Joint Usage of TSUBAME3.0
Partnership Resource Allocations

TSUBAME Industrial Use -Statistical InformationTSUBAME is open to academia and industries. Industrial use started in FY2007.
TSUBAME Resource Usage Profile
2011

75.63%

2012

72.34%

2013

62.01%

15.36%

22.63%

2014

56.25%

24.35%

19.40%

2015

55.40%

24.16%

20.44%

2016

58.31%

21.39%

20.30%

2017

49.51%

38.64%

11.85%

2018

63.08%

25.07%

11.85%

2019

58.96%

33.17%

7.87%

2020

70.76%

2021

82.76%

14.58% 2.66%

2022

78.67%

20.77% 0.56%

The Number of Industrial Projects
Subsidized Use

20.74%
23.45%

40

Paid Use-2015

Newly Accepted Continuations

2016-

HPCI (Full Year) HPCI (Half Year)

User Types

Disclosure
Nondisclosure(Permanent call for proposals)

Programs

Tokyo Tech Studentsand Faculty Member
Non-Tokyo Tech Users Partnership Resource(Academic andAllocations
Industrial Users)
HPCI/JHPCN

30

Industrial Users

20
Foreign Researchers

10

TSUBAME Services

Remarks

Menu

All Students have
TSUBAME accounts.

SubsidizedDisclosure
Use

4.66%

RemarksFree

Supported by MEXT

Disclosure$0.75/NodeH

Nondisclosure$2.24/NodeH

Exchange rate is calculated with $1 = ¥147.

Project for Creation of Research
Platforms and Sharing of AdvancedResearch Infrastructure ( - 2015)

Supported by MEXTHPCI/JHPCN (2016 - )Supported by MEXTIntellectual Property Rights are reserved completely bythe users and are not required to be shared with TokyoTech. “NodeH” is the unit for pricing. 1 NodeH is equivalent to 1 node for 1 hour.
For example, if you pay $75, you can use 100
nodes for 1 hour, or 1 node for 100 hours.
Each node has 2 Intel Xeon processors (28 cores) and 4
NVIDIA Tesla P100 GPUs, with 256GB Memory.
“Publicity: Disclosure” requires company name, division,
purpose to use and the report of result to be published.
“Publicity: Nondisclosure” only requires company name tobe published.

International Collaboration

202020212022202392018201720162015201420132012201120
102019200Price

Supported by MEXT

0200

Publicity

Pay UseResearch Collaboration based onCollaborators with
Tokyo Tech Professors Research Fund or Industrial Contracts

724.58%50

84.21%

2003.73%

How to Use TSUBAME?

Tokyo Tech Member
Academia (Non Tokyo Tech Member)
Industry

Cis-allosteric regulation of HIV-1 reverse transcriptase by Integrase
Takao Masuda (Tokyo Medical and Dental University), Osamu Kotani (National Institute of Infectious Diseases) et al.
F1P1 F2P2TbC

137N

138E

136N

RT
RTIN

RMSF（ Å）

Reverse transcriptase (RT) and integrase (IN)are encoded tandemly in the pol genes of retroviruses. This study examined the effect of INfusion on RT during reverse transcription by anin vitro cell-free assay, using recombinant
HIV-1 RTIN (rRTIN). It found that, compared torecombinant RT, rRTIN generated significantly
higher cDNAs under physiological concentrations of dNTPs. Then, analysis of molecular dynamics simulations suggested that IN can influence the structural dynamics of the RT active
center and the inhibitor binding pockets in cis.
Thus, This study demonstrated, for the firsttime, the cis-allosteric regulatory roles of IN in
RT structure and enzymatic activity.

aThis result is an excerpt from the reports at
an URL: https://doi.org/10.3390/v15010031

139T
140P
141G

RNA templatebinding sites

fingers

287K
65K
78R

285G

72R

284R

thumb

113D

151Q
115Y
185D

Amino acid residues

114A

112G

111V
110D

265N

Figure: Effects of IN fusion on fluctuations of RT protein.
RMSF values, which indicate the atomic fluctuations ofthe main chains of individual amino acids during MD
simulations. (a) Distributions of RMSF inRT. Numberson the horizontal axes indicate positions in the mature
RT of HIV-1 NL4-3. (b) Overall view of RT active center.

binding pocket fordNTP and NRTIs

YMDD motif

183Y

108V

230M

100L

181Y
188Y

107T
189V

palm

190G
106V 179V

101K

103K

binding pocket for
NNRTIs

HPCI Confederation
High Performance Computing Infrastructure- National grid infrastructure for HPC researchResources- 15 supercomputers in Japan, including TSUBAME3.0- 90PB global shared storage to share dataServices- One-stop sign up to all resources- Single sign on to all resources using Shibboleth & GSIStatus- 10 projects use TSUBAME3.0 for the HPCI project on FY2023

JHPCN
Joint Usage/Research Center for Interdisciplinary
Large-scale Information Infrastructures
The Network-Type Research Center aims to contribute to the advancement and permanent development of the academic and research infrastructure of Japan
Resources Provider
8 supercomputer centers in Japan, including TSUBAME3.0

For more details, please go to booth #1725“Research Organization for Information Science& Technology (RIST)”

Hokkaido University

GSI-SSH
Tohoku University

Single Sign On
GSI-SSHWeb Access(Shibboleth)

Kyushu University

HPCI Portal(HPCI Office)

45PBStorage

Global Shared Storage
Gfarm File System

45PBStorage

University of Tsukuba
AIST
The University of Tokyo
Shared Storage / East Hub
The University of Tokyo (Kashiwa)

ISM
Tokyo Institute of Technology

Kyoto University
RIKEN, AICSHPCI CA(NII)

File AccessOsaka University

JAMSTEC
Nagoya University

Shared Storage / West Hub
RIKEN, AICS (Kobe)

Call for Proposals of Joint Research Projects
Approximately 60 research projects in each year, including international & Industry joint research projects
Status7 projects use TSUBAME3.0, and total 68 projects are adopted as
JHPCN projects on FY2023

http://www.gsic.titech.ac.jp/sc23