MongoDB not using all memory in Windows server

The resident memory size represents the number of pages in memory actually touched by the mongod process. If that is significantly lower than the available memory and data exceeds the available memory (yours does), then it could be a case of simply not having actively touched enough pages yet.

To determine if this is the case, you should run free -m, the output should look something like this:

free -m
             total       used       free     shared    buffers     cached
Mem:          3709       3484        224          0         84       2412
-/+ buffers/cache:        987       2721
Swap:         3836        156       3680

In my example, cached is not close to the total, which means that not only has mongod not touched enough pages, the filesystem cache has not yet even been filled by pages being read from the disk in general.

A quick remedy for this would be the touch command (added in 2.2) - it should be used with caution on large data sets as it will attempt to load everything into RAM even if the data is far too large to fit (causing a lot of disk IO and page faults). It will certainly fill up the memory effectively though :)

If your cached value is close to the total available, then your issue is that a large number of pages being read into memory from disk are not relevant to (and hence not touched by) the mongod process. The usual candidate for this kind of discrepency is readahead. I've already covered that particular topic elsewhere in detail, so I'll just link those two answers for future reading if necessary.

Under Windows, in a worst case scenario, your pagefile size might have to be set to the size of your data files + physical memory size. So if your data files take up 50GB on disk, the rough guidance, in your case, is to set pagefile size to 53.5GB. This will improve with MongoDB 2.8 release since the new storage engine does not rely on virtual memory services provided by the OS. On a related subject, your memory size of 3.5GB sounds very low. Take a look at the Hard Page Faults per second under the Resource Monitor -- if the number is in hundreds, you need to dramatically increase your memory size