October 12, 2021 updated

Table of Contents

Within JAIST

  • JAIST is a famous national center of HPC (High Performance Computing) with variety of super computer architectures.
    Available machines at the present (2020.06) are,
- Cray-XC40 @ JAIST                 19728 cores (2017-)
- VPCC @ JAIST                       1536 cores (2016-)
- VPCC (P100 GPU) @ JAIST             256 cores + 16GPU
- VPCC (K40 GPU) @ JAIST               80 cores + 8GPU
- LargeMemoryCluster(12TB) @ JAIST     72 cores (2020-)
- LargeMemoryCluster(6TB) @ JAIST      72 cores (2020-)
- LargeMemoryCluster(1.5TB) @ JAIST  1920 cores (2020-)


Outside of JAIST

As a representative user of massive parallel simulation, we are using other HPC outside of JAIST,

  • K super computer
  • SR16000 at IMR


Used so far

  • Hitachi SR11000, SR8000, SR2201
  • SGI Altix, Origin
  • Fujitsu FX10, Prime_Power
  • NEC SX5
  • Cray T3E, XT3, XT4, XT5
  • IBM BlueGene
  • DEC Alpha
  • SGI-Altix3000, SGI-cluster(3920cores)
  • FujitsuCX250





cpu figure

写真:新たに組立てを待つ107個のIntel Core i7(空き箱ではありません)(2009年度)

自作クラスタ群(Intel_Core i7, Core2Quad)

64ビット対応LinuxOSの無料入手が容易となった08年度からは、Intel_Core2QuadやCore i7を搭載した自作PCをパーツから組み上げて、独力で並列クラスタを構築運用している。マザーボード当たり6-7万円程度で4coresのCPU資源が入手可能で、普段は、32並列規模の量子モンテカルロ計算が複数本数流れている。これら自作クラスタ群は、16台毎(64コア毎)に可搬ラック上に構築し、研究棟内に分散した各フロア拠点に移動可能としている。通常の100V電源で稼働し、騒音や発熱もさほどではないため、冬期は一部を居室に移動させ、暖房にも併用している。

fujitaCluster figure


clusters figure



Cores for MPI parallel calculation owned by my group/ 7TFlops相当

  • AMD EPYC 7702P, 64cores/node x 3nodes (192 cores)
  • Intel Core i9-9820X + RTX2080Ti, 40cores/nodes x 4node (160 cores) + 4 GPU
  • Intel Core i7-7700K, 12cores/nodes x 3node (42 cores)
  • Xeon E5-26220v4, 16cores/nodes x 2node (32 cores)

  • Intel Core2Quad x 48 cpus (192 cores),
  • Intel Core i7 x 112 cpus (448 cores, logically 896 cores)
  • AMD Phenom II X6 x 20 cpus (120 cores)

  • Apple Xserve (Xeon/3.0GHz), 4core/node x 29
  • Apple Xserve (Xeon/3.0GHz), 8core/node x 8

43MacintoshSetup/Homebrew version

How to setup your Macintosh for Homebrew


N.B.) Homebrew version is RECOMMENDED (on 22Apr2019).

00/Before upgrading/Caution on MacOS version upgrade...

  OSX     10.9  10.10  10.11  10.12  10.15  11.2
*sshfs       OK    [1]    [1]    OK     OK   OK
*pTeX        OK     OK     OK    OK     OK   OK
*xmgrace     OK     OK     OK    OK     OK   -
*gnuplot     OK     OK     OK    OK     OK   OK
*pukiwiki    OK     OK     OK    OK     -    -
*xcrysden    OK     OK     OK    OK     ?    -
*XQuartz     OK     OK     OK    [2]    OK   -
*MathType    OK     OK     OK    [3]    [4]  -
[1] It was no problem but some error recently confirmed on Yosemite Oct.15.
There appears error message, but somehow works.
[2] Installer gets stuck during its installation, but somehow it works.
[3] only for Word2011 & MathType6.7h
[4] Mathtype6 doesn’t work because the OS is now not accept any software with 32bit instructions.

01/Make them first to get comfortable typing/operations for faster completing setup...

  • OS update
  • Setup your iCloud account


You should always “maezono” as your account name (the name of home directory) on a mac computer.

02/Make them earlier because they takes a time (a couple of hours or days)...

These are possible to be executed parallel wise.

