Re: spark with breeze error of NoClassDefFoundError

[Ted Yu]

I don't have Spark 1.4 source code on hand.

You can use the following command:

mvn dependency:tree

to find out the answer to your question.

Cheers

On Wed, Nov 18, 2015 at 10:18 PM, Jack Yang <j...@uow.edu.au> wrote:

> Back to my question. If  I use “*provided*”, the jar file
> will expect some libraries are provided by the system.
>
> However, the “ *compiled *” is the default setting, which
> means the third-party library will be included inside jar file after
> compiling.
>
> So when I use “*provided*”, the error is they cannot find
> the Class, but with “compiled” the error is IncompatibleClassChangeError.
>
>
>
> Ok, so can someone tell me which version of breeze and breeze-math are
> used in spark 1.4?
>
>
>
> *From:* Zhiliang Zhu [mailto:zchl.j...@yahoo.com]
> *Sent:* Thursday, 19 November 2015 5:10 PM
> *To:* Ted Yu
> *Cc:* Jack Yang; Fengdong Yu; user@spark.apache.org
>
> *Subject:* Re: spark with breeze error of NoClassDefFoundError
>
>
>
> Dear Ted,
>
> I just looked at the link you provided, it is great!
>
>
>
> For my understanding, I could also directly use other Breeze part (except
> spark mllib package linalg ) in spark (scala or java ) program after
> importing Breeze package,
>
> it is right?
>
>
>
> Thanks a lot in advance again!
>
> Zhiliang
>
>
>
>
>
>
>
> On Thursday, November 19, 2015 1:46 PM, Ted Yu <yuzhih...@gmail.com>
> wrote:
>
>
>
> Have you looked at
>
> https://github.com/scalanlp/breeze/wiki
>
>
>
> Cheers
>
>
> On Nov 18, 2015, at 9:34 PM, Zhiliang Zhu <zchl.j...@yahoo.com> wrote:
>
> Dear Jack,
>
>
>
> As is known, Breeze is numerical calculation package wrote by scala ,
> spark mllib also use it as underlying package for algebra usage.
>
> Here I am also preparing to use Breeze for nonlinear equation
> optimization, however, it seemed that I could not find the exact doc or API
> for Breeze except spark linalg package...
>
>
>
> Could you help some to provide me the official doc or API website for
> Breeze ?
>
> Thank you in advance!
>
>
>
> Zhiliang
>
>
>
>
>
>
>
> On Thursday, November 19, 2015 7:32 AM, Jack Yang <j...@uow.edu.au> wrote:
>
>
>
> If I tried to change “provided” to “compile”.. then the error changed to :
>
>
>
> Exception in thread "main" java.lang.IncompatibleClassChangeError:
> Implementing class
>
> at java.lang.ClassLoader.defineClass1(Native Method)
>
> at java.lang.ClassLoader.defineClass(ClassLoader.java:800)
>
> at
> java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
>
> at java.net.URLClassLoader.defineClass(URLClassLoader.java:449)
>
> at java.net.URLClassLoader.access$100(URLClassLoader.java:71)
>
> at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
>
> at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
>
> at java.security.AccessController.doPrivileged(Native Method)
>
> at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
>
> at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
>
> at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
>
> at
> smartapp.smart.sparkwithscala.textMingApp.main(textMingApp.scala)
>
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>
> at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
>
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>
> at java.lang.reflect.Method.invoke(Method.java:606)
>
> at
> org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:664)
>
> at
> org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:169)
>
> at
> org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:192)
>
> at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:111)
>
> at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
>
> 15/11/19 10:28:29 INFO util.Utils: Shutdown hook called
>
>
>
> Meanwhile, I will prefer to use maven to compile the jar file rather than
> sbt, although it is indeed another option.
>
>
>
> Best regards,
>
> Jack
>
>
>
>
>
>
>
> *From:* Fengdong Yu [mailto:fengdo...@everstring.com
> <fengdo...@everstring.com>]
> *Sent:* Wednesday, 18 November 2015 7:30 PM
> *To:* Jack Yang
> *Cc:* Ted Yu; user@spark.apache.org
> *Subject:* Re

Re: spark with breeze error of NoClassDefFoundError

[Fengdong Yu]

The simplest way is remove all “provided” in your pom.

then ‘sbt assembly” to build your final package. then get rid of ‘—jars’ 
because assembly already includes all dependencies.






