Merge pull request #15 from firedrakeproject/connorjward/merge-upstream

Merge upstream

config/BuildSystem/config/package.py

@@ -345,7 +345,7 @@ def __remove_flag_pair(self, flags, flag_to_remove, pair_prefix):
     - flag_to_remove - the flag to remove
     - pair_prefix    - (Optional) if not None, indicates that FLAG_TO_REMOVE is in a pair, and
                        is prefixed by str(pair_prefix). For example, pair_prefix='-Xcompiler' indicates
-                       that the flag is specificied as <COMPILER_NAME> -Xcompiler FLAG_TO_REMOVE
+                       that the flag is specified as <COMPILER_NAME> -Xcompiler FLAG_TO_REMOVE
 
     Return
     ------

config/BuildSystem/config/packages/MFEM.py

@@ -4,15 +4,16 @@ class Configure(config.package.Package):
   def __init__(self, framework):
     config.package.Package.__init__(self, framework)
     #disable version checking
-    #self.minversion             = '4'
-    #self.version                = '4.0.0'
+    #self.minversion             = '4.6'
+    #self.version                = '4.6'
     #self.versionname            = 'MFEM_VERSION_STRING'
     #self.versioninclude         = 'mfem/config.hpp'
-    self.gitcommit              = 'v4.5.2'
+    self.gitcommit              = 'v4.6'
     self.download               = ['git://https://github.com/mfem/mfem.git','https://github.com/mfem/mfem/archive/'+self.gitcommit+'.tar.gz']
     self.linkedbypetsc          = 0
     self.downloadonWindows      = 1
     self.buildLanguages         = ['Cxx']
+    self.maxCxxVersion          = 'c++17'
     self.skippackagewithoptions = 1
     self.builtafterpetsc        = 1
     self.noMPIUni               = 1
@@ -57,7 +58,7 @@ def Install(self):
     if not os.path.exists(configDir):
       os.makedirs(configDir)
 
-    if self.framework.argDB['prefix']:
+    if self.framework.argDB['prefix'] and not 'package-prefix-hash' in self.argDB:
       PETSC_DIR  = os.path.abspath(os.path.expanduser(self.argDB['prefix']))
       PETSC_ARCH = ''
       prefix     = os.path.abspath(os.path.expanduser(self.argDB['prefix']))
@@ -70,16 +71,8 @@ def Install(self):
 
     self.pushLanguage('Cxx')
     cxx = self.getCompiler()
-    cxxflags = self.getCompilerFlags()
+    cxxflags = self.updatePackageCxxFlags(self.getCompilerFlags())
     self.popLanguage()
-    cxxflags = cxxflags.replace('-fvisibility=hidden','') # MFEM is currently broken with -fvisibility=hidden
-    # MFEM uses the macro MFEM_BUILD_DIR that builds a path by combining the directory plus other stuff but if the
-    # directory name contains  "-linux" this is converted by CPP to the value 1 since that is defined in Linux header files
-    # unless the -std=C++11 or -std=C++14 flag is used; we want to support MFEM without this flag
-    if '-linux' in self.packageDir:
-      cxxflags += ' -Dlinux=linux'
-    # MFEM adds C++ standard flags automatically
-    cxxflags = re.sub(r'-std=([^\s]+) ','',cxxflags)
     if 'download-mfem-ghv-cxx' in self.argDB and self.argDB['download-mfem-ghv-cxx']:
       ghv = self.argDB['download-mfem-ghv-cxx']
     else:
@@ -158,7 +151,7 @@ def Install(self):
         slepclib = '-L'+prefix+'/lib -lslepc'
         slepcext = ''
         g.write('SLEPC_LIB = '+petscrpt+' '+slepclib+' '+slepcext+' $(PETSC_LIB)\n')
-        if self.argDB['prefix']:
+        if self.argDB['prefix'] and not 'package-prefix-hash' in self.argDB:
           makedepend = 'slepc-install'
         else:
           makedepend = 'slepc-build'
@@ -173,16 +166,17 @@ def Install(self):
       if self.cuda.found:
         self.pushLanguage('CUDA')
         petscNvcc = self.getCompiler()
-        cudaFlags = self.getCompilerFlags()
+        cudaFlags = self.updatePackageCUDAFlags(self.getCompilerFlags())
         self.popLanguage()
         cudaFlags = re.sub(r'-std=([^\s]+) ','',cudaFlags)
         g.write('MFEM_USE_CUDA = YES\n')
         g.write('CUDA_CXX = '+petscNvcc+'\n')
         g.write('CXXFLAGS := '+cudaFlags+' $(addprefix -Xcompiler ,$(CXXFLAGS))\n')
+        g.write('CUDA_ARCH = sm_' + self.cuda.cudaArchSingle() + '\n')
       if self.hip.found:
         self.pushLanguage('HIP')
         hipcc = self.getCompiler()
-        hipFlags = self.getCompilerFlags()
+        hipFlags = self.updatePackageCxxFlags(self.getCompilerFlags())
         self.popLanguage()
         hipFlags = re.sub(r'-std=([^\s]+) ','',hipFlags)
         g.write('MFEM_USE_HIP = YES\n')
@@ -193,13 +187,22 @@ def Install(self):
         g.write('MPI_LIB = '+self.mpi.libpaths+' '+self.mpi.mpilibs+'\n')
       g.close()
 
