no jnind4jcpu in java.library.path when using version M2 of DeepLearning4j-CodePudding

I am working with DeepLearning4j library. I am running everything on HPC and I generate a jar file to submit with spark-submit. I was using the version beta7 and I didn't have any problem. Recently, I wanted to upgrade the version to M2 but I got this error:

        at org.nd4j.linalg.cpu.nativecpu.ops.NativeOpExecutioner.<init>(NativeOpExecutioner.java:79)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
        at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
        at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
        at java.lang.Class.newInstance(Class.java:442)
        at org.nd4j.linalg.factory.Nd4j.initWithBackend(Nd4j.java:5129)
        at org.nd4j.linalg.factory.Nd4j.initContext(Nd4j.java:5044)
        at org.nd4j.linalg.factory.Nd4j.<clinit>(Nd4j.java:269)
        at org.datavec.image.loader.NativeImageLoader.transformImage(NativeImageLoader.java:631)
        at org.datavec.image.loader.NativeImageLoader.asMatrix(NativeImageLoader.java:554)
        at org.datavec.image.loader.NativeImageLoader.asMatrix(NativeImageLoader.java:280)
        at org.datavec.image.loader.NativeImageLoader.asMatrix(NativeImageLoader.java:255)
        at org.datavec.image.loader.NativeImageLoader.asMatrix(NativeImageLoader.java:249)
        at org.datavec.image.recordreader.BaseImageRecordReader.next(BaseImageRecordReader.java:247)
        at org.datavec.image.recordreader.BaseImageRecordReader.nextRecord(BaseImageRecordReader.java:511)
        at org.deeplearning4j.datasets.datavec.RecordReaderDataSetIterator.initializeUnderlying(RecordReaderDataSetIterator.java:194)
        at org.deeplearning4j.datasets.datavec.RecordReaderDataSetIterator.next(RecordReaderDataSetIterator.java:341)
        at org.deeplearning4j.datasets.datavec.RecordReaderDataSetIterator.next(RecordReaderDataSetIterator.java:421)
        at org.deeplearning4j.datasets.datavec.RecordReaderDataSetIterator.next(RecordReaderDataSetIterator.java:53)
        at com.examples.DeepLearningOnSpark.imageNet_image.streaming.NetworkRetrainingMain.entryPoint(NetworkRetrainingMain.java:55)
        at com.examples.DeepLearningOnSpark.imageNet_image.streaming.NetworkRetrainingMain.main(NetworkRetrainingMain.java:31)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.apache.spark.deploy.JavaMainApplication.start(SparkApplication.scala:52)
        at org.apache.spark.deploy.SparkSubmit.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:928)
        at org.apache.spark.deploy.SparkSubmit.doRunMain$1(SparkSubmit.scala:180)
        at org.apache.spark.deploy.SparkSubmit.submit(SparkSubmit.scala:203)
        at org.apache.spark.deploy.SparkSubmit.doSubmit(SparkSubmit.scala:90)
        at org.apache.spark.deploy.SparkSubmit$$anon$2.doSubmit(SparkSubmit.scala:1007)
        at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:1016)
        at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
Caused by: java.lang.RuntimeException: ND4J is probably missing dependencies. For more information, please refer to: https://deeplearning4j.konduit.ai/nd4j/backend
        at org.nd4j.nativeblas.NativeOpsHolder.<init>(NativeOpsHolder.java:116)
        at org.nd4j.nativeblas.NativeOpsHolder.<clinit>(NativeOpsHolder.java:37)
        ... 34 more
Caused by: java.lang.UnsatisfiedLinkError: no jnind4jcpu in java.library.path
        at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1867)
        at java.lang.Runtime.loadLibrary0(Runtime.java:870)
        at java.lang.System.loadLibrary(System.java:1122)
        at org.bytedeco.javacpp.Loader.loadLibrary(Loader.java:1800)
        at org.bytedeco.javacpp.Loader.load(Loader.java:1402)
        at org.bytedeco.javacpp.Loader.load(Loader.java:1214)
        at org.bytedeco.javacpp.Loader.load(Loader.java:1190)
        at org.nd4j.linalg.cpu.nativecpu.bindings.Nd4jCpu.<clinit>(Nd4jCpu.java:14)
        at java.lang.Class.forName0(Native Method)
        at java.lang.Class.forName(Class.java:348)
        at org.nd4j.common.config.ND4JClassLoading.loadClassByName(ND4JClassLoading.java:62)
        at org.nd4j.common.config.ND4JClassLoading.loadClassByName(ND4JClassLoading.java:56)
        at org.nd4j.nativeblas.NativeOpsHolder.<init>(NativeOpsHolder.java:88)
        ... 35 more
Caused by: java.lang.UnsatisfiedLinkError: /home/h4/nore667e/.javacpp/cache/deepLearningSimpleOne-1.0-SNAPSHOT-jar-with-dependencies.jar/org/nd4j/linalg/cpu/nativecpu/bindings/linux-x86_64/libjnind4jcpu.so: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by /home/h4/nore667e/.javacpp/cache/deepLearningSimpleOne-1.0-SNAPSHOT-jar-with-dependencies.jar/org/nd4j/linalg/cpu/nativecpu/bindings/linux-x86_64/libnd4jcpu.so)
        at java.lang.ClassLoader$NativeLibrary.load(Native Method)
        at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1941)
        at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1824)
        at java.lang.Runtime.load0(Runtime.java:809)
        at java.lang.System.load(System.java:1086)
        at org.bytedeco.javacpp.Loader.loadLibrary(Loader.java:1747)
        ... 44 more

