Merge pull request #20 from firedrakeproject/connorjward/upstream-update

Upstream update

.gitignore

@@ -104,6 +104,7 @@ CMakeLists.txt
 petsc-doc-env
 doc/manualpages
 src/binding/petsc4py/.eggs
+src/binding/petsc4py/petsc4py.egg-info
 src/binding/petsc4py/src/include/petsc4py/petsc4py.PETSc.h
 src/binding/petsc4py/src/include/petsc4py/petsc4py.PETSc_api.h
 src/binding/petsc4py/src/libpetsc4py/libpetsc4py.c
@@ -180,7 +181,6 @@ src/benchmarks/streams/CUDAVersion
 src/benchmarks/streams/OpenMPVersion
 src/benchmarks/streams/PthreadVersion
 src/benchmarks/streams/scaling.png
-horse.ply
 /docs/
 **/f90module*.f90
 compile_commands.json

.gitlab-ci.yml

@@ -74,6 +74,8 @@ check-ci-settings:
     - if [ ! -z ${INIT_SCRIPT+x} ]; then echo "sourcing ${INIT_SCRIPT}"; if [ -f ${HOME}/${INIT_SCRIPT} ]; then source ${HOME}/${INIT_SCRIPT}; else source ${INIT_SCRIPT}; fi; fi
     - printf "PATH:$PATH\n"
     - printf "PYTHONPATH:$PYTHONPATH\n"
+    - printf "python:${PYTHON}\n"
+    - ${PYTHON} -m pip list --user
     - printf "CONFIG_OPTS:${CONFIG_OPTS}\n"
     - printf "PETSC_OPTIONS:$PETSC_OPTIONS\n"
     - if [ ! -z ${CI_MERGE_REQUEST_SOURCE_BRANCH_NAME+x} ]; then printf "CI_MERGE_REQUEST_SOURCE_BRANCH_NAME:$CI_MERGE_REQUEST_SOURCE_BRANCH_NAME\n" ;fi
@@ -83,7 +85,7 @@ check-ci-settings:
     - make CFLAGS="${MAKE_TEST_CFLAGS}" CXXFLAGS="${MAKE_TEST_CXXFLAGS}" FFLAGS="${MAKE_TEST_FFLAGS}" CUDAFLAGS="${MAKE_CUDAFLAGS}" allgtests-tap gmakesearch="${TEST_SEARCH}" TIMEOUT=${TIMEOUT}
   variables:
     PYTHON: python3
-    MAKE_CFLAGS: -Werror
+    MAKE_CFLAGS: -Werror -Wmissing-field-initializers
     MAKE_CXXFLAGS: -Werror -Wzero-as-null-pointer-constant
     MAKE_FFLAGS: -Werror
     MAKE_TEST_CFLAGS: -Werror
@@ -214,10 +216,17 @@ petsc4py-pip:
   script:
     - python3 -m venv pip-builds
     - source pip-builds/bin/activate
-    - python3 -m pip install --upgrade pip==23.0.1
-    - python3 -m pip install .
-    - python3 -m pip install src/binding/petsc4py
-    - python3 -m petsc4py
+    - python -m pip install --upgrade pip
+    - unset PETSC_DIR PETSC_ARCH
+    - export PIP_WHEEL_DIR="${PWD}/wheelhouse"
+    - export PIP_FIND_LINKS="${PIP_WHEEL_DIR}"
+    - mkdir -p "${PIP_WHEEL_DIR}"
+    - python -m pip wheel .
+    - python -m pip wheel src/binding/petsc4py
+    - python -m pip install --pre --no-index --no-cache-dir petsc4py
+    - python -m pip list
+    - python -m petsc --prefix
+    - python -m petsc4py
 
