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WebMO - Computational chemistry on the WWW
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October 1, 2014
Computational Chemistry Pre-Compiled Binaries for Linux

Pre-compiled binaries of computational chemistry programs can save the time and trouble of obtaining and compiling the program source code.

When using a pre-compiled binary, be aware that one must use a binary that is appropriate for one's particular hardware (e.g., x86 or ia32, Intel x86_64 or EM64T or Intel64, AMD x86_64 or Opteron, SGI MIPS R10000, etc.), operating system, (e.g., Linux, OS X, Windows, IRIX, AIX, Solaris, etc.), bitsize (32-bit or i4, 64-bit or i8), distribution/vendor (e.g., RHEL, CentOS, Fedora Core, RedHat, SuSE, SGI, Solaris, etc.), and version (4, 6.2, 7.2, 11, etc.).

GAMESS

GAMESS is currently no longer available for Linux as a pre-compiled binary, although it is available for other OS's. You must compile the source code on linux using a system compiler, e.g., f77, gfortran, or another popular compiler.

GAUSSIAN 09

  1. Obtain Gaussian 09
    Gaussian 09 is a commercial software product and must be purchased from Gaussian, Inc. Both source code and pre-compiled binary versions of Gaussian 09 are available.
  2. Setup gaussian group and add authorized users to this group
    $ su
    # cd /etc
    # cp -p group group.bak
    # cp -p gshadow gshadow.bak
    # grep 499 group
    # groupadd -g 499 gaussian
    # usermod -a -G gaussian webmo
    # usermod -a -G gaussian smith
    # usermod -a -G gaussian jones
  3. Copy binary distribution from CD-ROM
    # mount /mnt/cdrom
    # cd /usr/local
    # cp -p /mnt/cdom/tar/*.TGZ .
    # umount /mnt/cdrom
  4. Extract files
    # tar xzvf *.TGZ
    # chown -R root:gaussian g09
    # exit
  5. Run a test job from the command line
    $ cd ~
    $ mkdir g09
    $ cd g09
    $ vi g09setup
          export g09root=/usr/local
          export GAUSS_SCRDIR=/tmp
          source $g09root/g09/bsd/g09.profile
    $ cp -p /usr/local/g09/tests/com/test001.com test001.com
    $ cp -p /usr/local/g09/tests/ia64/test001.log test001.log.ia64
    $ source g09setup
    $ g09 < test001.com > test001.log.linux
    $ tail test001.log.ia64
    $ tail test001.log.linux
  6. Configure WebMO to use Gaussian09 as a computational engine
    • Login to WebMO as user 'admin'
    • Click 'Interface Manager' to enable the interfaces to any computational chemistry packages that you have installed on your system
    • Click the 'Enable' button for Gaussian
    • Click 'Edit' to configure the Gaussian interface
    • Verify that the first two entries are correct:
      • Gaussian Version: Gaussian 09
      • Gaussian root directory: /usr/local
    • Click the 'Suggest' button to fill the remining entries
    • Click the 'Submit' button for the changes to take effect
    • Click 'Return', 'Return to Admin', and 'Logout' to exit the WebMO administration page
  7. Login as a WebMO user, and run a test job using Gaussian as the computational engine
MOLPRO 2010