> On Nov 18, 2015, at 2:15 PM, Jack Yang <j...@uow.edu.au> wrote:
> 
> So weird. Is there anything wrong with the way I made the pom file (I 
> labelled them as provided)?
>  
> Is there missing jar I forget to add in “--jar”?
>  
> See the trace below:
>  
>  
>  
> Exception in thread "main" java.lang.NoClassDefFoundError: 
> breeze/storage/DefaultArrayValue
> at smartapp.smart.sparkwithscala.textMingApp.main(textMingApp.scala)
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at 
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
> at 
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:606)
> at 
> org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:664)
> at 
> org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:169)
> at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:192)
> at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:111)
> at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
> Caused by: java.lang.ClassNotFoundException: breeze.storage.DefaultArrayValue
> at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
> at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
> at java.security.AccessController.doPrivileged(Native Method)
> at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
> ... 10 more
> 15/11/18 17:15:15 INFO util.Utils: Shutdown hook called
>  
>  
> From: Ted Yu [mailto:yuzhih...@gmail.com] 
> Sent: Wednesday, 18 November 2015 4:01 PM
> To: Jack Yang
> Cc: user@spark.apache.org
> Subject: Re: spark with breeze error of NoClassDefFoundError
>  
> Looking in local maven repo, breeze_2.10-0.7.jar contains DefaultArrayValue :
>  
> jar tvf 
> /Users/tyu/.m2/repository//org/scalanlp/breeze_2.10/0.7/breeze_2.10-0.7.jar | 
> grep !$
> jar tvf 
> /Users/tyu/.m2/repository//org/scalanlp/breeze_2.10/0.7/breeze_2.10-0.7.jar | 
> grep DefaultArrayValue
>369 Wed Mar 19 11:18:32 PDT 2014 
> breeze/storage/DefaultArrayValue$mcZ$sp$class.class
>309 Wed Mar 19 11:18:32 PDT 2014 
> breeze/storage/DefaultArrayValue$mcJ$sp.class
>   2233 Wed Mar 19 11:18:32 PDT 2014 
> breeze/storage/DefaultArrayValue$DoubleDefaultArrayValue$.class
>  
> Can you show the complete stack trace ?
>  
> FYI
>  
> On Tue, Nov 17, 2015 at 8:33 PM, Jack Yang <j...@uow.edu.au 
> <mailto:j...@uow.edu.au>> wrote:
> Hi all,
> I am using spark 1.4.0, and building my codes using maven.
> So in one of my scala, I used:
>  
> import breeze.linalg._
> val v1 = new breeze.linalg.SparseVector(commonVector.indices, 
> commonVector.values, commonVector.size)   
> val v2 = new breeze.linalg.SparseVector(commonVector2.indices, 
> commonVector2.values, commonVector2.size)
> println (v1.dot(v2) / (norm(v1) * norm(v2)) )
>  
>  
>  
> in my pom.xml file, I used:
> 
>  org.scalanlp
>  
> breeze-math_2.10
>  0.4
>  provided
>   
>  
>   
>  org.scalanlp
>  
> breeze_2.10
>  0.11.2
>  provided
>   
>  
>  
> When submit, I included breeze jars (breeze_2.10-0.11.2.jar 
> breeze-math_2.10-0.4.jar breeze-natives_2.10-0.11.2.jar 
> breeze-process_2.10-0.3.jar) using “--jar” arguments, although I doubt it is 
> necessary to do that.
>  
> however, the error is
>  
> Exception in thread "main" java.lang.NoClassDefFoundError: 
> breeze/storage/DefaultArrayValue
>  
> Any thoughts?
>  
>  
>  
> Best regards,
> Jack

Re: spark with breeze error of NoClassDefFoundError

[金国栋]

Have you tried to change to scope to `compile` ?

2015-11-18 14:15 GMT+08:00 Jack Yang <j...@uow.edu.au>:

> So weird. Is there anything wrong with the way I made the pom file (I
> labelled them as *provided*)?
>
>
>
> Is there missing jar I forget to add in “--jar”?
>
>
>
> See the trace below:
>
>
>
>
>
>
>
> Exception in thread "main" java.lang.NoClassDefFoundError:
> breeze/storage/DefaultArrayValue
>
> at
> smartapp.smart.sparkwithscala.textMingApp.main(textMingApp.scala)
>
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>
> at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
>
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>
> at java.lang.reflect.Method.invoke(Method.java:606)
>
> at
> org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:664)
>
> at
> org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:169)
>
> at
> org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:192)
>
> at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:111)
>
> at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
>
> Caused by: java.lang.ClassNotFoundException:
> breeze.storage.DefaultArrayValue
>
> at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
>
> at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
>
> at java.security.AccessController.doPrivileged(Native Method)
>
> at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
>
> at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
>
> at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
>
> ... 10 more
>
> 15/11/18 17:15:15 INFO util.Utils: Shutdown hook called
>
>
>
>
>
> *From:* Ted Yu [mailto:yuzhih...@gmail.com]
> *Sent:* Wednesday, 18 November 2015 4:01 PM
> *To:* Jack Yang
> *Cc:* user@spark.apache.org
> *Subject:* Re: spark with breeze error of NoClassDefFoundError
>
>
>
> Looking in local maven repo, breeze_2.10-0.7.jar
> contains DefaultArrayValue :
>
>
>
> jar tvf
> /Users/tyu/.m2/repository//org/scalanlp/breeze_2.10/0.7/breeze_2.10-0.7.jar
> | grep !$
>
> jar tvf
> /Users/tyu/.m2/repository//org/scalanlp/breeze_2.10/0.7/breeze_2.10-0.7.jar
> | grep DefaultArrayValue
>
>369 Wed Mar 19 11:18:32 PDT 2014
> breeze/storage/DefaultArrayValue$mcZ$sp$class.class
>
>309 Wed Mar 19 11:18:32 PDT 2014
> breeze/storage/DefaultArrayValue$mcJ$sp.class
>
>   2233 Wed Mar 19 11:18:32 PDT 2014
> breeze/storage/DefaultArrayValue$DoubleDefaultArrayValue$.class
>
>
>
> Can you show the complete stack trace ?
>
>
>
> FYI
>
>
>
> On Tue, Nov 17, 2015 at 8:33 PM, Jack Yang <j...@uow.edu.au> wrote:
>
> Hi all,
>
> I am using spark 1.4.0, and building my codes using maven.
>
> So in one of my scala, I used:
>
>
>
> import breeze.linalg._
>
> val v1 = new breeze.linalg.SparseVector(commonVector.indices,
> commonVector.values, commonVector.size)
>
> val v2 = new breeze.linalg.SparseVector(commonVector2.indices,
> commonVector2.values, commonVector2.size)
>
> println (v1.dot(v2) / (norm(v1) * norm(v2)) )
>
>
>
>
>
>
>
> in my pom.xml file, I used:
>
> 
>
>
> org.scalanlp
>
>
> breeze-math_2.10
>
>  0.4
>
>  *provided*
>
>   
>
>
>
>   
>
>
> org.scalanlp
>
>
> breeze_2.10
>
>  0.11.2
>
>  *provided*
>
>   
>
>
>
>
>
> When submit, I included breeze jars (breeze_2.10-0.11.2.jar
> breeze-math_2.10-0.4.jar breeze-natives_2.10-0.11.2.jar
> breeze-process_2.10-0.3.jar) using “--jar” arguments, although I doubt it
> is necessary to do that.
>
>
>
> however, the error is
>
>
>
> Exception in thread "main" java.lang.NoClassDefFoundError:
> breeze/storage/DefaultArrayValue
>
>
>
> Any thoughts?
>
>
>
>
>
>
>
> Best regards,
>
> Jack
>
>
>
>
>

RE: spark with breeze error of NoClassDefFoundError

[Jack Yang]

If I tried to change “provided” to “compile”.. then the error changed to :

Exception in thread "main" java.lang.IncompatibleClassChangeError: Implementing 
class
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(ClassLoader.java:800)
at 
java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:449)
at java.net.URLClassLoader.access$100(URLClassLoader.java:71)
at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
at smartapp.smart.sparkwithscala.textMingApp.main(textMingApp.scala)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at 
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at 
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at 
org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:664)
at 
org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:169)
at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:192)
at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:111)
at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
15/11/19 10:28:29 INFO util.Utils: Shutdown hook called

Meanwhile, I will prefer to use maven to compile the jar file rather than sbt, 
although it is indeed another option.

Best regards,
Jack



From: Fengdong Yu [mailto:fengdo...@everstring.com]
Sent: Wednesday, 18 November 2015 7:30 PM
To: Jack Yang
Cc: Ted Yu; user@spark.apache.org
Subject: Re: spark with breeze error of NoClassDefFoundError

The simplest way is remove all “provided” in your pom.

then ‘sbt assembly” to build your final package. then get rid of ‘—jars’ 
because assembly already includes all dependencies.






