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Recent news
WebMO 8.0 is now available for free download!
WebMO 8.0 Pro and Enterprise have a variety of additional features and is available for
purchase.
WebMO can now be installed on Windows, Mac, and Unix servers!
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July 4, 2008
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Computational Chemistry Pre-Compiled Binaries for Linux
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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., Intel x86, SGI MIPS R10000, etc.), operating system, (e.g., Linux, IRIX, AIX, Solaris, Windows, etc.), distribution/vendor (e.g., RedHat, SuSE, SGI, Solaris, etc.), and version (6.2, 7.2, etc.).
GAUSSIAN 03
- Obtain Gaussian 03
Gaussian 03 is a commercial software product and must be purchased from Gaussian, Inc. Both source code and pre-compiled binary versions of Gaussian 03 are available.
- 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
- Copy binary distribution from CD-ROM
# mount /mnt/cdrom
# cd /usr/local
# cp -p /mnt/cdom/tar/*.TAZ .
# umount /mnt/cdrom
- Extract files and change permissions
# tar xzvf *.TAZ
# chown -R root:gaussian g03
# chmod -R o-rwx g03
# exit
- Optionally, setup gaussian environment
$ cd ~
$ mkdir g03
$ cd g03
$ vi g03setup_sh
export g03root=/usr/local
export GAUSS_SCRDIR=/tmp
. $g03root/g03/bsd/g03.profile
- Optionally, run a test job from the command line
$ cd ~/g03
$ cp -p /usr/local/g03/tests/com/test001.com test001.com
$ cp -p /usr/local/g03/tests/sgi/test001.log test001.log.sgi
$ . g03setup_sh
$ g03 < test001.com > test001.log.linux
$ tail test001.log.sgi
$ tail test001.log.linux
- Configure WebMO to use Gaussian03 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 03
- 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
- Login as a WebMO user, and run a test job using Gaussian as the computational engine
GAMESS
- Request a copy of the GAMESS source code
Visit the GAMESS homepage and request a copy of the source code distribution for "GAMESS ver. Mmm. DD, YYYY running on Intel compatable PC running Linux" (Apparently, there is no option to request a pre-compiled binary distribution for Linux; however, this option becomes available in the next step)
- Obtain the GAMESS binary
Download the pre-compiled binary file, linux.current.tar.gz, using the username "source" and the password in the email message that you received
- Uncompress the archive
% su
# cd /usr/local
# tar xzvf /{download_dir}/linux.current.tar.gz
# chown -R root:root gamess
- Add a symbolic link to the gamess binary
# cd gamess
# ln -s gamess.*.x gamess.00.x
- Configure WebMO to use GAMESS 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 GAMESS
- Click 'Edit' to configure the Gamess interface
- Verify that the entries are correct; if necessary, edit entries and click Submit
- Gamess Version: Mmm DD YYYY
- Gamess directory: /usr/local/gamess
- Gamess binary: gamess.00.x
- Ddikick binary: ddikick.x
- Click 'Return to Admin', followed by 'Logout' to exit the WebMO administration page
- Login as a WebMO user, and run a test job using GAMESS as the computational engine
MOPAC 7
- 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
- Uncompress the archive
$ su
# cd /usr/local
# tar xzvf /{download_dir}/mopac7.exe.tar.z
# chown -R root:root mopac7
- 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
- Login as a WebMO user, and run a test job using MOPAC as the computational engine
MOLPRO 2006
- 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.
- 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. Under the latest version of Molpro for which binary versions exist, download the rpm appropriate for your hardware architecture. (Note that mpp versions will run on a single processor as well as in parallel.)
