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Merged development into dev_atiken_update

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Nikhil Rao
2025-10-13 18:50:46 +00:00
parent f39d9d02ed 91e5480c29
commit 04761fde85
38 changed files with 802 additions and 606 deletions
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0
scripts/makeitso/makeitso.py Normal file → Executable file
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20
src/base/arrayutil.F90
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@@ -15,7 +15,7 @@ module arrayutil
subroutine fillArray1D_R(array, val)
real(rp), dimension(:), allocatable, intent(inout) :: array
real(rp), dimension(:), intent(inout) :: array
real(rp), intent(in) :: val
integer :: lbds(1),ubds(1),i
@@ -37,7 +37,7 @@ module arrayutil
end subroutine fillArray1D_R
subroutine fillArray1D_I(array, val)
integer, dimension(:), allocatable, intent(inout) :: array
integer, dimension(:), intent(inout) :: array
integer, intent(in) :: val
integer :: lbds(1),ubds(1),i
@@ -59,7 +59,7 @@ module arrayutil
end subroutine fillArray1D_I
subroutine fillArray2D_R(array, val)
real(rp), dimension(:,:), allocatable, intent(inout) :: array
real(rp), dimension(:,:), intent(inout) :: array
real(rp), intent(in) :: val
integer :: lbds(2),ubds(2),i,j
@@ -83,7 +83,7 @@ module arrayutil
end subroutine fillArray2D_R
subroutine fillArray2D_I(array, val)
integer, dimension(:,:), allocatable, intent(inout) :: array
integer, dimension(:,:), intent(inout) :: array
integer, intent(in) :: val
integer :: lbds(2),ubds(2),i,j
@@ -107,7 +107,7 @@ module arrayutil
end subroutine fillArray2D_I
subroutine fillArray3D_R(array, val)
real(rp), dimension(:,:,:), allocatable, intent(inout) :: array
real(rp), dimension(:,:,:), intent(inout) :: array
real(rp), intent(in) :: val
integer :: lbds(3),ubds(3),i,j,k
@@ -133,7 +133,7 @@ module arrayutil
end subroutine fillArray3D_R
subroutine fillArray3D_I(array, val)
integer, dimension(:,:,:), allocatable, intent(inout) :: array
integer, dimension(:,:,:), intent(inout) :: array
integer, intent(in) :: val
integer :: lbds(3),ubds(3),i,j,k
@@ -159,7 +159,7 @@ module arrayutil
end subroutine fillArray3D_I
subroutine fillArray4D_R(array, val)
real(rp), dimension(:,:,:,:), allocatable, intent(inout) :: array
real(rp), dimension(:,:,:,:), intent(inout) :: array
real(rp), intent(in) :: val
integer :: lbds(4),ubds(4),i,j,k
@@ -185,7 +185,7 @@ module arrayutil
end subroutine fillArray4D_R
subroutine fillArray4D_I(array, val)
integer, dimension(:,:,:,:), allocatable, intent(inout) :: array
integer, dimension(:,:,:,:), intent(inout) :: array
integer, intent(in) :: val
integer :: lbds(4),ubds(4),i,j,k
@@ -211,7 +211,7 @@ module arrayutil
end subroutine fillArray4D_I
subroutine fillArray5D_R(array, val)
real(rp), dimension(:,:,:,:,:), allocatable, intent(inout) :: array
real(rp), dimension(:,:,:,:,:), intent(inout) :: array
real(rp), intent(in) :: val
integer :: lbds(5),ubds(5),i,j,k
@@ -237,7 +237,7 @@ module arrayutil
end subroutine fillArray5D_R
subroutine fillArray5D_I(array, val)
integer, dimension(:,:,:,:,:), allocatable, intent(inout) :: array
integer, dimension(:,:,:,:,:), intent(inout) :: array
integer, intent(in) :: val
integer :: lbds(5),ubds(5),i,j,k

1
src/base/defs/raijudefs.F90
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@@ -70,6 +70,7 @@ module raijudefs
real(rp), parameter :: def_cfl = 0.3
real(rp), parameter :: cflMax = 0.3
logical, parameter :: def_doUseVelLRs = .true.
logical, parameter :: def_doSmoothGrads = .true.
! Domain limits
! Buffer not allowed beyond min of maxTail and maxSun

7
src/base/types/raijuTypes.F90
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@@ -147,6 +147,11 @@ module raijutypes
!--- State ---!
logical :: doCS_next_preAdv = .false.
!! Signal to run coldstart next time raiju preAdvances
real(rp) :: modelDst_next_preAdv = 0.0_rp
!! Target Dst [nT] when we run coldstart next
logical :: doneFirstCS = .false.
!! Have we executed once already?
real(rp) :: lastEval = -1*HUGE
@@ -221,6 +226,8 @@ module raijutypes
!! For debug
logical :: writeGhosts
!! For debug
logical :: doSmoothGrads
!! Whether or not we smooth variables (bvol and electric potential) before taking gradients
logical :: doClockConsoleOut
!! If we are driving, output clock info
logical :: doOutput_potGrads

13
src/chimp/chmpfields.F90
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@@ -65,22 +65,19 @@ module chmpfields
allocate(By(Nip,Njp,Nkp))
allocate(Bz(Nip,Njp,Nkp))
allocate(Vx(Nip,Njp,Nkp,0:Model%nSpc))
allocate(Vy(Nip,Njp,Nkp,0:Model%nSpc))
allocate(Vz(Nip,Njp,Nkp,0:Model%nSpc))
if (Model%doMHD) then
allocate(D (Nip,Njp,Nkp,0:Model%nSpc))
allocate(P (Nip,Njp,Nkp,0:Model%nSpc))
allocate(Vx(Nip,Njp,Nkp,0:Model%nSpc))
allocate(Vy(Nip,Njp,Nkp,0:Model%nSpc))
allocate(Vz(Nip,Njp,Nkp,0:Model%nSpc))
else
allocate(Vx(Nip,Njp,Nkp,0))
allocate(Vy(Nip,Njp,Nkp,0))
allocate(Vz(Nip,Njp,Nkp,0))
endif
if (Model%doJ) then
allocate(Jx(Nip,Njp,Nkp))
allocate(Jy(Nip,Njp,Nkp))
allocate(Jz(Nip,Njp,Nkp))
endif
!------------

28
src/raiju/raijuBCs.F90
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@@ -5,6 +5,7 @@ module raijuBCs
use raijutypes
use raijuetautils
use raijudomain
use raijuColdStartHelper
implicit none
@@ -29,12 +30,15 @@ module raijuBCs
doWholeDomain = .false.
endif
! Now that topo is set, we can calculate active domain
call setActiveDomain(Model, Grid, State)
call calcMomentIngestionLocs(Model, Grid, State, doWholeDomain, doMomentIngest)
call applyMomentIngestion(Model, Grid, State, doMomentIngest)
if (State%coldStarter%doCS_next_preAdv) then
call raijuGeoColdStart(Model, Grid, State, State%t, State%coldStarter%modelDst_next_preAdv, doAccumulateO=.true.)
State%coldStarter%doCS_next_preAdv = .false.
endif
if (Model%doActiveShell ) then
! Do first round of determining active shells for each k
@@ -64,9 +68,18 @@ module raijuBCs
doMomentIngest = .false.
! Determine where to do BCs
if(doWholeDomain) then
where (State%active .ne. RAIJUINACTIVE)
doMomentIngest = .true.
end where
!where (State%active .ne. RAIJUINACTIVE)
! doMomentIngest = .true.
!end where
associate(sh=>Grid%shGrid)
do j=sh%jsg,sh%jeg
do i=sh%isg,sh%ieg
if (State%active(i,j) .ne. RAIJUINACTIVE) then
doMomentIngest(i,j) = .true.
endif
enddo
enddo
end associate
else
associate(sh=>Grid%shGrid)
@@ -118,7 +131,6 @@ module raijuBCs
psphIdx = spcIdx(Grid, F_PSPH)
eleIdx = spcIdx(Grid, F_HOTE)
!$OMP PARALLEL DO default(shared) &
!$OMP schedule(dynamic) &
!$OMP private(i,j,s,fIdx,fm,vm,kT,etaBelow,tmp_kti,tmp_kte,eMin,tmp_D,tmp_P)
do j=Grid%shGrid%jsg,Grid%shGrid%jeg
do i=Grid%shGrid%isg,Grid%shGrid%ieg
@@ -215,8 +227,8 @@ module raijuBCs
press2D = State%Pavg (i-2:i+2, j-2:j+2, fIdx)
wgt2D = State%domWeights(i-2:i+2, j-2:j+2)
isG2D = State%active (i-2:i+2, j-2:j+2) .ne. RAIJUINACTIVE
D = sum(den2D * wgt2D, mask=isG2D)/sum(wgt2D, mask=isG2D)
P = sum(press2D* wgt2D, mask=isG2D)/sum(wgt2D, mask=isG2D)
D = sum(den2D * wgt2D, mask=isG2D)/max( sum(wgt2D, mask=isG2D), TINY)
P = sum(press2D* wgt2D, mask=isG2D)/max( sum(wgt2D, mask=isG2D), TINY)
endif
end subroutine getDomWeightedMoments