On Nov 18, 2015, at 2:15 PM, Jack Yang 
<j...@uow.edu.au<mailto:j...@uow.edu.au>> wrote:

So weird. Is there anything wrong with the way I made the pom file (I labelled 
them as provided)?

Is there missing jar I forget to add in “--jar”?

See the trace below:



Exception in thread "main" java.lang.NoClassDefFoundError: 
breeze/storage/DefaultArrayValue
at smartapp.smart.sparkwithscala.textMingApp.main(textMingApp.scala)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at 
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at 
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at 
org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:664)
at 
org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:169)
at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:192)
at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:111)
at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
Caused by: java.lang.ClassNotFoundException: breeze.storage.DefaultArrayValue
at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
... 10 more
15/11/18 17:15:15 INFO util.Utils: Shutdown hook called


From: Ted Yu [mailto:yuzhih...@gmail.com]
Sent: Wednesday, 18 November 2015 4:01 PM
To: Jack Yang
Cc: user@spark.apache.org<mailto:user@spark.apache.org>
Subject: Re: spark with breeze error of NoClassDefFoundError

Looking in local maven repo, breeze_2.10-0.7.jar contains DefaultArrayValue :

jar tvf 
/Users/tyu/.m2/repository//org/scalanlp/breeze_2.10/0.7/breeze_2.10-0.7.jar | 
grep !$
jar tvf 
/Users/tyu/.m2/repository//org/scalanlp/breeze_2.10/0.7/breeze_2.10-0.7.jar | 
grep DefaultArrayValue
   369 Wed Mar 19 11:18:32 PDT 2014 
breeze/storage/DefaultArrayValue$mcZ$sp$class.class
   309 Wed Mar 19 11:18:32 PDT 2014 
breeze/storage/DefaultArrayValue$mcJ$sp.class
  2233 Wed Mar 19 11:18:32 PDT 2014 
breeze/storage/DefaultArrayValue$DoubleDefaultArrayValue$.class

Can you show the complete stack trace ?

FYI

On Tue, Nov 17, 2015 at 8:33 PM, Jack Yang 
<j...@uow.edu.au<

Re: spark with breeze error of NoClassDefFoundError

[Zhiliang Zhu]

Dear Ted,I just looked at the link you provided, it is great!
For my understanding, I could also directly use other Breeze part (except spark 
mllib package linalg ) in spark (scala or java ) program after importing Breeze 
package,it is right?
Thanks a lot in advance again!Zhiliang  


 On Thursday, November 19, 2015 1:46 PM, Ted Yu <yuzhih...@gmail.com> wrote:
   

 Have you looked athttps://github.com/scalanlp/breeze/wiki
Cheers
On Nov 18, 2015, at 9:34 PM, Zhiliang Zhu <zchl.j...@yahoo.com> wrote:


Dear Jack,
As is known, Breeze is numerical calculation package wrote by scala , spark 
mllib also use it as underlying package for algebra usage.Here I am also 
preparing to use Breeze for nonlinear equation optimization, however, it seemed 
that I could not find the exact doc or API for Breeze except spark linalg 
package...
Could you help some to provide me the official doc or API website for Breeze 
?Thank you in advance!
Zhiliang 
 


 On Thursday, November 19, 2015 7:32 AM, Jack Yang <j...@uow.edu.au> wrote:
   

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72.0pt;}#yiv6155504207 div.yiv6155504207WordSection1 {}#yiv6155504207 If I 
tried to change “provided” to “compile”.. then the error changed to :    
Exception in thread "main" java.lang.IncompatibleClassChangeError: Implementing 
class     at java.lang.ClassLoader.defineClass1(Native Method)     at 
java.lang.ClassLoader.defineClass(ClassLoader.java:800)     at 
java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)     
at java.net.URLClassLoader.defineClass(URLClassLoader.java:449)     at 
java.net.URLClassLoader.access$100(URLClassLoader.java:71)     at 
java.net.URLClassLoader$1.run(URLClassLoader.java:361)     at 
java.net.URLClassLoader$1.run(URLClassLoader.java:355)     at 
java.security.AccessController.doPrivileged(Native Method)     at 
java.net.URLClassLoader.findClass(URLClassLoader.java:354)     at 
java.lang.ClassLoader.loadClass(ClassLoader.java:425)     at 
java.lang.ClassLoader.loadClass(ClassLoader.java:358)     
atsmartapp.smart.sparkwithscala.textMingApp.main(textMingApp.scala)     at 
sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)     at 
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)   
  at 
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
     at java.lang.reflect.Method.invoke(Method.java:606)     at 
org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:664)
     at 
org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:169)     
at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:192)     
at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:111)     at 
org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala) 15/11/19 10:28:29 
INFO util.Utils: Shutdown hook called    Meanwhile, I will prefer to use maven 
to compile the jar file rather than sbt, although it is indeed another option.  
  Best regards, Jack          From: Fengdong Yu 
[mailto:fengdo...@everstring.com]
Sent: Wednesday, 18 November 2015 7:30 PM
To: Jack Yang
Cc: Ted Yu; user@spark.apache.org
Subject: Re: spark with breeze error of NoClassDefFoundError    The simplest 
way is remove all “provided” in your pom.    then ‘sbt assembly” to build your 
final package. then get rid of ‘—jars’ because assembly already includes all 
dependencies.                   
On Nov 18, 2015, at 2:15 PM, Jack Yang <j...@uow.edu.au> wrote:    So weird. Is 
there anything wrong with the way I made the pom file (I labelled them as 
provided)?   Is there missing jar I forget to add 

