goldorak,
Dual CPU's >
1. the principal advantage to a dual CU system is when working with software that can use every thread. It's a complicated decision and my suggestion is to look into each application you use for multi-core use and assign a priority to it. If your primary application were rendering, which can use every thread, then yes, the dual Xeon would be useful and faster. A lot of analysis / simulation software as well as very complex 3D modeling, scientific like NAMD and MATLAB, and simulation can use all the threads too. Still, a surprising number of big complex programs are single-threaded such as Autodesk and Solidworks.
2. Besides more threads, dual CPU's also provide more PCIe lanes and RAM memory. If you are going to be using coprocessors like Tesla or Xeon Phi, then dual CPUs can get you up to seven PCIe x16 slots and there are quite a few dual motherboards off the shelf (Intel C602) that support 512GB of DDR3 ECC 1600.
Single CPU >
1. However, if your primary need is for speed in single-threaded programs, then the single CPU at a higher clock speed will be be an advantage. I use a dual Xeon quad core 3.16GHz Dell Precision, which I configured for rendering, but it seems rendering is less than 10% of my time, so the new system has a lowly quad core E5-1620 but that will run on the first two cores at 3.8GHz. It also much faster memory (1600 instead of 667) and disk system ( SSD and SATA III instead of mech'l and SATA II), so the experience of the new system is of a much, much faster one. It really shifts the polygons!
A little analysis of the options>
The dual quad-core are offering 50% more threads than the single six-core and the two E5-1643's cost about $2,800 to the E5-1660 at about $1,100. In Passmark CPU Benchmarks , dual E5-2643's are rated at No. 18 with a score of 13759.
http://www.cpubenchmark.net/cpu_list.php
The Xeon E5-1660 is No. 9, scoring 12468. That is, the E5-2643's perform at 110% of the E5-1660, but at more than 250% of the cost. This is a bit raw in terms of cost/ performance consideration, but means that the additional cores / threads need to be quite important to your work to justify the cost alone. In single-threaded program the E5-1660 will be faster due to the higher clock speed.
A suggestion:
If you find the eight cores / sixteen threads are an advantage, or in fact the more the better, consider buying a dual CPU system but populating it with a single Xeon E5-2687W. That runs at a slightly higher clock speed (3.1 /3.8) than the 2643 (3.3 / 3.5) and, importantly, has 8 cores / sixteen threads at a raw cost of about $1,950 as compared to the dual 2643's at $2,800. In passmark a single E5-2687W is rated No. 1, scoring 14586. This is compared to the dual 2643's at 13759, meaning that you can have the same core / thread count with higher performance at 70% of the cost. There is an upcoming E5-2687W V2 that is 3.4 / 4.0GHz >
http://ark.intel.com/products/76161/Intel-Xeon-Processor-E5-2687W-v2-25M-Cache-3_40-GHz
It may a bit more than the original version.
This is disregarding the possible need for more PCIe slots, but I believe you could have a good Quadro- I'd suggest the K4000 (3GB), and perhaps an LSI SAS/ SATA RAID controller, and if necessary a network / port card, and so on. There should still be at least one or two more X16 slots for a Tesla or PHI co-processor.
In summary, unless Lenovo charges a huge premium for it, a single E5-2687W seems to solve every contingency with very high capabilities at a reasonable cost.
I might mention too, that there is the Xeon E5-1650 six-core @ 3.2 / 3.8 GHz and these sell for under $600 as OEM. There are a lot of Precision T3600's with these that do very well. The soon to be released E5-1660 V2 will run it's first core at 3.7GHz, but the 1650 top rate is still faster at 3.8GHz., so that's experientially the same or better performance at 54% of the cost.
E5-1650
http://ark.intel.com/products/64601
Cheers,
BambiBoom
1. Dell Precision T5400 (2009)> 2X Xeon X5460 quad core @3.16GHz > 16 GB ECC 667> Quadro FX 4800 (1.5GB) > WD RE4 / Segt Brcda 500GB > Windows 7 Ultimate 64-bit > HP 2711x 27" 1920 x 1080 > AutoCad, Revit, Solidworks, Sketchup Pro, Corel Technical Designer, Adobe CS MC, WordP Office, MS Office > architecture, industrial design, graphic design, rendering, writing
2. HP z420 (2013)> Xeon E5-1620 quad core @ 3.6 / 3.9GHz > 24GB ECC RAM > Firepro V4900 (Soon quadro K4000) > Samsung 840 SSD 250GB / Seagate Barracuda 500GB > Windows 7 Professional 64 > to be loaded > AutoCad, Revit, Inventor, Maya (2011), Solidworks 2010, Adobe CS4, Corel Technical Design X-5, Sketchup Pro, WordP Office X-5, MS Office