Installation of Quantum Chemistry Software

installation of software

• Linux,
• Mac,
• Windows 32-bit and 64-bit

• Linux

  To complete some of the steps requires being able to act as root or superuser.

  1. Install Avogadro.
     options
     • If one is fortunate, the operating system's software installer (e.g., yum) may install Avogadro when asked to.
     • If not, one can download the source code from http://avogadro.openmolecules.net/wiki/Get_Avogadro Select the latest source release. Save the zipped archive. Open it. Follow instructions to install. Hope for good luck.
  2. Install GAMESS
     1. Check that csh is installed. For example, the command

        csh --version

        executed at a command prompt in a terminal, will return the version of csh that is installed. If csh is not installed, install it.
     2. Check that a fortran compiler, gfortran or f77 or g77, is installed. For example, the command

        gfortran

        executed at a command prompt in a terminal, will return an error message of "no input files" if the compiler is installed. Likewise, the f77 or g77 command. If no fortran compiler is found, install gfortran. Note: More advanced compilers such as Intel's F90 are also fine.
     3. Check that either MKL or ATLAS math libraries are installed. For example, the command

        whereis atlas

        will return the location of ATLAS libraries, if installed. If neither MKL nor ATLAS is installed, install ATLAS.
     4. Check that the BLAS (basic linear algebra subroutines) library is installed. For example, the command

        yum list blas

        may return the version and location of BLAS. If BLAS is not installed, install BLAS.
     5. Place the tar file gamess-current.tar.gz in a directory in which you will install it. For example, gamess-current.tar.gz might be moved to /usr/local or $HOME.
     6. untar and unpack the file, using the command

        tar -xvzf gamess-current.tar.gz

        Untarring will create a gamess subdirectory plus numerous subdirectories within the gamess subdirectory.
     7. It may be necessary to change the SysV shared memory allocation, because GAMESS requires considerable shared memory. Detailed instructions for checking and changing this value are in the gamess/ddi/readme.ddi file. Allow at least 160525768.
        Briefly, here are the linux instructions from readme.ddi
        • As root or superuser, edit the file /etc/sysctl.conf
        • add these lines at the end of the file
          # increase shmmax for GAMESS
          kernel.shmmax = 1610612736
        • reboot
     8. Follow the step-by-step installation instructions in the file gamess/machines/readme.unix.
        • ./config: As of November 2012, the newest version of gfortran known to the configuration script was 4.6, so even if your version is 4.7 enter 4.6.
        • ddi compddi
        • compall
     9. It is the shell script rungms that will be used to run GAMESS calculations. Edit the file gamess/rungms .
        • Find the line that begins "set SCR=".
          Change the scratch directory to the location of your choice (e.g., /tmp/scr) and then create the directory if it does not already exist.
        • Find the comment line that starts "# data left over from a previous run might be precious"
          Above that line, enter the following code, which will remove any such data left over, regardless of its preciousness.
          

          #    data left over from a previous run should be deleted
          if (-e $PUNCH)   rm -f $PUNCH   endif
          if (-e $MAKEFP)  rm -f $MAKEFP  endif
          if (-e $TRAJECT) rm -f $TRAJECT endif
          if (-e $RESTART) rm -f $RESTART endif
                                   

  3. Install MacMolPlt

     If one is fortunate, the operating system's software installer (e.g., yum) may install macmolplt when asked to. (Mine did.)

     If not, then connect to http://www.scl.ameslab.gov/MacMolPlt/, choose "Downloading MacMolPlt", and then select either the source code or a pre-built binary.

  Especially if problems arise, one might like to read Professor Jan Jensen's blog entry Installing GAMESS on a linux PC. The entry is part of his generally helpful blog entitled "Molecular Modeling Basics."

• Mac

  These instructions have been tested only twice, on Macs running OS X. Updates and corrections are welcome.
  1. Download and install Avogadro from http://avogadro.openmolecules.net/wiki/Get_Avogadro Choose the Mac Application. Install Avogadro.
  2. Download and install GAMESS
     GAMESS is developed and hosted by Professor Mark Gordon and his group at Iowa State University.
     1. The first step in downloading a copy is the license agreement. Then enter your email address and select the pre-compiled version you want. For example, select
            GAMESS version August 11, 2011 R1 for Apple MacOS X
     2. Professor Jan Jensen posted a screencast about downloading and installing GAMESS on a Mac. http://molecularmodelingbasics.blogspot.com/2009/07/installing-gamess-on-mac.html
     3. A key step in the installation, as mentioned by Prof Jensen, seems to be moving the gamess folder into the Mac's Applications folder.
     4. Note: The program GamessQ is a queueing program to run GAMESS jobs sequentially. It is packaged with GAMESS for Mac but is not essential. GAMESS can also be run using rungms at a command prompt.
  3. Install MacMolPlt

     This program, too, is hosted at Iowa State University. Simply connect to http://www.scl.ameslab.gov/MacMolPlt/, choose "Downloading MacMolPlt", and select a Universal binary file.

