NWChem: Benchmark of DFT Calculation running on Ryzen Threadripper
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