SPECFEM3D

Description

From the SPECFEM3D web site: SPECFEM3D Cartesian simulates acoustic (fluid), elastic (solid), coupled acoustic/elastic, poroelastic or seismic wave propagation in any type of conforming mesh of hexahedra (structured or not.) It can, for instance, model seismic waves propagating in sedimentary basins or any other regional geological model following earthquakes. It can also be used for non-destructive testing or for ocean acoustics.

Version

3.0

Authorized Users

CIRCE account holders
RRA account holders
SC account holders

Platforms

CIRCE cluster
RRA cluster
SC cluster

Modules

SPECFEM3D requires the following module file to run:

apps/specfem3d/3.0

See Modules for more information.

Running SPECFEM3D on CIRCE/SC

The SPECFEM3D user guide is essential to understanding the application and making the most of it. The guide and this page should help you to get started with your simulations. Please refer to the Documentation section for a link to the guide.

Note on CIRCE: Make sure to run your jobs from your $WORK directory!
Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.

How to Submit Jobs

Provided are directions for running an interactive job and a batch script for running SPECFEM3D as a multi-processor job. These scripts are provided as examples only.

Using the GUI Tools

Establishing a GUI connection to CIRCE/SC

To use SPECFEM3D, you will need to connect to CIRCE/SC with GUI redirection, either using:

CIRCE/SC Desktop Environment
SSH with X11 redirection
- If connecting from OSX or Linux via SSH, please ensure that you use one of the following commands to properly redirect X11:
  - ```
  [user@localhost ~]$ ssh -X circe.rc.usf.edu
```
  or
- ```
[user@localhost ~]$ ssh -X sc.rc.usf.edu
```

Once connected to CIRCE, you can open SPECFEM3D using the steps below :

[user@login0 ~]$ srun --time=10:00:00 --nodes=1 --ntasks-per-node=4 --pty /bin/bash
[user@wh-520-4-1 ~]$ module add apps/specfem3d/3.0
[user@wh-520-4-1 ~]$ xspecfem3D

Distributed Parallel

This script (for this example, call it "specfem3d-test.sh") can be copied into your job directory (the folder with your input files and database files) and modified so that you can submit batch processes to the queues.

#!/bin/sh
#SBATCH --job-name=specfem3d_job_name
#SBATCH --time=01:00:00
#SBATCH --ntasks=8

#### SLURM 8 processor SPECFEM3D test to run for 1 hour.


module load apps/specfem3d/3.0

mpirun xspecfem3D input.file

Next, you can change to your job’s directory, and run the sbatch command to submit the job:

[user@login0 ~]$ cd my/jobdir
[user@login0 jobdir]$ sbatch ./specfem3d-test.sh

You can view the status of your job with the “squeue -u <username>” command

Documentation

Home Page, User Guides, and Manuals

SPECFEM3D Home Page:
- https://geodynamics.org/cig/software/specfem3d/
SPECFEM3D Documentation:
- https://geodynamics.org/cig/software/specfem3d/specfem3d-manual.pdf
- /apps/specfem3d/3.0/doc

Benchmarks, Known Tests, Examples, Tutorials, and Other Resources

SPECFEM3D Examples
- /apps/specfem3d/3.0/EXAMPLES

More Job Information

See the following for more detailed job submission information:

Reporting Bugs

Report bugs with SPECFEM3D to the IT Help Desk: rc-help@usf.edu