Once again, I had fun.
I had a nice opportunity to visit academia again. Colleagues from the old times at the university were organizing a workshop at this years EGEV 2020, the VisGap 2020 — The Gap between Visualization Research and Visualization Software — and they invited me to give a cap stone presentation. I was honored by the invite, and luckily, my company agreed to my participation as well.
Now, with our current COVID-19 situation, the conference and the workshop did not take place in Norrköping in Sweden as planned. Instead the whole conference and all workshops were converted to virtual events. As a result attendance was free. And, all sessions are freely available on YouTube. So, if you like to see my talk, be my guest:
Each year at the renowned international conference for visualization, the IEEE VIS, the so called SciVis Contest takes place. This year, we, the staff of the Computer Graphics and Visualisation Group of the TU Dresden, together with colleagues from the Visualization Research Centre of the University of Stuttgart, have won the contest.
With the SciVis Contest the visualization community can confront themselves with challenging visual analysis tasks on real data scenarios. This year’s contest asked questions about large ensemble data sets of chemical processes of salt dissolution, namely the appearance and influence of viscous fingers. The entry by TU Dresden was deemed being the most wholesome and versatile solution, and thus gained the winning edge over its competitors.
GPU-based interactive Visualization of Large Particle Data
At the end of October, the largest conference on scientific visualization – the IEEE VIS 2015 – took place in Chicago. This is an anual venue for experts from all over the world to present current research and discuss future challenges. With more than 1100 participants, the conference is considered the largest and most important international forum in this domain.
This year, Michael Krone and Guido Reina from the group of Prof. Ertl, together with Sebastian Grottel (TU Dresden) and Martin Falk (Linköping University, Sweden) organized a tutorial on interactive GPU-based Visualization of large particle data. They explained the technical aspects for ensuring high quality and interactivity of particle visualizaton, which are nowadays accepted as state of the art. Part of these techniques have been developed in the SFB716. Additionally, the presentation included details on abstractions required by continuosly growing data sets. Such abstractions were disucssed in the context of biomolecules and material surfaces as well as in the context of whole cell visualization.
The tutorial was very well received with over 50 participants. The course materials distributed there, including slides, source code and example data sets can be downloaded here.
The IEEE VIS 2015 reached its end. And she was great once again. Good papers, good ideas, and good people to meet. It really was worth it.
My own tutorial was a big success, too. We had a much bigger audience than anticipated, and we received a whole lot of very positive feedback. I am very pleased.
And tired. Such a conference is always exhausting. And I do not have the time to relax yet. The next projects are already waiting.
Most new data sets for my scientific visualization find their way to my desk in form of arbitrarily structures text files. This is not really a problem. The first sensible step is converting them into a fast binary format for the visual analysis. With this, however, I face the problem of understanding the structure of 11 Gigabytes text files (no exaggeration here!). But, such files do have structure. So, only the few first and few last lines really matter. The bits in-between will be roughly the same way. What I need are the Linux-known commands “head” and “tail”. However, I am a Windows guy. So? The Powershell comes to the rescue:
gc log.txt | select -first 10 # head
gc log.txt | select -last 10 # tail
I found these on: http://stackoverflow.com/a/9682594 (where else)
At least the “head” version was fast and sufficient for me. I am happy.
We updated MegaMol to use cmake to build on Linux OS. This greatly improved the build process on Linux. But this also makes some more uncommon scenarios difficult to realize. For example, cmake usually automatically detects required dependencies. But, in some scenarios you need to override this magic.
In this article I show how to compile a second MegaMol on a system on which a MegaMol already has been compiled and installed. This is useful when working with experimental versions.
VISlib and visglut
First off you build the visglut the usual way. I assume here, that the installed MegaMol uses a different visglut as the one you want to build now:
mkdir megamol_x2 cd megamol_x2 svn co https://svn.vis.uni-stuttgart.de/utilities/visglut/tags/forMegaMol11 visglut cd visglut/build_linux_make make
If everything worked you can find the following files:
GL/freeglut_ext.h GL/freeglut.h GL/freeglut_std.h GL/glut.h visglut.h visglutversion.h
and in megamol_x2/visglut/lib:
If so, let’s continue with the VISlib:
cd megamol_x2 svn co https://svn.vis.uni-stuttgart.de/utilities/vislib/tags/release_2_0 vislib cd vislib
Now, there is the first action which is different from the default build process. As usual we will use the script cmake_build.sh. This script, however, per default registers the build directories in the cmake package registry. This enables cmake to find this package in its build trees. In this scenario, however, we do not want this special build to be automatically found, because we do not want to get in the way of our system-installed MegaMol. We thus deactivate the package registry.
