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If it's a something.bin file, that's not a Linux binary. That's the firmware image. There's lots of info in this thread and others on SVTH on using flint (part of MFT tools) or mlxup to update the firmware. If you're burning a newer version of the existing firmware, it's straightforward with...

The easiest way to change port type is via the Mellanox script connectx_port_config which is buried deep in the Mellanox OFED distribution downloads (http://www.mellanox.com/page/products_dyn?product_family=26). As background, the way the script changes the port type is by writing a value to the...

You're probably done by now :) If by box you mean a PC for flashing cards, I'm personally looking at one of these for future flashing: Supermicro | Products | SuperServers | Mini 1U | E300-8D Supermicro | Products | SuperServers | Mini 1U | E300-9A Only takes 1 PCIe card at a time, so requires...

Make sure you've rebooted the machine after flashing or changing firmware. It depends on what you mean by port is not there. Maybe it's not yet configured with IPv4 or v6 settings, or maybe there is no cable plugged into it, or maybe the port was automatically set to IB (inifiniband) mode...