271
src/raiju/raijuColdStartHelper.F90
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@@ -4,6 +4,7 @@ module raijuColdStartHelper
use raijutypes
use imaghelper
use earthhelper
use arrayutil
use raijuetautils
use raijuloss_CX
@@ -32,6 +33,8 @@ module raijuColdStartHelper
call iXML%Set_Val(coldStarter%tEnd,'coldStarter/tEnd',coldStarter%evalCadence-TINY) ! Don't do any updates as default
endif
coldStarter%doneFirstCS = .false.
end subroutine initRaijuColdStarter
@@ -41,7 +44,7 @@ module raijuColdStartHelper
! Worker routines
!------
subroutine raijuGeoColdStart(Model, Grid, State, t0, dstModel)
subroutine raijuGeoColdStart(Model, Grid, State, t0, dstModel, doAccumulateO)
!! Cold start RAIJU assuming we are at Earth sometime around 21st century
type(raijuModel_T), intent(in) :: Model
type(raijuGrid_T), intent(in) :: Grid
@@ -50,26 +53,31 @@ module raijuColdStartHelper
!! Target time to pull SW values from
real(rp), intent(in) :: dstModel
!! Current dst of global model
logical, optional, intent(in) :: doAccumulateO
!! If true, keep State%eta and add coldstart to it.
!! If false, replace State%eta with coldStart info
!! Default: false
logical :: isFirstCS
logical :: doInitRC, doAccumulate
integer :: i,j,k
integer :: s, sIdx_p, sIdx_e
real(rp) :: dstReal, dstTarget
real(rp) :: dps_current, dps_preCX, dps_postCX, dps_rescale, dps_ele
real(rp) :: etaScale
logical, dimension(Grid%shGrid%isg:Grid%shGrid%ieg, Grid%shGrid%jsg:Grid%shGrid%jeg) :: isGood
logical , dimension(Grid%shGrid%isg:Grid%shGrid%ieg, Grid%shGrid%jsg:Grid%shGrid%jeg) :: isGood
real(rp), dimension(Grid%shGrid%isg:Grid%shGrid%ieg, Grid%shGrid%jsg:Grid%shGrid%jeg, Grid%Nk) :: etaCS
associate(cs=>State%coldStarter)
!write(*,*)"Coldstart running..."
isFirstCS = .not. State%coldStarter%doneFirstCS
if (.not. isFirstCS .and. .not. cs%doUpdate) then
return
if (present(doAccumulateO)) then
doAccumulate = doAccumulateO
else
doAccumulate = .false.
endif
call fillArray(etaCS, 0.0_rp)
where (State%active .eq. RAIJUACTIVE)
associate(cs=>State%coldStarter)
where (State%active .ne. RAIJUINACTIVE)
isGood = .true.
elsewhere
isGood = .false.
@@ -77,102 +85,154 @@ module raijuColdStartHelper
sIdx_p = spcIdx(Grid, F_HOTP)
sIdx_e = spcIdx(Grid, F_HOTE)
if (isFirstCS) then
! Start by nuking all etas we will set up ourselves
do s=1,Grid%nSpc
!! Skip plasmashere, let that be handled on its own
!if ( Grid%spc(s)%flav == F_PSPH) then
! continue
!endif
State%eta(:,:,Grid%spc(s)%kStart:Grid%spc(s)%kEnd) = 0.0
enddo
endif
!! Init psphere
!if (isFirstCS .or. cs%doPsphUpdate) then
! call setRaijuInitPsphere(Model, Grid, State, Model%psphInitKp)
!endif
! Update Dst target
dstReal = GetSWVal('symh', Model%tsF, t0)
if (isFirstCS) then
if (cs%doneFirstCS) then
write(*,*)"Already coldstarted once, you shouldn't be here "
return
else
! On first try, we assume there is no existing ring current, and its our job to make up the entire difference
dstTarget = dstReal - dstModel
else if (t0 > (cs%lastEval + cs%evalCadence)) then
! If we are updating, there should already be some ring current
! If dstReal - dstModel is still < 0, we need to add ADDITIONAL pressure to get them to match
dps_current = spcEta2DPS(Model, Grid, State, Grid%spc(sIdx_p), isGood) + spcEta2DPS(Model, Grid, State, Grid%spc(sIdx_e), isGood)
dstTarget = dstReal - (dstModel - dps_current)
else
! Otherwise we have nothing to do, just chill til next update time
return
endif
cs%lastEval = t0
cs%lastTarget = dstTarget
cs%doneFirstCS = .true. ! Whether we do anything or not, we were at least called once
if (dstTarget > 0) then ! We got nothing to contribute
! Now decide if we need to add a starter ring current
if (dstTarget >= 0) then ! We've got nothing to contribute
write(*,*)"RAIJU coldstart not adding starter ring current"
return
endif
if (isFirstCS) then
! Init psphere
call setRaijuInitPsphere(Model, Grid, State, Model%psphInitKp)
! Init hot protons
call raiColdStart_initHOTP(Model, Grid, State, t0, dstTarget)
dps_preCX = spcEta2DPS(Model, Grid, State, Grid%spc(sIdx_p), isGood)
! Hit it with some charge exchange
if (cs%doCX) then
call raiColdStart_applyCX(Model, Grid, State, Grid%spc(sIdx_p))
endif
dps_postCX = spcEta2DPS(Model, Grid, State, Grid%spc(sIdx_p), isGood)
! Calc moments to update pressure and density
call EvalMoments(Grid, State)
! Use HOTP moments to set electrons
call raiColdStart_initHOTE(Model, Grid, State)
dps_ele = spcEta2DPS(Model, Grid, State, Grid%spc(sIdx_e), isGood)
dps_current = dps_postCX ! Note: if using fudge we're gonna lose electrons immediately, don't include them in current dst for now
! Init hot protons
call raiColdStart_initHOTP(Model, Grid, State, t0, dstTarget, etaCS)
!call raiColdStart_initHOTP_RCOnly(Model, Grid, State, t0, dstTarget, etaCS)
dps_preCX = spcEta2DPS(Model, Grid, State%bvol_cc, etaCS, Grid%spc(sIdx_p), isGood)
! Hit it with some charge exchange
if (cs%doCX) then
call raiColdStart_applyCX(Model, Grid, State, Grid%spc(sIdx_p), etaCS)
endif
dps_postCX = spcEta2DPS(Model, Grid, State%bvol_cc, etaCS, Grid%spc(sIdx_p), isGood)
! Use HOTP moments to set electrons
call raiColdStart_initHOTE(Model, Grid, State, etaCS)
dps_ele = spcEta2DPS(Model, Grid, State%bvol_cc, etaCS, Grid%spc(sIdx_e), isGood)
dps_current = dps_postCX ! Note: if using fudge we're gonna lose electrons immediately, don't include them in current dst for now
etaScale = abs(dstTarget / dps_current)
State%eta(:,:,Grid%spc(sIdx_p)%kStart:Grid%spc(sIdx_p)%kEnd) = etaScale*State%eta(:,:,Grid%spc(sIdx_p)%kStart:Grid%spc(sIdx_p)%kEnd)
dps_rescale = spcEta2DPS(Model, Grid, State, Grid%spc(sIdx_p), isGood)
if (isfirstCS) then
write(*,*) "RAIJU Cold starting..."
write(*,'(a,f7.2)') " Real Dst : ",dstReal
write(*,'(a,f7.2)') " Model Dst : ",dstModel
write(*,'(a,f7.2)') " Target DPS-Dst : ",dstTarget
write(*,'(a,f7.2)') " Hot proton pre-loss : ",dps_preCX
write(*,'(a,f7.2)') " post-loss : ",dps_postCX
write(*,'(a,f7.2)') " post-rescale : ",dps_rescale
write(*,'(a,f7.2)') " Hot electron DPS-Dst : ",dps_ele
if (dstTarget < 0) then
etaScale = abs(dstTarget / dps_current)
etaCS(:,:,Grid%spc(sIdx_p)%kStart:Grid%spc(sIdx_p)%kEnd) = etaScale*etaCS(:,:,Grid%spc(sIdx_p)%kStart:Grid%spc(sIdx_p)%kEnd)
dps_rescale = spcEta2DPS(Model, Grid, State%bvol_cc, etaCS, Grid%spc(sIdx_p), isGood)
else
write(*,'(a,f7.2)') " Real Dst : ",dstReal
write(*,'(a,f7.2)') " Model Dst : ",dstModel
write(*,'(a,f7.2)') " Current DPS-Dst : ",dps_current
write(*,'(a,f7.2)') " Target DPS-Dst : ",dstTarget
write(*,'(a,f7.2)') " post-rescale : ",dps_rescale
write(*,'(a,f7.2)') " Hot electron DPS-Dst : ",dps_ele
dps_rescale = dps_current
endif
write(*,*) "RAIJU Cold starting..."
write(*,'(a,f7.2)') " Real Dst : ",dstReal
write(*,'(a,f7.2)') " Model Dst : ",dstModel
write(*,'(a,f7.2)') " Target DPS-Dst : ",dstTarget
write(*,'(a,f7.2)') " Hot proton pre-loss : ",dps_preCX
write(*,'(a,f7.2)') " post-loss : ",dps_postCX
write(*,'(a,f7.2)') " post-rescale : ",dps_rescale
write(*,'(a,f7.2)') " Hot electron DPS-Dst : ",dps_ele
end associate
State%coldStarter%doneFirstCS = .true.
! finally, put it into raiju state
if(doAccumulate) then
!$OMP PARALLEL DO default(shared) &
!$OMP private(i,j,k)
do j=Grid%shGrid%jsg,Grid%shGrid%jeg
do i=Grid%shGrid%isg,Grid%shGrid%ieg
do k=1,Grid%Nk
if(etaCS(i,j,k) > State%eta(i,j,k)) then
State%eta(i,j,k) = etaCS(i,j,k)
endif
enddo
enddo
enddo
else
State%eta = etaCS
endif
end subroutine raijuGeoColdStart
subroutine raiColdStart_initHOTP(Model, Grid, State, t0, dstTarget)
subroutine raiColdStart_initHOTP_RCOnly(Model, Grid, State, t0, dstTarget, etaCS)
type(raijuModel_T), intent(in) :: Model
type(raijuGrid_T), intent(in) :: Grid
type(raijuState_T), intent(inout) :: State
type(raijuState_T), intent(in) :: State
real(rp), intent(in) :: t0
!! Target time to pull SW values from
real(rp), intent(in) :: dstTarget
real(rp), dimension(Grid%shGrid%isg:Grid%shGrid%ieg, Grid%shGrid%jsg:Grid%shGrid%jeg, Grid%Nk), intent(inout) :: etaCS
real(rp) :: dstTarget_p
logical :: isInTM03
integer :: i,j,sIdx
integer, dimension(2) :: ij_TM
real(rp) :: vSW, dSW, dPS_emp, pPS_emp, ktPS_emp
real(rp) :: x0_TM, y0_TM, T0_TM, Bvol0_TM, P0_ps, N0_ps
real(rp) :: L, vm, P_rc, D_rc, kt_rc
sIdx = spcIdx(Grid, F_HOTP)
associate(sh=>Grid%shGrid, spc=>Grid%spc(sIdx))
! Set everything to zero to start
etaCS(:,:,spc%kStart:spc%kEnd) = 0.0_rp
! Scale target Dst down to account for electrons contributing stuff later
dstTarget_p = dstTarget / (1.0 + 1.0/Model%tiote)
call SetQTRC(dstTarget_p,doVerbO=.false.) ! This sets a global QTRC_P0 inside earthhelper.F90
! Get reference TM value at -10 Re
x0_TM = -10.0-TINY
y0_TM = 0.0
! Empirical temperature
call EvalTM03([x0_TM,y0_TM,0.0_rp],N0_ps,P0_ps,isInTM03)
T0_TM = DP2kT(N0_ps, P0_ps)
! Model FTV
ij_TM = minloc( sqrt( (State%xyzMincc(:,:,XDIR)-x0_TM)**2 + (State%xyzMincc(:,:,YDIR)**2) ) )
Bvol0_TM = State%bvol_cc(ij_TM(IDIR), ij_TM(JDIR))
! Now set our initial density and pressure profile
do j=sh%jsg,sh%jeg
do i=sh%isg,sh%ie ! Note: Not setting low lat ghosts, we want them to be zero
if (State%active(i,j) .eq. RAIJUINACTIVE) cycle
L = norm2(State%xyzMincc(i,j,XDIR:YDIR))
vm = State%bvol_cc(i,j)**(-2./3.)
kt_rc = T0_TM*(Bvol0_TM/State%bvol_cc(i,j))**(2./3.)
kt_rc = min(kt_rc, 4.0*T0_TM) ! Limit cap. Not a big fan, but without cap we get stuff that's too energetic and won't go away (until FLC maybe)
P_rc = P_QTRC(L) ! From earthhelper.F90
D_rc = PkT2Den(P_rc, kt_rc)
! Finally map it to HOTP etas
call DkT2SpcEta(Model, spc, etaCS(i,j,spc%kStart:spc%kEnd), D_rc, kt_rc, vm)
enddo
enddo
end associate
end subroutine raiColdStart_initHOTP_RCOnly
subroutine raiColdStart_initHOTP(Model, Grid, State, t0, dstTarget, etaCS)
type(raijuModel_T), intent(in) :: Model
type(raijuGrid_T), intent(in) :: Grid
type(raijuState_T), intent(in) :: State
real(rp), intent(in) :: t0
!! Target time to pull SW values from
real(rp), intent(in) :: dstTarget
real(rp), dimension(Grid%shGrid%isg:Grid%shGrid%ieg, Grid%shGrid%jsg:Grid%shGrid%jeg, Grid%Nk), intent(inout) :: etaCS
real(rp) :: dstTarget_p
logical :: isInTM03
@@ -192,8 +252,10 @@ module raijuColdStartHelper
call InitTM03(Model%tsF,t0)
! Scale target Dst down to account for electrons contributing stuff later
dstTarget_p = dstTarget / (1.0 + 1.0/Model%tiote)
call SetQTRC(dstTarget_p,doVerbO=.false.) ! This sets a global QTRC_P0 inside earthhelper.F90
if (dstTarget < 0) then
dstTarget_p = dstTarget / (1.0 + 1.0/Model%tiote)
call SetQTRC(dstTarget_p,doVerbO=.false.) ! This sets a global QTRC_P0 inside earthhelper.F90
endif
! Get Borovsky statistical values
vSW = abs(GetSWVal("Vx",Model%tsF,t0))
@@ -218,7 +280,7 @@ module raijuColdStartHelper
endif
! Set everything to zero to start
State%eta(:,:,spc%kStart:spc%kEnd) = 0.0_rp
etaCS(:,:,spc%kStart:spc%kEnd) = 0.0_rp
! Now set our initial density and pressure profile
do j=sh%jsg,sh%jeg
@@ -234,7 +296,11 @@ module raijuColdStartHelper
call EvalTM03_SM(State%xyzMincc(i,j,:),N0_ps,P0_ps,isInTM03)
P_rc = P_QTRC(L) ! From earthhelper.F90
if (dstTarget < 0) then
P_rc = P_QTRC(L) ! From earthhelper.F90
else
P_rc = 0.0
endif
if (.not. isInTM03) then
N0_ps = dPS_emp
@@ -250,7 +316,7 @@ module raijuColdStartHelper
endif
! Finally map it to HOTP etas
call DkT2SpcEta(Model, spc, State%eta(i,j,spc%kStart:spc%kEnd), D_final, kt_rc, vm)
call DkT2SpcEta(Model, spc, etaCS(i,j,spc%kStart:spc%kEnd), D_final, kt_rc, vm)
enddo
enddo
@@ -260,11 +326,12 @@ module raijuColdStartHelper
end subroutine raiColdStart_initHOTP
subroutine raiColdStart_applyCX(Model, Grid, State, spc)
subroutine raiColdStart_applyCX(Model, Grid, State, spc, etaCS)
type(raijuModel_T), intent(in) :: Model
type(raijuGrid_T), intent(in) :: Grid
type(raijuState_T), intent(inout) :: State
type(raijuState_T), intent(in) :: State
type(raijuSpecies_T), intent(in) :: spc
real(rp), dimension(Grid%shGrid%isg:Grid%shGrid%ieg, Grid%shGrid%jsg:Grid%shGrid%jeg, Grid%Nk), intent(inout) :: etaCS
integer :: i,j,k
type(raiLoss_CX_T) :: lossCX
@@ -275,13 +342,12 @@ module raijuColdStartHelper
call lossCX%doInit(Model, Grid, nullXML)
!$OMP PARALLEL DO default(shared) &
!$OMP schedule(dynamic) &
!$OMP private(i,j,tau)
!$OMP private(i,j,k,tau)
do j=Grid%shGrid%jsg,Grid%shGrid%jeg
do i=Grid%shGrid%isg,Grid%shGrid%ieg
do k = spc%kStart,spc%kEnd
tau = lossCX%calcTau(Model, Grid, State, i, j, k)
State%eta(i,j,k) = State%eta(i,j,k)*exp(-tCX/tau)
etaCS(i,j,k) = etaCS(i,j,k)*exp(-tCX/tau)
enddo
enddo
enddo
@@ -289,38 +355,49 @@ module raijuColdStartHelper
end subroutine raiColdStart_applyCX
subroutine raiColdStart_initHOTE(Model, Grid, State)
subroutine raiColdStart_initHOTE(Model, Grid, State, etaCS)
type(raijuModel_T), intent(in) :: Model
type(raijuGrid_T), intent(in) :: Grid
type(raijuState_T), intent(inout) :: State
type(raijuState_T), intent(in) :: State
real(rp), dimension(Grid%shGrid%isg:Grid%shGrid%ieg, Grid%shGrid%jsg:Grid%shGrid%jeg, Grid%Nk), intent(inout) :: etaCS
integer :: sIdx_e, sIdx_p
integer :: i,j
real(rp) :: press_p, den_p
real(rp) :: kt_p, kt_e, den, vm
sIdx_p = spcIdx(Grid, F_HOTP)
sIdx_e = spcIdx(Grid, F_HOTE)
associate(spc_p=>Grid%spc(sIdx_p), spc_e=>Grid%spc(sIdx_e))
! Set everything to zero to start
State%eta(:,:,Grid%spc(sIdx_e)%kStart:Grid%spc(sIdx_e)%kEnd) = 0.0_rp
etaCS(:,:,spc_e%kStart:spc_e%kEnd) = 0.0_rp
!$OMP PARALLEL DO default(shared) &
!$OMP schedule(dynamic) &
!$OMP private(i,j,vm,den,kt_p,kt_e)
!$OMP private(i,j,vm,den_p, press_p,kt_p,kt_e)
do j=Grid%shGrid%jsg,Grid%shGrid%jeg
do i=Grid%shGrid%isg,Grid%shGrid%ie ! Note: Not setting low lat ghosts, we want them to be zero
if (State%active(i,j) .eq. RAIJUINACTIVE) cycle
vm = State%bvol_cc(i,j)**(-2./3.)
den = State%Den(sIdx_p)%data(i,j)
kt_p = DP2kT(den, State%Press(sIdx_p)%data(i,j))
!den = State%Den(sIdx_p)%data(i,j)
!kt_p = DP2kT(den, State%Press(sIdx_p)%data(i,j))
den_p = SpcEta2Den (spc_p, etaCS(i,j,spc_p%kStart:spc_p%kEnd), State%bvol_cc(i,j))
press_p = SpcEta2Press(spc_p, etaCS(i,j,spc_p%kStart:spc_p%kEnd), State%bvol_cc(i,j))
kt_p = DP2kT(den_p, press_p)
kt_e = kt_p / Model%tiote
call DkT2SpcEta(Model, Grid%spc(sIdx_e), &
State%eta(i,j,Grid%spc(sIdx_e)%kStart:Grid%spc(sIdx_e)%kEnd), &
den, kt_e, vm)
etaCS(i,j,Grid%spc(sIdx_e)%kStart:Grid%spc(sIdx_e)%kEnd), &
den_p, kt_e, vm)
enddo
enddo
end associate
end subroutine raiColdStart_initHOTE

