# Start NEMO 5.0 simulation from NEMO 4.2.2 restarts (including AGRIF) **URL:** \ **Category:** Uncategorized\ **Tags:** AGRIF\ **Created:** [14 February 2025 13:50 UTC](https://nemo-ocean.discourse.group/t/start-nemo-5-0-simulation-from-nemo-4-2-2-restarts-including-agrif/843 "2025-02-14T13:50:21Z")\ **Posts on this page:** 20\ **Page:** 1
**Author:** ![Franziska](https://avatars.discourse-cdn.com/v4/letter/f/8797f3/32.png) [@Franziska](https://nemo-ocean.discourse.group/u/Franziska)\ **Post date:** [14 February 2025 13:50 UTC](https://nemo-ocean.discourse.group/t/start-nemo-5-0-simulation-from-nemo-4-2-2-restarts-including-agrif/843/1 "2025-02-14T13:50:21Z")
Hi, I’d like to start a nested simulation in NEMO 5.0 (using RK3) based on NEMO 4.2.2 restarts. Although I haven’t tried, this should be fine without AGRIF but fails with AGRIF using dynspg\_ts because of missing variables `[uv]b2_i_b` and `[uv]n_adv`. **Is it safe to initialse these variables with zeros instead of reading the fields** , similarly as done for other variables (e.g. sshbb\_e etc.). Changing lines 1143 ff in `dynspg_ts.F90` from ```fortran #if defined key_agrif ! Read time integrated fluxes IF ( .NOT.Agrif_Root() ) THEN CALL iom_get( numror, jpdom_auto, 'ub2_i_b' , ub2_i_b(:,:), cd_type = 'U', psgn = -1._wp ) CALL iom_get( numror, jpdom_auto, 'vb2_i_b' , vb2_i_b(:,:), cd_type = 'V', psgn = -1._wp ) ELSE ub2_i_b(:,:) = 0._wp ; vb2_i_b(:,:) = 0._wp ! used in the 1st update of agrif ENDIF # if defined key_RK3 CALL iom_get( numror, jpdom_auto, 'un_adv' , un_adv(:,:), cd_type = 'U', psgn = -1._wp ) CALL iom_get( numror, jpdom_auto, 'vn_adv' , vn_adv(:,:), cd_type = 'V', psgn = -1._wp ) # endif #endif ``` to ```fortran #if defined key_agrif ! Read time integrated fluxes IF ( .NOT.Agrif_Root() ) THEN IF( iom_varid( numror, 'ub2_i_b', ldstop = .FALSE. ) > 0 ) THEN CALL iom_get( numror, jpdom_auto, 'ub2_i_b' , ub2_i_b(:,:), cd_type = 'U', psgn = -1._wp ) CALL iom_get( numror, jpdom_auto, 'vb2_i_b' , vb2_i_b(:,:), cd_type = 'V', psgn = -1._wp ) ELSE ub2_i_b(:,:) = 0._wp ; vb2_i_b(:,:) = 0._wp ENDIF ELSE ub2_i_b(:,:) = 0._wp ; vb2_i_b(:,:) = 0._wp ! used in the 1st update of agrif ENDIF # if defined key_RK3 IF( iom_varid( numror, 'un_adv', ldstop = .FALSE. ) > 0 ) THEN CALL iom_get( numror, jpdom_auto, 'un_adv' , un_adv(:,:), cd_type = 'U', psgn = -1._wp ) CALL iom_get( numror, jpdom_auto, 'vn_adv' , vn_adv(:,:), cd_type = 'V', psgn = -1._wp ) ELSE un_adv(:,:) = 0._wp ; vn_adv(:,:) = 0._wp ENDIF # endif #endif ``` seems to work technically but is this a way to go or what am I “losing/missing” when doing so? Is there another way to start a nested NEMO 5.0 simulation using RK3 from NEMO 4.2.2 restarts? Thank you! Franziska ---
**Author:** ![jchanut](https://yyz2.discourse-cdn.com/free1/user_avatar/nemo-ocean.discourse.group/jchanut/32/9_2.png) [@jchanut](https://nemo-ocean.discourse.group/u/jchanut)\ **Post date:** [19 February 2025 11:08 UTC](https://nemo-ocean.discourse.group/t/start-nemo-5-0-simulation-from-nemo-4-2-2-restarts-including-agrif/843/2 "2025-02-19T11:08:56Z")
Hi Franziska, This has been (hopefully) clarified in [this related issue](https://forge.nemo-ocean.eu/nemo/nemo/-/issues/590). It should be ok starting from [this commit.](https://forge.nemo-ocean.eu/nemo/nemo/-/commit/fe4fa8b8c5d4b6d438e12f246541029d287434eb) Let me know, Jérôme ---