+    with open(os.path.join(configDir,'petsc.mk'),'w') as f:
+      f.write('''
+MAKEOVERRIDES := $(filter-out CXXFLAGS=%,$(MAKEOVERRIDES))
+unexport CXXFLAGS
+.PHONY: run-config
+run-config:
+\t$(MAKE) -f {mfile} config MFEM_DIR={mfemdir}
+'''.format(mfile=os.path.join(self.packageDir,'makefile'), mfemdir=self.packageDir))
+
     self.addDefine('HAVE_MFEM',1)
     self.addMakeMacro('MFEM','yes')
     self.addMakeRule('mfembuild',makedepend, \
                        ['@echo "*** Building MFEM ***"',\
                           '@${RM} ${PETSC_ARCH}/lib/petsc/conf/mfem.errorflg',\
                           '@(cd '+buildDir+' && \\\n\
-           ${OMAKE} -f '+self.packageDir+'/makefile config MFEM_DIR='+self.packageDir+' && \\\n\
+           ${OMAKE} -f '+configDir+'/petsc.mk run-config && \\\n\
            ${OMAKE} clean && \\\n\
            '+self.make.make_jnp+') > ${PETSC_ARCH}/lib/petsc/conf/mfem.log 2>&1 || \\\n\
              (echo "**************************ERROR*************************************" && \\\n\
@@ -216,7 +219,7 @@ def Install(self):
              echo "********************************************************************" && \\\n\
              exit 1)'])
 
-    if self.argDB['prefix']:
+    if self.argDB['prefix'] and not 'package-prefix-hash' in self.argDB:
       self.addMakeRule('mfem-build','')
       self.addMakeRule('mfem-install','mfembuild mfeminstall')
     else:

config/BuildSystem/config/packages/MPI.py

@@ -48,14 +48,11 @@ def __init__(self, framework):
     self.usingMPIUni      = 0
     self.shared           = 0
     # local state
-    self.commf2c          = 0
-    self.commc2f          = 0
     self.needBatchMPI     = 1
     self.alternativedownload = 'mpich'
+    self.haveReduceLocal  = 0
     # support MPI-3 process shared memory
     self.support_mpi3_shm = 0
-    # support MPI-3 non-blocking collectives
-    self.support_mpi3_nbc = 0
     self.mpi_pkg_version  = ''
     self.mpi_pkg          = '' # mpich,mpich2,mpich3,openmpi,intel,intel2,intel3
 
@@ -413,21 +410,12 @@ def configureMPI2(self):
     '''):
       raise RuntimeError('PETSc requires some of the MPI-2.0 (1997), MPI-2.1 (2008) functions - they are not available with the specified MPI library')
 