14
src/raiju/raijuEtautils.F90
View File

@@ -178,18 +178,19 @@ module raijuetautils
end function SpcEta2Press
function spcEta2DPS(Model, Grid, State, spc, isGood) result(dpsdst)
function spcEta2DPS(Model, Grid, bVol_cc, eta, spc, isGood) result(dpsdst)
!! Calculate total DPS-Dst for given species within the defined isGood domain
type(raijuModel_T), intent(in) :: Model
type(raijuGrid_T), intent(in) :: Grid
type(raijuState_T), intent(in) :: State
real(rp), dimension(Grid%shGrid%isg:Grid%shGrid%ieg, Grid%shGrid%jsg:Grid%shGrid%jeg), intent(in) :: bVol_cc
real(rp), dimension(Grid%shGrid%isg:Grid%shGrid%ieg, Grid%shGrid%jsg:Grid%shGrid%jeg, Grid%Nk), intent(in) :: eta
type(raijuSpecies_T), intent(in) :: spc
logical, dimension(Grid%shGrid%isg:Grid%shGrid%ieg, Grid%shGrid%jsg:Grid%shGrid%jeg), intent(in) :: isGood
!! Eval mask, true = point is included in calculation
real(rp) :: dpsdst
integer :: i,j,k
real(rp) :: press, bVol, energyDen, energy
integer :: i,j
real(rp) :: press, energyDen, energy
logical :: isDead = .false.
dpsdst = 0.0
@@ -197,9 +198,8 @@ module raijuetautils
do j=Grid%shGrid%jsg,Grid%shGrid%jeg
do i=Grid%shGrid%isg,Grid%shGrid%ieg
if (.not. isGood(i,j)) cycle
bVol = State%bvol_cc(i,j)
press = SpcEta2Press(spc, State%eta(i,j,spc%kStart:spc%kEnd), bVol) ! [nPa]
energyDen = (press*1.0D-9) * (bVol*Model%planet%rp_m*1.0D9) * (Grid%Brcc(i,j)*1.0D-9)/kev2J ! p[J/m^3] * bVol[m/T] * B[T] = [J/m^2] * keV/J = [keV/m^2]
press = SpcEta2Press(spc, eta(i,j,spc%kStart:spc%kEnd), bvol_cc(i,j)) ! [nPa]
energyDen = (press*1.0D-9) * (bVol_cc(i,j)*Model%planet%rp_m*1.0D9) * (Grid%Brcc(i,j)*1.0D-9)/kev2J ! p[J/m^3] * bVol[m/T] * B[T] = [J/m^2] * keV/J = [keV/m^2]
energy = energyDen*(Grid%areaCC(i,j)*Model%planet%ri_m**2) ! [keV/m^2]* Re^2[m^2] = [keV]
dpsdst = dpsdst - 4.2*(1.0D-30)*energy ! [nT]
enddo

13
src/raiju/raijuIO.F90
View File

@@ -16,7 +16,7 @@ module raijuIO
implicit none
integer, parameter, private :: MAXIOVAR = 70
integer, parameter, private :: MAXIOVAR = 100
logical, private :: doRoot = .true. !Whether root variables need to be written
logical, private :: doFat = .false. !Whether to output lots of extra datalogical, private :: doRoot = .true. !Whether root variables need to be written
@@ -503,6 +503,12 @@ module raijuIO
else
call AddOutVar(IOVars,"cs_doneFirstCS", 0)
endif
if (State%coldStarter%doCS_next_preAdv) then
call AddOutVar(IOVars,"cs_doCS_next_preAdv", 1)
else
call AddOutVar(IOVars,"cs_doCS_next_preAdv", 0)
endif
call AddOutVar(IOVars, "cs_modelDst_next_preAdv", State%coldStarter%modelDst_next_preAdv)
call AddOutVar(IOVars, "cs_lastEval", State%coldStarter%lastEval)
call AddOutVar(IOVars, "cs_lastTarget", State%coldStarter%lastTarget)
@@ -598,6 +604,8 @@ module raijuIO
call AddInVar(IOVars,"nRes")
call AddInVar(IOVars,"tRes")
call AddInVar(IOVars,"isFirstCpl")
call AddInVar(IOVars,"cs_doCS_next_preAdv")
call AddInVar(IOVars,"cs_modelDst_next_preAdv")
call AddInVar(IOVars,"cs_doneFirstCS")
call AddInVar(IOVars,"cs_lastEval")
call AddInVar(IOVars,"cs_lastTarget")
@@ -651,12 +659,15 @@ module raijuIO
! Coldstarter
State%coldStarter%lastEval = GetIOReal(IOVars, "cs_lastEval")
State%coldStarter%lastTarget = GetIOReal(IOVars, "cs_lastTarget")
State%coldStarter%modelDst_next_preAdv = GetIOReal(IOVars, "cs_modelDst_next_preAdv")
! Handle boolean attributes
tmpInt = GetIOInt(IOVars, "isFirstCpl")
State%isFirstCpl = tmpInt .eq. 1
tmpInt = GetIOInt(IOVars, "cs_doneFirstCS")
State%coldStarter%doneFirstCS = tmpInt .eq. 1
tmpInt = GetIOInt(IOVars, "cs_doCS_next_preAdv")
State%coldStarter%doCS_next_preAdv = tmpInt .eq. 1
call IOArray2DFill(IOVars, "xmin" , State%xyzMin(:,:,XDIR))
call IOArray2DFill(IOVars, "ymin" , State%xyzMin(:,:,YDIR))

2
src/raiju/raijuOut.F90
View File

@@ -131,7 +131,7 @@ module raijuOut
if (maxP_MLT > 24) maxP_MLT = maxP_MLT - 24D0
write(*,'(a,I0,a,f7.2,a,f7.2,a,f5.2,a,f5.2,a,f7.2)') ' ', &
Grid%spc(s)%flav, ': P =', maxPress,', D =',maxDen,' @ ',maxP_L,' Rp,',maxP_MLT, &
" MLT; DPS:",spcEta2DPS(Model, Grid, State, Grid%spc(sIdx), State%active .eq. RAIJUACTIVE)
" MLT; DPS:",spcEta2DPS(Model, Grid, State%bvol_cc, State%eta_avg, Grid%spc(sIdx), State%active .eq. RAIJUACTIVE)
enddo
write(*,'(a)',advance="no") ANSIRESET

31
src/raiju/raijuPreAdvancer.F90
View File

@@ -36,12 +36,18 @@ module raijuPreAdvancer
call fillArray(State%eta_avg, 0.0_rp)
! (losses handled in updateRaiLosses)
! Now that topo is set, we can calculate active domain
call setActiveDomain(Model, Grid, State)
! Moments to etas, initial active shell calculation
call Tic("BCs")
call applyRaijuBCs(Model, Grid, State, doWholeDomainO=State%isFirstCpl) ! If fullEtaMap=True, mom2eta map is applied to the whole domain
if (State%isFirstCpl) then
call setRaijuInitPsphere(Model, Grid, State, Model%psphInitKp)
endif
call Toc("BCs")
! Handle plasmaasphere refilling for the full step about to happen
! Handle plasmasphere refilling for the full step about to happen
call plasmasphereRefill(Model,Grid,State)
! Handle edge cases that may effect the validity of information carried over from last coupling period
@@ -261,7 +267,7 @@ module raijuPreAdvancer
associate(sh=>Grid%shGrid)
! Gauss-Green calculation of cell-averaged gradients
call potExB(Grid%shGrid, State, pExB, doSmoothO=.true., isGCornerO=isGCorner) ! [V]
call potExB(Grid%shGrid, State, pExB, doSmoothO=Model%doSmoothGrads, isGCornerO=isGCorner) ! [V]
call potCorot(Model%planet, Grid%shGrid, pCorot, Model%doGeoCorot) ! [V]
call calcGradIJ_cc(Model%planet%rp_m, Grid, isGCorner, pExB , State%gradPotE_cc , doLimO=.true. ) ! [V/m]
call calcGradIJ_cc(Model%planet%rp_m, Grid, isGCorner, pCorot, State%gradPotCorot_cc, doLimO=.false.) ! [V/m]
@@ -270,7 +276,7 @@ module raijuPreAdvancer
! lambda is constant, so just need grad(V^(-2/3) )
call calcGradVM_cc(Model%planet%rp_m, Model%planet%ri_m, Model%planet%magMoment, &
Grid, isGCorner, State%bvol, State%gradVM_cc, &
doSmoothO=.true., doLimO=.true.)
doSmoothO=Model%doSmoothGrads, doLimO=.true.)
end associate
end subroutine calcPotGrads_cc
@@ -304,7 +310,6 @@ module raijuPreAdvancer
associate(sh=>Grid%shGrid)
!$OMP PARALLEL DO default(shared) &
!$OMP schedule(dynamic) &
!$OMP private(i,j,qLow,qHigh)
do j=sh%jsg,sh%jeg
do i=sh%isg,sh%ieg
@@ -332,7 +337,6 @@ module raijuPreAdvancer
allocate(gradQtmp(sh%isg:sh%ieg,sh%jsg:sh%jeg, 2))
gradQtmp = gradQ
!$OMP PARALLEL DO default(shared) &
!$OMP schedule(dynamic) &
!$OMP private(i,j)
do j=sh%jsg+1,sh%jeg-1
do i=sh%isg+1,sh%ieg-1
@@ -483,13 +487,19 @@ module raijuPreAdvancer
gradVM(:,:,RAI_TH) = gradVM(:,:,RAI_TH) + dV0_dth
!$OMP PARALLEL DO default(shared) &
!$OMP schedule(dynamic) &
!$OMP private(i,j,bVolcc)
do j=sh%jsg,sh%jeg
do i=sh%isg,sh%ieg
bVolcc = toCenter2D(dV(i:i+1,j:j+1)) + DipFTV_colat(Grid%thcRp(i), B0) ! Will include smoothing of dV if enabled
!bVolcc = toCenter2D(V(i:i+1,j:j+1))
gradVM(i,j,:) = (-2./3.)*bVolcc**(-5./3.)*gradVM(i,j,:)
if(all(isGcorner(i:i+1,j:j+1))) then
!bVolcc = toCenter2D(dV(i:i+1,j:j+1)) + DipFTV_colat(Grid%thcRp(i), B0) ! Will include smoothing of dV if enabled
bVolcc = toCenter2D(V(i:i+1,j:j+1))
gradVM(i,j,:) = (-2./3.)*bVolcc**(-5./3.)*gradVM(i,j,:)
else
! gradVM should be zero for this point coming out of calcGradIJ_cc, but set to dipole value just in case
gradVM(i,j,RAI_PH) = 0.0
gradVM(i,j,RAI_TH) = 0.0
!gradVM(i,j,RAI_TH) = (-2./3.)*DipFTV_colat(Grid%thcRp(i), B0)**(-5./3.)*dV0_dth(i,j)
endif
enddo
enddo
@@ -564,7 +574,6 @@ module raijuPreAdvancer
enddo
! Now everyone else
!$OMP PARALLEL DO default(shared) &
!$OMP schedule(dynamic) &
!$OMP private(i,j)
do j=jsg+1,jeg
do i=isg+1,ieg
@@ -572,6 +581,8 @@ module raijuPreAdvancer
enddo
enddo
call wrapJcorners(sh, Vsm)
! Write back to provided array
V = Vsm
end associate

3
src/raiju/raijuStarter.F90
View File

@@ -175,6 +175,7 @@ module raijustarter
Model%activeDomRad = abs(Model%activeDomRad)
!---Solver ---!
call iXML%Set_Val(Model%doSmoothGrads,'sim/doSmoothGrads',def_doSmoothGrads)
call iXML%Set_Val(Model%doUseVelLRs,'sim/useVelLRs',def_doUseVelLRs)
call iXML%Set_Val(Model%maxItersPerSec,'sim/maxIter',def_maxItersPerSec)
call iXML%Set_Val(Model%maxOrder,'sim/maxOrder',7)
@@ -553,6 +554,8 @@ module raijustarter
! Similarly, set vaFrac to safe value in case stand-alone never writes to it
State%vaFrac = 1.0
State%isFirstCpl = .true.
! Init State sub-modules
if (Model%isSA) then
! If we are standalone, this is the place to get coldStarter settings

