Merge remote-tracking branch 'upstream/main' into connorjward/upstream-update

Author: connorjward

config/install.py

@@ -584,7 +584,11 @@ def runcopy(self):
 
   def runfix(self):
     self.fixConf()
-    if os.environ.get('PEP517_BUILD_BACKEND'):
+    using_build_backend = any(
+      os.environ.get(prefix + '_BUILD_BACKEND')
+      for prefix in ('_PYPROJECT_HOOKS', 'PEP517')
+    )
+    if using_build_backend:
       self.fixPythonWheel()
     return
 

config/packages/hpddm.py

@@ -17,7 +17,7 @@ def __init__(self,argdb,log):
     package.Package.__init__(self,argdb,log)
     self.packagename    = 'hpddm'
     self.downloadable   = True
-    self.gitcommit      = '28add19c6968c41497468f4f4ac156196b051ea9'
+    self.gitcommit      = '66c82a45db9fb64ece5a69de8b4d27896b96c30e'
     # self.version        = '2.3.0'
     obj = self.version if hasattr(self,'version') else self.gitcommit
     self.url            = 'https://github.com/hpddm/hpddm/archive/'+('v'+obj if hasattr(self,'version') else obj)+'.tar.gz'

config/packages/slepc.py

@@ -55,7 +55,7 @@ def Process(self,slepcconf,slepcvars,slepcrules,slepc,petsc,archdir=''):
     self.AddDefine(slepcconf,'PETSC_ARCH',petsc.arch)
     self.AddDefine(slepcconf,'DIR',slepc.dir)
     self.AddDefine(slepcconf,'LIB_DIR',os.path.join(slepc.prefixdir,'lib'))
-    if slepc.isrepo:
+    if slepc.isrepo and slepc.gitrev != 'unknown':
       self.AddDefine(slepcconf,'VERSION_GIT',slepc.gitrev)
       self.AddDefine(slepcconf,'VERSION_DATE_GIT',slepc.gitdate)
       self.AddDefine(slepcconf,'VERSION_BRANCH_GIT',slepc.branch)
@@ -69,7 +69,7 @@ def Process(self,slepcconf,slepcvars,slepcrules,slepc,petsc,archdir=''):
 
   def ShowInfo(self):
     self.log.Println('\nSLEPc directory:\n  '+self.dir)
-    if self.isrepo:
+    if self.isrepo and self.gitrev != 'unknown':
       self.log.Println('  It is a git repository on branch: '+self.branch)
     if self.isinstall:
       self.log.Println('SLEPc prefix directory:\n  '+self.prefixdir)
@@ -110,28 +110,36 @@ def LoadVersion(self):
     # Check whether this is a working copy of the repository
     self.isrepo = False
     if os.path.exists(os.path.join(self.dir,'src','docs')):
+      self.log.write('This appears to be a repository clone - src/docs exists')
       self.isrepo = True
-      (status, output) = self.RunCommand('git help')
-      if status:
-        self.log.Warn('SLEPC_DIR appears to be a git working copy, but git is not found in PATH')
-        self.gitrev = 'unknown'
-        self.gitdate = 'unknown'
-        self.branch = 'unknown'
-      else:
-        (status, output) = self.RunCommand('git rev-parse')
+      if os.path.exists(os.path.join(self.dir,'.git')):
+        self.log.write('.git directory exists')
+        (status, output) = self.RunCommand('git help')
         if status:
-          self.log.Warn('SLEPC_DIR appears to be a git working copy, but the .git folder is missing')
+          self.log.Warn('SLEPC_DIR appears to be a git working copy, but git is not found in PATH')
           self.gitrev = 'unknown'
           self.gitdate = 'unknown'
           self.branch = 'unknown'
         else:
-          (status, self.gitrev) = self.RunCommand('git describe')
+          (status, self.gitrev) = self.RunCommand('git describe --match=v*')
           if not self.gitrev:
             (status, self.gitrev) = self.RunCommand('git log -1 --pretty=format:%H')
           (status, self.gitdate) = self.RunCommand('git log -1 --pretty=format:%ci')
           (status, self.branch) = self.RunCommand('git describe --contains --all HEAD')
           if status:
-            self.branch = 'unknown'
+            (status, self.branch) = self.RunCommand('git rev-parse --abbrev-ref HEAD')
+            if status:
+              self.branch = 'unknown'
+      else:
+        self.log.write('This repository clone is obtained as a tarball as no .git dirs exist')
+        self.gitrev = 'unknown'
+        self.gitdate = 'unknown'
+        self.branch = 'unknown'
+    else:
+      if os.path.exists(os.path.join(self.dir,'.git')):
+        self.log.Exit('Your SLEPc source tree is broken. Use "git status" to check, or remove the entire directory and start all over again')
+      else:
+        self.log.write('This is a tarball installation')
 
