The VMD configure script in detail

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The VMD configure script in detail

Working with the configure script

VMD is designed to be portable to diverse operating systems, and to allow a person to individually include or exclude different optional features or modules. To make this possible, the configure script creates a Makefile in the src directory, using the selected architecture and any optional features that are enabled. This newly generated Makefile is then used to compile a VMD executable from the source code.

The configure script is found at the top level of the VMD working directory. This script has three purposes:

To adapt the Makefile to use the proper libraries and compiler options for the type of operating system being used.
To specify which ones of the many optional components of VMD should be included in the final executable, and to include in the Makefile the necessary files for the selected options.
To configure the VMD directories and source files to use the values for configurable parameters chosen by the user, i.e., the name of the final executable, the location for where the program is to be installed, etc.

The configure script accepts options by command line or by reading a file named 'configure.options' in the top level directory. The main attributes required by the configure script are the target platform, graphics library, and any optional features which are to be enabled.

A typical example of this would be to compile VMD for Solaris with the following command line:

The configuration can be set in two ways:

On the command line, as in:
```
./configure SOLARIS2 OPENGL FLTK TK IMD VRPN SILENT LIBBALL TCL PTHREADS ACTC LIBTACHYON FREEVR PYTHON NUMPY
```
This will save the options to the file ./configure.options so the next time you want to regenerate the Makefiles, you need but do
```
     ./configure
```
Alternatively, you may edit the file ./configure.options yourself. You may wish to keep your settings in several configure.options files, or as new target platformms in the top level VMD Makefile if you intend to compile VMD on multiple platforms. This is a convenience which can save time when you want to recompile VMD more than once.

After you've set the options in the file, run ./configure to propagate the new definitions to the Makefiles! The full list of compile-time options set by the configure script are:

Which OS are you running? VMD can be compiled under several operating systems. The configure time options for these OSs are:

  Option:    Tested with: 
       AIX5 -- IBM AIX 5.x (32-bit)
    AIX5_64 -- IBM AIX 5.x (64-bit)
     HPUX11 -- HPUX 11.0 
      IRIX6 -- SGI IRIX 6.5.4 
   IRIX6_64 -- SGI IRIX 6.5.4 (64-bit)
      LINUX -- Linux 
 LINUXALPHA -- Linux Alpha
 LINUXAMD64 -- Linux on AMD Athlon64/Opteron (64-bit)
  LINUXIA64 -- Linux on Intel Itanium (64-bit)
   LINUXPPC -- Linux PowerPC
     MACOSX -- MacOS X PowerPC
  MACOSXX86 -- MacOS X Intel x86 
   SOLARIS2 -- Solaris Sparc 
SOLARIS2_64 -- Solaris Sparc (64-bit)
 SOLARISX86 -- Solaris x86
      TRU64 -- Tru64 Unix 4.0 (64-bit)
      WIN32 -- Windows

VMD supports GPU acceleration of non-graphical calculations on systems with compatible hardware. GPUs can perform calculations up to 100 times faster than the host CPU in some cases. The configuration option is:

    Option:    GPU Acceleration Support:
       CUDA -- Enable NVIDIA CUDA GPU acceleration support



Which type of display graphics will you use?  There are several
options which will be explained below:
    Option:    Graphics Support:
     OPENGL -- OpenGL graphics library (overall best choice)
       MESA -- Free, Portable, Open Source, OpenGL workalike 




 OPENGL - VMD compiles with native OpenGL for DEC, HP, IBM, Sun, and SGI.  OpenGL offers the best rendering performance on new systems, and is best supported graphics option for VMD at this time. Contact your vendor or support service to get OpenGL for your system.



 



MESA - Mesa is a free OpenGL compatible library which can be used on systems which have no native OpenGL implementation.  Mesa normally performs all of its rendering in software, and may run significantly slower than a native OpenGL implementation. On systems using XFree86 4.0 or later, the new DRI interface can provide hardware-accelerated Mesa, which will speed up VMD significantly. With few exceptions, a native OpenGL implementation will provide the best rendering performance. We have compiled VMD with MESA 3.1 on all of the tested  OSs. The Mesa library is available for free via ftp from ftp.mesa3d.org in the mesa directory. Mesa is also mirrored on sunsite in the directory pub/packages/development/graphics/mesa. See the web address  

http://www.mesa3d.org/ for more information, and the README in ./lib/Mesa for information about how to get Mesa working with VMD. 

 

VMD can be compiled to run in the CAVE. If you don't know what the CAVE is, see http://www.vrco.com/ . To compile in the CAVE you will need to get the appropriate CAVE library.  VMD now only supports OpenGL, so you need to use libcave_ogl.a.



 To get the CAVE library, please contact VRCO Inc.  The VRCO page is at http://www.vrco.com/. We cannot distribute the CAVE libraries themselves, but the  standard SGI binary versions are compiled with the CAVE library.  To use the CAVE, start VMD with the run-time option -dispdev caveforms.



 The configuration options are: 

    Option:    Graphics Support:
       CAVE -- include run-time support for CAVE display (OpenGL).




  
Which kind of GUI do you want to use? (The GUI is nearly independent from the graphics display method.) They are:



 
    Option:    GUI Support:
       FLTK -- the standard FLTK GUI
         TK -- Support for user-written GUI elements in scripts etc.




 You should compile with FLTK, in which case you need to get the source or binaries from http://www.fltk.org/.



 VMD was compiled against Tcl/Tk version 8.4.1. You must have the 8.0 or better versions of both packages. The latest versions can be found at:



  Tcl/Tk 8.4.1 is at http://www.tcl.tk/




 Because Tcl and Tk are very useful tools, we make the assumption that these will be installed on your system.  To configure VMD to use the appropriate Tcl/Tk directory, you may have to edit ./configure and change a few variables. The current settings look in /usr/local/[include,lib] unless the corresponding environment variable is set. The variables are:



 From the configure script:

################ Tcl / Tk
# location of TCL library and include file.
# If left blank, standard system  directories will be searched.
$stock_tcl_include_dir=$ENV{"TCL_INCLUDE_DIR"} || "/usr/local/include";
$stock_tcl_library_dir=$ENV{"TCL_LIBRARY_DIR"} || "/usr/local/lib";

# location of Tk (for TK option)
$stock_tk_include_dir=$ENV{"TK_INCLUDE_DIR"} || "/usr/local/include";
$stock_tk_library_dir=$ENV{"TK_LIBRARY_DIR"} || "/usr/local/lib";




 Either change the default values or override them with the environment variables.



  
VMD uses Amitabh Varshney's SURF program to compute the molecular surface. This is actually an external program that VMD calls; it is not compiled into VMD. You will need to compile SURF yourself to use option. The configuration options are:    SURF -- add the external call to SURF (uses DrawMolItemSurf.{Ch}
           and adds the option to the graphics pop-up list)




 There is no reason not to compile SURF. It is actually distributed (with permission) as part of the VMD distribution. To compile surf, go to ./lib/surf and follow the instructions in README.VMD

(the README file if from surf itself). The end result will be a program named surf_$ARCH in that directory. Leave it there.



 For the main SURF distribution, see  

ftp://ftp.cs.unc.edu/pub/projects/GRIP/SURF/surf.tar.Z



  
In addition to the CAVE library, VMD can use the VRPN  library to get information about various 3DOF and 6DOF spatial trackers and other input devices. Our standard VMD builds now enable VRPN by default on most platforms. The configuration options for using VRPN input devices are:



 

      VRPN -- Use the VRPN library to support local and remote trackers 
              and other input devices.




 For more information about VRPN see  

http://www.cs.unc.edu/Research/vrpn



  
VMD can connect to NAMD to perform interactive simulations; the protocols related to this connection are referred to as Interactive Molecular Dynamics (IMD). The configuration option for IMD is enabled by default:    IMD -- use IMD for doing remote simulations




  
There are several compilation flags for VMD. They are:         LP64
 This option compiles VMD as a 64-bit application program, allowing it to address large amounts of virtual and physical memory, and to access large files.



         PTHREADS
 This option builds VMD with support for POSIX threads. Threads are used within VMD to accelerate IMD and for linkage against  multithreaded libraries such as Tachyon.



         SILENT or NOSILENT

 The default is SILENT, in which case you don't see the details of  the compilation as it suppresses the make command echo. All this  does is add or not add the line ".SILENT" near the top of the  produced Makefile.

Id:: pg_configure.dox,v 1.7 2020/02/24 18:05:20 johns Exp

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