0201/Homebrew install

Open ‘Terminal.app’ and type this command

% /usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
    N.B.) The website is `brew.sh/index_ja <https://brew.sh/index_ja>`_
    N.B.) 'If you have already downloaded macports, please make

        % mkdir ~/macports/
        % sudo mv /opt/local ~/macports/
(This is required because in Homebrew, some alias ‘/opt/local/’ needed to be change to ‘/usr/local/’
You still could use some macports software by ‘~/macports/local/bin/xxx’.)

0202/Dropbox Installation


% brew cask install dropbox
% open -a dropbox
  • N.B.) The syncing will takes hours.
  • N.B.) For temporary users, use the followings
    ID/PW = ask to a staff



Do NOT synchronise all the files simultaneously, but USE partial synchronisation step by step. First synchronise ONLY ../02Shared/07maezonoSettings/04commonSetup


SmartSync in available on a new version of Dropbox!!

Then increase the contents to be synchronised, otherwise you have to wait for a couple of days to get even a tiny text files until other heavy contents are completed to be downloaded....



  • Preference-> Viewing -> check Use classic layout
  • View -> Columns ->”attached file, receiving time, sender,mailbox,destination”
  • View -> uncheck “Organize by Conversition”
  • open /Users/maezono/Dropbox/02Shared/07maezonoSettings/04commonSetup/09otherUtilities/04mail/MoveMail2MailBox/How_to_install_this.doc, and follow the instruction.


classic layout (after Catalina)

View -> check use as Columns

View -> uncheck side preview

Restore all the older emails in PC

There is a procedure how to restore the older emails on Dropbox into your newly purchased PC.
Make your PC always possible to trace back to any of older communications.

03/Make them properly after the ‘02’ items...


% brew cask install emacs

0302/Change your default shell

From catalina, the default shell is set zsh. so, please switch to bash

% chsh -s /bin/bash
% cd
% echo "export BASH_SILENCE_DEPRECATION_WARNING=1" >> .bash_profile

0303/Getting and Setting ‘.bash_profile/.bashrc/.alias’

% pwd
% vi .bash_profile
  source ~/.bashrc
% vi .bashrc
  source ~/Dropbox/01backup/bin/bash_alias_private
  source ~/Dropbox/02Shared/07MaezonoSettings/04commonSetup/01bin/bash_alias_common_homebrew

0304/Setting RSA key

If you have already generated your RSA keys and you do not want to update them, please follow this instruction.

If you do not have RSA keys, go to 0703/ssh Key Generation and Key Authentication

% pwd
% mkdir .ssh
% cp YOUR RSAKEY (public and private)
% cp YOUR RSA_PUBLIC_KEY  ~/.ssh
% chmod 700 ~/.ssh/rsa*

0305/First command operations (This should be after all the dropbox sync has completed)

  • Visualization of Library
chflags nohidden ~/Library/
  • N.B.) If this doesn’t work, go to ‘home(maezono) on Finder’, and press ⌘+J, then check “Show Library Folder”

04/Make them during other downloading...

0401/Terminal Setting

  • put its shortcut (alias) into the ‘Dock’
  • Terminal Preferences
    • ‘General’
      ・set ‘New windows open with:’ to
      ‘Default profile’ and ‘Default Working Directory’
      ・set ‘New tabs open with:’ to
      ‘Default profile’ and ‘Default Working Directory’
    • ‘Profile’
      ・select ‘Pro’ and click ‘Default’
    • ‘Text’
      ・change ‘Font’ to ‘Monaco 18 pt.’
      and then check ‘Blink cursor’.
    • ‘Window’
      ・‘Window Size,’ modify ‘Column’ to ‘100,’ and ‘Rows’ to ‘35’
    • ‘Shell’
      ・‘When the shell exits: Close the window’
      ・check ‘Ask before closing:’ to ‘Never’
    • 選択部分は赤

