It seems I remember reading about a work-around for that on the Arduino forum 
but if you need to get something going immediately you can use software serial.




>________________________________
> From: Kirk Wallace <[email protected]>
>To: LinuxCNC Users List <[email protected]> 
>Sent: Wednesday, March 7, 2012 1:51 PM
>Subject: [Emc-users] Arduin woes
> 
>I'm working on a VFD controller using an AVR, and also looking into
>using an Arduino. I seem to have found that the Arduino has problems
>working with the serial port because the Rx and Tx pins are also tied to
>the USB interface, the BootLoader, in someway the serial port monitor
>and debugging. It seems if one's application causes serial data to
>stream on power up, the BootLoader takes this as something trying to
>talk to the BootLoader and loops without a time-out. Unfortunately, one
>needs to use this link in order to edit the application to stop it from
>streaming until after the BootLoader does its thing and gets out of the
>way. There is a USB chip update that is supposed to fix this, but
>requires some command line gymnastics and something called DFU. I don't
>know what I did, but I finally got the update loaded and it seems to
>work now, but this brings up the thought, considering the importance of
>the serial port to many CNC applications and the serial port resource
>sharing on the Arduino, is Arduino appropriate for LinuxCNC
>applications?
>
>-- 
>Kirk Wallace
>http://www.wallacecompany.com/machine_shop/
>http://www.wallacecompany.com/E45/index.html
>California, USA
>
>
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Virtualization & Cloud Management Using Capacity Planning
Cloud computing makes use of virtualization - but cloud computing 
also focuses on allowing computing to be delivered as a service.
http://www.accelacomm.com/jaw/sfnl/114/51521223/
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