PMID- 31515016
OWN - NLM
STAT- MEDLINE
DCOM- 20200129
LR  - 20200801
IS  - 1724-191X (Electronic)
IS  - 1120-1797 (Print)
IS  - 1120-1797 (Linking)
VI  - 64
DP  - 2019 Aug
TI  - Monte Carlo Processing on a Chip (MCoaC)-preliminary experiments toward the 
      realization of optimal-hardware for TOPAS/Geant4 to drive discovery.
PG  - 166-173
LID - S1120-1797(19)30152-8 [pii]
LID - 10.1016/j.ejmp.2019.06.016 [doi]
AB  - Amongst the scientific frameworks powered by the Monte Carlo (MC) toolkit Geant4 
      (Agostinelli et al., 2003), the TOPAS (Tool for Particle Simulation) (Perl et 
      al., 2012) is one. TOPAS focuses on providing ease of use, and has significant 
      implementation in the radiation oncology space at present. TOPAS functionality 
      extends across the full capacity of Geant4, is freely available to non-profit 
      users, and is being extended into radiobiology via TOPAS-nBIO (Ramos-Mendez et 
      al., 2018). A current "grand problem" in cancer therapy is to convert the dose of 
      treatment from physical dose to biological dose, optimized ultimately to the 
      individual context of administration of treatment. Biology MC calculations are 
      some of the most complex and require significant computational resources. In 
      order to enhance TOPAS's ability to become a critical tool to explore the 
      definition and application of biological dose in radiation therapy, we chose to 
      explore the use of Field Programmable Gate Array (FPGA) chips to speedup the 
      Geant4 calculations at the heart of TOPAS, because this approach called 
      "Reconfigurable Computing" (RC), has proven able to produce significant (around 
      90x) (Sajish et al., 2012) speed increases in scientific computing. Here, we 
      describe initial steps to port Geant4 and TOPAS to be used on FPGA. We provide 
      performance analysis of the current TOPAS/Geant4 code from an RC implementation 
      perspective. Baseline benchmarks are presented. Achievable performance figures of 
      the subsections of the code on optimal hardware are presented; Aspects of 
      practical implementation of "Monte Carlo on a chip" are also discussed.
CI  - Published by Elsevier Ltd.
FAU - Abhyankar, Yogindra S
AU  - Abhyankar YS
AD  - Centre for Development of Advanced Computing (C-DAC), Pune, India.
FAU - Dev, Sachin
AU  - Dev S
AD  - Open Health Systems Laboratory (OHSL), USA.
FAU - Sarun, O S
AU  - Sarun OS
AD  - Centre for Development of Advanced Computing (C-DAC), Pune, India.
FAU - Saxena, Amit
AU  - Saxena A
AD  - Centre for Development of Advanced Computing (C-DAC), Pune, India.
FAU - Joshi, Rajendra
AU  - Joshi R
AD  - Centre for Development of Advanced Computing (C-DAC), Pune, India.
FAU - Darbari, Hemant
AU  - Darbari H
AD  - Centre for Development of Advanced Computing (C-DAC), Pune, India.
FAU - Sajish, C
AU  - Sajish C
AD  - Centre for Development of Advanced Computing (C-DAC), Pune, India.
FAU - Sonavane, U B
AU  - Sonavane UB
AD  - Centre for Development of Advanced Computing (C-DAC), Pune, India.
FAU - Gavane, Vivek
AU  - Gavane V
AD  - Centre for Development of Advanced Computing (C-DAC), Pune, India.
FAU - Deshpande, Abhay
AU  - Deshpande A
AD  - Society for Applied Microwave Electronics Engineering & Research (SAMEER), 
      Mumbai, India.
FAU - Dixit, Tanuja
AU  - Dixit T
AD  - Society for Applied Microwave Electronics Engineering & Research (SAMEER), 
      Mumbai, India.
FAU - Harsh, Rajesh
AU  - Harsh R
AD  - Society for Applied Microwave Electronics Engineering & Research (SAMEER), 
      Mumbai, India.
FAU - Badwe, Rajendra
AU  - Badwe R
AD  - Tata Memorial Centre (TMC), Mumbai, India.
FAU - Rath, G K
AU  - Rath GK
AD  - All India Institute of Medical Sciences (AIIMS), Delhi, India.
FAU - Laskar, Siddhartha
AU  - Laskar S
AD  - Tata Memorial Centre (TMC), Mumbai, India.
FAU - Faddegon, Bruce
AU  - Faddegon B
AD  - University of California San Francisco, USA.
FAU - Perl, Joseph
AU  - Perl J
AD  - SLAC National Accelerator Laboratory, Menlo Park, USA.
FAU - Paganetti, Harald
AU  - Paganetti H
AD  - Massachusetts General Hospital and Harvard Medical School, Boston, USA.
FAU - Schuemann, Jan
AU  - Schuemann J
AD  - Massachusetts General Hospital and Harvard Medical School, Boston, USA.
FAU - Srivastava, Anil
AU  - Srivastava A
AD  - National Cancer Institute (NCI), Bethesda, USA.
FAU - Obcemea, Ceferino
AU  - Obcemea C
AD  - National Cancer Institute (NCI), Bethesda, USA.
FAU - Nath, Asheet K
AU  - Nath AK
AD  - Centre for Development of Advanced Computing (C-DAC), Pune, India.
FAU - Sharma, Ashok
AU  - Sharma A
AD  - All India Institute of Medical Sciences (AIIMS), Delhi, India.
FAU - Buchsbaum, Jeffrey
AU  - Buchsbaum J
AD  - National Cancer Institute (NCI), Bethesda, USA. Electronic address: 
      jeff.buchsbaum@nih.gov.
LA  - eng
GR  - U24 CA215123/CA/NCI NIH HHS/United States
PT  - Journal Article
DEP - 20190716
PL  - Italy
TA  - Phys Med
JT  - Physica medica : PM : an international journal devoted to the applications of 
      physics to medicine and biology : official journal of the Italian Association of 
      Biomedical Physics (AIFB)
JID - 9302888
SB  - IM
MH  - *Monte Carlo Method
MH  - Radiobiology/*instrumentation
MH  - Radiotherapy Planning, Computer-Assisted
MH  - Time Factors
PMC - PMC7238758
MID - NIHMS1580588
OTO - NOTNLM
OT  - FPGA
OT  - Geant4
OT  - Monte Carlo
OT  - Simulation
OT  - TOPAS
COIS- Conflicts of Interest: The authors have none to report.
EDAT- 2019/09/14 06:00
MHDA- 2020/01/30 06:00
PMCR- 2020/08/01
CRDT- 2019/09/14 06:00
PHST- 2019/01/29 00:00 [received]
PHST- 2019/05/21 00:00 [revised]
PHST- 2019/06/29 00:00 [accepted]
PHST- 2019/09/14 06:00 [entrez]
PHST- 2019/09/14 06:00 [pubmed]
PHST- 2020/01/30 06:00 [medline]
PHST- 2020/08/01 00:00 [pmc-release]
AID - S1120-1797(19)30152-8 [pii]
AID - 10.1016/j.ejmp.2019.06.016 [doi]
PST - ppublish
SO  - Phys Med. 2019 Aug;64:166-173. doi: 10.1016/j.ejmp.2019.06.016. Epub 2019 Jul 16.