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RE: Problem while running the parallel job.

Niraj Bal Tamang, modified 3 Years ago.

Problem while running the parallel job.

Advanced Augur Posts: 34 Join Date: 4/26/21 Recent Posts
I partitioned my morphodynamic model and uploaded all input files into the remote machine to run parallel. I submitted the batch job and it starts to work on the input files. But as the process reaches the "INFO:Start partitioning model", followed by  "INFO: added node-based ghostcells", the model stops progressing and stalls. It doesn't give any error message but just stalls at that INFO message for hours. Can anyone please tell me what can cause this and how this can be handled? I get the following error in the diagnostic file:
** INFO   : boundary: 'Inflow.pli' opened 0 cells.
** INFO   : sedfracbndSand Inflow.pli       0 nr of sedfrac bndcells
** ERROR  :     3 small flow links discarded. Run 'merge circumcenters' to remove small flow links or increase threshold
** INFO   : Closed file : FlowFM.ext
Thank you
Victor Chavarrias, modified 3 Years ago.

RE: Problem while running the parallel job.

Famous Fortune teller Posts: 97 Join Date: 4/24/20 Recent Posts
 The error states that the grid has some issues. A link is considered small when its length $L$ is shorter than 9% (by default, but can be changed) of the average square root of the areas of the adjacent cells ($L<0.9*0.5*(sqrt(ba_1)+sqrt(ba_2)$). Note that in a square grid of size $l$, links have length $l$ and the average of the cells areas are also $l$. The idea behind this threshold is to prevent cells that, while being orthogonal and of the same area (i.e., perfect smoothness), they are such that the midpoint of the link is far from the cell edge. In this case the accuracy is low. 

I would recommend you to inspect the grid. The GUI has the option to merge the links which are small, if I am not mistaken.  
Niraj Bal Tamang, modified 3 Years ago.

RE: Problem while running the parallel job.

Advanced Augur Posts: 34 Join Date: 4/26/21 Recent Posts
Thanks a lot. I checked it in the GUI and found the option in the RFGRID settings. I was wondering if this could be done in commandline as well. In the error, it was saying to run 'merge circumcenters' to remove small flow links. I realized how to change the threshold in the GUI but was wondering if this command can be used in the commandline with the Grid file.
Victor Chavarrias, modified 3 Years ago.

RE: Problem while running the parallel job.

Famous Fortune teller Posts: 97 Join Date: 4/24/20 Recent Posts
To my knowledge this is not a command-line feature. The option 'merge circumcenters' appears when running file-based because there is a developers GUI which has the option available.