Here is my pom.xml file:

    <artifactId>deepLearningSimpleOne</artifactId>
    <version>1.0-SNAPSHOT</version>

    <properties>
        <dl4j-master.version>1.0.0-M2</dl4j-master.version>
        <!-- Change the nd4j.backend property to nd4j-cuda-X-platform to use CUDA GPUs -->
        <!-- <nd4j.backend>nd4j-cuda-10.2-platform</nd4j.backend> -->
        <nd4j.backend>nd4j-native</nd4j.backend>
        <java.version>1.8</java.version>
        <shadedClassifier>bin</shadedClassifier>
        <scala.binary.version>2.12</scala.binary.version>
        <maven-compiler-plugin.version>3.8.1</maven-compiler-plugin.version>
        <maven.minimum.version>3.3.1</maven.minimum.version>
        <exec-maven-plugin.version>1.4.0</exec-maven-plugin.version>
        <maven-shade-plugin.version>2.4.3</maven-shade-plugin.version>
        <jcommon.version>1.0.23</jcommon.version>
        <jfreechart.version>1.0.13</jfreechart.version>
        <logback.version>1.1.7</logback.version>
        <jcommander.version>1.27</jcommander.version>
        <azure.hadoop.version>2.7.4</azure.hadoop.version>
        <azure.storage.version>2.0.0</azure.storage.version>
        <spark.version>2.4.8</spark.version>
        <aws.sdk.version>1.11.109</aws.sdk.version>
        <jackson.version>2.5.1</jackson.version>
        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
    </properties>
    
    <build>
        <plugins>


            <plugin>
                <groupId>org.codehaus.mojo</groupId>
                <artifactId>exec-maven-plugin</artifactId>
                <version>${exec-maven-plugin.version}</version>
                <executions>
                    <execution>
                        <goals>
                            <goal>exec</goal>
                        </goals>
                    </execution>
                </executions>
                <configuration>
                    <executable>java</executable>
                </configuration>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-shade-plugin</artifactId>
                <version>${maven-shade-plugin.version}</version>
                <configuration>
                    <shadedArtifactAttached>true</shadedArtifactAttached>
                    <shadedClassifierName>${shadedClassifier}</shadedClassifierName>
                    <createDependencyReducedPom>true</createDependencyReducedPom>
                    <filters>
                        <filter>
                            <artifact>*:*</artifact>
                            <excludes>
                                <exclude>org/datanucleus/**</exclude>
                                <exclude>META-INF/*.SF</exclude>
                                <exclude>META-INF/*.DSA</exclude>
                                <exclude>META-INF/*.RSA</exclude>
                            </excludes>
                        </filter>
                    </filters>
                </configuration>
                <executions>
                    <execution>
                        <phase>package</phase>
                        <goals>
                            <goal>shade</goal>
                        </goals>
                        <configuration>
                            <transformers>
                                <transformer implementation="org.apache.maven.plugins.shade.resource.AppendingTransformer">
                                    <resource>reference.conf</resource>
                                </transformer>
                                <transformer implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer"/>
                                <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
                                </transformer>
                            </transformers>
                        </configuration>
                    </execution>
                </executions>
            </plugin>
            <!--      Added to enable jar creation using mvn command-->
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-assembly-plugin</artifactId>
                <version>3.3.0</version>
                <configuration>
                    <archive>
                        <manifest>
                            <mainClass>fully.qualified.MainClass</mainClass>
                        </manifest>
                    </archive>
                    <descriptorRefs>
                        <descriptorRef>jar-with-dependencies</descriptorRef>
                    </descriptorRefs>
                </configuration>
                <executions>
                    <execution>
                        <id>make-assembly</id>
                        <!-- bind to the packaging phase -->
                        <phase>package</phase>
                        <goals>
                            <goal>single</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>


