Miroslav,

I have chronyd 2.4.1 running on FreeBSD 11.0 release and it's working fine.
All refclocks are internet servers and data is received normally.
I have just compiled chrony 3.0-pre1 and it fails to receive any timestamp data 
from the internet refclocks.
I tried again with the latest master from git and it fails in the same way,
This is some debug output from the git master version and it seems there is an 
almost immediate timeout on both send and receiving data from any socket.

2016-12-14T15:25:22Z ntp_core.c:1056:(transmit_timeout) Transmit timeout for 
[194.171.167.130:123]
2016-12-14T15:25:22Z ntp_io.c:830:(NIO_SendPacket) Sent 48 bytes to 
194.171.167.130:123 from [UNSPEC] fd 7
2016-12-14T15:25:22Z ntp_io.c:668:(process_message) Received 0 bytes from 
194.171.167.130:123 to [UNSPEC] fd=7 if=-1 tss=1 delay=0.000104191
2016-12-14T15:25:22Z ntp_core.c:1056:(transmit_timeout) Transmit timeout for 
[80.94.65.10:123]
2016-12-14T15:25:22Z ntp_io.c:830:(NIO_SendPacket) Sent 48 bytes to 
80.94.65.10:123 from [UNSPEC] fd 8
2016-12-14T15:25:22Z ntp_io.c:668:(process_message) Received 0 bytes from 
80.94.65.10:123 to [UNSPEC] fd=8 if=-1 tss=1 delay=0.000099536

If there is anything I can do to test or provide more information, please let 
me know.

Adri,.

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