Quantum Chemistry (QC) on GPUs · 2017-10-13 · 3 MD vs. QC on GPUs “Classical” Molecular Dynamics Quantum Chemistry (MO, PW, DFT, Semi-Emp) Simulates positions of atoms over

October 2017

Quantum Chemistry (QC) on GPUs

2

Overview of Life & Material Accelerated Apps

MD: All key codes are GPU-accelerated

Great multi-GPU performance

Focus on dense (up to 16) GPU nodes &/or large # of

GPU nodes

ACEMD*, AMBER (PMEMD)*, BAND, CHARMM, DESMOND, ESPResso,

Folding@Home, GPUgrid.net, GROMACS, HALMD, HTMD, HOOMD-

Blue*, LAMMPS, Lattice Microbes*, mdcore, MELD, miniMD, NAMD,

OpenMM, PolyFTS, SOP-GPU* & more

QC: All key codes are ported or optimizing

Focus on using GPU-accelerated math libraries,

OpenACC directives

GPU-accelerated and available today:

ABINIT, ACES III, ADF, BigDFT, CP2K, GAMESS, GAMESS-

UK, GPAW, LATTE, LSDalton, LSMS, MOLCAS, MOPAC2012,

NWChem, OCTOPUS*, PEtot, QUICK, Q-Chem, QMCPack,

Quantum Espresso/PWscf, QUICK, TeraChem*

Active GPU acceleration projects:

CASTEP, GAMESS, Gaussian, ONETEP, Quantum

Supercharger Library*, VASP & more

green* = application where >90% of the workload is on GPU

3

MD vs. QC on GPUs

“Classical” Molecular Dynamics Quantum Chemistry (MO, PW, DFT, Semi-Emp)Simulates positions of atoms over time;

chemical-biological or chemical-material behaviors

Calculates electronic properties; ground state, excited states, spectral properties,

making/breaking bonds, physical properties

Forces calculated from simple empirical formulas (bond rearrangement generally forbidden)

Forces derived from electron wave function (bond rearrangement OK, e.g., bond energies)

Up to millions of atoms Up to a few thousand atoms

Solvent included without difficulty Generally in a vacuum but if needed, solvent treated classically (QM/MM)

or using implicit methods

Single precision dominated Double precision is important

Uses cuBLAS, cuFFT, CUDA Uses cuBLAS, cuFFT, OpenACC

Geforce (Accademics), Tesla (Servers) Tesla recommended

ECC off ECC on

4

Accelerating Discoveries

Using a supercomputer powered by the Tesla

Platform with over 3,000 Tesla accelerators,

University of Illinois scientists performed the first

all-atom simulation of the HIV virus and discovered

the chemical structure of its capsid — “the perfect

target for fighting the infection.”

Without gpu, the supercomputer would need to be

5x larger for similar performance.

5

GPU-Accelerated Quantum Chemistry Apps

Abinit

ACES III

ADF

BigDFT

CP2K

GAMESS-US

Gaussian

GPAW

LATTE

LSDalton

MOLCAS

Mopac2012

NWChem

Green Lettering Indicates Performance Slides Included

GPU Perf compared against dual multi-core x86 CPU socket.

Quantum SuperChargerLibrary

RMG

TeraChem

UNM

VASP

WL-LSMS

Octopus

ONETEP

Petot

Q-Chem

QMCPACK

Quantum Espresso

ABINIT

ABINIT on GPUS

Speed in the parallel version:

For ground-state calculations, GPUs can be used. This is based on

CUDA+MAGMA

For ground-state calculations, the wavelet part of ABINIT (which is BigDFT) is

also very well parallelized : MPI band parallelism, combined with GPUs

BigDFT

Courtesy of BigDFTteam @ CEA






April 2017

Gaussian 16

16

GAUSSIAN 16

Using OpenACC allowed us to continue

development of our fundamental

algorithms and software capabilities

simultaneously with the GPU-related

work. In the end, we could use the

same code base for SMP, cluster/

network and GPU parallelism. PGI's

compilers were essential to the

success of our efforts.

Mike Frisch, Ph.D.President and CEOGaussian, Inc.

Parallelization Strategy

Within Gaussian 16, GPUs are used for a small fraction of code that consumes a large

fraction of the execution time. T e implementation of GPU parallelism conforms

to Gaussian’s general parallelization strategy. Its main tenets are to avoid changing

the underlying source code and to avoid modif cations which negatively af ect CPU

performance. For these reasons, OpenACC was used for GPU parallelization.

T e Gaussian approach to parallelization relies on environment-specif c parallelization frameworks and tools: OpenMP for shared-memory, Linda for cluster and network parallelization across discrete nodes, and OpenACC for GPUs.

