Anton 3: Twenty Microseconds of Molecular Dynamics Simulation Before Lunch
Anton 3 is the newest member in a family of supercomputers specially designed for atomic-level simulation of molecules relevant to biology (e.g., DNA, proteins, and drug molecules). Anton 3 achieves order-of-magnitude improvements in time-to-solution over its predecessor, Anton 2 (the current state...
Saved in:
| Published in: | SC21: International Conference for High Performance Computing, Networking, Storage and Analysis pp. 1 - 11 |
|---|---|
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
| Format: | Conference Proceeding |
| Language: | English |
| Published: |
ACM
14.11.2021
|
| Subjects: | |
| ISSN: | 2167-4337 |
| Online Access: | Get full text |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| Abstract | Anton 3 is the newest member in a family of supercomputers specially designed for atomic-level simulation of molecules relevant to biology (e.g., DNA, proteins, and drug molecules). Anton 3 achieves order-of-magnitude improvements in time-to-solution over its predecessor, Anton 2 (the current state of the art), and is over 100-fold faster than any other currently available supercomputer, thereby enabling broad new avenues of research on critical questions in biology and drug discovery. This speedup means that a 512-node Anton 3 simulates a million atoms at over 100 microseconds per day. Furthermore, Anton 3 attains this performance while consuming an order of magnitude less energy per simulated microsecond than any other machine. Like its predecessors, Anton 3 was designed from the ground up around a new custom chip to best exploit the capabilities offered by new technologies. We present here the main architectural and algorithmic developments that were necessary to achieve such significant advances. |
|---|---|
| AbstractList | Anton 3 is the newest member in a family of supercomputers specially designed for atomic-level simulation of molecules relevant to biology (e.g., DNA, proteins, and drug molecules). Anton 3 achieves order-of-magnitude improvements in time-to-solution over its predecessor, Anton 2 (the current state of the art), and is over 100-fold faster than any other currently available supercomputer, thereby enabling broad new avenues of research on critical questions in biology and drug discovery. This speedup means that a 512-node Anton 3 simulates a million atoms at over 100 microseconds per day. Furthermore, Anton 3 attains this performance while consuming an order of magnitude less energy per simulated microsecond than any other machine. Like its predecessors, Anton 3 was designed from the ground up around a new custom chip to best exploit the capabilities offered by new technologies. We present here the main architectural and algorithmic developments that were necessary to achieve such significant advances. |
| Author | Nasrb, Mohamed H. Peticolas, Jon L. Gill, Gennette Dirks, Robert M. Dror, Ron O. Adams, Peter J. Parker, Andrew Gagliardo, Joseph McLaughlin, Adam Salmon, John K. Bergdorf, Michael Correia, Timothy Ierardi, Douglas J. Butts, J. Adam Williams, John M. Kirk, Mollie M. O'Donnell, Lief Johnson, Nick P. Forte, Anthony Gullingsrud, Justin Iserovich, Lev Quan, Terry Predescu, Cristian Tabladillo, Raymond Bell, Alistair Gorlatova, Maria Mackenzie, Kenneth M. Moraes, Mark A. McGowen, Richard Fenn, Michael Theobald, Michael Wang, Stanley C. Towles, Brian Heily, Mark Shim, Keun Sup Hunt, Jeremy Wazlowski, Michael Shaw, David E. Tartler, Reinhard Yuh, Kevin A. Hasenplaugh, William Weingarten, Madeleine J. Szalay, Tamas Even, Amos Schwink, Carl Klepeis, John L. Spengler, Jochen Azaria, Asaph Grossman, J.P. Edwards, Bruce Bhatt, Jhanvi Bank, Joseph A. Feldmann, Peter Mader, Roy J. Pocina, Goran Siddique, Naseer Vick, William Batson, Brannon Fenton, Christopher H. Jackson, Bryan L. Heshmat, Benjamin Colin Taube, Andrew G. Greskamp, Brian Harper, Anissa Eastwood, |