   def CreateFile(self,basedir,fname):
     ''' Create file basedir/fname and return path string '''

config/packages/sowing.py

@@ -18,8 +18,8 @@ def __init__(self,argdb,log):
     self.packagename  = 'sowing'
     self.downloadable = True
     self.inplace      = False
-    #self.gitcommit    = '2fe1f1f12257b274cbb0b4425f2994965bcc9bde'
-    self.version      = '1.1.26.9'
+    #self.gitcommit    = '3a410fa51a7bb531676f16deb8bc0c1ded8293c3'
+    self.version      = '1.1.26.12'
     obj = self.version if hasattr(self,'version') else self.gitcommit
     self.url          = 'https://bitbucket.org/petsc/pkg-sowing/get/'+('v'+obj if hasattr(self,'version') else obj)+'.tar.gz'
     self.archive      = 'sowing-'+obj+'.tar.gz'
@@ -69,7 +69,7 @@ def Process(self,slepcconf,slepcvars,slepcrules,slepc,petsc,archdir=''):
         self.log.write('Using BFORT='+bfort)
         sys.path.insert(0, os.path.abspath(os.path.join('lib','slepc','bin','maint')))
         import generatefortranstubs
-        generatefortranstubs.main(slepc.dir,'' if self.inplace else petsc.archname,bfort,os.path.join(slepc.dir,'src'),0)
+        generatefortranstubs.main(slepc.dir,'' if self.inplace else petsc.archname,bfort,slepc.dir,0)
         generatefortranstubs.processf90interfaces(slepc.dir,'' if self.inplace else petsc.archname,0)
       except:
         self.log.Exit('Try configuring with --download-sowing or use a Git version of PETSc')

gmakefile.test

@@ -289,7 +289,11 @@ $(foreach pkg, $(pkgs), $(call concattestlang,$(pkg),F F90)) : $(libslepcall)
 # Testing convenience targets
 .PHONY: test pre-clean
 
-test: report_tests
+# The Fortran compiler may use out-dated module files in the tutorial and test directories so delete them all
+remove-test-mod-files:
+	-@find src -name "*.mod" -not -path "src/binding/*" -delete
+
+test: remove-test-mod-files report_tests
 
 pre-clean:
 	@$(RM) -rf $(TESTDIR)/counts $(TESTLOGTAPFILE) $(TESTLOGERRFILE)

include/slepc/private/slepcimpl.h

@@ -17,7 +17,7 @@
 
 SLEPC_INTERN PetscBool SlepcBeganPetsc;
 
-/*@C
+/*MC
     SlepcHeaderCreate - Creates a SLEPc object
 
     Input Parameters:
@@ -37,7 +37,7 @@ SLEPC_INTERN PetscBool SlepcBeganPetsc;
     has been called.
 
     Level: developer
-@*/
+M*/
 #define SlepcHeaderCreate(h,classid,class_name,descr,mansec,comm,destroy,view) \
     ((PetscErrorCode)((!SlepcInitializeCalled && \
                        PetscError(comm,__LINE__,PETSC_FUNCTION_NAME,__FILE__,PETSC_ERR_ORDER,PETSC_ERROR_INITIAL, \

lib/slepc/bin/maint/generatefortranstubs.py

@@ -28,9 +28,9 @@ def findLineCol(filename, string):
 
   data = re.subn('\00','',data)[0]
   data = re.subn('\nvoid ','\nSLEPC_EXTERN void ',data)[0]
-  data = re.subn('\nPetscErrorCode ','\nSLEPC_EXTERN void ',data)[0]
+  data = re.subn('\n[ ]*PetscErrorCode ','\nSLEPC_EXTERN void ',data)[0]
   data = re.subn(r'Petsc([ToRm]*)Pointer\(int\)','Petsc\\1Pointer(void*)',data)[0]
-  data = re.subn(r'PetscToPointer\(a\) \(a\)','PetscToPointer(a) (*(PetscFortranAddr *)(a))',data)[0]
+  data = re.subn(r'PetscToPointer\(a\) \(a\)','PetscToPointer(a) (a ? *(PetscFortranAddr *)(a) : 0)',data)[0]
   data = re.subn(r'PetscFromPointer\(a\) \(int\)\(a\)','PetscFromPointer(a) (PetscFortranAddr)(a)',data)[0]
   data = re.subn(r'PetscToPointer\( \*\(int\*\)','PetscToPointer(',data)[0]
   data = re.subn('MPI_Comm comm','MPI_Comm *comm',data)[0]
@@ -46,6 +46,7 @@ def findLineCol(filename, string):
   with open(filename, 'w') as ff:
     ff.write('#include "petscsys.h"\n#include "petscfix.h"\n#include "petsc/private/fortranimpl.h"\n'+data)
 
