RE: Setting variable value in Compute class and using it in the next superstep
Hello again, As Tom and Matthew suggested I wrote my own custom vertex value class and input format class. I followed Matthew's example to create my own custom vertex class but now I'm getting the following error while running the program java.lang.IllegalStateException: newInstance: Illegal access org.apache.giraph.examples.DeltaVertexWritable at org.apache.giraph.utils.ReflectionUtils.newInstance(ReflectionUtils.java:84) at org.apache.giraph.utils.WritableUtils.createWritable(WritableUtils.java:68) at org.apache.giraph.factories.DefaultVertexValueFactory.newInstance(DefaultVertexValueFactory.java:48) at org.apache.giraph.conf.ImmutableClassesGiraphConfiguration.createVertexValue(ImmutableClassesGiraphConfiguration.java:729) at org.apache.giraph.utils.VertexIterator.resetEmptyVertex(VertexIterator.java:69) at org.apache.giraph.utils.VertexIterator.init(VertexIterator.java:60) at org.apache.giraph.comm.requests.SendWorkerVerticesRequest.doRequest(SendWorkerVerticesRequest.java:108) at org.apache.giraph.comm.netty.NettyWorkerClientRequestProcessor.doRequest(NettyWorkerClientRequestProcessor.java:466) at org.apache.giraph.comm.netty.NettyWorkerClientRequestProcessor.flush(NettyWorkerClientRequestProcessor.java:412) at org.apache.giraph.worker.InputSplitsCallable.call(InputSplitsCallable.java:241) at org.apache.giraph.worker.InputSplitsCallable.call(InputSplitsCallable.java:60) at org.apache.giraph.utils.LogStacktraceCallable.call(LogStacktraceCallable.java:51) at java.util.concurrent.FutureTask.run(FutureTask.java:262) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) at java.lang.Thread.run(Thread.java:744) Here is my DeltaVertexWritable class - https://gist.github.com/sar-vivek/df09cca17cc3f6b5ac60 I tried digging a bit but I couldn't get any success [at the first place I even didn't understand the error message!] Thank you. Vivek From: Sardeshmukh, Vivek vivek-sardeshm...@uiowa.edu Sent: Monday, July 21, 2014 6:06 PM To: user@giraph.apache.org Subject: RE: Setting variable value in Compute class and using it in the next superstep Thank you Matthew. Now writing a custom vertex class and input format seems doable! Thank you. -- Vivek From: Matthew Saltz sal...@gmail.com Sent: Monday, July 21, 2014 5:50 PM To: user@giraph.apache.org Subject: Re: Setting variable value in Compute class and using it in the next superstep Yeah, that's true. Sorry I forgot that part. Luckily, it isn't too tricky either, depending on the input format of your graph. Here's another examplehttps://gist.github.com/saltzm/ab7172c57dec927061be to get you started, for a very simple input format for edges with no values. I basically took the code straight from herehttp://giraph.apache.org/apidocs/org/apache/giraph/io/formats/LongLongNullTextInputFormat.html and modified where I needed to it to return the InputFormat that I needed for my code. You'll probably be better off digging through some of the already implemented InputFormat classes that come with Giraph to do something similar, since I'm guessing your input files will be different than mine. Take a look at the subclasses of TextVertexInputFormathttp://giraph.apache.org/apidocs/org/apache/giraph/io/formats/TextVertexInputFormat.html, since they deal with a lot of common input format styles, and see if you can modify their code to work with your custom vertex data format. Now, the example I give you is also easy because I just use the default constructor of the class, but if you need to load additional data from the file into your vertex data and the default constructor isn't appropriate, you may have to do some extra parsing and legwork for that. Best of luck, Matthew On Tue, Jul 22, 2014 at 12:28 AM, Sardeshmukh, Vivek vivek-sardeshm...@uiowa.edumailto:vivek-sardeshm...@uiowa.edu wrote: Thank you Matthew for the example link. It is helpful. I'll give it a shot. If I have a custom vertex class isn't it necessary to change the VertexInputFormat class too? Since this class loads the data into the vertex and if vertex has a custom value field then it doesn't know how to load the input. Am I right? Vivek From: Schweiger, Tom thschwei...@ebay.commailto:thschwei...@ebay.com Sent: Monday, July 21, 2014 5:16 PM To: user@giraph.apache.orgmailto:user@giraph.apache.org Subject: RE: Setting variable value in Compute class and using it in the next superstep For more than one flag, a custom class is necessary (unless you're able to, say, toggle the sign bit to get double usage out or a value). I've started a private thread with Vivek to get a better understanding of what he was trying to solve. And you are also correct that there isn't much to
RE: Setting variable value in Compute class and using it in the next superstep