This command configures and builds the VISlib, both for debug and release version:
As always, if you encounter build problems due to the multi-job make, reduce the number of compile jobs:
./cmake_build.she -dcmnj 1
Note that I do not specify an install directory. I do not plan to install this special MegaMol. I just want to build, for example for a bug hunt.
It’s now time for the core.
cd megamol_x2 svn co https://svn.vis.uni-stuttgart.de/projects/megamol/core/branches/v1.1rc core cd core
We first test the configuration by only configuring release and not building anything:
./cmake_build.sh -cv ../vislib -C -DCMAKE_DISABLE_FIND_PACKAGE_MPI=TRUE
Note that I also disabled MPI-Support here. The system I am building on has MPI installed, but I don’t want this MegaMol to use it.
The output should contain this line:
-- Found vislib: /home/sgrottel/megamol20150726/vislib/build.release/libvislib.a
This points to the right vislib, the one we specified. So all is well. We can build MegaMol, again without registering it’s build trees in the cmake package repository:
./cmake_build.sh -dcmnv ../vislib -C -DCMAKE_DISABLE_FIND_PACKAGE_MPI=TRUE
When all worked you got yourself the binaries:
Get yourself a working copy of the console:
cd megamol_x2 svn co https://svn.vis.uni-stuttgart.de/projects/megamol/frontends/console/branches/v1.1rc console cd console
Again, we test if everything works by only configuring release and not building:
./cmake_build.sh -c -f ../core
The Console does not register its build tree per default, since no other project depends on the console. So we are fine here.
The output should contain these lines:
-- Looking for MegaMolCore with hints: ../core;../core/build.release;../core/share/cmake/MegaMolCore -- Found MegaMolCore: /home/sgrottel/megamol20150726/core/build.release/libMegaMolCore.so -- MegaMolCore suggests vislib at: /home/sgrottel/megamol20150726/vislib/build.release -- MegaMolCore suggests install prefix: /usr/local -- Using MegaMolCore install prefix -- Found vislib: /home/sgrottel/megamol20150726/vislib/build.release/libvislib.a -- Found AntTweakBar: /home/sgrottel/AntTweakBar/lib/libAntTweakBar.so -- Found visglut: /home/sgrottel/megamol20150726/visglut/lib/libvisglut64.a
If the directories for other libraries are wrong, for example the AntTweakBar or the visglut use the cmake-typical DIR variable to give a search hint. Remember, relative paths might be confusion. Better use absolute paths. I don’t:
./cmake_build.sh -c -f ../core -C -Dvisglut_DIR=~/megamol20150709/visglut -C -DAntTweakBar_DIR=../../AntTweakBar
But in my case the cmake-magic worked fine in the first place. So, I configure both build types again:
./cmake_build.sh -dc -f ../core
Double check the output. Make sure the core, the vislib and the visglut are found in all the right places. If they are, built it:
At this point you can quickly test your MegaMol. First open the megamol.cfg configuration file in a text editor and adjust the paths in there to yours. Then run MegaMol:
cd build.release ./MegaMolCon
If this seems ok, and if you have a local graphics card you can run the demo renderer:
./MegaMolCon -i demospheres s
Some MegaMol Plugin
Finally we need a plugin. I go for the mmstd_moldyn:
cd megamol_x2 svn co https://svn.vis.uni-stuttgart.de/projects/megamol/plugins/mmstd_moldyn/branches/v1.1rc mmstd_moldyn cd mmstd_moldyn
The process is now exactly the same as with the console:
./cmake_build.sh -dcf ../core
The double check the directories for the core and the VISlib. If they are good, build the plugin:
To test this plugin we go back to the console, and adjust the config file to load the plugin:
Include the following lines in the config file. Obviously adjust the paths to what you need:
<plugin path="/home/dude/megamol_x2/mmstd_moldyn/build.release" name="mmstd_moldyn.mmplg" action="include" /> <shaderdir path="/home/dude/megamol_x2/mmstd_moldyn/Shaders" />
If you now run MegaMol it will try to load your plugin and will report it. The output console should contain something like:
200|Plugin mmstd_moldyn loaded: 11 Modules, 0 Calls 200|Plugin "mmstd_moldyn" (/home/sgrottel/megamol20150726/mmstd_moldyn/build.release/mmstd_moldyn.mmplg) loaded: 11 Modules, 0 Calls registered
And that’s it.
This Monday and Thursday the VII. Annual Meeting of the Boltzmann-Zuse-Society for Computational Molecular Engineering takes place in Kaiserslautern, organized by Martin Horsch. Basically it is a meeting for the groups from Stuttgart (VISUS, HLRS), Paderborn, Kaiserslautern and Dresden, to talk about simulation, analysis and visualization of molecular dynamics data. And to discuss our joint research and development projects. Of course, Joachim and I will be talking about current works with and on MegaMol. By the way: http://megamol.org