 checksource:
   extends: .test-basic
@@ -229,10 +238,12 @@ checksource:
     - vermin --version
     - make vermin
     - PATH=/nfs/gce/projects/petsc/soft/u22.04/spack-2024-03-06/opt/spack/linux-ubuntu22.04-x86_64/gcc-11.4.0/llvm-18.1.0-7hsf4hzma6aebqsd4ifb5brchcooktkp/bin:$PATH make checkclangformat SHELL=bash
+    - PATH=/nfs/gce/projects/petsc/soft/u22.04/spack-2024-03-06/opt/spack/linux-ubuntu22.04-x86_64/gcc-11.4.0/llvm-18.1.5-ug2n4c7cb3xrf3dxn7fkffuvcgfdzzpk/bin:$PATH make checkclangformat SHELL=bash
     - make checkbadSource SHELL=bash
     - make checkbadFileChange SHELL=bash
     - make -f gmakefile check_output SHELL=bash
     - make check_petsc4py_rst
+    - make -C src/binding/petsc4py lint
   artifacts:
     name: "$CI_JOB_NAME"
     when: always
@@ -1199,7 +1210,7 @@ analyze-pipeline:
       python3 -m venv $VENV &&
       . $VENV/bin/activate &&
       cd doc &&
-      python3 -m pip install -r requirements.txt
+      python -m pip install -r requirements.txt
 
 #
 # Build documentation and make available for review using GitLab pages

.gitlab/CODEOWNERS

@@ -18,6 +18,7 @@ src/ts/event/             @abhyshr @caidao22 @BarrySmith
 /src/ksp/pc/impls/gamg/   @markadams4 @jedbrown
 /src/ksp/pc/impls/hpddm/  @prj- @stefanozampini
 /src/ksp/ksp/impls/hpddm/ @prj- @stefanozampini
+/src/ksp/ksp/utils/lmvm/  @hsuh @tisaac
 
 /src/binding/petsc4py/    @dalcinl @wence @pefarrell @joseroman @jedbrown @knepley @psanan @stefanozampini
 

config/BuildSystem/config/compilers.py

@@ -249,11 +249,15 @@ def checkCLibraries(self):
         # Intel 11 has a bogus -long_double option
         if arg == '-long_double':
           continue
-        # if options of type -L foobar
         if arg == '-lto_library':
           lib = next(argIter)
           self.logPrint('Skipping Apple LLVM linker option -lto_library '+lib)
           continue
+        # ASan
+        if arg in ['-lasan', '-lubsan']:
+          self.logPrint('Skipping ASan libraries')
+          continue
+        # if options of type -L foobar
         if arg == '-L':
           lib = next(argIter)
           self.logPrint('Found -L '+lib, 4, 'compilers')
@@ -581,6 +585,10 @@ def checkCxxLibraries(self):
         if arg == '-long_double':
           continue
 
+        # ASan
+        if arg in ['-lasan', '-lubsan']:
+          self.logPrint('Skipping ASan libraries')
+          continue
         # if options of type -L foobar
         if arg == '-L':
           lib = next(argIter)
@@ -982,6 +990,7 @@ def checkFortranLibraries(self):
       while 1:
         arg = next(argIter)
         self.logPrint( 'Checking arg '+arg, 4, 'compilers')
+
         # Intel compiler sometimes puts " " around an option like "-lsomething"
         if arg.startswith('"') and arg.endswith('"'):
           arg = arg[1:-1]
@@ -990,6 +999,10 @@ def checkFortranLibraries(self):
         if arg.endswith('"') and arg[:-1].find('"') == -1:
           arg = arg[:-1]
 
+        # ASan
+        if arg in ['-lasan', '-lubsan']:
+          self.logPrint('Skipping ASan libraries')
+          continue
         if arg == '-lto_library':
           lib = next(argIter)
           self.logPrint('Skipping Apple LLVM linker option -lto_library '+lib)
@@ -1077,6 +1090,9 @@ def checkFortranLibraries(self):
               continue
             elif arg == '-lLTO' and self.setCompilers.isDarwin(self.log):
               self.logPrint('Skipping -lTO')
+            elif arg == '-lnvc':
+              self.logPrint('Skipping -lnvc: https://forums.developer.nvidia.com/t/failed-cuda-device-detection-when-explicitly-linking-libnvc/203225')
+              continue
             elif arg.find('-libpath:')>=0:
               self.logPrint('Skipping Intel oneAPI ifort (on Microsoft Windows) compiler option: '+arg)
               continue

