# AGRIF: Subscript #1 of the array IBUF\_SNDS has value **URL:** \ **Category:** nesting\ **Tags:** nesting\ **Created:** [January 9, 2026, 9:37am UTC](https://forum.croco-ocean.org/t/agrif-subscript-1-of-the-array-ibuf-snds-has-value/7531 "2026-01-09T09:37:56Z")\ **Posts on this page:** 7\ **Page:** 1
**Author:** ![ctroupin1](https://forum.croco-ocean.org/user_avatar/forum.croco-ocean.org/ctroupin1/32/778_2.png) [@ctroupin1](https://forum.croco-ocean.org/u/ctroupin1)\ **Post date:** [January 9, 2026, 9:37am UTC](https://forum.croco-ocean.org/t/agrif-subscript-1-of-the-array-ibuf-snds-has-value/7531/1 "2026-01-09T09:37:56Z")
Hello, I’m running a simulation using a parent grid (884 X 800 X 32 points) and a child grid (702 X 606 X 32). All the files were generated with the [croco\_pytools](https://croco-ocean.gitlabpages.inria.fr/croco_pytools/). The simulation without the AGRIF nesting works without any error and provides the expected output files. But when I use AGRIF, I get this error: ```auto malloc(): unsorted double linked list corrupted ``` I recompiled with more flags (`-check bounds -check pointers -check uninit -traceback`) to get more info, and get this ```auto forrtl: severe (408): fort: (2): Subscript #1 of the array IBUF_SNDS has value 450 which is greater than the upper bound of 449 Image PC Routine Line Source croco_test 0000000001069EC6 sub_loop_messpass 1529 MessPass2D_.f croco_test 0000000001063F12 messpass2d_3pts_t 1035 MessPass2D_.f croco_test 00000000010BAE05 sub_loop_exchange 869 exchange_.f croco_test 00000000010B9B6E exchange_r2d_3pts 534 exchange_.f croco_test 00000000007BE657 sub_loop_setup_gr 885 setup_grid1_.f croco_test 00000000007A87F2 setup_grid1_tile_ 362 setup_grid1_.f croco_test 00000000007A39A7 sub_loop_setup_gr 237 setup_grid1_.f croco_test 00000000007A3791 setup_grid1_ 66 setup_grid1_.f croco_test 00000000004D6593 sub_loop_main_ 1133 main_.f croco_test 00000000004D2369 MAIN__ 208 main_.f croco_test 000000000040E54D Unknown Unknown Unknown libc-2.28.so 000015050E5D9D85 __libc_start_main Unknown Unknown croco_test 000000000040E46E Unknown Unknown Unknown ``` It seems that the error comes from an allocation in `MessPass2D.F`, around line 52: ```auto sub_X=Lm size_X=Npts*(sub_X+2*Npts)-1 !7+Npts*sub_X sub_E=Mm size_E=Npts*(sub_E+2*Npts)-1 !7+Npts*sub_E ``` If I increase the value of `size_X` and `size_E` and run again the simulation, then it works (well, there is a similar issue with `MessPass3D.F` but could be _solved_ the same way) and I get some output files, yet the grid seems a bit messed up (probably due to the new & wrong allocation of `size_X` and `size_E`. ![Screenshot from 2026-01-09 10-34-50](https://forum.croco-ocean.org/uploads/default/original/1X/aade7c47e43f1be9d7561f536cdfdb566bbb99ef.png) The picture shows the surface temperature in the child grid, the northern boundary and the northeastern corner obviously have some issues. ## Compilation The code is compiled using intel compilers on a cluster and run on 32 nodes with MPI. The netCDF libraries are also compiled with the same compilers and options. ## Question Any idea about the origin of this issue? What other tests shall I run? Thanks ---
**Author:** ![eleboued](https://forum.croco-ocean.org/letter_avatar_proxy/v4/letter/e/51bf81/32.png) [@eleboued](https://forum.croco-ocean.org/u/eleboued)\ **Post date:** [January 13, 2026, 4:10pm UTC](https://forum.croco-ocean.org/t/agrif-subscript-1-of-the-array-ibuf-snds-has-value/7531/2 "2026-01-13T16:10:51Z")
Hi, I believe you get this error as you are using a 5th order scheme for advection (either WENo or UP5) ? If so the fix might be to change MessPass2D.F ```FORTRAN # ifdef AGRIF sub_X=Lm size_X=Npts*(sub_X+2*Npts)-1 !7+Npts*sub_X size_X=MAXNPTS*(sub_X+2*MAXNPTS)-1 !7+Npts*sub_X sub_E=Mm size_E=Npts*(sub_E+2*Npts)-1 !7+Npts*sub_E size_E=MAXNPTS*(sub_E+2*MAXNPTS)-1 !7+Npts*sub_E ``` and MessPass3D.F : ```fortran # ifdef AGRIF size_Z=Npts*Npts*(NP1) size_Z=MAXNPTS*MAXNPTS*(NP1) sub_X=(Lm+NSUB_X-1)/NSUB_X size_X=(NP1)*Npts*(sub_X+2*Npts) size_X=(NP1)*MAXNPTS*(sub_X+2*MAXNPTS) sub_E=(Mm+NSUB_E-1)/NSUB_E size_E=(NP1)*Npts*(sub_E+2*Npts) size_E=(NP1)*MAXNPTS*(sub_E+2*MAXNPTS) ``` Let me know if it helps, Enzo ---
**Author:** ![ctroupin1](https://forum.croco-ocean.org/user_avatar/forum.croco-ocean.org/ctroupin1/32/778_2.png) [@ctroupin1](https://forum.croco-ocean.org/u/ctroupin1)\ **Post date:** [January 14, 2026, 8:37am UTC](https://forum.croco-ocean.org/t/agrif-subscript-1-of-the-array-ibuf-snds-has-value/7531/3 "2026-01-14T08:37:29Z")
Hello Enzo, thanks a lot, you, indeed I was using WENO5. I tested with the suggested changes and the error did not appear. In addition I noticed that the issue shown in the figure was not related, not sure what was the origin but now it’s fixed as well. Cheers, Charles ---
**Author:** ![eleboued](https://forum.croco-ocean.org/letter_avatar_proxy/v4/letter/e/51bf81/32.png) [@eleboued](https://forum.croco-ocean.org/u/eleboued)\ **Post date:** [January 14, 2026, 8:59am UTC](https://forum.croco-ocean.org/t/agrif-subscript-1-of-the-array-ibuf-snds-has-value/7531/4 "2026-01-14T08:59:03Z")
Hi Charles ! Good to know that your problem is solved ! MPI buffers are currently initialized, in the AGRIF case, for numerical schemes needing 2 ghost points and not 3 as requested by WENO or UP5. It is a known issue and it will be fixed for the next release. Good luck for your work, Enzo ---
**Author:** ![hook-hulk](https://forum.croco-ocean.org/user_avatar/forum.croco-ocean.org/hook-hulk/32/783_2.png) [@hook-hulk](https://forum.croco-ocean.org/u/hook-hulk)\ **Post date:** [January 15, 2026, 7:56am UTC](https://forum.croco-ocean.org/t/agrif-subscript-1-of-the-array-ibuf-snds-has-value/7531/5 "2026-01-15T07:56:58Z")
Hi @eleboued @ctroupin1 , First of all thank you for a nice discussion. I am new here. UP5\_MASKING case i suspect there are some problems. can you please check it… during compilation I don’t get an error but reading the code _ **I feel the following changes are needed?** _ Thanks in advance for your reply. **Y direction →** > **[OCEAN/t3dadv\_order5.h · master · croco-ocean / croco · GitLab](https://gitlab.inria.fr/croco-ocean/croco/-/blob/master/OCEAN/t3dadv_order5.h?ref_type=heads#L82-L85)** > > Official repository for the CROCO model ELSE mask1=rmask(i,j+1)\*mask0 mask3=rmask(i,j+2)\*mask2 ENDIF _ **maybe I need to change:** _ ``` ELSE mask2=rmask(i,j+2)*mask0*rmask(i,j-1) mask1=rmask(i,j+2)*mask0 mask3=rmask(i,j+3)*mask2 ENDIF ``` **X direction →** > **[OCEAN/t3dadv\_order5.h · master · croco-ocean / croco · GitLab](https://gitlab.inria.fr/croco-ocean/croco/-/blob/master/OCEAN/t3dadv_order5.h?ref_type=heads#L193-L196)** > > Official repository for the CROCO model ELSE mask1=rmask(i+1,j)\*mask0 mask3=rmask(i+2,j)\*mask2 ENDIF _ **maybe I need to change:** _ ``` ESLE mask2=rmask(i+2,j)*mask0*rmask(i-1,j) mask1=rmask(i+2,j)*mask0 mask3=rmask(i+3,j)*mask2 ENDIF ``` Thanks. ---
**Author:** ![ctroupin1](https://forum.croco-ocean.org/user_avatar/forum.croco-ocean.org/ctroupin1/32/778_2.png) [@ctroupin1](https://forum.croco-ocean.org/u/ctroupin1)\ **Post date:** [January 20, 2026, 9:08am UTC](https://forum.croco-ocean.org/t/agrif-subscript-1-of-the-array-ibuf-snds-has-value/7531/6 "2026-01-20T09:08:24Z")
Hello @hook-hulk , I personally don’t have a sufficient knowledge of the CROCO code to know if the change you propose is needed, unfortunately. But maybe you can explain why you think there is an error there? Cheers, Charles ---
**Author:** ![hook-hulk](https://forum.croco-ocean.org/user_avatar/forum.croco-ocean.org/hook-hulk/32/783_2.png) [@hook-hulk](https://forum.croco-ocean.org/u/hook-hulk)\ **Post date:** [January 20, 2026, 12:47pm UTC](https://forum.croco-ocean.org/t/agrif-subscript-1-of-the-array-ibuf-snds-has-value/7531/7 "2026-01-20T12:47:52Z")
Hi @ctroupin1 For negative velocity, mask1 incorrectly checks i+1, i-1, i instead of the correct upstream points i+1, i+2, i. This causes wrong stencil validation and _ **incorrect fluxes near land masks** _ when flow goes left. 😃 Thank you.