org.apache.hadoop.util.QuickSort.sort(QuickSort.java:59) at org.apache.hadoop.mapred.MapTask$MapOutputBuffer.sortAndSpill(MapTask.java:1399) at org.apache.hadoop.mapred.MapTask$MapOutputBuffer.flush(MapTask.java:1298) at org.apache.hadoop.mapred.MapTask$NewOutputCollector.close(MapTask.java:699) at org.apache.hadoop.mapred.MapTask.runNewMapper(MapTask.java:766) at org.apache.hadoop.mapred.MapTask.run(MapTask.java:370) at org.apache.hadoop.mapred.Child$4.run(Child.java:255) at java.security.AccessController.doPrivileged(Native Method) at javax.security.auth.Subject.doAs(Subject.java:415) at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1149) at org.apache.hadoop.mapred.Child.main(Child.java:249)
Re: Job config before read fields
Personally, I don't know a way to access job configuration parameters in custom implementation of Writables ( at least not an elegant and appropriate one. Of course hacks of various kinds be done.) Maybe experts can chime in? One idea that I thought about was to use MapWritable (if you have not explored it already.) You can encode the 'custom metadata' for you 'data' as one byte symbols and move your data in the M/R flow as a map. Then while deserialization you will have the type (or your 'custom metadata') in the key part of the map and the value would be you actual data. This aligns with the efficient approach that is used natively in Hadoop for Strings/Text i.e. compact metadata (though I agree that you are not taking advantage of the other aspect of non-dependence between metadata and the data it defines.) Take a look at that: Page 96 of the Definitive Guide: http://books.google.com/books?id=Nff49D7vnJcCpg=PA96lpg=PA96dq=mapwritable+in+hadoopsource=blots=IiixYu7vXusig=4V6H7cY-MrNT7Rzs3WlODsDOoP4hl=ensa=Xei=aX4iUp2YGoaosASs_YCACQsqi=2ved=0CFUQ6AEwBA#v=onepageq=mapwritable%20in%20hadoopf=false and then this: http://www.chrisstucchio.com/blog/2011/mapwritable_sometimes_a_performance_hog.html and add your own custom types here (note that you are restricted by size of byte): http://hadoop.sourcearchive.com/documentation/0.20.2plus-pdfsg1-1/AbstractMapWritable_8java-source.html Regards, Shahab On Sat, Aug 31, 2013 at 5:38 AM, Adrian CAPDEFIER chivas314...@gmail.comwrote: Thank you for your help Shahab. I guess I wasn't being too clear. My logic is that I use a custom type as key and in order to deserialize it on the compute nodes, I need an extra piece of information (also a custom type). To use an analogy, a Text is serialized by writing the length of the string as a number and then the bytes that compose the actual string. When it is deserialized, the number informs the reader when to stop reading the string. This number is varies from string to string and it is compact so it makes sense to serialize it with the string. My use case is similar to it. I have a complex type (let's call this data), and in order to deserialize it, I need another complex type (let's call this second type metadata). The metadata is not closely tied to the data (i.e. if the data value changes, the metadata does not) and the metadata size is quite large. I ruled out a couple of options, but please let me know if you think I did so for the wrong reasons: 1. I could serialize each data value with it's own metadata value, but since the data value count is in the +tens of millions and the metadata value distinct count can be up to one hundred, it would waste resources in the system. 2. I could serialize the metadata and then the data as a collection property of the metadata. This would be an elegant solution code-wise, but then all the data would have to be read and kept in memory as a massive object before any reduce operations can happen. I wasn't able to find any info on this online so this is just a guess from peeking at the hadoop code. My solution was to serialize the data with a hash of the metadata and separately serialize the metadata and its hash in the job configuration (as key/value pairs). For this to work, I would need to be able to deserialize the metadata on the reduce node before the data is deserialized in the readFields() method. I think that for that to happen I need to hook into the code somewhere where a context or job configuration is used (before readFields()), but I'm stumped as to where that is. Cheers, Adi On Sat, Aug 31, 2013 at 3:42 AM, Shahab Yunus shahab.yu...@gmail.comwrote: What I meant was that you might have to split or redesign your logic or your usecase (which we don't know about)? Regards, Shahab On Fri, Aug 30, 2013 at 10:31 PM, Adrian CAPDEFIER chivas314...@gmail.com wrote: But how would the comparator have access to the job config? On Sat, Aug 31, 2013 at 2:38 AM, Shahab Yunus shahab.yu...@gmail.comwrote: I think you have to override/extend the Comparator to achieve that, something like what is done in Secondary Sort? Regards, Shahab On Fri, Aug 30, 2013 at 9:01 PM, Adrian CAPDEFIER chivas314...@gmail.com wrote: Howdy, I apologise for the lack of code in this message, but the code is fairly convoluted and it would obscure my problem. That being said, I can put together some sample code if really needed. I am trying to pass some metadata between the map reduce steps. This metadata is read and generated in the map step and stored in the job config. It also needs to be recreated on the reduce node before the key/ value fields can be read in the readFields function. I had assumed that I would be able to override the Reducer.setup() function and that would be it, but apparently the readFields function is called before the Reducer.setup() function. My question is what is any (the best) place on the
Job config before read fields
Howdy, I apologise for the lack of code in this message, but the code is fairly convoluted and it would obscure my problem. That being said, I can put together some sample code if really needed. I am trying to pass some metadata between the map reduce steps. This metadata is read and generated in the map step and stored in the job config. It also needs to be recreated on the reduce node before the key/ value fields can be read in the readFields function. I had assumed that I would be able to override the Reducer.setup() function and that would be it, but apparently the readFields function is called before the Reducer.setup() function. My question is what is any (the best) place on the reduce node where I can access the job configuration/ context before the readFields function is called? This is the stack trace: at org.apache.hadoop.io.WritableComparator.compare(WritableComparator.java:103) at org.apache.hadoop.mapred.MapTask$MapOutputBuffer.compare(MapTask.java:) at org.apache.hadoop.util.QuickSort.sortInternal(QuickSort.java:70) at org.apache.hadoop.util.QuickSort.sort(QuickSort.java:59) at org.apache.hadoop.mapred.MapTask$MapOutputBuffer.sortAndSpill(MapTask.java:1399) at org.apache.hadoop.mapred.MapTask$MapOutputBuffer.flush(MapTask.java:1298) at org.apache.hadoop.mapred.MapTask$NewOutputCollector.close(MapTask.java:699) at org.apache.hadoop.mapred.MapTask.runNewMapper(MapTask.java:766) at org.apache.hadoop.mapred.MapTask.run(MapTask.java:370) at org.apache.hadoop.mapred.Child$4.run(Child.java:255) at java.security.AccessController.doPrivileged(Native Method) at javax.security.auth.Subject.doAs(Subject.java:415) at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1149) at org.apache.hadoop.mapred.Child.main(Child.java:249)
Re: Job config before read fields
I think you have to override/extend the Comparator to achieve that, something like what is done in Secondary Sort? Regards, Shahab On Fri, Aug 30, 2013 at 9:01 PM, Adrian CAPDEFIER chivas314...@gmail.comwrote: Howdy, I apologise for the lack of code in this message, but the code is fairly convoluted and it would obscure my problem. That being said, I can put together some sample code if really needed. I am trying to pass some metadata between the map reduce steps. This metadata is read and generated in the map step and stored in the job config. It also needs to be recreated on the reduce node before the key/ value fields can be read in the readFields function. I had assumed that I would be able to override the Reducer.setup() function and that would be it, but apparently the readFields function is called before the Reducer.setup() function. My question is what is any (the best) place on the reduce node where I can access the job configuration/ context before the readFields function is called? This is the stack trace: at org.apache.hadoop.io.WritableComparator.compare(WritableComparator.java:103) at org.apache.hadoop.mapred.MapTask$MapOutputBuffer.compare(MapTask.java:) at org.apache.hadoop.util.QuickSort.sortInternal(QuickSort.java:70) at org.apache.hadoop.util.QuickSort.sort(QuickSort.java:59) at org.apache.hadoop.mapred.MapTask$MapOutputBuffer.sortAndSpill(MapTask.java:1399) at org.apache.hadoop.mapred.MapTask$MapOutputBuffer.flush(MapTask.java:1298) at org.apache.hadoop.mapred.MapTask$NewOutputCollector.close(MapTask.java:699) at org.apache.hadoop.mapred.MapTask.runNewMapper(MapTask.java:766) at org.apache.hadoop.mapred.MapTask.run(MapTask.java:370) at org.apache.hadoop.mapred.Child$4.run(Child.java:255) at java.security.AccessController.doPrivileged(Native Method) at javax.security.auth.Subject.doAs(Subject.java:415) at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1149) at org.apache.hadoop.mapred.Child.main(Child.java:249)
