Hello,
The 5911 can run in a multiple record mode which allows you to tell the 5911 ahead of time that you want to do a certain amount of acquisitions (32 in your case) and to re-arm (start the next acquisition) in hardware without software interaction. This allows for a very small dead time (time between acquistions). There are multiple record examples that ship with NI-Scope in all environments and more information on this mode is available in the the software users manual that should be installed on your computer. If you cannot find it, here is a link to it on NIs website: http://digital.ni.com/manuals.nsf/websearch/91C5DEA19ACC6F2586256A8F0072E86F?OpenDocument&node=132100_US
Currently there is no support for the NI 5911 on Linux.
Best Regards,
Bri
an