| Author_xml | – sequence: 1 givenname: David E. surname: Shaw fullname: Shaw, David E. email: David.Shaw@DEShawResearch.com organization: Columbia University,Department of Biochemistry and Molecular Biophysics,New York,NY,10032 – sequence: 2 givenname: Peter J. surname: Adams fullname: Adams, Peter J. organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 3 givenname: Asaph surname: Azaria fullname: Azaria, Asaph organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 4 givenname: Joseph A. surname: Bank fullname: Bank, Joseph A. organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 5 givenname: Brannon surname: Batson fullname: Batson, Brannon organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 6 givenname: Alistair surname: Bell fullname: Bell, Alistair organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 7 givenname: Michael surname: Bergdorf fullname: Bergdorf, Michael organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 8 givenname: Jhanvi surname: Bhatt fullname: Bhatt, Jhanvi organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 9 givenname: J. Adam surname: Butts fullname: Butts, J. Adam organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 10 givenname: Timothy surname: Correia fullname: Correia, Timothy organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 11 givenname: Robert M. surname: Dirks fullname: Dirks, Robert M. organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 12 givenname: Ron O. surname: Dror fullname: Dror, Ron O. organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 13 givenname: Michael P. surname: Eastwood fullname: Eastwood, Michael P. organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 14 givenname: Bruce surname: Edwards fullname: Edwards, Bruce organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 15 givenname: Amos surname: Even fullname: Even, Amos organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 16 givenname: Peter surname: Feldmann fullname: Feldmann, Peter organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 17 givenname: Michael surname: Fenn fullname: Fenn, Michael organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 18 givenname: Christopher H. surname: Fenton fullname: Fenton, Christopher H. organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 19 givenname: Anthony surname: Forte fullname: Forte, Anthony organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 20 givenname: Joseph surname: Gagliardo fullname: Gagliardo, Joseph organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 21 givenname: Gennette surname: Gill fullname: Gill, Gennette organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 22 givenname: Maria surname: Gorlatova fullname: Gorlatova, Maria organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 23 givenname: Brian surname: Greskamp fullname: Greskamp, Brian organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 24 givenname: J.P. surname: Grossman fullname: Grossman, J.P. organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 25 givenname: Justin surname: Gullingsrud fullname: Gullingsrud, Justin organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 26 givenname: Anissa surname: Harper fullname: Harper, Anissa organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 27 givenname: William surname: Hasenplaugh fullname: Hasenplaugh, William organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 28 givenname: Mark surname: Heily fullname: Heily, Mark organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 29 givenname: Benjamin Colin surname: Heshmat fullname: Heshmat, Benjamin Colin organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 30 givenname: Jeremy surname: Hunt fullname: Hunt, Jeremy organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 31 givenname: Douglas J. surname: Ierardi fullname: Ierardi, Douglas J. organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 32 givenname: Lev surname: Iserovich fullname: Iserovich, Lev organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 33 givenname: Bryan L. surname: Jackson fullname: Jackson, Bryan L. organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 34 givenname: Nick P. surname: Johnson fullname: Johnson, Nick P. organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 35 givenname: Mollie M. surname: Kirk fullname: Kirk, Mollie M. organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 36 givenname: John L. surname: Klepeis fullname: Klepeis, John L. organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 37 givenname: Jeffrey S. surname: Kuskin fullname: Kuskin, Jeffrey S. organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 38 givenname: Kenneth M. surname: Mackenzie fullname: Mackenzie, Kenneth M. organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 39 givenname: Roy J. surname: Mader fullname: Mader, Roy J. organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 40 givenname: Richard surname: McGowen fullname: McGowen, Richard organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 41 givenname: Adam surname: McLaughlin fullname: McLaughlin, Adam organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 42 givenname: Mark A. surname: Moraes fullname: Moraes, Mark A. organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 43 givenname: Mohamed H. surname: Nasrb fullname: Nasrb, Mohamed H. organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 44 givenname: Lawrence J. surname: Nociolo fullname: Nociolo, Lawrence J. organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 45 givenname: Lief surname: O'Donnell fullname: O'Donnell, Lief organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 46 givenname: Andrew surname: Parker fullname: Parker, Andrew organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 47 givenname: Jon L. surname: Peticolas fullname: Peticolas, Jon L. organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 48 givenname: Goran surname: Pocina fullname: Pocina, Goran organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 49 givenname: Cristian surname: Predescu fullname: Predescu, Cristian organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 50 givenname: Terry surname: Quan fullname: Quan, Terry organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 51 givenname: John K. surname: Salmon fullname: Salmon, John K. organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 52 givenname: Carl surname: Schwink fullname: Schwink, Carl organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 53 givenname: Keun Sup surname: Shim fullname: Shim, Keun Sup organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 54 givenname: Naseer surname: Siddique fullname: Siddique, Naseer organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 55 givenname: Jochen surname: Spengler fullname: Spengler, Jochen organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 56 givenname: Tamas surname: Szalay fullname: Szalay, Tamas organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 57 givenname: Raymond surname: Tabladillo fullname: Tabladillo, Raymond organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 58 givenname: Reinhard surname: Tartler fullname: Tartler, Reinhard organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 59 givenname: Andrew G. surname: Taube fullname: Taube, Andrew G. organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 60 givenname: Michael surname: Theobald fullname: Theobald, Michael organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 61 givenname: Brian surname: Towles fullname: Towles, Brian organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 62 givenname: William surname: Vick fullname: Vick, William organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 63 givenname: Stanley C. surname: Wang fullname: Wang, Stanley C. organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 64 givenname: Michael surname: Wazlowski fullname: Wazlowski, Michael organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 65 givenname: Madeleine J. surname: Weingarten fullname: Weingarten, Madeleine J. organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 66 givenname: John M. surname: Williams fullname: Williams, John M. organization: D. E. Shaw Research,New York,NY,USA,10036 – sequence: 67 givenname: Kevin A. surname: Yuh fullname: Yuh, Kevin A. organization: D. E. Shaw Research,New York,NY,USA,10036 |
| BookMark | eNotj81OwzAQhA0CiVJy5sDFL5Di9Tqxza20_CoVB8q5cuK1CGptlKRCeXsiwWVGmk8z0lyys5giMXYNYgGgiltUhTGgF6iMRqtPWGa1mYBAo5SEUzaTUOpcIeoLlvX9lxBCGg0oxYy9LuOQIsc7vv2hOIx80zZd6qlJ0fc8Bb5Je2qOe9fx9RjdoW16_t4epmBop949hdQRr46x-bxi58Hte8r-fc4-Hh-2q-e8ent6WS2r3EmlhzzogFRjYUXjFXgKpamtCc55QZMYPwEEAz4Eaf10rCwtaaplgKL2tsQ5u_nbbYlo9921B9eNO2tBiALwFxsfT3k |
| ContentType | Conference Proceeding |
| DBID | 6IE 6IL CBEJK RIE RIL |
| DOI | 10.1145/3458817.3487397 |