  1. Obtain a Molpro license
    MolPro is a commercial software product, and a license must be purchased from www.molpro.net. Registered licensees will receive a Molpro username and password, which grant access to the download area of the Molpro website.
  2. Download the Molpro binary and license token
    At the Molpro website, follow the For Licensees link, and supply your Molpro username and password. Download a copy of the license token. Follow the Download link. Download the latest binary version appropriate for your hardware architecture and operating system, for example, molpro-mpp-2010.1-13.Linux_x86_64.sh.gz for 64-bit Linux. (Note that mpp versions will run on a single processor as well as in parallel.)
  3. Install the molpro binary
    $ su -
    # mkdir /tmp/molpro
    # cd /tmp/molpro
    # cp -p {download_dir}/molpro-mpp-2010.1-13.Linux_x86_64.sh.gz .
    # gunzip molpro-mpp-2010.1-13.Linux_x86_64.sh.gz
    # chmod 755 molpro-mpp-2010.1-13.Linux_x86_64.sh
    # ./molpro-mpp-2010.1-13.Linux_x86_64.sh
    Enter installation directory for executable files [/usr/local/bin] /usr/local/molpro     <--WebMO standard location
    Enter installation directory for library files [/usr/local/lib/molprop_2010_1_Linux_x86_64_i8]
    directory /usr/local/lib/molprop_2010_1_Linux_x86_64_i8 does not exist, try to create [Y]/n
    Installation of Molpro files complete
    Please give your username for accessing molpro
    ******
    Please give your password for accessing molpro
    ********
    Token sucessfully downloaded and installed
  4. If Molpro license token was not automatically installed in last step, install license token manually
    # cp {download_dir}/.token /usr/local/lib/molprop_2010_1_Linux_x86_64_i8/.token
    # chmod 644 /usr/local/lib/molprop_2010_1_Linux_x86_64_i8/.token
  5. Fix file ownerships
    # chown -R root:root /usr/local/molpro
    # chown -R root:root chown -R root:root /usr/local/lib/molprop_2010_1_Linux_x86_64_i8
  6. Clean up
    # cd /tmp
    # rm -rf molpro
    # exit
  7. Run a test job from the command line
    $ /usr/local/molpro/molpro {inputfile}
  8. Configure WebMO to use Molpro as a computational engine
    • Login to WebMO as user 'admin'
    • Click 'Interface Manager' to enable the interfaces to any computational chemistry packages that you have installed on your system
    • Click the 'Enable interface' icon for Molpro
    • Click the 'Edit interface' icon to configure the Molpro interface
    • Verify that the entries are correct; if necessary, edit entries and click 'Submit'
      • Molpro version: 2010.1
      • Molpro path: /usr/local/molpro/molpro
      • LD library directory:
    • Click 'Return', 'Return to Admin', and 'Logout' to exit the WebMO administration page
  9. Login as a WebMO user, and run a test job using Molpro as the computational engine
  10. Notes
MOPAC 7

  1. Obtain the MOPAC 7 binary
    MOPAC 7 is public domain and the pre-compiled binary code mopac7.exe.tar.gz can be obtained from the WebMO website
  2. Uncompress the archive
    $ su
    # cd /usr/local
    # tar xzvf /{download_dir}/mopac7.exe.tar.gz
    # chown -R root:root mopac7
    # exit
  3. Configure WebMO to use MOPAC7 as a computational engine
    • Login to WebMO as user 'admin'
    • Click 'Interface Manager' to enable the interfaces to any computational chemistry packages that you have installed on your system
    • Click the 'Enable' button for MOPAC
    • Click 'Edit' to configure the MOPAC interface
    • Verify that the entries are correct; if necessary, edit entries and click Submit
      • Mopac version: Mopac 7
      • Mopac path: /usr/local/mopac7/mopac.exe
      • External parameter dir:
    • Click 'Return', 'Return to Admin', and 'Logout' to exit the WebMO administration page
  4. Login as a WebMO user, and run a test job using MOPAC as the computational engine
MOPAC 2009

