I recently shifted to Ubuntu@64bits and I have a problem with Matlab r2009a&memory.
The code makes use of a C file which is compiled via >mex name.c
In a 32bits architecture everything is fine. Under 64 bits the file is correctly compiled, but the programs stops with the error Function "mxGetIr_700" is obsolete in file "compat32.cpp", line 282. (64-bit mex files using sparse matrices must be rebuilt with the "-largeArrayDims" option. See the R2006b release notes for more details.)
I then compiled using the suggested option:
>mex -largeArrayDims name.c
and in this case I have an "out of memory" error.
The system has 4Gb of RAM, 4Gb of swap and the system monitor gives about 1Gb of used RAM while running Matlab...so I guess the problem is related to the quantity of ram allocated to Matlab.