Merge pull request #16 from firedrakeproject/angus-g/upstream-20231013

Merge upstream

config/BuildSystem/config/package.py

@@ -1227,7 +1227,7 @@ def infinitePatch(str):
 {x}
 #define  PetscXstr_(s) PetscStr_(s)
 #define  PetscStr_(s)  #s
-char     *ver = "petscpkgver(" PetscXstr_({y}) ")";
+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);
@@ -1241,20 +1241,18 @@ def infinitePatch(str):
       return
     self.popLanguage()
     setattr(self.compilers, flagsArg,oldFlags)
-    #strip #lines
-    output = re.sub('#.*\n','\n',output)
-    #strip newlines,spaces,quotes
-    output = re.sub('[\n "]*','',output)
-    #strip backslash. Mumps' version macro already has "" around it, giving output: char *ver = petscpkgver(" "\"5.4.1\"" ")";
-    output = output.replace('\\','')
-    #now split over ';'
-    loutput = output.split(';')
+    # 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 = ''
-    for i in loutput:
-      if i.find('petscpkgver') >=0:
-        self.log.write('Found version string: ' + i +'\n')
-        version = i.split('(')[1].split(')')[0]
-        break
+    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\"" ")";
+      for char in ['\\', ' ', '"']:
+          verLine = verLine.replace(char, '')
+      # get the string between the outer ()
+      version = verLine.split('(', 1)[-1].rsplit(')',1)[0]
+      self.log.write('This is the processed version string: ' + version +'\n')
     if not version:
       self.log.write('For '+self.package+' unable to find version information: output below, skipping version check\n')
       self.log.write(output)

config/BuildSystem/config/packages/cmake.py

@@ -4,7 +4,7 @@
 class Configure(config.package.GNUPackage):
   def __init__(self, framework):
     config.package.GNUPackage.__init__(self, framework)
-    self.version            = '3.27.6'
+    self.version            = '3.27.7'
     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',

config/BuildSystem/config/packages/hip.py

@@ -8,8 +8,9 @@ class Configure(config.package.Package):
   def __init__(self, framework):
     config.package.Package.__init__(self, framework)
 
-    self.minversion       = '4.1'
-    self.versionname      = 'HIP_VERSION_MAJOR.HIP_VERSION_MINOR'
+    self.minversion       = '4.1.0'
+    # HIP_VERSION_PATCH (e.g., 31061) is not necessarily the AMD advertised patch version, e.g., in 5.6.0
+    self.versionname      = 'HIP_VERSION_MAJOR.HIP_VERSION_MINOR.HIP_VERSION_PATCH'
     self.versioninclude   = 'hip/hip_version.h'
     self.requiresversion  = 1
     self.functionsCxx     = [1,'', 'rocblas_create']

config/BuildSystem/config/packages/hpddm.py

@@ -4,7 +4,7 @@ class Configure(config.package.Package):
   def __init__(self,framework):
     config.package.Package.__init__(self,framework)
     self.version                = '2.2.4'
-    self.gitcommit              = 'v'+self.version # main sep-15-2023
+    self.gitcommit              = '69bebeece9139b59524c70b88b60ccd4fba8a16a' # fix-saddle oct-10-2023
     self.download               = ['git://https://github.com/hpddm/hpddm','https://github.com/hpddm/hpddm/archive/'+self.gitcommit+'.tar.gz']
     self.minversion             = '2.2.1'
     self.versionname            = 'HPDDM_VERSION'

config/BuildSystem/config/packages/mpi4py.py

@@ -5,7 +5,7 @@
 class Configure(config.package.Package):
   def __init__(self, framework):
     config.package.Package.__init__(self, framework)
-    self.download          = ['https://github.com/mpi4py/mpi4py/releases/download/3.1.4/mpi4py-3.1.4.tar.gz']
+    self.download          = ['https://github.com/mpi4py/mpi4py/releases/download/3.1.5/mpi4py-3.1.5.tar.gz']
     self.functions         = []
     self.includes          = []
     self.useddirectly      = 0

config/BuildSystem/config/packages/sycl.py

@@ -6,9 +6,8 @@ def __init__(self, framework):
     config.package.Package.__init__(self, framework)
     self.minversion       = '20200101'
     self.versionname      = '__SYCL_COMPILER_VERSION' # The build date of the SYCL library, presented in the format YYYYMMDD.
-    self.versioninclude   = 'CL/sycl/version.hpp'
-    # CL/sycl.h is dpcpp.  Other SYCL impls may use SYCL/sycl.hpp -- defer
-    self.includes         = ['CL/sycl.hpp']
+    self.versioninclude   = 'sycl/version.hpp'
+    self.includes         = ['sycl/sycl.hpp']
     self.includedir       = 'include/sycl'
     self.functionsCxx     = [1,'namespace sycl = cl;','sycl::device::get_devices()']
     # Unlike CUDA or HIP, the blas issues are just part of MKL and handled as such.

