Merge pull request #745 from galacticusorg/featHDF1.14.5

Update code to work with v1.14.5 of the HDF5 library
galacticusorg · Dec 2, 2024 · a6a5c8c · a6a5c8c
2 parents e7a298f + 59a239b
commit a6a5c8c
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Showing 18 changed files with 684 additions and 678 deletions.
diff --git a/.github/actions/buildMacOS/action.yml b/.github/actions/buildMacOS/action.yml
@@ -106,19 +106,19 @@ runs:
     - name: Install HDF5
       shell: bash
       run: |
-        curl -L https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.20/src/hdf5-1.8.20.tar.gz --output hdf5-1.8.20.tar.gz
-        tar -vxzf hdf5-1.8.20.tar.gz 
-        cd hdf5-1.8.20
+        curl -L https://support.hdfgroup.org/releases/hdf5/v1_14/v1_14_5/downloads/hdf5-1.14.5.tar.gz --output hdf5-1.14.5.tar.gz
+        tar -vxzf hdf5-1.14.5.tar.gz 
+        cd hdf5-1.14.5
         if [[ "${OS_VER}" -eq 13 ]]; then
            # For MacOS 13 force use of the classic linker as the new linker does not support the '-commons' option - see https://trac.macports.org/ticket/68194#comment:15
-           CC=gcc-11 CXX=g++-11 FC=gfortran-11 LDFLAGS=-Wl,-ld_classic ./configure --prefix=/usr/local --enable-fortran --enable-production
+           CC=gcc-11 CXX=g++-11 FC=gfortran-11 LDFLAGS=-Wl,-ld_classic ./configure --prefix=/usr/local --enable-fortran --enable-build-mode=production
         else
-           CC=gcc-11 CXX=g++-11 FC=gfortran-11                         ./configure --prefix=/usr/local --enable-fortran --enable-production
+           CC=gcc-11 CXX=g++-11 FC=gfortran-11                         ./configure --prefix=/usr/local --enable-fortran --enable-build-mode=production
         fi
         make -j3
         sudo make install
         cd ..
-        rm -rf hdf5-1.8.20 hdf5-1.8.20.tar.gz
+        rm -rf hdf5-1.14.5 hdf5-1.14.5.tar.gz
     - name: Install FoX
       shell: bash
       run: |

diff --git a/.github/workflows/cicd.yml b/.github/workflows/cicd.yml
@@ -738,7 +738,8 @@ jobs:
     needs: Build-Executable-Linux
     uses: ./.github/workflows/testModel.yml
     with:
-      file: validate-darkMatterOnlySubhalos.pl
+      install: python3 python3-h5py python3-numpy python3-git
+      file: validate-darkMatterOnlySubhalos.py
       artifact: galacticus-exec
       runPath: ./testSuite
       cacheData: 0
@@ -749,7 +750,8 @@ jobs:
     needs: Build-Executable-Linux
     uses: ./.github/workflows/testModel.yml
     with:
-      file: validate-milkyWay.pl
+      install: python3 python3-h5py python3-numpy python3-git
+      file: validate-milkyWay.py
       artifact: galacticus-exec
       runPath: ./testSuite
       cacheData: 1
@@ -760,7 +762,8 @@ jobs:
     needs: Build-Executable-Linux
     uses: ./.github/workflows/testModel.yml
     with:
-      file: validate-PonosV.pl
+      install: python3 python3-h5py python3-numpy python3-git
+      file: validate-PonosV.py
       artifact: galacticus-exec
       runPath: ./testSuite
       cacheData: 0
@@ -771,7 +774,8 @@ jobs:
     needs: Build-Executable-Linux
     uses: ./.github/workflows/testModel.yml
     with:
-      file: validate-baryonicSuppression.pl
+      install: python3 python3-h5py python3-numpy python3-git
+      file: validate-baryonicSuppression.py
       artifact: galacticus-exec
       runPath: ./testSuite
       cacheData: 0

diff --git a/source/intergalactic_medium.state.RecFast.F90 b/source/intergalactic_medium.state.RecFast.F90
@@ -141,9 +141,9 @@ function recFastConstructorInternal(cosmologyFunctions_,cosmologyParameters_) re
     if (File_Exists(char(self%fileName))) then
        ! Check file version number.
        !$ call hdf5Access%set()
-       call outputFile%openFile     (char(self%fileName),overwrite=.false.          )
-       call outputFile%readAttribute('fileFormat'       ,          fileFormatVersion)
-       call outputFile%close        (                                               )
+       call outputFile%openFile     (char(self%fileName),overwrite=.false.          ,readOnly=.true.)
+       call outputFile%readAttribute('fileFormat'       ,          fileFormatVersion                )
+       call outputFile%close        (                                                               )
        !$ call hdf5Access%unset()
        buildFile=fileFormatVersion /= fileFormatVersionCurrent
     else

diff --git a/source/output.analyses.Local_Group.occupation_fraction.F90 b/source/output.analyses.Local_Group.occupation_fraction.F90
@@ -218,7 +218,7 @@ function localGroupOccupationFractionConstructorInternal(outputTimes_,positionTy
 
