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Fixing race conditions and uninitialized memory issues with raiju

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This commit is contained in:
Jeffrey Garretson
2025-07-30 21:35:10 -06:00
parent 88d6e53a1c
commit 2cc8c0215b
11 changed files with 96 additions and 16 deletions
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8
src/base/shellutils/shellInterp.F90
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@@ -106,7 +106,7 @@ module shellInterp
case(SHGR_CC)
!$OMP PARALLEL DO default(shared) &
!$OMP schedule(dynamic) &
!$OMP private(i,j)
!$OMP private(i,j,goodInterp)
do j=sgDest%jsg,sgDest%jeg
do i=sgDest%isg,sgDest%ieg
if (.not. varOut%mask(i,j)) cycle
@@ -125,7 +125,7 @@ module shellInterp
case(SHGR_CORNER)
!$OMP PARALLEL DO default(shared) &
!$OMP schedule(dynamic) &
!$OMP private(i,j)
!$OMP private(i,j,goodinterp)
do j=sgDest%jsg,sgDest%jeg+1
do i=sgDest%isg,sgDest%ieg+1
if (.not. varOut%mask(i,j)) cycle
@@ -142,7 +142,7 @@ module shellInterp
case(SHGR_FACE_THETA)
!$OMP PARALLEL DO default(shared) &
!$OMP schedule(dynamic) &
!$OMP private(i,j)
!$OMP private(i,j,goodInterp)
do j=sgDest%jsg,sgDest%jeg
do i=sgDest%isg,sgDest%ieg+1
if (.not. varOut%mask(i,j)) cycle
@@ -159,7 +159,7 @@ module shellInterp
case(SHGR_FACE_PHI)
!$OMP PARALLEL DO default(shared) &
!$OMP schedule(dynamic) &
!$OMP private(i,j)
!$OMP private(i,j,goodInterp)
do j=sgDest%jsg,sgDest%jeg+1
do i=sgDest%isg,sgDest%ieg
if (.not. varOut%mask(i,j)) cycle

4
src/raiju/raijuBCs.F90
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@@ -119,7 +119,7 @@ module raijuBCs
eleIdx = spcIdx(Grid, F_HOTE)
!$OMP PARALLEL DO default(shared) &
!$OMP schedule(dynamic) &
!$OMP private(i,j,s,fIdx,fm,vm,kT,etaBelow,tmp_kti,tmp_kte,tmp_D,tmp_P)
!$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
if (State%active(i,j) .eq. RAIJUINACTIVE) then
@@ -309,4 +309,4 @@ module raijuBCs
end subroutine setActiveShellsByContribution
end module raijuBCs
end module raijuBCs

