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From "RJ Nowling (JIRA)" <j...@apache.org>
Subject [jira] [Comment Edited] (SPARK-4816) Maven profile netlib-lgpl does not work
Date Mon, 14 Dec 2015 15:43:46 GMT

    [ https://issues.apache.org/jira/browse/SPARK-4816?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15056115#comment-15056115
] 

RJ Nowling edited comment on SPARK-4816 at 12/14/15 3:42 PM:
-------------------------------------------------------------

I tested it again to make sure and ran into the same issue:

{code}
$ mvn -version
Apache Maven 3.2.5 (12a6b3acb947671f09b81f49094c53f426d8cea1; 2014-12-14T17:29:23+00:00)
Maven home: /usr/share/apache-maven
Java version: 1.7.0_85, vendor: Oracle Corporation
Java home: /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.85-2.6.1.2.el7_1.x86_64/jre
Default locale: en_US, platform encoding: UTF-8
OS name: "linux", version: "3.10.0-229.1.2.el7.x86_64", arch: "amd64", family: "unix"

$ export MAVEN_OPTS="-Xmx2g -XX:MaxPermSize=512M -XX:ReservedCodeCacheSize=512m"
$ wget http://d3kbcqa49mib13.cloudfront.net/spark-1.4.1.tgz
$ tar -xzvf spark-1.4.1.tgz
$ cd spark-1.4.1
$ mvn -Pnetlib-lgpl -Phadoop-2.4 -Dhadoop.version=2.4.0 -DskipTests clean package
$ zipinfo -1 assembly/target/scala-2.10/spark-assembly-1.4.1-hadoop2.4.0.jar | grep netlib-native

(No output)
{code}

If I build the head from git {{branch-1.4}} and run {{zipinfo}}:

{code}
$ git clone https://github.com/apache/spark.git spark-1.4-netlib
$ cd spark-1.4-netlib
$ git checkout origin/branch-1.4
$ git log | head
commit c7c99857d47e4ca8373ee9ac59e108a9c443dd05
Author: Sean Owen <sowen@cloudera.com>
Date:   Tue Dec 8 14:34:47 2015 +0000