• Windows (32-bit and 64-bit)

  These instructions have been tested on Windows XP and Windows 7 and once on Windows 8. Updates and corrections are welcome.
  1. Download and install Avogadro from http://avogadro.openmolecules.net/wiki/Get_Avogadro Choose the Windows installer.
     • Install Avogadro.
       These options may be good:
       • Add Avogadro to the system path for all users
       • Create Avogadro Desktop Icon
     • On Windows 7, some graphical operations (e.g., changing a bond length) may crash Avogadro. It has been found that Avogadro works fine when run in Windows XP compatibility mode under Windows 7.
  2. Download and install GAMESS
     GAMESS is developed and hosted by Professor Mark Gordon and his group at Iowa State University.
     • GAMESS for 64-bit Windows

       The first step in downloading a copy is the license agreement. Then enter your email address and select the pre-compiled version you want. For example, select "GAMESS for Microsoft Windows". Submit. A password will be sent to your email address. When you receive the password, follow the instructions in the email to download GAMESS and the accompanying "setup guide.".

     • GAMESS for 32-bit Windows

       The 32-bit GAMESS offered by the GAMESS group is complicated to install and run, relying on CygWIN. If you need a 32-bit GAMESS please ask me for a copy of the slightly older (October 2012) GAMESS.Windows.32.msi self-installing file.

     • Open the setup guide (e.g., "WinGAMESS-setup-guide-64.pdf) Following the setup guide,
       • install C++ (but not on Windows 8)
         by downloading and installing
         • 64-bit vceredist_x64.exe from
           http://www.microsoft.com/downloads/en/details.aspx?familyid=ba9257ca-337f-4b40-8c14-157cfdffee4e
         • or 32-bit vcredist_x86.exe from
           http://www.microsoft.com/downloads/en/details.aspx?FamilyID=a7b7a05e-6de6-4d3a-a423-37bf0912db84.
       • install mpiexec by downloading either
         • 64-bit mpi_x64.msi and redist.txt from
           http://www.microsoft.com/downloads/en/details.aspx?FamilyID=ce888449-0e71-44f3-a2fc-947ec57ff90f
         • or 32-bit mpi_x86.msi and redist.txt from
           http://www.microsoft.com/downloads/en/details.aspx?FamilyID=ce888449-0e71-44f3-a2fc-947ec57ff90f.
       • install GAMESS
       GAMESS will be installed in C:\gamess.64 or C:\gamess.32 by default.
       The setup guide suggests giving the command

       runall.bat 11-32 1

       to run all 44 test jobs that were installed along with the program. That is OK but rather slow. Instructions below show how to run just one of the test jobs, "exam01".
     • Restart your computer so mpiexec will be added to your computer's executable-program path.
     • Download the small executable unix2dos.exe and move it to the GAMESS installation directory. This file changes end-of-line characters in GAMESS output so they can be read conveniently by MacMolPlot and text editors.
     • Customize C:\gamess.64\rungms.bat (or C:\gamess.32\rungms.bat) as follows:
       • Open rungms.bat with notepad or other similar editor.
         If the lines of the file appear run together in your editor, then exit the editor and use unix2dos to fix the end-of-line characters, as follows:
         1. Open a command-prompt window. (This can be done by entering cmd in the Windows Start/Run box.)
         2. cd C:\gamess.64 (or cd C:\gamess.32)
         3. unix2dos rungms.bat
         Then re-open rungms.bat with the editor. It should look OK.
       • In rungms.bat, find the line that says

         SET ERASEOLDFILES

         and set the value to true. The line should read

         @SET ERASEOLDFILES=TRUE 

       • Find the line that says

                           @IF NOT EXIST parameters.gms (
                           

         and change parameters.gms to C:\gamess.64\parameters.gms (or to C:\gamess.32\parameters.gms if you installed the 32-bit version of GAMESS).
         That is so GAMESS will find the parameters file even if GAMESS is executed from a directory other than the installation directory.
       • Find the line that says

