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Run the main program

Step 1: Connect to the server

As we did in the Configure SSH connection section Step 3.

Step 2: Create and open directory

  1. Create new folder in your temporary directory for running simulation. You don’t want to run any simulation directly in the work folder because it has slow disk RW speed and limited storage size.
cd scratch
mkdir test-run
  1. Click Open Folder and navigate to the folder you created, then click Ok.

Step 3: Create input files

For a quick start, you can copy input file from the example folder under your corresponding main program, such as for ferroelectric apps/muFerro/examples.

cp /storage/home/xuc116/work/PhaseFieldSDK/apps/PhaseFieldFerroelectric/examples/basic/*.toml .

If you copy the above command, remember to replace the user name with your own username.

Step 4: Test run the simulation

Before submitting a simulation job, you can first try running the simulation with a smaller system directly on the login node. Remember you have to shrink the size of these calculations, because login node has limit on memory. To do so, you need to open the input.toml file and update the values behind the simulation_grid keyword.

Since we have already configured the muferro alias in the previous step, you can simply call muferro within the test-run folder to start the ferroelectric program.

Step 5: Submit simulation jobs

  1. Prepare a pbs file, here is an example pbs file for PSU ACI server, let’s call it ferro.pbs
#PBS -l nodes=1:ppn=1
#PBS -l walltime=24:00:00
#PBS -l pmem=5g
#PBS -A open
#PBS -N jobname
#PBS -j oe
#PBS -M [email protected] -me

module load intel
module load mkl
module load impi

echo `date`
echo `date`
  1. Submit the job to pbs queue with qsub ferro.pbs