config/BuildSystem/config/compilersFortran.py

@@ -135,8 +135,11 @@ def checkFortranTypeInitialize(self):
 
   def checkFortranTypeStar(self):
     '''Determine whether the Fortran compiler handles type(*)'''
+    '''Newer nvfortran support (*) but they introduce extra arguments at the end that interfere with char * lengths'''
+    '''So it cannot be used in interface definitions'''
+    '''Not using type(*) :: b(:) prevents this compiler from certifying it has (*)'''
     self.pushLanguage('FC')
-    if self.checkCompile(body = '      interface\n      subroutine a(b)\n      type(*) :: b(:)\n      end subroutine\n      end interface\n'):
+    if self.checkCompile(body = '      interface\n      subroutine a(b)\n      type(*)  b\n      end subroutine\n      end interface\n'):
       self.addDefine('HAVE_FORTRAN_TYPE_STAR', 1)
       self.logPrint('Fortran compiler supports type(*)')
     else:

config/BuildSystem/config/framework.py

@@ -490,6 +490,8 @@ def filterCompileOutput(self, output,flag = '', filterAlways = 0):
     if output.find('warning: ISO C90 does not support') >= 0: return output
     if output.find('warning: ISO C does not support') >= 0: return output
     if output.find('warning #2650: attributes ignored here') >= 0: return output
+    if output.find('warning #3175: unrecognized gcc optimization level') >= 0: return output
+    if output.find('warning: unknown attribute') >= 0: return output
     if output.find('Warning: attribute visibility is unsupported and will be skipped') >= 0: return output
     if output.find('(E) Invalid statement found within an interface block. Executable statement, statement function or syntax error encountered.') >= 0: return output
     elif self.argDB['ignoreCompileOutput'] and not filterAlways:

config/BuildSystem/config/package.py

@@ -48,6 +48,7 @@ def __init__(self, framework):
     self.foundversion     = ''   # version of the package actually found
     self.version_tuple    = ''   # version of the package actually found (tuple)
     self.requiresversion  = 0    # error if the version information is not found
+    self.requirekandr     = 0    # package requires KandR compiler flags to build
 
     # These are specified for the package
     self.required               = 0    # 1 means the package is required
@@ -407,11 +408,8 @@ def updatePackageCFlags(self,flags):
     outflags = self.removeVisibilityFlag(flags.split())
     outflags = self.removeWarningFlags(outflags)
     outflags = self.removeCoverageFlag(outflags)
-    with self.Language('C'):
-      if config.setCompilers.Configure.isClang(self.getCompiler(), self.log):
-        outflags.append('-Wno-implicit-function-declaration')
-        if config.setCompilers.Configure.isDarwin(self.log):
-          outflags.append('-fno-common')
+    if self.requirekandr:
+      outflags += self.setCompilers.KandRFlags
     return ' '.join(outflags)
 
   def updatePackageFFlags(self,flags):
@@ -573,11 +571,11 @@ def generateLibList(self, directory, liblist = None):
       alllibs.append(libs)
     return alllibs
 
-  def getIncludeDirs(self, prefix, includeDir):
-    if isinstance(includeDir, list):
-      iDirs = [inc for inc in includeDir if os.path.isabs(inc)] + [os.path.join(prefix, inc) for inc in includeDir if not os.path.isabs(inc)]
-      return [inc for inc in iDirs if os.path.exists(inc)]
-    return os.path.join(prefix, includeDir)
+  def getIncludeDirs(self, prefix, includeDirs):
+    if not isinstance(includeDirs, list):
+      includeDirs = [includeDirs]
+    iDirs = [inc for inc in includeDirs if os.path.isabs(inc)] + [os.path.join(prefix, inc) for inc in includeDirs if not os.path.isabs(inc)]
+    return [inc for inc in iDirs if os.path.exists(inc)]
 
   def addToArgs(self,args,key,value):
     found = 0
@@ -1202,51 +1200,50 @@ def infinitePatch(str):
     setattr(self.compilers, flagsArg, oldFlags+extraFlags+' '+self.headers.toString(self.dinclude))
     self.compilers.saveLog()
 
-    # X.py uses a weird list of two headers.
+    # Multiple headers are tried in order
     if not isinstance(self.versioninclude,list):
       headerList = [self.versioninclude]
     else:
       headerList = self.versioninclude
 
-    includeLines = ''
     for header in headerList:
-      includeLines += '#include "'+header+'"\n'
-    try:
-      # We once used '#include "'+self.versioninclude+'"\npetscpkgver('+self.versionname+');\n',
-      # but some preprocessors are picky (ex. dpcpp -E), reporting errors on the code above even
-      # it is just supposed to do preprocessing:
-      #
-      #  error: C++ requires a type specifier for all declarations
-      #  petscpkgver(__SYCL_COMPILER_VERSION);
-      #  ^
-      #
-      # So we instead use this compilable code.
-      output = self.outputPreprocess(
+      try:
+        # We once used '#include "'+self.versioninclude+'"\npetscpkgver('+self.versionname+');\n',
+        # but some preprocessors are picky (ex. dpcpp -E), reporting errors on the code above even
+        # it is just supposed to do preprocessing:
+        #
+        #  error: C++ requires a type specifier for all declarations
+        #  petscpkgver(__SYCL_COMPILER_VERSION);
+        #  ^
+        #
+        # So we instead use this compilable code.
+        output = self.outputPreprocess(
 '''
-{x}
+#include "{x}"
 #define  PetscXstr_(s) PetscStr_(s)
 #define  PetscStr_(s)  #s
 const char *ver = "petscpkgver(" PetscXstr_({y}) ")";
-'''.format(x=includeLines, y=self.versionname))
-       # Ex. char *ver = "petscpkgver(" "20211206" ")";
-       # But after stripping spaces, quotes etc below, it becomes char*ver=petscpkgver(20211206);
-      self.logWrite(self.compilers.restoreLog())
-    except:
-      self.log.write('For '+self.package+' unable to run preprocessor to obtain version information, skipping version check\n')
+'''.format(x=header, y=self.versionname))
+         # Ex. char *ver = "petscpkgver(" "20211206" ")";
+         # But after stripping spaces, quotes etc below, it becomes char*ver=petscpkgver(20211206);
+      except:
+        output = None
       self.logWrite(self.compilers.restoreLog())
-      self.popLanguage()
-      setattr(self.compilers, flagsArg,oldFlags)
-      self.version = ''
-      return
+      if output:
+        break
     self.popLanguage()
     setattr(self.compilers, flagsArg,oldFlags)
+    if not output:
+        self.log.write('For '+self.package+' unable to run preprocessor to obtain version information, skipping version check\n')
+        self.version = ''
+        return
     # the preprocessor output might be very long, but the petscpkgver line should be at the end. Therefore, we partition it backwards
     [mid, right] = output.rpartition('petscpkgver')[1:]
     version = ''
     if mid: # if mid is not empty, then it should be 'petscpkgver', meaning we found the version string
       verLine = right.split(';',1)[0] # get the string before the first ';'. Preprocessor might dump multiline result.
       self.log.write('Found the raw version string: ' + verLine +'\n')
-      # strip backslashs, spaces and quotes. Note Mumps' version macro has "" around it, giving output: (" "\"5.4.1\"" ")";
+      # strip backslashes, spaces, and quotes. Note MUMPS' version macro has "" around it, giving output: (" "\"5.4.1\"" ")";
       for char in ['\\', ' ', '"']:
           verLine = verLine.replace(char, '')
       # get the string between the outer ()

config/BuildSystem/config/packages/AMReX.py

@@ -53,7 +53,7 @@ def formCMakeConfigureArgs(self):
     if self.cuda.found:
       GPUBackend = 'CUDA'
       # Prefer cmake options instead of -DAMReX_CUDA_ARCH
-      args.append('-DCMAKE_CUDA_ARCHITECTURES:STRING="{}"'.format(self.cuda.cmakeArch()))
+      args.extend(self.cuda.getCmakeCUDAArchFlag())
     elif self.hip.found:
       GPUBackend = 'HIP'
       args.append('-DCMAKE_HIP_ARCHITECTURES="'+self.hip.hipArch+'"')

config/BuildSystem/config/packages/Chaco.py

@@ -11,8 +11,9 @@ def __init__(self, framework):
     self.includes          = [] #Chaco does not have an include file
     self.liblist           = [['libchaco.a']]
     self.downloadonWindows = 1
-    self.requires32bitint  = 1;  # 1 means that the package will not work with 64-bit integers
+    self.requires32bitint  = 1   # 1 means that the package will not work with 64-bit integers
     self.hastests          = 1
+    self.requirekandr      = 1
     return
 
   def setupDependencies(self, framework):

config/BuildSystem/config/packages/MFEM.py

@@ -17,6 +17,7 @@ def __init__(self, framework):
     self.skippackagewithoptions = 1
     self.builtafterpetsc        = 1
     self.noMPIUni               = 1
+    self.precisions             = ['single', 'double']
     return
 
   def setupHelp(self, help):
@@ -35,6 +36,7 @@ def setupDependencies(self, framework):
     self.cuda   = framework.require('config.packages.cuda',self)
     self.hip    = framework.require('config.packages.hip',self)
     self.openmp = framework.require('config.packages.openmp',self)
+    self.scalar = framework.require('PETSc.options.scalarTypes',self)
     self.deps   = [self.mpi,self.hypre,self.metis]
     self.odeps  = [self.slepc,self.ceed,self.cuda,self.openmp]
     return
@@ -111,6 +113,8 @@ def Install(self):
       g.write('MFEM_MPIEXEC = '+self.mpi.getMakeMacro('MPIEXEC')+'\n')
       g.write('MFEM_USE_METIS_5 = YES\n')
       g.write('MFEM_USE_METIS = YES\n')
+      if self.scalar.precision == 'single':
+        g.write('MFEM_PRECISION = single\n')
       g.write('MFEM_USE_PETSC = YES\n')
       g.write('HYPRE_OPT = '+self.headers.toString(self.hypre.include)+'\n')
       g.write('HYPRE_LIB = '+self.libraries.toString(self.hypre.lib)+'\n')
@@ -218,6 +222,9 @@ def Install(self):
              echo "Error installing MFEM. Check ${PETSC_ARCH}/lib/petsc/conf/mfem.log" && \\\n\
              echo "********************************************************************" && \\\n\
              exit 1)'])
+    exampleDirBuild = os.path.join(buildDir, 'examples', 'petsc')
+    self.addMakeRule('mfem-check', '', ['@echo "Running MFEM/PETSc check examples"',\
+                                          '-@cd '+exampleDirBuild+' ; ${OMAKE} ex1p-test-par'])
 
     if self.argDB['prefix'] and not 'package-prefix-hash' in self.argDB:
       self.addMakeRule('mfem-build','')

config/BuildSystem/config/packages/MOAB.py

@@ -3,15 +3,14 @@
 class Configure(config.package.GNUPackage):
   def __init__(self, framework):
     config.package.GNUPackage.__init__(self, framework)
-    self.download          = ['https://web.cels.anl.gov/projects/petsc/download/externalpackages/moab-5.0.0.tar.gz']
+    self.download          = ['https://web.cels.anl.gov/projects/sigma/downloads/moab/moab-5.5.0.tar.gz']
     self.downloaddirnames  = ['moab']
     # Check for moab::Core and includes/libraries to verify build
     self.functions         = ['Core']
     self.functionsCxx      = [1, 'namespace moab {class Core {public: Core();};}','moab::Core *mb = new moab::Core()']
     self.includes          = ['moab/Core.hpp']
     self.liblist           = [['libiMesh.a', 'libMOAB.a'],['libMOAB.a']]
     self.buildLanguages    = ['Cxx']
-    self.maxCxxVersion     = 'c++14'
     self.precisions        = ['single','double']
     self.hastests          = 1
     self.useddirectly      = 0

