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MCX19 Laptop Preparation instructions

1.1. Laptop requirements
1.2. MCX software download and preparation
1.3. Test MCXCL in MCXStudio
1.4. Run a trial MCXCL simulation in MCXStudio
1.5. Configure MATLAB

In this workshop, we will use MCXCL (MCX-OpenCL) as the primary tool to teach our participants how to use our software. MCXCL can be executed on a wide range of CPUs and GPUs), therefore, we expect that every participant should be able to complete the training using only his/her own laptop.

1.1. Laptop requirements

Before coming to the workshop, we strongly encourage all participants preparing your laptop and make sure they can run our software. The requirements to the laptop is quite minimal - as long as you have an Intel CPU (preferably, newer than 4-th generation) or an AMD CPU made over the past 4 years, you will be able to run our software. Although, if you have access to a laptop with a discrete NVIDIA or AMD GPU, that will make the simulation much faster, but it is not required.

On the software side, your laptop must have

  1. a pre-installed MATLAB (if you do not have a license, you can get a trial version)
  2. the latest graphics (or GPU) driver. we assume you have a working graphics system (that can display 3D graphics), if your graphics is not working, please install the latest driver from the vendor's website

You DO NOT need to install CUDA run-time or other special libraries. Our software will contain all needed libraries.

1.2. MCX software download and preparation

We provided precompiled, ready-to-use packages for 64bit Linux, Windows and Mac OSX. You must download the latest all-in-one package - MCXStudio-*-nightlybuild.zip from our website

http://mcx.space/nightly/MCX19/

and unzip the all-in-one package to a directory - for example, you can unzip the package to Documents/MCXStudio/. We refer to this unzipped package top folder as the "<Root>" folder.

Special instructions for Windows

For Windows users, you need to navigate to the "<Root>/MCXSuite/mcx/setup/win64/" folder in the File Browser, and right-click on the "apply_timeout_registry_fix.bat" file, and select "Run as administrator". This will apply a patch to let your computer run MCX for more than 2 seconds. Once the patch is applied, you MUST REBOOT your laptop to activate the setting.

Special instructions for Mac

For Mac users, you need to open a terminal, cd the <Root> folder, and run

 xattr -dr com.apple.quarantine .

in the terminal. Otherwise, when you double click on the mcxstudio application, you will get an error.

1.3. Test MCXCL in MCXStudio

The next step of the preparation is to test a couple of MCXCL simulations in MCXStudio - a graphical user interface for MCX.

To start MCXStudio, go to the <Root> folder and double click on "mcxstudio.exe" (for Windows), "mcxstudio" (for Linux) or "mcxstudio" with a red-icon on the Mac.

You should see a the MCXStudio main window displayed. At the bottom of the window, you should see a line like

  EXEPATH=<Root>/MCXSuite/mcx/bin/mcx

where <Root> will be replaced by the actual local folder name.

To do a test, you need to

  1. click on the "New" button on the toolbar,
  2. select the 3rd option - "NVIDIA/AMD/Intel CPUs/GPUs (MCX-CL)",
  3. then type "test" in the session name,
  4. click OK,
  5. then click the "GPU" icon on the toolbar

Now, in the output area located at the bottom of the window, you should see at least 1 CPU or GPU information is printed. If you see any missing files or errors, you may have a partially installed driver or MCXStudio package. Please contact Dr. Fang for further help.

1.4. Run a trial MCXCL simulation in MCXStudio

If you can see a CPU or GPU is listed, you can simply select one of the listed CPU/GPU from the GPU settings\Run MCX on section, by checking the desired device. Then, you should click the "Validate" button on the toolbar. Then click "OK". This will start a default simulation with 10^6 photons. If everything goes well, you should see outputs in the Output area below. This simulation should typically be done within 5-20 seconds (depends on your device). If anything prevents the simulation to be completed, you should see an error message.

If the trial simulation completes without an error, you should now be able to plot the results. You should click on the "Plot" icon on the toolbar, and select "Plot fluence (mc2)". A volumetric rendering of the generated fluence map should be displayed.

1.5. Configure MATLAB

THe last step of the preparation is to

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