# What does these parameter mean? **URL:** \ **Category:** v4.2.x\ **Tags:** gyre\ **Created:** [19 March 2024 02:52 UTC](https://nemo-ocean.discourse.group/t/what-does-these-parameter-mean/642 "2024-03-19T02:52:37Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![Antonio](https://avatars.discourse-cdn.com/v4/letter/a/6de8d8/32.png) [@Antonio](https://nemo-ocean.discourse.group/u/Antonio)\ **Post date:** [19 March 2024 02:52 UTC](https://nemo-ocean.discourse.group/t/what-does-these-parameter-mean/642/1 "2024-03-19T02:52:37Z")
Hi, everyone. I’m a beginner. I want to use NEMO-4.2.2 as a workload to test my machine, which has 80 physical cores and 160 logical cores. I use OpenMPI and the GYRE\_PISCES configuration to test. And I ran the command `mpirun --use-hwthread-cpus -n 160 ./nemo` However, my terminal dispaly an ERROR: > ## Abort(123) on node 0 (rank 0 in comm 0): application called MPI\_Abort(MPI\_COMM\_WORLD, 123) - process 0 Abort(123) on node 0 (rank 0 in comm 0): application called MPI\_Abort(MPI\_COMM\_WORLD, 123) - process 0 Abort(123) on node 0 (rank 0 in comm 0): application called MPI\_Abort(MPI\_COMM\_WORLD, 123) - process 0 > > prterun detected that one or more processes exited with non-zero status, > thus causing the job to be terminated. The first process to do so was: > > ## Process name: [prterun-black-1592854@1,10] Exit code: 123 I only modified some parameters of namlist\_cfg and namlist\_ref. The namlist\_cfg, namlist\_ref and the ocean.output are following: **The modified part of namlist\_cfg is: nn\_GYRE, jpiglo, jpjglo, rn\_Dt** > !----------------------------------------------------------------------- > &namusr\_def ! GYRE user defined namelist > !----------------------------------------------------------------------- > nn\_GYRE = 4 ! GYRE resolution [1/degrees] > ln\_bench = .true. ! ! =T benchmark with gyre: the gridsize is kept constant > jpiglo = 1440 > jpjglo = 720 > jpkglo = 31 ! number of model levels > / > !----------------------------------------------------------------------- > &namdom ! time and space domain > !----------------------------------------------------------------------- > ln\_linssh = .true. ! =T linear free surface ==\>\> model level are fixed in time > ! > rn\_Dt = 1200. ! time step for the dynamics > / **The modified part of namlist\_ref is: jpni, jpnj** > !----------------------------------------------------------------------- > &nammpp ! Massively Parallel Processing > !----------------------------------------------------------------------- > ln\_listonly = .false. ! do nothing else than listing the best domain decompositions (with land domains suppression) > ! ! if T: the largest number of cores tested is defined by max(mppsize, jpni\*jpnj) > ln\_nnogather = .true. ! activate code to avoid mpi\_allgather use at the northfold > jpni = 10 ! number of processors following i (set automatically if \< 1), see also ln\_listonly = T > jpnj = 16 ! number of processors following j (set automatically if \< 1), see also ln\_listonly = T > nn\_hls = 1 ! halo width (applies to both rows and columns) > nn\_comm = 1 ! comm choice > / And the ocean.output is following: > AAAAAAAA > > par\_kind : wp = Working precision = dp = double-precision > > ```auto > > ===>>> : E R R O R > > =========== > > misspelled variable in namelist namusr_def in configuration namelist iostat = 5010 > > > usr_def_nam : read the user defined namelist (namusr_def) in namelist_cfg > > ``` > > ``` > Namelist namusr_def : GYRE case > GYRE used as Benchmark (=T) ln_bench = T > inverse resolution & implied domain size nn_GYRE = 4 > Ni0glo = 30*nn_GYRE Ni0glo = 122 > Nj0glo = 20*nn_GYRE Nj0glo = 82 > number of model levels jpkglo = 0 > > Namelist nammpp > processor grid extent in i jpni = 10 > processor grid extent in j jpnj = 16 > avoid use of mpi_allgather at the north fold ln_nnogather = T > halo width (applies to both rows and columns) nn_hls = 1 > choice of communication method nn_comm = 1 > > ``` > > mpp\_init: > > ```auto > The chosen domain decomposition 10 x 16 with 159 land subdomains > - uses a total of 1 mpi process > - has mpi subdomains with a maximum size of (jpi = 15, jpj = 8, jpi*jpj = 120) > The best domain decompostion 1 x 1 with 0 land subdomains > - uses a total of 1 mpi process > - has mpi subdomains with a maximum size of (jpi = 124, jpj = 84, jpi*jpj = 10416) > > ===>>> : E R R O R > > =========== > > With this specified domain decomposition: jpni = 10 jpnj = 16 > we can eliminate only 0 land mpi subdomains therefore > the number of ocean mpi subdomains ( 160) exceed the number of MPI processes: 1 > > ==>>> There is the list of best domain decompositions you should use: > > For your information: > list of the best partitions including land supression > ----------------------------------------------------- > > nb_cores oce: 1, land domains excluded: 0 ( 0.0%), largest oce domain: 10416 ( 124 x 84 ) > > ``` Can someone tell me what these parameters mean? How should I modify the parameters? Thank you very much. ---