config/BuildSystem/config/packages/MPI.py

@@ -739,17 +739,24 @@ def checkMPIDistro(self):
         MPI_VER  = '  '+MPICHPKG+'_VERSION: '+mpich_numversion
       except:
         self.logPrint('Unable to parse '+MPICHPKG+' version from header. Probably a buggy preprocessor')
-    for mpichpkg in ['i_mpi','mvapich2','mpich']:
-      MPICHPKG = mpichpkg.upper()
+    for MPICHPKG in ['MPICH', 'I_MPI', 'MVAPICH2']:
       mpich_test = '#include <mpi.h>\nint mpich_ver = '+MPICHPKG+'_NUMVERSION;\n'
       if self.checkCompile(mpich_test):
         buf = self.outputPreprocess(mpich_test)
         try:
           mpich_numversion = re.compile('\nint mpich_ver ='+HASHLINESPACE+'([0-9]+)'+HASHLINESPACE+';').search(buf).group(1)
-          self.addDefine('HAVE_'+MPICHPKG+'_NUMVERSION',mpich_numversion)
           MPI_VER += '  '+MPICHPKG+'_NUMVERSION: '+mpich_numversion
-          if mpichpkg == 'mpich': self.mpich_numversion = mpich_numversion
-          if mpichpkg == 'i_mpi': self.isIntelMPI = 1
+          self.addDefine('HAVE_'+MPICHPKG, 1)
+          # for I_MPI and MVAPICH2, we can not use petscpkg_version.h since they are not a petsc package yet.
+          # Anyway, we use PETSC_PKG_'MPICHPKG'_NUMVERSION to record the config time version for later compile time checking.
+          self.addDefine('PKG_'+MPICHPKG+'_NUMVERSION',mpich_numversion)
+          if MPICHPKG == 'MPICH':
+            self.mpich_numversion = mpich_numversion
+            MAJ = int(mpich_numversion)//10000000  # See comments in MPICH.py
+            MIN = int(mpich_numversion)//100000%100
+            REV = int(mpich_numversion)//1000%100
+            self.mpich.version_tuple = (MAJ, MIN, REV) # version_tuple makes mpich included in petscpkg_version.h
+          elif MPICHPKG == 'I_MPI': self.isIntelMPI = 1
         except:
           self.logPrint('Unable to parse '+MPICHPKG+' version from header. Probably a buggy preprocessor')
     if MPI_VER:
@@ -774,11 +781,10 @@ def checkMPIDistro(self):
         ompi_major_version = re.compile('\nint ompi_major ='+HASHLINESPACE+'([0-9]+)'+HASHLINESPACE+';').search(buf).group(1)
         ompi_minor_version = re.compile('\nint ompi_minor ='+HASHLINESPACE+'([0-9]+)'+HASHLINESPACE+';').search(buf).group(1)
         ompi_release_version = re.compile('\nint ompi_release ='+HASHLINESPACE+'([0-9]+)'+HASHLINESPACE+';').search(buf).group(1)
-        self.addDefine('HAVE_OMPI_MAJOR_VERSION',ompi_major_version)
-        self.addDefine('HAVE_OMPI_MINOR_VERSION',ompi_minor_version)
-        self.addDefine('HAVE_OMPI_RELEASE_VERSION',ompi_release_version)
         self.ompi_major_version = ompi_major_version
         self.ompi_version = tuple([int(i) for i in [ompi_major_version,ompi_minor_version,ompi_release_version]])
+        self.openmpi.version_tuple = self.ompi_version # version_tuple makes openmpi included by petscpkg_version.h, so one can uses macros defined there
+        self.addDefine('HAVE_OPENMPI', 1) # we have openmpi, though it is not necessarily installed by --download-openmpi
         self.mpi_pkg_version = '  OMPI_VERSION: '+ompi_major_version+'.'+ompi_minor_version+'.'+ompi_release_version+'\n'
         MPI_VER = '  OMPI_VERSION: '+ompi_major_version+'.'+ompi_minor_version+'.'+ompi_release_version
       except: