Merge pull request #19 from firedrakeproject/connorjward/merge-upstream

Merge upstream

.clang-format

@@ -99,6 +99,7 @@ IndentWidth: 2
 IndentWrappedFunctionNames: false
 InsertTrailingCommas: None
 KeepEmptyLinesAtTheStartOfBlocks: false
+KeepEmptyLinesAtEOF: false
 LambdaBodyIndentation: Signature
 MacroBlockBegin: ''
 MacroBlockEnd:   ''

.gitlab-ci.yml

@@ -153,9 +153,19 @@ c99-mlib-static-py:
 clang-uni:
   extends: .stage-1
   variables:
-    CONFIG_OPTS: --with-cc=clang --with-cxx=clang++ --with-mpi=0
+    CONFIG_OPTS: --with-cc=clang --with-cxx=clang++ --with-mpi=0 --with-strict-petscerrorcode
     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_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
+
 petsc4py-install:
   extends: .stage-2
   tags:
@@ -218,7 +228,7 @@ 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/clang+llvm-16.0.0-x86_64-linux-gnu-ubuntu-18.04/bin:$PATH make checkclangformat SHELL=bash
+    - PATH=/nfs/gce/projects/petsc/soft/u22.04/spack-2024-03-06/opt/spack/linux-ubuntu22.04-x86_64/gcc-11.4.0/llvm-18.1.0-7hsf4hzma6aebqsd4ifb5brchcooktkp/bin:$PATH make checkclangformat SHELL=bash
     - make checkbadSource SHELL=bash
     - make checkbadFileChange SHELL=bash
     - make -f gmakefile check_output SHELL=bash
@@ -833,7 +843,7 @@ check-each-commit:
   tags:
     - gce-u22-stage2
   script:
-    - export PATH=/nfs/gce/projects/petsc/soft/clang+llvm-16.0.0-x86_64-linux-gnu-ubuntu-18.04/bin:$PATH
+    - export PATH=/nfs/gce/projects/petsc/soft/u22.04/spack-2024-03-06/opt/spack/linux-ubuntu22.04-x86_64/gcc-11.4.0/llvm-18.1.0-7hsf4hzma6aebqsd4ifb5brchcooktkp/bin:$PATH
     - lib/petsc/bin/maint/check-each-commit.sh
   except:
     variables:

CODE_OF_CONDUCT.md

@@ -6,7 +6,7 @@ In the interest of fostering an open and welcoming environment, we as
 contributors and maintainers pledge to making participation in our project and
 our community a harassment-free experience for everyone, regardless of age, body
 size, disability, ethnicity, sex characteristics, gender identity and expression,
-level of experience, education, socio-economic status, nationality, personal
+level of experience, education, socioeconomic status, nationality, personal
 appearance, race, religion, or sexual identity and orientation.
 
 ## Our Standards

config/BuildSystem/config/compilerOptions.py

@@ -3,9 +3,9 @@
 import re
 import nargs
 
-re_win32fe_cl    = re.compile(r'win32fe\s+cl')
-re_win32fe_icl   = re.compile(r'win32fe\s+icl')
-re_win32fe_ifort = re.compile(r'win32fe\s+ifort')
+re_win32fe_cl    = re.compile(r'win32fe[\s_]+cl')
+re_win32fe_icl   = re.compile(r'win32fe[\s_]+ic[lx]')
+re_win32fe_ifort = re.compile(r'win32fe[\s_]+if(x|ort)')
 