**Author:** ![Franziska](https://avatars.discourse-cdn.com/v4/letter/f/8797f3/32.png) [@Franziska](https://nemo-ocean.discourse.group/u/Franziska)\ **Post date:** [19 February 2025 14:52 UTC](https://nemo-ocean.discourse.group/t/start-nemo-5-0-simulation-from-nemo-4-2-2-restarts-including-agrif/843/3 "2025-02-19T14:52:36Z")
Hi Jérôme, Thank you for your response. Unfortunately using the commit you shared doesn’t solve the issue but produces segmentation faults which seem to come from dynspg\_ts.F90. In my particular case here I start a configuration with a two-level nest from restarts of a configuration with only the first level nest and hot-start the secondary nest. In dynspg\_ts.F90 of the commit you shared there is no “ELSE” part for `IF( ln_rstart )` (line 1136) , which is present in tag 5.0 (but not in branch\_5.0\*) and I think this causes the segmentation fault. However, re-implementing this into your version brings me back to the initial issue of `[uv]b2_i_b` and `[uv]n_adv` not being present in the restarts I try to use. \* which brings me to the side-question: which version do I get when downloading the code following the instructions in the release notes `git clone --branch 5.0 https://forge.nemo-ocean.eu/nemo/nemo.git nemo_5.0` ? Is this the tagged version which doesn’t change or a branch which evolves? Best wishes Franziska ---
**Author:** ![jchanut](https://yyz2.discourse-cdn.com/free1/user_avatar/nemo-ocean.discourse.group/jchanut/32/9_2.png) [@jchanut](https://nemo-ocean.discourse.group/u/jchanut)\ **Post date:** [19 February 2025 15:35 UTC](https://nemo-ocean.discourse.group/t/start-nemo-5-0-simulation-from-nemo-4-2-2-restarts-including-agrif/843/4 "2025-02-19T15:35:19Z")
> which version do I get when downloading the code following the instructions in the release notes `git clone --branch 5.0 https://forge.nemo-ocean.eu/nemo/nemo.git nemo_5.0` Doing this, you get the tag, not the branch that evolves and that will (well is supposed to) contain bugfixes (such as the one we are talking about). Be sure to make your tests with the latest version of the branch. We agree that you use RK3, right ? `[uv]b2_i_b` and `[uv]n_adv` should be useless in that case. Using MLF, and setting` ln_1st_euler = .true.` (on all grids for security), should also make these fields useless at initialization. But I may have missed something. ---
**Author:** ![jchanut](https://yyz2.discourse-cdn.com/free1/user_avatar/nemo-ocean.discourse.group/jchanut/32/9_2.png) [@jchanut](https://nemo-ocean.discourse.group/u/jchanut)\ **Post date:** [19 February 2025 15:42 UTC](https://nemo-ocean.discourse.group/t/start-nemo-5-0-simulation-from-nemo-4-2-2-restarts-including-agrif/843/5 "2025-02-19T15:42:11Z")
> [@Franziska](#): > > In dynspg\_ts.F90 of the commit you shared there is no “ELSE” part for `IF( ln_rstart )` (line 1136) Why a `ELSE` would solve the problem ? It means you don’t have `ln_rstart=T` for all grids ? ---
**Author:** ![Franziska](https://avatars.discourse-cdn.com/v4/letter/f/8797f3/32.png) [@Franziska](https://nemo-ocean.discourse.group/u/Franziska)\ **Post date:** [19 February 2025 15:54 UTC](https://nemo-ocean.discourse.group/t/start-nemo-5-0-simulation-from-nemo-4-2-2-restarts-including-agrif/843/6 "2025-02-19T15:54:35Z")
Correct. I have `ln_rstart=F` for the inner-most grid and `ln_init_chfrpar = T`. ---
**Author:** ![Franziska](https://avatars.discourse-cdn.com/v4/letter/f/8797f3/32.png) [@Franziska](https://nemo-ocean.discourse.group/u/Franziska)\ **Post date:** [19 February 2025 16:00 UTC](https://nemo-ocean.discourse.group/t/start-nemo-5-0-simulation-from-nemo-4-2-2-restarts-including-agrif/843/7 "2025-02-19T16:00:05Z")
Good to know to get the tagged version! And I did the testing today in the commit you shared. Right, I use RK3. If these variables are useless in this case, removeing the respective lines in the code I’m using otherwise should be fine? So I would not need to initialize the fields with zeros (as I suggested initially) but simply not read them? ---