54
src/raiju/raijuStarter.F90
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@@ -5,6 +5,7 @@ module raijustarter
use shellgrid
use xml_input
use planethelper
use arrayutil
! Raiju
use raijudefs
@@ -382,71 +383,116 @@ module raijustarter
! dt for every lambda channel
allocate( State%dtk (Grid%Nk) )
call fillArray(State%dtk, 0.0_rp)
! nSteps for each channel
allocate( State%nStepk(Grid%Nk) )
call fillArray(State%nStepk, 0)
! Where we keep all our stuff
allocate( State%eta (sh%isg:sh%ieg, sh%jsg:sh%jeg, Grid%Nk) )
call fillArray(State%eta, 0.0_rp)
! Where we keep all our stuff but a half-step ahead of now
allocate( State%eta_half (sh%isg:sh%ieg, sh%jsg:sh%jeg, Grid%Nk) )
call fillArray(State%eta_half, 0.0_rp)
! Where we kept all our stuff one step ago
allocate( State%eta_last (sh%isg:sh%ieg, sh%jsg:sh%jeg, Grid%Nk) )
call fillArray(State%eta_last, 0.0_rp)
! Where all the stuff sorta was over the last State%dt
allocate( State%eta_avg (sh%isg:sh%ieg, sh%jsg:sh%jeg, Grid%Nk) )
call fillArray(State%eta_avg, 0.0_rp)
! I shells shat should be evolved for each k
allocate( State%activeShells (sh%isg:sh%ieg, Grid%Nk) )
State%activeShells = .false.
! Effective potential (used for output only)
allocate( State%pEff(sh%isg:sh%ieg+1, sh%jsg:sh%jeg+1, Grid%Nk) )
call fillArray(State%pEff, 0.0_rp)
! Gradient of ionspheric potential
allocate( State%gradPotE (sh%isg:sh%ieg+1, sh%jsg:sh%jeg+1, 2) )
call fillArray(State%gradPotE, 0.0_rp)
! Gradient of corotation potential
allocate( State%gradPotCorot (sh%isg:sh%ieg+1, sh%jsg:sh%jeg+1, 2) )
call fillArray(State%gradPotCorot, 0.0_rp)
! Gradient of (flux tube volume ^ -2/3)
allocate( State%gradVM (sh%isg:sh%ieg+1, sh%jsg:sh%jeg+1, 2) )
call fillArray(State%gradVM, 0.0_rp)
! Interface and cell velocities
allocate( State%gradPotE_cc (sh%isg:sh%ieg, sh%jsg:sh%jeg, 2) )
call fillArray(State%gradPotE_cc, 0.0_rp)
allocate( State%gradPotCorot_cc(sh%isg:sh%ieg, sh%jsg:sh%jeg, 2) )
call fillArray(State%gradPotCorot_cc, 0.0_rp)
allocate( State%gradVM_cc (sh%isg:sh%ieg, sh%jsg:sh%jeg, 2) )
call fillArray(State%gradVM_cc, 0.0_rp)
allocate( State%iVel (sh%isg:sh%ieg+1, sh%jsg:sh%jeg+1, Grid%Nk, 2) )
call fillArray(State%iVel, 0.0_rp)
allocate( State%iVelL(sh%isg:sh%ieg+1, sh%jsg:sh%jeg+1, Grid%Nk, 2) )
call fillArray(State%iVelL, 0.0_rp)
allocate( State%iVelR(sh%isg:sh%ieg+1, sh%jsg:sh%jeg+1, Grid%Nk, 2) )
call fillArray(State%iVelR, 0.0_rp)
allocate( State%cVel (sh%isg:sh%ieg , sh%jsg:sh%jeg , Grid%Nk, 2) )
call fillArray(State%cVel, 0.0_rp)
! Coupling input moments
allocate( State%Pavg(sh%isg:sh%ieg , sh%jsg:sh%jeg, 0:Grid%nFluidIn) )
call fillArray(State%Pavg, 0.0_rp)
allocate( State%Davg(sh%isg:sh%ieg , sh%jsg:sh%jeg, 0:Grid%nFluidIn) )
call fillArray(State%Davg, 0.0_rp)
allocate( State%Pstd(sh%isg:sh%ieg , sh%jsg:sh%jeg, 0:Grid%nFluidIn) )
call fillArray(State%Pstd, 0.0_rp)
allocate( State%Dstd(sh%isg:sh%ieg , sh%jsg:sh%jeg, 0:Grid%nFluidIn) )
call fillArray(State%Dstd, 0.0_rp)
allocate( State%domWeights(sh%isg:sh%ieg , sh%jsg:sh%jeg) )
call fillArray(State%domWeights, 0.0_rp)
allocate( State%tiote(sh%isg:sh%ieg , sh%jsg:sh%jeg) )
call fillArray(State%tiote, 0.0_rp)
call initShellVar(Grid%shGrid, SHGR_CC, State%Tb)
State%Tb%data = 0.0