**Author:** ![smasson](https://avatars.discourse-cdn.com/v4/letter/s/eb9ed0/32.png) [@smasson](https://nemo-ocean.discourse.group/u/smasson)\ **Post date:** [19 March 2024 14:02 UTC](https://nemo-ocean.discourse.group/t/what-does-these-parameter-mean/642/2 "2024-03-19T14:02:06Z")
Exit code 123 means that NEMO detected at least 1 error. As you saw, errors are reported in the ocean.output file. In your case, as written in your ocean.output file, NEMO detected 2 errors: 1. `misspelled variable in namelist namusr_def in configuration namelist` : which can be rephrased by: you have a typo somewhere in one of the variables name in the namusr\_def block on the file nameilist\_cfg. ```fortran jpiglo = 1440 jpjglo = 720 ``` are not part of namusr\_def and should not be there. 1. ` the number of ocean mpi subdomains ( 160) exceed the number of MPI processes: 1` : it says that you run NEMO on 1 MPI process instead of 160. In other words, you command `mpirun --use-hwthread-cpus -n 160 ./nemo` is not working as its attributes 1 MPI task to NEMO instead of 160… I would try `mpirun -np 80 ./nemo` (use only the physical cores if you want good performances). ---
**Author:** ![Antonio](https://avatars.discourse-cdn.com/v4/letter/a/6de8d8/32.png) [@Antonio](https://nemo-ocean.discourse.group/u/Antonio)\ **Post date:** [19 March 2024 14:38 UTC](https://nemo-ocean.discourse.group/t/what-does-these-parameter-mean/642/3 "2024-03-19T14:38:26Z")
Thank you for your reply. I just deleted jpiglo, jpjglo and used the command `mpirun -n 80 ./nemo` run the application again. However, it still display ERROR message: > ## Abort(123) on node 0 (rank 0 in comm 0): application called MPI\_Abort(MPI\_COMM\_WORLD, 123) - process 0 Abort(123) on node 0 (rank 0 in comm 0): application called MPI\_Abort(MPI\_COMM\_WORLD, 123) - process 0 … > > prterun detected that one or more processes exited with non-zero status, > thus causing the job to be terminated. The first process to do so was: > > ## Process name: [prterun-black-2885641@1,43] Exit code: 123 I have two conjectures: 1. The parameters`jpni, jpnj` I set it wrongly. If so, how should I set these two parameters? 2. The MPI process doesn’t match the physical core I’m trying to run, as the oputput shows `uses a total of 1 mpi process` but I use 80 physical cores. If so, how should I get the MPI process actually running from 1 to 80? Looking forward to your reply. ---
**Author:** ![smasson](https://avatars.discourse-cdn.com/v4/letter/s/eb9ed0/32.png) [@smasson](https://nemo-ocean.discourse.group/u/smasson)\ **Post date:** [19 March 2024 14:54 UTC](https://nemo-ocean.discourse.group/t/what-does-these-parameter-mean/642/4 "2024-03-19T14:54:47Z")
You must look at the error message in ocean.output file. You can keep the default definition of `jpni` and `jpnj` to 0. ---
**Author:** ![Antonio](https://avatars.discourse-cdn.com/v4/letter/a/6de8d8/32.png) [@Antonio](https://nemo-ocean.discourse.group/u/Antonio)\ **Post date:** [20 March 2024 10:37 UTC](https://nemo-ocean.discourse.group/t/what-does-these-parameter-mean/642/5 "2024-03-20T10:37:50Z")
I looked at the ocean.output file. Part of the document reads as follows: > mpp\_init: > > ```auto > The chosen domain decomposition 1 x 1 with -155 land subdomains > - uses a total of 156 mpi process > - has mpi subdomains with a maximum size of (jpi = 124, jpj = 84, jpi*jpj = 10416) > The best domain decompostion 13 x 12 with 0 land subdomains > - uses a total of 156 mpi process > - has mpi subdomains with a maximum size of (jpi = 12, jpj = 9, jpi*jpj = 108) > > ===>>> : W A R N I N G > > =============== > > ==> You could therefore have smaller mpi subdomains with the same number of mpi processes > > --- YOU ARE WASTING CPU... --- > > The number of mpi processes: 156 > exceeds the maximum number of subdomains (ocean+land) = 1 > defined by the following domain decomposition: jpni = 1 jpnj = 1 > You should: > - either properly prescribe your domain decomposition with jpni and jpnj > in order to be consistent with the number of mpi process you want to use > even IF it not the best choice... > - or use the automatic and optimal domain decomposition and pick up one of > the domain decomposition proposed in the list bellow > > For your information: > list of the best partitions including land supression > ----------------------------------------------------- > > ``` Therefore, I think I may have a problem with domain decomposition. The solution is either **prescribe my domain decomposition with jpni and jpnj** or **use the automatic and optimal domain decomposition**. I prefer the latter but I don’t know how to do. Can you help me? Thank you very much. ---
**Author:** ![smasson](https://avatars.discourse-cdn.com/v4/letter/s/eb9ed0/32.png) [@smasson](https://nemo-ocean.discourse.group/u/smasson)\ **Post date:** [20 March 2024 11:49 UTC](https://nemo-ocean.discourse.group/t/what-does-these-parameter-mean/642/6 "2024-03-20T11:49:40Z")
As I said, set `jpni` and `jpnj` to 0. ---
**Author:** ![Antonio](https://avatars.discourse-cdn.com/v4/letter/a/6de8d8/32.png) [@Antonio](https://nemo-ocean.discourse.group/u/Antonio)\ **Post date:** [20 March 2024 12:52 UTC](https://nemo-ocean.discourse.group/t/what-does-these-parameter-mean/642/7 "2024-03-20T12:52:18Z")
I run it successfully. Thank you very much. 🙏 ---
**Author:** ![smasson](https://avatars.discourse-cdn.com/v4/letter/s/eb9ed0/32.png) [@smasson](https://nemo-ocean.discourse.group/u/smasson)\ **Post date:** [21 March 2024 10:16 UTC](https://nemo-ocean.discourse.group/t/what-does-these-parameter-mean/642/8 "2024-03-21T10:16:09Z")