Python – Tensorflow Read from HDFS mac: java. lang. NoSuchFieldError: LOG

I’m trying to read an external Hadoop from TensorFlow on my Mac. I built TF with Hadoop support from source and Hadoop with native library support on my Mac. I get the following error

hdfsBuilderConnect(forceNewInstance=0, nn=192.168.60.53:9000, port=0, kerbTicketCachePath=(NULL), userName=(NULL)) error:
java.lang.NoSuchFieldError: LOG
    at org.apache.hadoop.ipc.ClientCache.getClient(ClientCache.java:62)
    at org.apache.hadoop.ipc.ProtobufRpcEngine$Invoker.<init>(ProtobufRpcEngine.java:145)
    at org.apache.hadoop.ipc.ProtobufRpcEngine$Invoker.<init>(ProtobufRpcEngine.java:133)
    at org.apache.hadoop.ipc.ProtobufRpcEngine$Invoker.<init>(ProtobufRpcEngine.java:119)
    at org.apache.hadoop.ipc.ProtobufRpcEngine.getProxy(ProtobufRpcEngine.java:102)
    at org.apache.hadoop.ipc.RPC.getProtocolProxy(RPC.java:579)
    at org.apache.hadoop.hdfs.NameNodeProxies.createNNProxyWithClientProtocol(NameNodeProxies.java:418)
    at org.apache.hadoop.hdfs.NameNodeProxies.createNonHAProxy(NameNodeProxies.java:314)
    at org.apache.hadoop.hdfs.NameNodeProxies.createProxy(NameNodeProxies.java:176)
    at org.apache.hadoop.hdfs.DFSClient.<init>(DFSClient.java:678)
    at org.apache.hadoop.hdfs.DFSClient.<init>(DFSClient.java:619)
    at org.apache.hadoop.hdfs.DistributedFileSystem.initialize(DistributedFileSystem.java:149)
    at org.apache.hadoop.fs.FileSystem.createFileSystem(FileSystem.java:2669)
    at org.apache.hadoop.fs.FileSystem.access$200(FileSystem.java:94)
    at org.apache.hadoop.fs.FileSystem$Cache.getInternal(FileSystem.java:2703)
    at org.apache.hadoop.fs.FileSystem$Cache.get(FileSystem.java:2685)
    at org.apache.hadoop.fs.FileSystem.get(FileSystem.java:373)
    at org.apache.hadoop.fs.FileSystem$1.run(FileSystem.java:162)
    at org.apache.hadoop.fs.FileSystem$1.run(FileSystem.java:159)
    at java.security.AccessController.doPrivileged(Native Method)
    at javax.security.auth.Subject.doAs(Subject.java:422)
    at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1698)
    at org.apache.hadoop.fs.FileSystem.get(FileSystem.java:159)
2018-10-05 16:01:21.867554: W tensorflow/core/kernels/queue_base.cc:277] _0_input_producer: Skipping cancelled enqueue attempt with queue not closed
Traceback (most recent call last):

Here is my code :

import tensorflow as tf

def create_file_reader_ops(filename_queue):
    reader = tf. TextLineReader(skip_header_lines=1)
    _, csv_row = reader.read(filename_queue)
    record_defaults = [[""], [""], [0], [0]]
    country, code, gold, silver = tf.decode_csv(csv_row, record_defaults=record_defaults)
    features = tf.stack([gold, silver])
    return features, country

filename_queue = tf.train.string_input_producer([
    "hdfs://192.168.60.53:9000/iris_data_multiclass.csv",
])
example, country = create_file_reader_ops(filename_queue)

with tf. Session() as sess:
    tf.global_variables_initializer().run()
    coord = tf.train.Coordinator()
    threads = tf.train.start_queue_runners(coord=coord)
    while True:
        try:
            example_data, country_name = sess.run([example, country])
            print(example_data, country_name)
        except tf.errors.OutOfRangeError:
            break

I built Hadoop from source on Mac.

$ hadoop version
Hadoop 2.7.3
Subversion https://github.com/apache/hadoop.git -r baa91f7c6bc9cb92be5982de4719c1c8af91ccff
Compiled by himaprasoon on 2018-10-04T11:09Z
Compiled with protoc 2.5.0
From source with checksum 2e4ce5f957ea4db193bce3734ff29ff4
This command was run using /Users/himaprasoon/git/hadoop/hadoop-dist/target/hadoop-2.7.3/share/hadoop/common/hadoop-common-2.7.3.jar

Hadoop checks native output

$ hadoop checknative
18/10/05 16:15:05 INFO bzip2. Bzip2Factory: Successfully loaded & initialized native-bzip2 library libbz2.dylib
18/10/05 16:15:05 INFO zlib. ZlibFactory: Successfully loaded & initialized native-zlib library
Native library checking:
hadoop:  true /Users/himaprasoon/git/hadoop/hadoop-dist/target/hadoop-2.7.3/lib/native/libhadoop.dylib
zlib:    true /usr/lib/libz.1.dylib
snappy:  true /usr/local/lib/libsnappy.1.dylib
lz4:     true revision:99
bzip2:   true /usr/lib/libbz2.1.0.dylib
openssl: true /usr/local/lib/libcrypto.dylib

tf version: 1.10.1
Any idea what I might have done wrong?

Here are my environment variables.

HADOOP_HOME=/Users/himaprasoon/git/hadoop/hadoop-dist/target/hadoop-2.7. 3/
HADOOP_MAPRED_HOME=$HADOOP_HOME
HADOOP_COMMON_HOME=$HADOOP_HOME
HADOOP_HDFS_HOME=$HADOOP_HOME
YARN_HOME=$HADOOP_HOME
HADOOP_COMMON_LIB_NATIVE_DIR=$HADOOP_HOME/lib/native
PATH=$PATH:$HADOOP_HOME/sbin: $HADOOP_HOME/bin
HADOOP_INSTALL=$HADOOP_HOME
OPENSSL_ROOT_DIR="/usr/local/opt/openssl"
LDFLAGS="-L${OPENSSL_ROOT_DIR}/lib"
CPPFLAGS="-I${OPENSSL_ROOT_DIR}/include"
PKG_CONFIG_PATH="${OPENSSL_ROOT_DIR}/lib/pkgconfig"
OPENSSL_INCLUDE_DIR="${OPENSSL_ROOT_DIR}/include"
PATH="/usr/local/opt/[email protected]/bin:$PATH
HADOOP_OPTS="-Djava.library.path=${HADOOP_HOME}/lib/native"
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:${HADOOP_HOME}/lib/native
JAVA_LIBRARY_PATH=$JAVA_LIBRARY_PATH:${HADOOP_HOME}/lib/native

This is how I run the program

CLASSPATH=$($HADOOP_HDFS_HOME/bin/hdfs classpath --glob) python3.6 myfile.py

References for building tf and hadoop

• Hadoop native libraries not found on OS/X
• https://medium.com/@s.matthew.english/build-hadoop-from-source-on-macos-a3fb2b958b6c
• Can Tensorflow read from HDFS on Mac?
• https://gist.github.com/zedar/f631ace0759c1d512573

Have you read this article?

Tensorflow Enqueue operation was cancelled

There seems to be a workaround for the same error message:

The problem happens at the very last stage when python tries to kill threads.
To do this properly you should create a train. Coordinator and pass it to your
queue_runner (no need to pass sess, as default session will be used>

with tf. Session() as sess:
    coord = tf.train.Coordinator()
    threads = tf.train.start_queue_runners(coord=coord)
     do your things
    coord.request_stop()
    coord.join(threads)

The last two lines should be added to your while loop to ensure that all threads are terminated properly.