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Fix a segfault associated with output of rank?VarLen datasets #511

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merged 3 commits into from
Dec 15, 2023
Merged

Fix a segfault associated with output of rank?VarLen datasets #511

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f9b9d35
fix: Fix a segfault associated with output of `rank?VarLen` datasets
abensonca Dec 14, 2023
174953b
feat: Add a new regression test for the `rank2VarLen` output segfault
abensonca Dec 14, 2023
73004ce
fix: Add new regression test to the dependencies for deployment
abensonca Dec 14, 2023
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37 changes: 37 additions & 0 deletions .github/workflows/cicd.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -8815,6 +8815,42 @@ jobs:
./Galacticus.exe testSuite/regressions/treeWithNoPrimaryProgenitor.xml 2>&1 | tee test.log
! grep -q FAIL test.log
- run: echo "This job's status is ${{ job.status }}."
Regressions-Output-Rank2VarLen-SegFault:
runs-on: ubuntu-latest
container: ghcr.io/galacticusorg/buildenv:latest
needs: Build-Executable-Linux
steps:
- run: echo "The job was automatically triggered by a ${{ github.event_name }} event."
- run: echo "This job is now running on a ${{ runner.os }} server."
- run: echo "The name of the branch is ${{ github.ref }} and the repository is ${{ github.repository }}."
- name: Check out repository code
uses: actions/checkout@v4
- name: Check out repository datasets
uses: actions/checkout@v4
with:
repository: galacticusorg/datasets
path: datasets
- run: echo "The ${{ github.repository }} repository has been cloned to the runner."
- name: "Set environmental variables"
run: |
echo "GALACTICUS_EXEC_PATH=$GITHUB_WORKSPACE" >> $GITHUB_ENV
echo "GALACTICUS_DATA_PATH=$GITHUB_WORKSPACE/datasets" >> $GITHUB_ENV
- name: Download executables
uses: actions/download-artifact@v3
with:
name: galacticus-exec
- name: Create test suite output directory
run: mkdir -p $GALACTICUS_EXEC_PATH/testSuite/outputs
- name: Run test
run: |
cd $GALACTICUS_EXEC_PATH
git config --global --add safe.directory $GALACTICUS_EXEC_PATH
chmod u=wrx ./Galacticus.exe
mkdir -p testSuite/outputs/regressions
set -o pipefail
./Galacticus.exe testSuite/regressions/outputRank2ExtendSegFault.xml 2>&1 | tee test.log
! grep -q FAIL test.log
- run: echo "This job's status is ${{ job.status }}."
Regressions-Bar-Instability-FPE:
runs-on: ubuntu-latest
container: ghcr.io/galacticusorg/buildenv:latest
Expand Down Expand Up @@ -10525,6 +10561,7 @@ jobs:
Regressions-Tree-With-Initial-Satellite-In-Progenitorless-Host,
Regressions-Tree-With-No-Primary-Progenitor,
Regressions-Bar-Instability-FPE,
Regressions-Output-Rank2VarLen-SegFault,
Test-Methods-01,
Test-Methods-02,
Test-Methods-03,
Expand Down
58 changes: 45 additions & 13 deletions source/merger_trees.outputter.standard.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -477,7 +477,7 @@ subroutine standardOutput(self,node,time)
doubleArray =extractor_%extract (node,time,instance)
do i=1,+extractor_%elementCount( time)
if ( allocated(self%doubleProperty (doubleProperty +i)%scalar)) deallocate(self%doubleProperty (doubleProperty +i)%scalar)
if ( allocated(self%doubleProperty (doubleProperty +i)%rank1 )) then
if ( allocated(self%doubleProperty (doubleProperty +i)%rank1 )) then
if (size(self%doubleProperty (doubleProperty +i)%rank1,dim=1) /= size(doubleArray,dim=1)) deallocate(self%doubleProperty (doubleProperty +i)%rank1 )
end if
if (.not.allocated(self%doubleProperty (doubleProperty +i)%rank1)) allocate(self%doubleProperty (doubleProperty +i)%rank1(size(doubleArray,dim=1),self%doubleBufferSize))
Expand Down Expand Up @@ -513,7 +513,11 @@ subroutine standardOutput(self,node,time)
if ( allocated(self%doubleProperty (doubleProperty +i)%rank1VarLen)) deallocate(self%doubleProperty (doubleProperty +i)%rank1VarLen)
if (.not.allocated(self%doubleProperty (doubleProperty +i)%rank2VarLen)) allocate(self%doubleProperty (doubleProperty +i)%rank2VarLen(self%doubleBufferSize))
if (associated(self%doubleProperty (doubleProperty +i)%rank2VarLen (self%doubleBufferCount )%row)) then
if (size(self%doubleProperty (doubleProperty +i)%rank2VarLen (self%doubleBufferCount )%row) /= size(doubleArray2D,dim=1)) deallocate(self%doubleProperty (doubleProperty +i)%rank2VarLen (self%doubleBufferCount )%row)
if ( &
& size(self%doubleProperty (doubleProperty +i)%rank2VarLen (self%doubleBufferCount )%row,dim=1) /= size(doubleArray2D,dim=1) &
& .or. &
& size(self%doubleProperty (doubleProperty +i)%rank2VarLen (self%doubleBufferCount )%row,dim=2) /= size(doubleArray2D,dim=2) &
& ) deallocate(self%doubleProperty (doubleProperty +i)%rank2VarLen (self%doubleBufferCount )%row)
end if
if (.not.associated(self%doubleProperty (doubleProperty +i)%rank2VarLen (self%doubleBufferCount )%row)) then
allocate(self%doubleProperty (doubleProperty +i)%rank2VarLen (self%doubleBufferCount )%row(size(doubleArray2D,dim=1),size(doubleArray2D,dim=2)))
Expand Down Expand Up @@ -573,7 +577,11 @@ subroutine standardOutput(self,node,time)
if (.not.allocated(self%doubleProperty(doubleProperty +i)%rank2VarLen)) allocate(self%doubleProperty (doubleProperty +i)%rank2VarLen(self%doubleBufferSize))
if (associated(self%doubleProperty (doubleProperty +i)%rank2VarLen (self%doubleBufferCount )%row)) then
shape_=doubleProperties(i)%shape()
if (size(self%doubleProperty (doubleProperty +i)%rank2VarLen (self%doubleBufferCount )%row) /= shape_(1)) deallocate(self%doubleProperty (doubleProperty +i)%rank2VarLen (self%doubleBufferCount )%row)
if ( &
& size(self%doubleProperty (doubleProperty +i)%rank2VarLen (self%doubleBufferCount )%row,dim=1) /= shape_(1) &
& .or. &
& size(self%doubleProperty (doubleProperty +i)%rank2VarLen (self%doubleBufferCount )%row,dim=2) /= shape_(2) &
& ) deallocate(self%doubleProperty (doubleProperty +i)%rank2VarLen (self%doubleBufferCount )%row)
deallocate(shape_)
end if
if (.not.associated(self%doubleProperty (doubleProperty +i)%rank2VarLen (self%doubleBufferCount )%row)) then
Expand Down Expand Up @@ -828,28 +836,52 @@ subroutine standardExtendDoubleBuffer(self)
!!{
Extend the size of the double buffer.
!!}
use :: IO_HDF5, only : hdf5VarDouble , hdf5VarDouble2D
implicit none
class (mergerTreeOutputterStandard), intent(inout) :: self
double precision , allocatable , dimension(: ) :: scalarTemporary
double precision , allocatable , dimension(:,:) :: rank1Temporary
integer :: i
type (hdf5VarDouble ), allocatable , dimension(: ) :: rank1VarLenTemporary
type (hdf5VarDouble2D ), allocatable , dimension(: ) :: rank2VarLenTemporary
integer :: i , j

