Experiences Porting NAMD to the Data Parallel C++ Programming Model

HPC applications have a growing need to leverage heterogeneous computing resources with a vendor-neutral programming paradigm. Data Parallel C++ is a programming language based on open standards SYCL, providing a vendor-neutral solution. We describe our experiences porting the NAMD molecular dynamic...

Celý popis

Uloženo v:
Podrobná bibliografie
Vydáno v:International Workshop on OpenCL Ročník 2022
Hlavní autoři: Hardy, David J, Choi, Jaemin, Jiang, Wei, Tajkhorshid, Emad
Médium: Journal Article
Jazyk:angličtina
Vydáno: United States 01.05.2022
Témata:
SYCL
Molecular Dynamics
oneAPI
DPC++
NAMD
On-line přístup:Zjistit podrobnosti o přístupu
Tagy: Přidat tag
Žádné tagy, Buďte první, kdo vytvoří štítek k tomuto záznamu!
Abstract HPC applications have a growing need to leverage heterogeneous computing resources with a vendor-neutral programming paradigm. Data Parallel C++ is a programming language based on open standards SYCL, providing a vendor-neutral solution. We describe our experiences porting the NAMD molecular dynamics application with its GPU-offload force kernels to SYCL/DPC++. Results are shown that demonstrate correctness of the porting effort.
AbstractList HPC applications have a growing need to leverage heterogeneous computing resources with a vendor-neutral programming paradigm. Data Parallel C++ is a programming language based on open standards SYCL, providing a vendor-neutral solution. We describe our experiences porting the NAMD molecular dynamics application with its GPU-offload force kernels to SYCL/DPC++. Results are shown that demonstrate correctness of the porting effort.
HPC applications have a growing need to leverage heterogeneous computing resources with a vendor-neutral programming paradigm. Data Parallel C++ is a programming language based on open standards SYCL, providing a vendor-neutral solution. We describe our experiences porting the NAMD molecular dynamics application with its GPU-offload force kernels to SYCL/DPC++. Results are shown that demonstrate correctness of the porting effort.HPC applications have a growing need to leverage heterogeneous computing resources with a vendor-neutral programming paradigm. Data Parallel C++ is a programming language based on open standards SYCL, providing a vendor-neutral solution. We describe our experiences porting the NAMD molecular dynamics application with its GPU-offload force kernels to SYCL/DPC++. Results are shown that demonstrate correctness of the porting effort.
Author Hardy, David J
Tajkhorshid, Emad
Jiang, Wei
Choi, Jaemin
Author_xml – sequence: 1
  givenname: David J
  surname: Hardy
  fullname: Hardy, David J
  organization: University of Illinois at Urbana-Champaign, Beckman Institute for Advanced Science and Technology, Urbana, Illinois, USA
– sequence: 2
  givenname: Jaemin
  surname: Choi
  fullname: Choi, Jaemin
  organization: University of Illinois at Urbana-Champaign, Department of Computer Science, Urbana, Illinois, USA
– sequence: 3
  givenname: Wei
  surname: Jiang
  fullname: Jiang, Wei
  organization: Argonne National Laboratory, Argonne Leadership Computing Facility, Lemont, Illinois, USA
– sequence: 4
  givenname: Emad
  surname: Tajkhorshid
  fullname: Tajkhorshid, Emad
  organization: University of Illinois at Urbana-Champaign, Beckman Institute for Advanced Science and Technology, Urbana, Illinois, USA
BackLink https://www.ncbi.nlm.nih.gov/pubmed/37334141$$D View this record in MEDLINE/PubMed