            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-compiler-plugin</artifactId>
                <version>3.5.1</version>
                <configuration>
                    <source>${java.version}</source>
                    <target>${java.version}</target>
                </configuration>
            </plugin>
        </plugins>
    </build>
    

    <dependencies>
        
        <dependency>
            <groupId>org.deeplearning4j</groupId>
            <artifactId>resources</artifactId>
            <version>${dl4j-master.version}</version>
        </dependency>

        <dependency>
            <groupId>org.apache.spark</groupId>
            <artifactId>spark-core_${scala.binary.version}</artifactId>
            <version>${spark.version}</version>
        </dependency>
        <dependency>
            <groupId>org.nd4j</groupId>
            <artifactId>${nd4j.backend}</artifactId>
            <version>${dl4j-master.version}</version>
        </dependency>
        <dependency>
            <groupId>org.datavec</groupId>
            <artifactId>datavec-spark_${scala.binary.version}</artifactId>
            <version>${dl4j-master.version}</version>
        </dependency>
        <dependency>
            <groupId>org.deeplearning4j</groupId>
            <artifactId>dl4j-spark_${scala.binary.version}</artifactId>
            <version>${dl4j-master.version}</version>
        </dependency>
        <dependency>
            <groupId>org.deeplearning4j</groupId>
            <artifactId>dl4j-spark-parameterserver_${scala.binary.version}</artifactId>
            <version>${dl4j-master.version}</version>
        </dependency>
        <dependency>
            <groupId>com.beust</groupId>
            <artifactId>jcommander</artifactId>
            <version>${jcommander.version}</version>
        </dependency>
        <!-- Used for patent classification example -->
        <dependency>
            <groupId>org.deeplearning4j</groupId>
            <artifactId>deeplearning4j-nlp</artifactId>
            <version>${dl4j-master.version}</version>
        </dependency>
        <dependency>
            <groupId>org.deeplearning4j</groupId>
            <artifactId>deeplearning4j-zoo</artifactId>
            <version>${dl4j-master.version}</version>
        </dependency>
        <dependency>
            <groupId>org.deeplearning4j</groupId>
            <artifactId>deeplearning4j-core</artifactId>
            <version>1.0.0-M2</version>
        </dependency>


        <dependency>
            <groupId>org.jsoup</groupId>
            <artifactId>jsoup</artifactId>
            <version>1.10.2</version>
        </dependency>

    </dependencies>

</project>

Anyone can help me please. Thank you!

CodePudding user response：

Caused by: java.lang.UnsatisfiedLinkError: /home/h4/nore667e/.javacpp/cache/deepLearningSimpleOne-1.0-SNAPSHOT-jar-with-dependencies.jar/org/nd4j/linalg/cpu/nativecpu/bindings/linux-x86_64/libjnind4jcpu.so: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by /home/h4/nore667e/.javacpp/cache/deepLearningSimpleOne-1.0-SNAPSHOT-jar-with-dependencies.jar/org/nd4j/linalg/cpu/nativecpu/bindings/linux-x86_64/libnd4jcpu.so)

Your stacktrace tells you exactly what the problem is.

This part in particular:

/lib64/libm.so.6: version `GLIBC_2.27' not found

That means that the operating system this is running on is too old (or rather its glibc version).

There is a binary that is still compatible with older releases.

You can get it by adding the following dependency (adapted to fit the style you've posted here):

        <dependency>
            <groupId>org.nd4j</groupId>
            <artifactId>${nd4j.backend}</artifactId>
            <version>${dl4j-master.version}</version>
            <classifier>linux-x86_64-compat</classifier>
        </dependency>

This new classifier exists since version M1.1: https://deeplearning4j.konduit.ai/release-notes/1.0.0-m1.1

Breaking default compatibility with old OS versions was necessary to enable the use of some speedups that are available on newer versions of glibc.