Bolt driver for Python "ValueError: filedescriptor out of range in select()"

Yo.Ahiru · March 2, 2020, 10:41am

Hi all,

I would like to ask you about Neo4j filedescriptor ERROR.
It says "ValueError: filedescriptor out of range in select()" after some loads.
Its environment is as follows.

Server: Amazon AWS
OS: Amazon Linux 2
Neo4j version: Enterprise 3.5.8
Bolt driver: 1.7 for Python
Python: 3.7.4 and we use multiprocessing

With some load, an error occurs like followings.
I changed LimitNOFILE from 1024 to 60000.
And I changed neo4j.conf.

dbms.memory.heap.initial_size=23g
dbms.memory.heap.max_size=23g
dbms.memory.pagecache.size=27400m
dbms.connector.bolt.thread_pool_min_size=500
dbms.connector.bolt.thread_pool_max_size=10000
dbms.connector.bolt.thread_pool_keep_alive=15m

Usually I start the Neo4j as a console. ex) "sudo /bin/neo4j start"
Still I meet the ERROR.

Could you tell me what to do?

debug.log

2020-02-20 06:28:15.721+0000 ERROR [o.n.b.t.TransportSelectionHandler] Fatal error occurred when initialising pipeline: [id: 0x6fd93f84, L:/172.31.41.6:7687 ! R:/150.249.195.153:51244] javax.net.ssl.SSLException: Received fatal alert: certificate_unknown
io.netty.handler.codec.DecoderException: javax.net.ssl.SSLException: Received fatal alert: certificate_unknown
        at io.netty.handler.codec.ByteToMessageDecoder.callDecode(ByteToMessageDecoder.java:472)
        at io.netty.handler.codec.ByteToMessageDecoder.channelRead(ByteToMessageDecoder.java:278)
        at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:362)
        at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:348)
        at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:340)
        at io.netty.channel.ChannelInboundHandlerAdapter.channelRead(ChannelInboundHandlerAdapter.java:86)
        at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:362)
        at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:348)
        at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:340)
        at io.netty.channel.DefaultChannelPipeline$HeadContext.channelRead(DefaultChannelPipeline.java:1434)
        at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:362)
        at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:348)
        at io.netty.channel.DefaultChannelPipeline.fireChannelRead(DefaultChannelPipeline.java:965)
        at io.netty.channel.epoll.AbstractEpollStreamChannel$EpollStreamUnsafe.epollInReady(AbstractEpollStreamChannel.java:799)
        at io.netty.channel.epoll.EpollEventLoop.processReady(EpollEventLoop.java:433)
        at io.netty.channel.epoll.EpollEventLoop.run(EpollEventLoop.java:330)
        at io.netty.util.concurrent.SingleThreadEventExecutor$5.run(SingleThreadEventExecutor.java:909)
        at java.lang.Thread.run(Thread.java:748)
Caused by: javax.net.ssl.SSLException: Received fatal alert: certificate_unknown
        at sun.security.ssl.Alerts.getSSLException(Alerts.java:208)
        at sun.security.ssl.SSLEngineImpl.fatal(SSLEngineImpl.java:1647)
        at sun.security.ssl.SSLEngineImpl.fatal(SSLEngineImpl.java:1615)
        at sun.security.ssl.SSLEngineImpl.recvAlert(SSLEngineImpl.java:1781)
        at sun.security.ssl.SSLEngineImpl.readRecord(SSLEngineImpl.java:1070)
        at sun.security.ssl.SSLEngineImpl.readNetRecord(SSLEngineImpl.java:896)
        at sun.security.ssl.SSLEngineImpl.unwrap(SSLEngineImpl.java:766)
        at javax.net.ssl.SSLEngine.unwrap(SSLEngine.java:624)
        at io.netty.handler.ssl.SslHandler$SslEngineType$3.unwrap(SslHandler.java:295)
        at io.netty.handler.ssl.SslHandler.unwrap(SslHandler.java:1301)
        at io.netty.handler.ssl.SslHandler.decodeJdkCompatible(SslHandler.java:1203)
        at io.netty.handler.ssl.SslHandler.decode(SslHandler.java:1247)
        at io.netty.handler.codec.ByteToMessageDecoder.decodeRemovalReentryProtection(ByteToMessageDecoder.java:502)
        at io.netty.handler.codec.ByteToMessageDecoder.callDecode(ByteToMessageDecoder.java:441)
        ... 17 more
2020-02-20 06:28:15.721+0000 ERROR [o.n.b.t.TransportSelectionHandler] Fatal error occurred when initialising pipeline: [id: 0x6fd93f84, L:/172.31.41.6:7687 ! R:/150.249.195.153:51244] javax.net.ssl.SSLException: Received fatal alert: certificate_unknown
io.netty.handler.codec.DecoderException: javax.net.ssl.SSLException: Received fatal alert: certificate_unknown
        at io.netty.handler.codec.ByteToMessageDecoder.callDecode(ByteToMessageDecoder.java:472)
        at io.netty.handler.codec.ByteToMessageDecoder.channelInputClosed(ByteToMessageDecoder.java:405)

