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Benchmarks performed with NWChem

This page contains a suite of benchmarks performed with NWChem. The benchmarks include a variety of computational chemistry methods on a variety of high performance computing platforms. The list of benchmarks available will evolve continuously as new data becomes available. If you have benchmark information you would like to add for your computing system, please contact one of the developers.

Hybrid density functional calculation on the C240 Buckyball

Performance of the Gaussian basis set DFT module in NWChem. This calculation involved performing a PBE0 calculation (in direct mode) on the on C240 system with the 6-31G* basis set (3600 basis functions) without symmetry. These calculations were performed on the Cascade supercomputer located at PNNL. Input and output files are available.

c240_web10.png

Parallel performance of Ab initio Molecular Dynamics using plane waves

AIMD Parallel timings for \(UO_2^{2+}\)+122\(H_2\)O. These calculations were performed on the Franklin Cray-XT4 computer system at NERSC.
PW

AIMD and AIMD/MM Parallel Timings for \(Zn^{2+}\)+64\(H_2\)O (unit cell parameters SC=12.4 Angs. and cutoff energy =100Ry). These calculations were performed on the Chinook HP computer system at MSCF EMSL, PNNL.
PWMD
Exact exchange timings – 80 atom cell of hematite (cutoff energy=100Ry). These calculations were performed on the Franklin Cray-XT4 computer system at NERSC.

Exact exchange timings – 576 atom cell of water (cutoff energy=100Ry). These calculations were performed on the Hopper Cray-XE6 computer system at NERSC.

Parallel performance of the CR-EOMCCSD(T) method (triples part)

An example of the scalability of the triples part of the CR-EOMCCSD(T) approach for Green Fluorescent Protein Chromophore (GFPC) described by cc-pVTZ basis set (648 basis functions) as obtained from NWChem. Timings were determined from calculations on the Franklin Cray-XT4 computer system at NERSC. See the input file for details.

And more recent scalability test of the CR-EOMCCSD(T) formalism (Jaguar Cray XT5 at ORNL, see K. Kowalski, S. Krishnamoorthy, R.M. Olson, V. Tipparaju, E. Aprà , SC2011, for details).

curve_bg_lumo.png

Parallel performance of the multireference coupled cluster (MRCC) methods

In collaboration with Dr. Jiri Pittner’s group from Heyrovsky Institute of Physical Chemistry implementations of two variants of state-specific MRCC approaches have been developed. During his internship at PNNL Jirka Brabec, using novel processor-group-based algorithms, implemented Brillouin-Wigner and Mukherjee MRCC models with singles and doubles. The scalabililty tests for the Brillouin-Wigner MRCCSD approach have been performed on Jaguar XT5 system at ORNL for \(\beta\)-carotene in 6-31 basis set (472 orbitals, 216 correlated electrons, 20 reference functions; see J.Brabec, J. Pittner, H.J.J. van Dam, E. Aprà, K. Kowalski, JCTC 2012, 8(2), pp 487–497). The input file and output files for runs at 6000 cores, at 12000 cores and at 24000 cores are available.

mrccsd_scalability.png

Former PNNL postdoctoral fellow Dr. Kiran Bhaskaran Nair developed perturbative MRCCSD(T) approaches, which accounts for the effect of triple excitations. Scaling of the triples part of the BW-MRCCSD(T) method for \(\beta\)” -carotene in 6-31 basis set (JCP 137, 094112 (2012)). The scalability tests of the BW-MRCCSD(T) implementation of NWChem have been performed on the Jaguar Cray-XK6 computer system of the National Center for Computational Sciences at Oak Ridge National Laboratory.

mrccsd_t_titan.png

Timings of CCSD/EOMCCSD for the oligoporphyrin dimer

CCSD/EOMCCSD timings for oligoporphyrin dimer (942 basis functions, 270 correlated electrons, D2h symmetry, excited-state calculations were performed for state of b1g symmetry, in all test calculation convergence threshold was relaxed, 1024 cores were used). See the input file for details.