| DatabaseName | IEEE Electronic Library (IEL) Conference Proceedings IEEE Xplore POP ALL IEEE Xplore All Conference Proceedings IEEE/IET Electronic Library (IEL) (UW System Shared) IEEE Proceedings Order Plans (POP All) 1998-Present |
| DatabaseTitleList | |
| Database_xml | – sequence: 1 dbid: RIE name: IEEE/IET Electronic Library (IEL) (UW System Shared) url: https://ieeexplore.ieee.org/ sourceTypes: Publisher |
| DeliveryMethod | fulltext_linktorsrc |
| Discipline | Computer Science |
| EISBN | 9781450384421 1450384420 |
| EISSN | 2167-4337 |
| EndPage | 11 |
| ExternalDocumentID | 9910051 |
| Genre | orig-research |
| GroupedDBID | 6IE 6IF 6IH 6IK 6IL 6IN AAWTH ABLEC ADZIZ ALMA_UNASSIGNED_HOLDINGS BEFXN BFFAM BGNUA BKEBE BPEOZ CBEJK CHZPO IEGSK IPLJI OCL RIE RIL |
| ID | FETCH-LOGICAL-a247t-f7f3eb3590cd41def68b98faad0eaad8d90c3181dff29d817669e7eb2f15bd963 |
| IEDL.DBID | RIE |
| ISICitedReferencesCount | 117 |
| ISICitedReferencesURI | http://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=Summon&SrcAuth=ProQuest&DestLinkType=CitingArticles&DestApp=WOS_CPL&KeyUT=000946520100012&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D |
| IngestDate | Wed Aug 27 02:51:44 EDT 2025 |
| IsDoiOpenAccess | false |
| IsOpenAccess | true |
| IsPeerReviewed | false |
| IsScholarly | false |
| Language | English |
| LinkModel | DirectLink |
| MergedId | FETCHMERGED-LOGICAL-a247t-f7f3eb3590cd41def68b98faad0eaad8d90c3181dff29d817669e7eb2f15bd963 |
| PageCount | 11 |
| ParticipantIDs | ieee_primary_9910051 |
| PublicationCentury | 2000 |
| PublicationDate | 2021-Nov.-14 |
| PublicationDateYYYYMMDD | 2021-11-14 |
| PublicationDate_xml | – month: 11 year: 2021 text: 2021-Nov.-14 day: 14 |
| PublicationDecade | 2020 |
| PublicationTitle | SC21: International Conference for High Performance Computing, Networking, Storage and Analysis |
| PublicationTitleAbbrev | SC |
| PublicationYear | 2021 |
| Publisher | ACM |
| Publisher_xml | – name: ACM |
| SSID | ssj0002871320 ssj0003204180 |
| Score | 2.271419 |
| Snippet | Anton 3 is the newest member in a family of supercomputers specially designed for atomic-level simulation of molecules relevant to biology (e.g., DNA,... |
| SourceID | ieee |
| SourceType | Publisher |
| StartPage | 1 |
| SubjectTerms | Analytical models Biological system modeling Computational modeling Drugs Heuristic algorithms High performance computing Proteins |
| Title | Anton 3: Twenty Microseconds of Molecular Dynamics Simulation Before Lunch |
| URI | https://ieeexplore.ieee.org/document/9910051 |
| WOSCitedRecordID | wos000946520100012&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 | |
| link | http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwlV1LTwIxEJ4A8eAJFYzv9ODRwpa229abL2IMEBIx4Ua6fUQOgmFB47-3XRaMiRcvTR9J07SdzDftzHwAl4Zyw7XiOEuoxvFjDmdCC0x0qrggPuVZwVrSE4OBHI_VsAJX21gY51zhfOZasVr85du5WcWnsnbAMvESVaEqRLqO1dq-p0TkT0voE9uhzohMymw-hPE2jUGZRLRowOhU_aZTKbRJt_6_dexB8ycsDw23CmcfKm52APUNLwMqxbQBTzeRGBjRazT6DBN9oX70usuj6WtzNPeov-HERfdrQvocPU_fSiIvdOsCkHWoFzTeaxNeug-ju0dcciZg3WFiib3wNNjHXCXGMmKdT2WmpNfaJi4U0oaBIMbEet9RVsb0kMqJYF57wjMbpPEQarP5zB0BYkakRktlpM2YUVZ57kXGHGHCWCn5MTTi1kze12kxJuWunPzdfQq7negOEj3o2BnUlouVO4cd87Gc5ouL4iy_AbWan00 |
| linkProvider | IEEE |
| linkToHtml | http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwlV1LTwIxEJ4gmugJFYxve_Do4nbbbltvvgjqQkjEhBvZ7SNyEAwLGv-97bJgTLx4afpImqbtZL5pZ-YDOFeEKZZKFmQhSQP_MRdkPOUBTmPJOLYxywrWkoR3u2IwkL0KXKxiYYwxhfOZafpq8ZevJ2run8ouHZbxl2gN1hmlUbiI1lq9qHjsT0rw49uuTrEIy3w-mLJL4sMyMW8Sh9KJ_E2oUuiTVu1_K9mGxk9gHuqtVM4OVMx4F2pLZgZUCmodHq89NTAiV6j_6Sb6Qh3vd5d741fnaGJRZ8mKi-4WlPQ5eh69lVRe6MY4KGtQ4nTeawNeWvf923ZQsiYEaUT5LLDcEmchMxkqTbE2NhaZFDZNdWhcIbQbcIKMtbWR1MIniJSGOwPbYpZpJ497UB1PxmYfEFU8VqmQSuiMKqmlZZZn1GDKlRaCHUDdb83wfZEYY1juyuHf3Wew2e53kmHy0H06gq3IO4d4fzp6DNXZdG5OYEN9zEb59LQ4128uW6KU |
| 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%3Abook&rft.genre=proceeding&rft.title=SC21%3A+International+Conference+for+High+Performance+Computing%2C+Networking%2C+Storage+and+Analysis&rft.atitle=Anton+3%3A+Twenty+Microseconds+of+Molecular+Dynamics+Simulation+Before+Lunch&rft.au=Shaw%2C+David+E.&rft.au=Adams%2C+Peter+J.&rft.au=Azaria%2C+Asaph&rft.au=Bank%2C+Joseph+A.&rft.date=2021-11-14&rft.pub=ACM&rft.eissn=2167-4337&rft.spage=1&rft.epage=11&rft_id=info:doi/10.1145%2F3458817.3487397&rft.externalDocID=9910051 |