     ! Construct the target distribution.
     !$ call hdf5Access%set  ()
-    call fileData%openFile(char(inputPath(pathTypeDataStatic))//"observations/stellarHaloMassRelation/fractionOccupation_Local_Group_Nadler2020.hdf5")
+    call fileData%openFile(char(inputPath(pathTypeDataStatic))//"observations/stellarHaloMassRelation/fractionOccupation_Local_Group_Nadler2020.hdf5",readOnly=.true.)
     call fileData%readDataset('massHalo'          ,massHaloData          )
     call fileData%readDataset('fractionOccupation',fractionOccupationData)
     call fileData%close      (                                           )

diff --git a/source/output.analyses.Local_Group.stellar_mass_halo_mass_relation.F90 b/source/output.analyses.Local_Group.stellar_mass_halo_mass_relation.F90
@@ -218,7 +218,7 @@ function localGroupStellarMassHaloMassRelationConstructorInternal(outputTimes_,p
 
     ! Construct the target distribution.
     !$ call hdf5Access%set  ()
-    call fileData%openFile(char(inputPath(pathTypeDataStatic))//"observations/stellarHaloMassRelation/stellarHaloMassRelation_Local_Group_Nadler2020.hdf5")
+    call fileData%openFile(char(inputPath(pathTypeDataStatic))//"observations/stellarHaloMassRelation/stellarHaloMassRelation_Local_Group_Nadler2020.hdf5",readOnly=.true.)
     call fileData%readDataset('massHalo'          ,massHaloData          )
     call fileData%readDataset('massStellar'       ,massStellarData       )
     call fileData%readDataset('massStellarScatter',massStellarScatterData)

diff --git a/source/output.analyses.stellar_vs_halo_mass_relation.COSMOS_Leauthaud2012.F90 b/source/output.analyses.stellar_vs_halo_mass_relation.COSMOS_Leauthaud2012.F90
@@ -292,7 +292,7 @@ function stellarVsHaloMassRelationLeauthaud2012ConstructorInternal(redshiftInter
     !!]
     ! Read observational data and convert masses to logarithmic.
     !$ call hdf5Access%set()
-    call fileData%openFile(char(inputPath(pathTypeDataStatic))//"observations/stellarHaloMassRelation/stellarHaloMassRelation_COSMOS_Leauthaud2012.hdf5")
+    call fileData%openFile(char(inputPath(pathTypeDataStatic))//"observations/stellarHaloMassRelation/stellarHaloMassRelation_COSMOS_Leauthaud2012.hdf5",readOnly=.true.)
     groupRedshiftName=var_str('redshiftInterval')//redshiftInterval
     groupRedshift=fileData%openGroup(char(groupRedshiftName))
     call groupRedshift%readDataset('massStellar' ,massStellarData )

