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MegaMol Manual

Contents


Overview

MegaMol is a visualization middleware used to visualize point-based molecular datasets. The MegaMol project was started in the Collaborative Research Center 716, subproject D.3, at the Visualization Research Center (VISUS), University of Stuttgart, Germany. Today, it is governed by a number of teams at the TU Dresden and the University of Stuttgart.

The goal of the project is to provide a software base for visualization research and to provide a stable environment to deploy newest visualization prototypes to application domain researchers. MegaMol is not a visualization tool. MegaMol is a platform for visualization research. Visit the project website for downloads and more information.

If you faced any trouble during installation or if you have any further questions concerning MegaMol, we encourage you to contact the developer team by opening an issue on github!


Installation and Setup

This chapter discusses installation and setup of MegaMol from source code. MegaMol targets Microsoft Windows (Windows 7 or newer, x64) and Linux (x64) as supported environments. Currently, Ubuntu is used as Linux distribution for development. Further platforms are not considered during the development. While MegaMol might work on further platforms, the development team will currently not grant any support for problems with these environments.

Building from Source

It is recommended to use the latest release 1.3 version of the source code. All bleeding edge features are available in the current main branch.

Note: The OSPRay plugin is currently disabled by default. See the plugins' readme for additional instructions on how to enable it.

Microsoft Windows

  1. Download and unzip the source code of the latest release into a new directory (e.g. megamol).
  2. You have to install CMake, and load the CMakeLists.txt present in the root directory of the repository.
  3. Create a new build directory.
  4. As generator, it is recommended to use the latest version of Visual Studio (Community Edition is free to use) with default native compilers and for the platform x64.
  5. Next, click Configure a few times (until all red entries disappear).
  6. Change the CMAKE_INSTALL_PREFIX in order to change the destination directory of the installed files and configure once more.
  7. Then click Generate to generate the build files.
  8. The configuration creates a megamol.sln file inside the build directory.
  9. Open the megamol.sln file with Visual Studio.
  10. Use the ALL_BUILD target to build MegaMol.
  11. Afterwards, use the INSTALL target to create your MegaMol installation.
  12. The binary megamol.exe is located in the default installation path ../megamol/build/install/bin.

CMake Windows Screenshot of cmake-gui after generating build files.

Linux (Ubuntu)

Since the full support of some C++17 functionality is required (e.g. std::filesystem), a gcc version equal or greater than 8 is required (with CMAKE_CXX_FLAGS appended by --std=c++17). Latest tested version:

$ cat /proc/version
Linux version 5.8.0-41-generic (buildd@lgw01-amd64-003) (gcc (Ubuntu 9.3.0-17ubuntu1~20.04) 9.3.0, GNU ld (GNU Binutils for Ubuntu) 2.34) #46~20.04.1-Ubuntu SMP Mon Jan 18 17:52:23 UTC 2021
  1. As prerequisites, following packages from the repository are required:

    $ sudo apt install cmake-curses-gui git libgl1-mesa-dev libncurses5-dev uuid-dev libexpat-dev libunwind-dev libxrandr-dev libxinerama-dev libxcursor-dev libxi-dev libglu1-mesa-dev

  2. First, download the source code from GitHub:

    $ mkdir megamol $ git clone https://github.com/UniStuttgart-VISUS/megamol.git megamol/ $ cd megamol/

  3. Checkout the latest release:

    $ git checkout tags/v1.3 -b latest_release

  4. Create a build directory and switch to it:

    $ mkdir build; cd build

  5. Check for required dependencies:

    $ cmake ..

  6. Start the ncurses gui for cmake:

    $ ccmake .

    • Configure the project repeatedly using c (and e) until no more changes are marked.
    • Change the CMAKE_INSTALL_PREFIX in order to change the destination directory of the installed files.
    • Then hit g to generate the build files.
  7. On the console prompt, start the building:

    $ make && make install

    • Hint: Use the -j option for make to run the build in parallel threads.
  8. The binary megamol is located in the default installation path ../megamol/build/install/bin.

Command Line Arguments

Providing additional command line arguments allow individual configuration of global MegaMol behavior and settings.

The following command line arguments are available:

Note: The khrdebug option is currently ignored and not applied.

    megamol.exe [OPTION...] <additional project files>

      --host arg      address of lua host server, default:
                      tcp://127.0.0.1:33333
      --example       load minimal test spheres example project
      --khrdebug      enable OpenGL KHR debug messages
      --vsync         enable VSync in OpenGL window
      --window arg    set the window size and position, accepted format:
                      WIDTHxHEIGHT[+POSX+POSY]
      --fullscreen    open maximized window
      --nodecoration  open window without decorations
      --topmost       open window that stays on top of all others
      --nocursor      do not show mouse cursor inside window
      --help          print help

Configuration File

After successfully compiling and installing MegaMol, you should have all executable files inside your bin directory (default: ../megamol/build/install/bin).