-    if self.checkLink('#include <mpi.h>\n', 'int count=2; int blocklens[2]={0,1}; MPI_Aint indices[2]={0,1}; MPI_Datatype old_types[2]={MPI_INT,MPI_DOUBLE}; MPI_Datatype *newtype = 0;\n \
+    if not self.checkLink('#include <mpi.h>\n', 'int count=2; int blocklens[2]={0,1}; MPI_Aint indices[2]={0,1}; MPI_Datatype old_types[2]={MPI_INT,MPI_DOUBLE}; MPI_Datatype *newtype = 0;\n \
                                              if (MPI_Type_create_struct(count, blocklens, indices, old_types, newtype)) { }\n'):
-      self.haveTypeCreateStruct = 1
-    else:
-      self.haveTypeCreateStruct = 0
       self.framework.addDefine('MPI_Type_create_struct(count,lens,displs,types,newtype)', 'MPI_Type_struct((count),(lens),(displs),(types),(newtype))')
-    if self.checkLink('#include <mpi.h>\n', 'MPI_Comm_errhandler_fn * p_err_fun = 0; MPI_Errhandler * p_errhandler = 0; if (MPI_Comm_create_errhandler(p_err_fun,p_errhandler)) { }\n'):
-      self.haveCommCreateErrhandler = 1
-    else:
-      self.haveCommCreateErrhandler = 0
+    if not self.checkLink('#include <mpi.h>\n', 'MPI_Comm_errhandler_fn * p_err_fun = 0; MPI_Errhandler * p_errhandler = 0; if (MPI_Comm_create_errhandler(p_err_fun,p_errhandler)) { }\n'):
       self.framework.addDefine('MPI_Comm_create_errhandler(p_err_fun,p_errhandler)', 'MPI_Errhandler_create((p_err_fun),(p_errhandler))')
-    if self.checkLink('#include <mpi.h>\n', 'if (MPI_Comm_set_errhandler(MPI_COMM_WORLD,MPI_ERRORS_RETURN)) { }\n'):
-      self.haveCommSetErrhandler = 1
-    else:
-      self.haveCommSetErrhandler = 0
+    if not self.checkLink('#include <mpi.h>\n', 'if (MPI_Comm_set_errhandler(MPI_COMM_WORLD,MPI_ERRORS_RETURN)) { }\n'):
       self.framework.addDefine('MPI_Comm_set_errhandler(comm,p_errhandler)', 'MPI_Errhandler_set((comm),(p_errhandler))')
     if self.checkLink('#include <mpi.h>\n', 'if (MPI_Reduce_local(0, 0, 0, MPI_INT, MPI_SUM)) { }\n'): # MPI_Reduce_local is in MPI-2.2
       self.haveReduceLocal = 1
@@ -499,7 +487,6 @@ def configureMPI3(self):
                         if (MPI_Ibarrier(MPI_COMM_WORLD,&req)) return 0;
                       '''):
       self.addDefine('HAVE_MPI_NONBLOCKING_COLLECTIVES', 1)
-      self.support_mpi3_nbc = 1
     if self.checkLink('#include <mpi.h>\n',
                       'MPI_Comm distcomm; \n\
                        MPI_Request req; \n\
@@ -635,8 +622,6 @@ def alternateConfigureLibrary(self):
     self.framework.addDefine('MPI_Comm_create_errhandler(p_err_fun,p_errhandler)', 'MPI_Errhandler_create((p_err_fun),(p_errhandler))')
     self.framework.addDefine('MPI_Comm_set_errhandler(comm,p_errhandler)', 'MPI_Errhandler_set((comm),(p_errhandler))')
     self.logWrite(self.framework.restoreLog())
-    self.commf2c = 1
-    self.commc2f = 1
     self.usingMPIUni = 1
     self.found = 1
     self.version = 'PETSc MPIUNI uniprocessor MPI replacement'
@@ -693,7 +678,6 @@ def FortranMPICheck(self):
     if self.fortran.fortranIsF90:
       self.log.write('Checking for mpi.mod\n')
       if self.libraries.check(self.lib,'', call = '       use mpi\n       integer(kind=selected_int_kind(5)) ierr,rank\n       call mpi_init(ierr)\n       call mpi_comm_rank(MPI_COMM_WORLD,rank,ierr)\n'):
-        self.havef90module = 1
         self.addDefine('HAVE_MPI_F90MODULE', 1)
     self.compilers.FPPFLAGS = oldFlags
     self.libraries.popLanguage()