diff --git a/source/structure_formation.cosmological_mass_variance.filtered_power_spectrum.F90 b/source/structure_formation.cosmological_mass_variance.filtered_power_spectrum.F90
@@ -1308,22 +1308,22 @@ subroutine filteredPowerFileRead(self)
     if (.not.File_Exists(char(self%fileName))) return
     call displayMessage('reading σ(M) data from: '//self%fileName,verbosityLevelWorking)
     !$ call hdf5Access%set()
-    call dataFile%openFile     (char(self%fileName)          ,overWrite                       =.false.)
-    call dataFile%readDataset  ('times'                      ,     timesTmp                           )
-    call dataFile%readDataset  ('mass'                       ,     massTmp                            )
-    call dataFile%readDataset  ('rootVariance'               ,     rootVarianceTmp                    )
-    call dataFile%readDataset  ('rootVarianceUnique'         ,     rootVarianceUniqueTmp              )
-    call dataFile%readDataset  ('indexUnique'                ,     indexTmp                           )
-    call dataFile%readDataset  ('uniqueSize'                 ,     uniqueSizeTmp                      )
-    call dataFile%readAttribute('sigma8'                     ,self%sigma8Value                        )
-    call dataFile%readAttribute('sigmaNormalization'         ,self%sigmaNormalization                 )
-    call dataFile%readAttribute('massMinimum'                ,self%massMinimum                        )
-    call dataFile%readAttribute('massMaximum'                ,self%massMaximum                        )
-    call dataFile%readAttribute('timeMinimum'                ,self%timeMinimum                        )
-    call dataFile%readAttribute('timeMaximum'                ,self%timeMaximum                        )
-    call dataFile%readAttribute('timeMinimumLogarithmic'     ,self%timeMinimumLogarithmic             )
-    call dataFile%readAttribute('timeLogarithmicDeltaInverse',self%timeLogarithmicDeltaInverse        )
-    call dataFile%close        (                                                                      )
+    call dataFile%openFile     (char(self%fileName)          ,overWrite                       =.false.,readOnly=.true.)
+    call dataFile%readDataset  ('times'                      ,     timesTmp                                           )
+    call dataFile%readDataset  ('mass'                       ,     massTmp                                            )
+    call dataFile%readDataset  ('rootVariance'               ,     rootVarianceTmp                                    )
+    call dataFile%readDataset  ('rootVarianceUnique'         ,     rootVarianceUniqueTmp                              )
+    call dataFile%readDataset  ('indexUnique'                ,     indexTmp                                           )
+    call dataFile%readDataset  ('uniqueSize'                 ,     uniqueSizeTmp                                      )
+    call dataFile%readAttribute('sigma8'                     ,self%sigma8Value                                        )
+    call dataFile%readAttribute('sigmaNormalization'         ,self%sigmaNormalization                                 )
+    call dataFile%readAttribute('massMinimum'                ,self%massMinimum                                        )
+    call dataFile%readAttribute('massMaximum'                ,self%massMaximum                                        )
+    call dataFile%readAttribute('timeMinimum'                ,self%timeMinimum                                        )
+    call dataFile%readAttribute('timeMaximum'                ,self%timeMaximum                                        )
+    call dataFile%readAttribute('timeMinimumLogarithmic'     ,self%timeMinimumLogarithmic                             )
+    call dataFile%readAttribute('timeLogarithmicDeltaInverse',self%timeLogarithmicDeltaInverse                        )
+    call dataFile%close        (                                                                                      )
     !$ call hdf5Access%unset()
     if (allocated(self%times                  )) deallocate(self%times                  )
     if (allocated(self%rootVarianceTable      )) deallocate(self%rootVarianceTable      )

diff --git a/source/tasks.halo_mass_function.F90 b/source/tasks.halo_mass_function.F90
@@ -79,7 +79,7 @@ Implementation of a task which computes and outputs the halo mass function and r
      double precision                                         , allocatable, dimension(:) :: fractionModeMasses
      type            (virialDensityContrastList              ), allocatable, dimension(:) :: virialDensityContrasts
      ! Pointer to the parameters for this task.
-     type            (inputParameters                        )                            :: parameters
+     type            (inputParameters                        ), pointer                   :: parameters                          => null()
    contains
      !![
      <methods>
@@ -401,8 +401,7 @@ function haloMassFunctionConstructorInternal(
     <constructorAssign variables="haloMassMinimum, haloMassMaximum, pointsPerDecade, outputGroup, includeUnevolvedSubhaloMassFunction, includeMassAccretionRate, massesRelativeToHalfModeMass, fractionModeMasses, *cosmologyParameters_, *cosmologyFunctions_, *virialDensityContrast_, *criticalOverdensity_, *linearGrowth_, *haloMassFunction_, *haloEnvironment_, *unevolvedSubhaloMassFunction_, *darkMatterHaloScale_, *darkMatterProfileScaleRadius_, *darkMatterProfileShape_, *darkMatterHaloMassAccretionHistory_, *cosmologicalMassVariance_, *darkMatterHaloBias_, *transferFunction_, *transferFunctionReference, *transferFunctionRelative, *outputTimes_, *randomNumberGenerator_"/>
     !!]
 
-    self%parameters=inputParameters(parameters)
-    call self%parameters%parametersGroupCopy(parameters)
+    self%parameters  => parameters
     allocate(self%virialDensityContrasts(size(virialDensityContrasts)))
     do i=1,size(virialDensityContrasts)
        self%virialDensityContrasts(i)%label=virialDensityContrasts(i)%label