In the bin directory, you can find the default configuration file megamolconfig.lua:

    -- Standard MegaMol Configuration File --
    print("Standard MegaMol Configuration:")

    basePath = "C:/megamol/build/install/"

    mmSetLogLevel("*") -- LogLevel: None=0,Error=1,Warn=100,INFO=200,ALL=*
    mmSetEchoLevel("*")
    -- mmSetLogFile("") 
    mmSetAppDir(basePath .. "bin")
    mmAddShaderDir(basePath .. "share/shaders")
    mmAddResourceDir(basePath .. "share/shaders")
    mmAddResourceDir(basePath .. "share/resources")
    mmPluginLoaderInfo(basePath .. "bin", "*.mmplg", "include")

    computer = mmGetMachineName()

    mmSetConfigValue("*-window",    "x5y35w1280h720")
    mmSetConfigValue("consolegui",  "on")
    mmSetConfigValue("topmost",     "off")
    mmSetConfigValue("fullscreen",  "off")
    mmSetConfigValue("vsync",       "off")
    mmSetConfigValue("useKHRdebug", "off")
    mmSetConfigValue("arcball",     "off")

The following paragraphs explain the essential steps of configuring MegaMol in more detail.

General Settings

Locate line 3 containing the variable basePath. Both relative and absolute path should work here fine. This path is set automatically and always has to fit the currently used execution path!

    basePath = "C:/megamol/build/install/"  

Logging

Line 4-6 configures the logging mechanism of MegaMol. Adjusting the value of EchoLevel changes the amount of log information printed on the console. Specifying a log file and the level informs MegaMol to write a log file and print the messages of the requested level into that file. The LogLevel is a numeric value. All messages with lower numeric values will be printed (or saved). The asterisk * stands for the highest numeric value, thus printing all messages.

    mmSetLogLevel('*') -- LogLevel: None=0,Error=1,Warn=100,INFO=200,ALL=*
    mmSetEchoLevel('*')
    -- mmSetLogFile("") 

Application, Shaders and Resources

Line 7-10 define the application, shader and resource directories:

    mmSetAppDir(basePath .. "bin")  
    mmAddShaderDir(basePath .. "share/shaders")
    mmAddResourceDir(basePath .. "share/shaders")
    mmAddResourceDir(basePath .. "share/resources")

The Add...Dir commands set the paths for the respective resources.

Plugins

Since we switched to static linking of plugin libraries into the MegaMol binary, the configuration of mmPluginLoaderInfo is DEPRECATED and no longer required.

Global Settings

The configuration file also specifies global settings variables which can modify the behavior of different modules.

  • The following settings variable activates (or deactivates) the arcball (orbiting) camera behavior. Set this option to on in order to use the arcball camera navigation.
    mmSetConfigValue("arcball",     "off")

All other configuration options are DEPRECATED and have currently no effect!

This concludes the information on building and the options on how to configure MegaMol. Test your installation following the description in the following section.


Test Installation

In order to test the installation, simply run the frontend executable.
Open a console (e.g Linux Terminal or Windows Powershell) and change your working directory to the MegaMol install directory containing the bin folder (default: ../megamol/build/install/bin) and execute the MegaMol binary:

Windows:

    > megamol.exe

Linux:

    $ ./megamol

If additional external libraries are required (e.g. when using the OSPRay plugin), for Linux you have to run the provided shell script ./megamol.sh instead. This script adds the required library path:

    #!/bin/bash
    #
    # MegaMol startup script
    # Copyright 2020, https://megamol.org/
    #

    BIN_DIR=$(dirname "$(readlink -f "${BASH_SOURCE[0]}")")
    cd "$BIN_DIR"

    LD_LIBRARY_PATH=../lib:$LD_LIBRARY_PATH ./megamol "$@"

MegaMol should start and print several messages to the console and an empty rendering window should appear. You can either check the console log messages or the messages printed in the Log Console window. The leading number of each line is the log level. There should be no error messages (log level 1). Some warnings (log level 100) might occur but are normal and indicate no failed installation or execution.

Examples

The example project script files are automatically available in the examples directory, which is installed next to the bin directory.