0402/Safari Environmental Setting

0403/System Preferences Setting

  • Dock
    • change ‘Position on screen’ to ‘Left’
    • check the following options:
      ‘Automatically hide and show the dock’
  • Security & Privacy
    • go to ‘Genral,’ click on the ‘Lock’ icon to activate the options
      check ‘Allow apps downloaded from’ to ‘Anywhere’
      You cannot find this item in OS sierra, but you can do equivalent operations by this command:
sudo spctl --master-disable
  • Mission Control
    ・Mission Control: F9
    ・Application windows: F10
    ・Show Desktop: F11
    ・Show Dashboard: F12
    • Hot Corners
      ・Upper Right: Mission Control
  • Keyboard
    • modify the ‘Key Repeat’ to ‘Fast’ and ‘Delay Until Repeat’ to ‘Short’
    • check ‘Show Keyboard & Character ...”
    • check ‘Use function keys...’
    • go to ‘Shortcuts/Spotlight,’ then uncheck both of those available options
    • go to ‘Shortcuts/Services,’ then uncheck ‘Searching-> Search With Google’ option
      leave command + shift + L for office (macOS Mojave)
    • go to ‘Shortcuts/Input sources’ then click the string at the left of ‘select previous input source’ and type command + space.
    • (If system language is English, first add Japanese to Input sources,
      otherwise ‘Shortcuts/Input sources’ doesn’t appear)
    • go to ‘Input source’ then check both of those available options
    • ‘Input Sources,’ only use ‘ひらがな(Google),’ ‘U.S.,’ and your own language
  • Accessibility
    • go to ‘Display,’ then modify ‘Cursor size’ to more than toward ‘Large’
  • Mouse
    • Point & Click
      ・uncheck ‘Scroll direction: natural’
      ・modify ‘Tracking speed,’ to the third speed from the right.
  • Trackpad
    • Point & Click
      ・check ‘Tap to click’,
      ・modify ‘Tracking speed’ to the third speed from the right.
    • Scroll & Zoom
      ・uncheck ‘Scroll direction: natural’
  • Sharing
    • under ‘Computer Name,’ please ask Maezono sensei for this.
    • check the following options
      ・’Screen Sharing’
      ・‘File Sharing’
      ・‘Remote Login’
  • Finder Option

0404/Microsoft Office Installation (Office365)

  • Office365のインストール
  • Installation
    Download office356 from the following webpage.
    Open the Word-app to initialise it, then close the app.
  • Replacing Normal.dotm file for standard shortcuts
    Next, copy ‘Normal_Office365_jpn_and_eng.dotm’ located at
    (Do not type ‘’ but use tab-compensation).
    Under the above ‘Templates.localized’ directory,
    remove original ‘Normal.dotm’ and then rename ‘Normal_Office365.dotm’
    into ‘Normal.dotm’.
  • Checking if the shortcuts are properly working...
    Be sure firstly whether the inherent shortcuts,
    Shift+Cmd+(H,J,K,L,N,Z), are deactivated from
    [System Preferences>Keyboard>Shortcuts>Services],
    those as
    • Searching->Search With Google (Shift+Command+L)
    • Text->Complete Citation (Shift+Command+J)
    • Text->Complete Cite Key (Shift+Command+K)
Open Word-app. again, then examine if the shortcuts like,
Shift+Cmd+(H,J,K,L,N,Z) are properly working.
[To see how the above shortcuts work, type ‘shortcuts’ in the terminal
(provided that ~/Dropbox/02Shared/07maezonoSettings/12docs/04ictTech/
has already synchronised)].


This should be done after the MS-Word has been installed.

MathType does NOT support Mac Catalina (on 04 June 2020)

% brew cask install mathtype
% mv /usr/local/Caskroom/mathtype/7.4.4/en /usr/local/Caskroom/mathtype/7.4.4/Mathtype.pkg
% open /usr/local/Caskroom/Mathtype/7.4.4/Mathtype.pkg
        ('7.3.1' would be changed to the latest version number)

Product keys (Since Oct.2018) for MathType 7 are found in this edit page (members only).

If you’ve already installed MathType, you can uninstall it by using the app located inside of MathType folder. Then you can reinstall MathType using brew cask reinstall mathtype.

It is observed on MacOS/10.14.6, PPT can not be opened whinging the error, “Compile error regarding
‘TestPDFScaling’”. In this case you can resolve the problem by uninstalling MathType,
but we don’t know yet how to make MathType and PPT coexist...

0406/Sketchy Draw

Can be installed from the Mac App Store.


Go to App store. before installing Intel C++ compiler

Xcodeのインストール後、command line toolを利用するために
Xcode -> Xcode -> preferences -> locations -> command line tool

0408/[Optional] ICSD (Inorganic Crystal Structure Database)

Inorganic Crystal Structure Database - ICSD is a commercial database. If you want to use this, please contact Prof. Nakano. (internal use only).

0409/[Optional] Crystal Maker

CrystalMaker is a commercial software. If you want to use this, please contact Prof. Nakano. (internal use only).

0410/[Optional] Intel C++ and fortran on Mac

Please install Intel compilers, if you have (commercial or educational) lisence.

Add the following source commands in ~/Dropbox/01backup/bin/bash_alias_private

# local intel setting
source /opt/intel/mkl/bin/mklvars.sh intel64
source /opt/intel/compilers_and_libraries/mac/bin/compilervars.sh intel64

0411/[Optional] Pycharm (Community)

Pycharm (Community) is a Python IDE. The community edition is Free/open-source.

