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hotfix - safeguard invalid scalar indices to prevent segmentation faults during LBC/IC generation #263

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hotfix - safeguard invalid scalar indices to prevent segmentation faults during LBC/IC generation #263

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e66493a
Safeguard invalid scalar indices to prevent segmentation faults durin…
guoqing-noaa Jun 19, 2026
21e6db8
Merge branch 'noaa/develop' into segfault_hotfix4ufs
guoqing-noaa Jul 26, 2026
9400e36
Change to a more robust safe guard
guoqing-noaa Jul 26, 2026
250ffc1
revert changes on index_nwfa, index_nifa outside the init_atm_case_lb…
guoqing-noaa Jul 26, 2026
dab4c63
fine tuning
guoqing-noaa Jul 26, 2026
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177 changes: 125 additions & 52 deletions src/core_init_atmosphere/mpas_init_atm_cases.F
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Original file line number Diff line number Diff line change
Expand Up @@ -7836,8 +7836,9 @@ subroutine init_atm_case_lbc(timestamp, block, mesh, nCells, nEdges, nVertLevels
integer :: nInterpPoints, ndims

integer :: nfglevels_actual
integer, pointer :: index_qv, index_qc, index_qr, index_qi, index_qs, index_qg,index_ni, index_nc, index_nr, index_ns, index_ng
integer, pointer :: index_nwfa, index_nifa
integer, pointer :: index_qv => null(), index_nwfa => null(), index_nifa => null()
integer, pointer :: index_qc => null(), index_qr => null(), index_qi => null(), index_qs => null(), index_qg => null()
integer, pointer :: index_nc => null(), index_ni => null(), index_nr => null(), index_ns => null(), index_ng => null()
! Chemistry
integer, pointer :: index_smoke_fine => null(), index_dust_fine => null(), index_dust_coarse => null()

Expand Down Expand Up @@ -8600,18 +8601,42 @@ subroutine init_atm_case_lbc(timestamp, block, mesh, nCells, nEdges, nVertLevels
if (associated(index_smoke_fine )) sorted_arrQ11(:,:) = -999.0
if (associated(index_dust_fine )) sorted_arrQ12(:,:) = -999.0
if (associated(index_dust_coarse )) sorted_arrQ13(:,:) = -999.0
scalars(index_nwfa,:,iCell) = 0._RKIND

@AndersJensen-NOAA AndersJensen-NOAA Jul 9, 2026

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see comment on suggested changes using the config variable, which is safer

@guoqing-noaa guoqing-noaa Jul 26, 2026

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@AndersJensen-NOAA I understand your preference to use config_lbc_hydrometeors_gfs/config_lbc_hydrometeors_rrfs to do the safe guard. However, why using the config_lbc options is safer? Could you elaborate more?

To my understanding, if (index_qc > 0) scalars(index_qc,:,iCell) = 0._RKIND is a more generic safe guard. Even one changes what variables exist for each different config_lbc options, the if (index_qc > 0) logic is still valid and don't need modifications.

scalars(index_nifa,:,iCell) = 0._RKIND
scalars(index_qc,:,iCell) = 0._RKIND
scalars(index_qr,:,iCell) = 0._RKIND
scalars(index_qi,:,iCell) = 0._RKIND
scalars(index_qs,:,iCell) = 0._RKIND
scalars(index_qg,:,iCell) = 0._RKIND
scalars(index_nc,:,iCell) = 0._RKIND
scalars(index_ni,:,iCell) = 0._RKIND
scalars(index_nr,:,iCell) = 0._RKIND
scalars(index_ns,:,iCell) = 0._RKIND
scalars(index_ng,:,iCell) = 0._RKIND
if (associated(index_nwfa)) then
if (index_nwfa > 0) scalars(index_nwfa,:,iCell) = 0._RKIND
end if
if (associated(index_nifa)) then
if (index_nifa > 0) scalars(index_nifa,:,iCell) = 0._RKIND
end if
if (associated(index_qc)) then
if (index_qc > 0) scalars(index_qc,:,iCell) = 0._RKIND
end if
if (associated(index_qr)) then
if (index_qr > 0) scalars(index_qr,:,iCell) = 0._RKIND
end if
if (associated(index_qi)) then
if (index_qi > 0) scalars(index_qi,:,iCell) = 0._RKIND
end if
if (associated(index_qs)) then
if (index_qs > 0) scalars(index_qs,:,iCell) = 0._RKIND
end if
if (associated(index_qg)) then
if (index_qg > 0) scalars(index_qg,:,iCell) = 0._RKIND
end if
if (associated(index_nc)) then
if (index_nc > 0) scalars(index_nc,:,iCell) = 0._RKIND
end if
if (associated(index_ni)) then
if (index_ni > 0) scalars(index_ni,:,iCell) = 0._RKIND
end if
if (associated(index_nr)) then
if (index_nr > 0) scalars(index_nr,:,iCell) = 0._RKIND
end if
if (associated(index_ns)) then
if (index_ns > 0) scalars(index_ns,:,iCell) = 0._RKIND
end if
if (associated(index_ng)) then
if (index_ng > 0) scalars(index_ng,:,iCell) = 0._RKIND
end if
! Chemistry
if (associated(index_smoke_fine )) then
if (index_smoke_fine > 0 ) scalars(index_smoke_fine,:,iCell) = 0._RKIND
Expand Down Expand Up @@ -8686,26 +8711,46 @@ subroutine init_atm_case_lbc(timestamp, block, mesh, nCells, nEdges, nVertLevels
if (associated(index_dust_coarse )) call mpas_quicksort(nfglevels_actual, sorted_arrQ13)
do k = nVertLevels, 1, -1
target_z = 0.5 * (zgrid(k,iCell) + zgrid(k+1,iCell))
scalars(index_nwfa,k,iCell) = vertical_interp(target_z, nfglevels_actual-1, &
sorted_arrQ9(:,1:nfglevels_actual-1), order=1, extrap=0)
scalars(index_nifa,k,iCell) = vertical_interp(target_z, nfglevels_actual-1, &
sorted_arrQ10(:,1:nfglevels_actual-1), order=1, extrap=0)
scalars(index_qc,k,iCell) = vertical_interp(target_z, nfglevels_actual-1, &
sorted_arrQ1(:,1:nfglevels_actual-1), order=1, extrap=0)
scalars(index_qr,k,iCell) = vertical_interp(target_z, nfglevels_actual-1, &
sorted_arrQ2(:,1:nfglevels_actual-1), order=1, extrap=0)
scalars(index_qi,k,iCell) = vertical_interp(target_z, nfglevels_actual-1, &
sorted_arrQ3(:,1:nfglevels_actual-1), order=1, extrap=0)
scalars(index_qs,k,iCell) = vertical_interp(target_z, nfglevels_actual-1, &
sorted_arrQ4(:,1:nfglevels_actual-1), order=1, extrap=0)
scalars(index_qg,k,iCell) = vertical_interp(target_z, nfglevels_actual-1, &
sorted_arrQ5(:,1:nfglevels_actual-1), order=1, extrap=0)
scalars(index_nc,k,iCell) = vertical_interp(target_z, nfglevels_actual-1, &
sorted_arrQ6(:,1:nfglevels_actual-1), order=1, extrap=0)
scalars(index_ni,k,iCell) = vertical_interp(target_z, nfglevels_actual-1, &
sorted_arrQ7(:,1:nfglevels_actual-1), order=1, extrap=0)
scalars(index_nr,k,iCell) = vertical_interp(target_z, nfglevels_actual-1, &
sorted_arrQ8(:,1:nfglevels_actual-1), order=1, extrap=0)
if (associated(index_nwfa)) then
if (index_nwfa > 0) scalars(index_nwfa,k,iCell) = vertical_interp(target_z, nfglevels_actual-1, &
sorted_arrQ9(:,1:nfglevels_actual-1), order=1, extrap=0)
end if
if (associated(index_nifa)) then
if (index_nifa > 0) scalars(index_nifa,k,iCell) = vertical_interp(target_z, nfglevels_actual-1, &
sorted_arrQ10(:,1:nfglevels_actual-1), order=1, extrap=0)
end if
if (associated(index_qc)) then
if (index_qc > 0) scalars(index_qc,k,iCell) = vertical_interp(target_z, nfglevels_actual-1, &
sorted_arrQ1(:,1:nfglevels_actual-1), order=1, extrap=0)
end if
if (associated(index_qr)) then
if (index_qr > 0) scalars(index_qr,k,iCell) = vertical_interp(target_z, nfglevels_actual-1, &
sorted_arrQ2(:,1:nfglevels_actual-1), order=1, extrap=0)
end if
if (associated(index_qi)) then
if (index_qi > 0) scalars(index_qi,k,iCell) = vertical_interp(target_z, nfglevels_actual-1, &
sorted_arrQ3(:,1:nfglevels_actual-1), order=1, extrap=0)
end if
if (associated(index_qs)) then
if (index_qs > 0) scalars(index_qs,k,iCell) = vertical_interp(target_z, nfglevels_actual-1, &
sorted_arrQ4(:,1:nfglevels_actual-1), order=1, extrap=0)
end if
if (associated(index_qg)) then
if (index_qg > 0) scalars(index_qg,k,iCell) = vertical_interp(target_z, nfglevels_actual-1, &
sorted_arrQ5(:,1:nfglevels_actual-1), order=1, extrap=0)
end if
if (associated(index_nc)) then
if (index_nc > 0) scalars(index_nc,k,iCell) = vertical_interp(target_z, nfglevels_actual-1, &
sorted_arrQ6(:,1:nfglevels_actual-1), order=1, extrap=0)
end if
if (associated(index_ni)) then
if (index_ni > 0) scalars(index_ni,k,iCell) = vertical_interp(target_z, nfglevels_actual-1, &
sorted_arrQ7(:,1:nfglevels_actual-1), order=1, extrap=0)
end if
if (associated(index_nr)) then
if (index_nr > 0) scalars(index_nr,k,iCell) = vertical_interp(target_z, nfglevels_actual-1, &
sorted_arrQ8(:,1:nfglevels_actual-1), order=1, extrap=0)
end if
! JLS
if ( associated(index_smoke_fine )) then
if ( index_smoke_fine > 0 ) scalars(index_smoke_fine,k,iCell) = conv_aer_kg2ug * vertical_interp(target_z, nfglevels_actual-1, &
Expand All @@ -8720,18 +8765,42 @@ subroutine init_atm_case_lbc(timestamp, block, mesh, nCells, nEdges, nVertLevels
sorted_arrQ13(:,1:nfglevels_actual-1), order=1, extrap=0)
endif
if (target_z < z_fg(1,iCell) .and. k < nVertLevels) then
scalars(index_nwfa,k,iCell) = scalars(index_nwfa,k+1,iCell)
scalars(index_nifa,k,iCell) = scalars(index_nifa,k+1,iCell)
scalars(index_qc,k,iCell) = scalars(index_qc,k+1,iCell)
scalars(index_qr,k,iCell) = scalars(index_qr,k+1,iCell)
scalars(index_qi,k,iCell) = scalars(index_qi,k+1,iCell)
scalars(index_qs,k,iCell) = scalars(index_qs,k+1,iCell)
scalars(index_qg,k,iCell) = scalars(index_qg,k+1,iCell)
scalars(index_nc,k,iCell) = scalars(index_nc,k+1,iCell)
scalars(index_ni,k,iCell) = scalars(index_ni,k+1,iCell)
scalars(index_nr,k,iCell) = scalars(index_nr,k+1,iCell)
scalars(index_ns,k,iCell) = scalars(index_ns,k+1,iCell)
scalars(index_ng,k,iCell) = scalars(index_ng,k+1,iCell)
if (associated(index_nwfa)) then
if (index_nwfa > 0) scalars(index_nwfa,k,iCell) = scalars(index_nwfa,k+1,iCell)
end if
if (associated(index_nifa)) then
if (index_nifa > 0) scalars(index_nifa,k,iCell) = scalars(index_nifa,k+1,iCell)
end if
if (associated(index_qc)) then
if (index_qc > 0) scalars(index_qc,k,iCell) = scalars(index_qc,k+1,iCell)
end if
if (associated(index_qr)) then
if (index_qr > 0) scalars(index_qr,k,iCell) = scalars(index_qr,k+1,iCell)
end if
if (associated(index_qi)) then
if (index_qi > 0) scalars(index_qi,k,iCell) = scalars(index_qi,k+1,iCell)
end if
if (associated(index_qs)) then
if (index_qs > 0) scalars(index_qs,k,iCell) = scalars(index_qs,k+1,iCell)
end if
if (associated(index_qg)) then
if (index_qg > 0) scalars(index_qg,k,iCell) = scalars(index_qg,k+1,iCell)
end if
if (associated(index_nc)) then
if (index_nc > 0) scalars(index_nc,k,iCell) = scalars(index_nc,k+1,iCell)
end if
if (associated(index_ni)) then
if (index_ni > 0) scalars(index_ni,k,iCell) = scalars(index_ni,k+1,iCell)
end if
if (associated(index_nr)) then
if (index_nr > 0) scalars(index_nr,k,iCell) = scalars(index_nr,k+1,iCell)
end if
if (associated(index_ns)) then
if (index_ns > 0) scalars(index_ns,k,iCell) = scalars(index_ns,k+1,iCell)
end if
if (associated(index_ng)) then
if (index_ng > 0) scalars(index_ng,k,iCell) = scalars(index_ng,k+1,iCell)
end if
! Chemistry
if ( associated(index_smoke_fine )) then
if (index_smoke_fine > 0 ) scalars(index_smoke_fine,k,iCell) = scalars(index_smoke_fine,k+1,iCell)
Expand Down Expand Up @@ -8855,14 +8924,18 @@ subroutine init_atm_case_lbc(timestamp, block, mesh, nCells, nEdges, nVertLevels
end do

