I would go for the i7 at 4 Ghz. In my own extensive testing, this jump has proved to be around twice as fast for imports. It is definitely not simply proportional to the number of GHz, i.e. 3 Ghz to 4 Ghz is not just a 33% gain. I did quite a bit of testing on a 24x intel xeon 2.5 GHz versus my i7 3.5 GHz desktop, and found my desktop around 2x faster using the same number of threads. Involving more threads (for parallel file import) could give the 24-core machine a bit of an edge, but this was tricky, mostly (I think) due to added garbage collection overhead. I was able to get over 2x as fast with 24-cores, but I had to use SkylineRunner command-line and multiple processes. Single process, multi-threaded peaked at just a percentage faster. The 24 core (48 thread) xeon machine also has 192 GB RAM and the fastest 750 GB SSD of all the machines I tested with CrystalDiskMark.
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CrystalDiskMark 5.1.0 x64 (C) 2007-2015 hiyohiyo
Crystal Dew World :
http://crystalmark.info/
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* MB/s = 1,000,000 bytes/s [SATA/600 = 600,000,000 bytes/s]
* KB = 1000 bytes, KiB = 1024 bytes
Sequential Read (Q= 32,T= 1) : 2891.801 MB/s
Sequential Write (Q= 32,T= 1) : 1415.197 MB/s
Random Read 4KiB (Q= 32,T= 1) : 687.117 MB/s [167753.2 IOPS]
Random Write 4KiB (Q= 32,T= 1) : 636.178 MB/s [155316.9 IOPS]
Sequential Read (T= 1) : 1232.987 MB/s
Sequential Write (T= 1) : 1339.985 MB/s
Random Read 4KiB (Q= 1,T= 1) : 40.323 MB/s [ 9844.5 IOPS]
Random Write 4KiB (Q= 1,T= 1) : 84.988 MB/s [ 20749.0 IOPS]
Test : 1024 MiB [D: 37.4% (279.1/745.2 GiB)] (x5) [Interval=5 sec]
Date : 2016/12/19 15:27:09
OS : Windows Server 2012 R2 Server Standard (full installation) [6.3 Build 9600] (x64)
The 128 GB RAM will give you a higher ceiling for memory use, but you'll need some really monster-sized files to need it. Nick was saying that your current file with 120 replicates uses around 20 GB on his 64 GB machine. So, it seems understandable that processing would go very, very slowly on your 16 GB machine because the OS will need to do a lot of swapping to disk to manage this. As long as you have enough memory to avoid forcing the OS thrash on the disk, you should be fine. In this case 64 GB versus 128 GB shouldn't make any difference. If you are thinking you would like to work on things 4x this size, then getting 128 GB may be a good idea.
On the SSD, actually, most of the time SSD versus HDD makes only a 10-20% difference in performance, and I process a lot of our data on HDD. We have worked very hard to make this the case for Skyline. But, occasionally, we do run into cases where SSD versus HDD makes more difference, e.g. I recently found an issue where the Thermo reader did much worse for DIA files on HDD, but that turned out to be only for Windows 7 and an external HDD (connected through USB 3). The problem returned to the normal 10% difference for either an internal HDD or Windows 10.
So, you shouldn't necessarily feel as if you need to store all data files on SSD which you are going to process. Run some of your own comparisons to see what kind of difference you see.
If it were me, I would say:
1. 4 Ghz i7 (too expensive to go NUMA, and too tricky to get better performance; easy to see worse, if you aren't careful)
2. Your choice of either 128 GB RAM or 1 TB SSD. Neither may give you immediate benefit but act more as insurance for future growth. Myself, I would probably get a 4 TB HDD and expect to do most of my processing from it, and take the RAM, as reconfiguring a system with 64 GB to 128 GB seems not as easy as getting more hard drive space, unless you know the machine has extra slots for adding memory later.
Those are my thoughts anyway.
--Brendan