- Install the molpro binary rpm
$ su -
# rpm -ivh {download_dir}/molpro-mpp-2006.1-52.amd64.rpm
- Install the Molpro license token
This can be done automatically
# /usr/local/bin/molpro-configure
or manually
# cp {download_dir}/.token /usr/local/lib/molpro-mpp-Linux-i686-i4-2006.1/.token
# chmod 644 /usr/local/lib/molpro-mpp-Linux-i686-i4-2006.1/.token
# exit
- Run a test job from the command line
$ TMPDIR=/tmp; export TMPDIR
$ molpro <inputfile>
- 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: 2006.1 (or appropriate version)
- Molpro path: /usr/local/bin/molpro
- LD library directory:
- Click 'Return', 'Return to Admin', and 'Logout' to exit the WebMO administration page
- Login as a WebMO user, and run a test job using Molpro as the computational engine
- Workarounds
- If library files cannot be found, define the LD_LIBRARY_PATH environmental variable to define their location, for example
$ LD_LIBRARY_PATH=/usr/pgi/linux86-64/6.1/libso; export LD_LIBRARY_PATH
and set the LD library directory location accordingly in the WebMO Molpro Interface Manager.
- Alternatively, if library files cannot be found, add the path to them to /etc/ld.so.conf (or to a new /etc/ld.so.conf.d/*.conf file) and then refresh the dynamic library loader
# vi /etc/ld.so.conf
# ldconfig
NWCHEM
- Request a copy of the NWChem binary
Visit the NWChem homepage and request a copy of NWChem from their download page. Fill out and submit the web-based registration form. Fill out license agreement sent to you by email, and mail/fax back according to instructions. After a few days, a fax will be sent back to you with a username and password that will allow you to download NWChem.
- Download NWChem binary
Log in as instructed, supply your name, email, and institution when requested. Download any desired NWChem binaries (e.g., nwchem-4.6-LINUXRHELWS3-G77-PIV.tgz). Optionally, download the NWChem User's Manual and/or Programmer's Manual
- Untar and copy binary files
A summary is available in the INSTALL.binbuilds file. Detailed instructions follow:
$ su
# cd ~/tmp
# mkdir nwchem-4.6-LINUXRHELWS3-G77-PIV
# cd nwchem-4.6-LINUXRHELWS3-G77-PIV
# tar xzf /{download_dir}/nwchem-4.6-LINUXRHELWS3-G77-PIV.tgz
# mkdir -p /usr/local/nwchem/bin
# cp -pr bin/* /usr/local/nwchem/bin/
# mkdir -p /usr/local/nwchem/data
# cp -pr usr.local.lib.nwchem/* /usr/local/nwchem/data/
# chown -R root:root /usr/local/nwchem
- Make a default .nwhcemrc file
# vi /usr/local/nwchem/data/default.nwchemrc
nwchem_basis_library /usr/local/nwchem/data/libraries/
ffield amber
amber_1 /usr/local/nwchem/data/amber_s/
amber_2 /usr/local/nwchem/data/amber_q/
amber_3 /usr/local/nwchem/data/amber_x/
amber_4 /usr/local/nwchem/data/amber_u/
spce /usr/local/nwchem/data/solvents/spce.rst
charmm_s /usr/local/nwchem/data/charmm_s/
charmm_x /usr/local/nwchem/data/charmm_x/
- Isolate this version of NWChem with a symbolic link
# cd /usr/local
# mv nwchem nwchem-4.6
# ln -s nwchem-4.6 nwchem
# exit
- Run test job
$ cd ~
$ ln -s /usr/local/nwchem/data/default.nwchemrc .nwchemrc
$ mkdir -p ~/test/nwchem
$ cd ~/test/nwchem
$ mkdir n2
$ cd n2
$ vi n2.in
title "Nitrogen cc-pvdz SCF geometry optimization"
geometry
n 0 0 0
n 0 0 1.08
end
basis
* library cc-pvdz
end
task scf optimize
$ /usr/local/nwchem/bin/nwchem n2.in > n2.out
$ more n2.out
$ cd ..
- 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: 4.6
- NWChem directory: /usr/local/nwchem
- Click 'Return', 'Return to Admin', and 'Logout' to exit the WebMO administration page
- Login as a WebMO user, and run a test job using NWChem as the computational engine
- Notes
Copyright © 2000, WebMO, LLC, all rights reserved.
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