State%Tb%mask = .false.
! Bmin surface
allocate( State%Bmin (sh%isg:sh%ieg+1, sh%jsg:sh%jeg+1, 3 ) )
call fillArray(State%Bmin, 0.0_rp)
allocate( State%xyzMin (sh%isg:sh%ieg+1, sh%jsg:sh%jeg+1, 3 ) )
call fillArray(State%xyzMin, 0.0_rp)
allocate( State%xyzMincc(sh%isg:sh%ieg , sh%jsg:sh%jeg , 3 ) )
call fillArray(State%xyzMincc, 0.0_rp)
allocate( State%thcon (sh%isg:sh%ieg+1, sh%jsg:sh%jeg+1 ) )
call fillArray(State%thcon, 0.0_rp)
allocate( State%phcon (sh%isg:sh%ieg+1, sh%jsg:sh%jeg+1 ) )
call fillArray(State%phcon, 0.0_rp)
! 2D corner quantities
allocate( State%topo (sh%isg:sh%ieg+1, sh%jsg:sh%jeg+1) )
call fillArray(State%topo, 0)
allocate( State%espot (sh%isg:sh%ieg+1, sh%jsg:sh%jeg+1) )
call fillArray(State%espot, 0.0_rp)
allocate( State%pot_corot(sh%isg:sh%ieg+1, sh%jsg:sh%jeg+1) )
call fillArray(State%pot_corot, 0.0_rp)
allocate( State%bvol (sh%isg:sh%ieg+1, sh%jsg:sh%jeg+1) )
call fillArray(State%bvol, 0.0_rp)
allocate( State%bvol_cc (sh%isg:sh%ieg , sh%jsg:sh%jeg ) )
call fillArray(State%bvol_cc, 0.0_rp)
allocate( State%vaFrac (sh%isg:sh%ieg+1, sh%jsg:sh%jeg+1) )
call fillArray(State%vaFrac, 0.0_rp)
! 1D cell-centered quantities
allocate( State%bndLoc(sh%jsg:sh%jeg) )
call fillArray(State%bndLoc, 0)
! 2D cell-centered quantities
allocate( State%active (sh%isg:sh%ieg, sh%jsg:sh%jeg) )
call fillArray(State%active, 0)
allocate( State%active_last (sh%isg:sh%ieg, sh%jsg:sh%jeg) )
call fillArray(State%active_last, 0)
allocate( State%OCBDist(sh%isg:sh%ieg, sh%jsg:sh%jeg) )
call fillArray(State%OCBDist, 0)
allocate( State%lossRates (sh%isg:sh%ieg, sh%jsg:sh%jeg, Grid%Nk) )
call fillArray(State%lossRates, 0.0_rp)
allocate( State%precipType_ele (sh%isg:sh%ieg, sh%jsg:sh%jeg, Grid%Nk) )
call fillArray(State%precipType_ele, 0.0_rp)
allocate( State%lossRatesPrecip(sh%isg:sh%ieg, sh%jsg:sh%jeg, Grid%Nk) )
call fillArray(State%lossRatesPrecip, 0.0_rp)
!allocate( State%precipNFlux (sh%isg:sh%ieg, sh%jsg:sh%jeg, Grid%Nk) )
!allocate( State%precipEFlux (sh%isg:sh%ieg, sh%jsg:sh%jeg, Grid%Nk) )
allocate( State%dEta_dt (sh%isg:sh%ieg, sh%jsg:sh%jeg, Grid%Nk) )
call fillArray(State%dEta_dt, 0.0_rp)
allocate( State%CCHeatFlux (sh%isg:sh%ieg, sh%jsg:sh%jeg, Grid%Nk) )
call fillArray(State%CCHeatFlux, 0.0_rp)
! Coupling output data
allocate(State%Den (0:Model%nSpc))
allocate(State%Press(0:Model%nSpc))
@@ -481,10 +527,15 @@ module raijustarter
! Only bother allocating persistent versions of debug stuff if we need them
if (Model%doOutput_debug) then
allocate( State%etaFaceReconL(sh%isg:sh%ieg+1, sh%jsg:sh%jeg+1, Grid%Nk, 2) )
call fillArray(State%etaFaceReconL, 0.0_rp)
allocate( State%etaFaceReconR(sh%isg:sh%ieg+1, sh%jsg:sh%jeg+1, Grid%Nk, 2) )
call fillArray(State%etaFaceReconR, 0.0_rp)
allocate( State%etaFacePDML (sh%isg:sh%ieg+1, sh%jsg:sh%jeg+1, Grid%Nk, 2) )
call fillArray(State%etaFacePDML, 0.0_rp)
allocate( State%etaFacePDMR (sh%isg:sh%ieg+1, sh%jsg:sh%jeg+1, Grid%Nk, 2) )
call fillArray(State%etaFacePDMR, 0.0_rp)
allocate( State%etaFlux (sh%isg:sh%ieg+1, sh%jsg:sh%jeg+1, Grid%Nk, 2) )
call fillArray(State%etaFlux, 0.0_rp)
endif
State%KpTS%wID = Model%tsF
@@ -492,7 +543,6 @@ module raijustarter
end associate
! For now, just set t to tStart and ts to 0
State%t = Model%t0
State%ts = 0

