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I am not sure why this is happening, but I suspect that this issue could be related to some sort of power management issues either on the server port or on the switch port. I would look for power saving features related to the ports on both ends of the link and disable them. If the speed drops with the accompanying loss of connectivity go away, then you can enable features one at a time until you find the setting that causes the drops.
Also check out the support file on the switch to see what the status is on the port when the connection stops working. Maybe there is a message in the log or on the port status that will give a clue about what the switch thinks happened.
Mark, thank you for reply.
Following you advise I disabled all Power Settings I could find but that did not fix the problem.
Then I connected a laptop directly to the server with a cross-over cable. I discovered that the problem only happens on embedded LAN Port-1. Second port works just fine - with or without a switch.
Then I borrowed an HP328T (Broadcom 5709) network card from a friend, installed it into empty PCI-Expressx4 slot. Again - no problem.
I think there is a manufacturing defect on mobo LAN port-1. I found out that Supermicro modified the EEPROM image to make LAN Port-1 a dual-function port : sharing data/ipmi. The second port uses the original INTEL eeprom image and it is running fine. Shame on Supermicro - I spent 3 weeks troubleshooting a brand new server board !!
And now we have to buy an extra LAN card to get that server online...
Yes that board does have a dedicated LAN port for ipmi and I already set ipmi configuration to use just that port. I also and made an extra cable. The is no way to disable ipmi per/port - it is only possible to disable ipmi with a jumper setting. I did that today and discovered that the LAN Port-1 is no longer dropping connection (with ipmi off). So in order to have reliable LAN-1 I must disable ipmi - great design from Supermicro.