--------------------------------------------------------
 Iter          Residuum       Correlation     Cpu    Wall
 --------------------------------------------------------
   1   0.7187071521175  -7.9406033677717   640.9   807.7
   ......
 MICROCYCLE DIIS UPDATE: 10 5
  11   0.0009737920958  -7.9953441809574   691.1   822.2
 --------------------------------------------------------
 Iterations converged
 CCSD correlation energy / hartree =        -7.995344180957357
 CCSD total energy / hartree       =     -2418.570838364838890

 EOM-CCSD right-hand side iterations
 --------------------------------------------------------------
      Residuum       Omega / hartree  Omega / eV    Cpu    Wall
 --------------------------------------------------------------
......
Iteration   2 using    6 trial vectors
  0.1584284659595   0.0882389635508    2.40111   865.3  1041.2
Iteration   3 using    7 trial vectors
  0.0575982107592   0.0810948687618    2.20670   918.0  1042.2

Performance tests of the GPU implementation of non-iterative part of the CCSD(T) approach

Recent tests of the GPU CCSD(T) implementation performed on Titan Cray XK7 1 system at ORNL (C22H14, 378 basis set functions, C1 symmetry; 98 nodes: 8 cores per node + 1GPU)

Using 8 CPU cores

Using CUDA CCSD(T) code 
Using 0 device(s) per node 
CCSD[T] correction energy / hartree = -0.150973754992986 
CCSD[T] correlation energy / hartree = -3.067917061062492 
CCSD[T] total energy / hartree = -844.403376796441080 
CCSD(T) correction energy / hartree = -0.147996460406684 
CCSD(T) correlation energy / hartree = -3.064939766476190 
CCSD(T) total energy / hartree = -844.400399501854849 
Cpu & wall time / sec 9229.9 9240.3

Using 7 CPU cores and one GPU

Using CUDA CCSD(T) code 
Using 1 device(s) per node  
CCSD[T] correction energy / hartree = -0.150973754993019 
CCSD[T] correlation energy / hartree = -3.067917061062597 
CCSD[T] total energy / hartree = -844.403376796441307 
CCSD(T) correction energy / hartree = -0.147996460406693 
CCSD(T) correlation energy / hartree = -3.064939766476270 
CCSD(T) total energy / hartree = -844.400399501854963 
Cpu & wall time / sec 1468.0 1630.7

Using 1 CPU core and one GPU

Using CUDA CCSD(T) code
Using 1 device(s) per node
CCSD[T] correction energy / hartree = -0.150973754993069
CCSD[T] correlation energy / hartree = -3.067917061063028
CCSD[T] total energy / hartree =  -844.***************
CCSD(T) correction energy / hartree = -0.147996460406749
CCSD(T) correlation energy / hartree = -3.064939766476708
CCSD(T) total energy / hartree = -844.400399501861216
Cpu & wall time / sec 1410.9 1756.5

Without GPU 9240.3 sec. With GPU 1630.7 sec.

Next release: GPU implementation of non-iterative part of the MRCCSD(T) approach (K. Bhaskarsan-Nair, W. Ma, S. Krishnamoorthy, O. Villa, H. van Dam, E. Aprà, K. Kowalski, J. Chem. Theory Comput. 9, 1949 (2013))

GPU_MRCCSD_T.png

Performance tests of the Xeon Phi implementation of non-iterative part of the CCSD(T) approach

Tests of the Xeon Phi CCSD(T) implementation performed on the EMSL cascade system at PNNL

Triplet_updated_feb2015.png

Aprà, E.; Klemm, M.; Kowalski, K., “Efficient Implementation of Many-Body Quantum Chemical Methods on the Intel® Xeon Phi Coprocessor,” High Performance Computing, Networking, Storage and Analysis, SC14: International Conference for , vol., no., pp.674-684, 16-21 Nov. 2014 http://dx.doi.org/10.1109/SC.2014.60

