Linux – lsof runs very slow in the server

Try the -n option:

-n This option inhibits the conversion of network numbers to host names for network files. Inhibiting conversion may make lsof run faster. It is also useful when host name lookup is not working properly.

flush is not "garbage collection in the kernel". I'm not sure where you read that but C has no garbage collector. There is no automatic memory management. C programmers have to manage their own memory allocations. Anyway...

flush is the process which the virtual memory subsystem uses to write dirty pages out to disk. This is called pdflush or bdflush in the EL kernels.

When you perform any (non-direct) IO, the file you access goes into the pagecache. If you read a text file from disk, that textfile now exists on the disk and in cache memory. If you make some changes and save that file, the actual write() system call that your text editor makes completes against the copy of the file in memory. This way, the system call returns quickly and your text editor can get back to accepting your input, rather than pausing while it writes data out to the (relatively) slow hard disk. The memory pages which that modified text file occupies are now called "dirty pages". The kernel worries about putting the actual block writes out to disk at a later time, this is called "syncing" or "flushing dirty pages".

You'd expect to see a flush process get high CPU usage at times, because the process will be performing IO to disk and will probably be spending most of its time in iowait.

There is nothing to worry about. Your system is behaving like every other Linux system.