TSUBAME Grand Challenge Programand SuperCon Programming Contest
TSUBAME Grand Challenge
The TSUBAME Grand Challenge solicits proposals for grandchallenge problems that can utilize all nodes of TSUBAME3.0 andhas two categories.
Category A: Exclusive use of all nodes for 24 hours
Category B: Exclusive use of 1/3 the nodes for up to 1 week
We started this program in 2011, and have continued to performthe Grand Challenge runs twice a year.
Under this program, we have adopted total 42 grand challenge
projects, some of which were awarded Gordon Bell prizes.

Project 1: Distributed Parallel Homology
Search System with Pwrake and Gfarm
Kenta Machida, Osamu Tatebe (University of Tsukuba)

Motivation
Metagenomics is a study of genetic material recovered directly fromenvironmental samples. The genomic sample data is acquired by
NGS (Next Generation Sequencer) and recently its size has been increasing rapidly. For that reason, existing homology search tools
such as BLAST have performance and memory problems in a studyof genome analysis due to increased execution time and memory
shortage.
Our approach to solve the problems- Distribute both query and DB and execute homology search inparallel on the platform consisting of Gfarm file system and Pwrake
workflow engine- Use GHOSTZ-GPU optimized for NVMe SSD
Results of Grand Challenge
In an experiment for large genomic data, input data were 62 GB ofDB provided by NCBI and 70 GB of queries provided by HMP. Although there were some problems found in a system, the proposedsystem completed all processing in about 2 hours.

Number of Accepted Proposals
2019

2018

2017

2016

2015

FSF

Category A00

Category B

1Total1SFSFS

F01

20112020102032112011 ACM Gordon Bell Prize: Special Achievements
in Scalability and Time-to-Solution“Peta-scale Phase-Field Simulation for Dendritic
Solidification on the TSUBAME 2.0 Supercomputer”

2014

2013

SFS

FS

F

S

FS

121201223423

11322110020

192253412225442

2011 ACM Gordon Bell Prize:
Honorable Mention
Large scale bioﬂuidics
simulations on TSUBAME2

2012

2011
Total

2011 Graph500 Challenge
on TSUBAME 2.0Project 2: Calculation of Various Atomic
Properties for Studies on Fundamental
Physics Using Large-scale HPC
Bhanu Pratap Das, Nanako Shitara, Kazuyuki Sanada, Toshio Watanabe(Tokyo Institute of Technology)

Motivation
Because the permanent electric dipole moment of the electron(eEDM) is a signature of CP-violation beyond the Standard Model(SM) of particle physics, its measurement is expected to reveal newphysics beyond the SM. To obtain an upper limit for the magnitudeof the eEDM, experimental measurements must be combined withtheoretical results, which often require computationally intensive calculations. In this work, we calculate the enhancement factor of thefrancium (Fr) atom, a promising eEDM search candidate.
MethodWe use the relativistic Coupled-Cluster (RCC) method to calculate
the wavefunction of the ground state of the Fr atom. The RCC wavefunction takes the Dirac-Fock (DF) state, which neglects correlation
effects between electrons, and adds terms corresponding to particle-hole excitations of the DF state, which reflect the effects of electron correlation.
Key Results
Included correction terms

Scalability of Execution Time

Scalability of Total Read Bandwidthin GHOSTZ Alignment Step

Enhancement factor R

Dirac-Coulomb (DC) Hamiltonian only

812.19DC Hamiltonian + Breit interaction terms

804.08DC Hamiltonian + approximate QED terms

811.57

SuperCon Programming Contest
The SuperCon programming contest is held every summer in cooperation with Osaka University, where high school students come toour campuses to compete in a programming contest using our supercomputers. SuperCon started back in 1995 and has been held
yearly. There is a qualifying round where students use their local environment to solve a given problem. About 10 teams consisting of
2-3 members each, will go on to the final round, which is held at
Tokyo Tech, and Osaka University, for teams from the east and westside of Japan, respectively.
This year the students solve a hierarchical N-body problem on
TSUBAME3.0 and most of them were able to utilize the GPU.

The following teams won the competition:
1st place: team Nerv (Hamamatsu Technical High School)
2nd place: team atKoder (High School at Komaba, U. Tsukuba)
3rd place: team supercon (Kaisei High School)

Teams at Tokyo Tech

Teams at Osaka University

https://www.gsic.titech.ac.jp/sc19