Working with the Configure Script

You must configure the compile time options you wish to use. These are set with the ./configure script which produces Makefiles for the src and $ARCH directories. After doing the configuration you will do the make. The configuration can be set in two ways:

• On the command line, as in:

       ./configure IRIX5 GL TK FORMS

  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 to the way you want it. (An advantage to keeping the information in a file is that we can set up several types of configurations and simply copy the one we want to use. For instance, for the SGI version with GL we do something like:

       cp ./configure.options.IRIX5 ./configure.options
       ./configure

  for the HP version with MESA we simply do

        cp ./configure.options.HPUX9 ./configure.options
        ./configure

  These files are included in the distribution.)

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 
      IRIX5 -- SGI IRIX 5.3, SGI IRIX 6.x (see comments below) 
      LINUX -- RedHat Linux 5, kernel 2.0.32
      HPUX9 -- HPUX 9, HPUX 10 (se comments below).

• Which type of display graphics will you use? There are four options which will be carefully explained below:

      GL  -- SGI's GL graphics library
      OPENGL -- OpenGL graphics library
      MESA -- API implementation of OpenGL (uses only X calls)
      NOGRAPHICS -- Do not use any display graphics

  GL - We have managed to get the GL version running on IRIX5 (of course), HPUX9 (using the NPGL GL emulator from Portable Graphics) and AIX3 using IBM's implementation of GL. Since we don't have access to an AIX machine, the binary is not distributed. On older SGIs, OpenGL is emulated via GL, so you should probably compile for GL on these platforms.
  
  OPENGL - VMD compiles with OpenGL for SGIs. On the newer SGIs, GL is implemented via OpenGL, so you should compile for OpenGL on these platforms. If you have a mix of GL and OpenGL-based machines in the same environment and want to get the best performance out of each, you'll have to do a bit of hackery to start the appropriate binary. Our suggestion is to compile and install one version as GL, and compile the OpenGL and rename the binary vmd_IRIX5_opengl. You can place that binary in the VMDDIR and modify the 'vmd' startup script to recognize which machine is running and start the appropriate application. To get GL or OpenGL if you do not already have it/them, contact your vendor or other support services.
  
  MESA - We have compiled VMD with MESA 2.6 on all of the tested OSs. The Mesa library is available for free via ftp from iris.ssec.wisc.edu in the pub/Mesa directory. Mesa is also mirrored on sunsite in the directory pub/packages/development/graphics/mesa. See the web address
  http://www.ssec.wisc.edu/ brianp/Mesa.html 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://evlweb.eecs.uic.edu/EVL/VR/ . To compile in the CAVE you will need to get the appropriate CAVE library. There are two, the GL (libcave.a) and OpenGL (libcave_ogl.a). VMD will compile in the correct one based on the type of graphics option you chose (GL or OPENGL), but so far will only compile with the GL version.

  To get access to the CAVE library, please contact them. We cannot distribute the library directly but the standard SGI binary distribution version is compiled with the CAVE library. To use that option, start VMD with the run-time option -dispdev cave. The CAVE libraries we used are old, and VMD will not compile with the newer libraries. We plan to interface VMD with the newer CAVE libraries in the final 1.2 version.

  The configuration options are:

       CAVE -- include run-time support for CAVE display (GL).
       CAVEOGL -- 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:

      XFORMS -- the standard (soon to be "old") GUI 
      TK -- (not yet supported) the rewrite of the XFORMS interface in Tk

  To date the GUI for VMD has been XForms or its GL-based predecessor, FORMS. In version 1.2b2 the GUI is still XForms based but we plan to convert to TK because of the increased flexibility available to scripts. For instance, this will allow user-scripts to create or modify the display on the fly; like drawing an RMSD plot in a new 2D graphics window. If you want to try out Tk, go ahead, but there will be no GUI or mouse control.

  You should compile with XForms, in which case you need to get the pre-built binaries from http://bragg.phys.uwm.edu/xforms/ or from the ftp site ftp://einstein.phys.uwm.edu/ . There are instructions in ./lib/xforms/README describing what you need to do.

  VMD was compiled against Tcl/Tk version 8.0 and TclX version 8.0.2 . You must have the 8.0 or better versions of both packages. The latest versions can be found at:

    Tcl/Tk 8.0 is at http://sunsite.sun.com/TclTkCore/8.0.html 
    TclX 8.0.2 is at ftp://www.neosoft.com/pub/tcl/TclX

  Because Tcl and TclX are very useful programs, we make the assumption that these will be installed on your system, so there is no ./lib/tcl directory. To configure VMD to use the appropriate Tcl/TclX 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";
  
  # location of TclX
  $stock_tclx_include_dir=$ENV{"TCLX_INCLUDE_DIR"} || "/usr/local/include";
  $stock_tclx_library_dir=$ENV{"TCLX_LIBRARY_DIR"} || "/usr/local/lib";

  Either change the default values or override them with the environment variables. As a note, if compiling TclX without Tk, you'll need use the option ./configure -with-tk=NO.

• 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

• As with SURF, the alpha shapes code in VMD calls a set of external programs. As before, you can configure VMD to use/not use alpha shapes. Because VMD's use of the code is rather primitive, we suggest you use it only if you are interested in seeing what it looks like. Also, the interface that VMD uses to talk to the Alpha shapes code is not publically available (we are trying to get ahold of the author) so there isn't anyway you can even get the code. The configuration options are:

        ALPHA -- Call the alpha shapes programs to compute the spectrum

  You can get the alpha shapes code yourself, but this does not include the library VMD uses to read the output of the alpha shape binaries. If you want them, see http://alpha.ncsa.uiuc.edu/alpha or the ftp site
  ftp.ncsa.uiuc.edu/Visualization/Alpha-shape .

• In addition to the CAVE library, VMD can use the UNC Tracker library to get information about various 3DOF and 6DOF spatial trackers. We use it internally to support our Polhemus Fastrack and it also supports Ascension Flock-of-Birds and the BOOM. However, because the CAVE library has more people working on it, we suggest your future work depends more on that than the UNC code. The configurations options for using the UNC tracker library are:

         UNC -- use it

  The standard VMD distribution for IRIX5 is compiled with UNC. We have not tested it with any other platforms. See ./lib/unc/ for more information about the library and how to set it up with VMD.

• We are working on interactive simulations whereby VMD can control a running simulations. The communications uses MDComm to connect to NAMD. For more information about this, see the MDComm web page at
  http://www.ks.uiuc.edu/Research/mdcomm/ .

  The configuration options for MDComm are: 
     REMOTE -- use MDComm for doing remote simulations

  Please read ./lib/mdcomm/README for information about setting up MDComm (and RAPP) for use in VMD.

• There are several compilation flags for VMD. They are:

           DEBUG or NODEBUG

  When turned on, these print all "msgdebug" messages. There are a lot of them and they really slow things down. (BTW, you can tell who wrote which sections of code by who uses msgDebug :) Also, set the -g flag when compiling. By default, VMD is compiled with NODEBUG. If you only want to add the -g flag, edit the configure script so the compiler is defined as "CC -g" (or "g++ -g").

           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.