And in answer of : This post also suggests (along with what I described above) to have a field in the vertex value itself. For that I need to change the vertex input format and also create my own custom vertex class. Is it really necessary? No, you don't need a custom vertex class or vertex input format. You can create/initialize the value at the beginning of the first superstep. From: Sardeshmukh, Vivek [vivek-sardeshm...@uiowa.edu] Sent: Monday, July 21, 2014 2:05 PM To: user@giraph.apache.org Subject: Setting variable value in Compute class and using it in the next superstep Hi, all-- In my algorithm, I need to set a flag if certain conditions hold (locally at a vertex v). If this flag is set then execute some other block of code *only once*, and do nothing until some other condition is hold. My question is, can I declare a flag variable in the class where I override compute function? I defined the flag as a public variable and setting it once the conditions are met but it seems the value is not carried over to the next superstep. I dig a little bit in this mailing list and found this https://www.mail-archive.com/user@giraph.apache.org/msg01266.html This post also suggests (along with what I described above) to have a field in the vertex value itself. For that I need to change the vertex input format and also create my own custom vertex class. Is it really necessary? By the way, I am using Giraph 1.1.0 compiled against Hadoop 1.0.3. I was able to run SimpleShortestPathComputation successfully. Here are more technical details of my algorithm: I am trying to implement Delta-stepping shortest path algorithm ( http://dl.acm.org/citation.cfm?id=740136 or http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.46.2200 ). This was mentioned in Pregel paper. A vertex relax light edges if it belongs to the minimum bucket index (of course, aggregators!). Once a vertex is done with relaxing light edges it relaxes heavy edges (here is where I need a flag) once. A vertex may be re-inserted to a newer bucket and may have to execute all the steps that I described here again. Thanks. Sincerely, Vivek A beginner in Giraph (and Java too!)
RE: Setting variable value in Compute class and using it in the next superstep
Thank you Tom for your prompt reply. If that is the case then I might be doing something wrong. I'll take a closer look with debug enabled and keep you posted. Thank you again. Vivek From: Schweiger, Tom thschwei...@ebay.com Sent: Monday, July 21, 2014 4:37 PM To: user@giraph.apache.org Subject: RE: Setting variable value in Compute class and using it in the next superstep And in answer of : This post also suggests (along with what I described above) to have a field in the vertex value itself. For that I need to change the vertex input format and also create my own custom vertex class. Is it really necessary? No, you don't need a custom vertex class or vertex input format. You can create/initialize the value at the beginning of the first superstep. From: Sardeshmukh, Vivek [vivek-sardeshm...@uiowa.edu] Sent: Monday, July 21, 2014 2:05 PM To: user@giraph.apache.org Subject: Setting variable value in Compute class and using it in the next superstep Hi, all-- In my algorithm, I need to set a flag if certain conditions hold (locally at a vertex v). If this flag is set then execute some other block of code *only once*, and do nothing until some other condition is hold. My question is, can I declare a flag variable in the class where I override compute function? I defined the flag as a public variable and setting it once the conditions are met but it seems the value is not carried over to the next superstep. I dig a little bit in this mailing list and found this https://www.mail-archive.com/user@giraph.apache.org/msg01266.html This post also suggests (along with what I described above) to have a field in the vertex value itself. For that I need to change the vertex input format and also create my own custom vertex class. Is it really necessary? By the way, I am using Giraph 1.1.0 compiled against Hadoop 1.0.3. I was able to run SimpleShortestPathComputation successfully. Here are more technical details of my algorithm: I am trying to implement Delta-stepping shortest path algorithm ( http://dl.acm.org/citation.cfm?id=740136 or http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.46.2200 ). This was mentioned in Pregel paper. A vertex relax light edges if it belongs to the minimum bucket index (of course, aggregators!). Once a vertex is done with relaxing light edges it relaxes heavy edges (here is where I need a flag) once. A vertex may be re-inserted to a newer bucket and may have to execute all the steps that I described here again. Thanks. Sincerely, Vivek A beginner in Giraph (and Java too!)