2
src/voltron/modelInterfaces/imag2mix_interface.F90
View File

@@ -231,7 +231,7 @@ module imag2mix_interface
imP_avg(RAI_EDEN) = imP_avg(RAI_EDEN )/nPnts**2
imP_avg(RAI_EPRE) = imP_avg(RAI_EPRE )/nPnts**2
imP_avg(RAI_NPSP) = imP_avg(RAI_NPSP )/nPnts**2
imP_avg(RAI_EAVG) = imP_avg(RAI_EFLUX) / imP_avg(RAI_ENFLX)
imP_avg(RAI_EAVG) = imP_avg(RAI_EFLUX) / max(TINY, imP_avg(RAI_ENFLX))
imP_avg(RAI_GTYPE) = imP_avg(RAI_GTYPE)/nGood
imP_avg(RAI_THCON) = imP_avg(RAI_THCON)/nGood
imP_avg(RAI_PHCON) = imP_avg(RAI_PHCON)/nGood

89
src/voltron/modelInterfaces/raiCplTypesSub.F90
View File

@@ -43,11 +43,7 @@ submodule (volttypes) raijuCplTypesSub
! Update MJD with whatever voltron handed us
! If we are restarting, this will get replaced with whatever's in file later
App%raiApp%State%mjd = App%opt%mjd0
write(*,*)"MJD0=",App%opt%mjd0
if (App%opt%doColdStart) then
! We are gonna cold start, so ignore plasma ingestion rules for first coupling
App%raiApp%State%isFirstCpl = .false.
endif
! Then allocate and initialize coupling variables based on raiju app
call raijuCpl_init(App, xml)
@@ -58,61 +54,29 @@ submodule (volttypes) raijuCplTypesSub
class(raijuCoupler_T), intent(inout) :: App
class(voltApp_T), intent(inout) :: vApp
logical :: doFirstColdStart
logical :: doUpdateColdStart
real(rp) :: BSDst
doFirstColdStart = .false.
doUpdateColdStart = .false.
associate(raiApp=>App%raiApp)
! If we are running realtime, its our job to get everything we need from vApp into raiCpl
if (.not. App%raiApp%Model%isSA) then
! First, determine if we should cold start, i.e. Completely reset raiju's eta's to match some target conditions
! Determine if we should cold start before packing coupler because it will set tLastUpdate to vApp%time and then we can't do the checks we want
! But actually do cold start after coupler packing completes so we can use real field line info
! Do we do our very first coldstart ever
if (App%opt%doColdStart .and. App%tLastUpdate < 0.0 .and. vApp%time >= 0.0) then
doFirstColdStart = .true.
endif
! Do we do "updates" to our coldstart during pre-conditioning period
if(App%opt%doColdStart .and. App%tLastUpdate > 0.0 .and. vApp%time < App%startup_blendTscl) then
doUpdateColdStart = .true.
endif
call packRaijuCoupler_RT(App, vApp)
endif
! Someone updated raiCpl's coupling variables by now, stuff it into RAIJU proper
call raiCpl2RAIJU(App)
if (.not. raiApp%State%coldStarter%doneFirstCS .or. vApp%time < raiApp%State%coldStarter%tEnd) then
!! Make sure we run at least once
call setActiveDomain(raiApp%Model, raiApp%Grid, raiApp%State)
! Calc voltron dst ourselves since vApp%BSDst is only set on console output
call EstDST(vApp%gApp%Model,vApp%gApp%Grid,vApp%gApp%State,BSDst0=BSDst)
call raijuGeoColdStart(raiApp%Model, raiApp%Grid, raiApp%State, vApp%time, BSDst)
endif
!if (doFirstColdStart) then
! ! Its happening, everybody stay calm
! write(*,*) "RAIJU Doing first cold start..."
! ! NOTE: By this point we have put coupling info into raiju (e.g. bVol, xyzmin, MHD moments)
! ! But haven't calculated active domain yet because that happens in preadvancer
! ! So we jump in and do it here so we have it for cold starting
! call setActiveDomain(raiApp%Model, raiApp%Grid, raiApp%State)
! ! Calc voltron dst ourselves since vApp%BSDst is only set on console output
! call EstDST(vApp%gApp%Model,vApp%gApp%Grid,vApp%gApp%State,BSDst0=BSDst)
! call raijuGeoColdStart(raiApp%Model, raiApp%Grid, raiApp%State, vApp%time, BSDst, doCXO=App%doColdstartCX,doPsphO=.true.)
!endif
!if (doUpdateColdStart) then
! write(*,*)"RAIJU doing update cold start at t=",vApp%time
! write(*,*)" (calculating model BSDst,)",vApp%time
! call setActiveDomain(raiApp%Model, raiApp%Grid, raiApp%State)
! call EstDST(vApp%gApp%Model,vApp%gApp%Grid,vApp%gApp%State,BSDst0=BSDst)
! call raijuGeoColdStart(raiApp%Model, raiApp%Grid, raiApp%State, vApp%time, BSDst, doCXO=App%doColdstartCX,doPsphO=.false.)
!endif
associate(cs=>raiApp%State%coldStarter)
if (.not. cs%doneFirstCS .or. (cs%doUpdate .and. vApp%time < cs%tEnd) ) then
!! Make sure we run at least once
! Calc voltron dst ourselves since vApp%BSDst is only set on console output
call EstDST(vApp%gApp%Model,vApp%gApp%Grid,vApp%gApp%State,BSDst0=BSDst)
raiApp%State%coldStarter%doCS_next_preAdv = .true.
raiApp%State%coldStarter%modelDst_next_preAdv = BSDst
!call setActiveDomain(raiApp%Model, raiApp%Grid, raiApp%State)
!call raijuGeoColdStart(raiApp%Model, raiApp%Grid, raiApp%State, vApp%time, BSDst)
endif
end associate
end associate
end subroutine volt2RAIJU
@@ -299,21 +263,22 @@ submodule (volttypes) raijuCplTypesSub
endif
enddo
! Mock up cold electrons balancing hot protons and see if it produces meaningful flux
call InterpShellVar_TSC_pnt(sh, State%Den_avg(idx_proton) , th, ph, d_ion)
call InterpShellVar_TSC_pnt(sh, State%Press_avg(idx_proton) , th, ph, p_ion)
pie_frac = 0.05 ! Fraction of ion pressure contained by these neutralizing electrons
pe_kT = DP2kT(d_ion, p_ion*pie_frac) ! [keV]
pe_nflux = imP(RAI_ENFLX)*d_ion/d_hot ! Scale number flux to same loss processes except there were d_ion density instead of d_electron density
pe_eflux = (pe_kT*kev2erg)*pe_nflux ! [erg/cm^2/s]
if (pe_eflux > imP(RAI_EFLUX)) then ! Use in place of normal flux only if energy flux for these are greater than hot electron channel fluxes
imP(RAI_EFLUX) = pe_eflux
imP(RAI_ENFLX) = pe_nflux
imP(RAI_EDEN ) = d_ion*1.0e6 ! [#/m^3]
imP(RAI_EPRE ) = p_ion*pie_frac*1.0e-9 ! [Pa]
endif
endif
!K: Removing this code for now, should be rewritten to use the MHD D,P => precip routines
! call InterpShellVar_TSC_pnt(sh, State%Den_avg(idx_proton) , th, ph, d_ion)
! call InterpShellVar_TSC_pnt(sh, State%Press_avg(idx_proton) , th, ph, p_ion)
! pie_frac = 0.05 ! Fraction of ion pressure contained by these neutralizing electrons
! pe_kT = DP2kT(d_ion, p_ion*pie_frac) ! [keV]
! pe_nflux = imP(RAI_ENFLX)*d_ion/d_hot ! Scale number flux to same loss processes except there were d_ion density instead of d_electron density
! pe_eflux = (pe_kT*kev2erg)*pe_nflux ! [erg/cm^2/s]
! if (pe_eflux > imP(RAI_EFLUX)) then ! Use in place of normal flux only if energy flux for these are greater than hot electron channel fluxes
! imP(RAI_EFLUX) = pe_eflux
! imP(RAI_ENFLX) = pe_nflux
! imP(RAI_EDEN ) = d_ion*1.0e6 ! [#/m^3]
! imP(RAI_EPRE ) = p_ion*pie_frac*1.0e-9 ! [Pa]
! endif
endif !spcList(s)%spcType == X
enddo
! derive mean energy where nflux is non-trivial.
if (imP(RAI_ENFLX) > TINY) imP(RAI_EAVG) = imP(RAI_EFLUX)/imP(RAI_ENFLX) * erg2kev ! Avg E [keV]

5
src/voltron/tubehelper.F90
View File

@@ -337,6 +337,11 @@ module tubehelper
bTube%nTrc = 0
!Zero pot
bTube%pot = 0.0
bTube%crpot = 0.0
bTube%potc = 0.0
end subroutine FreshenTube

35
src/voltron/voltapp.F90
View File

@@ -99,6 +99,8 @@ module voltapp
! adjust XMl reader root
call xmlInp%SetRootStr('Kaiju/Voltron')
! Make sure verbosity is still right after others do stuff with the reader
call xmlInp%SetVerbose(vApp%isLoud)
!Initialize planet information
call getPlanetParams(vApp%planet, xmlInp)
@@ -209,7 +211,7 @@ module voltapp
gApp%Model%t = vApp%time / gApp%Model%Units%gT0
gApp%State%time = gApp%Model%t
call genVoltShellGrid(vApp, xmlInp)
call genVoltShellGrid(vApp, xmlInp, gApp%Grid%Nkp)
call initVoltState(vApp)
endif
@@ -754,11 +756,14 @@ module voltapp
end subroutine init_volt2Chmp
subroutine genVoltShellGrid(vApp, xmlInp)
subroutine genVoltShellGrid(vApp, xmlInp, gamRes)
class(voltApp_T) , intent(inout) :: vApp
type(XML_Input_T), intent(in) :: xmlInp
integer, intent(in) :: gamRes
character(len=strLen) :: gType
integer :: Nt_def, Np_def
!! Default number of active cells in theta and phi unless xml says otherwise
integer :: Nt, Np
!! Number of active cells in theta and phi
integer :: Ng
@@ -786,8 +791,30 @@ module voltapp
! Note: Nt is for a single hemisphere, we will manually double it in a minute
! TODO: This means we will always have even number of total cells, and a cell interfce right on the equator
! Can upgrade to allow for odd number later
call xmlInp%Set_Val(Nt, "grid/Nt", 180 ) ! 1 deg res default for uniform grid
call xmlInp%Set_Val(Np, "grid/Np", 360) ! 1 deg res default
! First determine defaults
if (gamRes<=64) then
! DBL
Nt_def = 90
Np_def = 180
else if (gamRes<=128) then
! QUAD
Nt_def = 180
Np_def = 360
else if (gamRes<=256) then
! OCT
Nt_def = 360
Np_def = 720
else
! HEX or above
! Idk good luck
Nt_def = 540
Np_def = 1440
endif
call xmlInp%Set_Val(Nt, "grid/Nt", Nt_def) ! 1 deg res default for uniform grid
call xmlInp%Set_Val(Np, "grid/Np", Np_def) ! 1 deg res default
! Ghost cells
call xmlInp%Set_Val(Ng, "grid/Ng", 4) ! # of ghosts in every direction
nGhosts = 0

97
testingScripts/compare_mage_runs.py
View File

@@ -384,7 +384,7 @@ def create_magnetosphere_quicklook_plots(xml_files: list):
os.chdir(results_dir)
# Create the quicklook plot.
cmd = f"msphpic.py -id {runid}"
cmd = f"msphpic -id {runid}"
_ = subprocess.run(cmd, shell=True, check=True)
# Move back to the starting directory.
@@ -464,7 +464,7 @@ def create_REMIX_quicklook_plots(xml_files: list):
os.chdir(results_dir)
# Create the quicklook plots.
cmd = f"mixpic.py -id {runid}"
cmd = f"mixpic -id {runid}"
_ = subprocess.run(cmd, shell=True, check=True)
# Add the plots to the lists.
@@ -517,83 +517,6 @@ def merge_REMIX_quicklook_plots(plots_north: list, plots_south: list):
return merged_plot_north, merged_plot_south
def create_RCM_quicklook_plots(xml_files: list):
"""Create the RCM quicklook plot for each run.
Create the RCM quicklook plot for each run.
Parameters
----------
xml_files : list of str
List of XML files describing each run.
Returns
-------
quicklook_plots : list of str
Path to each quicklook file.
Raises
------
None
"""
# Save the current directory.
cwd = os.getcwd()
# Make the RCM quicklook plot for each run.
quicklook_plots = []
for xml_file in xml_files:
# Extract the run ID.
runid = common.extract_runid(xml_file)
# Compute the path to the results directory.
results_dir = os.path.split(xml_file)[0]
# Move to the results directory.
os.chdir(results_dir)
# Create the quicklook plot.
cmd = f"rcmpic.py -id {runid}"
_ = subprocess.run(cmd, shell=True, check=True)
# Add the plot to the list.
path = os.path.join(results_dir, "qkrcmpic.png")
quicklook_plots.append(path)
# Return to the original directory.
os.chdir(cwd)
# Return the list of quicklook plots.
return quicklook_plots
def merge_RCM_quicklook_plots(quicklook_plots: list):
"""Merge the RCM quicklook plots for all runs.
Merge the RCM quicklook plots for all runs.
Parameters
----------
quicklook_plots : list of str
List of quicklook plots to merge.
Returns
-------
merged_plot : str
Path to merged quicklook file.
Raises
------
None
"""
# Merge RCM quicklooks.
merged_plot = "combined_qkrcmpic.png"
cmd = f"convert {' '.join(quicklook_plots)} -append {merged_plot}"
print(f"cmd = {cmd}")
_ = subprocess.run(cmd, shell=True, check=True)
return merged_plot
def compare_mage_runs(args):
"""Compare a set of MAGE model runs.
@@ -710,20 +633,6 @@ def compare_mage_runs(args):
print(f"merged_remix_plot_n = {merged_remix_plot_n}")
print(f"merged_remix_plot_s = {merged_remix_plot_s}")
# Create the RCM quicklook plots.
if verbose:
print("Creating RCM quicklook plots.")
rcm_plots = create_RCM_quicklook_plots(run_xml_files)
if debug:
print(f"rcm_plots = {rcm_plots}")
# Create the merged RCM quicklook plots.
if verbose:
print("Creating merged RCM quicklook plot.")
rcm_merged_plots = merge_RCM_quicklook_plots(rcm_plots)
if debug:
print(f"rcm_merged_plots = {rcm_merged_plots}")
# ------------------------------------------------------------------------
# Post images to Slack.
@@ -736,7 +645,6 @@ def compare_mage_runs(args):
"combined_msphpic.png",
"combined_remix_n.png",
"combined_remix_s.png",
"combined_qkrcmpic.png",
]
comments_to_post = [
"Real-Time Performance\n\n",
@@ -745,7 +653,6 @@ def compare_mage_runs(args):
"Magnetosphere Quicklook Comparison Plots\n\n",
"REMIX (north) Quicklook Comparison Plots\n\n",
"REMIX (south) Quicklook Comparison Plots\n\n",
"RCM Quicklook Comparison Plots\n\n",
]
# If loud mode is on, post results to Slack.