do i=1,size(self%doubleProperty)
if (allocated(self%doubleProperty(i)%scalar)) then
call move_alloc(self%doubleProperty(i)%scalar,scalarTemporary)
allocate(self%doubleProperty(i)%scalar( self%doubleBufferSize+standardBufferSizeIncrement))
self%doubleProperty(i)%scalar( 1:self%doubleBufferSize)=scalarTemporary
if (allocated(self%doubleProperty(i)%scalar )) then
call move_alloc(self%doubleProperty(i)%scalar ,scalarTemporary)
allocate(self%doubleProperty(i)%scalar ( self%doubleBufferSize+standardBufferSizeIncrement))
self%doubleProperty(i)%scalar ( 1:self%doubleBufferSize)=scalarTemporary
deallocate(scalarTemporary)
end if
if (allocated(self%doubleProperty(i)%rank1 )) then
call move_alloc(self%doubleProperty(i)%rank1 ,rank1Temporary )
allocate(self%doubleProperty(i)%rank1 (size(rank1Temporary,dim=1),self%doubleBufferSize+standardBufferSizeIncrement))
self%doubleProperty(i)%rank1 (:,1:self%doubleBufferSize)=rank1Temporary
if (allocated(self%doubleProperty(i)%rank1 )) then
call move_alloc(self%doubleProperty(i)%rank1 ,rank1Temporary )
allocate(self%doubleProperty(i)%rank1 (size(rank1Temporary,dim=1),self%doubleBufferSize+standardBufferSizeIncrement))
self%doubleProperty(i)%rank1 (:,1:self%doubleBufferSize)=rank1Temporary
deallocate(rank1Temporary )
end if
if (allocated(self%doubleProperty(i)%rank1VarLen)) then
call move_alloc(self%doubleProperty(i)%rank1VarLen,rank1VarLenTemporary)
allocate(self%doubleProperty(i)%rank1VarLen( self%doubleBufferSize+standardBufferSizeIncrement))
self%doubleProperty(i)%rank1VarLen( 1:self%doubleBufferSize)=rank1VarLenTemporary
! Nullify row pointers in the temporary array to avoid the associated data being destroyed when our temporary array is
! deallocated.
do j=1,size(rank1VarLenTemporary)
rank1VarLenTemporary(j)%row => null()
end do
deallocate(rank1VarLenTemporary)
end if
if (allocated(self%doubleProperty(i)%rank2VarLen)) then
call move_alloc(self%doubleProperty(i)%rank2VarLen,rank2VarLenTemporary)
allocate(self%doubleProperty(i)%rank2VarLen( self%doubleBufferSize+standardBufferSizeIncrement))
self%doubleProperty(i)%rank2VarLen( 1:self%doubleBufferSize)=rank2VarLenTemporary
! Nullify row pointers in the temporary array to avoid the associated data being destroyed when our temporary array is
! deallocated.
do j=1,size(rank2VarLenTemporary)
rank2VarLenTemporary(j)%row => null()
end do
deallocate(rank2VarLenTemporary)
end if
end do
self%doubleBufferSize=self%doubleBufferSize+standardBufferSizeIncrement

return
end subroutine standardExtendDoubleBuffer

Expand Down
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