**Author:** ![jchanut](https://yyz2.discourse-cdn.com/free1/user_avatar/nemo-ocean.discourse.group/jchanut/32/9_2.png) [@jchanut](https://nemo-ocean.discourse.group/u/jchanut)\ **Post date:** [19 February 2025 16:43 UTC](https://nemo-ocean.discourse.group/t/start-nemo-5-0-simulation-from-nemo-4-2-2-restarts-including-agrif/843/8 "2025-02-19T16:43:58Z")
ok. The mixture of `ln_rstart=T/F` among grids leaves me a bit uncertain of what it can do… It makes me think that I should add a check that it is consistent for all grids 🙂 ---
**Author:** ![jchanut](https://yyz2.discourse-cdn.com/free1/user_avatar/nemo-ocean.discourse.group/jchanut/32/9_2.png) [@jchanut](https://nemo-ocean.discourse.group/u/jchanut)\ **Post date:** [19 February 2025 16:45 UTC](https://nemo-ocean.discourse.group/t/start-nemo-5-0-simulation-from-nemo-4-2-2-restarts-including-agrif/843/9 "2025-02-19T16:45:40Z")
There has been two commits concerning the initialization with agrif. So be sure not to use just one commit, but the branch as it is today. ---
**Author:** ![Franziska](https://avatars.discourse-cdn.com/v4/letter/f/8797f3/32.png) [@Franziska](https://nemo-ocean.discourse.group/u/Franziska)\ **Post date:** [19 February 2025 17:04 UTC](https://nemo-ocean.discourse.group/t/start-nemo-5-0-simulation-from-nemo-4-2-2-restarts-including-agrif/843/10 "2025-02-19T17:04:42Z")
That’s what I did, I used the branch as of today. ---
**Author:** ![jchanut](https://yyz2.discourse-cdn.com/free1/user_avatar/nemo-ocean.discourse.group/jchanut/32/9_2.png) [@jchanut](https://nemo-ocean.discourse.group/u/jchanut)\ **Post date:** [19 February 2025 17:36 UTC](https://nemo-ocean.discourse.group/t/start-nemo-5-0-simulation-from-nemo-4-2-2-restarts-including-agrif/843/11 "2025-02-19T17:36:11Z")
Could you please give the location of the segmentation fault (with debug options) ? ---
**Author:** ![Franziska](https://avatars.discourse-cdn.com/v4/letter/f/8797f3/32.png) [@Franziska](https://nemo-ocean.discourse.group/u/Franziska)\ **Post date:** [19 February 2025 19:08 UTC](https://nemo-ocean.discourse.group/t/start-nemo-5-0-simulation-from-nemo-4-2-2-restarts-including-agrif/843/12 "2025-02-19T19:08:40Z")
The error message is: ```auto forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PC Routine Line Source libpthread-2.28.s 0000145B55637D10 Unknown Unknown Unknown nemo 0000000000F5B6FE lbclnk_mp_load_pt 2756 lbclnk.f90 nemo 0000000000F5994E lbclnk_mp_sub_loo 2698 lbclnk.f90 nemo 0000000000F59420 lbclnk_mp_lbc_lnk 2353 lbclnk.f90 nemo 00000000007FDBCC agrif_all_update_ 241 agrif_all_update.f90 nemo 00000000007FC6AC agrif_all_update_ 179 agrif_all_update.f90 nemo 0000000000985C6D agrif_util_mp_agr 1135 modutil.f90 nemo 0000000000425A2E nemogcm_mp_nemo_g 274 nemogcm.f90 nemo 00000000004251C8 MAIN__ 44 nemo.f90 nemo 000000000042518D Unknown Unknown Unknown libc-2.28.so 0000145B54F077E5 __libc_start_main Unknown Unknown nemo 00000000004250AE Unknown Unknown Unknown ``` with line 241 in agrif\_all\_update.f90 ```auto CALL lbc_lnk( 'finalize_lbc_for_agrif', ssh(:,:, Kmm_a), 'T', 1._wp, & & ssh(:,:, Kbb_a), 'T', 1._wp, & & uu_b(:,:, Kmm_a), 'U',-1._wp, & & uu_b(:,:, Kbb_a), 'U',-1._wp, & & vv_b(:,:, Kmm_a), 'V',-1._wp, & & vv_b(:,:, Kbb_a), 'V',-1._wp, & & ub2_i_b(:,:), 'U',-1._wp, & & vb2_i_b(:,:), 'V',-1._wp ) ``` ---
