10 Jan 2019
Mac Setup

Mac setup for a computational material scientist (macOS Mojave 10.14).

Key APPS

Notion
Magnet
iTerm2
Dropbox and Box
Papers
Affinity designer
xQuartz

defaults write org.macosforge.xquartz.X11 enable_iglx -bool true
Slack (with dark mode)
SublimeText
- Package control, itg.flatland theme, sidebar enhancement, GitGutter, syntax highliters(python3, julia, Fortran)

Settings

ssh

#cp ~/Dropbox/SETUP/id_rsa* ~/.ssh
cp /Volume/USB_flash_drive/ssh ~/.ssh
chmod 400 ~/.ssh/id_rsa*

bash
```
ln -s ~/Dropbox/SETUP/.bash* ./ 
```

iTerm

ln -s ~/Dropbox/SETUP/iterm.json ~/Library/Application\ Support/iTerm2/DynamicProfiles/

To install Xcode make, xcode-select --install
To install python packages with anaconda (python3.7 because it’s 2018 soon 2019), make sure saying No to install Visual Studio code
```
conda install -c matsci pymatgen
conda install pandoc
```
To install Intel® Parallel Studio XE

To install openmpi

./configure -prefix=/usr/local/openmpi-X.X.X CC=icc CXX=icc FC=ifort F77=ifort  
make all  
sudo make install  
vi ~/.bash_profile  

  export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:/usr/local/openmpi-X.X.X/lib  
  export PATH=./:/usr/local/openmpi-X.X.X/bin:$PATH  
  export OMP_NUM_THREADS=1  

To install homebrew

/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

To install julia
```
brew cask install julia
```
To install jekyll with new gem replacing built-in gem at /usr/bin which requires root privilege.
```
brew install ruby
```

To install latex

brew tap caskroom/cask
brew cask install mactex

To set up backup

vi /Library/LaunchDaemons/mybackup.plist

  <?xml version="1.0" encoding="UTF-8"?
  <!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN"
    "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
  <plist version="1.0">
  <dict>
      <key>Label</key>
      <string>research_backup</string>
      <key>ProgramArguments</key>
      <array>
  <string>/Volumes/research_backup/backup.sh</string>
      </array>
      <key>StartCalendarInterval</key>
      <dict>
  <key>Hour</key>
  <integer>10</integer>
  <key>Minute</key>
  <integer>30</integer>
      </dict>
  </dict>
  </plist>

launchctl load -w /Library/LaunchDaemons/research_backup.plist

  #!/bin/sh
  # http://www.techrepublic.com/article/how-to-set-up-auto-rsync-backups-using-ssh/
  # automated backup with crontab (depreciated)
  # https://www.linux.com/learn/how-backup-files-linux-rsync-command-line
  # https://ubuntuforums.org/showthread.php?t=15082
  # Scripting OS X Launchd Agent to run a Backup Command
  # https://coolestguidesontheplanet.com/scripting-os-x-launchd-agent-to-run-a-backup-command/
    
  # THOMAS
  mkdir -p /Volumes/research_backup/THOMAS
  rsync  --exclude-from=$HOME/.rsync_exclude  -e 'ssh -p 22' -avzp mmm0035@thomas.rc.ucl.ac.uk:/scratch/scratch/mmm0035/00_PROJECT/ /Volumes/research_backup/THOMAS
    
  # ARCHER
  mkdir -p /Volumes/research_backup/ARCHER
  rsync  --exclude-from=$HOME/.rsync_exclude  -e 'ssh -p 22' -avzp skim18@login.archer.ac.uk:/home/e05/e05/skim18/work/ /Volumes/research_backup/ARCHER
    
  # MICHAEL
  mkdir -p /Volumes/research_backup/MICHAEL
  rsync  --exclude-from=$HOME/.rsync_exclude  -e 'ssh -p 22' -avzp mmm0035@michael.rc.ucl.ac.uk:/scratch/scratch/mmm0035/00_PROJECT/ /Volumes/research_backup/MICHAEL

  # $HOME/.rsync_exclude
  WAVECAR
  CHGCAR
  CHG
  core
  WAVEDER
  POTCAR*
  *.sublime-*
  LOCPOT

Reference

MacOS Sierra for Computational Materials Science in 2017

Til next time,
at 10:01

10 Jan 2019 Mac Setup

Key APPS

Settings

Reference

10 Jan 2019
Mac Setup