For a better test, you should invoke MegaMol loading an example project script requesting a simple rendering. Then you can be sure that the graphics drivers, graphics libraries, and shader codes are correctly found and are working. To do this, try:

Linux:

$ ./megamol ../examples/testspheres_megamol.lua

Windows:

> megamol.exe ..\examples\testspheres_megamol.lua

MegaMol should now open a rendering window showing a generated dataset with several colored spheres and the outline of the bounding box. Hitting the space key starts and stops the animation playback. In the GUI window Parameters you can find all available parameters of the running MegaMol instance grouped by the modules. For example, you can find the parameter speed in the group inst::view::anim. With this parameter, you can adjust the playback speed of the animation. In the parameter group anim of the view module you can adjust the animation speed.

Alternatively, you can also open an empty MegaMol rendering window and load the above example project script file via the menu File / Load Project.

All available options provided via the graphical user interface are described separately in the readme file of the GUI plugin.

Test Project Screenshot of MegaMol running the test spheres instance.


MegaMol Graph

In this chapter, we show the operating principle of MegaMol which is required to creating own custom projects for MegaMol.

Modules, Views and Calls

The runtime functionality of MegaMol is constructed by modules and calls. These two types of objects are instantiated at runtime, interconnected and build the module call graph. The figure given below, shows an example module call graph containing a view, the rendering content of a window, a renderer, a data source, and some modules providing additional information for the renderer. The modules are interconnected by the call objects. The connection endpoints at the modules are CallerSlots (outgoing, located on the right side of modules) or CalleeSlots (incoming, located on the left side of modules) shown as circled dots.

The module call graph follows the pull pattern. This means that modules request function invocation by other modules. For example, the view module needs to update the window content. The view module thus invokes the renderer module to provide a new rendering. The renderer calls the data source if new data is available or to provide the old cached data.

Left-most module view of class View3D_2 represents the rendering content of a window. The center module renderer of class BoundingBoxRenderer and SphererRenderer are called subsequently by the window using the corresponding call of type CallRenderer3D_2. The right modules provide data and additional information for the renderer, namely a color map transfer function and a clipping plane.

Example Graph

Example module call graph.

Modules and Calls

Modules are the functional entities of MegaMol. They provide several programmatic access points, the slots. Two types of these slots are shown in the above figure of an example graph as circled dots.

CalleeSlots are access points of modules, through which these can be called to perform a function. For example, modules of class SphererRenderer provide a CalleeSlot rendering through which the rendering function can be invoked. The counterparts are CallerSlots which are outgoing access points. These allow modules to call other modules. View modules of class View3D_2 provide a corresponding slot rendering to call a connected renderer. These two types of slots are connected using objects of call classes. Both CalleeSlots and CallerSlots specify types of calls they are compatible with. In the case of the above examples of renderings-relates slots, this is the type CallRender3D_2.

Calls should be lightweight. They are thin interfaces meant for data transport. For example, data to be visualized is loaded by data source modules. In the example graph figure the module data of class MMPLDDataSource loads a specified data set into main memory and provides the data through its CalleeSlot. The data is accessed through a MultiParticleDataCall. The call, however, does not copy the data but provides access to the data in terms of memory pointers, and metadata. This avoidance of copy operations is most important and one of the core design ideas of MegaMol.

Parameter Slots are the third type of slots. These are access points to exposed parameters controlling the functionality. Such parameters are automatically included in the frontend’s GUI. An example of such parameters is the setup of the virtual camera in modules of type View3D_2 or the dataset file name in data source modules.

The module call graph is configured for MegaMol using a project file. These files define modules and interconnecting calls for different instance specifications.

Views

Views are one of the two instance types MegaMol can run. They are specified by the corresponding tag in a MegaMol project file (see section Project Files). When a view is instantiated, a corresponding namespace will be created, and all modules instantiated as part of the view will be created inside this namespace.

View Interaction

The primary interaction with a view is controlling the camera with mouse and keyboard. The keyboard mapping is implemented by button parameters of the view module, also available in the GUI. Most parameters can be found in the sub-namespace viewKey inside the view name, e.g. RotLeft. The corresponding parameter button in the GUI also shows the associated hotkey. In the configuration file megamolconfig.lua the camera behaviour can be change be switching the arcball option on or off.

Some useful controls assuming the arcball option is set to on:

  • Hitting Home (aka Pos1) is associated with the button resetView. This function resets the view to default.
  • Hold the Left Mouse Button and move your mouse to rotate the view around the look-at point. The look-at point initially is placed in the center of the bounding box of the data set.
  • Hold Shift while holding and dragging the Left Mouse Button rolls the camera around the viewing direction.
  • Hold Control while holding and dragging the Left Mouse Button rotates the camera around its center point.
  • Hold Alt while holding and dragging the Left Mouse Button moves the camera orthogonally to the viewing direction.
  • Hold the Middle Mouse Button and move your mouse up or down to zoom the view by move the camera forwards or backwards. Note that if you zoom in too much, parts of the data set will be clipped by the near-clipping plane.
  • Hold Alt while holding and dragging the Middle Mouse Button zoom the view by changing the opening angle of the camera.
  • Hold Control while holding and dragging the Middle Mouse Button moves the look-at point forwards or backwards, changing the center of the corresponding rotation. Use the parameter showLookAt of the view to visualize the look-at point for better adjustment.

Project Files

Project files are lua scripts using special custom functions to define any module graph for MegaMol. Some predefined example project script files are available in the examples directory, which is installed next to the bin directory. Here you can see the example project script ..\examples\testspheres_megamol.lua:

    mmCreateView("testspheres", "View3D_2","::view")

    mmCreateModule("BoundingBoxRenderer","::bbox")
    mmCreateModule("DistantLight","::distantlight")
    mmCreateModule("SphereRenderer","::renderer")
    mmCreateModule("TestSpheresDataSource", "::data")

    mmSetParamValue("::renderer::renderMode", [=[Simple]=])

    mmCreateCall("CallRender3D_2", "::view::rendering", "::bbox::rendering")
    mmCreateCall("CallRender3D_2","::bbox::chainRendering","::renderer::rendering")
    mmCreateCall("MultiParticleDataCall", "::renderer::getData", "::data::getData")
    mmCreateCall("CallLight","::renderer::lights","::distantlight::deployLightSlot")

Project files can easily be created using the built in Configurator. It can be opened via the menu Windows / Configurator. You can either edit the currently running MegaMol graph (which might be empty) or you can create a new project starting a module graph by adding the main view module View3D_2. A detailed description of the configurator can be found in the readme file of the GUI plugin.


Making High-Resolution Screenshots

GUI

The GUI menu option Screenshot (hotkey F2) provides a basic screenshot functionality using the current viewport size. If screenshots are taken consecutively, the given file name is prepended by an incrementing suffix. This way, no new file name has to be set after each screenshot.

Project File

Within the LUA project file a screenshot can be triggered using the command mmScreenShot("screenshot_filename.png").

The following example shows how to take screenshots of various time steps:

for i=0,1 do
    mmSetParamValue("::View3D_2_1::anim::time", tostring(i))
    mmRenderNextFrame()
    mmScreenShot("screenshot_timestep_" .. string.format("%04d",i) .. ".png")
end

Framebuffer Size

The actual framebuffer size to use for a screenshot can be set in the following ways:

LUA Project File: mmSetFramebufferSize(width, height)
e.g. mmSetFramebufferSize(100, 100).

CLI Option: --window wxh+x+y
e.g. ./megamol.sh --window 100x100 for a window of size 100 x 100 pixels. Also see help output: ./megamol.sh -h

ScreenShooter Module

Offering more flexible options and special functions to create high-resolution screenshots of any rendering, you can add the ScreenShooter module to you project. The corresponding settings can be found in the modules parameters provided in the GUI (see figure of ScreenShooter parameters below).

In order to connect the ScreenShooter with your view, you need to set the module name of your view module in the corresponding variable ::screenshooter::view (e.g. to ::View3D_2_1). When making single screenshots, set the option makeAnim in the group ::screenshooter::anim to disabled, as shown in the figure. Ignore the remaining options in that group. These options will be explained in section Making Simple Videos, as they are used to produce videos.

The parameters imgWidth and imgHeight specify the size of the screenshot to be rendered. These values are not limited to the window size and can be, in theory, arbitrarily large. If these values are getting large, the image can be rendered in several tiles, i.e., sub-images. The size for these tiles is specified by tileWidth and tileHeight. However, many renderers have problems with producing these tiled images. It is, thus, recommended to set tileWidth and tileHeight to be at least as large as imgWidth and imgHeight. The values for tileWidth and tileHeight are limited by the maximum texture size, maximum frame buffer object size and graphics memory size of your graphics card. Thus, these values are often limited. The parameter file name specifies the path to the image file to be created. MegaMol only creates PNG files. Hit the button trigger to have MegaMol create the requested screenshot.

ScreenShooter


Making Simple Videos

MegaMol cannot create video files directly. However, MegaMol can create a sequence of screenshots of a time-dependent data set showing the different points-in-time. This functionality is provided and further described in the Cinematic plugin.


Reproducibility

MegaMol stores the active project and all parameter settings in the EXIF field of the saved screenshots. Please note that this field currently contains a simple zero-terminated string with the LUA code required to reproduce the state when the screenshot is taken, and not valid EXIF data. Such a project can be restored by simply loading the PNG file:

$ megamol.exe <something>.png

Also note that only Views with direct access to camera parameters (like View3D_2) can be properly restored.