Re: Setting variable value in Compute class and using it in the next superstep
Tom,
If it's necessary to store more than one flag though, for example, won't a
custom class be necessary? I'm a beginner too, so I apologize if I'm
incorrect about that. Just to be clarify, to keep persistent data for a
vertex from one superstep to the next, it is necessary to encapsulate it in
the type used for the 'V', right? In other words, if Vivek tries to use a
normal member variable for the Computation class, it won't work will it?
Also, just to point out, there actually isn't too much involved with
writing your own custom vertex class. Here's a quick example
https://gist.github.com/saltzm/692fba1d3aade035ce9c to get you started.
Within your compute() method you can access the data in this class by doing
SampleVertexData d = vertex.getValue();
and then using d.setFlag(true) or boolean currentFlag = d.getFlag() for
example. And your computation class is now something like
public class MyComputation extends BasicComputation*IdType, *
*SampleVertexData*, *EdgeType, MessageType* {
@Override
public void compute(Vertex*IdType, **SampleVertexData*, *EdgeType*
vertex, Iterable*MessageType messages) {.} *
*...*
}
As a warning, for this class I'm using Hadoop 0.20.203 and I'm also a
beginner, so take everything I say with a grain of salt, and Tom please
correct me if I'm wrong.
Best of luck,
Matthew
On Mon, Jul 21, 2014 at 11:37 PM, Schweiger, Tom thschwei...@ebay.com
wrote:
And in answer of :
This post also suggests (along with what I described above) to have a
field in the vertex value itself. For that I need to change the vertex
input format and also create my own custom vertex class. Is it really
necessary?
No, you don't need a custom vertex class or vertex input format. You can
create/initialize the value at the beginning of the first superstep.
--
*From:* Sardeshmukh, Vivek [vivek-sardeshm...@uiowa.edu]
*Sent:* Monday, July 21, 2014 2:05 PM
*To:* user@giraph.apache.org
*Subject:* Setting variable value in Compute class and using it in the
next superstep
Hi, all--
In my algorithm, I need to set a flag if certain conditions hold
(locally at a vertex v). If this flag is set then execute some other block
of code *only once*, and do nothing until some other condition is hold.
My question is, can I declare a flag variable in the class where I
override compute function? I defined the flag as a public variable and
setting it once the conditions are met but it seems the value is not
carried over to the next superstep.
I dig a little bit in this mailing list and found this
https://www.mail-archive.com/user@giraph.apache.org/msg01266.html
This post also suggests (along with what I described above) to have a
field in the vertex value itself. For that I need to change the vertex
input format and also create my own custom vertex class. Is it really
necessary?
By the way, I am using Giraph 1.1.0 compiled against Hadoop 1.0.3. I was
able to run SimpleShortestPathComputation successfully.
Here are more technical details of my algorithm: I am trying to
implement Delta-stepping shortest path algorithm (
http://dl.acm.org/citation.cfm?id=740136 or
http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.46.2200 ). This
was mentioned in Pregel paper. A vertex relax light edges if it belongs
to the minimum bucket index (of course, aggregators!). Once a vertex is
done with relaxing light edges it relaxes heavy edges (here is where I need
a flag) once. A vertex may be re-inserted to a newer bucket and may have
to execute all the steps that I described here again.
Thanks.
Sincerely,
Vivek
A beginner in Giraph (and Java too!)
RE: Setting variable value in Compute class and using it in the next superstep
For more than one flag, a custom class is necessary (unless you're able to,
say, toggle the sign bit to get double usage out or a value).
I've started a private thread with Vivek to get a better understanding of what
he was trying to solve.