Python program's log

2020-02-20 06:28:27,725 INFO
Process Process-1083:
Traceback (most recent call last):
  File "/usr/lib64/python3.7/multiprocessing/process.py", line 297, in _bootstrap
    self.run()
  File "/usr/lib64/python3.7/multiprocessing/process.py", line 99, in run
    self._target(*self._args, **self._kwargs)
  File "/home/ec2-user/graph/program.py", line 3514, in input_part
    Es1 = make_data(0, 0, UsId, OpId, 0, 0)
  File "/home/ec2-user/graph/program.py", line 123, in make_data
    driver = GraphDatabase.driver("bolt://localhost:7687", auth=("neo4j", driver_pass))
  File "/home/ec2-user/.local/lib/python3.7/site-packages/neo4j/__init__.py", line 116, in driver
    return Driver(uri, **config)
  File "/home/ec2-user/.local/lib/python3.7/site-packages/neo4j/__init__.py", line 157, in __new__
    return subclass(uri, **config)
  File "/home/ec2-user/.local/lib/python3.7/site-packages/neo4j/__init__.py", line 231, in __new__
    pool.release(pool.acquire())
  File "/home/ec2-user/.local/lib/python3.7/site-packages/neobolt/direct.py", line 719, in acquire
    return self.acquire_direct(self.address)
  File "/home/ec2-user/.local/lib/python3.7/site-packages/neobolt/direct.py", line 612, in acquire_direct
    connection = self.connector(address, error_handler=self.connection_error_handler)
  File "/home/ec2-user/.local/lib/python3.7/site-packages/neo4j/__init__.py", line 228, in connector
    return connect(address, **dict(config, **kwargs))
  File "/home/ec2-user/.local/lib/python3.7/site-packages/neobolt/direct.py", line 976, in connect
    raise last_error
  File "/home/ec2-user/.local/lib/python3.7/site-packages/neobolt/direct.py", line 968, in connect
    connection = _handshake(s, address, der_encoded_server_certificate, **config)
  File "/home/ec2-user/.local/lib/python3.7/site-packages/neobolt/direct.py", line 902, in _handshake
    ready_to_read, _, _ = select((s,), (), (), 1)
ValueError: filedescriptor out of range in select()
no label.wait...

anthapu · March 2, 2020, 12:48pm

This seems to be related to certificates and encryption. Are you using valid certificates on server?

Can you disable encryption and see if it works first?

Yo.Ahiru · March 3, 2020, 12:16pm

Hi Anthapu,

Thanks for your reply!
I am using two servers.
The other server says the following when " ValueError: filedescriptor out of range in select() " occurs.
Sorry, I should have written this log.

2020-02-28 16:09:26.008+0000 INFO [o.n.k.i.t.l.c.CheckPointerImpl] Checkpoint triggered by "Scheduled checkpoint for time threshold" @ txId: 9951392 checkpoint started...
2020-02-28 16:09:26.010+0000 INFO [o.n.k.i.s.c.CountsTracker] Rotated counts store at transaction 9951392 to [/var/lib/neo4j/data/databases/graph.db/neostore.counts.db.b], from [/var/lib/neo4j/data/databases/graph.db/neostore.counts.db.a].
2020-02-28 16:09:26.328+0000 INFO [o.n.k.i.t.l.c.CheckPointerImpl] Checkpoint triggered by "Scheduled checkpoint for time threshold" @ txId: 9951392 checkpoint completed in 320ms
2020-02-28 16:09:26.328+0000 INFO [o.n.k.i.t.l.p.LogPruningImpl] No log version pruned, last checkpoint was made in version 61
2020-02-28 16:20:06.397+0000 WARN [o.n.b.t.p.HouseKeeper] Fatal error occurred when handling a client connection, remote peer unexpectedly closed connection: [id: 0x35408957, L:/127.0.0.1:7687 - R:/127.0.0.1:49278]
2020-02-28 16:21:06.623+0000 WARN [o.n.b.t.p.HouseKeeper] Fatal error occurred when handling a client connection, remote peer unexpectedly closed connection: [id: 0x54ca9da9, L:/127.0.0.1:7687 - R:/127.0.0.1:49294]

Then, I noticed that Zhen says "some function that goes over all connections on server every 4h and kill all idle connections" in the following.
Fatal error occurred when handling a client connection causes crash
Should I make those functions?

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Bolt driver for Python "ValueError: filedescriptor out of range in select()"

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