Changes between Version 2 and Version 3 of cypress/MaterialsStudio

Timestamp:

05/08/18 17:14:07 (7 years ago)

Author:

hoang

Comment:

—

cypress/MaterialsStudio

@@ -1 +1 @@
 == Materials Studio ==
 
-Materials Studio is commercial, licensed software.  You must have a license to use it.
+[http://accelrys.com/products/collaborative-science/biovia-materials-studio/ Materials Studio] is a commercial software distributed by BIOVIA (formerly Accelrys) for simulation and modeling in materials science.  '''Only licensed users have access to Materials Studio on Cypress.'''
 
-To create input files for running jobs on Cypress, set up the simulation in Materials Studio Visualizer on your desktop.  For example, you can set up a "DMol3" calculation.  Instead of selecting the "Run" button to do a run on your desktop, you can select "Files" to instead just create the input files for a run, as shown below:
+The complete Materials Studio suite is only available for Windows workstations, but BIOVIA provides Linux versions of its computationally intensive routines, which allows you to make use of Cypress for computationally intensive calculations.  Here, we will show how to set up a calculation on your workstation in order to run on Cypress.
+
+The image below shows the setup for a typical calculation you would perform on your workstation, in this case, a quantum mechanical energy calculation.  You would push the "Run" button to run this on your workstation.  We will not do this.  Instead, we will show how to set up and run the calculation on Cypress.  First, we will create the input files needed.  Instead of "Run", we select "Files", as shown below:
 
 [[Image(create_files.png)]]
 
-Press "Save Files" to save the files:
+and then press "Save Files" to save the input files:
 
 [[Image(save_files.png)]]
 
-Locate the folder where Materials Studio saved the input files (*.input, *.car, etc.).  The folder should appear in the Project pane, where you can explore it.  Copy this folder to Cypress.
+Locate the folder where Materials Studio saved the input files (in this example, "benzene.input", "benzene.car", etc.).  The folder should appear in the Project pane, where you can explore it.  
 
 [[Image(files_folder.png)]]
 
-To run the job on Cypress, create a job script and submit it with the "sbatch" command.  An example job script follows:
+Copy these input files to Cypress using [https://wiki.hpc.tulane.edu/trac/wiki/cypress/FileTransfer one of the methods we explained earlier for file transfers to Cypress].  We now need to [[/wiki/cypress/using#SubmittingJobsonCypress|create a SLURM script]] to run our job.  Suppose we have copied the input files to our folder /home/joeuser/benzene.  Then, an example job script would be as follows:
 
 {{{
 #!/bin/bash
 #SBATCH --job-name=benzene
-#SBATCH --time=02:00:00
+#SBATCH --time=20:00:00
 #SBATCH --nodes=1
 #SBATCH --ntasks-per-node=20
 
-cd /path/to/input/files
-/path/to/materials/studio/etc/DMol3/bin/RunDMol3.sh  -np 20 "benzene"
+cd /home/joeuser/benzene
+/share/apps/materials_studio/2017R2/MaterialsStudio17.2/etc/DMol3/bin/RunDMol3.sh -np 20 "benzene"
 }}}
 
-This requests a node with 20 CPU cores to run the job, and uses the "RunDMol3.sh" script to do a parallel run with 20 cores.  Replace "/path/to/input/files" with the location of the input files (i.e. the *.input and *.car files) you copied over and "/path/to/materials/studio" with the location of your Materials Studio installation.
-
-For more details about submitting jobs on Cypress, please see our [[/wiki/cypress/using#SubmittingJobsonCypress|wiki section on submitting jobs on Cypress]].
+This requests a node with 20 CPU cores to run the job, and uses the "RunDMol3.sh" script to do a parallel run with 20 cores.  The location of the "RunDMol3.sh" may differ depending on your license.  If you were not given this location when we installed the program for you, please contact us.