And you are also correct that there isn't much to writing a custom vertex
class. The key is making sure you read and write in the same order. Likewise,
extending a vertex reader can be quite simple.
From: Matthew Saltz [sal...@gmail.com]
Sent: Monday, July 21, 2014 3:09 PM
To: user@giraph.apache.org
Subject: Re: Setting variable value in Compute class and using it in the next
superstep
Tom,
If it's necessary to store more than one flag though, for example, won't a
custom class be necessary? I'm a beginner too, so I apologize if I'm incorrect
about that. Just to be clarify, to keep persistent data for a vertex from one
superstep to the next, it is necessary to encapsulate it in the type used for
the 'V', right? In other words, if Vivek tries to use a normal member variable
for the Computation class, it won't work will it?
Also, just to point out, there actually isn't too much involved with writing
your own custom vertex class. Here's a quick
examplehttps://gist.github.com/saltzm/692fba1d3aade035ce9c to get you
started. Within your compute() method you can access the data in this class by
doing
SampleVertexData d = vertex.getValue();
and then using d.setFlag(true) or boolean currentFlag = d.getFlag() for
example. And your computation class is now something like
public class MyComputation extends BasicComputationIdType, SampleVertexData,
EdgeType, MessageType {
@Override
public void compute(VertexIdType, SampleVertexData, EdgeType vertex,
IterableMessageType messages) {.}
...
}
As a warning, for this class I'm using Hadoop 0.20.203 and I'm also a beginner,
so take everything I say with a grain of salt, and Tom please correct me if I'm
wrong.
Best of luck,
Matthew
On Mon, Jul 21, 2014 at 11:37 PM, Schweiger, Tom
thschwei...@ebay.commailto:thschwei...@ebay.com wrote:
And in answer of :
This post also suggests (along with what I described above) to have a field in
the vertex value itself. For that I need to change the vertex input format and
also create my own custom vertex class. Is it really necessary?
No, you don't need a custom vertex class or vertex input format. You can
create/initialize the value at the beginning of the first superstep.
From: Sardeshmukh, Vivek
[vivek-sardeshm...@uiowa.edumailto:vivek-sardeshm...@uiowa.edu]
Sent: Monday, July 21, 2014 2:05 PM
To: user@giraph.apache.orgmailto:user@giraph.apache.org
Subject: Setting variable value in Compute class and using it in the next
superstep
Hi, all--
In my algorithm, I need to set a flag if certain conditions hold (locally at a
vertex v). If this flag is set then execute some other block of code *only
once*, and do nothing until some other condition is hold.
My question is, can I declare a flag variable in the class where I override
compute function? I defined the flag as a public variable and setting it once
the conditions are met but it seems the value is not carried over to the next
superstep.
I dig a little bit in this mailing list and found this
https://www.mail-archive.com/user@giraph.apache.org/msg01266.html
This post also suggests (along with what I described above) to have a field in
the vertex value itself. For that I need to change the vertex input format and
also create my own custom vertex class. Is it really necessary?
By the way, I am using Giraph 1.1.0 compiled against Hadoop 1.0.3. I was able
to run SimpleShortestPathComputation successfully.
Here are more technical details of my algorithm: I am trying to implement
Delta-stepping shortest path algorithm (
http://dl.acm.org/citation.cfm?id=740136 or
http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.46.2200 ). This was
mentioned in Pregel paper. A vertex relax light edges if it belongs to the
minimum bucket index (of course, aggregators!). Once a vertex is done with
relaxing light edges it relaxes heavy edges (here is where I need a flag) once.
A vertex may be re-inserted to a newer bucket and may have to execute all the
steps that I described here again.
Thanks.
Sincerely,
Vivek
A beginner in Giraph (and Java too!)
Re: Setting variable value in Compute class and using it in the next superstep
Yeah, that's true. Sorry I forgot that part. Luckily, it isn't too tricky
either, depending on the input format of your graph. Here's another example
https://gist.github.com/saltzm/ab7172c57dec927061be to get you started,
for a very simple input format for edges with no values. I basically took
the code straight from here
http://giraph.apache.org/apidocs/org/apache/giraph/io/formats/LongLongNullTextInputFormat.html
and
modified where I needed to it to return the InputFormat that I needed for
my code. You'll probably be better off digging through some of the already
implemented InputFormat classes that come with Giraph to do something
similar, since I'm guessing your input files will be different than mine.