    [SPARK-11652][CORE] Remote code execution with InvokerTransformer

    Fix commons-collection group ID to commons-collections for version 3.x

    Patches earlier PR at https://github.com/apache/spark/pull/9731

$ zipinfo -1 assembly/target/scala-2.10/spark-assembly-1.4.3-SNAPSHOT-hadoop2.4.0.jar | grep
netlib-native
netlib-native_ref-osx-x86_64.jnilib
netlib-native_ref-osx-x86_64.jnilib.asc
netlib-native_ref-osx-x86_64.pom
netlib-native_ref-osx-x86_64.pom.asc
META-INF/maven/com.github.fommil.netlib/netlib-native_ref-osx-x86_64/
META-INF/maven/com.github.fommil.netlib/netlib-native_ref-osx-x86_64/pom.xml
META-INF/maven/com.github.fommil.netlib/netlib-native_ref-osx-x86_64/pom.properties
netlib-native_ref-linux-x86_64.so
META-INF/maven/com.github.fommil.netlib/netlib-native_ref-linux-x86_64/
META-INF/maven/com.github.fommil.netlib/netlib-native_ref-linux-x86_64/pom.xml
META-INF/maven/com.github.fommil.netlib/netlib-native_ref-linux-x86_64/pom.properties
netlib-native_ref-linux-i686.so
META-INF/maven/com.github.fommil.netlib/netlib-native_ref-linux-i686/
META-INF/maven/com.github.fommil.netlib/netlib-native_ref-linux-i686/pom.xml
META-INF/maven/com.github.fommil.netlib/netlib-native_ref-linux-i686/pom.properties
netlib-native_ref-win-x86_64.dll
netlib-native_ref-win-x86_64.dll.asc
netlib-native_ref-win-x86_64.pom
netlib-native_ref-win-x86_64.pom.asc
META-INF/maven/com.github.fommil.netlib/netlib-native_ref-win-x86_64/
META-INF/maven/com.github.fommil.netlib/netlib-native_ref-win-x86_64/pom.xml
META-INF/maven/com.github.fommil.netlib/netlib-native_ref-win-x86_64/pom.properties
netlib-native_ref-win-i686.dll
netlib-native_ref-win-i686.dll.asc
netlib-native_ref-win-i686.pom
netlib-native_ref-win-i686.pom.asc
META-INF/maven/com.github.fommil.netlib/netlib-native_ref-win-i686/
META-INF/maven/com.github.fommil.netlib/netlib-native_ref-win-i686/pom.xml
META-INF/maven/com.github.fommil.netlib/netlib-native_ref-win-i686/pom.properties
netlib-native_ref-linux-armhf.so
META-INF/maven/com.github.fommil.netlib/netlib-native_ref-linux-armhf/
META-INF/maven/com.github.fommil.netlib/netlib-native_ref-linux-armhf/pom.xml
META-INF/maven/com.github.fommil.netlib/netlib-native_ref-linux-armhf/pom.properties
netlib-native_system-osx-x86_64.jnilib
netlib-native_system-osx-x86_64.jnilib.asc
netlib-native_system-osx-x86_64.pom
netlib-native_system-osx-x86_64.pom.asc
META-INF/maven/com.github.fommil.netlib/netlib-native_system-osx-x86_64/
META-INF/maven/com.github.fommil.netlib/netlib-native_system-osx-x86_64/pom.xml
META-INF/maven/com.github.fommil.netlib/netlib-native_system-osx-x86_64/pom.properties
netlib-native_system-linux-x86_64.pom.asc
netlib-native_system-linux-x86_64.pom
netlib-native_system-linux-x86_64.so
netlib-native_system-linux-x86_64.so.asc
META-INF/maven/com.github.fommil.netlib/netlib-native_system-linux-x86_64/
META-INF/maven/com.github.fommil.netlib/netlib-native_system-linux-x86_64/pom.xml
META-INF/maven/com.github.fommil.netlib/netlib-native_system-linux-x86_64/pom.properties
netlib-native_system-linux-i686.pom
netlib-native_system-linux-i686.so.asc
netlib-native_system-linux-i686.pom.asc
netlib-native_system-linux-i686.so
META-INF/maven/com.github.fommil.netlib/netlib-native_system-linux-i686/
META-INF/maven/com.github.fommil.netlib/netlib-native_system-linux-i686/pom.xml
META-INF/maven/com.github.fommil.netlib/netlib-native_system-linux-i686/pom.properties
netlib-native_system-linux-armhf.pom
netlib-native_system-linux-armhf.so.asc
netlib-native_system-linux-armhf.pom.asc
netlib-native_system-linux-armhf.so
META-INF/maven/com.github.fommil.netlib/netlib-native_system-linux-armhf/
META-INF/maven/com.github.fommil.netlib/netlib-native_system-linux-armhf/pom.xml
META-INF/maven/com.github.fommil.netlib/netlib-native_system-linux-armhf/pom.properties
netlib-native_system-win-x86_64.dll
netlib-native_system-win-x86_64.dll.asc
netlib-native_system-win-x86_64.pom
netlib-native_system-win-x86_64.pom.asc
META-INF/maven/com.github.fommil.netlib/netlib-native_system-win-x86_64/
META-INF/maven/com.github.fommil.netlib/netlib-native_system-win-x86_64/pom.xml
META-INF/maven/com.github.fommil.netlib/netlib-native_system-win-x86_64/pom.properties
netlib-native_system-win-i686.dll
netlib-native_system-win-i686.dll.asc
netlib-native_system-win-i686.pom
netlib-native_system-win-i686.pom.asc
META-INF/maven/com.github.fommil.netlib/netlib-native_system-win-i686/
META-INF/maven/com.github.fommil.netlib/netlib-native_system-win-i686/pom.xml
META-INF/maven/com.github.fommil.netlib/netlib-native_system-win-i686/pom.properties
{code}

I'm testing on CentOS 7 but using a custom installed Maven version instead of the EPEL default.


was (Author: rnowling):
I tested it again to make sure and ran into the same issue:

{code}
$ mvn -version
Apache Maven 3.2.5 (12a6b3acb947671f09b81f49094c53f426d8cea1; 2014-12-14T17:29:23+00:00)
Maven home: /usr/share/apache-maven
Java version: 1.7.0_85, vendor: Oracle Corporation
Java home: /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.85-2.6.1.2.el7_1.x86_64/jre
Default locale: en_US, platform encoding: UTF-8
OS name: "linux", version: "3.10.0-229.1.2.el7.x86_64", arch: "amd64", family: "unix"

$ export MAVEN_OPTS="-Xmx2g -XX:MaxPermSize=512M -XX:ReservedCodeCacheSize=512m"
$ wget http://d3kbcqa49mib13.cloudfront.net/spark-1.4.1.tgz
$ tar -xzvf spark-1.4.1.tgz
$ cd spark-1.4.1
$ mvn -Pnetlib-lgpl -Phadoop-2.4 -Dhadoop.version=2.4.0 -DskipTests clean package
$ zipinfo -1 assembly/target/scala-2.10/spark-assembly-1.4.1-hadoop2.4.0.jar | grep netlib-native

(No output)
{code}

If I build the head from git {{branch-1.4}} and run {{zipinfo}}:

{code}
$ git log | head
commit c7c99857d47e4ca8373ee9ac59e108a9c443dd05
Author: Sean Owen <sowen@cloudera.com>
Date:   Tue Dec 8 14:34:47 2015 +0000