+  # https://gitlab.com/petsc/petsc/-/issues/360#note_231598172
   l, c = findLineCol(filename, '\00')
   if l > 0: print('WARNING: Found null character in generated Fortran stub file after generatefortranstubs.py processing:\n  %s:%d:%d\n' % (filename, l, c))
 
@@ -96,7 +97,6 @@ def FixDir(petscdir,petscarch,parentdir,dir,verbose):
   inbuf = fd.read()
   fd.close()
   cppflags = ""
-  libbase = ""
 
   # new makefile will be created from outbuf
   outbuf  =  '\n'
@@ -115,6 +115,10 @@ def FixDir(petscdir,petscarch,parentdir,dir,verbose):
     if line.find('MANSEC') >=0 and not line.find('SUBMANSEC') >=0:
       mansec = line.split('=')[1].lower().strip()
 
+  # this is a hack for the include directory and will be wrong for any
+  # non-sys static include functions
+  if mansec == 'unknown': mansec = 'sys'
+  if submansec == 'unknown': submansec = 'sys'
   if not bfortsubmansec == 'unknown':
     submansec = bfortsubmansec
 
@@ -135,7 +139,6 @@ def FixDir(petscdir,petscarch,parentdir,dir,verbose):
       txt = fd.read()
       fd.close()
       if txt:
-        if mansec == 'unknown': raise RuntimeError("Cannot have unknown mansec in " + parentdir)
         if mansec in ['bv','ds','fn','rg','st']:
           basedir = os.path.join(petscdir,petscarch,'src','sys','classes',mansec,'f90-mod','ftn-auto-interfaces')
         else:
@@ -165,6 +168,7 @@ def processDir(petscdir, petscarch, bfort, verbose, dirpath, dirnames, filenames
   ''' Runs bfort on a directory and then fixes the files generated by bfort including moving generated F90 fortran interface files'''
   if not dirpath.startswith(petscdir): raise RuntimeError("Error, the directory being processed "+dirpath+" does not begin with SLEPC_DIR "+petscdir)
   sdirpath = dirpath.replace(petscdir+'/','')
+  if sdirpath == 'include': sdirpath = os.path.join('src','sys')
   outdir = os.path.join(petscdir,petscarch,sdirpath,'ftn-auto')
   if filenames:
     PrepFtnDir(outdir)
@@ -247,22 +251,27 @@ def processf90interfaces(petscdir,petscarch,verbose):
           for sfile in os.listdir(tmpDir):
             if verbose: print('  Copying in '+sfile)
             with open(os.path.join(tmpDir,sfile),'r') as fdr:
-              for ibuf in fdr.read().split('      subroutine')[1:]:
+              buf =  fdr.read()
+              if buf.startswith('#if defined(PETSC_HAVE_FORTRAN_TYPE_STAR)'):
+                fd.write('#if defined(PETSC_HAVE_FORTRAN_TYPE_STAR)\n')
+              for ibuf in buf.split('      subroutine')[1:]:
                 ibuf = '      subroutine'+ibuf
                 ibuf = ibuf.replace('integer z','PetscErrorCode z')
                 ibuf = ibuf.replace('integer a ! MPI_Comm','MPI_Comm a ! MPI_Comm')
                 plist = [p for p in ptypes if ' '+p[1:]+' ' in ibuf]
+                if 'PetscObject' in ibuf: plist.append('tPetscObject')
                 if plist: ibuf = ibuf.replace(')',')\n       import '+','.join(set(plist)),1)
                 fd.write(ibuf)
         shutil.rmtree(tmpDir)
   # FixDir(petscdir,os.path.join(petscdir,'include','slepc','finclude','ftn-auto-interfaces'),verbose)
   return
 