  1. Request license (free for academic use) from MOPAC 2009 website:
        http://www.openmopac.net/download-c.html
    A license of the form 12345678a12345678 will be sent to you in an email message
  2. Download MOPAC2009 for Linux (MOPAC2009_for_Linux.zip) from
        http://www.openmopac.net/Download_MOPAC_Executable_Step2.html
  3. Install MOPAC2009 binary
    $ cd {download_dir}
    $ mkdir mopac2009
    $ cd mopac2009
    $ unzip ../MOPAC2009_for_Linux.zip
    $ su
    # cd /usr/local
    # mkdir mopac2009
    # cd mopac2009
    # cp -p {download_dir}/mopac2009/MOPAC2009.exe .
    # chown root:root MOPAC2009.exe
    # chmod 755 MOPAC2009.exe
  4. Install MOPAC2009 license
    # export MOPAC_LICENSE=/usr/local/mopac2009/
    # /usr/local/mopac2009/MOPAC2009.exe {license}
    (press {Return} twice, type "Yes", and press {Return} as prompted, which creates the file password_for_mopac2009)
    # exit
  5. Run a test job from the command line
    $ cd ~
    $ mkdir -p test/mopac2009
    $ cd test/mopac2009
    $ cp {download_dir}/mopac2009/Example\ data\ set.mop h2co.mop
    $ export MOPAC_LICENSE=/usr/local/mopac2009/
    $ /usr/local/mopac2009/MOPAC2009.exe h2co.mop
    $ more h2co.out
  6. Configure WebMO to use Mopac 2009 as a computational engine
    • Login to WebMO as user 'admin'
    • Click 'Interface Manager' to enable the interfaces to any computational chemistry packages that you have installed on your system
    • Click the 'Enable' button for Mopac
    • Click 'Edit' to configure the MOPAC interface
    • Verify that the entries are correct; if necessary, edit entries and click Submit
      • Mopac Version: Mopac 2009
      • Mopac path: /usr/local/mopac2009/MOPAC2009.exe
      • External parameter dir:
    • Click 'Return', 'Return to Admin', and 'Logout' to exit the WebMO administration page
  7. Login as a WebMO user, and run a test job using MOPAC as the computational engine
  8. MOPAC documentation
    The online manual for MOPAC2007 covers everything in MOPAC2009, except the MOZYME feature designed for linear scaling of larger molecules
NWCHEM 5.5

  1. Request a copy of the NWChem binary
    Visit the NWChem homepage and request a copy of NWChem from their download page. Create an EMSL user account by using the EMSL User Portal web-based registration form, and the temporary password send to your email address. Upon logging in to the EMSL User Portal, select Usage Type: Software Agreement and click Register for New Software. Fill out the Software User Info, choose to download NWChem (and possibly ECCE), and digitally sign the Software End User Agreement. After a few days, your request will be processed and your software agreement status will change from "pending" to "approved" if your meet the EMSL criteria (e.g., permanent faculty member/researcher in non-embargoed country).
  2. Download NWChem binary
    Visit the NWChem homepage and request a copy NWChem from their download page. Upon logging in to the EMSL User Portal with your email address and password specified above, select Usage Type: Software Agreement. Choose NWChem download, Binaries, and the latest version. Download the NWChem binary appropriate for your computer architecture (e.g., nwchem-5.1.1-LINUX64-RHELWS4-ifort-AMD64.tgz for 64-bit Linux running on an Opteron processor).
  3. Untar the binary files
    A summary of this procedure is available in the INSTALL.binbuilds file. Detailed instructions follow:
    $ su
    # cd /usr/local
    # mkdir nwchem-5.1.1
    # cd nwchem-5.1.1
    # tar xzf {download_dir}/nwchem-5.1.1-LINUX64-RHELWS4-ifort-AMD64.tgz
    # chown -R root:root /usr/local/nwchem-5.1.1
    # chmod 755 /usr/local/nwchem-5.1.1/bin/*
    # chmod 755 /usr/local/nwchem-5.1.1/etc/
  4. Make a default.nwchemrc file
    # cd /usr/local/nwchem-5.1.1/etc
    # ./gen_default.nwchemrc
  5. Define this version of NWChem as the default with a symbolic link
    # cd /usr/local
    # ln -s nwchem-5.1.1 nwchem
    # exit
  6. Run test job from the command line
    $ cd ~
    Specify the location of the nwchem with either
          $ ln -s /usr/local/nwchem/data/default.nwchemrc .nwchemrc
    or
          $ export NWCHEM_BASIS_LIBRARY=/usr/local/nwchem/usr.local.lib.nwchem/libraries/
    $ mkdir ~/nwchem
    $ cd ~/nwchem
    $ cp -p /usr/local/nwchem/examples/h2o/h2o.nw .
    $ /usr/local/nwchem/bin/nwchem h2o.nw > h2o.out
    $ more h2o.out
  7. Configure WebMO to use NWChem as a computational engine
    • Login to WebMO as user 'admin'
    • Click 'Interface Manager' to enable the interfaces to any computational chemistry packages that you have installed on your system
    • Click the 'Enable' button for NWChem
    • Click 'Edit' to configure the NWChem interface
    • Verify that the entries are correct; if necessary, edit entries and click 'Submit'
      • NWChem Version: 5.1.1
      • NWChem directory: /usr/local/nwchem
      • NWChem binary: /usr/local/nwchem/bin/nwchem
      • NWChem config file: /usr/local/nwchem/etc/default.nwchemrc
    • Click 'Return', 'Return to Admin', and 'Logout' to exit the WebMO administration page
  8. Login as a WebMO user, and run a test job using NWChem as the computational engine
  9. Notes
PQS 3.3

  1. Download PQS binary
    Visit the PQS homepage and download a copy of PQS from their software page. Choose an appropriate implementation and architecture, or choose the free 32-bit trial version, e.g., pqs_mpi2-3.3-19.i386.tar.gz. The following instructions are based on a TAR file download, not the RPM download.
  2. Untar the binary files
    $ su
    # cd /tmp
    # tar xzf {download_dir}/pqs_mpi2-3.3-19.i386.tar.gz
    # cd pqs_trial-3.3-19.i386
    # ./install.sh
    Please choose the installation type: 1 Multi-user install (requires root privileges)
    Enter the target directory for PQS install [/usr/local/share/PQS]: /usr/local/PQS
    Enter the scratch directory for PQS jobs [/scr]: /tmp
    Please choose one of the following actions: 1 Skip this step leaving PQS_SCRDIR = /tmp
    Now you can choose to create links to the PQS scripts. Do you want to proceed [y]: n
  3. Fix file ownerships
    # chown -R root:root /usr/local/PQS
  4. Clean up
    # cd /tmp
    # rm -rf pqs_trial-3.3-19.i386
    # exit
  5. Configure WebMO to use PQS as a computational engine
    • Login to WebMO as user 'admin'
    • Click 'Interface Manager' to enable the interfaces to any computational chemistry packages that you have installed on your system
    • Click the 'Enable' button for PQS
    • Click 'Edit' to configure the PQS interface
    • Verify that the entries are correct; if necessary, edit entries and click 'Submit'
      • PQS version: 3.3
      • PQS directory: /usr/local/PQS-3.3trial
      • PQS binary: /usr/local/PQS-3.3trial/pqs.x
    • Click 'Return', 'Return to Admin', and 'Logout' to exit the WebMO administration page
  6. Login as a WebMO user, and run a test job using PQS as the computational engine
Q-Chem 3.2

