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I have a NIC which is capable of 100BaseT/Full. But it negotiates a connection only on 100baseT/Half mode. Here is the output of mii-tool:

eth0: no autonegotiation, 100baseTx-HD, link ok

The Ethernet cable from the NIC connects to my ISP's MUX installed in our office. So, does it mean that ISP's MUX switch/hub can support only 100baseT/Half? Or can it be a issue with my NIC. It is a Athros Gigabit NIC. And the box (Ubuntu Server) has another NIC which is connected to my LAN switch, and it runs on 100BaseT/Full

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It may mean the box from you isp doesn't auto negotiate. – Zoredache Oct 28 '11 at 15:40
Maybe the ISP has accidentally set their end to HD instead of auto negotiate. Also check the cable quality. – jftuga Oct 28 '11 at 18:06

Did you try to set the NIC speed manually by executing:

# mii-tool eth0 -F 100baseTx-FD
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I think that you have a number of choices to pursue:

 Possibility that the cable is bad.
 Possibility that the ethernet board is bad.
 The switch port you are connected to has been "hardwired" for a certain speed 
     and duplex level and not auto.  So the system and the port are now talking
     assumming different speeds and duplex settings.  
 Possibility that the driver is not properly autonegotiating.

I have experienced all of these at one time or another in a problem such as this.

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If I'm reading the source code right, this means that the far end does not support or is not configured for autonegotiation. When this happens with 100base-TX, the usual safe default is 100 Mbps at half-duplex. You can get more information by running it with --verbose:

# mii-tool --verbose eth2
eth2: negotiated 100baseTx-FD, link ok
  product info: vendor 00:50:ef, model 60 rev 8
  basic mode:   autonegotiation enabled
  basic status: autonegotiation complete, link ok
  capabilities: 100baseTx-FD 100baseTx-HD 10baseT-FD 10baseT-HD
  advertising:  100baseTx-FD 100baseTx-HD 10baseT-FD 10baseT-HD
  link partner: 100baseTx-FD 100baseTx-HD 10baseT-FD 10baseT-HD
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