    [SPARK-11652][CORE] Remote code execution with InvokerTransformer

    Fix commons-collection group ID to commons-collections for version 3.x

    Patches earlier PR at https://github.com/apache/spark/pull/9731

$ zipinfo -1 assembly/target/scala-2.10/spark-assembly-1.4.3-SNAPSHOT-hadoop2.4.0.jar | grep
netlib-native
netlib-native_ref-osx-x86_64.jnilib
netlib-native_ref-osx-x86_64.jnilib.asc
netlib-native_ref-osx-x86_64.pom
netlib-native_ref-osx-x86_64.pom.asc
META-INF/maven/com.github.fommil.netlib/netlib-native_ref-osx-x86_64/
META-INF/maven/com.github.fommil.netlib/netlib-native_ref-osx-x86_64/pom.xml
META-INF/maven/com.github.fommil.netlib/netlib-native_ref-osx-x86_64/pom.properties
netlib-native_ref-linux-x86_64.so
META-INF/maven/com.github.fommil.netlib/netlib-native_ref-linux-x86_64/
META-INF/maven/com.github.fommil.netlib/netlib-native_ref-linux-x86_64/pom.xml
META-INF/maven/com.github.fommil.netlib/netlib-native_ref-linux-x86_64/pom.properties
netlib-native_ref-linux-i686.so
META-INF/maven/com.github.fommil.netlib/netlib-native_ref-linux-i686/
META-INF/maven/com.github.fommil.netlib/netlib-native_ref-linux-i686/pom.xml
META-INF/maven/com.github.fommil.netlib/netlib-native_ref-linux-i686/pom.properties
netlib-native_ref-win-x86_64.dll
netlib-native_ref-win-x86_64.dll.asc
netlib-native_ref-win-x86_64.pom
netlib-native_ref-win-x86_64.pom.asc
META-INF/maven/com.github.fommil.netlib/netlib-native_ref-win-x86_64/
META-INF/maven/com.github.fommil.netlib/netlib-native_ref-win-x86_64/pom.xml
META-INF/maven/com.github.fommil.netlib/netlib-native_ref-win-x86_64/pom.properties
netlib-native_ref-win-i686.dll
netlib-native_ref-win-i686.dll.asc
netlib-native_ref-win-i686.pom
netlib-native_ref-win-i686.pom.asc
META-INF/maven/com.github.fommil.netlib/netlib-native_ref-win-i686/
META-INF/maven/com.github.fommil.netlib/netlib-native_ref-win-i686/pom.xml
META-INF/maven/com.github.fommil.netlib/netlib-native_ref-win-i686/pom.properties
netlib-native_ref-linux-armhf.so
META-INF/maven/com.github.fommil.netlib/netlib-native_ref-linux-armhf/
META-INF/maven/com.github.fommil.netlib/netlib-native_ref-linux-armhf/pom.xml
META-INF/maven/com.github.fommil.netlib/netlib-native_ref-linux-armhf/pom.properties
netlib-native_system-osx-x86_64.jnilib
netlib-native_system-osx-x86_64.jnilib.asc
netlib-native_system-osx-x86_64.pom
netlib-native_system-osx-x86_64.pom.asc
META-INF/maven/com.github.fommil.netlib/netlib-native_system-osx-x86_64/
META-INF/maven/com.github.fommil.netlib/netlib-native_system-osx-x86_64/pom.xml
META-INF/maven/com.github.fommil.netlib/netlib-native_system-osx-x86_64/pom.properties
netlib-native_system-linux-x86_64.pom.asc
netlib-native_system-linux-x86_64.pom
netlib-native_system-linux-x86_64.so
netlib-native_system-linux-x86_64.so.asc
META-INF/maven/com.github.fommil.netlib/netlib-native_system-linux-x86_64/
META-INF/maven/com.github.fommil.netlib/netlib-native_system-linux-x86_64/pom.xml
META-INF/maven/com.github.fommil.netlib/netlib-native_system-linux-x86_64/pom.properties
netlib-native_system-linux-i686.pom
netlib-native_system-linux-i686.so.asc
netlib-native_system-linux-i686.pom.asc
netlib-native_system-linux-i686.so
META-INF/maven/com.github.fommil.netlib/netlib-native_system-linux-i686/
META-INF/maven/com.github.fommil.netlib/netlib-native_system-linux-i686/pom.xml
META-INF/maven/com.github.fommil.netlib/netlib-native_system-linux-i686/pom.properties
netlib-native_system-linux-armhf.pom
netlib-native_system-linux-armhf.so.asc
netlib-native_system-linux-armhf.pom.asc
netlib-native_system-linux-armhf.so
META-INF/maven/com.github.fommil.netlib/netlib-native_system-linux-armhf/
META-INF/maven/com.github.fommil.netlib/netlib-native_system-linux-armhf/pom.xml
META-INF/maven/com.github.fommil.netlib/netlib-native_system-linux-armhf/pom.properties
netlib-native_system-win-x86_64.dll
netlib-native_system-win-x86_64.dll.asc
netlib-native_system-win-x86_64.pom
netlib-native_system-win-x86_64.pom.asc
META-INF/maven/com.github.fommil.netlib/netlib-native_system-win-x86_64/
META-INF/maven/com.github.fommil.netlib/netlib-native_system-win-x86_64/pom.xml
META-INF/maven/com.github.fommil.netlib/netlib-native_system-win-x86_64/pom.properties
netlib-native_system-win-i686.dll
netlib-native_system-win-i686.dll.asc
netlib-native_system-win-i686.pom
netlib-native_system-win-i686.pom.asc
META-INF/maven/com.github.fommil.netlib/netlib-native_system-win-i686/
META-INF/maven/com.github.fommil.netlib/netlib-native_system-win-i686/pom.xml
META-INF/maven/com.github.fommil.netlib/netlib-native_system-win-i686/pom.properties
{code}

I'm testing on CentOS 7 but using a custom installed Maven version instead of the EPEL default.

> Maven profile netlib-lgpl does not work
> ---------------------------------------
>
>                 Key: SPARK-4816
>                 URL: https://issues.apache.org/jira/browse/SPARK-4816
>             Project: Spark
>          Issue Type: Bug
>          Components: Build
>    Affects Versions: 1.1.0
>         Environment: maven 3.0.5 / Ubuntu
>            Reporter: Guillaume Pitel
>            Priority: Minor
>             Fix For: 1.1.1
>
>
> When doing what the documentation recommends to recompile Spark with Netlib Native system
binding (i.e. to bind with openblas or, in my case, MKL), 
> mvn -Pnetlib-lgpl -Pyarn -Phadoop-2.3 -Dhadoop.version=2.3.0 -DskipTests clean package
> The resulting assembly jar still lacked the netlib-system class. (I checked the content
of spark-assembly...jar)
> When forcing the netlib-lgpl profile in MLLib package to be active, the jar is correctly
built.
> So I guess it's a problem with the way maven passes profiles activitations to children
modules.
> Also, despite the documentation claiming that if the job's jar contains netlib with necessary
bindings, it should works, it does not. The classloader must be unhappy with two occurrences
of netlib ?



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