BookMark eNo1jztPwzAURj2AeBRmNuQRqUrxK44zVml5SC1kgDm6Tm5KJCcuTiLRf0-AMp3l6HtckpPOd0jIDWcLzlV8L2ORxtIsfqnZGTmXiZSKK35BsvXXHkODXYk9zX0Ymm5HX5bbFR08HT6QrmAAmkMA59DRbD6nefC7AG37Y259he6KnNbgerw-ckbeH9Zv2VO0eX18zpabCKZeFiEwI60UrNKiBmEh5rVOua1ZqiuorNCxjZUykGBaqoSjMAyNZQg4bU1QzMjdX-4--M8R-6Fom75E56BDP_aFMCLRWglmJvX2qI62xarYh6aFcCj-j4tv9WlTHw
ContentType Journal Article
DBID NPM
7X8
DOI 10.1145/3529538.3529560
DatabaseName PubMed
MEDLINE - Academic
DatabaseTitle PubMed
MEDLINE - Academic
DatabaseTitleList PubMed
MEDLINE - Academic
Database_xml – sequence: 1
  dbid: NPM
  name: PubMed
  url: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed
  sourceTypes: Index Database
– sequence: 2
  dbid: 7X8
  name: MEDLINE - Academic
  url: https://search.proquest.com/medline
  sourceTypes: Aggregation Database
DeliveryMethod no_fulltext_linktorsrc
ExternalDocumentID 37334141
Genre Journal Article
GrantInformation_xml – fundername: NIGMS NIH HHS
  grantid: P41 GM104601
GroupedDBID NPM
7X8
ID FETCH-LOGICAL-a2950-ea083b320d62fa2ba51f691bf096dadb265b5448a7e9c471e280e8b0eae4147e2
IEDL.DBID 7X8
IngestDate Fri Jul 11 11:34:45 EDT 2025
Thu Jan 02 22:31:40 EST 2025
IsDoiOpenAccess false
IsOpenAccess true
IsPeerReviewed false
IsScholarly false
Keywords SYCL
Molecular Dynamics
oneAPI
DPC++
NAMD
Language English
LinkModel DirectLink
MergedId FETCHMERGED-LOGICAL-a2950-ea083b320d62fa2ba51f691bf096dadb265b5448a7e9c471e280e8b0eae4147e2
Notes ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
OpenAccessLink https://pmc.ncbi.nlm.nih.gov/articles/PMC10276636/pdf/nihms-1892994.pdf
PMID 37334141
PQID 2827664208
PQPubID 23479
ParticipantIDs proquest_miscellaneous_2827664208
pubmed_primary_37334141
PublicationCentury 2000
PublicationDate 20220501
PublicationDateYYYYMMDD 2022-05-01
PublicationDate_xml – month: 5
  year: 2022
  text: 20220501
  day: 1
PublicationDecade 2020
PublicationPlace United States
PublicationPlace_xml – name: United States
PublicationTitle International Workshop on OpenCL
PublicationTitleAlternate Int Workshop OpenCL
PublicationYear 2022
Score 1.8354379
Snippet HPC applications have a growing need to leverage heterogeneous computing resources with a vendor-neutral programming paradigm. Data Parallel C++ is a...
SourceID proquest
pubmed
SourceType Aggregation Database
Index Database
Title Experiences Porting NAMD to the Data Parallel C++ Programming Model
URI https://www.ncbi.nlm.nih.gov/pubmed/37334141
https://www.proquest.com/docview/2827664208
Volume 2022
hasFullText
inHoldings 1
isFullTextHit
isPrint
link http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwpV07T8MwELaAMrDwEK_ykpHYqtDEduxkQlVLxUCjDCB1i86JIyGVpDSF3885ccXCgMSSLInk3MV33_nuviPkLkfDGDDDvNi2uAuGMWukfe5BLKTQwmDo3JK4PqskiebzOHUHbo0rq9zYxNZQF3Vuz8iHGBooKW0y-GH54dmpUTa76kZobJMeRyhjS7rUPHIMPoEIh9zmsXh0394dDeWvMLJ1J9OD_y7kkOw7IElHneaPyJapjsn4h7m4obZIFB0TTUazCV3XFKEencAaaAorO0FlQceDAU27Aq13-6QdjLY4Ia_Tx5fxk-fGJHiAH-V7BhBGac78QrISmIYwKGUc6BKjkwIKzWSoQ4zCQJk4R19kWOQbVIgBIwKhDDslO1VdmXNCbV9sVPohGAXouhUoCRHjeZznDLEI9MntRiYZ_oY2twCVqT-b7EcqfXLWCTZbdnwZGVccfaUILv7w9iXZY7bBoC0pvCK9EjehuSa7-df6rVndtPrFa5LOvgFzzq9o
linkProvider ProQuest
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=Experiences+Porting+NAMD+to+the+Data+Parallel+C%2B%2B+Programming+Model&rft.jtitle=International+Workshop+on+OpenCL&rft.au=Hardy%2C+David+J&rft.au=Choi%2C+Jaemin&rft.au=Jiang%2C+Wei&rft.au=Tajkhorshid%2C+Emad&rft.date=2022-05-01&rft.volume=2022&rft_id=info:doi/10.1145%2F3529538.3529560&rft.externalDBID=NO_FULL_TEXT