Re: Job config before read fields
But how would the comparator have access to the job config? On Sat, Aug 31, 2013 at 2:38 AM, Shahab Yunus shahab.yu...@gmail.comwrote: I think you have to override/extend the Comparator to achieve that, something like what is done in Secondary Sort? Regards, Shahab On Fri, Aug 30, 2013 at 9:01 PM, Adrian CAPDEFIER chivas314...@gmail.comwrote: Howdy, I apologise for the lack of code in this message, but the code is fairly convoluted and it would obscure my problem. That being said, I can put together some sample code if really needed. I am trying to pass some metadata between the map reduce steps. This metadata is read and generated in the map step and stored in the job config. It also needs to be recreated on the reduce node before the key/ value fields can be read in the readFields function. I had assumed that I would be able to override the Reducer.setup() function and that would be it, but apparently the readFields function is called before the Reducer.setup() function. My question is what is any (the best) place on the reduce node where I can access the job configuration/ context before the readFields function is called? This is the stack trace: at org.apache.hadoop.io.WritableComparator.compare(WritableComparator.java:103) at org.apache.hadoop.mapred.MapTask$MapOutputBuffer.compare(MapTask.java:) at org.apache.hadoop.util.QuickSort.sortInternal(QuickSort.java:70) at org.apache.hadoop.util.QuickSort.sort(QuickSort.java:59) at org.apache.hadoop.mapred.MapTask$MapOutputBuffer.sortAndSpill(MapTask.java:1399) at org.apache.hadoop.mapred.MapTask$MapOutputBuffer.flush(MapTask.java:1298) at org.apache.hadoop.mapred.MapTask$NewOutputCollector.close(MapTask.java:699) at org.apache.hadoop.mapred.MapTask.runNewMapper(MapTask.java:766) at org.apache.hadoop.mapred.MapTask.run(MapTask.java:370) at org.apache.hadoop.mapred.Child$4.run(Child.java:255) at java.security.AccessController.doPrivileged(Native Method) at javax.security.auth.Subject.doAs(Subject.java:415) at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1149) at org.apache.hadoop.mapred.Child.main(Child.java:249)
Re: Job config before read fields
What I meant was that you might have to split or redesign your logic or your usecase (which we don't know about)? Regards, Shahab On Fri, Aug 30, 2013 at 10:31 PM, Adrian CAPDEFIER chivas314...@gmail.comwrote: But how would the comparator have access to the job config? On Sat, Aug 31, 2013 at 2:38 AM, Shahab Yunus shahab.yu...@gmail.comwrote: I think you have to override/extend the Comparator to achieve that, something like what is done in Secondary Sort? Regards, Shahab On Fri, Aug 30, 2013 at 9:01 PM, Adrian CAPDEFIER chivas314...@gmail.com wrote: Howdy, I apologise for the lack of code in this message, but the code is fairly convoluted and it would obscure my problem. That being said, I can put together some sample code if really needed. I am trying to pass some metadata between the map reduce steps. This metadata is read and generated in the map step and stored in the job config. It also needs to be recreated on the reduce node before the key/ value fields can be read in the readFields function. I had assumed that I would be able to override the Reducer.setup() function and that would be it, but apparently the readFields function is called before the Reducer.setup() function. My question is what is any (the best) place on the reduce node where I can access the job configuration/ context before the readFields function is called? This is the stack trace: at org.apache.hadoop.io.WritableComparator.compare(WritableComparator.java:103) at org.apache.hadoop.mapred.MapTask$MapOutputBuffer.compare(MapTask.java:) at org.apache.hadoop.util.QuickSort.sortInternal(QuickSort.java:70) at org.apache.hadoop.util.QuickSort.sort(QuickSort.java:59) at org.apache.hadoop.mapred.MapTask$MapOutputBuffer.sortAndSpill(MapTask.java:1399) at org.apache.hadoop.mapred.MapTask$MapOutputBuffer.flush(MapTask.java:1298) at org.apache.hadoop.mapred.MapTask$NewOutputCollector.close(MapTask.java:699) at org.apache.hadoop.mapred.MapTask.runNewMapper(MapTask.java:766) at org.apache.hadoop.mapred.MapTask.run(MapTask.java:370) at org.apache.hadoop.mapred.Child$4.run(Child.java:255) at java.security.AccessController.doPrivileged(Native Method) at javax.security.auth.Subject.doAs(Subject.java:415) at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1149) at org.apache.hadoop.mapred.Child.main(Child.java:249)
