# v4.2.x **URL:** https://nemo-ocean.discourse.group/c/versions/v4-2-x/12.md?page=2 [Latest](https://nemo-ocean.discourse.group/latest.md) · [Categories](https://nemo-ocean.discourse.group/categories.md) · [Tags](https://nemo-ocean.discourse.group/tags.md) **Page:** 3 --- ## [Junk domain input at high processor number](https://nemo-ocean.discourse.group/t/junk-domain-input-at-high-processor-number/468)
**Author:** [@nick.heavens-cgg](https://nemo-ocean.discourse.group/u/nick.heavens-cgg)\ **Replies:** 11\ **Last updated:** [18 October 2024 09:50 UTC](https://nemo-ocean.discourse.group/t/junk-domain-input-at-high-processor-number/468 "2024-10-18T09:50:46Z")
I am currently working with a coupled framework between NEMO 4.2 and WAVEWATCH III for the UK coastal shelf at 1.5 km (AMM15). I am porting this at the moment to a supercomputer and running it with far more processors th… --- ## [MPI & restart inconsistencies with activated solar light penetration](https://nemo-ocean.discourse.group/t/mpi-restart-inconsistencies-with-activated-solar-light-penetration/756)
**Author:** [@r-hartmann](https://nemo-ocean.discourse.group/u/r-hartmann)\ **Replies:** 7\ **Last updated:** [17 October 2024 18:27 UTC](https://nemo-ocean.discourse.group/t/mpi-restart-inconsistencies-with-activated-solar-light-penetration/756 "2024-10-17T18:27:38Z")
Hi everyone, I recently started to use NEMO. Unfortunately, I obtain different results, depending on the number of MPI tasks used, whenever solar light penetration is activated (ln\_traqsr = true, for both options ln\_qsr… --- ## [Trcrad: Bug in ocean.output regarding tracer conservation](https://nemo-ocean.discourse.group/t/trcrad-bug-in-ocean-output-regarding-tracer-conservation/762)
**Author:** [@mchoblet](https://nemo-ocean.discourse.group/u/mchoblet)\ **Replies:** 0\ **Last updated:** [25 September 2024 07:54 UTC](https://nemo-ocean.discourse.group/t/trcrad-bug-in-ocean-output-regarding-tracer-conservation/762 "2024-09-25T07:54:12Z")
Good morning, We noticed a small bug regarding the ocean.output lines written by the trcrad routine (src/TOP/TRP/trcrad.F90 · main · NEMO Workspace / Nemo · GitLab). I’m reporting it here before opening an issue on the … --- ## [MPP\_PREP tools deprecated in 4.2.x?](https://nemo-ocean.discourse.group/t/mpp-prep-tools-deprecated-in-4-2-x/757)
**Author:** [@dupontf](https://nemo-ocean.discourse.group/u/dupontf)\ **Replies:** 1\ **Last updated:** [17 September 2024 14:39 UTC](https://nemo-ocean.discourse.group/t/mpp-prep-tools-deprecated-in-4-2-x/757 "2024-09-17T14:39:34Z")
Hi all, I have started using mpp\_optimiz\_zoom\_nc.F90 for preparing in advance best MPI distributions but found out that the code does not seem to have been updated to 4.2.x: missing extended computational grid relative… --- ## [Shallow water configuration example](https://nemo-ocean.discourse.group/t/shallow-water-configuration-example/737)
**Author:** [@teekarna](https://nemo-ocean.discourse.group/u/teekarna)\ **Replies:** 2\ **Last updated:** [20 August 2024 12:49 UTC](https://nemo-ocean.discourse.group/t/shallow-water-configuration-example/737 "2024-08-20T12:49:02Z")
NEMO v4.2.x now includes the SWE 2D shallow water module. Documentation is lacking, however. Is there an example configuration somewhere that could be compiled and executed? A simple idealized test with closed boundarie… --- ## [Compiling NEMO 4.2.2 with Intel compilers version 2024](https://nemo-ocean.discourse.group/t/compiling-nemo-4-2-2-with-intel-compilers-version-2024/733)
