OS-X Mavericks for Scientific Computing

My Macbook Pro (Early 2011) running Snow Leopard was starting to get a little slow, so I decided to upgrade it with a 250Gb SSD, and use the opportunity of an empty disk to give a chance to OS-X Mavericks.
In this post, I am going to explain step by step how did I set up my laptop with Mavericks and some extra tools for enabling scientific computing and computational chemistry tasks.

First of all, I bought an SSD (Samsung SSD 840 ~140 €), a 2.5″ HD case for using the old 500Gb/5400 rpm hard disk as an external drive (~5 €) and a USB Flash drive (16Gb, because it was the cheapest option ~12€), for creating a bootable drive, in order to perform a clean install (not upgrade).

Creating the bootable drive was a little bit tricky, because most common option using “createinstallmedia” didn’t work for me. So I used an alternative procedure described here.

Once the bootable drive was created, I opened the back cover of my laptop and replaced the old HD with the SSD. At this point, the laptop was clean an ready to start the installation of OS-X Mavericks.

This are the steps I followed:

    • Turn on the laptop while holding the “option” key
    • Agree the terms of the license
    • Chose the disk for the installation

At this point, I noticed that there was no available disk, because as opposed to most of Gnu/Linux installers which display all the available (formatted and unformatted) disks, this one only displays the formatted ones, and as my new SSD was unformatted, there was nothing to chose. <br>
Fortunately, this issue can be easily solved by going to the menu on the top, and chosing “Utilities>Disk Utility” and once there, chose the SSD disk (or the one we want to install the OS in), go to the “Partition” tab, chose “Partition Layout” to 1, chose a name (i.e. local), format (i.e. Mac OS Extended) and apply changes. <br>
Now the disk will appear in the available disks list, so just click on it and the installation will begin and last for some 23 minutes. After that, the system will restart.

  • Once the computer restarts, it will ask us the typical questions about Country, Keyboard, WIFI/LAN network, syncronize information from other accounts (HDs), license agreement again, and finally create a user and password. All this tasks were completed in my laptop after 28 minutes.

The laptop is now up and successfully running OS-X Mavericks. Now we have to customize it a little bit.
Well… I won’t go through all the typical apps for non-scientific tasks (Firefox, Skype, …) because if you are reading this post, you know very well how to do that 😉

Next step is to install Xcode, which can be downloaded from Apple’s App store, but once again, as it happened before while trying to download Mavericks, for some reason, it didn’t not work for me. I do have an Apple ID which works fine with iTunes, but for some reason, when I enter it on the app store, it gets into an infinite loop after clicking on “Sign In” and does not allow me to go further. It does not give any error, and I don’t know how to track it. This is one of the things I really don’t like proprietary software.

The alternative to App store, is downloading the Xcode directly from the apple developer site:
https://developer.apple.com/downloads/index.action. (You still need an Apple ID to log in)

Once the Download is completed, install the package on the Applications folder and execute it to run the installer. Finally enable it on the terminal by typing “xcode-select --install” on a terminal and agree the license.
Xcode is now ready.

Next very useful tool is macports, which enables Gnu/Linux-like command-line installation of thousands of valuable open source packages together with their dependencies.
It can be downloaded from here. Installation is performed by simply opening the installer and following the default steps.

From now on, we can install tons of packages by typing “port search PACKAGE” and “port install PACKAGE” as root (or adding “sudo” at the beginning of the command).

My personal choice is:
port install MacVim py27-scipy ssh pssh gromacs jmol mplayer2 openssh htop

Macports apparently doesn’t include any good gfortran package (I didn’t found any full package), so I downloaded and installed the one from CRAN, from this link.

I use Latex for writing documents and articles, and this one can be installed also through macports, but in this case, I chose to install it with the Mactex package, available for download here.