0412/[Optional] CLion

CLion is a Cross-Platform IDE for C and C++ by JetBrains This is a commercial software. Please ask Prof. Nakano if you want to use (internal use only).


defaults write com.apple.screencapture location ~/Dropbox/

05/Brew downloading stuff..

0501/’mi’ editer (from below, if these are already installed, it just reported as that...)


% brew cask install mi

Setting the mi preferences-

  • Transfer the environment setup files
    to your ~/Library/Application Support/mi3/mode/
    from 01commonSetup
cp -r Dropbox/02Shared/07maezonosettings/04commonSetup/05mi/mi3/mode ~/Library/Application\ Support/mi3/
  • Or equivalently, setup your environment
    go to mi > Mode Preferences... > Normal
    • under ‘General’ tab
      Font: ‘Monaco, 18 pt’.
    • under ‘Edit’ tab
      Wrap mode: ‘Word Wrap with Window Width’
      Spell check: ‘Highlight misspelled word with red underline’
    • under ‘Display’ tab
      Control code display: check all
    • under ‘Indent’ tab
      Indent character: ‘Space characters, 4 characters’
    • under ‘Key Bind’ tab
      There is the ‘import’ button, from which you can import your preset.~
  • Macをダークモードで利用したい場合には、「Cmd+,」にて


% brew cask install google-japanese-ime

Then, take over your dictionary from Dropbox

% pwd
  /Users/maezono/Library/Application Support/Google
% mv JapaneseInput/ JapaneseInput_bak
% ln -s ~/Dropbox/01backup/JapaneseInput .
N.B.) To setup from scratch, first cp 'JapaneseInput' from the common dir. on Dropbox:

    % cd ~/Dropbox/02Shared/07maezonoSettings/04commonSetup/07StandardDictionary/
    % cp -r JapaneseInput ~/Dropbox/01backup/


% brew cask install skype


% brew cask install xquartz

After this installation, reboot your Mac once.

0505/VMware Horizon Client for Mac

% brew cask install vmware-horizon-client
  • Run the “VMware Horizon View Client” and add access server ”ts-portal.jaist.ac.jp”.
  • Login the JAIST Cloud Desktop (Windows system) using your JAIST ID/PWD.
    AD should be chosen as Domain.


% brew install wget


% brew cask install osxfuse
% brew install sshfs

to create mount point, please make directory

% mkdir -p ~/sshfs/unified
we can mount our ‘XXX’ server to the above directory by using ‘yamaXXX’ in .alias
after this server is mounted, we can use GUI in our mac to connect to the server.~


Just run

% brew install gnuplot
It is confirmed this command works with Mac OS Mojave,
letting one draw a graph from gnuplot terminal using qt visualizer.
When it does not work, you can try another way written in
First you need to install two different visualization softwares:

Aqua Term

x11 is highly functional and Aqua Term provides beautiful graphs.
Next you need to install gnuplot with links to x11 and Aqua Term:
% brew install gnuplot

You can change your visualization software, executing

% set terminal qt



% brew install grace

Test if it works:

% cp ~/Dropbox/02Shared/07maezonoSettings/04commonSetup/dmc.hist .
% xmgrace dmc.hist

0510/mpi Installation (based on gcc9)*

% brew install gcc # installs gcc9
% export HOMEBREW_CXX=g++-9
% export HOMEBREW_CC=gcc-9
% brew install open-mpi
# Build from source required to use homebrew compiled compilers as
# opposed to Apple CLANG. Check "mpicc -v" indicates Homebrew gcc

0511/xcrysden & openbabel

Can be installed by using command: .. % brew install openbabel

% brew tap agiliopadua/extras
% brew install xcrysden
% xcrysden

0512/unrar Installation

% brew install unrar

0513/nkf Installation

% brew install nkf

0514/Python environment


% brew install pyenv
% echo 'eval "$(pyenv init -)"' >> ~/Dropbox/01backup/bin/bash_alias_private
% exec $SHELL -l

Identify which version is available

% pyenv install -l | grep anaconda

Choosing the latest version [xxx], then install it by

% pyenv install anaconda[xxx]
% pyenv global anaconda[xxx]
[c.f./ You can override anaconda 2-> 3 by doing
        % pyenv install anaconda3-4.0.0
        % pyenv global anaconda3-4.0.0

Check python version

% python --version

Installing sphinx by doing

% pip install sphinx
% pip install sphinx_bootstrap_theme

0515/GitHub account

Please go to Github, and create your account.


