Materials Studio

De Wiki de Calcul Québec
Aller à : Navigation, rechercher
Cette page est une traduction de la page Materials Studio et la traduction est complétée à 100 % et à jour.

Autres langues :anglais 100% • ‎français 100%

Note: This documentation has been tested on Colosse. Some instructions may be different on other servers.

Sommaire

Description

Materials Studio is a complete environment for modelling and simulation designed to allow researchers in materials science and chemistry to predict and understand the relations between the atomic and molecular structure of a material and its properties.

Materials Studio is a commercial application, each research group that would like to use it at Calcul Québec must therefore provide its own license.

Usage on Colosse

Availability

To use Materials Studio on Colosse, make sure that your project manager does indeed have a license for this commercial software. To see quickly if Materials Studio is available for you, after connecting to Colosse by ssh enter the command

[nom@serveur $] module avail


to list all of the available applications. You should see it appear in general at the bottom of the screen.

apps/MaterialsStudio/6.0

Remember that the mere presence of the application doesn't necessarily give you the right to use it. Speak with your project manager to verify the availability of this software for your research group.

SSH Configuration and Keys

Materials Studio uses a job submission procedure which requires the installation of an automatic authentification process between the compute nodes. As no information can be entered by the user during the communication between the nodes, it may be necessary to generate ssh keys. On some servers this step may be done automatically. To check to see if that's the case, you can use the command

[nom@serveur $] ssh localhost


The SSH connection should work without asking you anything. If this is not the case, you should generate ssh keys.

List of Available Applications

  • RunAmorphousCell.sh
  • RunCASTEP.sh
  • RunDFTB.sh
  • RunDFTBpara.sh
  • RunDMol3.sh
  • RunDPD.sh
  • RunDiscover.sh
  • RunEquilibria.sh
  • RunGULP.sh
  • RunKinetix.sh
  • RunMatServer.sh
  • RunMesoDyn.sh
  • RunONETEP.sh
  • RunQMERA.sh
  • RunMatScript.sh
  • RunVAMP.sh

Running Materials Studio on Colosse

To submit jobs to the Moab scheduler, you need to create a job submission script as follows

File : submit.sh
#!/bin/bash
 
#PBS -N give_a_name     # The job name
#PBS -A aaa-111-aa     # Project to which the job is assigned
#PBS -l nodes=2:ppn=8        # Number of nodes and cores per node
#PBS -l walltime=15:00:00    # Maximal duration of the job (here, 15 hours)
 
module load apps/MaterialsStudio/6.0
 
# Run the job in the current directory
cd $PBS_O_WORKDIR
 
# Create a list of nodes to be used for the job
DSD_MachineList="machines.LINUX"
/clumeq/bin/moabhl2hl.py --format HP-MPI > $DSD_MachineList
export DSD_MachineList
 
# Count the number of CPU cores allocated
NN=$(wc -l < $PBS_NODEFILE)
 
# Job to run
RunDMol3.sh -np $NN benzene


Next you just need to submit the job with the command

[nom@serveur $] msub submit.sh


Outils personnels
Espaces de noms

Variantes
Actions
Navigation
Ressources de Calcul Québec
Outils
Partager