                           FOR /F "tokens=1,2 delims==" %%A IN 
                           

         and change "parameters.gms" as you did above.
       • Find the next line (about 40 lines down) that again says

                              FOR /F "tokens=1,2 delims==" %%A IN 
                           

         and change "parameters.gms" as you did above.
       • Find the line that says

         VERSION=00

         . The "00" must be changed to the actual version installed in your C:\gamess.64 or C:\gamess.32 directory.
         Determining the value of VERSION
         • Open a command prompt window.
         • cd C:\gamess.64 (or cd C:\gamess.32) to change to the installation directory
         • Type the command "dir". That will bring to the screen a list of the files in the directory. One executable file will have a name that starts with "gamess." and ends with ".exe". (The extension, ".exe" may not be displayed. That is OK). The text between "gamess." and ".exe" is the VERSION. VERSION might, for example, be one of these:
           • 12-64.pgi.fast
           • 12-64.intel.fast
           • 11-64
         In rungms.bat, change "00" to VERSION (the value you just found in the middle of your gamess executable's name). That is so you will not have to type the GAMESS version number every time you use rungms.bat.
       • Save rungms.bat.
     • You may want to put C:\gamess.64 (or C:\gamess.32) in the Windows Path, so the command "rungms" can be run from any directory. To modify the Path, go to the computer's system environment variables.

       My Computer, Properties, Advanced tab, environment variables

       Find "Path" in the defined variables and edit it. Different directories in the Path are separated by semicolons. For example,

       C:\Windows;C:\Program Files;C:\Windows\System32;C:\gamess.64

       For more instructions, see computerhope.
        
     • This step is just for a case in which gamess is being installed by an administrator for users who may not have write permission to C:\gamess.64 (or C:\gamess.32). This is an unusual case for a personal computer, so it is most likely not applicable.
       • Use Windows Explorer to locate the C:\gamess.64 (or C:\gamess.32) directory. Display its properties. "Readonly" must be unchecked. Apply the change to all files and subdirectories.
       • Change into the gamess directory. Uncheck "Readonly" in the properties of the tmp and scr directories. Apply to all files and subdirectories.
       
       
     • Now GAMESS is installed and ready to test. One of the sample input files that comes with GAMESS, "exam01.inp", makes a good test case. It optimizes the bond lengths and angles of CH₂. At the command prompt, in the directory C:\gamess.64 (or C:\gamess.32)

       copy tests\exam01.inp .

       to copy an example input file into the installation directory.
     • Again at the command prompt, ask GAMESS to read exam01.inp and calculate.

       rungms exam01  > exam01.log 

       Wait for "FORTRAN STOP" to appear. That may take 10-20 seconds.
     • Open exam01.log with notepad or another simple editor. Look near the end of the file for the comforting words EXECUTION OF GAMESS TERMINATED NORMALLY. If you find them, the job ran and your GAMESS installation is complete.
     
      
  3. Download and install MacMolPlt

     This program, too, is hosted at Iowa State University. Simply connect to http://www.scl.ameslab.gov/MacMolPlt/, choose "Downloading MacMolPlt", and select a windows installer. Download it.

     Administrative privileges may be needed to install MacMolPlt into the default directory C:\Program Files.

     Install MacMolPlt.

     Make a shortcut copy on the desktop.

Problems for which solutions are known

1. Problem: GAMESS fails because it cannot overwrite existing data files.
   Solutions:
   • One-time solution: Remove files from your personal GAMESS scratch directory ($HOME/scr on Linux). Then rerun the GAMESS job.
   • Permanent solution: Edit the file rungms (Linux, Mac) or the file rungms.bat (Windows). Delete or comment out the lines in which GAMESS checks for existing PUNCH, TRAJECT, etc., files. Then rerun the GAMESS job.
2. Problem: GAMESS fails and gives a ddikick TCP error.
   Work-around: Connect the computer to the internet. Then rerun the GAMESS calculation.
3. Problem: Avogadro crashes under Windows 7.
   Work-around: Run Avogadro in Windows XP compatibility mode.
4. Problem: Example exam44.inp fails.
   Word-around: Never mind.

• Return to main page.
• Go to tutorial for software use.
• Go to Avogadro home page.
• Go to GAMESS home page.
• Go to MacMolPlt home page.

Last Modified: Tuesday, 29-Jan-2013 07:12:16 CST