Unable to Run Delft3D-FM with Sigma Layers in Parallel on Linux Cluster - Forum - Delft3D Flexible Mesh
Hi all,
I'm currently trying to run a 3D Delft3D-FM (Version 2021.03) salinity simulation of an estuary using 10 sigma layers and struggling to get the simulation working on my Linux cluster. What's strange is that I'm able to get the simulation running in 2D on the same cluster and in full 3D on my person desktop (6 core machine) without any issues, but when I try and run it via DIMR on my 64 core cluster it doesn't work. I'm running it with 48 cores, and I get the following error:Unfortunately my .dia file isn't very informative either. I'm partitioning the model using the automatic partition exporter (METIS, PETSC algorithm) in the GUI. I've tried other partitioning methods to no success. I've attached the full error code and .dia files to this thread.
One thing I noticed is that my GUI does not contain the "contiguous domains" option which is present in the manual (see images below). Indeed, when I check my partition I see that there are some portions of the model which are discontinuous - is that what could be causing the issue?
My Delft3D-FM Partition Exporter Options:
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Manual Delft3D-FM Partition Exporter Options:
![]()
Example of my discontinuous mesh:
![]()
I'm currently trying to run a 3D Delft3D-FM (Version 2021.03) salinity simulation of an estuary using 10 sigma layers and struggling to get the simulation working on my Linux cluster. What's strange is that I'm able to get the simulation running in 2D on the same cluster and in full 3D on my person desktop (6 core machine) without any issues, but when I try and run it via DIMR on my 64 core cluster it doesn't work. I'm running it with 48 cores, and I get the following error:
=============================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= PID 72679 RUNNING AT dc011
= EXIT CODE: 11
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)
This typically refers to a problem with your application.
Please see the FAQ page for debugging suggestions
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= PID 72679 RUNNING AT dc011
= EXIT CODE: 11
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)
This typically refers to a problem with your application.
Please see the FAQ page for debugging suggestions
One thing I noticed is that my GUI does not contain the "contiguous domains" option which is present in the manual (see images below). Indeed, when I check my partition I see that there are some portions of the model which are discontinuous - is that what could be causing the issue?
My Delft3D-FM Partition Exporter Options:
Manual Delft3D-FM Partition Exporter Options:
Example of my discontinuous mesh:
