International Journal of High Performance Computing Applications, volume 33, issue 1, pages 212-224
An efficient MPI/OpenMP parallelization of the Hartree–Fock–Roothaan method for the first generation of Intel® Xeon Phi™ processor architecture
Publication type: Journal Article
Publication date: 2017-10-04
Quartile SCImago
Q2
Quartile WOS
Q2
Impact factor: 3.1
ISSN: 10943420, 17412846
Hardware and Architecture
Software
Theoretical Computer Science
Abstract
The Hartree–Fock method in the General Atomic and Molecular Structure System (GAMESS) quantum chemistry package represents one of the most irregular algorithms in computation today. Major steps in the calculation are the irregular computation of electron repulsion integrals and the building of the Fock matrix. These are the central components of the main self consistent field (SCF) loop, the key hot spot in electronic structure codes. By threading the Message Passing Interface (MPI) ranks in the official release of the GAMESS code, we not only speed up the main SCF loop (4× to 6× for large systems) but also achieve a significant ([Formula: see text]×) reduction in the overall memory footprint. These improvements are a direct consequence of memory access optimizations within the MPI ranks. We benchmark our implementation against the official release of the GAMESS code on the Intel® Xeon Phi™ supercomputer. Scaling numbers are reported on up to 7680 cores on Intel Xeon Phi coprocessors.
Citations by journals
|
1
2
3
4
|
|
|
Journal of Chemical Physics
|
Journal of Chemical Physics
4 publications, 26.67%
|
|
Journal of Chemical Theory and Computation
|
Journal of Chemical Theory and Computation
4 publications, 26.67%
|
|
International Journal of Quantum Chemistry
|
International Journal of Quantum Chemistry
1 publication, 6.67%
|
|
Parallel Computing
|
Parallel Computing
1 publication, 6.67%
|
|
Journal of Physical Chemistry A
|
Journal of Physical Chemistry A
1 publication, 6.67%
|
|
Chemical Reviews
|
Chemical Reviews
1 publication, 6.67%
|
|
Lecture Notes in Computer Science
|
Lecture Notes in Computer Science
1 publication, 6.67%
|
|
1
2
3
4
|
Citations by publishers
|
1
2
3
4
5
6
|
|
|
American Chemical Society (ACS)
|
American Chemical Society (ACS)
6 publications, 40%
|
|
American Institute of Physics (AIP)
|
American Institute of Physics (AIP)
4 publications, 26.67%
|
|
Wiley
|
Wiley
1 publication, 6.67%
|
|
Elsevier
|
Elsevier
1 publication, 6.67%
|
|
Springer Nature
|
Springer Nature
1 publication, 6.67%
|
|
1
2
3
4
5
6
|
- We do not take into account publications that without a DOI.
- Statistics recalculated only for publications connected to researchers, organizations and labs registered on the platform.
- Statistics recalculated weekly.
{"yearsCitations":{"type":"bar","data":{"show":true,"labels":[2018,2019,2020,2021,2022,2023,2024],"ids":[0,0,0,0,0,0,0],"codes":[0,0,0,0,0,0,0],"imageUrls":["","","","","","",""],"datasets":[{"label":"Citations number","data":[1,1,3,4,3,2,1],"backgroundColor":["#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6"],"percentage":["6.67","6.67","20","26.67","20","13.33","6.67"],"barThickness":null}]},"options":{"indexAxis":"x","maintainAspectRatio":true,"scales":{"y":{"ticks":{"precision":0,"autoSkip":false,"font":{"family":"Montserrat"},"color":"#000000"}},"x":{"ticks":{"stepSize":1,"precision":0,"font":{"family":"Montserrat"},"color":"#000000"}}},"plugins":{"legend":{"position":"top","labels":{"font":{"family":"Montserrat"},"color":"#000000"}},"title":{"display":true,"text":"Citations per year","font":{"size":24,"family":"Montserrat","weight":600},"color":"#000000"}}}},"journals":{"type":"bar","data":{"show":true,"labels":["Journal of Chemical Physics","Journal of Chemical Theory and Computation","International Journal of Quantum Chemistry","Parallel Computing","Journal of Physical Chemistry A","Chemical Reviews","Lecture Notes in Computer Science"],"ids":[544,58,15897,4056,15255,13718,1022],"codes":[0,0,0,0,0,0,0],"imageUrls":["\/storage\/images\/resized\/ARM4e6URKRsbRZvIF0vFis9DjxGloBjnBYJXbHmZ_medium.webp","\/storage\/images\/resized\/iLiQsFqFaSEx6chlGQ5fbAwF6VYU3WWa08hkss0g_medium.webp","\/storage\/images\/resized\/bRyGpdm98BkAUYiK1YFNpl5Z7hPu6Gd87gbIeuG3_medium.webp","\/storage\/images\/resized\/GDnYOu1UpMMfMMRV6Aqle4H0YLLsraeD9IP9qScG_medium.webp","\/storage\/images\/resized\/iLiQsFqFaSEx6chlGQ5fbAwF6VYU3WWa08hkss0g_medium.webp","\/storage\/images\/resized\/iLiQsFqFaSEx6chlGQ5fbAwF6VYU3WWa08hkss0g_medium.webp","\/storage\/images\/resized\/voXLqlsvTwv5p3iMQ8Dhs95nqB4AXOG7Taj7G4ra_medium.webp"],"datasets":[{"label":"","data":[4,4,1,1,1,1,1],"backgroundColor":["#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6"],"percentage":[26.67,26.67,6.67,6.67,6.67,6.67,6.67],"barThickness":13}]},"options":{"indexAxis":"y","maintainAspectRatio":false,"scales":{"y":{"ticks":{"precision":0,"autoSkip":false,"font":{"family":"Montserrat"},"color":"#000000"}},"x":{"ticks":{"stepSize":null,"precision":0,"font":{"family":"Montserrat"},"color":"#000000"}}},"plugins":{"legend":{"position":"top","labels":{"font":{"family":"Montserrat"},"color":"#000000"}},"title":{"display":true,"text":"Journals","font":{"size":24,"family":"Montserrat","weight":600},"color":"#000000"}}}},"publishers":{"type":"bar","data":{"show":true,"labels":["American Chemical Society (ACS)","American Institute of Physics (AIP)","Wiley","Elsevier","Springer Nature"],"ids":[40,250,11,17,8],"codes":[0,0,0,0,0],"imageUrls":["\/storage\/images\/resized\/iLiQsFqFaSEx6chlGQ5fbAwF6VYU3WWa08hkss0g_medium.webp","\/storage\/images\/resized\/ARM4e6URKRsbRZvIF0vFis9DjxGloBjnBYJXbHmZ_medium.webp","\/storage\/images\/resized\/bRyGpdm98BkAUYiK1YFNpl5Z7hPu6Gd87gbIeuG3_medium.webp","\/storage\/images\/resized\/GDnYOu1UpMMfMMRV6Aqle4H0YLLsraeD9IP9qScG_medium.webp","\/storage\/images\/resized\/voXLqlsvTwv5p3iMQ8Dhs95nqB4AXOG7Taj7G4ra_medium.webp"],"datasets":[{"label":"","data":[6,4,1,1,1],"backgroundColor":["#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6"],"percentage":[40,26.67,6.67,6.67,6.67],"barThickness":13}]},"options":{"indexAxis":"y","maintainAspectRatio":false,"scales":{"y":{"ticks":{"precision":0,"autoSkip":false,"font":{"family":"Montserrat"},"color":"#000000"}},"x":{"ticks":{"stepSize":null,"precision":0,"font":{"family":"Montserrat"},"color":"#000000"}}},"plugins":{"legend":{"position":"top","labels":{"font":{"family":"Montserrat"},"color":"#000000"}},"title":{"display":true,"text":"Publishers","font":{"size":24,"family":"Montserrat","weight":600},"color":"#000000"}}}}}
Metrics
Cite this
GOST |
RIS |
BibTex |
MLA
Cite this
GOST
Copy
Mironov V. et al. An efficient MPI/OpenMP parallelization of the Hartree–Fock–Roothaan method for the first generation of Intel® Xeon Phi™ processor architecture // International Journal of High Performance Computing Applications. 2017. Vol. 33. No. 1. pp. 212-224.
GOST all authors (up to 50)
Copy
Mironov V., Moskovsky A., Dmello M. J., Alexeev Y. An efficient MPI/OpenMP parallelization of the Hartree–Fock–Roothaan method for the first generation of Intel® Xeon Phi™ processor architecture // International Journal of High Performance Computing Applications. 2017. Vol. 33. No. 1. pp. 212-224.
Cite this
RIS
Copy
TY - JOUR
DO - 10.1177/1094342017732628
UR - https://doi.org/10.1177%2F1094342017732628
TI - An efficient MPI/OpenMP parallelization of the Hartree–Fock–Roothaan method for the first generation of Intel® Xeon Phi™ processor architecture
T2 - International Journal of High Performance Computing Applications
AU - Moskovsky, Alexander
AU - Mironov, Vladimir
AU - Dmello, Michael J
AU - Alexeev, Yuri
PY - 2017
DA - 2017/10/04 00:00:00
PB - SAGE
SP - 212-224
IS - 1
VL - 33
SN - 1094-3420
SN - 1741-2846
ER -
Cite this
BibTex
Copy
@article{2017_Mironov,
author = {Alexander Moskovsky and Vladimir Mironov and Michael J Dmello and Yuri Alexeev},
title = {An efficient MPI/OpenMP parallelization of the Hartree–Fock–Roothaan method for the first generation of Intel® Xeon Phi™ processor architecture},
journal = {International Journal of High Performance Computing Applications},
year = {2017},
volume = {33},
publisher = {SAGE},
month = {oct},
url = {https://doi.org/10.1177%2F1094342017732628},
number = {1},
pages = {212--224},
doi = {10.1177/1094342017732628}
}
Cite this
MLA
Copy
Mironov, Vladimir, et al. “An efficient MPI/OpenMP parallelization of the Hartree–Fock–Roothaan method for the first generation of Intel® Xeon Phi™ processor architecture.” International Journal of High Performance Computing Applications, vol. 33, no. 1, Oct. 2017, pp. 212-224. https://doi.org/10.1177%2F1094342017732628.
Profiles