Re: spark with breeze error of NoClassDefFoundError

[Zhiliang Zhu]

Dear Jack,
As is known, Breeze is numerical calculation package wrote by scala , spark 
mllib also use it as underlying package for algebra usage.Here I am also 
preparing to use Breeze for nonlinear equation optimization, however, it seemed 
that I could not find the exact doc or API for Breeze except spark linalg 
package...
Could you help some to provide me the official doc or API website for Breeze 
?Thank you in advance!
Zhiliang 
 


 On Thursday, November 19, 2015 7:32 AM, Jack Yang <j...@uow.edu.au> wrote:
   

  If I tried to change 
“provided” to “compile”.. then the error changed to :    Exception in thread 
"main" java.lang.IncompatibleClassChangeError: Implementing class     at 
java.lang.ClassLoader.defineClass1(Native Method)     at 
java.lang.ClassLoader.defineClass(ClassLoader.java:800)     at 
java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)     
at java.net.URLClassLoader.defineClass(URLClassLoader.java:449)     at 
java.net.URLClassLoader.access$100(URLClassLoader.java:71)     at 
java.net.URLClassLoader$1.run(URLClassLoader.java:361)     at 
java.net.URLClassLoader$1.run(URLClassLoader.java:355)     at 
java.security.AccessController.doPrivileged(Native Method)     at 
java.net.URLClassLoader.findClass(URLClassLoader.java:354)     at 
java.lang.ClassLoader.loadClass(ClassLoader.java:425)     at 
java.lang.ClassLoader.loadClass(ClassLoader.java:358)     
atsmartapp.smart.sparkwithscala.textMingApp.main(textMingApp.scala)     at 
sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)     at 
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)   
  at 
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
     at java.lang.reflect.Method.invoke(Method.java:606)     at 
org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:664)
     at 
org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:169)     
at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:192)     
at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:111)     at 
org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala) 15/11/19 10:28:29 
INFO util.Utils: Shutdown hook called    Meanwhile, I will prefer to use maven 
to compile the jar file rather than sbt, although it is indeed another option.  
  Best regards, Jack          From: Fengdong Yu 
[mailto:fengdo...@everstring.com]
Sent: Wednesday, 18 November 2015 7:30 PM
To: Jack Yang
Cc: Ted Yu; user@spark.apache.org
Subject: Re: spark with breeze error of NoClassDefFoundError    The simplest 
way is remove all “provided” in your pom.    then ‘sbt assembly” to build your 
final package. then get rid of ‘—jars’ because assembly already includes all 
dependencies.                   
On Nov 18, 2015, at 2:15 PM, Jack Yang <j...@uow.edu.au> wrote:    So weird. Is 
there anything wrong with the way I made the pom file (I labelled them as 
provided)?   Is there missing jar I forget to add in “--jar”?   
See the trace below:       Exception in thread "main" 
java.lang.NoClassDefFoundError: breeze/storage/DefaultArrayValue     at 
smartapp.smart.sparkwithscala.textMingApp.main(textMingApp.scala)     at 
sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)     at 
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)   
  at 
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
     at java.lang.reflect.Method.invoke(Method.java:606)     at 
org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:664)
     at 
org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:169)     
at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:192)     
at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:111)     at 
org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala) Caused by: 
java.lang.ClassNotFoundException: breeze.storage.DefaultArrayValue     at 
java.net.URLClassLoader$1.run(URLClassLoader.java:366)     at 
java.net.URLClassLoader$1.run(URLClassLoader.java:355)     at 
java.security.AccessController.doPrivileged(Native Method)     at 
java.net.URLClassLoader.findClass(URLClassLoader.java:354)     at 
java.lang.ClassLoader.loadClass(ClassLoader.java:425)     at 
java.lang.ClassLoader.loadClass(ClassLoader.java:358)     ... 10 more 
15/11/18 17:15:15 INFO util.Utils: Shutdown hook called     From: Ted Yu 
[mailto:yuzhih...@gmail.com] 
Sent: Wednesday, 18 November 2015 4:01 PM
To: Jack Yang
Cc: user@spark.apache.org
Subject: Re: spark with breeze error of NoClassDefFoundError   Looking in local 
maven repo, breeze_2.10-0.7.jar contains DefaultArrayValue :   jar tvf 
/Users/tyu/.m2/reposito

Re: spark with breeze error of NoClassDefFoundError

[Ted Yu]

Have you looked at
https://github.com/scalanlp/breeze/wiki

Cheers

> On Nov 18, 2015, at 9:34 PM, Zhiliang Zhu <zchl.j...@yahoo.com> wrote:
> 
> Dear Jack,
> 
> As is known, Breeze is numerical calculation package wrote by scala , spark 
> mllib also use it as underlying package for algebra usage.
> Here I am also preparing to use Breeze for nonlinear equation optimization, 
> however, it seemed that I could not find the exact doc or API for Breeze 
> except spark linalg package...
> 
> Could you help some to provide me the official doc or API website for Breeze ?
> Thank you in advance!
> 
> Zhiliang 
> 
> 
> 
> 
> On Thursday, November 19, 2015 7:32 AM, Jack Yang <j...@uow.edu.au> wrote:
> 
> 
> If I tried to change “provided” to “compile”.. then the error changed to :
>  
> Exception in thread "main" java.lang.IncompatibleClassChangeError: 
> Implementing class
> at java.lang.ClassLoader.defineClass1(Native Method)
> at java.lang.ClassLoader.defineClass(ClassLoader.java:800)
> at 
> java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
> at java.net.URLClassLoader.defineClass(URLClassLoader.java:449)
> at java.net.URLClassLoader.access$100(URLClassLoader.java:71)
> at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
> at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
> at java.security.AccessController.doPrivileged(Native Method)
> at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
> at smartapp.smart.sparkwithscala.textMingApp.main(textMingApp.scala)
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at 
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
> at 
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:606)
> at 
> org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:664)
> at 
> org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:169)
> at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:192)
> at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:111)
> at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
> 15/11/19 10:28:29 INFO util.Utils: Shutdown hook called
>  
> Meanwhile, I will prefer to use maven to compile the jar file rather than 
> sbt, although it is indeed another option.
>  
> Best regards,
> Jack
>  
>  
>  
> From: Fengdong Yu [mailto:fengdo...@everstring.com] 
> Sent: Wednesday, 18 November 2015 7:30 PM
> To: Jack Yang
> Cc: Ted Yu; user@spark.apache.org
> Subject: Re: spark with breeze error of NoClassDefFoundError
>  
> The simplest way is remove all “provided” in your pom.
>  
> then ‘sbt assembly” to build your final package. then get rid of ‘—jars’ 
> because assembly already includes all dependencies.
>  
>  
>  
>  
>  
>  
> On Nov 18, 2015, at 2:15 PM, Jack Yang <j...@uow.edu.au> wrote:
>  
> So weird. Is there anything wrong with the way I made the pom file (I 
> labelled them as provided)?
>  
> Is there missing jar I forget to add in “--jar”?
>  
> See the trace below:
>  
>  
>  
> Exception in thread "main" java.lang.NoClassDefFoundError: 
> breeze/storage/DefaultArrayValue
> at smartapp.smart.sparkwithscala.textMingApp.main(textMingApp.scala)
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at 
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
> at 
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:606)
> at 
> org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:664)
> at 
> org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:169)
> at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:192)
> at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:111)
> at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
> Caused by: java.lang.ClassNotFoundException: breeze.storage.DefaultArrayValue
> at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
> at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
> at java.security.Access

RE: spark with breeze error of NoClassDefFoundError

[Jack Yang]

Back to my question. If  I use “provided”, the jar file will 
expect some libraries are provided by the system.
However, the “ compiled ” is the default setting, which means 
the third-party library will be included inside jar file after compiling.
So when I use “provided”, the error is they cannot find the 
Class, but with “compiled” the error is IncompatibleClassChangeError.

