Merge pull request #22 from firedrakeproject/JDBetteridge/merge_upstream

JDBetteridge/merge upstream

Author: dham

.clang-format

@@ -172,6 +172,16 @@ StatementMacros:
   - PETSC_PRAGMA_DIAGNOSTIC_IGNORED_END
   - PETSC_PRAGMA_DIAGNOSTIC_IGNORED_END_
   - _Pragma
+TypeNames:
+  - PetscScalar
+  - PetscComplex
+  - PetscReal
+  - PetscInt
+  - PetscMPIInt
+  - PetscBLASInt
+  - PetscErrorCode
+  - PetscBool
+  - PetscBool3
 TabWidth: 2
 UseCRLF: false
 UseTab: Never

.gitignore

@@ -1,3 +1,4 @@
+bfort-petsc.txt
 *.bkp
 *.info
 *.gcov

.gitlab-ci.yml

@@ -78,6 +78,7 @@ check-ci-settings:
     - ${PYTHON} -m pip list --user
     - printf "CONFIG_OPTS:${CONFIG_OPTS}\n"
     - printf "PETSC_OPTIONS:$PETSC_OPTIONS\n"
+    - printf "MODULEPATH:$MODULEPATH\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
     - ${PYTHON} ./configure --with-debugging=0 COPTFLAGS='-O3 -march=native' CXXOPTFLAGS='-O3 -march=native' FOPTFLAGS='-O3 -march=native' ${CONFIG_OPTS}
     - make CFLAGS="${MAKE_CFLAGS}" CXXFLAGS="${MAKE_CXXFLAGS}" FFLAGS="${MAKE_FFLAGS}" CUDAFLAGS="${MAKE_CUDAFLAGS}"
@@ -156,14 +157,16 @@ clang-uni:
   extends: .stage-1
   variables:
     CONFIG_OPTS: --with-cc=clang --with-cxx=clang++ --with-mpi=0 --with-strict-petscerrorcode
+    MAKE_CFLAGS: -Werror -Wmissing-field-initializers -Wundef -Wextra-semi-stmt
+    MAKE_CXXFLAGS: -Werror -Wzero-as-null-pointer-constant -Wundef -Wextra-semi-stmt -Wextra-semi
     TEST_SEARCH: snes_tutorials-ex48%
 
 gcc-lto:
   extends: .stage-1
   variables:
     CONFIG_OPTS: CFLAGS= CXXFLAGS= FFLAGS=
     MAKE_CFLAGS: -Werror -flto=4 -Werror=odr -Werror=lto-type-mismatch
-    MAKE_CXXFLAGS: -Werror -flto=4 -Werror=odr -Werror=lto-type-mismatch
+    MAKE_CXXFLAGS: -Werror -Wextra-semi -flto=4 -Werror=odr -Werror=lto-type-mismatch
     MAKE_FFLAGS: -Werror -flto=4 -Werror=odr -Werror=lto-type-mismatch
     TEST_SEARCH: snes_tutorials-ex19% snes_tutorials-ex5f%
     LOAD_MODULES: gcc/12.1.0 mpich/4.1-gcc-12.1.0
@@ -237,8 +240,7 @@ checksource:
     - python3 ./configure --with-mpi=0 --with-fc=0 --with-cxx=0 --with-x=0 --with-bison=0 --with-cmake=0 --with-pthread=0 --with-regex=0
     - 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
+    - PATH=/nfs/gce/projects/petsc/soft/u22.04/spack-2024-09-18/opt/spack/linux-ubuntu22.04-x86_64/gcc-11.4.0/llvm-19.1.0-dqibzqq5utu2fba2me2bodbnaj5y7c36/bin:$PATH make checkclangformat SHELL=bash
     - make checkbadSource SHELL=bash
     - make checkbadFileChange SHELL=bash
     - make -f gmakefile check_output SHELL=bash
@@ -300,7 +302,7 @@ pause-for-approval:
         printf "RUN_GCOV_OPTIONS:$RUN_GCOV_OPTIONS\n";
         gcovr --version;
       fi
-    - if [ -d ${HOME}/petsc-hash-pkgs/ ]; then find ${HOME}/petsc-hash-pkgs/ -maxdepth 1 -mindepth 1 -type d -mtime +25 -exec rm -rf {} \; ; fi
+    - if [ -d ${HOME}/petsc-hash-pkgs/ ]; then find ${HOME}/petsc-hash-pkgs/ -maxdepth 1 -mindepth 1 -type d -mtime +25 -exec touch {} \; -exec rm -rf {} \; ; fi
     - printf "PATH:$PATH\n"
     - printf "PYTHONPATH:$PYTHONPATH\n"
     - printf "PETSC_OPTIONS:$PETSC_OPTIONS\n"
@@ -734,6 +736,8 @@ linux-cxx-cmplx-pkgs-64idx:
   variables:
     TEST_ARCH: arch-ci-linux-cxx-cmplx-pkgs-64idx
     PETSC_OPTIONS: -fp_trap
+    MODULEPATH: /nfs/gce/projects/petsc/soft/u22.04/spack-2024-08-30/modules/linux-ubuntu22.04-x86_64/Core
+    LOAD_MODULES: python/3.13.0rc1-rayc5m7 py-setuptools/69.2.0-6yku3zk python-venv/1.0-bnbfk2n py-pip/23.1.2-o7dlzno
 
 # Set env vars for 'Kokkos + OpenMP' tests, so that they won't give warnings
 linux-pkgs-dbg-ftn-interfaces:
@@ -810,7 +814,8 @@ linux-pgi:
     - gce-u22-stage3, linux-mcpu
   variables:
     TEST_ARCH: arch-ci-linux-pgi
-    LOAD_MODULES: nvhpc/22.3
+    MODULEPATH: /nfs/gce/projects/petsc/soft/u22.04/spack-2024-09-18/modules/linux-ubuntu22.04-x86_64/Core
+    LOAD_MODULES: nvhpc/24.7-nypdnhf
 
 # If the Nag license server fails then ${PETSC_DIR}/naglicenseproblem is created and the job is marked as failed but allow_failure
 linux-nagfor:
@@ -854,7 +859,7 @@ check-each-commit:
   tags:
     - gce-u22-stage2
   script:
-    - export PATH=/nfs/gce/projects/petsc/soft/u22.04/spack-2024-03-06/opt/spack/linux-ubuntu22.04-x86_64/gcc-11.4.0/llvm-18.1.0-7hsf4hzma6aebqsd4ifb5brchcooktkp/bin:$PATH
+    - export PATH=/nfs/gce/projects/petsc/soft/u22.04/spack-2024-09-18/opt/spack/linux-ubuntu22.04-x86_64/gcc-11.4.0/llvm-19.1.0-dqibzqq5utu2fba2me2bodbnaj5y7c36/bin:$PATH
     - lib/petsc/bin/maint/check-each-commit.sh
   except:
     variables:
@@ -964,6 +969,8 @@ linux-opt-cxx-quad:
     - gce-u22-stage3
   variables:
     TEST_ARCH: arch-ci-linux-opt-cxx-quad
+    MODULEPATH: /nfs/gce/projects/petsc/soft/u22.04/spack-2024-08-30/modules/linux-ubuntu22.04-x86_64/Core
+    LOAD_MODULES: python/3.13.0rc1-rayc5m7
 
 linux-ILP64:
   extends:

config/BuildSystem/RDict.py

@@ -83,7 +83,6 @@ class RDict(dict):
   def __init__(self, parentAddr = None, parentDirectory = None, load = 1, autoShutdown = 1, readonly = False):
     import atexit
     import time
-    import xdrlib
 
     self.logFile         = None
     self.setupLogFile()
@@ -98,8 +97,6 @@ def __init__(self, parentAddr = None, parentDirectory = None, load = 1, autoShut
     self.isServer        = 0
     self.readonly        = readonly
     self.parentDirectory = parentDirectory
-    self.packer          = xdrlib.Packer()
-    self.unpacker        = xdrlib.Unpacker('')
     self.stopCmd         = pickle.dumps(('stop',))
     self.writeLogLine('Greetings')
     self.connectParent(self.parentAddr, self.parentDirectory)
@@ -110,25 +107,20 @@ def __init__(self, parentAddr = None, parentDirectory = None, load = 1, autoShut
     return
 
   def __getstate__(self):
-    '''Remove any parent socket object, the XDR translators, and the log file from the dictionary before pickling'''
+    '''Remove any parent socket object, and the log file from the dictionary before pickling'''
     self.writeLogLine('Pickling RDict')
     d = self.__dict__.copy()
     if 'parent'    in d: del d['parent']
     if 'saveTimer' in d: del d['saveTimer']
     if '_setCommandLine' in d: del d['_setCommandLine']
-    del d['packer']
-    del d['unpacker']
     del d['logFile']
     return d
 
   def __setstate__(self, d):
-    '''Reconnect the parent socket object, recreate the XDR translators and reopen the log file after unpickling'''
+    '''Reconnect the parent socket object and reopen the log file after unpickling'''
     self.logFile  = open('RDict.log', 'a')
     self.writeLogLine('Unpickling RDict')
     self.__dict__.update(d)
-    import xdrlib
-    self.packer   = xdrlib.Packer()
-    self.unpacker = xdrlib.Unpacker('')
     self.connectParent(self.parentAddr, self.parentDirectory)
     return
 
@@ -477,13 +469,9 @@ def sendPacket(self, s, packet, source = 'Unknown', isPickled = 0):
       p = packet
     else:
       p = pickle.dumps(packet)
-    self.packer.reset()
-    self.packer.pack_uint(len(p))
     if hasattr(s, 'write'):
-      s.write(self.packer.get_buffer())
       s.write(p)
     else:
-      s.sendall(self.packer.get_buffer())
       s.sendall(p)
     self.writeLogLine(source+': Sent packet')
     return
@@ -495,9 +483,6 @@ def recvPacket(self, s, source = 'Unknown'):
       s.read(4)
       value = pickle.load(s)
     else:
-      # I probably need to check that it actually read these 4 bytes
-      self.unpacker.reset(s.recv(4))
-      length    = self.unpacker.unpack_uint()
       objString = ''
       while len(objString) < length:
         objString += s.recv(length - len(objString))

config/BuildSystem/config/compilerOptions.py

@@ -26,6 +26,9 @@ def getCFlags(self, compiler, bopt, language):
     if config.setCompilers.Configure.isGNU(compiler, self.log) or config.setCompilers.Configure.isClang(compiler, self.log):
       if bopt == '':
         flags.extend(['-Wall', '-Wwrite-strings', '-Wno-unknown-pragmas', '-Wno-lto-type-mismatch'])
+        if config.setCompilers.Configure.isClang(compiler, self.log):
+          # gcc does not support -Wno-implicit-float-conversion so -Wconversion is always noisy
+          flags.extend(['-Wconversion', '-Wno-sign-conversion', '-Wno-float-conversion', '-Wno-implicit-float-conversion'])
         if config.setCompilers.Configure.isGcc110plus(compiler, self.log):
           flags.extend(['-Wno-stringop-overflow'])
         # skip -fstack-protector for brew gcc - as this gives SEGV

config/BuildSystem/config/compilers.py

@@ -188,7 +188,7 @@ def checkCLibraries(self):
     if hasattr(self.setCompilers, 'CXX'):
       self.setCompilers.saveLog()
       try:
-        if self.checkCrossLink('#include <stdio.h>\nvoid asub(void)\n{char s[16];printf("testing %s",s);}\n',"int main(int argc,char **args)\n{return 0;}\n",language1='C',language2='C++'):
+        if self.checkCrossLink('#include <stdio.h>\nvoid asub(void)\n{char s[16];printf("testing %s",s);}\n',"int main(int argc,char **args)\n{(void)argc, (void)args; return 0;}\n",language1='C',language2='C++'):
           self.logWrite(self.setCompilers.restoreLog())
           self.logPrint('C libraries are not needed when using C++ linker')
         else:
@@ -853,8 +853,8 @@ def checkFortranLibraries(self):
     skipfortranlibraries = 1
     self.setCompilers.saveLog()
     asub=self.mangleFortranFunction("asub")
-    cbody = "extern void "+asub+"(void);\nint main(int argc,char **args)\n{\n  "+asub+"();\n  return 0;\n}\n";
-    cxxbody = 'extern "C" void '+asub+'(void);\nint main(int argc,char **args)\n{\n  '+asub+'();\n  return 0;\n}\n';
+    cbody = "extern void "+asub+"(void);\nint main(int argc,char **args)\n{\n  "+asub+"();\n  (void)argc, (void)args;\n  return 0;\n}\n";
+    cxxbody = 'extern "C" void '+asub+'(void);\nint main(int argc,char **args)\n{\n  '+asub+'();\n  (void)argc, (void)args;\n  return 0;\n}\n';
     self.pushLanguage('FC')
     if self.checkLink(body='      use mpi\n      call MPI_Allreduce()\n'):
       fbody = "      subroutine asub()\n      use mpi\n      print*,'testing'\n      call MPI_Allreduce()\n      return\n      end\n"

config/BuildSystem/config/framework.py

@@ -454,6 +454,7 @@ def filterPreprocessOutput(self,output, log = None):
     lines = [s for s in lines if s.find("icc: command line remark #10148: option '-i-dynamic' not supported") < 0]
     lines = [s for s in lines if s.find("[: unexpected operator") < 0]  # Deals with error in mpiicc and mpiicpc wrappers from some versions of Intel MPI.
     lines = [s for s in lines if s.find(': remark #10441:') < 0]
+    lines = [s for s in lines if s.find("'linker' input unused") < 0]
     # IBM:
     lines = [s for s in lines if not s.startswith('cc_r:')]
     # PGI: Ignore warning about temporary license
@@ -469,6 +470,8 @@ def filterPreprocessOutput(self,output, log = None):
     lines = [s for s in lines if s.find('The -gpu option has no effect unless a language-specific option to enable GPU code generation is used') < 0]
     # pgi dumps filename on stderr - but returns 0 errorcode'
     lines = [s for s in lines if lines != 'conftest.c:']
+    # nvcc
+    lines = [s for s in lines if s.find('incompatible redefinition for option \'compiler-bindir\', the last value of this option was used') < 0]
 
     lines = [s for s in lines if len(s)]
     if lines: output = '\n'.join(lines)
@@ -517,6 +520,7 @@ def filterCompileOutput(self, output,flag = '', filterAlways = 0):
       # Intel
       lines = [s for s in lines if s.find("icc: command line remark #10148: option '-i-dynamic' not supported") < 0]
       lines = [s for s in lines if s.find(': remark #10441:') < 0]
+      lines = [s for s in lines if s.find("'linker' input unused") < 0]
       # PGI: Ignore warning about temporary license
       lines = [s for s in lines if s.find('license.dat') < 0]
       # Cray XT3
@@ -531,8 +535,9 @@ def filterCompileOutput(self, output,flag = '', filterAlways = 0):
       lines = [s for s in lines if s.find('The -gpu option has no effect unless a language-specific option to enable GPU code generation is used') < 0]
       # pgi dumps filename on stderr - but returns 0 errorcode'
       lines = [s for s in lines if lines != 'conftest.c:']
-
       lines = [s for s in lines if len(s)]
+      # nvcc
+      lines = [s for s in lines if s.find('incompatible redefinition for option \'compiler-bindir\', the last value of this option was used') < 0]
       if lines: output = '\n'.join(lines)
       else: output = ''
       self.log.write("Compiler output after filtering:\n"+(output if not output else output+'\n'))
@@ -595,6 +600,7 @@ def filterLinkOutput(self, output, filterAlways = 0):
       lines = [s for s in lines if s.find('ld: warning: -undefined dynamic_lookup may not work with chained fixups') < 0]
       # Nvidia linker
       lines = [s for s in lines if s.find('nvhpc.ld contains output sections') < 0]
+      lines = [s for s in lines if s.find('incompatible redefinition for option \'compiler-bindir\', the last value of this option was used') < 0]
       # Intel dpcpp linker
       # Ex. clang-offload-bundler: error: '/home/jczhang/mpich/lib': Is a directory
       lines = [s for s in lines if s.find('clang-offload-bundler: error:') < 0]

config/BuildSystem/config/functions.py

@@ -28,7 +28,7 @@ def check(self, funcs, libraries = None, examineOutput=lambda ret,out,err:None):
     if isinstance(funcs, str): funcs = [funcs]
     self.log.write('Checking for functions ['+' '.join(funcs)+']\n')
     def genIncludes(funcName):
-      return 'char %s();\n' % funcName
+      return 'char %s(void);\n' % funcName
     def genBody(funcName):
       # The GNU C library defines __stub_* for functions that it implements
       # to always fail with ENOSYS.  Some functions are actually named
@@ -112,7 +112,7 @@ def checkVSNPrintf(self):
   def checkSignalHandlerType(self):
     '''Checks the type of C++ signals handlers, and defines SIGNAL_CAST to the correct value'''
     self.pushLanguage('C++')
-    if not self.checkLink('#include <signal.h>\nstatic void myhandler(int sig) {}\n', 'signal(SIGFPE,myhandler)'):
+    if not self.checkLink('#include <signal.h>\nstatic void myhandler(int sig) { (void)sig; }\n', 'signal(SIGFPE,myhandler)'):
       self.addDefine('SIGNAL_CAST', '(void (*)(int))')
     else:
       self.addDefine('SIGNAL_CAST', ' ')
@@ -147,7 +147,7 @@ def checkMemmove(self):
 
   def checkMmap(self):
     '''Check for functional mmap() to allocate shared memory and define HAVE_MMAP'''
-    if self.checkLink('#include <sys/mman.h>\n#include <sys/types.h>\n#include <sys/stat.h>\n#include <fcntl.h>\n','int fd;\n fd=open("/tmp/file",O_RDWR);\n mmap((void*)0,100,PROT_READ|PROT_WRITE,MAP_SHARED,fd,0)'):
+    if self.checkLink('#include <sys/mman.h>\n#include <sys/types.h>\n#include <sys/stat.h>\n#include <fcntl.h>\n','int fd;\n fd=open("/tmp/file",O_RDWR);\n mmap(NULL,100,PROT_READ|PROT_WRITE,MAP_SHARED,fd,0)'):
       self.addDefine('HAVE_MMAP', 1)
     return
 

config/BuildSystem/config/libraries.py

@@ -575,13 +575,13 @@ def checkExportedSymbols(self, flags, checkLink = None, libraries = [], defaultA
 
 #define PETSC_DLLEXPORT %s
 
-extern PETSC_DLLEXPORT int foo() {
+extern PETSC_DLLEXPORT int foo(void) {
   return 42;
 }
     ''' % (guard, visibility)
     body = '''
   void *lib;
-  int (*foo)();
+  int (*foo)(void);
 
   lib = dlopen(NULL, RTLD_LAZY);
   if (!lib) {
@@ -627,6 +627,24 @@ def isBGL(self):
         self._isBGL = 0
     return self._isBGL
 
+  def checkPthreadMutex(self):
+    '''Check for pthread mutex support'''
+    funcs = ['pthread_mutex_unlock']
+    prototypes = ['#include <pthread.h>']
+    self.pthreadmutex = []
+    calls = ['pthread_mutex_t m; pthread_mutex_unlock(&m)']
+    if self.check('', funcs, prototype=prototypes, call=calls):
+      self.logPrint('pthread mutex are linked in by default')
+      self.pthreadmutex = []
+      self.addDefine('HAVE_PTHREAD_MUTEX',1)
+    elif self.check('pthread', funcs, prototype=prototypes, call=calls):
+      self.logPrint('Using libpthread for the mutex')
+      self.pthreadmutex = ['libpthread.a']
+      self.addDefine('HAVE_PTHREAD_MUTEX',1)
+    else:
+      self.logPrint('No pthread mutex support found')
+    return
+
   def checkExecutableExportFlag(self):
     '''Checks for the flag that allows executables to export symbols to dlsym()'''
     # Right now, we just check some compilers, but we should make a test trying to load a symbol from the executable
@@ -648,6 +666,7 @@ def configure(self):
     self.executeTest(self.checkMathLog2)
     self.executeTest(self.checkRealtime)
     self.executeTest(self.checkDynamic)
+    self.executeTest(self.checkPthreadMutex)
     if not self.argDB['with-batch']:
       self.executeTest(self.checkExecutableExportFlag)
     return

config/BuildSystem/config/package.py

@@ -305,13 +305,15 @@ def rmArgsPair(self,args,rejects,remove_ahead=True):
     return nargs
 
   def rmArgsStartsWith(self,args,rejectstarts):
+    '''Remove an argument that starts with given strings'''
     rejects = []
     if not isinstance(rejectstarts, list): rejectstarts = [rejectstarts]
     for i in rejectstarts:
       rejects.extend([arg for arg in args if arg.startswith(i)])
     return self.rmArgs(args,rejects)
 
   def addArgStartsWith(self,args,sw,value):
+    '''Adds another value with the argument that starts with sw, create sw if it does not exist'''
     keep = []
     found = 0
     for i in args:
@@ -323,13 +325,24 @@ def addArgStartsWith(self,args,sw,value):
       keep.append(sw+'="' + value + '"')
     return keep
 
+  def rmValueArgStartsWith(self,args,sw,value):
+    '''Remove a value from arguements that start with sw'''
+    if not isinstance(sw, list): sw = [sw]
+    keep = []
+    for i in args:
+      for j in sw:
+        if i.startswith(j+'="'):
+          i = i.replace(value,'')
+      keep.append(i)
+    return keep
+
   def removeWarningFlags(self,flags):
     flags = self.rmArgs(
       flags,
       {
         '-Werror', '-Wall', '-Wwrite-strings', '-Wno-strict-aliasing', '-Wno-unknown-pragmas',
         '-Wno-unused-variable', '-Wno-unused-dummy-argument', '-std=c89', '-pedantic','--coverage',
-        '-Mfree', '-fdefault-integer-8', '-fsanitize=address', '-fstack-protector'
+        '-Mfree', '-fdefault-integer-8', '-fsanitize=address', '-fstack-protector', '-Wconversion'
       }
     )
     return ['-g' if f == '-g3' else f for f in flags]
@@ -374,6 +387,13 @@ def removeCoverageFlag(self, flags, pair_prefix=None):
     """Remove --coverage from flags."""
     return self.__remove_flag_pair(flags, '--coverage', pair_prefix)
 
+  def removeOpenMPFlag(self, flags, pair_prefix=None):
+    """Remove -fopenmp from flags."""
+    if hasattr(self,'openmp') and hasattr(self.openmp,'ompflag'):
+      return self.__remove_flag_pair(flags, self.openmp.ompflag, pair_prefix)
+    else:
+      return flags
+
   def removeStdCxxFlag(self,flags):
     '''Remove the -std=[CXX_VERSION] flag from the list of flags, but only for CMake packages'''
     if issubclass(type(self),config.package.CMakePackage):