Linux equivalent for Microsoft Visio

You might want to look at SimPy. I haven't used SimPy in maybe 4 years, but I think it could do what you want. It may be a bit more basic, not including all the bells and whistles that your Windows software does.

The console standby for this is top, but there are alternatives like my favorite htop that give you a little more display flexibility and allow you a few more operations on the processes.

A less interactive view that is better for use in scripts would be the ps program and all it's relatives.

Edit: Based on your clarified question, you might note that strace handles watching system calls made by a given process including all read-write operations and os function calls. You can activate it on the command line before the program you want to track or attach to a running process by hitting s on a process selected in htop.