 class CompilerOptions(config.base.Configure):
   def getCFlags(self, compiler, bopt, language):
@@ -50,7 +50,7 @@ def getCFlags(self, compiler, bopt, language):
           flags.append('-O')
     else:
       # Linux Intel
-      if config.setCompilers.Configure.isIntel(compiler, self.log) and not compiler.find('win32fe') >=0:
+      if config.setCompilers.Configure.isIntel(compiler, self.log) and not re_win32fe_icl.search(compiler):
         if bopt == '':
           flags.extend(['-wd1572', '-Wno-unknown-pragmas'])
           # next one fails in OpenMP build and we don't use it anyway so remove
@@ -61,7 +61,7 @@ def getCFlags(self, compiler, bopt, language):
           flags.append('-g')
           flags.append('-O3')
       # Windows Intel
-      elif 'win_icl' in compiler or re_win32fe_icl.search(compiler):
+      elif re_win32fe_icl.search(compiler):
         if bopt == '':
           flags.extend(['-Qstd=c99'])
           if self.argDB['with-shared-libraries']:
@@ -73,7 +73,7 @@ def getCFlags(self, compiler, bopt, language):
         elif bopt == 'O':
           flags.extend(['-O3', '-QxW'])
       # Windows Microsoft
-      elif 'win_cl' in compiler or re_win32fe_cl.search(compiler):
+      elif re_win32fe_cl.search(compiler):
         if bopt == '':
           dir(self)
           # cause compiler to generate only a single copy of static strings; needed usage of __func__ in PETSc
@@ -176,7 +176,7 @@ def getCxxFlags(self, compiler, bopt, language):
         flags.append('-O')
     else:
       # Linux Intel
-      if config.setCompilers.Configure.isIntel(compiler, self.log) and not compiler.find('win32fe') >=0:
+      if config.setCompilers.Configure.isIntel(compiler, self.log) and not re_win32fe_icl.search(compiler):
         if bopt == '':
           flags.append('-wd1572')
         elif bopt == 'g':
@@ -185,7 +185,7 @@ def getCxxFlags(self, compiler, bopt, language):
           flags.append('-g')
           flags.append('-O3')
       # Windows Intel
-      elif 'win_icl' in compiler or re_win32fe_icl.search(compiler):
+      elif re_win32fe_icl.search(compiler):
         if bopt == '':
           if self.argDB['with-shared-libraries']:
             flags.extend(['-MD','-GR','-EHsc'])
@@ -196,7 +196,7 @@ def getCxxFlags(self, compiler, bopt, language):
         elif bopt in ['O']:
           flags.extend(['-O3', '-QxW'])
       # Windows Microsoft
-      elif 'win_cl' in compiler or re_win32fe_cl.search(compiler):
+      elif re_win32fe_cl.search(compiler):
         if bopt == '':
           # cause compiler to generate only a single copy of static strings; needed usage of __func__ in PETSc
           flags.extend(['-GF'])
@@ -274,14 +274,14 @@ def getFortranFlags(self, compiler, bopt):
         elif bopt == 'O':
           flags.extend(['-fast', '-Mnoframe'])
       # Linux Intel
-      if config.setCompilers.Configure.isIntel(compiler, self.log) and not compiler.find('win32fe') >=0:
+      if config.setCompilers.Configure.isIntel(compiler, self.log) and not re_win32fe_ifort.search(compiler):
         if bopt == 'g':
           flags.extend(['-g','-O0'])
         elif bopt == 'O':
           flags.append('-g')
           flags.append('-O3')
       # Windows Intel
-      elif 'win_ifort' in compiler or re_win32fe_ifort.search(compiler):
+      elif re_win32fe_ifort.search(compiler):
         if bopt == '':
           if self.argDB['with-shared-libraries']:
             flags.extend(['-MD'])

