There are two different issues. The first issue is that a successfully built CUDA app fails when running and the second is that building a CUDA app fails due to an invalid build environment.
The message,
MapSMtoCores undefined SM 3.5 is undefined (please update to the latest SDK)!
is output when an app (normally one of the CUDA samples) that uses the CUDA samples framework (helper_cuda.h) is run on a device of compute capability 3.5 and the app was built with a version of the samples framework that has not been updated to cover that compute capability.
If CUDA 5 is installed, then it seems likely that the app was built with an earlier version of the SDK.
The second message,
..src/cudaconv2/filter_acts.cu(1179) : getLastCudaError() CUDA error : filterActs: kernel execution failed : (9) invalid configuration argument.
is likely caused by the app not having detected the first error and then going on with trying to launch a kernel with invalid values returned by the function that printed the first error.
The other errors are build errors. These are caused by copying the CUDA SDK to your home folder and attempting to build from there without updating the CUDA environment variables.
Building the CUDA samples outside of their native locations may be a lot of work and should not be necessary to get the "filter acts" app working. To get the "filter acts" working on a machine with a compute capability 3.5 device, you will need to rebuild it with CUDA 5.0 or newer or modify it to no longer rely on the CUDA samples framework (which would be better).
So, you should first establish if you have an actual working CUDA 5 build environment. If you do not have that, someone that has root access should fix it. With a working build environment, you should then be able to rebuild the app.