**Author:** [@joakim](https://nemo-ocean.discourse.group/u/joakim)\ **Replies:** 1\ **Last updated:** [5 August 2024 07:28 UTC](https://nemo-ocean.discourse.group/t/compiling-nemo-4-2-2-with-intel-compilers-version-2024/733 "2024-08-05T07:28:01Z")
Good afternoon I’m trying to compile NEMO 4.2.2 on a machine that only has the latest Intel compilers (v 2024.2). With the new versions, the names of the compilers have changed as follows: icc → icx ifort → ifx As I … --- ## [AGRIF - DOMAINcfg generated 1\_domain\_cfg.nc file has 2 exact longitude points](https://nemo-ocean.discourse.group/t/agrif-domaincfg-generated-1-domain-cfg-nc-file-has-2-exact-longitude-points/728)
**Author:** [@murat.gunduz](https://nemo-ocean.discourse.group/u/murat.gunduz)\ **Replies:** 1\ **Last updated:** [17 July 2024 08:37 UTC](https://nemo-ocean.discourse.group/t/agrif-domaincfg-generated-1-domain-cfg-nc-file-has-2-exact-longitude-points/728 "2024-07-17T08:37:54Z")
Dear NEMO users, I am using DOMAINcfg tools (compiled with the key\_agrif) to generate the child bathymetry domain file (i.e. 1\_domain\_cfg.nc). The generated file longitudes have the exact same longitude in the first tw… --- ## [Zos : sea\_surface\_height\_above\_geoid in NEMO](https://nemo-ocean.discourse.group/t/zos-sea-surface-height-above-geoid-in-nemo/515)
**Author:** [@amrtalaat](https://nemo-ocean.discourse.group/u/amrtalaat)\ **Replies:** 4\ **Last updated:** [6 July 2024 16:57 UTC](https://nemo-ocean.discourse.group/t/zos-sea-surface-height-above-geoid-in-nemo/515 "2024-07-06T16:57:51Z")
I have the variable zos being saved in a grid\_T.nc file. Based on the standard name, this variable represents the “sea surface height above geoid” which is the Absolute Dynamic Topography (ADT) : Since, ADT = SLAp + MD… --- ## [Help!Running NEMO 4.2.2 with XIOS is slower than running it without XIOS](https://nemo-ocean.discourse.group/t/help-running-nemo-4-2-2-with-xios-is-slower-than-running-it-without-xios/718)
**Author:** [@xhjhggybz](https://nemo-ocean.discourse.group/u/xhjhggybz)\ **Replies:** 1\ **Last updated:** [4 July 2024 12:13 UTC](https://nemo-ocean.discourse.group/t/help-running-nemo-4-2-2-with-xios-is-slower-than-running-it-without-xios/718 "2024-07-04T12:13:39Z")
Hello everyone, When running the GYRE\_PISCES case at 1/4° resolution, I found that using XIOS is much slower than not using it. I am using the initial XIOS configuration provided with NEMO. I would like to know how I ca… --- ## [Cold start initial velocity at nest boundary](https://nemo-ocean.discourse.group/t/cold-start-initial-velocity-at-nest-boundary/716)
**Author:** [@mhilt](https://nemo-ocean.discourse.group/u/mhilt)\ **Replies:** 0\ **Last updated:** [27 June 2024 14:18 UTC](https://nemo-ocean.discourse.group/t/cold-start-initial-velocity-at-nest-boundary/716 "2024-06-27T14:18:43Z")
Hello Nemo community, I am starting to run 2-way nested simulations with Nemo4.2.1-Agrif, I’ve started with a simple test in my regional configuration of a nest with no temporal nor spatial refinement. Child is initiali… --- ## [NEMO4.2: execution time spikes for some ts](https://nemo-ocean.discourse.group/t/nemo4-2-execution-time-spikes-for-some-ts/650)
**Author:** [@ngrivault](https://nemo-ocean.discourse.group/u/ngrivault)\ **Replies:** 3\ **Last updated:** [20 June 2024 09:45 UTC](https://nemo-ocean.discourse.group/t/nemo4-2-execution-time-spikes-for-some-ts/650 "2024-06-20T09:45:45Z")
Hello, Due to significant execution time difference between two of our HPCs, I am looking at how much time takes each individual time steps from the timing.output file, in function of the frequency of outputs (hourly, d… --- ## [AGRIF nest & no cyclic east-west boundaries (host)](https://nemo-ocean.discourse.group/t/agrif-nest-no-cyclic-east-west-boundaries-host/706)
**Author:** [@sykim](https://nemo-ocean.discourse.group/u/sykim)\ **Replies:** 4\ **Last updated:** [14 June 2024 04:29 UTC](https://nemo-ocean.discourse.group/t/agrif-nest-no-cyclic-east-west-boundaries-host/706 "2024-06-14T04:29:13Z")
Hi all, I’m trying to refine a northwestern Pacific with NEMO4.2.x. Below is AGRIF\_FixedGrids.in 1 65 210 250 416 5 5 3 0 The parent domain (ORCA05) has no cyclic east-west boundaries (nx = 720 & ny = 510). Howeve… --- ## [Ice initialization from SST](https://nemo-ocean.discourse.group/t/ice-initialization-from-sst/699)
**Author:** [@Iljamal](https://nemo-ocean.discourse.group/u/Iljamal)\ **Replies:** 1\ **Last updated:** [28 May 2024 16:12 UTC](https://nemo-ocean.discourse.group/t/ice-initialization-from-sst/699 "2024-05-28T16:12:24Z")
report for what seems to be bug: It seems that sea level (zos) is sensitive to initial fields for v4.2.2 Namely: If the model is initialized with initial fields where temperature is \< 2, the sea level drops to some … --- ## [How small are the "large water bodies" that NEMO can simulate](https://nemo-ocean.discourse.group/t/how-small-are-the-large-water-bodies-that-nemo-can-simulate/652)
**Author:** [@nick.heavens-cgg](https://nemo-ocean.discourse.group/u/nick.heavens-cgg)\ **Replies:** 2\ **Last updated:** [23 May 2024 10:49 UTC](https://nemo-ocean.discourse.group/t/how-small-are-the-large-water-bodies-that-nemo-can-simulate/652 "2024-05-23T10:49:42Z")
I am trying to refine a global coupled model I have developed. Somewhere in one of the NEMO manuals it says, " When a global ocean is coupled to an atmospheric model it is better to represent all large water bodies (e.… --- ## [Help with fldread.F90 for surface boundary conditions](https://nemo-ocean.discourse.group/t/help-with-fldread-f90-for-surface-boundary-conditions/692)
**Author:** [@David](https://nemo-ocean.discourse.group/u/David)\ **Replies:** 2\ **Last updated:** [6 May 2024 09:21 UTC](https://nemo-ocean.discourse.group/t/help-with-fldread-f90-for-surface-boundary-conditions/692 "2024-05-06T09:21:12Z")
Hi all, I used to force my configuration with yearly climatological emp fields at daily frequency, which worked fine. Now I’m trying to go to fields at monthly frequency, making use of the time-interpolation implemente… --- ## [Does NEMO support OpenMP?](https://nemo-ocean.discourse.group/t/does-nemo-support-openmp/669)
**Author:** [@Antonio](https://nemo-ocean.discourse.group/u/Antonio)\ **Replies:** 2\ **Last updated:** [28 April 2024 07:50 UTC](https://nemo-ocean.discourse.group/t/does-nemo-support-openmp/669 "2024-04-28T07:50:14Z")
Hello everyone! I’m a beginner and I’d like to use NEMO as a benchmark to test my HPC system and CPU. My system has 2 sockets, 80 physical cores and 160 logical cores. I use MPICH 4.2.0 and NEMO 4.2.2. When I run the co… --- ## [How to change the output directory of mesh\_mask\_XXX files and ocean.output\_XXX files?](https://nemo-ocean.discourse.group/t/how-to-change-the-output-directory-of-mesh-mask-xxx-files-and-ocean-output-xxx-files/646)
**Author:** [@Antonio](https://nemo-ocean.discourse.group/u/Antonio)\ **Replies:** 2\ **Last updated:** [21 March 2024 12:48 UTC](https://nemo-ocean.discourse.group/t/how-to-change-the-output-directory-of-mesh-mask-xxx-files-and-ocean-output-xxx-files/646 "2024-03-21T12:48:45Z")
Hi everyone! I am a beginner for NEMO. After running nemo successfully, a lot of files were generated, but these files are all placed in the current directory, which I don’t think it’s easy to find other files for me. Ju… --- ## [What does these parameter mean?](https://nemo-ocean.discourse.group/t/what-does-these-parameter-mean/642)
**Author:** [@Antonio](https://nemo-ocean.discourse.group/u/Antonio)\ **Replies:** 6\ **Last updated:** [20 March 2024 12:52 UTC](https://nemo-ocean.discourse.group/t/what-does-these-parameter-mean/642 "2024-03-20T12:52:18Z")
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 … --- ## [BDY segments with NEMO4.2+](https://nemo-ocean.discourse.group/t/bdy-segments-with-nemo4-2/632)