T e process of implementing GPU support involved many dif erent aspects:

Identifying places where GPUs could be benef cial. T ese are a subset of areas which

are parallelized for other execution contexts because using GPUs requires f ne grained

parallelism.

Understanding and optimizing data movement/storage at a high level to maximize

GPU ef ciency.

Gaussian, Inc.340 Quinnipiac St. Bldg. 40Wallingford, CT 06492 [email protected]

Gaussian is a registered trademark of Gaussian, Inc. All other trademarks and registered trademarks are the properties of their respective holders. Specif cations subject to change without notice.

Copyright © 2017, Gaussian, Inc. All rights reserved.

Roberto GompertsNVIDIA

Michael FrischGaussian

Brent LebackNVIDIA/PGI

Giovanni ScalmaniGaussian

Project Contributors

PGI Accelerator Compilers with OpenACCPGI compilers fully support the current OpenACC standard as well as important extensions to it. PGI is an important contributor to the ongoing development of OpenACC.

OpenACC enables developers to implement GPU parallelism by adding compiler directives to their source code, of en eliminating the need for rewriting or restructuring. For example, the following Fortran compiler directive identif es a loop which the compiler should parallelize:

! $ a c c p a r a l l e l l o o p

Other directives allocate GPU memory, copy data to/from GPUs, specify data to remain on the GPU, combine or split loops and other code sections, and generally provide hints for optimal work distribution management, and more.

T e OpenACC project is very active, and the specif cations and tools are changing fairly rapidly. T is has been true throughout the lifetime of this project. Indeed, one of its major challenges has been using OpenACC in the midst of its development. T e talented people at PGI were instrumental in addressing issues that arose in one of the very f rst uses of OpenACC for a large commercial sof ware package.

Specifying GPUs to Gaussian 16

T e GPU implementation in Gaussian 16 is sophisticated and complex but using it is simple and straightforward. GPUs are specif ed with

1 additional Link 0 command (or equivalent Default.Route f le entry/command line option). For example, the following commands tell

Gaussian to run the calculation using 24 compute cores plus 8 GPUs+8 controlling cores (32 cores total):

%CPU= 0 - 3 1 Request 32 CPUs for the calculation: 24 cores for computation, and 8 cores to control GPUs (see below). %GPUCPU= 0 - 7 = 0 - 7 Use GPUs 0-7 with CPUs 0-7 as their controllers.

Detailed information is available on our website.

PGI’s sophisticated prof ling and performance evaluation tools were vital to the success of the ef ort.

ValinomycinwB97xD/6-311+(2d,p) Freq

2.25X speedup

Hardware: HPE server with dual Intel Xeon E5-2698 v3 CPUs (2.30GHz ; 16 cores/chip), 256GB memory and 4 Tesla K80 dual GPU boards (boost clocks: MEM 2505 and SM 875). Gaussian source code compiled with PGI Accelerator Compilers (16.5) with OpenACC (2.5 standard).

A Leading Computation Chemistry Code

17

GPU-ACCELERATED GAUSSIAN 16 AVAILABLE

• Gaussian is a Top Ten HPC (Quantum Chemistry) Application.

• 80-85% of use cases are GPU-accelerated (Hartree-Fock and DFT: energies, 1st derivatives (gradients) and 2nd derivatives). More functionality to come.

• K40, K80 support; P100 support coming as a minor release, performance “good”, faster wall clock times. Early P100 results promising.

• No pricing difference between Gaussian CPU and GPU versions.

• Existing Gaussian 09 customers under maintenance contract get (free) upgrade.

• Existing non-maintenance customers required to pay upgrade fee.

• To get the bits or to ask about the upgrade fee, please contact Gaussian, Inc.’s Jim Hess, Operations Manager; [email protected].

100% PGI OpenACC Port (no CUDA)

mailto:[email protected]

18

rg-a25 on K80s

Running Gaussian version 16

The blue node contains Dual Intel Xeon E5-2698 [email protected] (Haswell) CPUs

The green nodes contain Dual Intel Xeon E5-2698 [email protected] (Haswell) CPUs + Tesla K80 (autoboost) GPUs

Alanine 25. Two steps: Force and Frequency. APFD 6-31G*

nAtoms = 259, nBasis = 2195

7.4 hrs 6.4 hrs 5.8 hrs 5.1 hrs0.0x

0.2x

0.4x

0.6x

0.8x

1.0x

1.2x

1.4x

1.6x

1 Haswell node 1 node +1x K80 per node

1 node +2x K80 per node


Speed-u

p v

s D

ual H

asw

ell

rg-a25

19

rg-a25td on K80s




Alanine 25. Two Time-Dependent (TD) steps: Force and Frequency. APFD 6-31G*


27.9 hrs 25.8 hrs 22.6 hrs 20.1 hrs0.0x

0.2x

0.4x

0.6x

0.8x

1.0x

1.2x

1.4x

1.6x




Speed-u

p v

s D

ual H

asw

ell

rg-a25td

20

rg-on on K80s




GFP ONIOM. Two steps: Force and Frequency. APFD/6-

311+G(2d,p):amber=softfirst)=embednAtoms = 3715 (48/3667), nBasis = 813

2.5 hrs 2.1 hrs 1.7 hrs 1.5 hrs0.0x

0.2x

0.4x

0.6x

0.8x

1.0x

1.2x

1.4x

1.6x

1.8x




Speed-u

p v

s D

ual H

asw

ell

rg-on

21

rg-ontd on K80s




GFP ONIOM. Two Time-Dependent (TD) steps: Force and Frequency. APFD/6-311+G(2d,p):amber=softfirst)=embed

nAtoms = 3715 (48/3667), nBasis = 813

55.4 hrs 43.6 hrs 33.7 hrs 26.8 hrs0.0x

0.5x

1.0x

1.5x

2.0x

2.5x




Speed-u

p v

s D

ual H

asw

ell

rg-ontd

22

rg-val on K80s




Valinomycin. Two steps: Force and Frequency. APFD 6-311+G(2d,p)


229.0 hrs 168.4 hrs 141.7 hrs 101.5 hrs0.0x

0.5x

1.0x

1.5x

2.0x

2.5x




Speed-u

p v

s D

ual H

asw

ell

rg-val

23

Effects of using K80s7.4

hrs

27.9

hrs

2.5

hrs

55.4

hrs

229.0

hrs

6.4

hrs

25.8

hrs

2.1

hrs

43.6

hrs

168.4

hrs

5.8

hrs

22.6

hrs

1.7

hrs

33.7

hrs

141.7

hrs

5.1

hrs

20.1

hrs

1.5

hrs

26.8

hrs

101.5

hrs

0.0x

0.3x

0.5x

0.8x

1.0x

1.3x

1.5x

1.8x

2.0x

2.3x

2.5x

rg-a25 rg-a25td rg-on rg-ontd rg-val

Speed-u

p o

ver

run w

ithout

GPU

s

Number of K80 boards

Effects of using K80 boardsHaswell E5-2698 [email protected]

0 1 2 4

24

Gaussian 16 Supported Platforms

• 4-way collaboration; Gaussian, Inc., PGI, NVIDIA and HPE

• HPE, NVIDIA and PGI is the development platform

• All released/certified x86_64 versions of Gaussian 16 use the PGI compilers

• Certified versions of Gaussian 16 use Intel only for Itanium, XLF for some IBM platforms, Fujitsu compilers for some SPARC-based machines and PGI for the rest (including some Apple products)

• GINC is collaborating with IBM, PGI (and NVIDIA) to release an OpenPower version of Gaussian that also uses the PGI compiler

• See Gaussian Supported Platforms for more details: http://gaussian.com/g16/g16_plat.pdf

http://gaussian.com/g16/g16_plat.pdf

25

CLOSING REMARKS

Significant Progress has been made in enabling Gaussian on GPUs with OpenACC

OpenACC is increasingly becoming more versatile

Significant work lies ahead to improve performance

Expand feature set:

PBC, Solvation, MP2, ONIOM, triples-Corrections

26

ACKNOWLEDGEMENTS

Development is taking place with:

Hewlett-Packard (HP) Series SL2500 Servers (Intel® Xeon® E5-2680 v2 (2.8GHz/10-core/25MB/8.0GT-s QPI/115W, DDR3-1866)

NVIDIA® Tesla® GPUs (K40 and later)

PGI Accelerator Compilers (16.x) with OpenACC (2.5 standard)

10/12/2017

GPAW

Increase Performance with Kepler

Running GPAW 10258

The blue nodes contain 1x E5-2687W CPU (8

Cores per CPU).

The green nodes contain 1x E5-2687W CPU (8

Cores per CPU) and 1x or 2x NVIDIA K20X for

the GPU.

0

0.5

1

1.5

2

2.5

3

3.5

Silicon K=1 Silicon K=2 Silicon K=3

Sp

eed

up

Co

mp

are

d t

o C

PU

On

ly

1.4

2.5

1.5

2.7

1.6

3.0

1 1 1


0

0.5

1

1.5

2

2.5

3


Sp

eed

up

Co

mp

are

d t

o C

PU

On

ly

1.7x

2.2x

2.4x

Running GPAW 10258

The blue nodes contain 1x E5-2687W CPU (8

Cores per CPU).

The green nodes contain 1x E5-2687W CPUs (8

Cores per CPU) and 2x NVIDIA K20 or K20X for

the GPU.


Running GPAW 10258

The blue nodes contain 2x E5-2687W CPUs (8

Cores per CPU).

The green nodes contain 2x E5-2687W CPUs (8

Cores per CPU) and 2x NVIDIA K20 or K20X for

the GPU.

0

0.2

0.4

0.6

0.8

1

1.2

1.4

1.6


Sp

eed

up

Co

mp

are

d t

o C

PU

On

ly

1.3x

1.4x

1.4x

Used with

permission from

Samuli Hakala

35

36

37

38

39

40

LSDALTON

42

Janus Juul Eriksen, PhD Fellow

qLEAP Center for Theoretical Chemistry, Aarhus University

“

OpenACC makes GPU computing approachable for

domain scientists. Initial OpenACC implementation

required only minor effort, and more importantly,

no modifications of our existing CPU implementation.

“

LSDALTON

Large-scale application for calculating high-accuracy molecular energies

Lines of Code

Modified

# of Weeks

Required

# of Codes to

Maintain

<100 Lines 1 Week 1 Source

Big Performance

7.9x8.9x

11.7x

ALANINE-113 ATOMS

ALANINE-223 ATOMS

ALANINE-333 ATOMS

Speedup v

s C

PU

Minimal Effort

LS-DALTON CCSD(T) ModuleBenchmarked on Titan Supercomputer (AMD CPU vs Tesla K20X)

https://developer.nvidia.com/openacc/success-stories

https://developer.nvidia.com/openacc/success-stories

NWChem

NWChem 6.3 Release with GPU Acceleration

Addresses large complex and challenging molecular-scale scientific

problems in the areas of catalysis, materials, geochemistry and

biochemistry on highly scalable, parallel computing platforms to

obtain the fastest time-to-solution

Researchers can for the first time be able to perform large scale

coupled cluster with perturbative triples calculations utilizing the

NVIDIA GPU technology. A highly scalable multi-reference coupled

cluster capability will also be available in NWChem 6.3.

The software, released under the Educational Community License

2.0, can be downloaded from the NWChem website at

www.nwchem-sw.org

http://www.nwchem-sw.org/

System: cluster consisting

of dual-socket nodes

constructed from:

• 8-core AMD Interlagos

processors

• 64 GB of memory

• Tesla M2090 (Fermi)

GPUs

The nodes are connected

using a high-performance

QDR Infiniband interconnect

Courtesy of Kowolski, K.,

Bhaskaran-Nair, at al @

PNNL, JCTC (submitted)

NWChem - Speedup of the non-iterative calculation for various configurations/tile sizes

Kepler, Faster Performance (NWChem)

0

20

40

60

80

100

120

140

160

180

CPU Only CPU + 1x K20X CPU + 2x K20X

Tim

e t

o S

olu

tio

n (

sec

on

ds

)

165

81

54

Uracil

Uracil Molecule

Performance improves by 2x with one GPU and by 3.1x with 2 GPUs

December 2016

Quantum Espresso 5.4.0

48

QUANTUM ESPRESSO

CUDA Fortran gives us the full

performance potential of the CUDA

programming model and NVIDIA GPUs.

!$CUF KERNELS directives give us

productivity and source code

maintainability. It’s the best of both

worlds.

Filippo SpigaHead of Research Software EngineeringUniversity of CambridgeQuantum Chemistry Suite

www.quantum-espresso.org

http://www.quantum-espresso.org/

49

AUSURF112 on K80s

Running Quantum Espresso version 5.4.0

The blue node contains Dual Intel Xeon E5-2690 [email protected] [3.5GHz Turbo]

(Broadwell) CPUs

The green node contains Dual Intel Xeon E5-2690 [email protected] [3.5GHz Turbo]

(Broadwell) CPUs + Tesla K80 (autoboost) GPUs

606.00

528.20

480

500

520

540

560

580

600

620

1 Broadwell node 1 node +4x K80 per node

seconds

AUSURF112*Lower is better

1.1X

50

AUSURF112 on P100s PCIe

606.00

515.70

486.90

0

100

200

300

400

500

600

700

1 Broadwell node 1 node +4x P100 PCIe per node

1 node +8x P100 PCIe per node

seconds

AUSURF1120

Running Quantum Espresso version 5.4.0


(Broadwell) CPUs

The green nodes contain Dual Intel Xeon E5-2690 [email protected] [3.5GHz Turbo]