config/BuildSystem/config/packages/MPICH.py

@@ -7,7 +7,7 @@ def __init__(self, framework):
     self.version          = '4.1.2'
     self.download         = ['https://github.com/pmodels/mpich/releases/download/v'+self.version+'/mpich-'+self.version+'.tar.gz',
                              'https://www.mpich.org/static/downloads/'+self.version+'/mpich-'+self.version+'.tar.gz', # does not always work from Python? So add in ftp.mcs URL below
-                             'https://ftp.mcs.anl.gov/pub/petsc/externalpackages'+'/mpich-'+self.version+'.tar.gz']
+                             'https://web.cels.anl.gov/projects/petsc/download/externalpackages'+'/mpich-'+self.version+'.tar.gz']
     self.download_git     = ['git://https://github.com/pmodels/mpich.git']
     self.gitsubmodules    = ['.']
     self.downloaddirnames = ['mpich']

config/BuildSystem/config/packages/MUMPS.py

@@ -9,7 +9,7 @@ def __init__(self, framework):
     self.requiresversion  = 1
     self.gitcommit        = 'v'+self.version
     self.download         = ['https://graal.ens-lyon.fr/MUMPS/MUMPS_'+self.version+'.tar.gz',
-                             'http://ftp.mcs.anl.gov/pub/petsc/externalpackages/MUMPS_'+self.version+'.tar.gz']
+                             'https://web.cels.anl.gov/projects/petsc/download/externalpackages/MUMPS_'+self.version+'.tar.gz']
     self.downloaddirnames = ['petsc-pkg-mumps','MUMPS']
     self.buildLanguages   = ['C','FC']
     self.precisions       = ['single','double']

config/BuildSystem/config/packages/OpenMPI.py

@@ -4,9 +4,9 @@
 class Configure(config.package.GNUPackage):
   def __init__(self, framework):
     config.package.GNUPackage.__init__(self, framework)
-    self.version                = '4.1.5'
+    self.version                = '4.1.6'
     self.download               = ['https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-'+self.version+'.tar.gz',
-                                   'http://ftp.mcs.anl.gov/pub/petsc/externalpackages/openmpi-'+self.version+'.tar.gz']
+                                   'https://web.cels.anl.gov/projects/petsc/download/externalpackages/openmpi-'+self.version+'.tar.gz']
     self.downloaddirnames       = ['openmpi','ompi']
     self.skippackagewithoptions = 1
     self.isMPI                  = 1

config/BuildSystem/config/packages/PTScotch.py

@@ -8,7 +8,7 @@ def __init__(self, framework):
     self.gitcommit        = 'v'+self.version
     self.download         = ['git://https://gitlab.inria.fr/scotch/scotch.git',
                              'https://gitlab.inria.fr/scotch/scotch/-/archive/'+self.gitcommit+'/scotch-'+self.gitcommit+'.tar.gz',
-                             'http://ftp.mcs.anl.gov/pub/petsc/externalpackages/scotch-'+self.gitcommit+'.tar.gz']
+                             'https://web.cels.anl.gov/projects/petsc/download/externalpackages/scotch-'+self.gitcommit+'.tar.gz']
     self.downloaddirnames = ['scotch','petsc-pkg-scotch']
     self.liblist          = [['libptesmumps.a','libptscotchparmetisv3.a','libptscotch.a','libptscotcherr.a','libesmumps.a','libscotch.a','libscotcherr.a'],['libptesmumps.a','libptscotchparmetis.a','libptscotch.a','libptscotcherr.a','libesmumps.a','libscotch.a','libscotcherr.a'],
                              ['libptesmumps.a','libptscotchparmetis.a','libptscotch.a','libptscotcherr.a','libesmumps.a','libscotch.a','libscotcherr.a']]

config/BuildSystem/config/packages/PaStiX.py

@@ -6,7 +6,7 @@ def __init__(self, framework):
     self.version          = '5.2.3'
     self.versionname      = 'PASTIX_MAJOR_VERSION.PASTIX_MEDIUM_VERSION.PASTIX_MINOR_VERSION'
     # 'https://gforge.inria.fr/frs/download.php/file/36212/pastix_'+self.version+'.tar.bz2',
-    self.download         = ['http://ftp.mcs.anl.gov/pub/petsc/externalpackages/pastix_'+self.version+'.tar.bz2']
+    self.download         = ['https://web.cels.anl.gov/projects/petsc/download/externalpackages/pastix_'+self.version+'.tar.bz2']
     self.liblist          = [['libpastix.a'],
                             ['libpastix.a','libpthread.a','librt.a']]
     self.functions        = ['pastix']

config/BuildSystem/config/packages/SAMRAI.py

@@ -3,7 +3,7 @@
 class Configure(config.package.GNUPackage):
   def __init__(self, framework):
     config.package.GNUPackage.__init__(self, framework)
-    self.download  = ['http://ftp.mcs.anl.gov/pub/petsc/externalpackages/SAMRAI-v2.4.4p.tar.gz', 'https://computation-rnd.llnl.gov/SAMRAI/download/SAMRAI-v2.4.4.tar.gz']
+    self.download  = ['https://web.cels.anl.gov/projects/petsc/download/externalpackages/SAMRAI-v2.4.4p.tar.gz', 'https://computation-rnd.llnl.gov/SAMRAI/download/SAMRAI-v2.4.4.tar.gz']
     self.functions = []
     self.includes  = ['Box.h']
     self.liblist   = [['libSAMRAI.a']]

config/BuildSystem/config/packages/SuperLU.py

@@ -7,8 +7,7 @@ def __init__(self, framework):
     self.version          = '6.0.1'
     self.minversion       = '5.2.1' # bugs in 5.2.0 prevent it from functioning
     self.versionname      = 'SUPERLU_MAJOR_VERSION.SUPERLU_MINOR_VERSION.SUPERLU_PATCH_VERSION'
-    # self.gitcommit        = 'v'+self.version
-    self.gitcommit        = 'baeea941129895a3718b558a2b8f2c65df1be15f' # master, may-7-2023
+    self.gitcommit        = 'v'+self.version
     self.download         = ['git://https://github.com/xiaoyeli/superlu','https://github.com/xiaoyeli/superlu/archive/'+self.gitcommit+'.tar.gz']
     self.functions        = ['set_default_options']
     self.includes         = ['slu_ddefs.h']
@@ -33,7 +32,7 @@ def setupDependencies(self, framework):
   def formCMakeConfigureArgs(self):
     args = config.package.CMakePackage.formCMakeConfigureArgs(self)
     args.append('-DUSE_XSDK_DEFAULTS=YES')
-
+    args.append('-DCMAKE_DISABLE_FIND_PACKAGE_Doxygen=TRUE')
     args.append('-DTPL_BLAS_LIBRARIES="'+self.libraries.toString(self.blasLapack.dlib)+'"')
 
     #  Tests are broken on Apple since they depend on a shared library that is not resolved against BLAS

config/BuildSystem/config/packages/Zoltan.py

@@ -6,7 +6,7 @@ def __init__(self, framework):
     config.package.GNUPackage.__init__(self, framework)
     self.version     = '3.83'
     self.versionname = 'ZOLTAN_VERSION_NUMBER'
-    self.download    = ['http://ftp.mcs.anl.gov/pub/petsc/externalpackages/zoltan_distrib_v'+self.version+'.tar.gz']
+    self.download    = ['https://web.cels.anl.gov/projects/petsc/download/externalpackages/zoltan_distrib_v'+self.version+'.tar.gz']
     self.functions   = ['Zoltan_LB_Partition']
     self.includes    = ['zoltan.h']
     self.liblist     = [['libzoltan.a']]

config/BuildSystem/config/packages/boost.py

@@ -5,7 +5,7 @@ class Configure(config.package.Package):
   def __init__(self, framework):
     config.package.Package.__init__(self, framework)
     self.download          = ['https://downloads.sourceforge.net/project/boost/boost/1.78.0/boost_1_78_0.tar.gz',
-                              'https://ftp.mcs.anl.gov/pub/petsc/externalpackages/boost_1_78_0.tar.gz']
+                              'https://web.cels.anl.gov/projects/petsc/download/externalpackages/boost_1_78_0.tar.gz']
     self.includes          = ['boost/multi_index_container.hpp']
     self.liblist           = []
     self.buildLanguages    = ['Cxx']

config/BuildSystem/config/packages/cmake.py

@@ -4,11 +4,11 @@
 class Configure(config.package.GNUPackage):
   def __init__(self, framework):
     config.package.GNUPackage.__init__(self, framework)
-    self.version            = '3.27.4'
+    self.version            = '3.27.6'
     self.download           = ['https://github.com/Kitware/CMake/releases/download/v'+self.version+'/cmake-'+self.version+'.tar.gz',
                               'https://gitlab.kitware.com/cmake/cmake/-/archive/v'+self.version+'/cmake-v'+self.version+'.tar.gz']
     self.download_solaris   = ['https://cmake.org/files/v3.11/cmake-3.11.4.tar.gz',
-                               'http://ftp.mcs.anl.gov/pub/petsc/externalpackages/cmake-3.11.4.tar.gz']
+                               'https://web.cels.anl.gov/projects/petsc/download/externalpackages/cmake-3.11.4.tar.gz']
     self.downloadonWindows  = 1
     self.lookforbydefault   = 1
     self.publicInstall      = 0  # always install in PETSC_DIR/PETSC_ARCH (not --prefix) since this is not used by users

config/BuildSystem/config/packages/concurrencykit.py

@@ -5,7 +5,7 @@ class Configure(config.package.GNUPackage):
   def __init__(self, framework):
     config.package.GNUPackage.__init__(self, framework)
     self.download          = ['http://concurrencykit.org/releases/ck-0.4.5.tar.gz',
-                              'http://ftp.mcs.anl.gov/pub/petsc/externalpackages/ck-0.4.5.tar.gz']
+                              'https://web.cels.anl.gov/projects/petsc/download/externalpackages/ck-0.4.5.tar.gz']
     self.functions         = []
     self.includes          = ['ck_spinlock.h']
     self.liblist           = [['libck.a']]

config/BuildSystem/config/packages/eigen.py

@@ -8,7 +8,7 @@ def __init__(self, framework):
     self.gitcommit     = self.version
     self.download      = ['git://https://gitlab.com/libeigen/eigen.git',
                           'https://gitlab.com/libeigen/eigen/-/archive/'+self.gitcommit+'/eigen-'+self.gitcommit+'.tar.gz',
-                          'http://ftp.mcs.anl.gov/pub/petsc/externalpackages/eigen-'+self.gitcommit+'.tar.gz']
+                          'https://web.cels.anl.gov/projects/petsc/download/externalpackages/eigen-'+self.gitcommit+'.tar.gz']
     self.functions     = []
     self.includes      = ['Eigen/Core']
     self.liblist       = []

config/BuildSystem/config/packages/f2cblaslapack.py

@@ -3,7 +3,7 @@
 class Configure(config.package.Package):
   def __init__(self, framework):
     config.package.Package.__init__(self, framework)
-    self.download               = ['http://ftp.mcs.anl.gov/pub/petsc/externalpackages/f2cblaslapack-3.8.0.q2.tar.gz']
+    self.download               = ['https://web.cels.anl.gov/projects/petsc/download/externalpackages/f2cblaslapack-3.8.0.q2.tar.gz']
     self.downloadonWindows      = 1
     self.skippackagewithoptions = 1
 

config/BuildSystem/config/packages/fftw.py

@@ -5,7 +5,7 @@ def __init__(self, framework):
     config.package.GNUPackage.__init__(self, framework)
     # host locally as fftw.org url can expire after new release.
     self.download   = ['http://www.fftw.org/fftw-3.3.10.tar.gz',
-                       'http://ftp.mcs.anl.gov/pub/petsc/externalpackages/fftw-3.3.8.tar.gz']
+                       'https://web.cels.anl.gov/projects/petsc/download/externalpackages/fftw-3.3.8.tar.gz']
     self.functions  = ['fftw_malloc']
     self.includes   = ['fftw3.h']
     self.liblist    = [['libfftw3_mpi.a','libfftw3.a'],['libfftw3.a']]