Technical Aspects

Contents

I Introduction to command-line environment 2

I.I How to open the terminal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

I.II Paths and useful commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

I.III Text editors (suggestions) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

II How to install gfortran 5

III How to install NetCDF libraries 6

IV How to connect remotely to a computer 9

V How to install Canopy-python 10

I Introduction to command-line environment

I.I How to open the terminal

GNU/Linux

You can either:

X Open the Dash by clicking the Ubuntu icon in the upper-left, typer ”terminal”, and select the

Terminal application from the results that appear.

X Hit the keyboard shortcut

Ctrl

Alt

MacOS

X Press

cmd /

+ . The search bar will open.

X Write ”terminal” and press the return key

Windows

X Press +

to open RUN dialog box.

X Write ”cmd”,and click/tap on OK.

I Introduction to command-line environment

I.II Paths and useful commands

GNU/Linux and MacOS are based on UNIX, therefore all the commands are similar for both OS. Windows, on the other

hand, uses diﬀerent command lines.

Path

Comment

Paths are written using ”/” Paths are written using ”\”

Example

/Users/user/Desktop

c:\Users\user\Desktop

Change directory

Command

Example

cd dirname

Create a new directory

Command

mkdir

Example

mkdir dirname

View the contents of a directory Command

dir

Print current working directory Command

pwd

Move (rename) a ﬁle/directory

Command

move

Example

mv inﬁle outﬁle

move inﬁle outﬁle

Copy a ﬁle

Command

copy

Example

cp ﬁle ﬁlecopy

copy ﬁle ﬁlecopy

Copy a directory

Command

cp -r

xcopy

Example

cp -r dir dircopy

xcopy dir dircopy

Remove a ﬁle

Command

del

Example

rm ﬁlename

del ﬁlername

Remove a directory

Command

rm -r

Example

rm -r dirname

rddirname

I Introduction to command-line environment

I.III Text editors (suggestions)

This is a list of some text editor that may be useful for this course.

GNU/Linux

X You can use the default text editors in GNU/Linux: Emacs or Vim.

Quick reference cards:

1. Emacs reference card 

2. Vim quick reference card 

MacOS

X You can install Emacs or Vim for Mac.

- Emacs: https://emacsformacosx.com 

- Vim (macVim): https://github.com/macvim-dev/macvim 

X Another alternative is to install Xcode (it may be useful in the future).

- Open up the App Store application and search for ”Xcode - the suite of tools for developers”

- Agree to Xcode licence. Once Xcode is downloaded, open up the Terminal app and type:

sudo xcodebuild -license

- Hit spacebar a few times as directed and then type: ’agree’.

Windows

X You can use the default text editors in Windows: Notepad or Wordpad.

X Another recommended alternative is Notepad++. You can downloaded it from:

https://notepad-plus-plus.org/download/v7.3.html 

II How to install gfortran

GNU/Linux

X GNU/Linux should include by default the gfortran libraries. However, in case it is not installed,

open up the terminal and type:

sudo apt-get install gfortran

MacOS

X The ”GCC Wiki” implementation described in the following procedure is typically the newest

binary release of gfortran, but requires that you download a version appropriate for your architec-

ture.

I - Visit the GCC Wiki GFortranBinaries  page and scroll to the MacOS section.

II - Download gfortran-macosx-x86.dmg  (Intel) or gfortran-macosx-ppc.dmg  (PowerPC).

III - If your browser did not automatically mount the disk image, the double-click the dmg ﬁle to

mount and open it.

IV - Open the unmounted gfortran-macosx-{architecture}-{version} folder, double-click

gfortran.pkg, and follow the prompts to install it.

Windows

X Stand-alone gfortran binaries  for Windows are available as an installer  .

I - Download the installer, and run it.

II - Accept the GNU Public License, choose an directory to install gfortran, and let it work for you.

III - The installer sets your PATH environment variable, so that simply typing gfortran in a com-

mand prompt will run the compiler.

III How to install NetCDF libraries

GNU/Linux

X Alternative I - Use a package manager to download libraries

This approach is generally the easiest one provided you ﬁnd a library which was compiled with

the same compile you plan to use (gnu gfortran for example). Make sure you install development

libraries and Fortran interface libraries.

X Alternative II - Download the libraries from the source page

You can download the gzipped tar ﬁle with the source code from:

http://www.unidata.ucar.edu/downloads/netcdf/index.jsp 

To install it do the following. Untar the downloaded ﬁle and enter the directory with downloaded

code:

tar -xzf netcdf-3.6.3.tar.gz

cd netcdf-3.6.3

Choose a directory where you want to install NetCDF, say ”/opt/netcdf/3.6.3” (make sure that

directory above it exists and is writable to you). Make sure that Fortran compiler is installed and is

functional. Now, start the installation process. Inform the system which Fortran compiler you are

going to use

export FC=gfortran

Conﬁgure the package giving it the desired location for installation

./configure —prefix=/opt/netcdf/3.6.3

Compile and install the package

make

make install

III How to install NetCDF libraries

MacOS

Taken from http://mazamascience.com/WorkingWithData/?p=1474 

I - Install Xcode

Open up the App Store application and search for Xcode — the suite of tools for developers.

II - Agree to Xcode license

Once Xcode is downloaded, open up the Terminal app and type:

sudo xcodebuild -license

Hit spacebar a few times as directed and then type: ‘agree’.

III - Install MacPorts

Download the appropriate version of MacPorts from www.macports.org/install.php  . Then click on the

package to open up the package installer. After installation has ﬁnished you should close any Terminal

windows and open up a new one that will now be aware of the new port command. Try it out with:

port help

...

port info netcdf

IV - Install netcdf libraries and associated tools

Each of the following installations will automatically install any dependencies.

sudo port install netcdf

...

port port install ncview

V - Make sure you have X11

To install X11 just open the Utilities folder on your machine and click on the X11 icon. If X11 is not installed

you will be prompted to install it. This will take you to the https://xquartz.macosforge.org  where you

can download the disk image for the latest version of XQuartz.

Once the download is ﬁnished, double click on the XQuartz.dmg ﬁle and again on the XQuartz package and

walk through the installer. The last instruction is to log out and back in again.

III How to install NetCDF libraries

Windows

Instructions provided by Jimmy Thelander

I - Download MSYS2:

32 bit: http://repo.msys2.org/distrib/i686/msys2-i686-20161025.exe 

64 bit: http://repo.msys2.org/distrib/x86_64/msys2-x86_64-20161025.exe 

II - Install MSYS2

III - Start MSYS2

IV - Install compilers and dependencies

Type in the MSYS2 terminal (all in one line):

For 32-bit:

pacman -S mingw-w64-i686-gcc mingw-w64-i686-hdf5 gcc gcc-fortran tar zlib make

For 64-bit:

pacman -S mingw-w64-x86_64-gcc mingw-w64-x86_64-hdf5 gcc gcc-fortran tar zlib make

V - Download NetCDF

cd ~

wget ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.4.1.1.tar.gz

VI - Build netcdf (replace mingw64 with mingw32 if 32-bit system)

tar xfvz netcdf-4.4.1.1.tar.gz

cd netcdf-4.4.1.1

The following command goes in one single line:

LDFLAGS="-L/mingw64/lib" CFLAGS="-I/mingw64/include" CPPFLAGS="-I/mingw64/include"

./configure --prefix=/mingw64/

make

make install

VII - Download NetCDF-Fortran

cd ~

wget ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-4.4.4.tar.gz

VIII - Build NetCDF-Fortran (replace mingw64 with mingw32 if 32-bit system)

tar xfvz netcdf-fortran-4.4.4.tar.gz

cd netcdf-fortran-4.4.4

The following command goes in one single line:

LDFLAGS="-L/mingw64/lib" CFLAGS="-I/mingw64/include" CPPFLAGS="-I/mingw64/include"

./configure --prefix=/mingw64/

make

make install

IV How to connect remotely to a computer

GNU/Linux and MacOS

X Mac and Linux come with SSH clients that can help connecting to remote servers. However, X11

(the graphical user interface) is no longer included with OS X. X11 server and client libraries for

OS X are available from the XQuartz project (http://xquartz.macosforge.org  ).

I - Login by typing

ssh -XY <userid>@<hostname> <press enter>

<remote_password> <press enter>

Windows

X Both SSH and the graphical user interface X11 are not included by default in Windows. There are

many options available but in this guide we will present how to install PuTTY. PuTTY is a free

implementation of Telnet and SSH for Windows, along with a xterm terminal emulator:

I - Download and install XMing:

http://sourceforge.net/projects/xming/ 

Select Multiple Windows and type the number 0 for Display number.

II - Download and install PuTTY:

https://the.earth.li/ sgtatham/putty/latest/x86/putty.exe 

After you have downloaded the installer for Windows, run it, and follow through the steps.

Unless you know what you are doing, stick with the default installation options. After download

completes, you are done with the installation.

To connect to a remote server using PuTTY, provide the hostname of the remote server and

the port number on which the SSH server is listening. The default port is 22. Make sure the

connection type is ssh.

III - Conﬁgure the X11 forwarding.

Scroll to Connection > SSH > X11. Check the box next to Enable X11 Forwarding. By

default the X Display location is empty. You can enter localhost:0. The remote authentication

should be set to MIT-Magic-Cookie-1.

IV - Login to the remote server

Go back to Session. Click Open to bring up the terminal and login using your userid/password.

V How to install Canopy-python

Instructions taken from http://docs.enthought.com/canopy/quick-start 

GNU/Linux

I - Download Canopy:

Canopy 2.7 for LINUX: https://store.enthought.com/downloads/installer/74/ 

II - Install Canopy

Open the terminal and type the following commands:

cd ~/Downloads

bash canopy-2.0.0-rh5-64.sh

III - Launch Canopy

Canopy can be launched by executing the following command in the terminal:

~/Canopy/canopy

MacOS

I - Download Canopy:

Canopy 2.7 for MacOS: https://store.enthought.com/downloads/installer/70/ 

II - Install Canopy

The Mac OSX version of Canopy is distributed as a disk image (.dmg) ﬁle. Opening this ﬁle displays the

installation window shown below. Canopy can be installed by dragging the Canopy icon to the Applications

folder in the window, to the computer Desktop, or to another folder. If you drag it to the Applications

folder, it will show as “Canopy” along with your other applications.

Windows

I - Download Canopy:

32 bit: https://store.enthought.com/downloads/installer/78/ 

64 bit: https://store.enthought.com/downloads/installer/82/ 

II - Install Canopy

To start the installer, double-click the downloaded ﬁle. Verify that the publisher is listed as Enthought, Inc.

and click Run.

Environment Setup for all OS:

When Canopy is launched for the ﬁrst time, it will automatically conﬁgure your Python environment in the default location unless

speciﬁed otherwise by a command-line option or a preference setting.

V How to install Canopy-python

NOTE: Make sure you have the following Python Packages installed in the Canopy after installation

1. NumPy

2. SciPy

3. matplotlib

4. Basemap

5. netCDF4

6. Pandas

7. TkInter

8. Jupyter

Installing packages in Canopy for all OS:

In the editor window of Canopy, go to Tools>Package Manager. A new window will pop-up, you can search

the desired package here and then just click on install. The majority of the packages listed above are already

installed by default.