(Triplet state of Si4C3N2H12, 706 basis set functions, C1 symmetry)

Non-iterative part of the CCSD(T) approach: Comparing Xeon Phi and NVidia K20X performance

Wall time to solution (in seconds) of non-iterative triples part of the single-reference CCSD(T) approach for the pentacene molecule using Intel MIC and Nvidia GPU implementations. Tests were performed using 96 compute nodes on the Cascade system at EMSL (Intel® Xeon™ Phi 5110P) and Titan system at ORNL (NVIDIA Tesla® K20X).

( input file)

Tilesize Intel Xeon Phi 5110P Nvidia K20X
18 1806.4 1824.9
21 1652.2 1699.3
24 1453.3 1554.4

Current developments for high accuracy: alternative task schedulers (ATS)

Currently various development efforts are underway for high accuracy methods that will be available in future releases of NWChem. The examples below shows the first results of the performance of the triples part of Reg-CCSD(T) on GPGPUs (left two examples) and of using alternative task schedules for the iterative CCSD and EOMCCSD.

Scalability of the triples part of the Reg-CCSD(T) approach for Spiro cation described by the Sadlej’s TZ basis set (POL1). The calculations were performed using Barracuda cluster at EMSL. Speedup of GPU over CPU of the (T) part of the (T) part of the Reg-CCSD(T) approach as a function of the tile size for the uracil molecule. The calculations were performed using Barracuda cluster at EMSL.
*Comparison of the CCSD/EOMCCSD iteration times for BacterioChlorophyll (BChl, Mg O6 N4 C 36 H38) for various tile sizes. Calculations were performed for 3-21G basis set (503 basis functions, C1 symmetry, 240 correlated electrons, 1020 cores).

bchl_6_311G_ccsd.png *Time per CCSD iteration for BChl in 6-311G basis set (733 basis functions, C1 symmetry, 240 correlated electrons, 1020 cores) as a function of tile size. Scalability of the CCSD/EOMCCSD codes for BChl in 6-311G basis set (733 basis functions; tilesize=40, C1 symmetry, 240 correlated electrons).

Other tests:

The impact of the tilesize on the CCSD(ATS) timings: All tests have been performed for uracil trimer (6-31G* basis set; all core electrons frozen) on Hopper using 25 nodes (600 cores). One can observe almost 10-fold speedup of the CCSD(ATS) code for tilesize=40 compared to standard TCE CCSD implementation using tilesize=12.

uracil_trimer.png

Performance tests for water clusters

CTF.png

Luciferin (aug-cc-pVDZ basis set; RHF reference; frozen core) - time per CCSD iteration ( input file)

 tilesize = 30 
   256 cores      644 sec.
   512            378 sec.
   664            314 sec.
  1020            278 sec.
  1300            237 sec.

 tilesize = 40
    128             998 sec.
    256             575 sec.

Sucrose (6-311G** basis set; RHF reference; frozen core) - time per CCSD iteration ( input file)

tilesize = 40
   256 cores   1486 sec. 
   512          910 sec.
  1024          608 sec.

Cytosine-OH (POL1; UHF reference; frozen core) - time per EOMCCSD iteration ( input file)

 tilesize = 30
 256 cores    44.5 sec.

 tilesize = 40
 128 cores    55.6 sec.

Density functional calculation of a zeolite fragment

Benchmark results with NWChem 7.0.0 for LDA calculations (energy plus gradient) on a 533 atoms siosi8 zeolite fragment. The input uses an atomic orbital basis set with 7108 functions and a charge density fitting basis with 16501 functions. The input file is available at this link.

computer # nodes cores/node total # cores Wall time (seconds)
cascade 9 16 144 1247
cascade 20 16 320 703
tahoma 4 36 144 927
tahoma 9 36 324 524


Hardware used:

benchmarks/siosi8.png