**Author:** ![jchanut](https://yyz2.discourse-cdn.com/free1/user_avatar/nemo-ocean.discourse.group/jchanut/32/9_2.png) [@jchanut](https://nemo-ocean.discourse.group/u/jchanut)\ **Post date:** [20 February 2025 08:43 UTC](https://nemo-ocean.discourse.group/t/start-nemo-5-0-simulation-from-nemo-4-2-2-restarts-including-agrif/843/13 "2025-02-20T08:43:18Z")
Thanks. There’s indeed a bug. One should not perform mpp exchange for `[uv]b2_i_b` arrays with RK3, and not on the root grid for MLF (they are not allocated). The correct code from [this line](https://forge.nemo-ocean.eu/nemo/nemo/-/blob/branch_5.0/src/NST/agrif_all_update.F90?ref_type=heads#L103) should be: ```auto CALL lbc_lnk( 'finalize_lbc_for_agrif', ssh(:,:, Kmm_a), 'T', 1._wp, & & ssh(:,:, Kbb_a), 'T', 1._wp, & & uu_b(:,:, Kmm_a), 'U',-1._wp, & & uu_b(:,:, Kbb_a), 'U',-1._wp, & & vv_b(:,:, Kmm_a), 'V',-1._wp, & & vv_b(:,:, Kbb_a), 'V',-1._wp ) # if ! defined key_RK3 CALL lbc_lnk( 'finalize_lbc_for_agrif', ub2_b(:,:), 'U',-1._wp, & & un_bf(:,:), 'U',-1._wp, & & vb2_b(:,:), 'V',-1._wp, & & vn_bf(:,:), 'V',-1._wp. ) IF (.NOT.Agrif_root()) THEN CALL lbc_lnk( 'finalize_lbc_for_agrif', ub2_i_b(:,:), 'U',-1._wp, & & vb2_i_b(:,:), 'V',-1._wp ) END IF #endif ``` I will correct this in [branch\_5.0](https://forge.nemo-ocean.eu/nemo/nemo/-/tree/branch_5.0?ref_type=heads) and let you know. This said, if you pass in this code, it means that you have a zoom with cyclic boundaries, right ? Could you tell me more about your setup ? ---
**Author:** ![Franziska](https://avatars.discourse-cdn.com/v4/letter/f/8797f3/32.png) [@Franziska](https://nemo-ocean.discourse.group/u/Franziska)\ **Post date:** [20 February 2025 08:56 UTC](https://nemo-ocean.discourse.group/t/start-nemo-5-0-simulation-from-nemo-4-2-2-restarts-including-agrif/843/14 "2025-02-20T08:56:05Z")
Thank you Jérôme! I actually don’tr have cyclic boundaries in the zooms\*. The configuration is basically an update of [INALT60](https://gmd.copernicus.org/articles/12/3329/2019/gmd-12-3329-2019-f02-web.png) ([respective paper](https://gmd.copernicus.org/articles/12/3329/2019/)) with eORCA025 as global parent grid, a primary nest at 1/20° resoultion (similar to INALT20 but extended southward) and a secondary nest at 1/100° around southern Africa. \* addition: the first nest, however crosses the east-west folding line ---
**Author:** ![jchanut](https://yyz2.discourse-cdn.com/free1/user_avatar/nemo-ocean.discourse.group/jchanut/32/9_2.png) [@jchanut](https://nemo-ocean.discourse.group/u/jchanut)\ **Post date:** [20 February 2025 10:01 UTC](https://nemo-ocean.discourse.group/t/start-nemo-5-0-simulation-from-nemo-4-2-2-restarts-including-agrif/843/15 "2025-02-20T10:01:24Z")
ok. Well, you’re in a special case (with a zoom crossing a parent east-west cyclic boundary), this is what I meant. This case does require extra mpp links on parent grid to feed ghost points there (agrif update is not done on cyclic ghost points). Good to know that this functionnality (not really fully tested, I admit) is usefull. Talking about this, there may be a (small) issue in such a case with “interface separation” which is defined [here](https://forge.nemo-ocean.eu/nemo/nemo/-/blob/branch_5.0/src/NST/agrif_oce_update.F90?ref_type=heads#L1). “Interface separation” implies agrif update from parent is not performed at the closest points to the dynamical boundary of the nest (see [debreu et al 2012](https://www.sciencedirect.com/science/article/pii/S1463500312000480) for explanation). This tends to reduce artefacts near the interface as can be appreciated in the VORTEX test case. I’m not 100% sure, but it is likely that in your case, it also prevents from an update of parent near its west/east folding line which should not be the case. You can still disable this by setting `#undef DECAL_FEEDBACK` in place of `#define DECAL_FEEDBACK` `in agrif_oce_update.F90`. It should not be a real problem anyway. Solving these tiny details and, more generally, an assessment of agrif related numerical choices (interpolation/update schemes) is underway. But I will communicate on the forum about it. ---
**Author:** ![Franziska](https://avatars.discourse-cdn.com/v4/letter/f/8797f3/32.png) [@Franziska](https://nemo-ocean.discourse.group/u/Franziska)\ **Post date:** [24 February 2025 05:33 UTC](https://nemo-ocean.discourse.group/t/start-nemo-5-0-simulation-from-nemo-4-2-2-restarts-including-agrif/843/16 "2025-02-24T05:33:11Z")
I can confirm that correcting the code as suggested solves the initial issue. Thanks! ---
**Author:** ![Franziska](https://avatars.discourse-cdn.com/v4/letter/f/8797f3/32.png) [@Franziska](https://nemo-ocean.discourse.group/u/Franziska)\ **Post date:** [24 February 2025 05:35 UTC](https://nemo-ocean.discourse.group/t/start-nemo-5-0-simulation-from-nemo-4-2-2-restarts-including-agrif/843/17 "2025-02-24T05:35:08Z")
I will have a look into this and let you know. ---
**Author:** ![jchanut](https://yyz2.discourse-cdn.com/free1/user_avatar/nemo-ocean.discourse.group/jchanut/32/9_2.png) [@jchanut](https://nemo-ocean.discourse.group/u/jchanut)\ **Post date:** [24 February 2025 10:48 UTC](https://nemo-ocean.discourse.group/t/start-nemo-5-0-simulation-from-nemo-4-2-2-restarts-including-agrif/843/18 "2025-02-24T10:48:32Z")
ok. Commited [here](https://forge.nemo-ocean.eu/nemo/nemo/-/commit/403cbb596b6b5f8054ab60ade367723c93308880). ---
**Author:** ![Franziska](https://avatars.discourse-cdn.com/v4/letter/f/8797f3/32.png) [@Franziska](https://nemo-ocean.discourse.group/u/Franziska)\ **Post date:** [24 February 2025 14:54 UTC](https://nemo-ocean.discourse.group/t/start-nemo-5-0-simulation-from-nemo-4-2-2-restarts-including-agrif/843/19 "2025-02-24T14:54:44Z")
I didn’t dig deeper into the code but ran a short experiment with `#undef DECAL_FEEDBACK` in `agrif_oce_update.F90` and compared the solutions to an otherwise identical run after a few days. They only differ marginally everywhere - as expected. The plot here shows absolute values of SST difference from the two experiments on a logarithmic scale (to actually see something) for a small region around the North-Eastern corner of the nest. Black lines mark the nest boundaries, white line at 73°E the east-west cyclic boundary. ![sst_parent_diff_day5_log](https://global.discourse-cdn.com/free1/uploads/nemo_ocean/original/1X/b6004cb0fdf6eacefe23866e24fe4f913df42a05.png) The nest boundaries show up with higher differences, while the cyclic boundary on the parent grid does not. Patterns are similar for velocities. From this I would conclude that the parent receives an update at its east-west cyclic boundary in both versions. If you agree on this, which version would you then recommend to use? From what you say above, I assume `#define DECAL_FEEDBACK` (which I used before and was quite happy with the dynamics along the boundaries - in line with what you expect from that option). ---
**Author:** ![Franziska](https://avatars.discourse-cdn.com/v4/letter/f/8797f3/32.png) [@Franziska](https://nemo-ocean.discourse.group/u/Franziska)\ **Post date:** [24 February 2025 14:55 UTC](https://nemo-ocean.discourse.group/t/start-nemo-5-0-simulation-from-nemo-4-2-2-restarts-including-agrif/843/20 "2025-02-24T14:55:32Z")
Great, thank you Jérôme! [Next page](https://nemo-ocean.discourse.group/t/start-nemo-5-0-simulation-from-nemo-4-2-2-restarts-including-agrif/843.md?page=2)