144
testingScripts/compare_mage_runs_numerical.py
View File

@@ -125,67 +125,6 @@ def compare_GAMERA_results(runxml1: str, runxml2: str, verbose: bool = False):
return TEST_PASS
def compare_MHDRCM_results(runxml1: str, runxml2: str, verbose: bool = False):
"""Numerically compare the MHD RCM output files from two runs.
Numerically compare the MHD RCM output files from two runs.
Parameters
----------
runxm1 : str
Path to XML file describing 1st run.
runxm2 : str
Path to XML file describing 2nd run.
verbose : bool
Set to True to print verbose information during comparison.
Returns
-------
TEST_PASS or TEST_FAIL : str
Description of result of comparison.
Raises
------
None
"""
# Determine the directories containing the sets of results.
dir1 = os.path.split(runxml1)[0]
dir2 = os.path.split(runxml2)[0]
# Generate a sorted list of output files for the 1st run.
pattern1 = os.path.join(dir1, "*.mhdrcm.h5")
files1 = glob.glob(pattern1)
files = [os.path.split(f)[1] for f in files1]
files.sort()
# Compare each output file in the two directories.
# Comparisons are done with h5diff, which must be in the PATH.
# Attributes of the steps and other top-level groups are excluded from
# comparison.
for filename in files:
file1 = os.path.join(dir1, filename)
file2 = os.path.join(dir2, filename)
if verbose:
print(f"Numerically comparing {file1} to {file2}.")
# Compare each step, without attributes.
_, step_ids = kaiH5.cntSteps(file1)
for step_id in step_ids:
step_path = f"/Step#{step_id}"
if verbose:
print(f" Comparing {step_path}.")
cmd = (
f"h5diff --exclude-attribute {step_path} {file1} {file2} "
f"{step_path}"
)
cproc = subprocess.run(cmd, shell=True, check=True)
if cproc.returncode != 0:
return TEST_FAIL
# Return the result of the comparison.
return TEST_PASS
def compare_REMIX_results(runxml1: str, runxml2: str, verbose: bool = False):
"""Numerically compare the REMIX output files from two runs.
@@ -247,67 +186,6 @@ def compare_REMIX_results(runxml1: str, runxml2: str, verbose: bool = False):
return TEST_PASS
def compare_RCM_results(runxml1: str, runxml2: str, verbose: bool = False):
"""Numerically compare the RCM output files from two runs.
Numerically compare the RCM output files from two runs.
Parameters
----------
runxm1 : str
Path to XML file describing 1st run.
runxm2 : str
Path to XML file describing 2nd run.
verbose : bool
Set to True to print verbose information during comparison.
Returns
-------
TEST_PASS or TEST_FAIL : str
Description of result of comparison.
Raises
------
None
"""
# Determine the directories containing the sets of results.
dir1 = os.path.split(runxml1)[0]
dir2 = os.path.split(runxml2)[0]
# Generate a sorted list of output files for the 1st run.
pattern1 = os.path.join(dir1, "*.rcm.h5")
files1 = glob.glob(pattern1)
files = [os.path.split(f)[1] for f in files1]
files.sort()
# Compare each result file in the two directories.
# Comparisons are done with h5diff, which must be in the PATH.
# Attributes of the steps and other top-level groups are excluded from
# comparison.
for filename in files:
file1 = os.path.join(dir1, filename)
file2 = os.path.join(dir2, filename)
if verbose:
print(f"Numerically comparing {file1} to {file2}.")
# Compare each step, without attributes.
_, step_ids = kaiH5.cntSteps(file1)
for step_id in step_ids:
step_path = f"/Step#{step_id}"
if verbose:
print(f" Comparing {step_path}.")
cmd = (
f"h5diff --exclude-attribute {step_path} {file1} {file2} "
f"{step_path}"
)
cproc = subprocess.run(cmd, shell=True, check=True)
if cproc.returncode != 0:
return TEST_FAIL
# Return the result of the comparison.
return TEST_PASS
def compare_VOLTRON_results(runxml1: str, runxml2: str, verbose: bool = False):
"""Numerically compare the VOLTRON output files from two runs.
@@ -417,14 +295,6 @@ def compare_mage_runs_numerical(args: dict):
print(f"comparison_result = {comparison_result}")
comparison_results.append(comparison_result)
# Compare the MHD RCM output files.
if verbose:
print("Comparing MHD RCM output files.")
comparison_result = compare_MHDRCM_results(runxml1, runxml2, verbose)
if debug:
print(f"comparison_result = {comparison_result}")
comparison_results.append(comparison_result)
# Compare the REMIX output files.
if verbose:
print("Comparing REMIX output files.")
@@ -433,14 +303,6 @@ def compare_mage_runs_numerical(args: dict):
print(f"comparison_result = {comparison_result}")
comparison_results.append(comparison_result)
# Compare the RCM output files.
if verbose:
print("Comparing RCM output files.")
comparison_result = compare_RCM_results(runxml1, runxml2, verbose)
if debug:
print(f"comparison_result = {comparison_result}")
comparison_results.append(comparison_result)
# Compare the VOLTRON output files.
if verbose:
print("Comparing VOLTRON output files.")
@@ -454,10 +316,8 @@ def compare_mage_runs_numerical(args: dict):
# Detail the test results.
test_report_details_string = ""
test_report_details_string += f"GAMERA: *{comparison_results[0]}*\n"
test_report_details_string += f"MHD RCM: *{comparison_results[1]}*\n"
test_report_details_string += f"REMIX: *{comparison_results[2]}*\n"
test_report_details_string += f"RCM: *{comparison_results[3]}*\n"
test_report_details_string += f"VOLTRON: *{comparison_results[4]}*\n"
test_report_details_string += f"REMIX: *{comparison_results[1]}*\n"
test_report_details_string += f"VOLTRON: *{comparison_results[2]}*\n"
# Summarize the test results.
if run_description is not None:

3
testingScripts/crontab
View File

@@ -16,8 +16,7 @@
# source tree). Job submission reports to Slack only on failure, report run
# in Slack-on-fail (-s) mode.
15 00 * * * ssh derecho "/glade/campaign/hao/msphere/automated_kaiju_tests/kaiju-private/testingScripts/run_mage_tests.sh -v -b development 'unitTest.py -sv'" >> /glade/campaign/hao/msphere/automated_kaiju_tests/logs/nightly-tests-2-development.out 2>&1
# Disable master unit test for now since it hangs.
# 20 00 * * * ssh derecho "/glade/campaign/hao/msphere/automated_kaiju_tests/kaiju-private/testingScripts/run_mage_tests.sh -v -b master 'unitTest.py -sv'" >> /glade/campaign/hao/msphere/automated_kaiju_tests/logs/nightly-tests-2-master.out 2>&1
20 00 * * * ssh derecho "/glade/campaign/hao/msphere/automated_kaiju_tests/kaiju-private/testingScripts/run_mage_tests.sh -v -b master 'unitTest.py -sv'" >> /glade/campaign/hao/msphere/automated_kaiju_tests/logs/nightly-tests-2-master.out 2>&1
# Run a weekly dash every Sunday morning for the development branch and
# compare to reference development run listed in reference_runs.txt.

27
testingScripts/derecho_configuration_check-template.pbs
View File

@@ -20,21 +20,18 @@ echo 'The currently loaded modules are:'
module list
echo 'Loading python environment.'
export CONDARC="{{ condarc }}"
export CONDA_ENVS_PATH="{{ conda_envs_path }}"
mage_miniconda3="{{ mage_test_root }}/miniconda3"
mage_conda="${mage_miniconda3}/bin/conda"
__conda_setup="$($mage_conda 'shell.bash' 'hook' 2> /dev/null)"
__conda_setup="$('/glade/u/home/ewinter/miniconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
eval "$__conda_setup"
else
if [ -f "$mage_miniconda3/etc/profile.d/conda.sh" ]; then
. "$mage_miniconda3/etc/profile.d/conda.sh"
if [ -f "/glade/u/home/ewinter/miniconda3/etc/profile.d/conda.sh" ]; then
. "/glade/u/home/ewinter/miniconda3/etc/profile.d/conda.sh"
else
export PATH="$mage_miniconda3/bin:$PATH"
export PATH="/glade/u/home/ewinter/miniconda3/bin:$PATH"
fi
fi
unset __conda_setup
conda activate {{ conda_environment }}
echo "The current conda environment is ${CONDA_PREFIX}."
@@ -42,10 +39,6 @@ echo 'Setting up MAGE environment.'
source {{ kaijuhome }}/scripts/setupEnvironment.sh
echo "The kaiju software is located at ${KAIJUHOME}."
echo 'Setting up kaipy environment.'
source {{ kaipy_private_root }}/kaipy/scripts/setupEnvironment.sh
echo "The kaipy software is located at ${KAIPYHOME}."
echo 'Setting environment variables.'
export TMPDIR={{ tmpdir }}
export SLACK_BOT_TOKEN={{ slack_bot_token }}
@@ -82,10 +75,10 @@ echo 'Generating the solar wind boundary condition file.'
{{ cda2wind_cmd }}
echo "The solar wind boundary condition file is `ls bcwind.h5`."
# Generate the RCM configuration file.
echo 'Generating the RCM configuration file.'
{{ genRCM_cmd }}
echo "The RCM configuration file is `ls rcmconfig.h5`."
# Generate the RAIJU configuration file.
echo 'Generating the RAIJU configuration file.'
genRAIJU
echo "The RAIJU configuration file is `ls raijuconfig.h5`."
# Moved this setting here to avoid error from genLFM.py.
export OMP_NUM_THREADS=128
@@ -99,7 +92,7 @@ eval $cmd
# Run the comparison. Post results to Slack if any test fails.
reference_run=`cat /glade/u/home/ewinter/mage_testing/test_runs/derecho_configuration_check_runs.txt`
cmd="python $KAIJUHOME/testingScripts/compare_mage_runs_numerical.py -sv --run_description='`derecho` configuration check' $reference_run `pwd`/weeklyDashGo.xml >& compare_mage_runs_numerical.out"
cmd="python $KAIJUHOME/testingScripts/compare_mage_runs_numerical.py -sv --run_description='derecho configuration check' $reference_run `pwd`/weeklyDashGo.xml >& compare_mage_runs_numerical.out"
echo "Run comparison command is:"
echo $cmd
eval $cmd

11
testingScripts/derecho_configuration_check.py
View File

@@ -143,16 +143,13 @@ def derecho_configuration_check(args: dict):
make_cmd = "make voltron_mpi.x"
# Create the command to generate the LFM grid.
genLFM_cmd = "genLFM.py -gid Q"
genLFM_cmd = "genLFM -gid Q"
# Create the command to generate the solar wind boundary condition file.
cda2wind_cmd = (
"cda2wind.py -t0 2016-08-09T02:00:00 -t1 2016-08-09T12:00:00"
"cda2wind -t0 2016-08-09T02:00:00 -t1 2016-08-09T12:00:00"
)
# Create the command to generate the RCM configuration.
genRCM_cmd = "genRCM.py"
# Create the command for launching an MPI program.
mpiexec_cmd = f"mpiexec {KAIJUHOME}/scripts/preproc/pinCpuCores.sh"
@@ -179,13 +176,10 @@ def derecho_configuration_check(args: dict):
pbs_options["job_priority"] = os.environ["DERECHO_TESTING_PRIORITY"]
pbs_options["walltime"] = "08:00:00"
pbs_options["modules"] = module_names
pbs_options["condarc"] = os.environ["CONDARC"]
pbs_options["conda_envs_path"] = os.environ["CONDA_ENVS_PATH"]
pbs_options["conda_environment"] = os.environ["CONDA_ENVIRONMENT"]
pbs_options["mage_test_root"] = os.environ["MAGE_TEST_ROOT"]
pbs_options["mage_test_set_root"] = os.environ["MAGE_TEST_SET_ROOT"]
pbs_options["kaijuhome"] = KAIJUHOME
pbs_options["kaipy_private_root"] = os.environ["KAIPY_PRIVATE_ROOT"]
pbs_options["tmpdir"] = os.environ["TMPDIR"]
pbs_options["slack_bot_token"] = os.environ["SLACK_BOT_TOKEN"]
pbs_options["branch_or_commit"] = os.environ["BRANCH_OR_COMMIT"]
@@ -193,7 +187,6 @@ def derecho_configuration_check(args: dict):
pbs_options["make_cmd"] = make_cmd
pbs_options["genLFM_cmd"] = genLFM_cmd
pbs_options["cda2wind_cmd"] = cda2wind_cmd
pbs_options["genRCM_cmd"] = genRCM_cmd
pbs_options["mpiexec_cmd"] = mpiexec_cmd
pbs_options["voltron_cmd"] = voltron_cmd