9
src/voltron/modelInterfaces/imag2mhd_interface.F90
View File

@@ -293,10 +293,11 @@ module imag2mhd_interface
do i=Gr%isg,Gr%ieg
isActive = (j >= Gr%js) .and. (j <= Gr%je) .and. &
(k >= Gr%ks) .and. (k <= Gr%ks)
if (isActive) cycle
!If still here map this ghost to active and set value based on active
call lfmIJKcc(Model,Gr,i,j,k,ip,jp,kp)
Q(i,j,k) = Q(ip,jp,kp)
if(.not. isActive) then
!If still here map this ghost to active and set value based on active
call lfmIJKcc(Model,Gr,i,j,k,ip,jp,kp)
Q(i,j,k) = Q(ip,jp,kp)
endif
enddo
enddo !j
enddo !k

7
testingScripts/ICtest.py
View File

@@ -360,7 +360,12 @@ def main():
)
if debug:
print(f"slack_response_summary = {slack_response_summary}")
# Also write a summary file to the root folder of this test
with open(os.path.join(MAGE_TEST_SET_ROOT,'testSummary.out'), 'w', encoding='utf-8') as f:
f.write(test_report_details_string)
f.write('\n')
# ------------------------------------------------------------------------
if debug:

7
testingScripts/buildTest.py
View File

@@ -378,7 +378,12 @@ def main():
)
if debug:
print(f"slack_response_summary = {slack_response_summary}")
# Also write a summary file to the root folder of this test
with open(os.path.join(MAGE_TEST_SET_ROOT,'testSummary.out'), 'w', encoding='utf-8') as f:
f.write(test_report_details_string)
f.write('\n')
# ------------------------------------------------------------------------
if debug:

1
testingScripts/intelCheckSubmitReport-template.pbs
View File

@@ -52,6 +52,7 @@ export TMPDIR={{ tmpdir }}
export SLACK_BOT_TOKEN={{ slack_bot_token }}
export DERECHO_TESTING_ACCOUNT={{ account }}
export BRANCH_OR_COMMIT={{ branch_or_commit }}
export MAGE_TEST_SET_ROOT={{ mage_test_set_root }}
echo 'The active environment variables are:'
printenv

2
testingScripts/intelChecks.py
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@@ -378,6 +378,8 @@ def intelChecks(args: dict):
pbs_options["slack_bot_token"] = os.environ["SLACK_BOT_TOKEN"]
pbs_options["mage_test_root"] = os.environ["MAGE_TEST_ROOT"]
pbs_options["branch_or_commit"] = BRANCH_OR_COMMIT
pbs_options["mage_test_set_root"] = os.environ["MAGE_TEST_SET_ROOT"]
pbs_options["conda_environment"] = os.environ["CONDA_ENVIRONMENT"]
# Set options specific to the memory check, then render the template.
pbs_options["job_name"] = "mage_intelCheckSubmitMem"

10
testingScripts/intelChecksReport.py
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@@ -35,6 +35,9 @@ DESCRIPTION = 'Create report for Intel Inspector tests.'
# Branch or commit (or tag) used for testing.
BRANCH_OR_COMMIT = os.environ['BRANCH_OR_COMMIT']
# Root of directory tree for this set of tests.
MAGE_TEST_SET_ROOT = os.environ["MAGE_TEST_SET_ROOT"]
def main():
"""Begin main program.
@@ -255,7 +258,12 @@ def main():
)
if debug:
print(f"slack_response_summary = {slack_response_summary}")
# Also write a summary file to the root folder of this test
with open(os.path.join(MAGE_TEST_SET_ROOT,'testSummary.out'), 'w', encoding='utf-8') as f:
f.write(test_report_details_string)
f.write('\n')
# ------------------------------------------------------------------------
if debug:

3
testingScripts/relCasePost-template.pbs
View File

@@ -56,5 +56,8 @@ 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
# copy output video to test root folder
cp {{ frameFolder }}/{{ caseName }}.mp4 $MAGE_TEST_SET_ROOT/.
echo "Job $PBS_JOBID ended at `date` on `hostname` in directory `pwd`."

7
testingScripts/unitTestReport.py
View File

@@ -234,7 +234,12 @@ def main():
)
if debug:
print(f"slack_response_summary = {slack_response_summary}")
# Also write a summary file to the root folder of this test
with open(os.path.join(MAGE_TEST_SET_ROOT,'testSummary.out'), 'w', encoding='utf-8') as f:
f.write(test_report_details_string)
f.write('\n')
# ------------------------------------------------------------------------
if debug: