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- December 13, 2002 Psi has been updated to 3.2(alpha)
Jaguar is an ab initio quantum chemistry software package developed
by Schrodinger, Inc.
For information
on program's capabilities refer to
Jaguar's website.
User's manual is available here.
The current installation of Jaguar is a trial version, therefore this information may change
once the full copy of Jaguar is installed.
To be able to use Jaguar on the CCMST SP you need to initialize some environmental variables first.
This is usually achieved by adding a line source /cgate/common/etc/cshrc.schrodinger to your
.cshrc shell initialization file. This line has probably beed added to the file
for you, but if it is not there, append it to the end of the file. After you update your shell
initialization file it is safest to log out and log in again.
Now you are ready to submit Jaguar jobs.
To submit a Jaguar job to LoadLeveler you have to construct a LoadLeveler command file (see
Facilities). Unlike other programs,
Jaguar jobs can only be submitted with jaguar as the LoadLeveler class name.
Once we obtain the full version of Jaguar you will need to use the usual classes
described in Facilities section.
The command to execute Jaguar is jaguar run file
where file is the name of Jaguar input file without the .in
suffix. The job output will go to files file.out and file.log.
Note that Maestro, the molecule builder and a graphical user interface to the Schrodinger
family of programs,
cannot be started on cgate like other X-Windows programs due to heavy bandwidth requirements.
However, you may use the graphical user interface to Jaguar from a remote computer with an X-Windows
server (see Facilities) by typing jaguar gui file.
The GUI will let you set up Jaguar input files. NEVER start jobs from within GUI because they will
run interactively, instead use the GUI to save the resulting Jaguar input
file and use a LoadLeveler command file to run the job.
MOLCAS 5.0 is an ab initio quantum chemistry software package developed at
the Department of Theoretical Chemistry, Lund University, Sweden.
For information
on program's capabilities and user manual refer to
Molcas' website.
All environmental variables required to execute a MOLCAS job are setup in
the script runmolcas,
which is located in /cgate/common/bin/. The command and command parameters
for executing MOLCAS
is
runmolcas file.in
where file.in is the name of the molcas input file.
Output from MOLCAS is
automatically sent to file.out without having to specify it as a command
parameter. To submit
a MOLCAS job to LoadLeveler construct a LoadLeveler command file.
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Psi is an ab initio code that is used for most in-house development at the CCMST. Refer to
the official Psi site for more info.
To use Psi on the CCMST SP you need to add /cgate/common/software/psi3/powerpc-ibm-aix4.3.3.0-stable/bin,
the location of its executables, to your shell's PATH variable. The most recent Psi code, not
necessarily tested, is kept under
/cgate/common/software/psi3/powerpc-ibm-aix4.3.3.0-latest/bin.
Q-Chem is a powerful software package that computes properties of
molecular systems ab initio. Q-Chem is distributed by Q-Chem, Inc. For information
on program's capabilities and user manual refer to Q-Chem's website.
To be able to use Q-Chem on the CCMST SP you need to initialize some environmental variables first.
This is usually achieved by adding a line source /cgate/common/etc/cshrc.qchem to your
.cshrc shell initialization file. This line has probably beed added to the file
for you, but if it is not there, append it to the end of the file. After you update your shell
initialization file it is safest to log out and log in again.
Now you are ready to submit Q-Chem jobs.
The command to execute qchem is runqchem file.in file.out
where file.in is the name of Q-Chem input file, and file.out will store job's output.
To submit a Q-Chem job to LoadLeveler you may either use a LoadLeveler command file (see
Facilities)
, or you may use an automated Q-Chem submitter jqsub useful to streamline the process.
For example, to submit a Q-Chem job using h2o.in as an input file you need to execute jqsub as follows:
jqsub cpuaccountname jobclass h2o.in
where cpuaccountname is your CCMST CPU account name, jobclass is the LoadLeveler class
(currently, you may use jqsub only is you use classes interactive, quick,
or cpu). The output of this job will be written into file h2o.out, stdout will go into
h2o.stdout, and, as an additional benefit, jqsub will store the LoadLeveler command
file it created in h2o.cmd.
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Portable, Extensible Toolkit for Scientific Computation
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Patched version 2.1.1 of the toolkit is installed under /cgate/common/software/PETSs/petsc-2.1.1.
Only the parallel 32-bit version of the toolkit (PETSC_ARCH=rs6000_sp) is installed.
Therefore programs compiled using this installation of PETSc can only be submitted through LoadLeveler
and run under POE as explained in Facilities section.
For PETSc user's manual and other documentation refer to
the official PETSc website.
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They are not intended to nor do they constitute an endorsement by the
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Center for Computational Molecular Science and
Technology
Georgia Institute of Technology
Last Modified: October 20, 2005