5
testingScripts/intelCheckSubmitReport-template.pbs
View File

@@ -19,11 +19,9 @@ module load {{ module }}
module list
echo 'Loading python environment.'
mage_test_root=$HOME
if [ -d "${mage_test_root}/miniconda3" ]; then
echo 'Loading local miniconda3'
mage_test_root='{{ mage_test_root }}'
export CONDARC="${mage_test_root}/.condarc"
export CONDA_ENVS_PATH="${mage_test_root}/.conda"
mage_miniconda3="${mage_test_root}/miniconda3"
mage_conda="${mage_miniconda3}/bin/conda"
__conda_setup="$($mage_conda 'shell.bash' 'hook' 2> /dev/null)"
@@ -45,7 +43,6 @@ conda activate {{ conda_environment }}
echo 'Setting up MAGE environment.'
source {{ kaijuhome }}/scripts/setupEnvironment.sh
source {{ kaipyhome }}/kaipy/scripts/setupEnvironment.sh
echo 'Setting environment variables.'
export TMPDIR={{ tmpdir }}

13
testingScripts/intelChecks.py
View File

@@ -305,7 +305,7 @@ def intelChecks(args: dict):
# Generate bcwind data file.
if verbose:
print("Creating bcwind data file.")
cmd = "cda2wind.py -t0 2016-08-09T09:00:00 -t1 2016-08-09T11:00:00"
cmd = "cda2wind -t0 2016-08-09T09:00:00 -t1 2016-08-09T11:00:00"
if debug:
print(f"cmd = {cmd}")
try:
@@ -315,7 +315,7 @@ def intelChecks(args: dict):
f"{module_set_name}.\n"
f"e.cmd = {e.cmd}\n"
f"e.returncode = {e.returncode}\n"
"See testing log for output from cda2wind.py.\n"
"See testing log for output from cda2wind.\n"
"Skipping remaining steps for module set"
f"{module_set_name}\n")
continue
@@ -325,7 +325,7 @@ def intelChecks(args: dict):
# Generate the LFM grid file.
if verbose:
print("Creating LFM grid file.")
cmd = "genLFM.py -gid D"
cmd = "genLFM -gid D"
if debug:
print(f"cmd = {cmd}")
try:
@@ -335,7 +335,7 @@ def intelChecks(args: dict):
f"{module_set_name}.\n"
f"e.cmd = {e.cmd}\n"
f"e.returncode = {e.returncode}\n"
"See testing log for output from genLFM.py.\n"
"See testing log for output from genLFM.\n"
"Skipping remaining steps for module set"
f"{module_set_name}\n")
continue
@@ -345,7 +345,7 @@ def intelChecks(args: dict):
# Generate the Raiju configuration file.
if verbose:
print("Creating Raiju configuration file.")
cmd = "genRAIJU.py"
cmd = "genRAIJU"
if debug:
print(f"cmd = {cmd}")
try:
@@ -355,7 +355,7 @@ def intelChecks(args: dict):
f" for module set {module_set_name}.\n"
f"e.cmd = {e.cmd}\n"
f"e.returncode = {e.returncode}\n"
"See testing log for output from genRAIJU.py.\n"
"See testing log for output from genRAIJU.\n"
"Skipping remaining steps for module set "
f"{module_set_name}\n")
continue
@@ -373,7 +373,6 @@ def intelChecks(args: dict):
pbs_options["job_priority"] = os.environ["DERECHO_TESTING_PRIORITY"]
pbs_options["modules"] = module_names
pbs_options["kaijuhome"] = KAIJUHOME
pbs_options["kaipyhome"] = os.environ["KAIPYHOME"]
pbs_options["tmpdir"] = os.environ["TMPDIR"]
pbs_options["slack_bot_token"] = os.environ["SLACK_BOT_TOKEN"]
pbs_options["mage_test_root"] = os.environ["MAGE_TEST_ROOT"]

10
testingScripts/mage_reproducibility_check-template.pbs
View File

@@ -19,11 +19,11 @@ module load {{ module }}
echo 'The currently loaded modules are:'
module list
echo 'Loading python environment.'
mage_test_root=$HOME
if [ -d "${mage_test_root}/miniconda3" ]; then
echo 'Loading local miniconda3'
export CONDARC="{{ condarc }}"
export CONDA_ENVS_PATH="{{ conda_envs_path }}"
mage_miniconda3="{{ mage_test_root }}/miniconda3"
mage_miniconda3="${mage_test_root}/miniconda3"
mage_conda="${mage_miniconda3}/bin/conda"
__conda_setup="$($mage_conda 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
@@ -47,10 +47,6 @@ echo 'Setting up MAGE environment.'
source {{ kaijuhome }}/scripts/setupEnvironment.sh
echo "The kaiju software is located at ${KAIJUHOME}."
echo 'Setting up kaipy environment.'
source {{ kaipy_private_root }}/kaipy/scripts/setupEnvironment.sh
echo "The kaipy software is located at ${KAIPYHOME}."
echo 'Setting environment variables.'
export TMPDIR={{ tmpdir }}
export SLACK_BOT_TOKEN={{ slack_bot_token }}

50
testingScripts/mage_reproducibility_check.py
View File

@@ -84,6 +84,35 @@ MAGE_REPRODUCIBILITY_CHECK_PBS_TEMPLATE_FILE = os.path.join(
MAGE_REPRODUCIBILITY_CHECK_PBS_SCRIPT = "mage_reproducibility_check.pbs"
def create_command_line_parser():
"""Create the command-line argument parser.
Create the parser for command-line arguments.
Parameters
----------
None
Returns
-------
parser : argparse.ArgumentParser
Command-line argument parser for this script.
Raises
------
None
"""
parser = common.create_command_line_parser(DESCRIPTION)
parser.add_argument(
"--module_set_file", "-f", default=DEFAULT_MODULE_SET_FILE,
help=(
"Path to text file containing set of modules to build with "
"(default: %(default)s)"
)
)
return parser
def mage_reproducibility_check(args: dict):
"""Perform a MAGE reproducibility check.
@@ -146,7 +175,6 @@ def mage_reproducibility_check(args: dict):
module_names, cmake_environment, cmake_options = (
common.read_build_module_list_file(module_set_file)
)
print(f"module_names = {module_names}")
# Extract the name of the list.
module_set_name = os.path.split(module_set_file)[-1].rstrip(".lst")
@@ -213,12 +241,11 @@ def mage_reproducibility_check(args: dict):
pbs_template = Template(template_content)
# Assemble commands needed in the PBS script.
genLFM_cmd = "genLFM.py -gid Q"
genLFM_cmd = "genLFM -gid Q"
cda2wind_cmd = (
"cda2wind.py -t0 2016-08-09T02:00:00 -t1 2016-08-09T12:00:00"
"cda2wind -t0 2016-08-09T02:00:00 -t1 2016-08-09T12:00:00"
)
genRCM_cmd = "genRCM.py"
genRaiju_cmd = "genRAIJU.py"
genRaiju_cmd = "genRAIJU"
mpiexec_cmd = f"mpiexec {KAIJUHOME}/scripts/preproc/pinCpuCores.sh"
voltron_cmd = "../bin/voltron_mpi.x weeklyDashGo.xml"
@@ -241,13 +268,10 @@ def mage_reproducibility_check(args: dict):
pbs_options["job_priority"] = os.environ["DERECHO_TESTING_PRIORITY"]
pbs_options["walltime"] = "08:00:00"
pbs_options["modules"] = module_names
pbs_options["condarc"] = os.environ["CONDARC"]
pbs_options["conda_envs_path"] = os.environ["CONDA_ENVS_PATH"]
pbs_options["conda_environment"] = os.environ["CONDA_ENVIRONMENT"]
pbs_options["mage_test_root"] = os.environ["MAGE_TEST_ROOT"]
pbs_options["mage_test_set_root"] = os.environ["MAGE_TEST_SET_ROOT"]
pbs_options["conda_environment"] = os.environ["CONDA_ENVIRONMENT"]
pbs_options["kaijuhome"] = KAIJUHOME
pbs_options["kaipy_private_root"] = os.environ["KAIPY_PRIVATE_ROOT"]
pbs_options["tmpdir"] = os.environ["TMPDIR"]
pbs_options["slack_bot_token"] = os.environ["SLACK_BOT_TOKEN"]
pbs_options["branch_or_commit"] = os.environ["BRANCH_OR_COMMIT"]
@@ -255,7 +279,6 @@ def mage_reproducibility_check(args: dict):
pbs_options["make_cmd"] = make_cmd
pbs_options["genLFM_cmd"] = genLFM_cmd
pbs_options["cda2wind_cmd"] = cda2wind_cmd
pbs_options["genRCM_cmd"] = genRCM_cmd
pbs_options["genRaiju_cmd"] = genRaiju_cmd
pbs_options["mpiexec_cmd"] = mpiexec_cmd
pbs_options["voltron_cmd"] = voltron_cmd
@@ -326,13 +349,10 @@ def mage_reproducibility_check(args: dict):
pbs_options["job_priority"] = os.environ["DERECHO_TESTING_PRIORITY"]
pbs_options["walltime"] = "02:00:00"
pbs_options["modules"] = module_names
pbs_options["condarc"] = os.environ["CONDARC"]
pbs_options["conda_envs_path"] = os.environ["CONDA_ENVS_PATH"]
pbs_options["conda_environment"] = os.environ["CONDA_ENVIRONMENT"]
pbs_options["mage_test_root"] = os.environ["MAGE_TEST_ROOT"]
pbs_options["mage_test_set_root"] = os.environ["MAGE_TEST_SET_ROOT"]
pbs_options["conda_environment"] = os.environ["CONDA_ENVIRONMENT"]
pbs_options["kaijuhome"] = KAIJUHOME
pbs_options["kaipy_private_root"] = os.environ["KAIPY_PRIVATE_ROOT"]
pbs_options["tmpdir"] = os.environ["TMPDIR"]
pbs_options["slack_bot_token"] = os.environ["SLACK_BOT_TOKEN"]
pbs_options["branch_or_commit"] = os.environ["BRANCH_OR_COMMIT"]
@@ -403,7 +423,7 @@ def mage_reproducibility_check(args: dict):
def main():
"""Driver for command-line version of code."""
# Set up the command-line parser.
parser = common.create_command_line_parser(DESCRIPTION)
parser = create_command_line_parser()
# # Add additional arguments specific to this script.
# parser.add_argument(

4
testingScripts/relCasePost-template.pbs
View File

@@ -12,9 +12,9 @@
echo "Job $PBS_JOBID started at `date` on `hostname` in directory `pwd`."
echo 'Loading python environment.'
mage_test_root=$HOME
if [ -d "${mage_test_root}/miniconda3" ]; then
echo 'Loading local miniconda3'
mage_test_root='{{ mage_test_root }}'
export CONDARC="${mage_test_root}/.condarc"
export CONDA_ENVS_PATH="${mage_test_root}/.conda"
mage_miniconda3="${mage_test_root}/miniconda3"
@@ -54,7 +54,7 @@ echo 'The active environment variables are:'
printenv
# Process the data and generate the output video
python $KAIPYHOME/kaipy/scripts/quicklook/gamerrVid.py -d1 {{ case1F }} -id1 {{ case1id }} -d2 {{ case2F }} -id2 {{ case2id }} -o {{ frameFolder }}/{{ caseName }} -ts {{ ts }} -te {{ te }} -dt {{ dt }} -Nth 9 >& {{ caseName }}.out
gamerrVid -d1 {{ case1F }} -id1 {{ case1id }} -d2 {{ case2F }} -id2 {{ case2id }} -o {{ frameFolder }}/{{ caseName }} -ts {{ ts }} -te {{ te }} -dt {{ dt }} -Nth 9 >& {{ caseName }}.out
# copy output video to test root folder
cp {{ frameFolder }}/{{ caseName }}.mp4 $MAGE_TEST_SET_ROOT/.

