Building and running SOFI3D - ()
SOFI3D is used for processing three dimensional seismic data.
Building SOFI3D
-
Clone the git repository where SOFI3D is located
git clone https://git.scc.kit.edu/GPIAG-Software/SOFI3D.git
-
Load one of the MPI GCC Modules
module load mpich/ge/gcc
ORmodule load openmpi/gcc
-
Unload the default C compiler
module unload gcc
-
Change to the SOFI3D src directory
cd SOFI3D/src
-
Run the
make all
command and watch out for errors.
If you don't get any errors, SOFI3D has been successfully built.
- NOTE: There may be some warnings about variables being set but not used. This should be fine.
Running SOFI3D on a Cluster
When running in parallel SOFI will decompose the domain you are working on and split
it into smaller chunks for each processor to work on. The number of chunks will depend
on the number of nodes and tasks you set in the submission file (see below) and in
the SOFI3D/par/in_and_out/sofi3D.json
parameter file. It is recommended to split the domain into relatively square/cubic
sections.
The parameters file creates by default will not necessarily work with the settings
you want to use to submit the job to the queue. You will need to edit it before attempting
to submit to the cluster. The default parameters file can be found at SOFI3D/par/in_and_out/sofi3D.json
. Under Domain Decomposition
, the variables NPROCX
, NPROCY
, and NPROCZ
must have their variables changed such that NPROCX * NPROCY * NPROCZ = Number of processors requested
.
- For the example submission script below
NPROCX * NPROCY * NPROCZ = 8 = (4 tasks per node) * (2 nodes)
Use the following script as a template submission script. Adjust paths and resource requirements where necessary.
SOFI3D/par/in_and_out/sofi3D.json:
#________________________________- #JSON PARAMETER FILE FOR SOFI3D #________________________________- # description: example of json input file # description/name of the model: homogeneous full space (hh.c) # { "Domain Decomposition" : "comment", "NPROCX" : "2", "NPROCY" : "2", "NPROCZ" : "2", ...}Sbatch submission script sofi3DSubmission.sh
:
After you've created your submission script and modified the sofi2D.json parameters file you can submit your job using sbatch.
sbatch sofi3DSubmission.shSee the Slurm tutorial for more instructions on how to submit jobs.