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C [libtensorflow_framework.so.1+0x744da9] _GLOBAL__sub_I_loader.cc+0x99 #2256

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leeivan opened this issue Feb 7, 2021 · 9 comments
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C [libtensorflow_framework.so.1+0x744da9] _GLOBAL__sub_I_loader.cc+0x99 #2256

leeivan opened this issue Feb 7, 2021 · 9 comments
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@albertoandreottiATgmail @maziyarpanahi
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@leeivan
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leeivan commented Feb 7, 2021 •
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#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGILL (0x4) at pc=0x00007eff1b96eda9, pid=12627, tid=0x00007effe75f1700
#
# JRE version: OpenJDK Runtime Environment (8.0_282-b08) (build 1.8.0_282-b08)
# Java VM: OpenJDK 64-Bit Server VM (25.282-b08 mixed mode linux-amd64 compressed oops)
# Problematic frame:
# C  [libtensorflow_framework.so.1+0x744da9]  _GLOBAL__sub_I_loader.cc+0x99
#
# Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
#
# If you would like to submit a bug report, please visit:
#   https://bugzilla.redhat.com/enter_bug.cgi?product=Red%20Hat%20Enterprise%20Linux%207&component=java-1.8.0-openjdk
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#

---------------  T H R E A D  ---------------

Current thread (0x00007effd400a000):  JavaThread "Thread-5" [_thread_in_native, id=12674, stack(0x00007effe74f1000,0x00007effe75f2000)]

siginfo: si_signo: 4 (SIGILL), si_code: 2 (ILL_ILLOPN), si_addr: 0x00007eff1b96eda9

Registers:
RAX=0x00007effd9b67500, RBX=0x00007effe75ed550, RCX=0x0000000000000000, RDX=0x0000000000000001
RSP=0x00007effe75ed500, RBP=0x00007effe75ed610, RSI=0x00007effe75ed440, RDI=0x00007effe75ed530
R8 =0x00007effd9b67580, R9 =0x00007effd9b67390, R10=0x0000000000000002, R11=0x000000000000001f
R12=0x00007ffcb5fbe1b8, R13=0x00007eff1cb86018, R14=0x0000000000000001, R15=0x00007eff1cb84510
RIP=0x00007eff1b96eda9, EFLAGS=0x0000000000010202, CSGSFS=0x0000000000000033, ERR=0x0000000000000000
  TRAPNO=0x0000000000000006

Top of Stack: (sp=0x00007effe75ed500)
0x00007effe75ed500:   00007eff1d3038d8 0000000000000007
0x00007effe75ed510:   00007eff1cc3a1a8 00007eff25f02ff0

v  ~StubRoutines::call_stub
j  com.johnsnowlabs.ml.tensorflow.TensorflowWrapper$.readGraph(Ljava/lang/String;)Lorg/tensorflow/Graph;+12
j  com.johnsnowlabs.ml.tensorflow.TensorflowWrapper$.read(Ljava/lang/String;ZZ[Ljava/lang/String;Z)Lcom/johnsnowlabs/ml/tensorflow/Tensorflo$
j  com.johnsnowlabs.ml.tensorflow.ReadTensorflowModel$class.readTensorflowModel(Lcom/johnsnowlabs/ml/tensorflow/ReadTensorflowModel;Ljava/la$
j  com.johnsnowlabs.nlp.embeddings.BertEmbeddings$.readTensorflowModel(Ljava/lang/String;Lorg/apache/spark/sql/SparkSession;Ljava/lang/Strin$
j  com.johnsnowlabs.nlp.embeddings.ReadBertTensorflowModel$class.readTensorflow(Lcom/johnsnowlabs/nlp/embeddings/ReadBertTensorflowModel;Lco$
j  com.johnsnowlabs.nlp.embeddings.BertEmbeddings$.readTensorflow(Lcom/johnsnowlabs/nlp/embeddings/BertEmbeddings;Ljava/lang/String;Lorg/apa$
j  com.johnsnowlabs.nlp.embeddings.ReadBertTensorflowModel$$anonfun$4.apply(Lcom/johnsnowlabs/nlp/embeddings/BertEmbeddings;Ljava/lang/Strin$
j  com.johnsnowlabs.nlp.embeddings.ReadBertTensorflowModel$$anonfun$4.apply(Ljava/lang/Object;Ljava/lang/Object;Ljava/lang/Object;)Ljava/lan$
j  com.johnsnowlabs.nlp.ParamsAndFeaturesReadable$$anonfun$com$johnsnowlabs$nlp$ParamsAndFeaturesReadable$$onRead$1.apply(Lscala/Function3;)$
j  com.johnsnowlabs.nlp.ParamsAndFeaturesReadable$$anonfun$com$johnsnowlabs$nlp$ParamsAndFeaturesReadable$$onRead$1.apply(Ljava/lang/Object;$
J 4635 C2 scala.collection.mutable.ArrayBuffer.foreach(Lscala/Function1;)V (6 bytes) @ 0x00007f00856531a8 [0x00007f0085653120+0x88]
j  com.johnsnowlabs.nlp.ParamsAndFeaturesReadable$class.com$johnsnowlabs$nlp$ParamsAndFeaturesReadable$$onRead(Lcom/johnsnowlabs/nlp/ParamsA$
j  com.johnsnowlabs.nlp.ParamsAndFeaturesReadable$$anonfun$read$1.apply(Lcom/johnsnowlabs/nlp/HasFeatures;Ljava/lang/String;Lorg/apache/spar$
j  com.johnsnowlabs.nlp.ParamsAndFeaturesReadable$$anonfun$read$1.apply(Ljava/lang/Object;Ljava/lang/Object;Ljava/lang/Object;)Ljava/lang/Ob$
j  com.johnsnowlabs.nlp.FeaturesReader.load(Ljava/lang/String;)Lcom/johnsnowlabs/nlp/HasFeatures;+40
j  com.johnsnowlabs.nlp.FeaturesReader.load(Ljava/lang/String;)Ljava/lang/Object;+2
j  com.johnsnowlabs.nlp.pretrained.ResourceDownloader$.downloadModel(Lorg/apache/spark/ml/util/DefaultParamsReadable;Lcom/johnsnowlabs/nlp/p$
j  com.johnsnowlabs.nlp.pretrained.ResourceDownloader$.downloadModel(Lorg/apache/spark/ml/util/DefaultParamsReadable;Ljava/lang/String;Lscal$
j  com.johnsnowlabs.nlp.pretrained.PythonResourceDownloader$.downloadModel(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Ljava/lang/$
j  com.johnsnowlabs.nlp.pretrained.PythonResourceDownloader.downloadModel(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Ljava/lang/S$
v  ~StubRoutines::call_stub
J 9825  sun.reflect.NativeMethodAccessorImpl.invoke0(Ljava/lang/reflect/Method;Ljava/lang/Object;[Ljava/lang/Object;)Ljava/lang/Object; (0 b$
J 4145 C1 sun.reflect.NativeMethodAccessorImpl.invoke(Ljava/lang/Object;[Ljava/lang/Object;)Ljava/lang/Object; (104 bytes) @ 0x00007f0085bfc$
J 5089 C2 java.lang.reflect.Method.invoke(Ljava/lang/Object;[Ljava/lang/Object;)Ljava/lang/Object; (62 bytes) @ 0x00007f0085cd2cec [0x00007f$
j  py4j.reflection.MethodInvoker.invoke(Ljava/lang/Object;[Ljava/lang/Object;)Ljava/lang/Object;+91
j  py4j.reflection.ReflectionEngine.invoke(Ljava/lang/Object;Lpy4j/reflection/MethodInvoker;[Ljava/lang/Object;)Ljava/lang/Object;+6
j  py4j.Gateway.invoke(Ljava/lang/String;Ljava/lang/String;Ljava/util/List;)Lpy4j/ReturnObject;+151
j  py4j.commands.AbstractCommand.invokeMethod(Ljava/lang/String;Ljava/lang/String;Ljava/util/List;)Lpy4j/ReturnObject;+10
j  py4j.commands.CallCommand.execute(Ljava/lang/String;Ljava/io/BufferedReader;Ljava/io/BufferedWriter;)V+26
j  py4j.GatewayConnection.run()V+126
j  java.lang.Thread.run()V+11
v  ~StubRoutines::call_stub

---------------  P R O C E S S  ---------------

Java Threads: ( => current thread )
  0x00007effd9be6000 JavaThread "process reaper" daemon [_thread_blocked, id=13067, stack(0x00007f000414a000,0x00007f0004183000)]
  0x00007effbc008800 JavaThread "task-result-getter-3" daemon [_thread_blocked, id=12923, stack(0x00007eff26194000,0x00007eff26295000)]
  0x00007effcc009000 JavaThread "task-result-getter-2" daemon [_thread_blocked, id=12922, stack(0x00007eff26295000,0x00007eff26396000)]
  0x00007effcc007800 JavaThread "task-result-getter-1" daemon [_thread_blocked, id=12903, stack(0x00007eff2779b000,0x00007eff2789c000)]
  0x00007eff3801b800 JavaThread "shuffle-server-7-2" daemon [_thread_in_native, id=12902, stack(0x00007eff27498000,0x00007eff27599000)]
  0x00007effd4011000 JavaThread "ForkJoinPool-1-worker-9" daemon [_thread_blocked, id=12899, stack(0x00007eff27599000,0x00007eff2769a000)]
  0x00007effd9a14000 JavaThread "java-sdk-http-connection-reaper" daemon [_thread_blocked, id=12870, stack(0x00007eff340fc000,0x00007eff341f$
  0x00007effd9842000 JavaThread "IPC Parameter Sending Thread #1" daemon [_thread_blocked, id=12869, stack(0x00007eff400ed000,0x00007eff401e$
  0x00007effbc00f800 JavaThread "task-result-getter-0" daemon [_thread_blocked, id=12867, stack(0x00007effe442f000,0x00007effe4530000)]
  0x00007eff3801a800 JavaThread "shuffle-server-7-1" daemon [_thread_in_native, id=12866, stack(0x00007effe4631000,0x00007effe4732000)]
  0x00007effd8954000 JavaThread "org.apache.hadoop.hdfs.PeerCache@3153baf" daemon [_thread_blocked, id=12865, stack(0x00007eff401ee000,0x000$
  0x00007effac015800 JavaThread "rpc-server-4-8" daemon [_thread_in_native, id=12855, stack(0x00007eff409f0000,0x00007eff40af1000)]
  0x00007effac013800 JavaThread "rpc-server-4-7" daemon [_thread_in_native, id=12854, stack(0x00007eff40af1000,0x00007eff40bf2000)]
  0x00007effac011800 JavaThread "rpc-server-4-6" daemon [_thread_in_native, id=12853, stack(0x00007eff40bf2000,0x00007eff40cf3000)]
  0x00007effac010000 JavaThread "rpc-server-4-5" daemon [_thread_in_native, id=12836, stack(0x00007eff40cf3000,0x00007eff40df4000)]
  0x00007effac00e000 JavaThread "rpc-server-4-4" daemon [_thread_in_native, id=12835, stack(0x00007eff41df5000,0x00007eff41ef6000)]
@leeivan
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leeivan commented Feb 7, 2021

The above is hs_err_pid12627.log, which was produced when executing:

    val bert = BertEmbeddings.pretrained("biobert_clinical_base_cased", "en")
      .setInputCols("sentence", "token")
      .setOutputCol("bert")
      .setCaseSensitive(false)

This error happened whatever in scala and python.

@leeivan
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leeivan commented Feb 7, 2021 •
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I had two spark standalone cluster env:
The one is ubuntu20.04, using one VM, this is right,
The other is centos 7, using five VMs, this is wrong.

I guess this problem is at spark cluster environment or OS.

@maziyarpanahi
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Our TensorFlow version doesn't support Centos 7.

@leeivan
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leeivan commented Feb 7, 2021 •
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Thanks, but I want to keep trying. Can you give me some suggestion ? @maziyarpanahi

@maziyarpanahi
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Of course, these might help:

@maziyarpanahi
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Hi @albertoandreottiATgmail

Is this error related to the libstdc or some other dependencies/packages on the machine? If all happen in CentOS it is fine. (I've seen similar issues reported on TensorFlow GitHub, but not exactly the same since this is via Java/C++)

@albertoandreottiATgmail
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Hi guys,

yes, it seems like a native library version mismatch, take a look at a similar error reported here,

https://stackoverflow.com/questions/46836882/access-tensorflow-from-tomcat-on-centos-linux/49568814

Probably changing the version of the system libraries will help.

Alberto.

@leeivan
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leeivan commented Feb 12, 2021 •
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@maziyarpanahi , I found the reason about this question, it is that the regency CUP of VM is not support AVX instruction set, AVX is advanced function to new-brand intel cpu. I recompiled tensorflow jar at the native VM with the below guide:
https://github.com/tensorflow/tensorflow/tree/master/tensorflow/java

@maziyarpanahi
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This is very interesting! Didn't know not being compatible with AVX will result in that error. It's hard to find a CPU that doesn't support AVX if they were produced after 2011, but there must be some CPUs or virtualized environments that don't support it.

Many thanks for the update @leeivan, it will be very helpful to the future users 👍🏼

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