1
testingScripts/relCaseReport-template.pbs
View File

@@ -12,6 +12,7 @@
echo "Job $PBS_JOBID started at `date` on `hostname` in directory `pwd`."
echo 'Loading python environment.'
mage_test_root=$HOME
if [ -d "${mage_test_root}/miniconda3" ]; then
echo 'Loading local miniconda3'
mage_test_root='{{ mage_test_root }}'

1
testingScripts/relativeCase-template.pbs
View File

@@ -23,6 +23,7 @@ module load {{ module }}
module list
echo 'Loading python environment.'
mage_test_root=$HOME
if [ -d "${mage_test_root}/miniconda3" ]; then
echo 'Loading local miniconda3'
mage_test_root='{{ mage_test_root }}'

4
testingScripts/relativeCaseGo-template.xml
View File

@@ -3,7 +3,7 @@
<Kaiju>
<VOLTRON>
<time tFin="7201.0"/>
<spinup doSpin="T" tSpin="3600.0"/>
<spinup doSpin="T" tSpin="3600.0" tIO="-600.0"/>
<output dtOut="60.0" tsOut="100"/>
<coupling dtCouple="5.0" imType="RAIJU" doQkSquish="F" qkSquishStride="2" doAsyncCoupling="F" doSerial="{{ serial_coupling }}"/>
<restart dtRes="3600.0"/>
@@ -41,7 +41,7 @@
<output loudConsole="T" doFat="F" doLossExtras="F" doDebug="F" writeGhosts="F"/>
<grid gType="SHGRID" ThetaL="15" ThetaU="50"/>
<domain tail_buffer="15.0" sun_buffer="15.0" tail_active="12.0" sun_active="12.0"/>
<sim pdmb="0.75"/>
<sim pdmb="0.75" doSmoothgrads="F"/>
<config fname="raijuconfig.h5"/>
<plasmasphere doPsphere="T" doExcessMap="T"/>
<losses doLosses="T" doCX="T" doSS="T" doCC="T"/>

16
testingScripts/relativeTests.py
View File

@@ -39,9 +39,6 @@ TEST_DIRECTORY = os.path.join(MAGE_TEST_SET_ROOT, 'compTest')
# Home directory of kaiju installation
KAIJUHOME = os.environ['KAIJUHOME']
# Home directory of kaipy installation
KAIPYHOME = os.environ['KAIPYHOME']
# Path to directory containing the test scripts
TEST_SCRIPTS_DIRECTORY = os.path.join(KAIJUHOME, 'testingScripts')
@@ -610,7 +607,7 @@ def main():
# Generate the LFM grid file.
if verbose:
print('Creating LFM grid file.')
cmd = 'genLFM.py -gid D'
cmd = 'genLFM -gid D'
if debug:
print(f"cmd = {cmd}")
try:
@@ -620,7 +617,7 @@ def main():
f"{module_set_name}.\n"
f"e.cmd = {e.cmd}\n"
f"e.returncode = {e.returncode}\n"
'See testing log for output from genLFM.py.\n'
'See testing log for output from genLFM.\n'
'Skipping remaining steps for module set'
f"{module_set_name}\n")
continue
@@ -628,7 +625,7 @@ def main():
# Generate the solar wind boundary condition file.
if verbose:
print('Creating solar wind initial conditions file.')
cmd = 'cda2wind.py -t0 2016-08-09T02:00:00 -t1 2016-08-09T12:00:00'
cmd = 'cda2wind -t0 2016-08-09T02:00:00 -t1 2016-08-09T12:00:00'
if debug:
print(f"cmd = {cmd}")
try:
@@ -638,7 +635,7 @@ def main():
f" for module set {module_set_name}.\n"
f"e.cmd = {e.cmd}\n"
f"e.returncode = {e.returncode}\n"
'See testing log for output from cda2wind.py.\n'
'See testing log for output from cda2wind.\n'
'Skipping remaining steps for module set'
f"{module_set_name}\n")
continue
@@ -646,7 +643,7 @@ def main():
# Generate the Raiju configuration file.
if verbose:
print('Creating Raiju configuration file.')
cmd = 'genRAIJU.py'
cmd = 'genRAIJU'
if debug:
print(f"cmd = {cmd}")
try:
@@ -656,7 +653,7 @@ def main():
f" for module set {module_set_name}.\n"
f"e.cmd = {e.cmd}\n"
f"e.returncode = {e.returncode}\n"
'See testing log for output from genRCM.py.\n'
'See testing log for output from genRAIJU.\n'
'Skipping remaining steps for module set '
f"{module_set_name}\n")
continue
@@ -668,7 +665,6 @@ def main():
base_pbs_options['job_priority'] = os.environ['DERECHO_TESTING_PRIORITY']
base_pbs_options['modules'] = module_names
base_pbs_options['kaijuhome'] = KAIJUHOME
base_pbs_options['kaipyhome'] = KAIPYHOME
base_pbs_options['tmpdir'] = os.environ['TMPDIR']
base_pbs_options['slack_bot_token'] = os.environ['SLACK_BOT_TOKEN']
base_pbs_options['mage_test_root'] = os.environ['MAGE_TEST_ROOT']

10
testingScripts/run_mage-template.pbs
View File

@@ -19,11 +19,11 @@ module load {{ module }}
echo 'The currently loaded modules are:'
module list
echo 'Loading python environment.'
mage_test_root=$HOME
if [ -d "${mage_test_root}/miniconda3" ]; then
echo 'Loading local miniconda3'
export CONDARC="{{ condarc }}"
export CONDA_ENVS_PATH="{{ conda_envs_path }}"
mage_miniconda3="{{ mage_test_root }}/miniconda3"
mage_miniconda3="${mage_test_root}/miniconda3"
mage_conda="${mage_miniconda3}/bin/conda"
__conda_setup="$($mage_conda 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
@@ -47,10 +47,6 @@ echo 'Setting up MAGE environment.'
source {{ kaijuhome }}/scripts/setupEnvironment.sh
echo "The kaiju software is located at ${KAIJUHOME}."
echo 'Setting up kaipy environment.'
source {{ kaipy_private_root }}/kaipy/scripts/setupEnvironment.sh
echo "The kaipy software is located at ${KAIPYHOME}."
echo 'Setting environment variables.'
export TMPDIR={{ tmpdir }}
export SLACK_BOT_TOKEN={{ slack_bot_token }}

381
testingScripts/run_mage_tests.sh Executable file
View File

@@ -0,0 +1,381 @@
#!/usr/bin/bash
# ############################################################################
# IMPORTANT NOTES:
# This bash script was designed to run from a cron job on the 'cron' host at
# NCAR, using ssh to execute this script on a derecho login node. See
# kaiju/testingScripts/crontab for an example of how to invoke this script.
# SSH must be configured so that ssh from cron to derecho does not require a
# password.
# ############################################################################
echo '***********************************************************************'
echo "Starting $0 at `date` on `hostname`."
# ############################################################################
# Force this script to exit on any failure.
set -e
# ----------------------------------------------------------------------------
# These *should* be the only variables you have to change when moving the
# testing environment around or changing python environments.
# Root of kaiju testing environment - *everything* goes under here, except
# for the outputs from the individual test runs.
export MAGE_TEST_ROOT='/glade/campaign/hao/msphere/automated_kaiju_tests'
# Root of kaiju test results tree.
export MAGE_TEST_RESULTS_ROOT='/glade/derecho/scratch/ewinter/mage_testing'
# Location of the miniconda installation used for testing.
export MAGE_MINICONDA='/glade/u/home/ewinter/miniconda3'
# Setup command for conda.
__conda_setup="$('/glade/u/home/ewinter/miniconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
# conda environment for testing
export CONDA_ENVIRONMENT='kaiju-3.12-testing'
# ----------------------------------------------------------------------------
# Other exported environment variables
# Path to directory containing the dateime-stamped directories for individual
# sets of test runs.
export MAGE_TEST_RUNS_ROOT="${MAGE_TEST_RESULTS_ROOT}/test_runs"
# PBS account to use for running tests on derecho
export DERECHO_TESTING_ACCOUNT='P28100045'
# PBS queue to use for running tests on derecho
export DERECHO_TESTING_QUEUE='main'
# PBS priority to use for running tests on derecho
export DERECHO_TESTING_PRIORITY='economy'
# Set the token for sending messages to Slack.
export SLACK_BOT_TOKEN=`cat $HOME/.ssh/slack.txt`
# IMPORTANT: Set this environment variable to force the python print()
# function to automatically flush its output in all of the testing scripts.
# This will ensure that output from the testing scripts is logged in the order
# that it is created.
export PYTHONUNBUFFERED='TRUE'
# ----------------------------------------------------------------------------
# Non-exported variables used by this script
# Path to the SSH key to use for running the tests. The key must have no
# passphrase. This is needed to allow passwordless access to BitBucket.
ssh_key_for_testing='/glade/u/home/ewinter/.ssh/id_rsa_kaiju_testing'
# Setup script for CDF code
cdf_setup_script="${MAGE_TEST_ROOT}/local/cdf/3.9.0/bin/definitions.B"
# Address of kaiju-private repository on BitBucket.
kaiju_repository='git@bitbucket.org:aplkaiju/kaiju-private.git'
# Name of local directory containing clone of repository.
local_kaiju_name='kaiju'
# Default kaiju code branch to test if no branch, commit, or tag is specified.
default_branch_to_test='development'
# Output string to separate results from different tests.
test_output_separator='------------------------------------------------------'
# ############################################################################
# Define the command-line help function.
Help()
{
# Display Help
echo 'Control script for running MAGE tests via cron and ssh.'
echo
echo "Syntax: run_mage_tests.sh [-b branch] [-c commit] [-d] [-h] [-v] 'test1[,test2,...]'"
echo 'options:'
echo 'b branch Run tests using this branch'
echo 'c commit Run tests using this commit (or tag)'
echo 'd Use debug mode.'
echo 'h Print this help message.'
echo 'v Use verbose mode.'
echo
echo 'If no branch or commit is specified, the latest commit on the development branch will be used for the tests.'
echo "Each test can have its own options, e.g. 'buildTest.py -d,unitTest.py -lv'"
}
# Process command-line options.
branch=''
commit=''
debug=false
verbose=false
while getopts ':b:c:dhv' option; do
case $option in
b) # Test a specific branch
branch=$OPTARG;;
c) # Test a specific commit or tag
commit=$OPTARG;;
d) # debug mode
debug=true;;
h) # display Help
Help
exit;;
v) # verbose mode
verbose=true;;
\?) # Invalid option
echo 'Error: Invalid option'
exit 1;;
esac
done
if $debug; then
echo "branch=${branch}"
echo "commit=${commit}"
echo "debug=${debug}"
echo "help=${help}"
echo "verbose=${verbose}"
fi
# Fetch the branch or commit to test. If neither specified, use the default.
if [[ -n $branch && -n $commit ]]; then
echo 'Cannot specify branch and commit together!'
exit 1
fi
if [[ -z $branch && -z $commit ]]; then
branch=$default_branch_to_test
fi
# At this point, either branch is specified, or commit/tag is specified.
# There should be no case where both are unspecified, or both are specified.
if [[ -n $branch ]]; then
export BRANCH_OR_COMMIT=$branch
else
export BRANCH_OR_COMMIT=$commit
fi
if $debug; then
echo "BRANCH_OR_COMMIT=${BRANCH_OR_COMMIT}"
fi
# Fetch the list of tests to run.
tests_to_run_str=$BASH_ARGV
if $debug; then
echo "tests_to_run_str=${tests_to_run_str}"
fi
# Split the test list string into an array.
# Tests are separated by comma, no spaces.
IFS="," tests_to_run=($tests_to_run_str)
if $debug; then
echo 'The test commands to run are:'
for test_cmd in "${tests_to_run[@]}"
do
echo $test_cmd
done
fi
# ############################################################################
# Load the SSH private key for testing. This is needed for BitBucket access.
# Note that this key does not have a passphrase, so it can easily be used
# from a cron job.
if $verbose; then
echo 'Loading SSH key into key agent.'
fi
eval `ssh-agent -s`
ssh-add $ssh_key_for_testing
# ############################################################################
# Set up the module system (needed when running from cron, harmless
# otherwise).
if $verbose; then
echo 'Setting up module system.'
fi
source /etc/profile.d/z00_modules.sh
# List at-start modules.
# The 2>&1 (no spaces!) is needed since the 'module' command sends
# output to stderr by default, and so it is lost when stdout is sent
# back to the user.
if $verbose; then
echo 'At start, the loaded modules are:'
module list 2>&1
fi
# ############################################################################
# Activate the conda installation for MAGE testing.
if $verbose; then
echo "Setting up conda environment for MAGE testing ${CONDA_ENVIRONMENT}."
fi
# This code is based on the code that the miniconda installer puts into
# ~/.bashrc or ~/.bash_profile when a user installs miniconda.
# This code is needed since $HOME/.bashrc is not run.
if [ $? -eq 0 ]; then
eval "$__conda_setup"
else
if [ -f "${MAGE_MINICONDA}/etc/profile.d/conda.sh" ]; then
. "${MAGE_MINICONDA}/etc/profile.d/conda.sh"
else
export PATH="${MAGE_MINICONDA}/bin:$PATH"
fi
fi
unset __conda_setup
conda activate $CONDA_ENVIRONMENT
if $verbose; then
echo "conda environment is `echo $CONDA_PREFIX`"
fi
if $verbose; then
echo 'The installed version of kaipy in this environment is:'
conda list kaipy
fi
# ############################################################################
# Make the CDF library available (needed by the satellite comparison
# python scripts).
if $verbose; then
echo 'Sourcing CDF setup script.'
fi
source $cdf_setup_script
# ############################################################################
# Create the ISO 8601 datetime stamp for this set of tests.
testing_datetime=`date --iso-8601=seconds`
if $debug; then
echo "testing_datetime=${testing_datetime}"
fi
# <HACK>
# The make tool cannot handle file or directory names that contain a colon
# (':'). Process the ISO 8601 date time string from the ISO 8601 form:
# YYYY-MM-DDTHH:mm:ss[+-]hh:mm
# into the more compact form:
# YYYYMMDD_HHMMSS
# The sed commands to do this are, in order:
# s/.\{6\}$// - Remove the time zone offset (last 6 characters)
# s/-//g - Delete all '-'.
# s/\://g - Delete all ':'.
# s/T/_/ - Convert 'T' separating date and time to underscore.
testing_datetime=`echo $testing_datetime | sed -e 's/.\{6\}$//' -e 's/-//g' -e 's/\://g' -e 's/T/_/'`
if $debug; then
echo "testing_datetime=${testing_datetime}"
fi
# </HACK>
# Create a directory to hold all of the tests for this set of tests.
test_set_dir="${testing_datetime}-${BRANCH_OR_COMMIT}"
if $debug; then
echo "test_set_dir=${test_set_dir}"
fi
export MAGE_TEST_SET_ROOT="${MAGE_TEST_RUNS_ROOT}/${test_set_dir}"
if $verbose; then
echo "Creating directory for this set of tests at ${MAGE_TEST_SET_ROOT}."
fi
mkdir $MAGE_TEST_SET_ROOT
# ############################################################################
# Move to the directory for this set of tests.
cd $MAGE_TEST_SET_ROOT
# Clone the kaiju-private repository, call it kaiju locally.
if $verbose; then
echo "Cloning repository ${kaiju_repository}."
fi
git clone $kaiju_repository $local_kaiju_name
# Move into the repository clone.
cd $local_kaiju_name
# If a branch was requested, switch to that branch. Otherwise, if a commit
# or tag was requested, check out that commit or tag.
if $verbose; then
echo "Checking out branch/commit/tag ${BRANCH_OR_COMMIT}."
fi
git checkout $BRANCH_OR_COMMIT
# ############################################################################
# <HACK>
# Back up existing test code, since we need to use test code that is under
# development.
mkdir TEST_CODE_BACKUP
mv testingScripts TEST_CODE_BACKUP/
mv tests TEST_CODE_BACKUP/
# Copy latest test code.
new_test_code_root="${MAGE_TEST_ROOT}/kaiju-private"
if $verbose; then
echo "Copying updated test files from ${new_test_code_root}."
fi
cp -rp $new_test_code_root/testingScripts ./testingScripts
cp -rp $new_test_code_root/tests ./tests
# </HACK>
# ############################################################################
# Set up the kaiju environment using the just-checked-out code.
kaiju_setup_script="${MAGE_TEST_SET_ROOT}/${local_kaiju_name}/scripts/setupEnvironment.sh"
if $verbose; then
echo "Sourcing kaiju setup script ${kaiju_setup_script}."
fi
source $kaiju_setup_script
if $verbose; then
echo "KAIJUHOME is ${KAIJUHOME}."
fi
# ############################################################################
# List at-start environment variables.
if $debug; then
echo 'At start, the environment variables are:'
printenv
fi
# ############################################################################
# Compute the location of the test scripts.
kaiju_test_scripts_dir="${KAIJUHOME}/testingScripts"
if $debug; then
echo "kaiju_test_scripts_dir=${kaiju_test_scripts_dir}"
fi
# Run each test.
for mage_test in ${tests_to_run[@]}
do
echo $test_output_separator
if $verbose; then
echo "Moving to ${MAGE_TEST_SET_ROOT}."
fi
cd $MAGE_TEST_SET_ROOT
cmd="python ${kaiju_test_scripts_dir}/${mage_test}"
if $verbose; then
echo "Running test '${cmd}' at `date` on `hostname`."
fi
eval "${cmd}"
done
echo $test_output_separator
# ############################################################################
# Shut down the SSH agent.
if $verbose; then
echo "Shutting down SSH key agent."
fi
ssh-agent -k
# ############################################################################
echo "Ending $0 at `date` on `hostname`."
echo '***********************************************************************'

8
testingScripts/unitTest.py
View File

@@ -145,7 +145,7 @@ UNIT_TEST_DATA_INPUT_FILES = [
'bcwind.h5',
'geo_mpi.xml',
'lfmD.h5',
'rcmconfig.h5',
'raijuconfig.h5',
]
# Names of PBS scripts to create from templates.
@@ -425,17 +425,17 @@ def main():
print(f"Copying {from_path} to {to_path}.")
shutil.copyfile(from_path, to_path)
else:
cmd = "cda2wind.py -t0 2016-08-09T09:00:00 -t1 2016-08-09T11:00:00"
cmd = "cda2wind -t0 2016-08-09T09:00:00 -t1 2016-08-09T11:00:00"
if debug:
print(f"cmd = {cmd}")
cproc = subprocess.run(cmd, shell=True, check=True,
text=True, capture_output=True)
cmd = "genLFM.py"
cmd = "genLFM"
if debug:
print(f"cmd = {cmd}")
cproc = subprocess.run(cmd, shell=True, check=True,
text=True, capture_output=True)
cmd = "genRAIJU.py"
cmd = "genRAIJU"
if debug:
print(f"cmd = {cmd}")
cproc = subprocess.run(cmd, shell=True, check=True,

16
testingScripts/weeklyDash-template.pbs
View File

@@ -20,9 +20,7 @@ echo 'The currently loaded modules are:'
module list
echo 'Loading python environment.'
export CONDARC="{{ condarc }}"
export CONDA_ENVS_PATH="{{ conda_envs_path }}"
mage_miniconda3="{{ mage_test_root }}/miniconda3"
mage_miniconda3="${HOME}/miniconda3"
mage_conda="${mage_miniconda3}/bin/conda"
__conda_setup="$($mage_conda 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
@@ -42,10 +40,6 @@ echo 'Setting up MAGE environment.'
source {{ kaijuhome }}/scripts/setupEnvironment.sh
echo "The kaiju software is located at ${KAIJUHOME}."
echo 'Setting up kaipy environment.'
source {{ kaipy_private_root }}/kaipy/scripts/setupEnvironment.sh
echo "The kaipy software is located at ${KAIPYHOME}."
echo 'Setting environment variables.'
export TMPDIR={{ tmpdir }}
export SLACK_BOT_TOKEN={{ slack_bot_token }}
@@ -83,10 +77,10 @@ echo 'Generating the solar wind boundary condition file.'
{{ cda2wind_cmd }}
echo "The solar wind boundary condition file is `ls bcwind.h5`."
# Generate the RCM configuration file.
echo 'Generating the RCM configuration file.'
{{ genRCM_cmd }}
echo "The RCM configuration file is `ls rcmconfig.h5`."
# Generate the raiju configuration file.
echo 'Generating the raiju configuration file.'
{{ genRAIJU_cmd }}
echo "The RAIJU configuration file is `ls raijuconfig.h5`."
# Run the model.
MPICOMMAND="{{ mpiexec_cmd }}"

13
testingScripts/weeklyDash.py
View File

@@ -142,15 +142,15 @@ def weekly_dash(args: dict):
make_cmd = "make voltron_mpi.x"
# Create the command to generate the LFM grid.
genLFM_cmd = "genLFM.py -gid Q"
genLFM_cmd = "genLFM -gid Q"
# Create the command to generate the solar wind boundary condition file.
cda2wind_cmd = (
"cda2wind.py -t0 2016-08-09T02:00:00 -t1 2016-08-09T12:00:00"
"cda2wind -t0 2016-08-09T02:00:00 -t1 2016-08-09T12:00:00"
)
# Create the command to generate the RCM configuration.
genRCM_cmd = "genRCM.py"
# Create the command to generate the raiju configuration.
genRAIJU_cmd = "genRAIJU"
# Create the command for launching an MPI program.
mpiexec_cmd = f"mpiexec {KAIJUHOME}/scripts/preproc/pinCpuCores.sh"
@@ -178,13 +178,10 @@ def weekly_dash(args: dict):
pbs_options["job_priority"] = os.environ["DERECHO_TESTING_PRIORITY"]
pbs_options["walltime"] = "08:00:00"
pbs_options["modules"] = module_names
pbs_options["condarc"] = os.environ["CONDARC"]
pbs_options["conda_envs_path"] = os.environ["CONDA_ENVS_PATH"]
pbs_options["conda_environment"] = os.environ["CONDA_ENVIRONMENT"]
pbs_options["mage_test_root"] = os.environ["MAGE_TEST_ROOT"]
pbs_options["mage_test_set_root"] = os.environ["MAGE_TEST_SET_ROOT"]
pbs_options["kaijuhome"] = KAIJUHOME
pbs_options["kaipy_private_root"] = os.environ["KAIPY_PRIVATE_ROOT"]
pbs_options["tmpdir"] = os.environ["TMPDIR"]
pbs_options["slack_bot_token"] = os.environ["SLACK_BOT_TOKEN"]
pbs_options["branch_or_commit"] = os.environ["BRANCH_OR_COMMIT"]
@@ -192,7 +189,7 @@ def weekly_dash(args: dict):
pbs_options["make_cmd"] = make_cmd
pbs_options["genLFM_cmd"] = genLFM_cmd
pbs_options["cda2wind_cmd"] = cda2wind_cmd
pbs_options["genRCM_cmd"] = genRCM_cmd
pbs_options["genRAIJU_cmd"] = genRAIJU_cmd
pbs_options["mpiexec_cmd"] = mpiexec_cmd
pbs_options["voltron_cmd"] = voltron_cmd

50
testingScripts/weeklyDashReport.py
View File

@@ -121,9 +121,6 @@ REMIX_NORTH_QUICKLOOK_MASTER = os.path.join(
REMIX_SOUTH_QUICKLOOK_MASTER = os.path.join(
REFERENCE_RESULTS_DIRECTORY_MASTER, 'remix_s.png'
)
RCM_QUICKLOOK_MASTER = os.path.join(
REFERENCE_RESULTS_DIRECTORY_MASTER, 'qkrcmpic.png'
)
# Compute the paths to the quicklook plots for the development branch.
MAGNETOSPHERE_QUICKLOOK_DEVELOPMENT = os.path.join(
@@ -135,9 +132,6 @@ REMIX_NORTH_QUICKLOOK_DEVELOPMENT = os.path.join(
REMIX_SOUTH_QUICKLOOK_DEVELOPMENT = os.path.join(
REFERENCE_RESULTS_DIRECTORY_DEVELOPMENT, 'remix_s.png'
)
RCM_QUICKLOOK_DEVELOPMENT = os.path.join(
REFERENCE_RESULTS_DIRECTORY_DEVELOPMENT, 'qkrcmpic.png'
)
def main():
@@ -908,27 +902,6 @@ def main():
# ------------------------------------------------------------------------
# Make the RCM quick-look plot.
if verbose:
print(f"Creating RCM quicklook plot for {os.getcwd()}.")
# Create the plot.
cmd = 'rcmpic.py'
if debug:
print(f"cmd = {cmd}")
try:
_ = subprocess.run(cmd, shell=True, check=True)
except subprocess.CalledProcessError as e:
print(
'ERROR: Unable to create RCM quicklook plot.\n'
f"e.cmd = {e.cmd}\n"
f"e.returncode = {e.returncode}\n"
f'See log for output.\n',
file=sys.stderr
)
# ------------------------------------------------------------------------
# Create merged images for the quicklook plots.
# Merge magnetosphere quicklooks.
@@ -988,25 +961,6 @@ def main():
file=sys.stderr
)
# Merge RCM quicklooks.
cmd = (
f"convert {RCM_QUICKLOOK_MASTER}"
f" {RCM_QUICKLOOK_DEVELOPMENT}"
' qkrcmpic.png -append combined_qkrcmpic.png'
)
if debug:
print(f"cmd = {cmd}")
try:
cproc = subprocess.run(cmd, shell=True, check=True)
except subprocess.CalledProcessError as e:
print(
'ERROR: Unable to combine RCM quicklook plots.\n'
f"e.cmd = {e.cmd}\n"
f"e.returncode = {e.returncode}\n"
f'See log for output.\n',
file=sys.stderr
)
# ------------------------------------------------------------------------
# List the files to post and their comments.
@@ -1017,11 +971,9 @@ def main():
'qkmsphpic.png',
'remix_n.png',
'remix_s.png',
'qkrcmpic.png',
'combined_msphpic.png',
'combined_remix_n.png',
'combined_remix_s.png',
'combined_qkrcmpic.png'
]
comments_to_post = [
'Real-Time Performance\n\n',
@@ -1030,11 +982,9 @@ def main():
'Magnetosphere Quicklook Plots\n\n',
'REMIX (north) Quicklook Plots\n\n',
'REMIX (south) Quicklook Plots\n\n',
'RCM Quicklook Plots\n\n',
'Magnetosphere Quicklook Comparison Plots\n\n',
'REMIX (north) Quicklook Comparison Plots\n\n',
'REMIX (south) Quicklook Comparison Plots\n\n',
'RCM Quicklook Comparison Plots\n\n'
]
# If loud mode is on, post results to Slack.

4
tests/unitTestReport-template.pbs
View File

@@ -19,11 +19,9 @@ module load {{ module }}
module list
echo 'Loading python environment.'
mage_test_root=$HOME
if [ -d "${mage_test_root}/miniconda3" ]; then
echo 'Loading local miniconda3'
mage_test_root='{{ mage_test_root }}'
export CONDARC="${mage_test_root}/.condarc"
export CONDA_ENVS_PATH="${mage_test_root}/.conda"
mage_miniconda3="${mage_test_root}/miniconda3"
mage_conda="${mage_miniconda3}/bin/conda"
__conda_setup="$($mage_conda 'shell.bash' 'hook' 2> /dev/null)"

6
tests/voltron/testVoltGridGen.pf
View File

@@ -9,6 +9,8 @@ module testVoltGridGen
implicit none
character(len=strLen) :: xmlName = 'voltGridTests.xml'
integer, parameter :: gamRes = 64
!! genVoltShellGrid expects a gamera resolution to determine defaults for its own
contains
@@ -36,7 +38,7 @@ module testVoltGridGen
call xmlInp%Set_Val(Nt, "grid/Nt", -1) ! -1 so things blow up if xml isn't set properly
call xmlInp%Set_Val(Np, "grid/Np", -1) ! -1 so things blow up if xml isn't set properly
call genVoltShellGrid(vApp, xmlInp)
call genVoltShellGrid(vApp, xmlInp, gamRes)
@assertEqual(vApp%shGrid%Nt, 2*Nt, "Wrong amount of theta cells")
@assertEqual(vApp%shGrid%Np, Np , "Wrong amount of phi cells")
@@ -62,7 +64,7 @@ module testVoltGridGen
call xmlInp%Set_Val(Nt, "grid/Nt", -1) ! -1 so things blow up if xml isn't set properly
call xmlInp%Set_Val(Np, "grid/Np", -1) ! -1 so things blow up if xml isn't set properly
call genVoltShellGrid(vApp, xmlInp)
call genVoltShellGrid(vApp, xmlInp, gamRes)
@assertEqual(2*Nt, vApp%shGrid%Nt, "Wrong amount of theta cells")
@assertEqual( Np, vApp%shGrid%Np, "Wrong amount of phi cells")