43MacintoshSetup/MacPorts version¶

011/Starting up¶

• 0111/OS update

• 0112/Setup your iCloud account

012/Dropbox Installation¶

• User Setting

  ID/PW ask to a staff

013/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’.
    • 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

014/Installation of Google-Japanese (This should be after all the dropbox sync has completed)¶

Download the installation file from the web page from here

• Dropbox-nize your dictionary for Google-Japanese

% 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/

015/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

016/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/Input sources’ then click the string at the right 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/共有

  • under ‘Computer Name(コンピュータ名)’, set ‘meiwaku19pc01’ (for example).

  • check the following options

    • ‘Screen Sharing’

    • ‘File Sharing’

    • ‘Remote Login’

017/Finder Option¶

• ‘Finder/Preferences/General’

  • under ‘Show these items on the desktop:’ check all available options.

  • under ‘New Finder windows show:’ select ‘Desktop’

• ‘Sidebar’

  • check ‘maezono’

• ‘Advanced’

  • change ‘Search This Mac’ to ‘Search the Current Folder’

  • check ‘Display extensions’

021/First command operations¶

• Visualization of Library

  • by typing this command in the terminal:

chflags nohidden ~/Library/

022/Getting and Setting ‘.bash_profile/.bashrc/.alias’¶

% pwd
    /Users/maezono
% cat .bash_profile
   source ~/.bashrc
% cat .bashrc
   source ~/Dropbox/01backup/bin/bash_alias_private
   source ~/Dropbox/02Shared/07MaezonoSettings/04commonSetup/01bin/bash_alias_common

023/Xcode¶

• Free installation from Mac App Store.

  Open ‘App Store,’ then search for ‘Xcode,’ and then click ‘get’
• ‘Command Line Tools’ installation
• Xcode > Preferences > Download Command Line Tools

  open ‘Terminal,’ and type this command:

% xcode-select --install

% sudo xcodebuild -license

then type ‘agree’

1. macport

• Download from this website:

  http://www.macports.org/

• After installing it, execute the followings from Terminal:

% sudo port sync
% sudo port selfupdate

2. wget

% sudo port install wget

3. Install XQuartz

4. Install emacs

http://emacsformacosx.com/

5. sshfs

% sudo port install sshfs

to create mount point, please make directory

% mkdir -p ~/sshfs/unified

High Sierra (10.13)

% cd /Applications/Xcode.app/Contents/Developer/Toolchains
% sudo ln -s XcodeDefault.xctoolchain OSX10.13.xctoolchain

Mojave (10.14)

% sudo mkdir /usr/local/lib
% sudo ln -s "$(xcode-select -p)/Toolchains/XcodeDefault.xctoolchain/usr/lib/libclang.dylib" /usr/local/lib

reference page (both): https://trac.macports.org/ticket/54939

6. GNUPLOT

• 141/gnuplot Installation

% sudo port install gnuplot

• 142/gnuplot Setting

% cd /Users/maezono
% echo "set term x11" > .gnuplot
% cat .gnuplot
  set term x11

7. xmgrace

% sudo port install xorg-libXt +flat_namespace
% sudo port install grace

Test if it works:

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

8. openmpi Installation (based on gcc6)

   In order to install openmpi, please use the MacPort (as of 09Mar16):

% sudo port install gcc6
% sudo port select --set gcc mp-gcc6
% sudo port install openmpi-gcc6
% sudo port select --set mpi openmpi-gcc6-fortran

If the installation failed, you may try these steps:

• download fixed syslog.h file from here (or modify it by yourself, see diff)

  https://trac.macports.org/attachment/ticket/54993/syslog.h
• enter recovery mode by pressing ⌘+R while rebooting
• open terminal, find the the label of and mount “Macintosh HD”/”MACOSX/名称未設定” (may has different names according to your language setting)

% diskutil list
% diskutil apfs unlockVolume [Macintosh HD"/"MACOSX/名称未設定]

• backup and replace original syslog.h

% cd [Macintosh HD"/"MACOSX/名称未設定]/usr/include/sys/
% mv syslog.h syslog.h.bak
% cp [downloaded syslog.h] syslog.h

• reboot, and then before continuing installation, clean the previous build of openmpi

% sudo port clean openmpi-gcc6
% sudo port install openmpi-gcc6

reference page: https://trac.macports.org/ticket/54993

9. xcrysden & openbabel

   can be installed by using command:

% sudo port install openbabel
% sudo port install py-openbabel
% sudo port install xcrysden

Environmental setups are:

% mkdir ~/.xcrysden
% echo 'set xcMisc(babel) /opt/local/bin/babel' > ~/.xcrysden/custom-definitions
% export XCRYSDEN_TOPDIR=/opt/local/share/xcrysden-1.5.60/

Then test it:

% /opt/local/share/xcrysden-1.5.60/tests/run_test.sh structures

10. Resuming of wdworker

% sudo mdutil -a -i on

11. unrar Installation

% sudo port install unrar

12. nkf Installation

% sudo port install nkf

13. MATLAB installation(If you need.)

    Install MATLAB following this webpage

    http://isc-w3.jaist.ac.jp/iscenter/index.php?id=771#c4404

14. python2.7 environment

%  sudo port install py27-numpy py27-scipy py27-matplotlib py27-ipython +notebook py27-pandas py27-sympy py27-nose

and include the below statement to your alias

export PYTHONPATH=/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages

15. macMolPlot

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

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

031/Install and setup ’mi’ editor.¶

• Download from web site and install it.

  http://www.mimikaki.net/download/
• Setting the mi preferences~

version 3.x

• 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/

Go to mi > Application Preferences… > Print

• under ‘Print’ tab

  Check ‘Use Font for Print Instead of Font foe Display’.

  Change ‘Font’ to ‘Monaco 9.0 pt.’

(2019/04/11現在、上記の方法で設定すると、インデントがdeleteで一括で消えてしまう。これを避けるには「mi > モードの毎設定 > 標準 > インデント > インデントのオプション」 の「前一文字削除時の左シフト:行頭で前一文字削除したときは左シフトする」をアンチェックする。この設定をmodeファイルに書けるのかは不明。)

• 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.~

version 2.x

• Transfer the environment setup files

  to your ~/Library/Application Support/mi/mode/

  from 01commonSetup

cp -r Dropbox/02Shared/01Maezono_Group01/04commonSetup/05mi/mi2/mode ~/Library/Application\ Support/mi/

• Or equivalently, setup your environment

  • go to Mode Preference > Default

    change ‘Font: (Default Font)’ and ‘Size: 18 pt’.

    Wrap with Window Width.
  • go to ‘Display’ tab

    Under ‘Display Code Characters:’ check all of available code options
  • go to ‘Edit’ tab, and check ‘Input Space Character instead of Tab …’
  • go to ‘Edit’ tab, and check ‘Display Red Underline at Misspelled Word’
• Keyboard short cuts.

  From ‘Mode setting’ found as a button, you’ll find ‘key-bind’.

  There is the ‘import’ button, from which you can import your preset.

033/Skype Installation¶

Download the installation file from Skype web page , and then execute this file.

034/Microsoft Office Installation¶

• Installation

  (office365)

  If you are student of JAIST, please download office356 as follow webpage.

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

• Setting

  Override your ‘Normal.dotm’ by that located in the common folder:

(office365)

cp ~/Dropbox/02Shared/07maezonoSettings/04commonSetup/04Office/office356/Normal.dotm ~/Library/Group\ Containers/UBF8T346G9.Office/User\ Content.localized/Templates.localized/Normal.dotm

• Be sure whether the following ‘system shortcuts’ are deactivated.

  These can be deactivated from ‘System Preferences->Keyboard->Shortcuts->Services’ as,

  • Searching->Search With Google (Shift+Command+L)

  • Text->Complete Citation (Shift+Command+J)

  • Text->Complete Cite Key (Shift+Command+K)

• See if the following shortcuts work (All usage for shortcuts are found by typing ‘shortcuts’ from terminal).

  • Enter Normal: Osaka 5 Line spacing: single

  • Shift+Command+h 正文: Osaka 12 Left: 0.35 cm

  • Shift+Command+j 第一見出し: MS Gothic 20 Left: 0.35 cm

  • Shift+Command+k 第二見出し: MS Gothic 18 Left: 0.35 cm

  • Shift+Command+l 第三見出し: MS Gothic 14 Left: 0.35 cm

  • Shift+Command+n 数式等numerical: Monaco 10 Left: 3.53 cm

  • Shift+command+z 図番: Osaka 10 Centered

• Note that these settings sometimes will not apply on previously created documents.

  In such case, copy styles from the Normal.dotm using Tools -> Templates and Add-ins -> Organizer menu.

035/MathType¶

• go to the following web to begin download the installer.

  https://store.wiris.com/en/products/downloads/mathtype/installer/mac/en
• do the normal installation of dmg format.
• when being asked for authentication, use the following information:

  Product keys (Since Oct.2018) for MathType 7

036/Sketchy Draw¶

can be installed from the Mac App Store.

041/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.

042/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

043/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 ~/

044/CASINO (confirmed on Sierra, Dec2016)¶

% which gfortran
/opt/local/bin/gfortran

% cd
% pwd
 /Users/maezono
% mkdir applications/

% pwd
/Users/maezono/applications
% cp /Users/maezono/Dropbox/02Shared/07maezonoSettings/04commonSetup/v213pl713_noex.tar.gz .
% tar -xzvf v213pl713_noex.tar.gz
% l
v213pl713/          v213pl713_noex.tar.gz

export QMC_ARCH=intelmac-gcc
export CASINO_ARCH=intelmac-gcc
% fixal

% pwd
 /Users/maezono/applications/v213pl713
% rm -rf bin_qmc/
% make -j 4

% cd
% l
Desktop/ Downloads/ ...
% ln -s applications/v213pl713 currentCASINO
% l
Desktop/ Downloads/ ...  currentCASINO@ ...

% setal
PATH="$PATH":$HOME/currentCASINO/bin_qmc/utils/intelmac-gcc/
% fixal
# Check the operation of utility, for example, reblock, graphit, etc.
% pwd
/Users/maezono/Downloads
% l
... dmc.hist ...
% reblock
% graphit

045/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.

046/VMware Horizon Client for Mac¶

• Go to the following web and download the installer.

  https://my.vmware.com/web/vmware/details?downloadGroup=VIEWCLIENTS_MAC_35&productId=421&rPId=9324

• Do the normal installation of dmg format.

• 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.

047/Mail¶

Account admin.

Archiving email communications

Do not accumulate all in icloud server

Restore all the older emails in PC

environment setting > display tab > choose use classic layout
display>display items >"attached file, receiving time, sender,mailbox,destination"
display> uncheck "gathering per thread"

051/TeXLive Installation¶

% sudo port install texlive +full

N.B. RevTeX and ACS style are automatically installed via the above TeXLive installation. Don’t worry. (as of June/26/2017 by KH)

1. aspell (Spell Checker)

% sudo port install aspell aspell-dict-en

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=$1
 PATH=/opt/local/bin/:$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