0201/Homebrew install¶

Open ‘Terminal.app’ and type this command

% /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
% cd
% echo 'eval "$(/opt/homebrew/bin/brew shellenv)"' >> .bash_profile

0202/Dropbox Installation¶

Installation

% brew install --cask 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

Synchronisation

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….

0203/Mail¶

Setup

• Preference-> Viewing -> check Use column 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.

Restore all the older emails in PC

0301/emacs¶

% brew install --cask 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
  /Users/maezono
% 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
  /Users/maezono
% mkdir .ssh
% cp YOUR RSAKEY (public and private)
% cp YOUR RSA_PRIVATE_KEY ~/.ssh
% 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”

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’

    ・キーボードのタブに行き「代替スクリーンをスクロール」のチェックを外す
  • ‘Text’

    ・change ‘Font’ to ‘Monaco 18 pt.’

    and then check ‘Blink cursor’.

    ・カーソルも選択部分も赤色
  • ‘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¶

• Go to Safari > Preference > General

  and uncheck ‘Open “safe” file after downloading…’

  (If you don’t do this setting, an inconvenient problem will occur because

  ‘xxx.zip’ file will unzip (self- extracting) automatically when we download

  ‘xxx.zip’ file, such as the ACS format files. By removing the check from default,

  then it will not be self-extracting.)
• 表示＞お気に入りバーを表示
• Show favorites bar on the top of the window.
  • Shift+cmd+B
• Edit the favorites.
  • opt+cmd+B

    add the following contents.
    01前園グループ

    http://www.jaist.ac.jp/is/labs/maezono-lab
    02JAIST 北陸先端科学技術大学院大学

    http://www.jaist.ac.jp/index.html
    03Macのスクリーンショット機能のキーボードショートカットまとめ(17種類)/Inforati

    http://inforati.jp/apple/mac-tips-techniques/system-hints/how-to-use-mac-screenshot-with-keyboard-shortcut.html
    04Trello

    https://trello.com/
    05Google

    https://www.google.co.jp
    06Apple

    https://www.apple.com/jp/
    07Amazon

    https://www.amazon.co.jp
    08ReserachGate

    https://www.researchgate.net
• You can show the these web site by using following command.
  • opt+cmd+[1-9]

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
  • System Settings＞Keyboard＞Keyboard Shortcuts>＞Input Sources＞Select the previous input source＞「Cmd+Space」setting
• 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

  「アプリを入手」のほうではなく「ログイン」の方を選択し、

  xxx@jaist.ac.jp

  でログインする。

  そうすると、一旦、jaistのログインページに遷移し、

  ここで認証される。

  その先に遷移したページの右上に「officeをインストール」

  というボタンがあり、ここからダウンロードされる。
• Installation

  Download office356 from the following webpage.

  https://www.jaist.ac.jp/iscenter/software/microsoft/office365/

  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

  ‘~/Dropbox/02Shared/07maezonoSettings/04commonSetup/04Office/’

  into

  ‘~/Library/GroupContainers/UBF8T346G9.Office/UserContent.localized/Templates.localized/’

  (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)

0405/MathType¶

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

0406/Sketchy Draw¶

Can be installed from the Mac App Store.

0407/Xcode¶

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

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).

0413/[Optional] macMolPlot¶

http://brettbode.github.io/wxmacmolplt/downloads.html

0414/[Optional] MATLAB installation(If you need.)¶

0415/スクショの保存位置¶

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

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

Installation

% brew install --cask 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

  環境設定＞一般

  とたどり、

  「ダークモード用の色セット」＞モード設定で設定した色

  「ライト/ダークモードの切替」＞常にライトモード

  とするのが吉。そうしないと、

  範囲設定したときの色目が見えづらい。

0503/Skype¶

% brew install --cask skype

0504/XQuartz¶

% brew install --cask xquartz

After this installation, reboot your Mac once.

0505/VMware Horizon Client for Mac¶

% brew install --cask 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.

0506/wget¶

% brew install wget

0507/yamaUnifiedまわりの設定¶

See the link for the latest information.

0508/GNUPLOT¶

Just run

% brew install gnuplot

http://mashiroyuya.hatenablog.com/entry/installgnuplot

https://sourceforge.net/projects/aquaterm/files/

Aqua Term

http://xquartz.macosforge.org/

% brew install gnuplot

You can change your visualization software, executing

% set terminal qt

respectively.

0509/xmgrace¶

% 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/openbabel¶

Can be installed by using command:

% brew install openbabel

0512/unrar Installation¶

% brew install rar

0513/nkf Installation¶

% brew install nkf

0514/Python environment¶

Preparation

% brew install pyenv
% exec $SHELL -l

Identify which version is available

% pyenv install -l | grep anaconda

Choosing the latest version [xxx] (e.g., 4.0.0), then install it by

% pyenv install anaconda3-4.0.0
% pyenv global anaconda3-4.0.0

** Note for [OS12.x] (confirmed in OS12.5) **
ターミナルアプリに対して、Cmd+Iでアプリ設定で「Rossettaで開く」にチェックを入れる。その後に、
    % pyenv install anaconda[xxx]
    % pyenv global anaconda[xxx]
を実行すること。Rossetta対応をしないと、
    % pyenv install anaconda3-5.3.1
        ERROR: The binary distribution of Anaconda3 is not available for MacOSX-arm64.
といった顛末になる。

上記の設定が済んだら、再度、ロゼッタのチェックは外しておく(さもないと今度はsetal/setacなどが効かなくなる)。

bash_alias_privateに下記の記載があることを確認
    %----------------------
    eval "$(pyenv init -)"

    # python setup
    export PYENV_ROOT="$HOME/.pyenv"
    export PATH="$PYENV_ROOT/bin:$PATH"
    eval "$(pyenv init --path)"
    %----------------------

そうしたら、
    % python --version
        Python 2.7.18
    % fixal
    % python --version
        Python 3.7.0
として、Python3系に切り替わっていることを確認。

Check python version

% python --version

Installing sphinx by doing

% conda install sphinx
% pip install --upgrade pip
% pip install sphinx_bootstrap_theme

0515/GitHub account¶

Please go to Github, and create your account.

0516/supercell¶

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

0601/TeXLive Installation¶

% brew install --cask mactex

1. aspell (Spell Checker)

% brew install aspell

2. ‘’Setting for TeX_via_Emacs’’

% 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

3. How to typeset

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

% texcompile.sh filename

% cat texcompile.sh
  #!/bin/sh
  target=$1
  PATH=/Library/TeX/texbin/:$PATH
  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

4. 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"

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):

  http://www.jaist.ac.jp/iscenter/en/digital-certificate/client/#c902
• 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”):

  http://www.jaist.ac.jp/iscenter/en/network/wireless/

  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¶

• reference page: http://www.itmedia.co.jp/help/tips/linux/l0402.html
• 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,

%cd
%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 ~/

0705/Scanner&NameCardAdmin¶

• Prepare the environment so that you can connect your PC with ScanSnap.
• Goto the directory

  /Users/maezono/Dropbox/02Shared/01Maezono_Group01/04commonSetup/09otherUtilities/scansnap

  Execute installation from 01…, 02…
• Confirm if your NameCard DB is correctly reproduced.

0706/Install docker and run¶

% brew install --cask 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¶

• below is the reference web page but in Japanese

  http://blancbooth.com/archives/62
• execute this command in Terminal:

% 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