do k=1,nVertLevels
IF ( index_qs > 0 .and. index_ns > 0 ) THEN
IF ( scalars(index_qs,k,iCell) > 0.0 .and. scalars(index_ns,k,iCell) == 0.0 ) THEN
scalars(index_ns,k,iCell) = calcnfromq(qsw=scalars(index_qs,k,iCell),dn=rho_zz(k,iCell) )
IF ( associated(index_qs) .and. associated(index_ns) ) THEN
IF ( index_qs > 0 .and. index_ns > 0 ) THEN
IF ( scalars(index_qs,k,iCell) > 0.0 .and. scalars(index_ns,k,iCell) == 0.0 ) THEN
scalars(index_ns,k,iCell) = calcnfromq(qsw=scalars(index_qs,k,iCell),dn=rho_zz(k,iCell) )
ENDIF
ENDIF
ENDIF
IF ( index_qg > 0 .and. index_ng > 0 ) THEN
IF ( scalars(index_qg,k,iCell) > 0.0 .and. scalars(index_ng,k,iCell) == 0.0 ) THEN
scalars(index_ng,k,iCell) = calcnfromq(qhw=scalars(index_qg,k,iCell),dn=rho_zz(k,iCell) )
IF ( associated(index_qg) .and. associated(index_ng) ) THEN
IF ( index_qg > 0 .and. index_ng > 0 ) THEN
IF ( scalars(index_qg,k,iCell) > 0.0 .and. scalars(index_ng,k,iCell) == 0.0 ) THEN
scalars(index_ng,k,iCell) = calcnfromq(qhw=scalars(index_qg,k,iCell),dn=rho_zz(k,iCell) )
ENDIF
ENDIF
ENDIF
! IF ( index_qr > 0 .and. index_nr > 0 ) THEN
Expand Down
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