Take a look at the subclasses of TextVertexInputFormat
http://giraph.apache.org/apidocs/org/apache/giraph/io/formats/TextVertexInputFormat.html,
since they deal with a lot of common input format styles, and see if you
can modify their code to work with your custom vertex data format. Now, the
example I give you is also easy because I just use the default constructor
of the class, but if you need to load additional data from the file into
your vertex data and the default constructor isn't appropriate, you may
have to do some extra parsing and legwork for that.
Best of luck,
Matthew
On Tue, Jul 22, 2014 at 12:28 AM, Sardeshmukh, Vivek
vivek-sardeshm...@uiowa.edu wrote:
Thank you Matthew for the example link. It is helpful. I'll give it a
shot.
If I have a custom vertex class isn't it necessary to change the
VertexInputFormat class too? Since this class loads the data into the
vertex and if vertex has a custom value field then it doesn't know how to
load the input. Am I right?
Vivek
--
*From:* Schweiger, Tom thschwei...@ebay.com
*Sent:* Monday, July 21, 2014 5:16 PM
*To:* user@giraph.apache.org
*Subject:* RE: Setting variable value in Compute class and using it in
the next superstep
For more than one flag, a custom class is necessary (unless you're able
to, say, toggle the sign bit to get double usage out or a value).
I've started a private thread with Vivek to get a better understanding of
what he was trying to solve.
And you are also correct that there isn't much to writing a custom vertex
class. The key is making sure you read and write in the same order.
Likewise, extending a vertex reader can be quite simple.
--
*From:* Matthew Saltz [sal...@gmail.com]
*Sent:* Monday, July 21, 2014 3:09 PM
*To:* user@giraph.apache.org
*Subject:* Re: Setting variable value in Compute class and using it in
the next superstep
Tom,
If it's necessary to store more than one flag though, for example, won't
a custom class be necessary? I'm a beginner too, so I apologize if I'm
incorrect about that. Just to be clarify, to keep persistent data for a
vertex from one superstep to the next, it is necessary to encapsulate it in
the type used for the 'V', right? In other words, if Vivek tries to use a
normal member variable for the Computation class, it won't work will it?
Also, just to point out, there actually isn't too much involved with
writing your own custom vertex class. Here's a quick example
https://gist.github.com/saltzm/692fba1d3aade035ce9c to get you started.
Within your compute() method you can access the data in this class by doing
SampleVertexData d = vertex.getValue();
and then using d.setFlag(true) or boolean currentFlag = d.getFlag() for
example. And your computation class is now something like
public class MyComputation extends BasicComputation*IdType, *
*SampleVertexData*, *EdgeType, MessageType* {
@Override
public void compute(Vertex*IdType, **SampleVertexData*, *EdgeType*
vertex, Iterable*MessageType messages) {.} *
*...*
}
As a warning, for this class I'm using Hadoop 0.20.203 and I'm also a
beginner, so take everything I say with a grain of salt, and Tom please
correct me if I'm wrong.
Best of luck,
Matthew
On Mon, Jul 21, 2014 at 11:37 PM, Schweiger, Tom thschwei...@ebay.com
wrote:
And in answer of :
This post also suggests (along with what I described above) to have a
field in the vertex value itself. For that I need to change the vertex
input format and also create my own custom vertex class. Is it really
necessary?
No, you don't need a custom vertex class or vertex input format. You can
create/initialize the value at the beginning of the first superstep.
--
*From:* Sardeshmukh, Vivek [vivek-sardeshm...@uiowa.edu]
*Sent:* Monday, July 21, 2014 2:05 PM
*To:* user@giraph.apache.org
*Subject:* Setting variable value in Compute class and using it in the
next superstep
Hi, all--
In my algorithm, I need to set a flag if certain conditions hold
(locally at a vertex v). If this flag is set then execute some other block
of code *only once*, and do nothing until some other condition is