config/BuildSystem/config/compilers.py

@@ -36,7 +36,10 @@ def getSkipDefaultPaths(self):
     if len(self.skipdefaultpaths):
       return self.skipdefaultpaths
     else:
-      self.skipdefaultpaths = ['/usr/lib','/lib','/usr/lib64','/lib64','/usr/lib/x86_64-linux-gnu','/lib/x86_64-linux-gnu','/usr/lib/i386-linux-gnu']
+      self.skipdefaultpaths = ['/usr/lib','/lib','/usr/lib64','/lib64']
+      for loc in ['/usr/lib','/lib']:
+        for arch in ['x86_64','i386','aarch64']:
+          self.skipdefaultpaths.append(os.path.join(loc,arch+'-linux-gnu'))
       conda_sysrt = os.getenv('CONDA_BUILD_SYSROOT')
       if conda_sysrt:
         conda_sysrt = os.path.abspath(conda_sysrt)
@@ -622,6 +625,9 @@ def checkCxxLibraries(self):
             elif arg == '-lLTO' and self.setCompilers.isDarwin(self.log):
               self.logPrint('Skipping -lTO')
               continue
+            elif arg.find('-libpath:')>=0:
+              self.logPrint('Skipping Intel oneAPI icx (on Microsoft Windows) compiler option: '+arg)
+              continue
             elif iscray and (arg == '-lsci_cray_mpi' or arg == '-lsci_cray' or arg == '-lsci_cray_mp'):
               self.logPrint('Skipping CRAY LIBSCI library: '+arg, 4, 'compilers')
               continue
@@ -850,6 +856,7 @@ def checkFortranLibraries(self):
       fbody = "      subroutine asub()\n      print*,'testing'\n      return\n      end\n"
     self.popLanguage()
     iscray = config.setCompilers.Configure.isCray(self.getCompiler('FC'), self.log)
+    isintel = config.setCompilers.Configure.isIntel(self.getCompiler('C'), self.log)
     try:
       if self.checkCrossLink(fbody,cbody,language1='FC',language2='C'):
         self.logWrite(self.setCompilers.restoreLog())
@@ -858,34 +865,25 @@ def checkFortranLibraries(self):
         skipfortranlibraries = 0
         self.logWrite(self.setCompilers.restoreLog())
         oldLibs = self.setCompilers.LIBS
-        self.setCompilers.LIBS = '-lgfortran '+self.setCompilers.LIBS
-        self.setCompilers.saveLog()
-        if self.checkCrossLink(fbody,cbody,language1='FC',language2='C'):
-          self.logWrite(self.setCompilers.restoreLog())
-          self.logPrint('Fortran requires -lgfortran to link with C compiler', 3, 'compilers')
-          self.setCompilers.LIBS = oldLibs
-          self.flibs.append('-lgfortran')
-          skipfortranlibraries = 1
-        else:
-          self.logWrite(self.setCompilers.restoreLog())
-          self.setCompilers.LIBS = oldLibs
-          self.logPrint('Fortran code cannot directly be linked with C linker, therefore will determine needed Fortran libraries')
-          skipfortranlibraries = 0
-        if iscray:
-          oldLibs = self.setCompilers.LIBS
-          self.setCompilers.LIBS = '-lmpifort_cray '+self.setCompilers.LIBS
+        testlibs = ['-lgfortran']
+        if iscray: testlibs.append('-lmpifort_cray')
+        if isintel: testlibs.append('-fortlib')
+        for testlib in testlibs:
+          self.setCompilers.LIBS = testlib+' '+self.setCompilers.LIBS
           self.setCompilers.saveLog()
           if self.checkCrossLink(fbody,cbody,language1='FC',language2='C'):
             self.logWrite(self.setCompilers.restoreLog())
-            self.logPrint('Fortran requires -lmpifort_cray to link with C compiler', 3, 'compilers')
+            self.logPrint('Fortran requires '+testlib+' to link with C compiler', 3, 'compilers')
             self.setCompilers.LIBS = oldLibs
-            self.flibs.append('-lmpifort_cray')
+            self.flibs.append(testlib)
             skipfortranlibraries = 1
+            break
           else:
             self.logWrite(self.setCompilers.restoreLog())
             self.setCompilers.LIBS = oldLibs
-            self.logPrint('Fortran code cannot directly be linked with C linker, therefore will determine needed Fortran libraries')
             skipfortranlibraries = 0
+        if not skipfortranlibraries:
+          self.logPrint('Fortran code cannot directly be linked with C linker, therefore will determine needed Fortran libraries')
     except RuntimeError as e:
       self.logWrite(self.setCompilers.restoreLog())
       self.logPrint('Error message from compiling {'+str(e)+'}', 4, 'compilers')
@@ -1061,10 +1059,6 @@ def checkFortranLibraries(self):
           if not lib == '-LLTO' or not self.setCompilers.isDarwin(self.log):
             flibs.append(lib)
           continue
-        # intel windows compilers can use -libpath argument
-        if arg.find('-libpath:')>=0:
-          self.logPrint('Skipping win32 ifort option: '+arg)
-          continue
         # Check for special library arguments
         m = re.match(r'^-l.*$', arg)
         if m:
@@ -1083,6 +1077,9 @@ def checkFortranLibraries(self):
               continue
             elif arg == '-lLTO' and self.setCompilers.isDarwin(self.log):
               self.logPrint('Skipping -lTO')
+            elif arg.find('-libpath:')>=0:
+              self.logPrint('Skipping Intel oneAPI ifort (on Microsoft Windows) compiler option: '+arg)
+              continue
             elif iscray and (arg == '-lsci_cray_mpi' or arg == '-lsci_cray' or arg == '-lsci_cray_mp'):
               self.logPrint('Skipping CRAY LIBSCI library: '+arg, 4, 'compilers')
               continue

config/BuildSystem/config/compilersFortran.py

@@ -420,7 +420,7 @@ def checkFortranModuleOutput(self):
     self.popLanguage()
     if modname: os.remove(os.path.join(testdir, modname))
     os.rmdir(testdir)
-    # Flag not used by PETSc - do do not flag a runtime error
+    # Flag not used by PETSc - do not flag a runtime error
     #if not found:
     #  raise RuntimeError('Cannot determine Fortran module output flag')
     return

config/BuildSystem/config/framework.py

@@ -936,7 +936,10 @@ def outputMakeRuleHeader(self, name):
 
   def processPackageListDefine(self, defineDict):
     key = 'PETSC_HAVE_PACKAGES'
-    pkglist = sorted(set([pkg.pkgname.lower() for pkg in self.packages]))
+    pkglist = []
+    for pkg in self.packages:
+      pkglist.extend(pkg.pkgname.lower().split())
+    pkglist.sort()
     str = '":' + ':'.join(pkglist) + ':"'
     defineDict[key] = (key, str)
 

config/BuildSystem/config/libraries.py

@@ -38,21 +38,39 @@ def getLibArgumentList(self, library, with_rpath=True):
       return [library] if with_rpath else []
     if library.startswith('${FC_LINKER_SLFLAG}'):
       return [library] if with_rpath else []
+    flagName  = self.language[-1]+'SharedLinkerFlag'
+    flagSubst = self.language[-1].upper()+'_LINKER_SLFLAG'
+    rpathFlag = ''
+    if hasattr(self.setCompilers, flagName) and not getattr(self.setCompilers, flagName) is None:
+      rpathFlag = getattr(self.setCompilers, flagName)
+    elif flagSubst in self.argDB:
+      rpathFlag = self.argDB[flagSubst]
+    if library.startswith('-L'):
+      dirname = library[2:]
+      if not dirname.startswith('$') and not os.path.isdir(dirname): self.logPrint('Warning! getLibArgumentList(): could not locate dir '+ dirname)
+      if dirname in self.sysDirs:
+          return []
+      elif with_rpath and rpathFlag and not dirname in self.rpathSkipDirs:
+        return [rpathFlag+dirname,library]
+      else:
+        return [library]
     if library.lstrip()[0] == '-':
       return [library]
     if len(library) > 3 and library[-4:] == '.lib':
       return [library.replace('\\ ',' ').replace(' ', '\\ ').replace('\\(','(').replace('(', '\\(').replace('\\)',')').replace(')', '\\)')]
     if os.path.basename(library).startswith('lib'):
       name = self.getLibName(library)
       if ((len(library) > 2 and library[1] == ':') or os.path.isabs(library)):
-        flagName  = self.language[-1]+'SharedLinkerFlag'
-        flagSubst = self.language[-1].upper()+'_LINKER_SLFLAG'
         dirname   = os.path.dirname(library).replace('\\ ',' ').replace(' ', '\\ ').replace('\\(','(').replace('(', '\\(').replace('\\)',')').replace(')', '\\)')
         if dirname in self.sysDirs:
           return [library]
         if with_rpath and not dirname in self.rpathSkipDirs:
           if hasattr(self.setCompilers, flagName) and not getattr(self.setCompilers, flagName) is None:
-            return [getattr(self.setCompilers, flagName)+dirname,'-L'+dirname,'-l'+name]
+            import pathlib
+            if pathlib.Path(library).suffix[1:].isnumeric(): # libfoo.so.1.0
+              return [getattr(self.setCompilers, flagName)+dirname,library]
+            else:
+              return [getattr(self.setCompilers, flagName)+dirname,'-L'+dirname,'-l'+name]
           if flagSubst in self.argDB:
             return [self.argDB[flagSubst]+dirname,'-L'+dirname,'-l'+name]
         return ['-L'+dirname,'-l'+name]
@@ -182,10 +200,10 @@ def genPreamble(f, funcName):
           pre = prototype[f]
       else:
         # We use char because int might match the return type of a gcc2 builtin and its argument prototype would still apply.
-        pre = 'char '+funcName+'();'
+        pre = 'char '+funcName+'(void);'
       # Capture the function call in a static function so that any local variables are isolated from
       # calls to other library functions.
-      return pre + '\nstatic void _check_%s() { %s }' % (funcName, genCall(f, funcName, pre=True))
+      return pre + '\nstatic void _check_%s(void) { %s }' % (funcName, genCall(f, funcName, pre=True))
     def genCall(f, funcName, pre=False):
       if self.language[-1] != 'FC' and not pre:
         return '_check_' + funcName + '();'
@@ -302,10 +320,10 @@ def checkMath(self):
                   '#include <stdio.h>\ndouble floor(double);',
                   '#include <stdio.h>\ndouble log10(double);',
                   '#include <stdio.h>\ndouble pow(double, double);']
-    calls = ['double x,y; int s = scanf("%lf",&x); y = sin(x); printf("%f %d",y,s);\n',
-             'double x,y; int s = scanf("%lf",&x); y = floor(x); printf("%f %d",y,s);\n',
-             'double x,y; int s = scanf("%lf",&x); y = log10(x); printf("%f %d",y,s);\n',
-             'double x,y; int s = scanf("%lf",&x); y = pow(x,x); printf("%f %d",y,s);\n']
+    calls = ['double x,y; int s = scanf("%lf",&x); y = sin(x); printf("%f %d",y,s)',
+             'double x,y; int s = scanf("%lf",&x); y = floor(x); printf("%f %d",y,s)',
+             'double x,y; int s = scanf("%lf",&x); y = log10(x); printf("%f %d",y,s)',
+             'double x,y; int s = scanf("%lf",&x); y = pow(x,x); printf("%f %d",y,s)']
     if self.check('', funcs, prototype = prototypes, call = calls):
       self.math = []
     elif self.check('m', funcs, prototype = prototypes, call = calls):
@@ -348,11 +366,11 @@ def checkMathLgamma(self):
 
   def checkMathFenv(self):
     '''Checks if <fenv.h> can be used with FE_DFL_ENV'''
-    if not self.math is None and self.check(self.math, ['fesetenv'], prototype = ['#include <fenv.h>'], call = ['fesetenv(FE_DFL_ENV);']):
+    if not self.math is None and self.check(self.math, ['fesetenv'], prototype = ['#include <fenv.h>'], call = ['fesetenv(FE_DFL_ENV)']):
       self.addDefine('HAVE_FENV_H', 1)
     else:
       self.logPrint('<fenv.h> with FE_DFL_ENV not found')
-    if not self.math is None and self.check(self.math, ['feclearexcept'], prototype = ['#include <fenv.h>'], call = ['feclearexcept(FE_INEXACT);']):
+    if not self.math is None and self.check(self.math, ['feclearexcept'], prototype = ['#include <fenv.h>'], call = ['feclearexcept(FE_INEXACT)']):
       self.addDefine('HAVE_FE_VALUES', 1)
     else:
       self.logPrint('<fenv.h> with FE_INEXACT not found')
@@ -372,7 +390,7 @@ def checkRealtime(self):
     self.rt = None
     funcs = ['clock_gettime']
     prototypes = ['#include <time.h>']
-    calls = ['struct timespec tp; clock_gettime(CLOCK_REALTIME,&tp);']
+    calls = ['struct timespec tp; clock_gettime(CLOCK_REALTIME,&tp)']
     if self.check('', funcs, prototype=prototypes, call=calls):
       self.logPrint('realtime functions are linked in by default')
       self.rt = []