Ultrafast scalable parallel algorithm for the radial distribution function histogramming using MPI maps

In the present paper, an ultrafast and scalable parallel program for the Radial Pair Function (RPF) is presented via pure Message Passing Interface (MPI) paradigm. The parallel code computes the radial distribution function for the single-component as well as multi-component systems. The single-comp...

Celý popis

Uložené v:

Podrobná bibliografia
Vydané v:	The Journal of supercomputing Ročník 73; číslo 4; s. 1629 - 1653
Hlavní autori:	Kouetcha, Daniella Nguemalieu, Ramézani, Hamidréza, Cohaut, Nathalie
Médium:	Journal Article
Jazyk:	English
Vydavateľské údaje:	New York Springer US 01.04.2017 Springer Nature B.V Springer Verlag
Predmet:	Algorithms C (programming language) Compilers Computer Science Computer simulation Computing time Condensed Matter Distribution functions Interpreters Message passing Optimization Parallel programming Physics Processor Architectures Programming Languages Radial distribution Single wall carbon nanotubes Stochastic approach Parallel computing Statistical mechanics Radial distribution function Monte Carlo simulation MPI
ISSN:	0920-8542, 1573-0484
On-line prístup:	Získať plný text
Tagy:	Pridať tag Žiadne tagy, Buďte prvý, kto otaguje tento záznam!

Abstract	In the present paper, an ultrafast and scalable parallel program for the Radial Pair Function (RPF) is presented via pure Message Passing Interface (MPI) paradigm. The parallel code computes the radial distribution function for the single-component as well as multi-component systems. The single-component and multi-component systems have been extracted for benchmarking purposes by means of user-written codes in C++ for the Graphite structure and MPI C++ for hydrogen adsorption via Grand Canonical Monte Carlo (GCMC) in the Single-Walled Carbon Nanotube (SWNT), respectively. The speedup and efficiency curves substantiate an excellent performance in terms of computing time and computation size as well. Additionally, the mentioned MPI paradigms are nearly five times (single-component systems) and two times (multi-component systems) faster than the relevant parallel codes using a machine with 48 CPUs and NVIDIA Quadro K5200/PCIe/SSE2. Some conclusions and outlooks pertaining to the numerical implementations, algorithm optimization involving the space decomposition idea have been discussed and provided.
AbstractList	In the present paper, an ultrafast and scalable parallel program for the Radial Pair Function (RPF) is presented via pure Message Passing Interface (MPI) paradigm. The parallel code computes the radial distribution function for the single-component as well as multi-component systems. The single-component and multi-component systems have been extracted for benchmarking purposes by means of user-written codes in C++ for the Graphite structure and MPI C++ for hydrogen adsorption via Grand Canonical Monte Carlo (GCMC) in the Single-Walled Carbon Nanotube (SWNT), respectively. The speedup and efficiency curves substantiate an excellent performance in terms of computing time and computation size as well. Additionally, the mentioned MPI paradigms are nearly five times (single-component systems) and two times (multi-component systems) faster than the relevant parallel codes using a machine with 48 CPUs and NVIDIA Quadro K5200/PCIe/SSE2. Some conclusions and outlooks pertaining to the numerical implementations, algorithm optimization involving the space decomposition idea have been discussed and provided.
Author	Kouetcha, Daniella Nguemalieu Cohaut, Nathalie Ramézani, Hamidréza
Author_xml	– sequence: 1 givenname: Daniella Nguemalieu surname: Kouetcha fullname: Kouetcha, Daniella Nguemalieu organization: Université d’Orléans, ICMN,UMR CNRS 7374, Interfaces, Confinement, Matériaux et Nanostructures – sequence: 2 givenname: Hamidréza surname: Ramézani fullname: Ramézani, Hamidréza email: hamidreza.ramezani@univ-orleans.fr organization: École Polytechnique de l’Université d’Orléans, Université d’Orléans, ICMN, UMR CNRS 7374, Interfaces, Confinement, Matériaux et Nanostructures – sequence: 3 givenname: Nathalie surname: Cohaut fullname: Cohaut, Nathalie organization: Université d’Orléans, ICMN,UMR CNRS 7374, Interfaces, Confinement, Matériaux et Nanostructures
BackLink	https://hal.science/hal-01885745$$DView record in HAL
BookMark	eNp9kMGL1TAQxoOs4NvVP8BbwJOH6kyTNu1xWXR34Yke3HOYtmlflrR5Jqngf2-6FRFBL5Nh8v2-Gb5LdrH4xTD2GuEdAqj3EbEsVQFYF9hUsoBn7ICVEgXIRl6wA7QlFPmjfMEuY3wEACmUOLDpwaVAI8XEY0-OOmf4mQI5ZxwnN_lg02nmow88nQwPNFhyfLAxBdutyfqFj-vSPzWnPPVToHm2y8TXuNVPX-75TOf4kj0fyUXz6td7xR4-fvh6c1ccP9_e31wfi15UkIrG4GAMqlq2poKuAom9qjpqUNFgWiVrHLtS1KakFuWIY2uoro3oykFV1Ahxxd7uvidy-hzsTOGH9mT13fVRbzPApqmUrL5j1r7Ztefgv60mJv3o17Dk83QWgZKifXLEXdUHH2Mw429bBL1lr_fss3Ott-w1ZEb9xfQ20RZSDtu6_5LlTsa8ZZlM-OOmf0I_ARMgmq4
CitedBy_id	crossref_primary_10_1007_s10450_020_00227_2 crossref_primary_10_1016_j_colsurfa_2023_131645 crossref_primary_10_1080_07391102_2022_2084456 crossref_primary_10_1080_07391102_2024_2316790 crossref_primary_10_1007_s00707_017_1863_y crossref_primary_10_3390_ijerph182413290 crossref_primary_10_1016_j_colsurfa_2024_133373 crossref_primary_10_1016_j_molliq_2020_113612 crossref_primary_10_1016_j_molliq_2021_117548 crossref_primary_10_1016_j_commatsci_2018_04_029 crossref_primary_10_1016_j_commatsci_2021_110572 crossref_primary_10_1016_j_ejps_2020_105258 crossref_primary_10_1016_j_jobe_2019_01_038 crossref_primary_10_1016_j_jcou_2021_101564 crossref_primary_10_1080_19648189_2021_1928555
Cites_doi	10.1007/s10035-008-0116-0 10.1016/0743-7315(90)90028-N 10.1023/A:1022804606389 10.1007/BF01391926 10.1143/PTP.53.400 10.4319/lom.2006.4.382 10.1023/B:JOMC.0000044223.40611.00 10.1016/0378-3812(93)85015-E 10.1017/CBO9780511812583 10.1016/j.cpc.2014.07.012 10.1007/s11227-014-1209-7 10.1063/1.1742004 10.1002/jcc.20829 10.1016/j.tca.2014.06.019 10.1016/j.jmgm.2010.06.010 10.1016/0167-8191(95)00032-9 10.1016/j.parco.2014.04.002 10.1016/j.jcp.2013.11.012 10.1016/j.cma.2010.01.016 10.1007/s11227-016-1707-x 10.1016/j.jtice.2015.06.027 10.1021/la800351d 10.1016/j.tca.2016.01.001 10.1016/j.cpc.2011.04.026 10.1007/BF00130109 10.1524/zkri.218.2.132.20664 10.1109/71.584095 10.1093/comjnl/30.5.425 10.1016/j.powtec.2016.02.051 10.1006/jpdc.1995.1011 10.1016/0263-7855(96)00018-5 10.1143/PTP.26.45 10.1016/j.parco.2008.12.004 10.1007/978-3-319-21903-5 10.1111/j.1467-8659.1989.tb00448.x 10.1063/1.470654 10.1016/j.cpc.2015.08.011 10.1016/j.jcp.2011.01.048 10.1016/j.apsusc.2009.12.108 10.1016/j.cemconcomp.2013.03.005 10.2514/6.2000-213 10.1016/j.compfluid.2014.12.016 10.1103/PhysRevE.50.1317 10.1016/j.jcp.2014.10.055 10.1107/S0021889809051929 10.1016/j.commatsci.2011.02.009 10.1140/epjst/e2015-02500-2 10.1016/j.jcp.2012.07.038 10.1103/PhysRevA.39.4098