Ok, so can someone tell me which version of breeze and breeze-math are used in 
spark 1.4?

From: Zhiliang Zhu [mailto:zchl.j...@yahoo.com]
Sent: Thursday, 19 November 2015 5:10 PM
To: Ted Yu
Cc: Jack Yang; Fengdong Yu; user@spark.apache.org
Subject: Re: spark with breeze error of NoClassDefFoundError

Dear Ted,
I just looked at the link you provided, it is great!

For my understanding, I could also directly use other Breeze part (except spark 
mllib package linalg ) in spark (scala or java ) program after importing Breeze 
package,
it is right?

Thanks a lot in advance again!
Zhiliang



On Thursday, November 19, 2015 1:46 PM, Ted Yu 
<yuzhih...@gmail.com<mailto:yuzhih...@gmail.com>> wrote:

Have you looked at
https://github.com/scalanlp/breeze/wiki

Cheers

On Nov 18, 2015, at 9:34 PM, Zhiliang Zhu 
<zchl.j...@yahoo.com<mailto:zchl.j...@yahoo.com>> wrote:
Dear Jack,

As is known, Breeze is numerical calculation package wrote by scala , spark 
mllib also use it as underlying package for algebra usage.
Here I am also preparing to use Breeze for nonlinear equation optimization, 
however, it seemed that I could not find the exact doc or API for Breeze except 
spark linalg package...

Could you help some to provide me the official doc or API website for Breeze ?
Thank you in advance!

Zhiliang



On Thursday, November 19, 2015 7:32 AM, Jack Yang 
<j...@uow.edu.au<mailto:j...@uow.edu.au>> wrote:

If I tried to change “provided” to “compile”.. then the error changed to :

Exception in thread "main" java.lang.IncompatibleClassChangeError: Implementing 
class
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(ClassLoader.java:800)
at 
java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:449)
at java.net.URLClassLoader.access$100(URLClassLoader.java:71)
at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
at smartapp.smart.sparkwithscala.textMingApp.main(textMingApp.scala)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at 
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at 
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at 
org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:664)
at 
org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:169)
at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:192)
at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:111)
at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
15/11/19 10:28:29 INFO util.Utils: Shutdown hook called

Meanwhile, I will prefer to use maven to compile the jar file rather than sbt, 
although it is indeed another option.

Best regards,
Jack



From: Fengdong Yu [mailto:fengdo...@everstring.com]
Sent: Wednesday, 18 November 2015 7:30 PM
To: Jack Yang
Cc: Ted Yu; user@spark.apache.org<mailto:user@spark.apache.org>
Subject: Re: spark with breeze error of NoClassDefFoundError

The simplest way is remove all “provided” in your pom.

then ‘sbt assembly” to build your final package. then get rid of ‘—jars’ 
because assembly already includes all dependencies.






On Nov 18, 2015, at 2:15 PM, Jack Yang 
<j...@uow.edu.au<mailto:j...@uow.edu.au>> wrote:

So weird. Is there anything wrong with the way I made the pom file (I labelled 
them as provided)?

Is there missing jar I forget to add in “--jar”?

See the trace below:



Exception in thread "main" java.lang.NoClassDefFoundError: 
breeze/storage/DefaultArrayValue
at smartapp.smart.sparkwithscala.textMingApp.main(textMingApp.scala)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at 
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at 
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at

Re: spark with breeze error of NoClassDefFoundError

[Ted Yu]

Looking in local maven repo, breeze_2.10-0.7.jar contains DefaultArrayValue
:

jar tvf
/Users/tyu/.m2/repository//org/scalanlp/breeze_2.10/0.7/breeze_2.10-0.7.jar
| grep !$
jar tvf
/Users/tyu/.m2/repository//org/scalanlp/breeze_2.10/0.7/breeze_2.10-0.7.jar
| grep DefaultArrayValue
   369 Wed Mar 19 11:18:32 PDT 2014
breeze/storage/DefaultArrayValue$mcZ$sp$class.class
   309 Wed Mar 19 11:18:32 PDT 2014
breeze/storage/DefaultArrayValue$mcJ$sp.class
  2233 Wed Mar 19 11:18:32 PDT 2014
breeze/storage/DefaultArrayValue$DoubleDefaultArrayValue$.class

Can you show the complete stack trace ?

