VMD 1.8.6 Linux Release Notes

VMD Linux Installation Notes:

  • Linux kernel versions
    Some versions of the linux kernel incorrectly send a SIGHUP signal to the main VMD thread when child threads exit. Anyone experiencing this problem will need to update to a current kernel. VMD works well with RHEL4 update 4 with current kernels (e.g. 2.6.9-42).
  • Support for GLSL rendering mode
    VMD 1.8.6 uses OpenGL Shading Language shaders written for the version 1.10 version of the standard (now a few years old). Some early GPUs which are now 3 or 4 years old may not support the entire GLSL standard, and thus will not allow the use of GLSL shading with the standard VMD shaders. The most significant change to the VMD GLSL shaders is that they now require support for the gl_FrontFacing shader attribute. GPUs which do not support gl_FrontFacing will not be able to run the most recent versions of VMD in GLSL mode. If you have one of these older cards and would like to use GLSL (with some shading artifacts as a result of the hardware limitations) we can provide you with a special version of the VMD shaders. NVIDIA provides a GLSL compatibility document which describes what features are supported on the various hardware and driver versions: NVIDIA GLSL Release Notes
  • Linux graphics driver bugs
    VMD users should be aware that specific versions of ATI, nVidia, and other graphics drivers have serious problems and that you'll need to install a known-stable driver version in order to get good results with VMD. If you encounter problems, please report them to nVidia and ATI on their respective web sites.
    ATI Linux driver support site
    nVidia Linux driver support site
  • If you have problems running VMD (i.e. console window briefly pops up and then immediately disappears again) it is usually caused by one of two problems, either a graphics driver problem, or a C++ library problem. The easy way to determine which is the cause, is to run VMD in text mode with the command: vmd -dispdev text If VMD fails to run in text mode, this usually indicates a C++ (or other) dynamic link library problem, which is typically solved as described in this list below by installing missing libraries.
  • If VMD runs in text mode, but fails to start in graphics mode, the next thing to do is to run the Linux command glxinfo, which will access OpenGL and report on the installed hardware, software, and all supported video modes and extensions. If there are fundamental problems with the OpenGL installation the glxinfo output may contain errors or warnings. Generally speaking, if glxinfo reports serious problems, then there's no way VMD or other graphics programs can run correctly until they are solved. In a few rare cases, users may encounter bugs in their OpenGL drivers which only manifest themselves when VMD is actually being used, causing crashes or garbled output. This kind of problem can be debugged by running VMD with the command: vmd -debug This will start a debugging session on VMD. When the debugger is ready and presents a prompt, simply type the command: run At this point, you can run VMD as usual until the crashing or other problems occur again. If the program terminates unexpectedly, type this command in the debugger, and email the output to the VMD development team for analysis: where This will tell the VMD developers what VMD was doing when the crash occured, and can be very helpful in localizing bugs in graphics drivers and related software, and even in VMD itself.
  • With Fedora Core 5, Fedora Core 6, and other recent distributions, users of the 32-bit VMD binary may have to install an additional libstdc++ backward-compatibility package as the 32-bit versions of VMD are compiled on an old Redhat 9 machine, which allows individuals with similarly old Linux installations to run these binaries. With more recent distributions, one may have to add a missing libstdc++.so.5 shared library. On Fedora Core 5, this is done with the command: 
      yum install compat-libstdc++-33
  • With Fedora Core 5, and other recent distributions, the SELinux may cause problems for dynamically loaded VMD plugins. If you don't want to disable SELinux, I suggest you try running this command on the VMD installation directory (Assumes the VMD directory is local to the machine... If you're mounting over NFS, this may or may not work. If not, then you may have to disable SELinux as described below) 
      cd /usr/local/lib/vmd
  find . -name \*.so -exec chcon -t texrel_shlib_t {} \;
    If you'd rather just turn SELinux off, try setting this line in your /etc/sysconfig/selinux and then reboot the machine: 
      SELINUX=disabled
  • Suse 10.x users may experience problems using the Tk input fields of VMD as a result of known problems with Tcl/Tk and SCIM (which Suses uses by default): The only solutions currently available for this problem are either to disable SCIM, or to recompile VMD against the new Tcl 8.4.13 versions that include SCIM input fixes. SCIM can be disabled (for VMD) with: XMODIFIERS=@im=local
  • In order to use the built-in Python interpreter in VMD, you'll need to install the matching Python library distribution.
  • The XFree86 docs cover various info on checking your installation to make sure that the OpenGL/DRI support is working correctly. See their docs (www.xfree86.org) for more info.
  • In order to run VMD, you may have to have a Mesa 4.x RPM installed on your system. This is sometimes needed in order to get the GLU libraries on your system, which are needed by VMD. For Mesa, go to: www.mesa3d.org
  • In order to achieve hardware accelerated 3-D rendering, your video board must have an XFree 4.x "DRI" type video driver. Once you have an appropriate driver, you may need to set the board it to a particular video mode in order to enable the hardware acceleration features. The instructions that come with the video driver should mention what modes are fully accelerated.
  • A "Howto" on setting up stereo for VMD with NVidia cards