(Broadwell) CPUs + Tesla P100 PCIe GPUs

*Lower is better

1.2X 1.2X

Speaker, Date

TeraChem 1.5K

TrpCage6-31GRHF

1604 bfn284 atoms

TrpCage6-31G**

RHF2900 bfn

284 atoms

Ru ComplexLANL2DZ

B3LYP4512 bfn

1013 atoms

BPTISTO-3G

RHF2706 bfn

882 atoms

Olestra6-31G*

RHF3181 bfn

453 atoms

Olestra6-31G*

BLYP3181 bfn

453 atoms

3.7x

2.8x 3.3x

2.7x2.3x

2.8x

All timings for complete energyand gradient Calculations

K80 = 1 GPU on Board, not both

Slide courtesy of PetaChem LLC / Todd Martinez

53

TERACHEM 1.5K; TRIPCAGE ON TESLA K40S

0

40

80

120

160

200

2 x Xeon E5-2697 [email protected] + 1 xTesla K40@875Mhz (1 node)




TeraChem 1.5K; TripCage on Tesla K40s & IVB CPUs(Total Processing Time in Seconds)

54

TERACHEM 1.5K; TRIPCAGE ON TESLA K40S & HASWELL CPUS

0

40

80

120

160

200

2 x Xeon E5-2698 [email protected] + 1 x TeslaK40@875Mhz (1 node)



TeraChem 1.5K; TripCage on Tesla K40s & Haswell CPUs(Total Processing Time in Seconds)

55

TERACHEM 1.5K; TRIPCAGE ON TESLA K80S & IVB CPUS

0

40

80

120

2 x Xeon E5-2697 [email protected] + 1 x Tesla K80 board(1 node)

2 x Xeon E5-2697 [email protected] + 2 x Tesla K80 boards(1 node)

2 x Xeon E5-2697 [email protected] + 4 x Tesla K80 boards(1 node)

TeraChem 1.5K; TripCage on Tesla K80s & IVB CPUs(Total Processing Time in Seconds)

56

TERACHEM 1.5K; TRIPCAGE ON TESLA K80S & HASWELL CPUS

0

30

60

90

120

2 x Xeon E5-2698 [email protected] + 1 x Tesla K80board (1 node)

2 x Xeon E5-2698 [email protected] + 2 x Tesla K80boards (1 node)


TeraChem 1.5K; TripCage on Tesla K80s & Haswell CPUs(Total Processing Time in Seconds)

57

TERACHEM 1.5K; BPTI ON TESLA K40S & IVB CPUS

0

2000

4000

6000

8000

10000

12000





TeraChem 1.5K; BPTI on Tesla K40s & IVB CPUs(Total Processing Time in Seconds)

58


0

2000

4000

6000

8000

2 x Xeon E5-2697 [email protected] + 1 x Tesla K80board (1 node)



TeraChem 1.5K; BPTI on Tesla K80s & IVB CPUs(Total Processing Time in Seconds)

59


0

2000

4000

6000

8000

10000

12000




TeraChem 1.5K; BPTI on Tesla K40s & Haswell CPUs(Total Processing Time in Seconds)

60

TERACHEM 1.5K; BPTI ON TESLA K80S & HASWELL CPUS

0

2000

4000

6000

2 x Xeon E5-2698 [email protected] + 1 x Tesla K80 board(1 node)



TeraChem 1.5K; BPTI on Tesla K80s & Haswell CPUs(Total Processing Time in Seconds)

TeraChemSupercomputer Speeds on GPUs

0

10

20

30

40

50

60

70

80

90

100

4096 Quad Core CPUs ($19,000,000) 8 C2050 ($31,000)

Tim

e (

Seco

nd

s)

Time for SCF Step

TeraChem running on 8 C2050s on 1 node

NWChem running on 4096 Quad Core CPUs

In the Chinook Supercomputer

Giant Fullerene C240 Molecule

Similar performance from just a handful of GPUs

TeraChemBang for the Buck

1

493

0

100

200

300

400

500

600

4096 Quad Core CPUs ($19,000,000) 8 C2050 ($31,000)

Pri

ce/P

erf

orm

an

ce r

ela

tiv

e t

o S

up

erc

om

pu

ter

Performance/Price

Dollars spent on GPUs do 500x more science than those spent on CPUs

TeraChem running on 8 C2050s on 1 node

NWChem running on 4096 Quad Core

CPUs

In the Chinook Supercomputer

Giant Fullerene C240 Molecule

Note: Typical CPU and GPU node pricing

used. Pricing may vary depending on node

configuration. Contact your preferred HW

vendor for actual pricing.

Kepler’s Even Better

Kepler performs 2x faster than Tesla

TeraChem running on C2050 and K20C

First graph is of BLYP/G-31(d)

Second is B3LYP/6-31G(d)

0

100

200

300

400

500

600

700

800

C2050 K20C

Seco

nd

s

Olestra BLYP 453 Atoms

0

200

400

600

800

1000

1200

1400

1600

1800

2000

C2050 K20C

Seco

nd

s

B3LYP/6-31G(d)

October 2017

VASP 5.4.4

65

Silica IFPEN on V100s PCIe

0.00210

0.00418

0.00537

0.00628

0.00000

0.00100

0.00200

0.00300

0.00400

0.00500

0.00600

0.00700

1 Broadwell node 1 node +2x V100 PCIe

per node (16GB)

1 node +4x V100 PCIe

per node (16GB)


per node (16GB)

1/se

conds

(Untuned on Volta)Running VASP version 5.4.4


(Broadwell) CPUs

The green nodes contain Dual Intel Xeon E5-2690 [email protected] [3.5GHz

Turbo] (Broadwell) CPUs + Tesla V100 PCIe (16GB) GPUs

240 ions, cristobalite (high) bulk720 bands

? plane wavesALGO = Very Fast (RMM-DIIS)

2.0X

2.6X

3.0X

66

Silica IFPEN on V100s SXM2

0.00210

0.00423

0.00541

0.00580

0.00000

0.00100

0.00200

0.00300

0.00400

0.00500

0.00600

0.00700

1 Broadwell node 1 node +2x V100 SXM2

per node (16GB)

1 node +4x V100 SXM2

per node (16GB)


per node (16GB)

1/se

conds



(Broadwell) CPUs


Turbo] (Broadwell) CPUs + Tesla V100 SXM2 (16GB) GPUs



2.0X

2.6X

2.8X

67

Si-Huge on V100s PCIe

0.00017

0.00045

0.00057

0.00065

0.00000

0.00010

0.00020

0.00030

0.00040

0.00050

0.00060

0.00070


per node (16GB)


per node (16GB)


per node (16GB)

1/se

conds



(Broadwell) CPUs



512 Si atoms1282 bands

864000 Plane WavesAlgo = Normal (blocked Davidson)

2.6X

3.4X

3.8X

68

Si-Huge on V100s SXM2

0.00017

0.00044

0.00056

0.00067

0.00000

0.00010

0.00020

0.00030

0.00040

0.00050

0.00060

0.00070

0.00080


per node (16GB)


per node (16GB)


per node (16GB)

1/se

conds



(Broadwell) CPUs





2.6X3.3X

4.0X

69

SupportedSystems on V100s PCIe

0.0037

0.0068

0.0087

0.0000

0.0010

0.0020

0.0030

0.0040

0.0050

0.0060

0.0070

0.0080

0.0090

0.0100


per node (16GB)


per node (16GB)

1/se

conds



(Broadwell) CPUs



267 ions788 bands

762048 plane wavesALGO = Fast (Davidson + RMM-DIIS)

1.8X

2.4X

70

SupportedSystems on V100s SXM2

0.0037

0.0068

0.0087

0.0100

0.0000

0.0020

0.0040

0.0060

0.0080

0.0100

0.0120


per node (16GB)


per node (16GB)


per node (16GB)

1/se

conds



(Broadwell) CPUs



267 ions788 bands


1.8X

2.4X

2.7X

71

NiAl-MD on V100s PCIe

0.0031

0.0063

0.0068

0.0000

0.0010

0.0020

0.0030

0.0040

0.0050

0.0060

0.0070

0.0080


per node (16GB)


per node (16GB)

1/se

conds



(Broadwell) CPUs



500 ions3200 bands


2.0X2.2X

72

NiAl-MD on V100s SXM2

0.0031

0.0064

0.0070

0.0074

0.0000

0.0010

0.0020

0.0030

0.0040

0.0050

0.0060

0.0070

0.0080


per node (16GB)


per node (16GB)


per node (16GB)

1/se

conds



(Broadwell) CPUs



500 ions3200 bands


2.1X

2.3X2.4X

73

B.hR105 on V100s PCIe

0.0008

0.0077

0.0112

0.0119

0.0000

0.0020

0.0040

0.0060

0.0080

0.0100

0.0120

0.0140


per node (16GB)


per node (16GB)


per node (16GB)

1/se

conds



(Broadwell) CPUs



105 Boron atoms (β-rhombohedral structure)216 bands

110592 plane wavesHybrid Functional with blocked Davicson

(ALGO=Normal)LHFCALC=.True. (Exact Exchange)

9.6X

14.0X14.9X

74

B.hR105 on V100s SXM2

0.0008

0.0079

0.0116

0.0128

0.0000

0.0020

0.0040

0.0060

0.0080

0.0100

0.0120

0.0140


per node (16GB)


per node (16GB)


per node (16GB)

1/se

conds



(Broadwell) CPUs






9.9X

14.5X

16.0X

75

B.aP107 on V100s PCIe

0.000038

0.000323

0.000462

0.000490

0.000000

0.000100

0.000200

0.000300

0.000400

0.000500

0.000600


per node (16GB)


per node (16GB)


per node (16GB)

1/se

conds



(Broadwell) CPUs



107 Boron atoms (symmetry broken 107-atom β′ variant)216 bands

110592 plane wavesHybrid functional calculation (exact

exchange) with blocked Davidson. No KPointparallelization.

Hybrid Functional with blocked Davidson (ALGO=Normal)

LHFCALC=.True. (Exact Exchange)

8.5X

12.2X

12.9X

76

B.aP107 on V100s SXM2

0.000038

0.000324

0.000465

0.000523

0.000000

0.000100

0.000200

0.000300

0.000400

0.000500

0.000600


per node (16GB)


per node (16GB)


per node (16GB)

1/se

conds



(Broadwell) CPUs



107 Boron atoms (symmetry broken 107-atom β′ variant)216 bands

110592 plane wavesHybrid functional calculation (exact

exchange) with blocked Davidson. No KPointparallelization.



8.5X

12.2X

13.8X

February 2017

VASP 5.4.1

78

Interface on P100s PCIe

Running VASP version 5.4.1


(Broadwell) CPUs


Turbo] (Broadwell) CPUs + Tesla P100 PCIe GPUs

➢ 1x P100 PCIe is paired with Single Intel Xeon E5-2699 [email protected]

[3.6GHz Turbo] (Broadwell)

Interface between a platinum slab Pt(111) (108 atoms) and liquid water (120 water

molecules) (468 ions)

1256 bands762048 plane waves

ALGO = Fast (Davidson + RMM-DIIS)

0.00171

0.00228

0.00308

0.00359

0.00434

0.00000

0.00050

0.00100

0.00150

0.00200

0.00250

0.00300

0.00350

0.00400

0.00450

0.00500

1 Broadwell node 1 node +1x P100 PCIe

per node

1 node +2x P100 PCIe

per node


per node


per node

1/se

conds

Interface

1.3X

1.8X2.1X

2.5X

79

Interface on P100s SXM2



(Broadwell) CPUs


Turbo] (Broadwell) CPUs + Tesla P100 SXM2 GPUs

➢ 1x P100 SXM2 is paired with Single Intel Xeon E5-2698 [email protected]


Interface between a platinum slab Pt(111) (108 atoms) and liquid water (120 water

molecules) (468 ions)


ALGO = Fast (Davidson + RMM-DIIS)