ContentType	Journal Article
Copyright	Springer Science+Business Media New York 2016 Copyright Springer Science & Business Media 2017 Distributed under a Creative Commons Attribution 4.0 International License
Copyright_xml	– notice: Springer Science+Business Media New York 2016 – notice: Copyright Springer Science & Business Media 2017 – notice: Distributed under a Creative Commons Attribution 4.0 International License
DBID	AAYXX CITATION JQ2 1XC
DOI	10.1007/s11227-016-1854-0
DatabaseName	CrossRef ProQuest Computer Science Collection Hyper Article en Ligne (HAL)
DatabaseTitle	CrossRef ProQuest Computer Science Collection
DatabaseTitleList	ProQuest Computer Science Collection
DeliveryMethod	fulltext_linktorsrc
Discipline	Computer Science Physics
EISSN	1573-0484
EndPage	1653
ExternalDocumentID	oai:HAL:hal-01885745v1 10_1007_s11227_016_1854_0
GroupedDBID	-4Z -59 -5G -BR -EM -Y2 -~C .4S .86 .DC .VR 06D 0R~ 0VY 123 199 1N0 1SB 2.D 203 28- 29L 2J2 2JN 2JY 2KG 2KM 2LR 2P1 2VQ 2~H 30V 4.4 406 408 409 40D 40E 5QI 5VS 67Z 6NX 78A 8TC 8UJ 95- 95. 95~ 96X AAAVM AABHQ AACDK AAHNG AAIAL AAJBT AAJKR AANZL AAOBN AARHV AARTL AASML AATNV AATVU AAUYE AAWCG AAYIU AAYOK AAYQN AAYTO AAYZH ABAKF ABBBX ABBXA ABDBF ABDPE ABDZT ABECU ABFTD ABFTV ABHLI ABHQN ABJNI ABJOX ABKCH ABKTR ABMNI ABMQK ABNWP ABQBU ABQSL ABSXP ABTEG ABTHY ABTKH ABTMW ABULA ABWNU ABXPI ACAOD ACBXY ACDTI ACGFS ACHSB ACHXU ACKNC ACMDZ ACMLO ACOKC ACOMO ACPIV ACUHS ACZOJ ADHHG ADHIR ADIMF ADINQ ADKNI ADKPE ADMLS ADQRH ADRFC ADTPH ADURQ ADYFF ADZKW AEBTG AEFIE AEFQL AEGAL AEGNC AEJHL AEJRE AEKMD AEMSY AENEX AEOHA AEPYU AESKC AETLH AEVLU AEXYK AFBBN AFEXP AFGCZ AFLOW AFQWF AFWTZ AFZKB AGAYW AGDGC AGGDS AGJBK AGMZJ AGQEE AGQMX AGRTI AGWIL AGWZB AGYKE AHAVH AHBYD AHSBF AHYZX AI. AIAKS AIGIU AIIXL AILAN AITGF AJBLW AJRNO AJZVZ ALMA_UNASSIGNED_HOLDINGS ALWAN AMKLP AMXSW AMYLF AMYQR AOCGG ARCSS ARMRJ ASPBG AVWKF AXYYD AYJHY AZFZN B-. B0M BA0 BBWZM BDATZ BGNMA BSONS CAG COF CS3 CSCUP DDRTE DL5 DNIVK DPUIP DU5 EAD EAP EAS EBD EBLON EBS EDO EIOEI EJD EMK EPL ESBYG ESX F5P FEDTE FERAY FFXSO FIGPU FINBP FNLPD FRRFC FSGXE FWDCC GGCAI GGRSB GJIRD GNWQR GQ6 GQ7 GQ8 GXS H13 HF~ HG5 HG6 HMJXF HQYDN HRMNR HVGLF HZ~ H~9 I-F I09 IHE IJ- IKXTQ ITM IWAJR IXC IZIGR IZQ I~X I~Z J-C J0Z JBSCW JCJTX JZLTJ KDC KOV KOW LAK LLZTM M4Y MA- N2Q N9A NB0 NDZJH NPVJJ NQJWS NU0 O9- O93 O9G O9I O9J OAM OVD P19 P2P P9O PF0 PT4 PT5 QOK QOS R4E R89 R9I RHV RNI ROL RPX RSV RZC RZE RZK S16 S1Z S26 S27 S28 S3B SAP SCJ SCLPG SCO SDH SDM SHX SISQX SJYHP SNE SNPRN SNX SOHCF SOJ SPISZ SRMVM SSLCW STPWE SZN T13 T16 TEORI TSG TSK TSV TUC TUS U2A UG4 UOJIU UTJUX UZXMN VC2 VFIZW VH1 W23 W48 WH7 WK8 YLTOR Z45 Z7R Z7X Z7Z Z83 Z88 Z8M Z8N Z8R Z8T Z8W Z92 ZMTXR ~8M ~EX AAPKM AAYXX ABBRH ABDBE ABFSG ABJCF ABRTQ ACSTC ADHKG ADKFA AEZWR AFDZB AFFHD AFHIU AFKRA AFOHR AGQPQ AHPBZ AHWEU AIXLP ARAPS ATHPR AYFIA BENPR BGLVJ CCPQU CITATION HCIFZ K7- M7S PHGZM PHGZT PQGLB PTHSS JQ2 1XC
ID	FETCH-LOGICAL-c350t-8e1dee17649e50b5041c75ba817ade97461fb236e2a914f1f9ea66e3b2d75a833
IEDL.DBID	RSV
ISICitedReferencesCount	16
ISICitedReferencesURI	http://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=Summon&SrcAuth=ProQuest&DestLinkType=CitingArticles&DestApp=WOS_CPL&KeyUT=000398748700016&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D
ISSN	0920-8542
IngestDate	Tue Oct 14 20:37:11 EDT 2025 Thu Sep 25 00:39:33 EDT 2025 Sat Nov 29 06:13:10 EST 2025 Tue Nov 18 22:01:02 EST 2025 Fri Feb 21 02:27:32 EST 2025
IsPeerReviewed	true
IsScholarly	true
Issue	4
Keywords	Stochastic approach Parallel computing Statistical mechanics Radial distribution function Monte Carlo simulation MPI
Language	English
License	Distributed under a Creative Commons Attribution 4.0 International License: http://creativecommons.org/licenses/by/4.0
LinkModel	DirectLink
MergedId	FETCHMERGED-LOGICAL-c350t-8e1dee17649e50b5041c75ba817ade97461fb236e2a914f1f9ea66e3b2d75a833
Notes	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14
ORCID	0000-0002-4788-9252
PQID	1880743983
PQPubID	2043774
PageCount	25
ParticipantIDs	hal_primary_oai_HAL_hal_01885745v1 proquest_journals_1880743983 crossref_primary_10_1007_s11227_016_1854_0 crossref_citationtrail_10_1007_s11227_016_1854_0 springer_journals_10_1007_s11227_016_1854_0
PublicationCentury	2000
PublicationDate	2017-04-01
PublicationDateYYYYMMDD	2017-04-01
PublicationDate_xml	– month: 04 year: 2017 text: 2017-04-01 day: 01
PublicationDecade	2010
PublicationPlace	New York
PublicationPlace_xml	– name: New York
PublicationSubtitle	An International Journal of High-Performance Computer Design, Analysis, and Use
PublicationTitle	The Journal of supercomputing
PublicationTitleAbbrev	J Supercomput
PublicationYear	2017
Publisher	Springer US Springer Nature B.V Springer Verlag
Publisher_xml	– name: Springer US – name: Springer Nature B.V – name: Springer Verlag
References	KantorALLongLNMicciMMMolecular dynamics simulation of dissociation kinetics2000PennsylvaniaThe Pennsylvania State University10.2514/6.2000-213 GotziasAHeiberg-AndersenHKainourgiakisMSteriotisThGrand canonical monte carlo simulations of hydrogen adsorption in carbon conesAppl Surf Sci2010256175226523110.1016/j.apsusc.2009.12.108 Ramézani H, Kouetcha DN, Cohaut N (2016) Scalable parallel grand canonical monte carlo simulation using MPI maps: micro-pollutant adsorption objective. In: WCCM-APCOM 2016 Congress, 24–29 July SergeyKIgorKNikitaNAlexanderNYuliaSagdeevaScalable hybrid implementation of the schur complement method for multi-GPU systemsJ Supercomput2014691818810.1007/s11227-014-1209-7 Arif WaniMArabniaHRParallel edge-region-based segmentation algorithm targeted at reconfigurable multiring networkJ Supercomput2003251436210.1023/A:10228046063891021.68099 Barney B (2015) Message passing interface (MPI). Lawrence Livermore National Laboratory JeongJRamézaniHLeklouNThermo-chemical heterogeneous hydration gradient modeling of concrete and aggregates size effect on ITZThermochim Acta201459016518010.1016/j.tca.2014.06.019 