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RE: "Number of nodes/links read unequal to nodes/links in model" in paralle
Niraj Bal Tamang, modified 3 Years ago.
"Number of nodes/links read unequal to nodes/links in model" in parallel
Advanced Augur Posts: 34 Join Date: 4/26/21 Recent Posts
My morphodynamic model works fine when run in a single file but when I partition, it is giving me different errors every time. the recent one is the "Number of nodes/links read unequal to nodes/links in model" at the start of the run. I think I am making a mistake from the partition step to running parallel in the supercomputer. Can anyone please share the steps of partitioning morphodynamic model including input file feed, so that i can check where I am making the mistake?
Thank you
Thank you
Victor Chavarrias, modified 3 Years ago.
RE: "Number of nodes/links read unequal to nodes/links in model" in paralle
Famous Fortune teller Posts: 97 Join Date: 4/24/20 Recent Posts
The error seems to indicate that you are restarting a partitioned run. Is this true? The restart-files need to match each partition. Are the restart-files from a hydrodynamic simulation with the same partitioning?
Niraj Bal Tamang, modified 3 Years ago.
RE: "Number of nodes/links read unequal to nodes/links in model" in paralle
Advanced Augur Posts: 34 Join Date: 4/26/21 Recent Posts
Yes. I tried both ways as mentioned in the manual (using partitioned restart files as well as merging them and using a single restart file). I used the same polygon file to partition the morphodynamic model. I ran the hydrodynamic model in both partitioned and single run just to make the parallel run of morphodynamic model work. I tried both ways one at a time in the morphodynamic model but it didn't work. But the model is working without partitioning although takes a longer time.
Victor Chavarrias, modified 3 Years ago.
RE: "Number of nodes/links read unequal to nodes/links in model" in paralle
Famous Fortune teller Posts: 97 Join Date: 4/24/20 Recent Posts
The partitioned hydrodynamic run will create restart-files such as <simname_0000_20181112_000000_rst.nc>. Be sure to create the partition-polygon file (e.g. <simname_part.pol>).
For restarting in parallel:
In the mdu-file of the morphodynamic simulation, refer to the partition-polygon file in flag <PartitionFile> in block [geometry] as:
For restarting in parallel:
- Create a new folder for the morphodynamic run.
- Create the morphodynamic mdu-file in that folder.
- Add the partition-polygon file to the folder.
- Create a folder inside called, for instance, <rst>.
| 1 | [restart] |
| 2 | RestartFile = ./rst/simname_20181112_000000_rst.nc |
In the mdu-file of the morphodynamic simulation, refer to the partition-polygon file in flag <PartitionFile> in block [geometry] as:
| 1 | [geometry] |
| 2 | PartitionFile = simname_part.pol |
Niraj Bal Tamang, modified 3 Years ago.
RE: "Number of nodes/links read unequal to nodes/links in model" in paralle
Advanced Augur Posts: 34 Join Date: 4/26/21 Recent Posts
Thank you. I will give it a try. One more question regarding the icgsolver while partitioning. If I am partitioning the file in command prompt and later uploading them in Linux system, should the icgsolver be assigned as 6 or 7?
Victor Chavarrias, modified 3 Years ago.
RE: "Number of nodes/links read unequal to nodes/links in model" in paralle
Famous Fortune teller Posts: 97 Join Date: 4/24/20 Recent Posts
I would do the partitioning already in the cluster immediately before running. <icgsolver> needs to be set to 6 (petsc) for parallel in Linux.
Niraj Bal Tamang, modified 3 Years ago.
RE: "Number of nodes/links read unequal to nodes/links in model" in paralle
Advanced Augur Posts: 34 Join Date: 4/26/21 Recent Posts
Oh. May be this is where i might have made the mistake. I was using (run_dflowfm.bat "--partition:ndomains=36:genpolygon=1:icgsolver=6" <mdu file> <partition polygon file>) command for partitioning. So, does that mean i need to remove the icgsolver from the command and run it first to get the partition and again run it after adding the icgsolver part?
Victor Chavarrias, modified 3 Years ago.
RE: "Number of nodes/links read unequal to nodes/links in model" in paralle
Famous Fortune teller Posts: 97 Join Date: 4/24/20 Recent Posts
I am not fully sure I am understanding your workflow. The <icgsolver> flag is set when partitioning, as this is the step when the mdu-files are created. Is the partitioning succesfull? Do you see all the partitioned mdu-files with their correct restart file, partition-polygon-file, and <icgsolver> flag?