As shown above, the licenses for modules Discover, Compass, DPD, and Amorphous Cell have been purchased by the proposal grant of Prof. Ahmed Al-Ostaz whereas the licenses for modules Dmol3 and Vamp have been purchased by the proposal grant of Prof. Paige Phillips; hence any researcher affiliated with these researchers has the priority of usage of Materials Studio in our systems. For more information on Accelrys and white papers on research, please visit Materials Studio of Accelrys.
Using Materials Studio with PBS on MCSR Systems
Currently, Materials Studio, MSI, version 4.0 is installed sweetgum and mimosa. Within the next month, the installation of MSI on redwood will be completed, and a script will be written by MCSR consultants for the submission of Materials Studio calculations. This script, similar to the g03sub script for submitting Gaussian 03 calculations, will do some error checking and then create and submit a PBS job to run your calculation, injecting a two-digit code into the PBS job name, so that our PBS jobs datawarehouse will recognize your job as a Materials Studio calculation of a given module, and allow this job to distinguishable from others in the My MCSR Jobs portal. In the meantime, you will need to write your own PBS scripts to run the calculations, and encode your PBS jobname as described further below. MSI has been installed under the directories /usr/local/apps/MSI and /usr/local/appl/MSI in mimosa and sweetgum, respectively. There are two test folders, one each for "Discover" and "Dmol3" modules, located under the MSI directory under the MSI_testjobs folder. Each folder contains essential input files for each module and a pbs script to run the jobs. You can simply submit these jobs via qsub command of PBS after copying the folders and files to your account directory and modifying "cd " lines of pbs files by changing the directory paths to your account path. You may follow the steps below to run Discover test on sweetgum:
Once you login to the system, you will receive a command prompt as
sweetgum % , then
please follow the steps below;
cp -Rf /usr/local/appl/MSI/MSI_testjobs .
cd /usr/local/appl/MSI/MSI_testjobs/Discover" to "
cd /ptmp/(user login name)/MSI_testjobs/Discover":
Each Materials Studio job needs to have a specific name code assigned depending on the
the module being used by adding the PBS command, "
#PBS -N" in your script,
i.e. For Discover test job above, #PBS -N Zstest command line has been added to the
discover.pbs script. Hence, here are the PBS name codes need to be given according to modules:
For more information on PBS commands, you may visit PBS Batch Script Web Site. For further information on Accelrys, please contact MCSR Consultancy Group via emailing assist at mcsr.olemiss.edu.