Tanaka S, Nakano M (2013) Classical density functional calculation of radial distribution functions of liquid water. Chem Phys 430 GroppWLuskESkjellumAUsing MPI: portable parallel programming with the message-passing interface. Scientific and engineering computation2014USAMIT Press Kouetcha D, Ramézani H, Cohaut N (2015) Etude structurale et détermination de la fonction de corrélation de paire du graphène et du graphite. In: Colloque Francophone du Carbone GFEC–2015. Karellis, Savoie, France, May (in French) Hasanov K, Lastovetsky A (2016) Hierarchical redesign of classic MPI reduction algorithms. J Supercomput 01–13 GroppWHoeflerTLuskEThakurRUsing advanced MPI: modern features of the message-passing interface. Computer science and intelligent systems2014USAMIT Press BillingeSJLThe atomic pair distribution function: past and present2003MichiganDepartment of Physics and Astronomy, Michigan State University GriebelMKnapekSZumbuschGWNumerical simulation in molecular dynamics: numerics, algorithms, parallelization, applications. Texts in computational science and engineering2007BerlinSpringer1131.76001 Proffen T, Page KL, McLainand SE,Clausen B, Darling TW, TenCate JA, Lee Seung-Yub, Ustundag E (2005) Atomic pair distribution function analysis of materials containing crystalline and amorphous phases. Zeitschrift für Kristallographie, p 220 GlassCWReiserSRutkaiGDeubleinSKösterAndreasGuevara-CarrionGabrielaWafaiAmerHorschMartinBernreutherMartinWindmannThorstenHasseHansVrabecJadranms2: a molecular simulation tool for thermodynamic properties, new version releaseComput Phys Commun2014185123302330610.1016/j.cpc.2014.07.012 Jerier JF (2009) Modélisation de la compression haute densité des poudres métalliques ductiles par la méthode des éléments discrets. PhD thesis, Université Joseph Fourier de Grenoble, Grenoble, France, Novembre (in French) LuoTLloydJRGrand canonical monte carlo simulation of hydrogen adsorption in different carbon nano structures2014MichiganMichigan State University Menshov I, Pavlukhin P (2016) Highly scalable implementation of an implicit matrix-free solver for gas dynamics on GPU-accelerated clusters. J Supercomput 1–8 JeongJRamézaniHSardiniPKondoDPonsonLaurentSiitari-KauppiMarjaPorous media modeling and micro-structurally motivated material moduli determination via the micro-dilatation theoryEur Phys J Spec Topics201522491805181610.1140/epjst/e2015-02500-2 Arabnia HR (1996) A distributed stereocorrelation algorithm. In: Selected papers from the Third International Conference on Computer Communications and Networks Distributed stereo-correlation algorithm, vol 19, pp 707–711 BhandarkarSMArabniaHRThe hough transform on a reconfigurable multi-ring networkJ Parallel Distrib Comput199524110711410.1006/jpdc.1995.1011 Kambayashi S, Chihara J (1994) Extraction of the bridge function for simple liquids from a molecular dynamics simulation and its application for correcting the pair distribution function. Am Phys Soc StoneJEHardyDJUfimtsevISSchultenKGPU-accelerated molecular modeling coming of ageJ Mol Graph Model201029211612510.1016/j.jmgm.2010.06.010 LevineBGStoneJEKohlmeyerAFast analysis of molecular dynamics trajectories with graphics processing units-radial distribution function histogrammingJ Comput Phys201123093556356910.1016/j.jcp.2011.01.0481221.82010 NielsenFIntroduction to HPC with MPI for data science. Undergraduate topics in computer science2016BerlinSpringer International Publishing10.1007/978-3-319-21903-5 LimT-CConnection among classical interatomic potential functionsJ Math Chem200436326126910.1023/B:JOMC.0000044223.40611.001068.920512101449 NguyenTXCohautNBaeJ-SBhatiaSKNew method for atomistic modeling of the microstructure of activated carbons using hybrid reverse monte carlo simulationLangmuir200824157912792210.1021/la800351d Alder BJ, Frankel SP, Lewinson VA (1955) Radial distribution function calculated by the monte carlo method for a hard sphere fluid. J Chem Phys 23(3) RamézaniHMounangaPJeongJBouaskerMRole of cement paste composition on the self induced stress in early-age mortars: application of the cosserat size numberCement Concrete Compos201339435910.1016/j.cemconcomp.2013.03.005 AbrahamssonPJSasicSRasmusonAOn continuum modelling of dense inelastic granular flows of relevance for high shear granulationPowder Technol201629432332910.1016/j.powtec.2016.02.051 Ueda S (1961) The pair correlation function of an imperfect electron gas in high densities. Prog Theor Phys 26 Gerhard N (2004) The physics of colloidal soft matter. Inst Fundam Technol Res Li K, Li D, Liang J, Ye Y, Liao Y, Liu R, Mo Y (2015) Performance analysis of parallel algorithms in physics simulation for molecular dynamics simulation liquid metals solidification processes. Comput Fluids 110:19–26. ParCFD 2013 HosseiniSYFattahiMAhmadiGCFD study of hydrodynamic and heat transfer in a 2d spouted bedJ Taiwan Inst Chem Eng20165810711610.1016/j.jtice.2015.06.027 GramaAYGuptaAKumarVIsoefficiency: measuring the scalability of parallel algorithms and architectures1993MinnesotaUniversity of Minnesota Chihara J (1974) Calculation of pair correlations in a degenerate electron liquid. Prog Theor Phys 53(2) Matteoli E, Mansoori GA (1995) A simple expression for radial distribution functions of pure fluids and mixtures. J Chem Phy ZuweiXZhaoHZhengCAccelerating population balance-monte carlo simulation for coagulation dynamics from the markov jump model, stochastic algorithm and GPU parallel computingJ Comput Phys201528184486310.1016/j.jcp.2014.10.0551351.820943281998 DeubleinSEcklBStollJLishchukSVGuevara-CarrionGabrielaGlassColin WMerkerThorstenBernreutherMartinHasseHansVrabecJadranms2: a molecular simulation tool for thermodynamic propertiesComput Phys Commun2011182112350236710.1016/j.cpc.2011.04.026 HallCJiWBlaisten-BarojasEThe metropolis monte carlo method with CUDA enabled graphic processing unitsJ Comput Phys201425887187910.1016/j.jcp.2013.11.0121349.65013 ArabniaHROliverMAA transputer network for fast operations on digitised imagesComput Graph Forum19898131110.1111/j.1467-8659.1989.tb00448.x Le RouxSPetkovVISAACS—interactive structure analysis of amorphous and crystalline systemsJ Appl Crystallogr201043118118510.1107/S0021889809051929 JerierJFRichefeuVImbaultDDonzéFVPacking spherical discrete elements for large scale simulationsComput Methods Appl Mech Eng201019925–281668167610.1016/j.cma.2010.01.0161231.74480 Konstantakou M, Gotzias A, Kainourgiakis M, Stubos Ak, Steriotis TA (2011) Applications of Monte Carlo method in science and engineering: GCMC simulations of gas adsorption in carbon pore structures. Chapter 26. InTech, pp 653–676 JeongJRamézaniHLeklouNWhy does the modified arrhenius’ law fail to describe the hydration modeling of recycled aggregate?Thermochim Acta2016626133010.1016/j.tca.2016.01.001 Proffen TH, Billinge SJL, Egami T, Louca D, Kristallogr Z (2003) Structural analysis of complex materials using the atomic pair distribution function—a practical guide 218 HumphreyWDalkeASchultenKVmd: visual molecular dynamicsJ Mol Graph1996141333810.1016/0263-7855(96)00018-5 ArabniaHRBhandarkarSMParallel stereocorrelation on a reconfigurable multi-ring networkJ Supercomput199610324326910.1007/BF001301091067.68510 Meredith JS, Alvarez G, Maier TA, Schulthess TC, Vetter JS (2009) Accuracy and performance of graphics processors: A quantum monte carlo application case study. Parallel Comput 35(3):151–163 (Revolutionary Technologies for Acceleration of Emerging Petascale Applications) LiboffRLCorrelation functions in statistical mechanics and astrophysicsPhys Rev A1989394098410210.1103/PhysRevA.39.4098996598 ZettiliNQuantum mechanics: concepts and applications2009USAWiley Ramézani H, Chuta E (2014) Hydrogen adsorption simulation in the single-wall carbon nanotube (SWNT) network. In: Matériaux 2014, Montpellier, France, November Fédération Française des Matériaux (FFM) (in English) ZernikeFPrinsJADie beugung von röntgenstrahlen in flüssigkeiten als effekt der molekülanordnungZeitschrift für Physik192741218419410.1007/BF01391926(in German) BhandarkarSMArabniaHRParallel computer vision on a reconfigurable multiprocessor networkIEEE Trans Parallel Distrib Syst19978329230910.1109/71.584095 BhandarkarSMArabniaHRThe REFINE multiprocessor—theoretical properties and algorithmsParallel Comput199521111783180510.1016/0167-8191(95)00032-9 Stone JE, Phillips JC, Freddolino PL, Hardy DJ, Trabuco LG, Schulten K (2007) Accelerating molecular modeling applications with graphics processors. J Comput Chem 28 Konstantakou M et al (2011) Applications of Monte Carlo method in science and engineering MarendicPLemeireJVucinicDSchelkensPA novel MPI reduction algorithm resilient to imbalances in process arrival timesJ Supercomput20167251973201310.1007/s11227-016-1707-x YoungeKJohnstonBChristensonCBoharaAJacobsonJButlerNMSaulnierPThe use of radial distribution and pair-correlation functions to analyz A Gotzias (1854_CR52) 2010; 256 C Dimitroulis (1854_CR37) 2015; 197 SM Bhandarkar (1854_CR48) 1997; 8 RL Liboff (1854_CR14) 1989; 39 JF Jerier (1854_CR15) 2009; 11 1854_CR28 T Luo (1854_CR61) 2014 1854_CR26 1854_CR1 AY Grama (1854_CR54) 1993 1854_CR60 1854_CR2 HR Arabnia (1854_CR47) 1996; 10 1854_CR65 1854_CR5 PJ Abrahamsson (1854_CR18) 2016; 294 1854_CR64 1854_CR6 1854_CR63 C Hall (1854_CR69) 2014; 258 1854_CR7 1854_CR62 SY Hosseini (1854_CR24) 2016; 58 GA Mansoori (1854_CR25) 1993; 87 N Zettili (1854_CR59) 2009 W Humphrey (1854_CR38) 1996; 14 CW Glass (1854_CR9) 2014; 185 D Frenkel (1854_CR13) 2002 SM Bhandarkar (1854_CR45) 1995; 24 X Zuwei (1854_CR71) 2015; 281 K Sergey (1854_CR70) 2014; 69 BG Levine (1854_CR67) 2011; 230 J Jeong (1854_CR19) 2011; 50 1854_CR39 F Zernike (1854_CR4) 1927; 41 1854_CR72 M Arif Wani (1854_CR49) 2003; 25 1854_CR73 M Griebel (1854_CR27) 2007 HR Arabnia (1854_CR41) 1989; 8 G Karniadakis (1854_CR31) 2003 AL Kantor (1854_CR56) 2000 1854_CR46 S Deublein (1854_CR8) 2011; 182 P Marendic (1854_CR74) 2016; 72 W Gropp (1854_CR34) 2014 J Jeong (1854_CR23) 2016; 626 F Nielsen (1854_CR35) 2016 1854_CR43 J Jeong (1854_CR21) 2014; 590 T-C Lim (1854_CR57) 2004; 36 HR Arabnia (1854_CR40) 1987; 30 HR Arabnia (1854_CR42) 1990; 10 J Jeong (1854_CR22) 2015; 224 H Ramézani (1854_CR20) 2013; 39 1854_CR58 Ivan Teixidó (1854_CR32) 2014; 40 C-C Su (1854_CR68) 2012; 231 1854_CR12 K Younge (1854_CR29) 2006; 4 1854_CR11 JF Jerier (1854_CR17) 2010; 199 M Snir (1854_CR30) 1998 1854_CR55 1854_CR16 SM Bhandarkar (1854_CR44) 1995; 21 SJL Billinge (1854_CR3) 2003 S Roux Le (1854_CR36) 2010; 43 W Gropp (1854_CR33) 2014 1854_CR50 1854_CR10 TX Nguyen (1854_CR51) 2008; 24 1854_CR53 JE Stone (1854_CR66) 2010; 29
References_xml	– reference: DimitroulisCRaptisTRaptisVPOLYANA-A tool for the calculation of molecular radial distribution functions based on molecular dynamics trajectoriesComput Phys Commun201519722022610.1016/j.cpc.2015.08.011 – reference: HallCJiWBlaisten-BarojasEThe metropolis monte carlo method with CUDA enabled graphic processing unitsJ Comput Phys201425887187910.1016/j.jcp.2013.11.0121349.65013 – reference: JeongJRamézaniHLeklouNWhy does the modified arrhenius’ law fail to describe the hydration modeling of recycled aggregate?Thermochim Acta2016626133010.1016/j.tca.2016.01.001 – reference: Matteoli E, Mansoori GA (1995) A simple expression for radial distribution functions of pure fluids and mixtures. J Chem Phy – reference: Meredith JS, Alvarez G, Maier TA, Schulthess TC, Vetter JS (2009) Accuracy and performance of graphics processors: A quantum monte carlo application case study. Parallel Comput 35(3):151–163 (Revolutionary Technologies for Acceleration of Emerging Petascale Applications) – reference: KantorALLongLNMicciMMMolecular dynamics simulation of dissociation kinetics2000PennsylvaniaThe Pennsylvania State University10.2514/6.2000-213 – reference: GramaAYGuptaAKumarVIsoefficiency: measuring the scalability of parallel algorithms and architectures1993MinnesotaUniversity of Minnesota – reference: BillingeSJLThe atomic pair distribution function: past and present2003MichiganDepartment of Physics and Astronomy, Michigan State University – reference: Ueda S (1961) The pair correlation function of an imperfect electron gas in high densities. Prog Theor Phys 26 – reference: StoneJEHardyDJUfimtsevISSchultenKGPU-accelerated molecular modeling coming of ageJ Mol Graph Model201029211612510.1016/j.jmgm.2010.06.010 – reference: Ramézani H, Chuta E (2014) Hydrogen adsorption simulation in the single-wall carbon nanotube (SWNT) network. In: Matériaux 2014, Montpellier, France, November Fédération Française des Matériaux (FFM) (in English) – reference: MarendicPLemeireJVucinicDSchelkensPA novel MPI reduction algorithm resilient to imbalances in process arrival timesJ Supercomput20167251973201310.1007/s11227-016-1707-x – reference: Ramézani H, Kouetcha DN, Cohaut N (2016) Scalable parallel grand canonical monte carlo simulation using MPI maps: micro-pollutant adsorption objective. In: WCCM-APCOM 2016 Congress, 24–29 July – reference: JerierJFRichefeuVImbaultDDonzéFVPacking spherical discrete elements for large scale simulationsComput Methods Appl Mech Eng201019925–281668167610.1016/j.cma.2010.01.0161231.74480 – reference: Tanaka S, Nakano M (2013) Classical density functional calculation of radial distribution functions of liquid water. Chem Phys 430 – reference: Proffen TH, Billinge SJL, Egami T, Louca D, Kristallogr Z (2003) Structural analysis of complex materials using the atomic pair distribution function—a practical guide 218 – reference: HosseiniSYFattahiMAhmadiGCFD study of hydrodynamic and heat transfer in a 2d spouted bedJ Taiwan Inst Chem Eng20165810711610.1016/j.jtice.2015.06.027 – reference: BhandarkarSMArabniaHRThe hough transform on a reconfigurable multi-ring networkJ Parallel Distrib Comput199524110711410.1006/jpdc.1995.1011 – reference: SergeyKIgorKNikitaNAlexanderNYuliaSagdeevaScalable hybrid implementation of the schur complement method for multi-GPU systemsJ Supercomput2014691818810.1007/s11227-014-1209-7 – reference: Barney B (2015) Message passing interface (MPI). Lawrence Livermore National Laboratory – reference: ArabniaHRA parallel algorithm for the arbitrary rotation of digitized images using process-and-data-decomposition approachJ Parallel Distrib Comput199010218819210.1016/0743-7315(90)90028-N – reference: LevineBGStoneJEKohlmeyerAFast analysis of molecular dynamics trajectories with graphics processing units-radial distribution function histogrammingJ Comput Phys201123093556356910.1016/j.jcp.2011.01.0481221.82010 – reference: Kouetcha DN, Ramézani H, Cohaut N (2015) Lennard-jones potential determination via the schrödinger equation. In: Scientific committee of European Comsol Conference in Grenoble-France, editor. Excerpt from the Proceedings of the COMSOL Conference 2015. Grenoble, France, October 14–16 – reference: YoungeKJohnstonBChristensonCBoharaAJacobsonJButlerNMSaulnierPThe use of radial distribution and pair-correlation functions to analyze and describe biological aggregations -Limnol Oceanogr Methods2006438239110.4319/lom.2006.4.382 – reference: Konstantakou M et al (2011) Applications of Monte Carlo method in science and engineering – reference: NguyenTXCohautNBaeJ-SBhatiaSKNew method for atomistic modeling of the microstructure of activated carbons using hybrid reverse monte carlo simulationLangmuir200824157912792210.1021/la800351d – reference: NielsenFIntroduction to HPC with MPI for data science. Undergraduate topics in computer science2016BerlinSpringer International Publishing10.1007/978-3-319-21903-5 – reference: Kurniawan Y, Bhatia SK, Rudolph V (2005) Monte carlo simulation of binary mixture adsorption of methane and carbon dioxide in carbon slit pores. Technical report, University of Queensland – reference: Le RouxSPetkovVISAACS—interactive structure analysis of amorphous and crystalline systemsJ Appl Crystallogr201043118118510.1107/S0021889809051929 – reference: Konstantakou M, Gotzias A, Kainourgiakis M, Stubos Ak, Steriotis TA (2011) Applications of Monte Carlo method in science and engineering: GCMC simulations of gas adsorption in carbon pore structures. Chapter 26. InTech, pp 653–676 – reference: JeongJRamézaniHSardiniPKondoDPonsonLaurentSiitari-KauppiMarjaPorous media modeling and micro-structurally motivated material moduli determination via the micro-dilatation theoryEur Phys J Spec Topics201522491805181610.1140/epjst/e2015-02500-2 – reference: MansooriGARadial distribution functions and their role in modeling of mixtures behaviorFluid Phase Equ19938712210.1016/0378-3812(93)85015-E – reference: HumphreyWDalkeASchultenKVmd: visual molecular dynamicsJ Mol Graph1996141333810.1016/0263-7855(96)00018-5 – reference: FrenkelDSmitBUnderstanding molecular simulation: from algorithms to applications. Computational science2002USAAcademic Press0889.65132 – reference: GroppWHoeflerTLuskEThakurRUsing advanced MPI: modern features of the message-passing interface. Computer science and intelligent systems2014USAMIT Press – reference: Jerier JF (2009) Modélisation de la compression haute densité des poudres métalliques ductiles par la méthode des éléments discrets. PhD thesis, Université Joseph Fourier de Grenoble, Grenoble, France, Novembre (in French) – reference: AbrahamssonPJSasicSRasmusonAOn continuum modelling of dense inelastic granular flows of relevance for high shear granulationPowder Technol201629432332910.1016/j.powtec.2016.02.051 – reference: GotziasAHeiberg-AndersenHKainourgiakisMSteriotisThGrand canonical monte carlo simulations of hydrogen adsorption in carbon conesAppl Surf Sci2010256175226523110.1016/j.apsusc.2009.12.108 – reference: LimT-CConnection among classical interatomic potential functionsJ Math Chem200436326126910.1023/B:JOMC.0000044223.40611.001068.920512101449 – reference: ZuweiXZhaoHZhengCAccelerating population balance-monte carlo simulation for coagulation dynamics from the markov jump model, stochastic algorithm and GPU parallel computingJ Comput Phys201528184486310.1016/j.jcp.2014.10.0551351.820943281998 – reference: GroppWLuskESkjellumAUsing MPI: portable parallel programming with the message-passing interface. Scientific and engineering computation2014USAMIT Press – reference: Arabnia HR (1996) A distributed stereocorrelation algorithm. In: Selected papers from the Third International Conference on Computer Communications and Networks Distributed stereo-correlation algorithm, vol 19, pp 707–711 – reference: Kouetcha D, Ramézani H, Cohaut N (2015) Etude structurale et détermination de la fonction de corrélation de paire du graphène et du graphite. In: Colloque Francophone du Carbone GFEC–2015. Karellis, Savoie, France, May (in French) – reference: DeubleinSEcklBStollJLishchukSVGuevara-CarrionGabrielaGlassColin WMerkerThorstenBernreutherMartinHasseHansVrabecJadranms2: a molecular simulation tool for thermodynamic propertiesComput Phys Commun2011182112350236710.1016/j.cpc.2011.04.026 – reference: ZettiliNQuantum mechanics: concepts and applications2009USAWiley – reference: Menshov I, Pavlukhin P (2016) Highly scalable implementation of an implicit matrix-free solver for gas dynamics on GPU-accelerated clusters. J Supercomput 1–8 – reference: ArabniaHRBhandarkarSMParallel stereocorrelation on a reconfigurable multi-ring networkJ Supercomput199610324326910.1007/BF001301091067.68510 – reference: LuoTLloydJRGrand canonical monte carlo simulation of hydrogen adsorption in different carbon nano structures2014MichiganMichigan State University – reference: Kambayashi S, Chihara J (1994) Extraction of the bridge function for simple liquids from a molecular dynamics simulation and its application for correcting the pair distribution function. Am Phys Soc – reference: JeongJMounangaPRamézaniHBouaskerMA new multi-scale modeling approach based on hygro-Cosserat theory for self-induced stress in hydrating cementitious mortarsComput Mater Sci20115072063207410.1016/j.commatsci.2011.02.009 – reference: BhandarkarSMArabniaHRThe REFINE multiprocessor—theoretical properties and algorithmsParallel Comput199521111783180510.1016/0167-8191(95)00032-9 – reference: ZernikeFPrinsJADie beugung von röntgenstrahlen in flüssigkeiten als effekt der molekülanordnungZeitschrift für Physik192741218419410.1007/BF01391926(in German) – reference: Hasanov K, Lastovetsky A (2016) Hierarchical redesign of classic MPI reduction algorithms. J Supercomput 01–13 – reference: JerierJFImbaultDDonzéFVDoremusPA geometric algorithm based on tetrahedral meshes to generate a dense polydisperse sphere packingGranular Matter2009111435210.1007/s10035-008-0116-01258.74211 – reference: Arif WaniMArabniaHRParallel edge-region-based segmentation algorithm targeted at reconfigurable multiring networkJ Supercomput2003251436210.1023/A:10228046063891021.68099 – reference: ArabniaHROliverMAA transputer network for fast operations on digitised imagesComput Graph Forum19898131110.1111/j.1467-8659.1989.tb00448.x – reference: TeixidóIvanSebéFrancescCondeJosepSolsonaFrancescMPI-based implementation of an enhanced algorithm to solve the LPN problem in a memory-constrained environmentParallel Comput2014405–610011210.1016/j.parco.2014.04.002 – reference: LiboffRLCorrelation functions in statistical mechanics and astrophysicsPhys Rev A1989394098410210.1103/PhysRevA.39.4098996598 – reference: Chihara J (1974) Calculation of pair correlations in a degenerate electron liquid. Prog Theor Phys 53(2) – reference: ArabniaHROliverMAA transputer network for the arbitrary rotation of digitised imagesComput J198730542543210.1093/comjnl/30.5.425 – reference: Li K, Li D, Liang J, Ye Y, Liao Y, Liu R, Mo Y (2015) Performance analysis of parallel algorithms in physics simulation for molecular dynamics simulation liquid metals solidification processes. Comput Fluids 110:19–26. ParCFD 2013 – reference: Gerhard N (2004) The physics of colloidal soft matter. Inst Fundam Technol Res – reference: BhandarkarSMArabniaHRParallel computer vision on a reconfigurable multiprocessor networkIEEE Trans Parallel Distrib Syst19978329230910.1109/71.584095 – reference: Alder BJ, Frankel SP, Lewinson VA (1955) Radial distribution function calculated by the monte carlo method for a hard sphere fluid. J Chem Phys 23(3) – reference: GriebelMKnapekSZumbuschGWNumerical simulation in molecular dynamics: numerics, algorithms, parallelization, applications. Texts in computational science and engineering2007BerlinSpringer1131.76001 – reference: RamézaniHMounangaPJeongJBouaskerMRole of cement paste composition on the self induced stress in early-age mortars: application of the cosserat size numberCement Concrete Compos201339435910.1016/j.cemconcomp.2013.03.005 – reference: KarniadakisGKirbyRMParallel scientific computing in C++ and MPI: a seamless approach to parallel algorithms and their implementation2003CambridgeCambridge University Press10.1017/CBO97805118125831027.68023 – reference: JeongJRamézaniHLeklouNThermo-chemical heterogeneous hydration gradient modeling of concrete and aggregates size effect on ITZThermochim Acta201459016518010.1016/j.tca.2014.06.019 – reference: Arabnia HR, Smith JW (1993) A reconfigurable interconnection network for imaging operations and its implementation using a multi-stage switching box. In: Proceedings of the 7th Annual International High Performance Computing Conference. The 1993 High Performance Computing: New Horizons Supercomputing SymposiumCalgary, Alberta, Canada, pp 349–357 – reference: Stone JE, Phillips JC, Freddolino PL, Hardy DJ, Trabuco LG, Schulten K (2007) Accelerating molecular modeling applications with graphics processors. J Comput Chem 28 – reference: SnirMMPI the complete reference: the MPI Core1998USAMIT Press – reference: GlassCWReiserSRutkaiGDeubleinSKösterAndreasGuevara-CarrionGabrielaWafaiAmerHorschMartinBernreutherMartinWindmannThorstenHasseHansVrabecJadranms2: a molecular simulation tool for thermodynamic properties, new version releaseComput Phys Commun2014185123302330610.1016/j.cpc.2014.07.012 – reference: Proffen T, Page KL, McLainand SE,Clausen B, Darling TW, TenCate JA, Lee Seung-Yub, Ustundag E (2005) Atomic pair distribution function analysis of materials containing crystalline and amorphous phases. Zeitschrift für Kristallographie, p 220 – reference: SuC-CSmithMRKuoF-AWuJ-SHsiehC-WTsengK-CLarge-scale simulations on multiple graphics processing units (GPUs) for the direct simulation monte carlo methodJ Comput Phys2012231237932795810.1016/j.jcp.2012.07.0382972876 – volume: 11 start-page: 43 issue: 1 year: 2009 ident: 1854_CR15 publication-title: Granular Matter doi: 10.1007/s10035-008-0116-0 – volume: 10 start-page: 188 issue: 2 year: 1990 ident: 1854_CR42 publication-title: J Parallel Distrib Comput doi: 10.1016/0743-7315(90)90028-N – volume: 25 start-page: 43 issue: 1 year: 2003 ident: 1854_CR49 publication-title: J Supercomput doi: 10.1023/A:1022804606389 – volume: 41 start-page: 184 issue: 2 year: 1927 ident: 1854_CR4 publication-title: Zeitschrift für Physik doi: 10.1007/BF01391926 – ident: 1854_CR62 – ident: 1854_CR6 doi: 10.1143/PTP.53.400 – volume-title: Grand canonical monte carlo simulation of hydrogen adsorption in different carbon nano structures year: 2014 ident: 1854_CR61 – volume: 4 start-page: 382 year: 2006 ident: 1854_CR29 publication-title: Limnol Oceanogr Methods doi: 10.4319/lom.2006.4.382 – volume: 36 start-page: 261 issue: 3 year: 2004 ident: 1854_CR57 publication-title: J Math Chem doi: 10.1023/B:JOMC.0000044223.40611.00 – volume: 87 start-page: 1 year: 1993 ident: 1854_CR25 publication-title: Fluid Phase Equ doi: 10.1016/0378-3812(93)85015-E – ident: 1854_CR43 – volume-title: Parallel scientific computing in C++ and MPI: a seamless approach to parallel algorithms and their implementation year: 2003 ident: 1854_CR31 doi: 10.1017/CBO9780511812583 – volume: 185 start-page: 3302 issue: 12 year: 2014 ident: 1854_CR9 publication-title: Comput Phys Commun doi: 10.1016/j.cpc.2014.07.012 – volume: 69 start-page: 81 issue: 1 year: 2014 ident: 1854_CR70 publication-title: J Supercomput doi: 10.1007/s11227-014-1209-7 – ident: 1854_CR11 doi: 10.1063/1.1742004 – ident: 1854_CR64 doi: 10.1002/jcc.20829 – volume: 590 start-page: 165 year: 2014 ident: 1854_CR21 publication-title: Thermochim Acta doi: 10.1016/j.tca.2014.06.019 – volume-title: Understanding molecular simulation: from algorithms to applications. Computational science year: 2002 ident: 1854_CR13 – volume: 29 start-page: 116 issue: 2 year: 2010 ident: 1854_CR66 publication-title: J Mol Graph Model doi: 10.1016/j.jmgm.2010.06.010 – ident: 1854_CR53 – ident: 1854_CR63 – volume: 21 start-page: 1783 issue: 11 year: 1995 ident: 1854_CR44 publication-title: Parallel Comput doi: 10.1016/0167-8191(95)00032-9 – volume-title: The atomic pair distribution function: past and present year: 2003 ident: 1854_CR3 – volume: 40 start-page: 100 issue: 5–6 year: 2014 ident: 1854_CR32 publication-title: Parallel Comput doi: 10.1016/j.parco.2014.04.002 – volume: 258 start-page: 871 year: 2014 ident: 1854_CR69 publication-title: J Comput Phys doi: 10.1016/j.jcp.2013.11.012 – volume: 199 start-page: 1668 issue: 25–28 year: 2010 ident: 1854_CR17 publication-title: Comput Methods Appl Mech Eng doi: 10.1016/j.cma.2010.01.016 – ident: 1854_CR46 – volume: 72 start-page: 1973 issue: 5 year: 2016 ident: 1854_CR74 publication-title: J Supercomput doi: 10.1007/s11227-016-1707-x – volume: 58 start-page: 107 year: 2016 ident: 1854_CR24 publication-title: J Taiwan Inst Chem Eng doi: 10.1016/j.jtice.2015.06.027 – volume: 24 start-page: 7912 issue: 15 year: 2008 ident: 1854_CR51 publication-title: Langmuir doi: 10.1021/la800351d – volume-title: Using MPI: portable parallel programming with the message-passing interface. Scientific and engineering computation year: 2014 ident: 1854_CR33 – volume: 626 start-page: 13 year: 2016 ident: 1854_CR23 publication-title: Thermochim Acta doi: 10.1016/j.tca.2016.01.001 – volume-title: Isoefficiency: measuring the scalability of parallel algorithms and architectures year: 1993 ident: 1854_CR54 – ident: 1854_CR58 – volume: 182 start-page: 2350 issue: 11 year: 2011 ident: 1854_CR8 publication-title: Comput Phys Commun doi: 10.1016/j.cpc.2011.04.026 – volume: 10 start-page: 243 issue: 3 year: 1996 ident: 1854_CR47 publication-title: J Supercomput doi: 10.1007/BF00130109 – ident: 1854_CR60 – volume-title: Using advanced MPI: modern features of the message-passing interface. Computer science and intelligent systems year: 2014 ident: 1854_CR34 – ident: 1854_CR39 – ident: 1854_CR1 doi: 10.1524/zkri.218.2.132.20664 – volume: 8 start-page: 292 issue: 3 year: 1997 ident: 1854_CR48 publication-title: IEEE Trans Parallel Distrib Syst doi: 10.1109/71.584095 – volume-title: Numerical simulation in molecular dynamics: numerics, algorithms, parallelization, applications. Texts in computational science and engineering year: 2007 ident: 1854_CR27 – volume-title: MPI the complete reference: the MPI Core year: 1998 ident: 1854_CR30 – volume: 30 start-page: 425 issue: 5 year: 1987 ident: 1854_CR40 publication-title: Comput J doi: 10.1093/comjnl/30.5.425 – volume: 294 start-page: 323 year: 2016 ident: 1854_CR18 publication-title: Powder Technol doi: 10.1016/j.powtec.2016.02.051 – volume: 24 start-page: 107 issue: 1 year: 1995 ident: 1854_CR45 publication-title: J Parallel Distrib Comput doi: 10.1006/jpdc.1995.1011 – ident: 1854_CR73 – volume: 14 start-page: 33 issue: 1 year: 1996 ident: 1854_CR38 publication-title: J Mol Graph doi: 10.1016/0263-7855(96)00018-5 – ident: 1854_CR50 – ident: 1854_CR5 doi: 10.1143/PTP.26.45 – ident: 1854_CR65 doi: 10.1016/j.parco.2008.12.004 – volume-title: Introduction to HPC with MPI for data science. Undergraduate topics in computer science year: 2016 ident: 1854_CR35 doi: 10.1007/978-3-319-21903-5 – volume: 8 start-page: 3 issue: 1 year: 1989 ident: 1854_CR41 publication-title: Comput Graph Forum doi: 10.1111/j.1467-8659.1989.tb00448.x – ident: 1854_CR16 – ident: 1854_CR26 doi: 10.1063/1.470654 – volume: 197 start-page: 220 year: 2015 ident: 1854_CR37 publication-title: Comput Phys Commun doi: 10.1016/j.cpc.2015.08.011 – ident: 1854_CR12 – volume: 230 start-page: 3556 issue: 9 year: 2011 ident: 1854_CR67 publication-title: J Comput Phys doi: 10.1016/j.jcp.2011.01.048 – volume: 256 start-page: 5226 issue: 17 year: 2010 ident: 1854_CR52 publication-title: Appl Surf Sci doi: 10.1016/j.apsusc.2009.12.108 – ident: 1854_CR55 – ident: 1854_CR28 – ident: 1854_CR2 – volume: 39 start-page: 43 year: 2013 ident: 1854_CR20 publication-title: Cement Concrete Compos doi: 10.1016/j.cemconcomp.2013.03.005 – volume-title: Molecular dynamics simulation of dissociation kinetics year: 2000 ident: 1854_CR56 doi: 10.2514/6.2000-213 – ident: 1854_CR10 doi: 10.1016/j.compfluid.2014.12.016 – ident: 1854_CR7 doi: 10.1103/PhysRevE.50.1317 – volume: 281 start-page: 844 year: 2015 ident: 1854_CR71 publication-title: J Comput Phys doi: 10.1016/j.jcp.2014.10.055 – volume: 43 start-page: 181 issue: 1 year: 2010 ident: 1854_CR36 publication-title: J Appl Crystallogr doi: 10.1107/S0021889809051929 – volume: 50 start-page: 2063 issue: 7 year: 2011 ident: 1854_CR19 publication-title: Comput Mater Sci doi: 10.1016/j.commatsci.2011.02.009 – ident: 1854_CR72 – volume: 224 start-page: 1805 issue: 9 year: 2015 ident: 1854_CR22 publication-title: Eur Phys J Spec Topics doi: 10.1140/epjst/e2015-02500-2 – volume: 231 start-page: 7932 issue: 23 year: 2012 ident: 1854_CR68 publication-title: J Comput Phys doi: 10.1016/j.jcp.2012.07.038 – volume-title: Quantum mechanics: concepts and applications year: 2009 ident: 1854_CR59 – volume: 39 start-page: 4098 year: 1989 ident: 1854_CR14 publication-title: Phys Rev A doi: 10.1103/PhysRevA.39.4098
SSID	ssj0004373
Score	2.1868122
Snippet	In the present paper, an ultrafast and scalable parallel program for the Radial Pair Function (RPF) is presented via pure Message Passing Interface (MPI)...
SourceID	hal proquest crossref springer
SourceType	Open Access Repository Aggregation Database Enrichment Source Index Database Publisher
StartPage	1629
SubjectTerms	Algorithms C (programming language) Compilers Computer Science Computer simulation Computing time Condensed Matter Distribution functions Interpreters Message passing Optimization Parallel programming Physics Processor Architectures Programming Languages Radial distribution Single wall carbon nanotubes
Title	Ultrafast scalable parallel algorithm for the radial distribution function histogramming using MPI maps
URI	https://link.springer.com/article/10.1007/s11227-016-1854-0 https://www.proquest.com/docview/1880743983 https://hal.science/hal-01885745
Volume	73
WOSCitedRecordID	wos000398748700016&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D
hasFullText	1
inHoldings	1
isFullTextHit
isPrint
journalDatabaseRights	– providerCode: PRVAVX databaseName: SpringerLINK Contemporary 1997-Present customDbUrl: eissn: 1573-0484 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0004373 issn: 0920-8542 databaseCode: RSV dateStart: 19970101 isFulltext: true titleUrlDefault: https://link.springer.com/search?facet-content-type=%22Journal%22 providerName: Springer Nature
link	http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV3dS8MwEA86ffDFb3F-EcQnpZCPJk0ehzgUdAy_8K2kbToH3SZt9e8317Vuigr6VtprG3JJ7673u98hdCJ1nBDOuCdd2Ob5mmtPWS3gR74AvjIRGFI1mwh6PfX0pPt1HXfRoN2blGT1pZ4Vu1HGACYpPWdjfM_F6UvO2ino13B79zgrhuTTtLJ2cZGTY00q87tHfDJGi88AhZzzM7-kRiuL013711jX0WrtYOLOdEVsoAU73kRrTfMGXO_lLTR4yMrcpKYoceH0BBVUGHjAs8xm2GSDST4sn0fY-bTY-Yg4Bw6DDCfAs1u3yMJgE6uDirQYYF4jN0gMUPoBvulf4ZF5KbbRQ_fi_vzSq7sueDEXpHSqoom1NJC-toJEgvg0DkRkFA1MYl34IWkaMS4tM5r6KU21NVJaHrEkEEZxvoNa48nY7iLsQkEuFbEMvAjK3Dee2YTSyNIoTWOm2og00x_GNSU5dMbIwhmZMkxkCDA0mMiQtNHpxy0vUz6O34SPnU4_5IBJ-7JzHcI5QpVbh754o2100Kg8rPdvEQJLHYRqirfRWaPiucs_vXHvT9L7aIWBl1ABgQ5Qq8xf7SFajt_KYZEfVcv6HbqH79M
linkProvider	Springer Nature
linkToHtml	http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV3fb9MwED6xgTReGLAhOgpYiKdNkfwjduLHCVG1oq0qaFHfIidx2kppNyVhf_98adIWBJPYW5RcEstn5-5y330H8FnpJKWCC0-5sM3ztdBeaLXEH_kS-cpkYGjdbCIYj8P5XE-aOu6yRbu3Kcn6S70vdmOcI0xSec7G-J6L05_6zmAhYf73Hz_3xZBim1bWLi5ycrxNZf7tEb8Zo6MlQiEP_Mw_UqO1xemdPmqsL-FF42CS6-2KeAVP7OY1nLbNG0izl89gMcurwmSmrEjp9IQVVAR5wPPc5sTki5tiVS3XxPm0xPmIpEAOg5ykyLPbtMgiaBPrg5q0GGFeazdIglD6BRlNBmRtbstzmPW-Tr_0vabrgpcISSunKpZaywLlaytpLKnPkkDGJmSBSa0LPxTLYi6U5UYzP2OZtkYpK2KeBtKEQryB483Nxr4F4kJBoUJqOXoRjLtvPLcpY7FlcZYlPOwAbac_ShpKcuyMkUd7MmWcyAhhaDiREe3A5e6W2y0fx0PCn5xOd3LIpN2_HkZ4jrLQrUNf3rEOdFuVR83-LSNkqcNQLRQduGpVfHD5X2-8-C_pj3DSn46G0XAw_vYOnnP0GGpQUBeOq-KXfQ_PkrtqVRYf6iV-D__H8rc
linkToPdf	http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwpV3dS9xAEB_8KNKX2vqBZ21dxKdKcD-ym-yjaA8Pr8eBWnwLm2RzCrkPkvT-fndyiaelFcS3kEySZWc3M5P5zW8AjpVOUiq48JQL2zxfC-2FVkv8kS-Rr0wGhtbNJoLBILy708Omz2nZot3blOSipgFZmibV6SzNTpeFb4xzhEwqz9kb33Mx-7qPOHoM169_LwsjxSLFrF2M5OR4m9b81yNeGKbVe4RFPvM5_0qT1tanu_nucX-GT43jSc4WK-ULrNjJFmy2TR1Is8e3YXSbV4XJTFmR0ukPK6sI8oPnuc2JyUfT4qG6HxPn6xLnO5ICuQ1ykiL_btM6i6CtrA9qMmOEf43dgAlC7Efk17BHxmZW7sBt9-fN-aXXdGPwEiFp5VTIUmtZoHxtJY0l9VkSyNiELDCpdWGJYlnMhbLcaOZnLNPWKGVFzNNAmlCIXVibTCd2D4gLEYUKqeXoXTDuvv3cpozFlsVZlvCwA7RVRZQ0VOXYMSOPliTLOJERwtNwIiPagR9Pt8wWPB2vCR85_T7JIcP25Vk_wnOUhW59-nLOOnDQqj9q9nUZIXsdhnCh6MBJq-5nl__3xv03SR_CxvCiG_V7g6uv8JGjI1FjhQ5grSr-2G_wIZlXD2XxvV7tj1dF-5s
openUrl	ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Ultrafast+scalable+parallel+algorithm+for+the+radial+distribution+function+histogramming+using+MPI+maps&rft.jtitle=The+Journal+of+supercomputing&rft.au=Kouetcha%2C+Daniella+Nguemalieu&rft.au=Ram%C3%A9zani%2C+Hamidr%C3%A9za&rft.au=Cohaut%2C+Nathalie&rft.date=2017-04-01&rft.pub=Springer+US&rft.issn=0920-8542&rft.eissn=1573-0484&rft.volume=73&rft.issue=4&rft.spage=1629&rft.epage=1653&rft_id=info:doi/10.1007%2Fs11227-016-1854-0&rft.externalDocID=10_1007_s11227_016_1854_0
thumbnail_l	http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=0920-8542&client=summon
thumbnail_m	http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=0920-8542&client=summon
thumbnail_s	http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=0920-8542&client=summon