 def main(petscdir,petscarch,bfort,dir,verbose):
-  for dirpath, dirnames, filenames in os.walk(dir, topdown=True):
-    filenames = [i for i in filenames if not i.find('#') > -1 and os.path.splitext(i)[1] in ['.c','.h','.cxx','.cu']]
-    dirnames[:] = [d for d in dirnames if d not in ['output','tutorials','tests','binding','benchmarks'] and not d.startswith('ftn-') and not d.startswith('f90-')]
-    processDir(petscdir, petscarch,bfort, verbose, dirpath, dirnames, filenames)
+  for p in [ os.path.join(dir,'include'), os.path.join(dir,'src') ]:
+    for dirpath, dirnames, filenames in os.walk(p, topdown=True):
+      filenames = [i for i in filenames if not i.find('#') > -1 and os.path.splitext(i)[1] in ['.c','.h','.cxx','.cu']]
+      dirnames[:] = [d for d in dirnames if d not in ['output', 'binding', 'tests', 'tutorials', 'yaml']]
+      processDir(petscdir, petscarch,bfort, verbose, dirpath, dirnames, filenames)
   return
 #
 # generatefortranstubs bfortexectuable -verbose            -----  generates fortran stubs for a directory and all its children
@@ -308,5 +317,5 @@ def not_empty(v):
     assert isinstance(args.bfort, (list, tuple))
     bfort_exec = args.bfort[0]
     assert isinstance(bfort_exec, str)
-    ret = main(args.slepc_dir, args.petsc_arch, bfort_exec, os.path.join(args.slepc_dir, 'src'), args.verbose)
+    ret = main(args.slepc_dir, args.petsc_arch, bfort_exec, args.slepc_dir, args.verbose)
   sys.exit(ret)

lib/slepc/conf/bfort-petsc.txt

@@ -3,9 +3,12 @@
 # petscao.h
 nativeptr AO
 
-# petscbag.h
+# petscbag.h  This is not a PETSc object
 nativeptr PetscBag
 
+# this is not a PETSc object
+native PetscSFNode
+
 # petscdt.h
 native    PetscDTNodeType
 
@@ -46,8 +49,6 @@ native    DMDALocalInfo
 native    DMDAInterpolationType
 native    DMDAElementType
 
-nativeptr PetscGLL
-
 # dmlabel.h
 nativeptr DMLabel
 
@@ -144,7 +145,6 @@ native    MatSTRUMPACKCompressionType
 
 # petscpc.h
 nativeptr PC
-nativeptr PCType
 
 native    PCSide
 native    PCJacobiType
@@ -176,7 +176,7 @@ nativeptr PetscConvEst
 native    SNESConvergedReason
 native    SNESLineSearchReason
 nativeptr MatMFFD
-nativeptr MatMFFDType
+native    MatMFFDType
 nativeptr SNESLineSearch
 native    SNESLineSearchOrder
 native    SNESNormSchedule
@@ -209,6 +209,9 @@ native    PetscOffset
 native    PetscFortranAddr
 native    PetscCount
 
+nativeptr PetscDevice
+nativeptr PetscDeviceContext
+
 native    PetscInt
 native    PetscInt64
 native    PetscObjectState
@@ -241,7 +244,7 @@ native    PetscReal
 
 
 native    MatScalar
-native    PetscObject
+nativeptr PetscObject
 native    PetscLogDouble
 
 nativeptr PetscMatlabEngine

setup.py

@@ -156,6 +156,32 @@ def config(prefix, dry_run=False):
     status = os.system(" ".join(command))
     if status != 0:
         raise RuntimeError(status)
+    # Fix SLEPc configuration
+    using_build_backend = any(
+        os.environ.get(prefix + '_BUILD_BACKEND')
+        for prefix in ('_PYPROJECT_HOOKS', 'PEP517')
+    )
+    if using_build_backend:
+        pdir = os.environ['SLEPC_DIR']
+        parch = os.environ['PETSC_ARCH']
+        if not parch:
+            makefile = os.path.join(pdir, 'lib', 'slepc', 'conf', 'slepcvariables')
+            with open(makefile, 'r') as mfile:
+                contents = mfile.readlines()
+            for line in contents:
+                if line.startswith('PETSC_ARCH'):
+                    parch = line.split('=')[1].strip()
+                    break
+        include = os.path.join(pdir, parch, 'include')
+        for filename in (
+            'slepcconf.h',
+        ):
+            filename = os.path.join(include, filename)
+            with open(filename, 'r') as old_fh:
+                contents = old_fh.read()
+            contents = contents.replace(prefix, '${SLEPC_DIR}')
+            with open(filename, 'w') as new_fh:
+                new_fh.write(contents)
 
 
 def build(dry_run=False):

src/eps/f90-mod/slepceps.h

@@ -11,8 +11,7 @@
 !
 #include "slepc/finclude/slepceps.h"
 
-      type tEPS
-        PetscFortranAddr:: v PETSC_FORTRAN_TYPE_INITIALIZE
+      type, extends(tPetscObject) :: tEPS
       end type tEPS
 
       EPS, parameter :: SLEPC_NULL_EPS = tEPS(0)