**Author:** [@dupontf](https://nemo-ocean.discourse.group/u/dupontf)\ **Replies:** 7\ **Last updated:** [7 March 2024 16:38 UTC](https://nemo-ocean.discourse.group/t/bdy-segments-with-nemo4-2/632 "2024-03-07T16:38:51Z")
Hi all, I have a sort of philosophical question regarding the convention for BDY segments in NEMO4.2+. Reading the documentation (that mostly applies to global configurations) and the code, jpiglo is now calculated from… --- ## [AGRIF and optimization levels](https://nemo-ocean.discourse.group/t/agrif-and-optimization-levels/625)
**Author:** [@Franziska](https://nemo-ocean.discourse.group/u/Franziska)\ **Replies:** 3\ **Last updated:** [4 March 2024 14:56 UTC](https://nemo-ocean.discourse.group/t/agrif-and-optimization-levels/625 "2024-03-04T14:56:39Z")
Hi, with previous code versions it was recommended to not go beyond optimization level -O1 when compiling a configuration with AGRIF. Is this still the case in NEMO4.2(.2)? How far can one go with the optimization witho… --- ## [DOMAINcfg tool produces crashed domain and mask files](https://nemo-ocean.discourse.group/t/domaincfg-tool-produces-crashed-domain-and-mask-files/408)
**Author:** [@m-n-o](https://nemo-ocean.discourse.group/u/m-n-o)\ **Replies:** 8\ **Last updated:** [19 February 2024 09:48 UTC](https://nemo-ocean.discourse.group/t/domaincfg-tool-produces-crashed-domain-and-mask-files/408 "2024-02-19T09:48:28Z")
Hello! I’m trying to create a domain and mask files via DOMAINcfg tool. Coordinate mesh\_mask is cut from the ORCA\_R025 (min lat ~ 53 N) and I use GEBCO\_2022 (min lat ~45 N) as a bathymetry data. Input coordinates and b… --- ## [AGRIF and complex nest geometries](https://nemo-ocean.discourse.group/t/agrif-and-complex-nest-geometries/617)
**Author:** [@Franziska](https://nemo-ocean.discourse.group/u/Franziska)\ **Replies:** 0\ **Last updated:** [18 January 2024 17:09 UTC](https://nemo-ocean.discourse.group/t/agrif-and-complex-nest-geometries/617 "2024-01-18T17:09:45Z")
Hi all, I’m planning new nested configurations, building on INALT20 and VIKING20X respectively. Although I might build on those configurations directly, I was wondering whether there might be a way to improve the settin… --- ## [File DOME\_domcfg.nc\* not found](https://nemo-ocean.discourse.group/t/file-dome-domcfg-nc-not-found/582)
**Author:** [@banmianyu](https://nemo-ocean.discourse.group/u/banmianyu)\ **Replies:** 6\ **Last updated:** [14 December 2023 14:49 UTC](https://nemo-ocean.discourse.group/t/file-dome-domcfg-nc-not-found/582 "2023-12-14T14:49:42Z")
Hi everyone I want to run the test “DOME” in NMEO-4.2.0. The compilation went very smoothly, but when I ran the ./nemo, ocean.output file showed an error “File DOME\_domcfg.nc\* not found”. Anyone can tell me how can I f… --- ## [Agrif and vertical remap](https://nemo-ocean.discourse.group/t/agrif-and-vertical-remap/588)
**Author:** [@Luc](https://nemo-ocean.discourse.group/u/Luc)\ **Replies:** 4\ **Last updated:** [24 November 2023 09:46 UTC](https://nemo-ocean.discourse.group/t/agrif-and-vertical-remap/588 "2023-11-24T09:46:49Z")
Hello all, I use DOMAINcfg to define a parent grid mesh, and some children. I define the vertical zps layers by specifying ppkt, ppacr, ppdzmin, pphmax in the &namdom namelist. Then, in &namcfg , I define jpkdta and jp… --- ## [Very poor scaling with OpenIFS + NEMO 4.2 + XIOS 3 (slow)](https://nemo-ocean.discourse.group/t/very-poor-scaling-with-openifs-nemo-4-2-xios-3-slow/576)
