How to prepare your laptop for the upcoming MCX workshop

To participate the MCX training workshop, you need to bring a laptop (Windows, Linux or Mac). In addition, a set of software tools are needed to run simulations on our servers or on your own laptop. The below instructions describe the steps to prepare your laptop for this event.

We strongly recommend you to configure and test your laptop before the event to avoid delays. We will also hold a 2-hour session on Aug. 7 (Monday) between 4-6PM in ISEC RM 232 (second floor of 805 Columbus Ave, Boston) to troubleshoot issues when setting up the software on your laptop. If you have difficulty installing the tools based on the below instructions, please email the organizer or stop by ISEC on Monday afternoon.

1. Step 1. Install X2go, a remote desktop for accessing GPU servers
2. Step 2. Modify system search path to use X2go utilities
3. Step 3. Download MCXTraining software package
4. Step 4. Configure MATLAB and add paths to MCX tools
5. Step 5. Installing GNU Octave
6. Step 6. Configure Octave and add paths to MCX tools
7. Step 7. Add MATLAB and Octave's executable path to you system search path

Video tutorial can be found here and Part 2.

1. Step 1. Install X2go, a remote desktop for accessing GPU servers

  1. Download and install x2go client from this link. Choose the file for your OS
  2. Once installed, start x2go by double-clicking on the icon
  3. Create a new session. In the Session tab, type the assigned remote desktop server name, username, and set XFCE as the session type; in the Connection tab, set compression method to "16m-png-jpeg" and compression level 7; in the Media tab, disable "Sound" and "Client side printing"
  4. Click on the session created, and type in the assigned username and password (will be sent in an email before the event).
  5. Once login the remote server, click on the "MCX Studio" icon, and test if you can see the GUI.

The procedures are similar for Linux, Windows and Mac. If you use Ubuntu Linux, you can install x2go client using the below command 

 sudo apt-get install x2goclient

2. Step 2. Modify system search path to use X2go utilities

For Windows computers

  1. Type "environment" in the start-menu, and click on "Edit environment variable for your account"
  2. Double click on the "Path" variable, if does not exist, create it
  3. Click on "New" to add a new path, browse the folder containing x2goclient utilities; if you use default settings, this path is "C:\Program Files (x86)\x2goclient"
  4. Save your path settings;
  5. To verify, open the command window by typing "cmd" in the start-up menu; in the command window, type "plink" or "pscp" and type enter, you should see help info; if not, your path is not set correctly.

For Linux and Mac

open a terminal, and type "ssh" and enter, if you see the help info, you don't need to do anything; also type "scp" followed by enter, you should also see help info printed. By default, these utilities are already installed.

3. Step 3. Download MCXTraining software package

  1. Please browse this link to download the MCXTraining.zip package for your operating system; 3 operating systems are supported.
    1. For 64bit Windows, click on this link,
    2. For 64bit Linux (Ubuntu), click on this link,
    3. For 64bit Mac with Intel processors, click on this link.
  2. Once you download the package, unzip it to your home directory under a workfolder. For Windows users, the recommended location is inside the Documents folder in your home folder (C:\Users\my_account\Documents\).

4. Step 4. Configure MATLAB and add paths to MCX tools

We assume you have already installed MATLAB in your system. Please open MATLAB, and type the below two commands 

 addpath(genpath('/path/to/MCXTraining/Software'));
 savepath;

For example, if you use Windows, and the MCXTraining folder were extracted under your Documents directory, you should type 

 addpath(genpath('C:\Users\my_account\Documents\MCXTraining\Software'));
 savepath;

Alternatively, you can type "pathtool", and add all subfolders to MCXTraining to MATLAB using the GUI. See our tutorials for details.

To verify, please type 

 help mcxlab
 help mmclab
 help s2m

any one of the commands should output the corresponding help info.

5. Step 5. Installing GNU Octave

If you don't have MATLAB, Steps 5 and 6 are required if you want to use the plotting feature (this feature is experimental).

An optional component is the GNU Octave - an open-source clone of MATLAB. You can download and install the latest version from this link. Version 4.0 or newer is required.

For Ubuntu Linux, you may install the v4.0 octave by using the following commands: 

  sudo add-apt-repository ppa:octave/stable
  sudo apt-get update
  sudo apt-get install octave

6. Step 6. Configure Octave and add paths to MCX tools

You need to follow the same commands as in Step 4 to add MCX utility paths to Octave. See preparation tutorial part 2 for details.

7. Step 7. Add MATLAB and Octave's executable path to you system search path

For Windows

Following the same steps as Step 2, you should add the path containing matlab.exe and octave.exe to your system Path variable. Typically, you can find matlab.exe under "C:\Program Files\MATLAB\RXXXXx\bin" folder; and for Octave, the typical path is "C:\Octave\Octave-X.X.X\bin" where XXX represents the installed version.

For Linux and Mac

type matlab or octave in your terminal, if you see matlab and octave windows, the path has already been added. No need to do anything.
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