Download supercell binary from the Website,

Go to the directory, and move it to the Application directory.

% cd /Users/maezono/Downloads
% mkdir supercell
% tar -xzf supercell-osx.tar -C supercell
% chmod -R 755 supercell
% mv supercell /Applications/
% vi ~/Dropbox/01backup/bin/bash_alias_private
    export PATH=$PATH:/Applications/supercell
    export BABEL_DATADIR=/Applications/supercell

Can be installed by using command: .. % brew install openbabel

% brew tap agiliopadua/extras
% brew install xcrysden
% xcrysden

06/TeX stuff (confirmed on Sierra, June2017)

0601/TeXLive Installation

% brew cask install mactex
  1. aspell (Spell Checker)
% brew install aspell
  1. ‘’Setting for TeX_via_Emacs’‘
% cd
% cd
% sudo ln -s ~/Dropbox/02Shared/07maezonoSettings/dotEmacs/init.el .emacs
% sudo ln -s ~/Dropbox/02Shared/07maezonoSettings/dotEmacs/.aspell.en.pws .aspell.en.pws
% sudo ln -s ~/Dropbox/02Shared/07maezonoSettings/dotEmacs/dot_aspell.conf .aspell.conf
% sudo ln -s ~/Dropbox/02Shared/07maezonoSettings/dotEmacs/dot_template .template
  1. How to typeset

When you typeset ‘filename.tex’, the corresponding command is

% texcompile.sh filename
Test files are located at
% cat texcompile.sh
  platex --kanji=sjis $target
  pbibtex --kanji=sjis $target
  platex --kanji=sjis $target
  pbibtex --kanji=sjis $target
  platex --kanji=sjis $target
  dvipdfmx $target.dvi
  open $target.pdf
  1. Trouble shooting

When installing MacTeX via homebrew, you might encounter an installation failure, more precisely, download error from the default repository. In this case, replace the default download site with the JAIST mirror site, and then retry:

% cd /usr/local/Homebrew/Library/Taps/homebrew/homebrew-cask/Casks
% mnw mactex.rb
#  url "http://mirror.ctan.org/systems/mac/mactex/mactex-#{version.no_dots}.pkg"
url "http://ftp.jaist.ac.jp/pub/CTAN/systems/mac/mactex/mactex-#{version.no_dots}.pkg"

07/Establishing Environments

0701/Registration of Digital Certification

  • Get your digital certificate.

  • Put/keep the certificate on your Dropbox using such a name ‘NIICertificateTil18May.p12’.

  • Click the certificate. By answering PW asked, then it will be kept in your key-chain.
    For more details, vist the following site (see “Others manuals” and select your appropriate browser):
  • Try connecting JAIST(eduroam) wifi to see if it works. For more details,
    visit the following web site (“Settings for Wi-Fi connection in JAIST”):
    N.B. “eduroam” is available at many world-wide academic institutes and then recommended to be setup.

0702/Import to your iPhone

  • Send your digital certification to your iCloud email address
  • Tap the certification on the email, then “Profile” will appear.
  • Follow its instruction, e.g. enter your password, etc.

0703/ssh Key Generation and Key Authentication

  • in Terminal, please type ‘ssh-keygen’
    then you can get the public key in the ‘.ssh’ directory
    you will be prompted to the passphrase,
    but you have to skip this by pressing ‘return’ (enter) key
  • register ‘.ssh/id_rsa.pub’ to ‘.ssh/authorized_keys’ in each server
    for example, unified server, supercomputer, or youmono server

0704/Sharing Desktop with your subPC

From mainPC,

%sudo mv Desktop Dropbox/
% ln -s Dropbox/Desktop ~/

From SubPC, after moving all the contents on the Desktop onto Dropbox/Desktop, then

%sudo rm -r ~/Desktop
% ln -s Dropbox/Desktop ~/


  • Prepare the environment so that you can connect your PC with ScanSnap.
  • Goto the directory
    Execute installation from 01..., 02...
  • Confirm if your NameCard DB is correctly reproduced.

0706/Install docker and run

% brew cask install docker
% open -a docker
% docker run -d -p 9000:80  --name php56-apache  -v ~/Sites/wiki/:/var/www/html php:5.6-apache
% open http://localhost:9000


0801/To avoid making .DS_Store

% defaults write com.apple.desktopservices DSDontWriteNetworkStores true
  • how to delete existing ‘.DS_store’
% find Desktop/target directory -name ".DS_Store" -print -exec rm {} ";"

Restart Finder

% killall Finder

10Available Softwares

Simulation Softwares