FYI

On Tue, Nov 17, 2015 at 8:33 PM, Jack Yang  wrote:

> Hi all,
>
> I am using spark 1.4.0, and building my codes using maven.
>
> So in one of my scala, I used:
>
>
>
> import breeze.linalg._
>
> val v1 = new breeze.linalg.SparseVector(commonVector.indices,
> commonVector.values, commonVector.size)
>
> val v2 = new breeze.linalg.SparseVector(commonVector2.indices,
> commonVector2.values, commonVector2.size)
>
> println (v1.dot(v2) / (norm(v1) * norm(v2)) )
>
>
>
>
>
>
>
> in my pom.xml file, I used:
>
> 
>
>
> org.scalanlp
>
>
> breeze-math_2.10
>
>  0.4
>
>  *provided*
>
>   
>
>
>
>   
>
>
> org.scalanlp
>
>
> breeze_2.10
>
>  0.11.2
>
>  *provided*
>
>   
>
>
>
>
>
> When submit, I included breeze jars (breeze_2.10-0.11.2.jar
> breeze-math_2.10-0.4.jar breeze-natives_2.10-0.11.2.jar
> breeze-process_2.10-0.3.jar) using “--jar” arguments, although I doubt it
> is necessary to do that.
>
>
>
> however, the error is
>
>
>
> Exception in thread "main" java.lang.NoClassDefFoundError:
> breeze/storage/DefaultArrayValue
>
>
>
> Any thoughts?
>
>
>
>
>
>
>
> Best regards,
>
> Jack
>
>
>

RE: spark with breeze error of NoClassDefFoundError

[Jack Yang]

So weird. Is there anything wrong with the way I made the pom file (I labelled 
them as provided)?

Is there missing jar I forget to add in “--jar”?

See the trace below:



Exception in thread "main" java.lang.NoClassDefFoundError: 
breeze/storage/DefaultArrayValue
at smartapp.smart.sparkwithscala.textMingApp.main(textMingApp.scala)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at 
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at 
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at 
org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:664)
at 
org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:169)
at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:192)
at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:111)
at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
Caused by: java.lang.ClassNotFoundException: breeze.storage.DefaultArrayValue
at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
... 10 more
15/11/18 17:15:15 INFO util.Utils: Shutdown hook called


From: Ted Yu [mailto:yuzhih...@gmail.com]
Sent: Wednesday, 18 November 2015 4:01 PM
To: Jack Yang
Cc: user@spark.apache.org
Subject: Re: spark with breeze error of NoClassDefFoundError

Looking in local maven repo, breeze_2.10-0.7.jar contains DefaultArrayValue :

jar tvf 
/Users/tyu/.m2/repository//org/scalanlp/breeze_2.10/0.7/breeze_2.10-0.7.jar | 
grep !$
jar tvf 
/Users/tyu/.m2/repository//org/scalanlp/breeze_2.10/0.7/breeze_2.10-0.7.jar | 
grep DefaultArrayValue
   369 Wed Mar 19 11:18:32 PDT 2014 
breeze/storage/DefaultArrayValue$mcZ$sp$class.class
   309 Wed Mar 19 11:18:32 PDT 2014 
breeze/storage/DefaultArrayValue$mcJ$sp.class
  2233 Wed Mar 19 11:18:32 PDT 2014 
breeze/storage/DefaultArrayValue$DoubleDefaultArrayValue$.class

Can you show the complete stack trace ?

FYI

On Tue, Nov 17, 2015 at 8:33 PM, Jack Yang 
<j...@uow.edu.au<mailto:j...@uow.edu.au>> wrote:
Hi all,
I am using spark 1.4.0, and building my codes using maven.
So in one of my scala, I used:

import breeze.linalg._
val v1 = new breeze.linalg.SparseVector(commonVector.indices, 
commonVector.values, commonVector.size)
val v2 = new breeze.linalg.SparseVector(commonVector2.indices, 
commonVector2.values, commonVector2.size)
println (v1.dot(v2) / (norm(v1) * norm(v2)) )



in my pom.xml file, I used:

 org.scalanlp
 
breeze-math_2.10
 0.4
 provided
  

  
 org.scalanlp
 
breeze_2.10
 0.11.2
 provided
  


When submit, I included breeze jars (breeze_2.10-0.11.2.jar 
breeze-math_2.10-0.4.jar breeze-natives_2.10-0.11.2.jar 
breeze-process_2.10-0.3.jar) using “--jar” arguments, although I doubt it is 
necessary to do that.

however, the error is

Exception in thread "main" java.lang.NoClassDefFoundError: 
breeze/storage/DefaultArrayValue

Any thoughts?



Best regards,
Jack