**Author:** [@joakim](https://nemo-ocean.discourse.group/u/joakim)\ **Replies:** 10\ **Last updated:** [17 November 2023 12:34 UTC](https://nemo-ocean.discourse.group/t/very-poor-scaling-with-openifs-nemo-4-2-xios-3-slow/576 "2023-11-17T12:34:40Z")
Good afternoon I recently did some test runs with a coupled model with OpenIFS 43r3 + NEMO 4.2 + XIOS 3. The resolutions are 100 km (OpenIFS) and eORCA025 L75, and output from both OpenIFS and NEMO are handled by XIOS. … --- ## [Internal wave-driven mixing parameterization input fields changed](https://nemo-ocean.discourse.group/t/internal-wave-driven-mixing-parameterization-input-fields-changed/589)
**Author:** [@rabbit](https://nemo-ocean.discourse.group/u/rabbit)\ **Replies:** 2\ **Last updated:** [16 November 2023 12:18 UTC](https://nemo-ocean.discourse.group/t/internal-wave-driven-mixing-parameterization-input-fields-changed/589 "2023-11-16T12:18:45Z")
Tidal mixing parameterization (activated with ln\_zdfiwm = .true.; input files prescribed in &namzdf\_iwm) has been reworked in v4.2. In previous versions it required 5 input fields (usually provided as 5 NetCDF files: m… --- ## [DOMAINcfg 1-way nesting](https://nemo-ocean.discourse.group/t/domaincfg-1-way-nesting/450)
**Author:** [@qtqw](https://nemo-ocean.discourse.group/u/qtqw)\ **Replies:** 3\ **Last updated:** [24 October 2023 13:04 UTC](https://nemo-ocean.discourse.group/t/domaincfg-1-way-nesting/450 "2023-10-24T13:04:55Z")
I use DOMAINcfg to create a nested domain, e.g. files 1\_domain\_cfg.nc and domain\_cfg.nc I found that while creating a nested domain DOMAINcfg also changes bathymetry in parent domain in the area where nested domain is s… --- ## [Seg. fault after compiling XIOS and NEMO with openmpi 4.1 and intel 18](https://nemo-ocean.discourse.group/t/seg-fault-after-compiling-xios-and-nemo-with-openmpi-4-1-and-intel-18/573)
**Author:** [@spence-cgg](https://nemo-ocean.discourse.group/u/spence-cgg)\ **Replies:** 2\ **Last updated:** [17 October 2023 08:24 UTC](https://nemo-ocean.discourse.group/t/seg-fault-after-compiling-xios-and-nemo-with-openmpi-4-1-and-intel-18/573 "2023-10-17T08:24:19Z")
Hi, I appreciate this probably isn’t an easy one without giving a lot of information about my environment and compilation settings, but I’m at a loss so any suggestions would be welcome… I’m using openmpi 4.1.0 with in… --- ## [Contrasting Behaviour in Reading bdydtav files between GNU and PGI Builds](https://nemo-ocean.discourse.group/t/contrasting-behaviour-in-reading-bdydtav-files-between-gnu-and-pgi-builds/565)
**Author:** [@nick.heavens-cgg](https://nemo-ocean.discourse.group/u/nick.heavens-cgg)\ **Replies:** 0\ **Last updated:** [2 October 2023 08:55 UTC](https://nemo-ocean.discourse.group/t/contrasting-behaviour-in-reading-bdydtav-files-between-gnu-and-pgi-builds/565 "2023-10-02T08:55:48Z")
I have been trying to build NEMO with the legacy Portland Group compilers (part of the Nvidia HPC SDK version 23.7). I found the issue three years ago documented in #2579 (PGI compiler does allow read values from namelis… --- ## [Restart fails with ice variables not found](https://nemo-ocean.discourse.group/t/restart-fails-with-ice-variables-not-found/541)
**Author:** [@knaughten](https://nemo-ocean.discourse.group/u/knaughten)\ **Replies:** 4\ **Last updated:** [2 August 2023 16:32 UTC](https://nemo-ocean.discourse.group/t/restart-fails-with-ice-variables-not-found/541 "2023-08-02T16:32:57Z")
Hello, I am new to NEMO so apologies if this is a beginner question! I am trying out a colleague’s configuration on a different HPC facility, using NEMO 4.2. When I try to restart with the restart files he provided, it … [Previous page](https://nemo-ocean.discourse.group/c/versions/v4-2-x/12.md?page=1) [Next page](https://nemo-ocean.discourse.group/c/versions/v4-2-x/12.md?page=3)