0.00171

0.00228

0.00270

0.00326

0.00462

0.00000

0.00050

0.00100

0.00150

0.00200

0.00250

0.00300

0.00350

0.00400

0.00450

0.00500

1 Broadwell node 1 node +1x P100 SXM2

per node

1 node +2x P100 SXM2

per node


per node


per node

1/se

conds

Interface

1.3X1.6X

1.9X

2.7X

80

Silica IFPEN on P100s PCIe



(Broadwell) CPUs







0.00273

0.00380

0.00474

0.00616

0.00674

0.00000

0.00100

0.00200

0.00300

0.00400

0.00500

0.00600

0.00700

0.00800


per node


per node


per node


per node

1/se

conds

Silica IFPEN

1.4X

1.7X

2.3X

2.5X

81

Silica IFPEN on P100s SXM2



(Broadwell) CPUs







0.00273

0.00352

0.00475

0.00616

0.00692

0.00000

0.00100

0.00200

0.00300

0.00400

0.00500

0.00600

0.00700

0.00800


per node


per node


per node


per node

1/se

conds

Silica IFPEN

1.3X

1.7X

2.3X2.5X

82

Si-Huge on P100s PCIe



(Broadwell) CPUs







0.00019

0.00034

0.00044

0.00058

0.00074

0.00000

0.00010

0.00020

0.00030

0.00040

0.00050

0.00060

0.00070

0.00080


per node


per node


per node


per node

1/se

conds

Si-Huge

1.8X

2.3X

3.1X

3.9X

83

Si-Huge on P100s SXM2



(Broadwell) CPUs







0.00019

0.00033

0.00040

0.00045

0.00066

0.00000

0.00010

0.00020

0.00030

0.00040

0.00050

0.00060

0.00070


per node


per node


per node


per node

1/se

conds

Si-Huge

1.7X

2.1X2.4X

3.5X

84

SupportedSystems on P100s PCIe



(Broadwell) CPUs





267 ions788 bands


0.00413

0.00518

0.00651

0.00794 0.00796

0.00000

0.00200

0.00400

0.00600

0.00800

0.01000


per node


per node


per node


per node

1/se

conds

SupportedSystems

1.3X

1.6X

1.9X 1.9X

85

SupportedSystems on P100s SXM2



(Broadwell) CPUs





267 ions788 bands


0.00413

0.00516

0.00570

0.00692

0.00938

0.00000

0.00100

0.00200

0.00300

0.00400

0.00500

0.00600

0.00700

0.00800

0.00900

0.01000


per node


per node


per node


per node

1/se

conds

SupportedSystems

1.2X1.4X

1.7X

2.3X

86

NiAl-MD on P100s PCIe



(Broadwell) CPUs





500 ions3200 bands


0.00347

0.00577

0.00731

0.009020.00936

0.00000

0.00100

0.00200

0.00300

0.00400

0.00500

0.00600

0.00700

0.00800

0.00900

0.01000


per node


per node


per node


per node

1/se

conds

NiAl-MD

1.7X

2.1X2.6X

2.7X

87

NiAl-MD on P100s SXM2



(Broadwell) CPUs





500 ions3200 bands


0.0035

0.0057

0.0074

0.0081

0.0090

0.0000

0.0010

0.0020

0.0030

0.0040

0.0050

0.0060

0.0070

0.0080

0.0090

0.0100


per node


per node


per node


per node

1/se

conds

NiAl-MD

1.6X

2.1X2.3X

2.6X

88

LiZnO on P100s PCIe



(Broadwell) CPUs



500 ions3200 bands


0.00106

0.00137

0.00153

0.00000

0.00020

0.00040

0.00060

0.00080

0.00100

0.00120

0.00140

0.00160

0.00180


per node


per node

1/se

conds

LiZnO

1.3X1.4X

89

LiZnO on P100s SXM2



(Broadwell) CPUs





500 ions3200 bands


0.00110.0011

0.0013

0.0015

0.0018

0.0000

0.0002

0.0004

0.0006

0.0008

0.0010

0.0012

0.0014

0.0016

0.0018

0.0020


per node


per node


per node


per node

1/se

conds

LiZnO

1.0X1.2X

1.4X1.6X

90

B.hR105 on P100s PCIe



(Broadwell) CPUs








0.00090

0.00223

0.00371

0.00560

0.00702

0.00000

0.00100

0.00200

0.00300

0.00400

0.00500

0.00600

0.00700

0.00800


per node


per node


per node


per node

1/se

conds

B.hR105

2.5X

4.1X

6.2X

7.8X

91

B.hR105 on P100s SXM2



(Broadwell) CPUs








0.0009

0.0024

0.0039

0.0059

0.0078

0.0000

0.0010

0.0020

0.0030

0.0040

0.0050

0.0060

0.0070

0.0080

0.0090


per node


per node


per node


per node

1/se

cpnds

B.hR105

2.7X

4.3X

6.6X

8.7X

92

B.aP107 on P100s PCIe



(Broadwell) CPUs





107 Boron atoms (symmetry broken 107-atom β′ variant)


Hybrid functional calculation (exact exchange) with blocked Davidson. No KPoint parallelization.



0.00003

0.00012

0.00021

0.00031

0.00041

0.00000

0.00005

0.00010

0.00015

0.00020

0.00025

0.00030

0.00035

0.00040

0.00045


per node


per node


per node


per node

1/se

conds

B.aP107

4.0X

7.0X

10.3X

13.7X

93

B.aP107 on P100s SXM2



(Broadwell) CPUs





107 Boron atoms (symmetry broken 107-atom β′ variant)


Hybrid functional calculation (exact exchange) with blocked Davidson. No KPoint parallelization.



0.00003

0.00011

0.00020

0.00027

0.00044

0.00000

0.00005

0.00010

0.00015

0.00020

0.00025

0.00030

0.00035

0.00040

0.00045

0.00050


per node


per node


per node


per node

1/se

conds

B.aP107

3.7X

6.7X9.0X

14.7X

Dec, 19, 2016

Quantum Chemistry (QC) on GPUs

95

GPU-Accelerated Molecular Dynamics Apps

ACEMD

AMBER

CHARMM

DESMOND

ESPResSO

Folding@Home

GENESIS

GPUGrid.net

GROMACS

HALMD

HOOMD-Blue

HTMD

Green Lettering Indicates Performance Slides Included

GPU Perf compared against dual multi-core x86 CPU socket.

LAMMPS

mdcore

MELD

NAMD

OpenMM

PolyFTS

Documents

Quantum Chemistry (QC) on GPUs · 2017-10-13 · 3 MD vs. QC on GPUs “Classical” Molecular Dynamics Quantum Chemistry (MO, PW, DFT, Semi-Emp) Simulates positions of atoms over