  1. Obtain a Q-Chem license and binaries
    Q-Chem is a commercial software product, and a license must be purchased from www.q-chem.com. A CD-ROM with Q-Chem binaries will be mailed to the customer, or binaries may be downloaded from www.q-chem.com/download.htm.
  2. Mount CD-ROM
    # mount /mnt/cdrom
    # cd /mnt/cdrom
    or untar downloaded binary
    # mkdir -p /tmp/qchem
    # cd /tmp/qchem
    # tar xf {download_dir}/qc3202-LINUX64S.tar
  3. Install Q-Chem software
    # ./INSTALL.sh
    Answer questions as appropriate. Some responses might be:
    • Specify the path of the new Q-Chem directory: /usr/local/qchem
    • Choose serial installation of Q-Chem for appropriate hardware
    • Specify a directory (full path) for storing scratch files: /tmp
    • Set default limit for the amount of system memory that Q-Chem to less than maximum amount of available memory, e.g., for 2000 MB (2 GB) of memory, set upper memory limit to 1000.
    • Enter order number (or 0) and user information so a license.data file can be created
  4. Unmount CD-ROM
    # cd /usr/local/qchem
    # umount /mnt/cdrom
    or
    # rm -rf /tmp/qchem
  5. Obtain and install license key
    Email the file /usr/local/qchem/license.data to license@q-chem.com. The returned email will have an attached file qchem.license.dat.computer_name.txt. Copy this file to
        /usr/local/qchem/aux/license/qchem.license.dat
  6. Optionally, isolate version of qchem with a symbolic link (only if you have multiple versions of qchem on your system)
    # cd /usr/local
    # mv qchem qchem-3.2-64S (or appropriate version)
    # ln -s qchem-3.2-64S qchem
    # cd qchem/config
    # cp -p shellvar.txt shellvar.txt.000
    # cp -p qchemrc.sh qchemrc.sh.000
    # cp -p qchemrc.csh qchemrc.csh.000
    # vi shellvar.txt
          change "QC /usr/local/qchem" to "QC /usr/local/qchem-3.2-64S"
          change all other instances of "/usr/local/qchem" to "$QC"
    # ../bin/write_source.sh /usr/local/qchem
  7. Set up Q-Chem environment
    $ cd ~
    $ mkdir qchem
    $ cd qchem
    $ vi qchemsetup
          QC=/usr/local/qchem; export QC
          source $QC/bin/qchem.setup.sh
  8. Run a test job from the command line
    $ cd ~/qchem
    $ source qchemsetup
    $ cp -p /usr/local/qchem/samples/HF_water.in .
    $ cp -p /usr/local/qchem/samples/qcref/HF_water.out HF_water.ref
    qchem HF_water.in HF_water.out
    diff HF_water.ref HF_water.out
  9. Configure WebMO to use Q-Chem as a computational engine
    • Login to WebMO as user 'admin'
    • Click 'Interface Manager' to enable the interfaces to any computational chemistry packages that you have installed on your system
    • Click the 'Enable' button for QChem
    • Click 'Edit' to configure the QChem interface
    • Verify that the entries are correct; if necessary, edit entries and click 'Submit'
      • QChem version: 3.2
      • QChem directory: /usr/local/qchem
    • Click 'Return', 'Return to Admin', and 'Logout' to exit the WebMO administration page
  10. Login as a WebMO user, and run a test job using Q-Chem as the computational engine
  11. Workarounds
    • Could NOT read file: /usr/local/qchem/aux/license/qchem.license.dat.
      ReadLicense failed.
      Q-Chem fatal error occurred in module qink_init.C, line 331:
      License check failed!
      This message occurs because the license files have not been installed; copy the license file to /usr/local/qchem/aux/license/qchem.license.dat
    • /usr/local/qchem/exe/progman.exe: Command not found.
      This message occurs because environmental variables have not been correctly defined; check them as follows
      $ printenv
      Make sure that QC, QCAUC, QCPLATFORM, QCSCRATCH, PATH, ONEEXE, and RUNCPP are properly defined (which is usually done by $QC/bin/qchem.setup.sh and $QC/config/qchemrc.sh)
    • /usr/local/qchem/exe/qcprog.exe: error while loading shared libraries: libstdc++.so.5: cannot open shared object file: No such file or directory
      This message occurs because the correct version of libstdc++ is not available, e.g., the 64-bit version is needed, and only the 32-bit version is installed; install the needed version
      # rpm -qa --queryformat="%{n}-%{v}-%{r}.%{arch}\n" | grep compat-libstdc++
      compat-libstdc++-296-2.96-132.fc4.i386
      compat-libstdc++-33-3.2.3-47.fc4.i386
      # yum install compat-libstdc++-33.x86_64
      # rpm -qa --queryformat="%{n}-%{v}-%{r}.%{arch}\n" | grep compat-libstdc++
      compat-libstdc++-296-2.96-132.fc4.i386
      compat-libstdc++-33-3.2.3-47.fc4.i386
      compat-libstdc++-33-3.2.3-47.fc4.x86_64

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