NWChem: Benchmark of DFT Calculation running on Ryzen Threadripper

Ryzen Threadripper 1950X

Ref: https://www.anandtech.com

In this post I am going to show the benchmark results of performance testing of Ryzen Threadripper 1950X CPU for quantum chemistry calculation using NWChem program package. Ryzen Threadripper is state-of-the-art CPU of AMD. 1950X is the top class of Threadripper series. It has 16 cores/32 threads, which is a dark horse candidate in the war between AMD and Intel! I am so excited for this test of using the AMD's CPU for DFT calculation. The following is resource of machine and CPU specification that I use. Another candidate is Intel Xeon Co-processor E5-2697 v.3. Can't wait? Go down for read!

AMD Ryzen™ Threadripper 1950X

Architecture:          x86_64

CPU op-mode(s):        32-bit, 64-bit

Byte Order:            Little Endian

CPU(s):                32

On-line CPU(s) list:   0-31

Thread(s) per core:    2

Core(s) per socket:    16

Socket(s):             1

NUMA node(s):          2

Vendor ID:             AuthenticAMD

CPU family:            23

Model:                 1

Model name:            AMD Ryzen Threadripper 1950X 16-Core Processor

Stepping:              1

CPU MHz:               2200.000

CPU max MHz:           3400.0000

CPU min MHz:           2200.0000

BogoMIPS:              6786.58

Virtualization:        AMD-V

L1d cache:             32K

L1i cache:             64K

L2 cache:              512K

L3 cache:              8192K

NUMA node0 CPU(s):     0-7,16-23

NUMA node1 CPU(s):     8-15,24-31

Intel® Xeon® Processor E5-2697 v3

Architecture:          x86_64

CPU op-mode(s):        32-bit, 64-bit

Byte Order:            Little Endian

CPU(s):                28

On-line CPU(s) list:   0-27

Thread(s) per core:    1

Core(s) per socket:    14

Socket(s):             2

NUMA node(s):          4

Vendor ID:             GenuineIntel

CPU family:            6

Model:                 63

Stepping:              2

CPU MHz:               2593.971

BogoMIPS:              5187.58

Virtualization:        VT-x

L1d cache:             32K

L1i cache:             32K

L2 cache:              256K

L3 cache:              17920K

NUMA node0 CPU(s):     0,2,4,6,8,10,12

NUMA node1 CPU(s):     1,3,5,7,9,11,13

NUMA node2 CPU(s):     14,16,18,20,22,24,26

NUMA node3 CPU(s):     15,17,19,21,23,25,27

Program compilation

NWChem 6.8.1 was used in this test and was compiled manually with OpenMPI.

https://github.com/rangsimanketkaew/Auto-NWChem/tree/master/script

Tested molecule and calculation setup

Molecule: Tryptophan

Method: Density functional theory

Task: Single-point energy calculation

Functional: B3LYP and M06-2X

Basis set: 6-311++G(d,p)

Basis functions: 429

Charge: 0

Spin state: Singlet

Integral approach: Direct (on-the-fly)

Tryptophan

Input file

echo

start tryp-b3lyp-6-311++Gdp

memory stack 600 mb heap 50 mb global 400 mb noverify

scratch_dir /scratch/rangsiman/nwchem

permanent_dir .

geometry units angstrom noautoz

  symmetry c1

C       0.2699104420    -1.0108865836    -0.3683130952

C      -1.1717252744    -0.8428104535    -0.6503439320

H      -1.6792014443    -1.8288725326    -0.6137671086

H      -1.2877723491    -0.4791725466    -1.6914105077

C      -1.8459588054     0.1499150058     0.3112067480

N      -1.7959317480    -0.2468329763     1.7377821167

H      -2.2161720921    -1.1448059777     1.8585129306

H      -0.8394916844    -0.2879496005     2.0220904138

C      -3.3065223884     0.3106051815    -0.0869777892

O      -4.1944847211    -0.5221564648    -0.1054323635

O      -3.6537704097     1.5539926964    -0.4899646874

H      -4.5802415103     1.5796675292    -0.7087540852

H      -1.3128990822     1.1406738377     0.2349841455

C       1.2474179299     0.0408346940    -0.2193620936

C       1.1555245659     1.4391072316    -0.2186973930

C       2.3081955252     2.1747669480    -0.0390077626

C       3.5576637434     1.5487271836     0.1399510886

C       3.6811726255     0.1743154306     0.1469359543

C       2.5117189698    -0.5776612422    -0.0342040773

N       2.3171955667    -1.9742551771    -0.1274834562

C       0.9334831586    -2.2180739422    -0.2646030476

H       0.5181836619    -3.2254029279    -0.3238168600

H       2.9606157503    -2.6398109623     0.2168686362

H       4.6508019433    -0.3124295201     0.2889135247

H       4.4464013075     2.1732956451     0.2793431837

H       2.2595898801     3.2691493913    -0.0301538306

H       0.1720969826     1.9155481639    -0.3412322606

end

basis cartesian

* library 6-311++G**

end

dft

  xc b3lyp

  direct

end

task dft energy ignore

Benchmark Results

**To be fair, keep in mind that the Ryzen Threadripper 1950X has 16 physical cores (2 threads per core), while Xeon 2697 v.3 has 28 physical cores (1 thread / cores) !

Therefore, I recommend you to consider the results for only 1 - 16 processors.

Table and figure above are preliminary results. I have to check results again and again to ensure that all published results are correct.

To do list.

Write discussion.
Re-calculate the calculation to confirm results.
Check memory dependence.
Re-compile NWChem for Ryzen site with MVAPICH2 v. 2.2b, the current version was compiled with OpenMPI.
Perform DFT calculation with M06-2X.

Rangsiman Ketkaew

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