config/BuildSystem/config/packages/zlib.py

@@ -3,9 +3,10 @@
 class Configure(config.package.Package):
   def __init__(self, framework):
     config.package.Package.__init__(self, framework)
-    self.version      = '1.2.13'
+    self.version      = '1.3'
     self.versionname  = 'ZLIB_VERSION'
     self.download     = ['http://www.zlib.net/zlib-'+self.version+'.tar.gz',
+                         'https://github.com/madler/zlib/releases/download/v'+self.version+'/zlib-'+self.version+'.tar.gz',
                          'https://web.cels.anl.gov/projects/petsc/download/externalpackages/zlib-'+self.version+'.tar.gz']
     self.functions    = ['compress', 'uncompress']
     self.includes     = ['zlib.h']
@@ -44,7 +45,7 @@ def Install(self):
     self.log.write('zlibDir = '+self.packageDir+' installDir '+self.installDir+'\n')
     self.logPrintBox('Building and installing zlib; this may take several minutes')
     try:
-      output,err,ret  = config.base.Configure.executeShellCommand('cd '+self.packageDir+' && ' + args + ' ./configure '+cargs+' && '+self.make.make_jnp+' && '+self.make.make+' install', timeout=600, log = self.log)
+      output,err,ret = config.base.Configure.executeShellCommand('cd '+self.packageDir+' && ' + args + ' ./configure '+cargs+' && '+self.make.make_jnp+' && '+self.make.make+' install', timeout=600, log = self.log)
     except RuntimeError as e:
       raise RuntimeError('Error building/install zlib files from '+os.path.join(self.packageDir, 'zlib')+' to '+self.packageDir)
     self.postInstall(output+err,conffile)

doc/changes/dev.rst

@@ -41,6 +41,8 @@ Changes: Development
 
 .. rubric:: PC:
 
+- Add ``PCGAMGSetLowMemoryFilter()`` with corresponding option ``-pc_gamg_low_memory_threshold_filter``. Use the system ``MatFilter`` graph/matrix filter, without a temporary copy of the graph, otherwise use method that can be faster
+
 .. rubric:: KSP:
 
 .. rubric:: SNES:

doc/faq/index.rst

@@ -669,8 +669,8 @@ PETSc also contains a balancing Neumann-Neumann type preconditioner, see the man
 for ``PCBDDC``. This requires matrices be constructed with ``MatCreateIS()`` via the finite
 element method. See ``src/ksp/ksp/tests/ex59.c`` for an example.
 
-You have ``MATAIJ`` and ``MATBAIJ`` matrix formats, and ``MATSBAIJ`` for symmetric storage, how come no `MATSAIJ``?
--------------------------------------------------------------------------------------------------------------------
+You have ``MATAIJ`` and ``MATBAIJ`` matrix formats, and ``MATSBAIJ`` for symmetric storage, how come no ``MATSAIJ``?
+--------------------------------------------------------------------------------------------------------------------
 
 Just for historical reasons; the ``MATSBAIJ`` format with blocksize one is just as efficient as
 a `MATSAIJ` would be.

doc/manual/ksp.rst

@@ -1484,7 +1484,7 @@ scaling, available via the command line switch
 ``PCISSetSubdomainScalingFactor()``,
 ``PCISSetSubdomainDiagonalScaling()`` or
 ``PCISSetUseStiffnessScaling()``. However, the convergence properties of
-the `PCBDDC`` method degrades in presence of large jumps in the material
+the ``PCBDDC`` method degrades in presence of large jumps in the material
 coefficients not aligned with the interface; for such cases, PETSc has
 the capability of adaptively computing the primal constraints. Adaptive
 selection of constraints could be requested by specifying a threshold

doc/manual/mat.rst

@@ -209,7 +209,7 @@ Note that for
 most PETSc matrices the values returned by ``MatGetOwnershipIS()`` are the same as those returned by  ``MatGetOwnershipRange()`` and
 ``MatGetOwnershipRangeColumn()``.
 
-The PETSc object ``PetscLayout`` contains the ownership information that is provided by ``VecGetOwnershipRange()`` and with ``MatGetOwnershipRange()``, ``MatGetOwnershipRangeColumn()``. Each vector has one layout, which can be obtained with ``VecGetLayout()`` and ``MatGetLayouts()``. Layouts support the routines ``PetscLayoutGetLocalSize()``, ``PetscLayoutGetSize()``, ``PetscLayoutGetBlockSize()``, ``PetscLayoutGetRanges()``, ``PetscLayoutCompare()`` as well as a variety of creation routines. These are used by the ``Vec`` and ``Mat`` and so are rarely needed directly. Finally ``PetscSplitOwnership()`` is a utility routine that does the same splitting of ownership ranges as `PetscLayout``.
+The PETSc object ``PetscLayout`` contains the ownership information that is provided by ``VecGetOwnershipRange()`` and with ``MatGetOwnershipRange()``, ``MatGetOwnershipRangeColumn()``. Each vector has one layout, which can be obtained with ``VecGetLayout()`` and ``MatGetLayouts()``. Layouts support the routines ``PetscLayoutGetLocalSize()``, ``PetscLayoutGetSize()``, ``PetscLayoutGetBlockSize()``, ``PetscLayoutGetRanges()``, ``PetscLayoutCompare()`` as well as a variety of creation routines. These are used by the ``Vec`` and ``Mat`` and so are rarely needed directly. Finally ``PetscSplitOwnership()`` is a utility routine that does the same splitting of ownership ranges as ``PetscLayout``.
 
 
 .. _sec_matsparse:

gmakefile

@@ -64,7 +64,7 @@ $(generated) : $(petscconf) $(petscvariables) config/gmakegen.py
 	$(PYTHON) ./config/gmakegen.py --petsc-arch=$(PETSC_ARCH)
 
 # Skip including generated files (which triggers rebuilding them) when we're just going to clean anyway.
-ifneq ($(filter-out alletags deletefortranstubs allfortranstubs allfortranstubsinplace help clean check info gmakeinfo,$(MAKECMDGOALS:clean%=clean)),)
+ifneq ($(filter-out alletags deletefortranstubs allfortranstubs allfortranstubsinplace help clean distclean check info gmakeinfo,$(MAKECMDGOALS:clean%=clean)),)
 include $(generated)
 endif
 

gmakefile.test

@@ -101,7 +101,7 @@ endif
 $(generatedtest) : $(petscconf) $(petscvariables) $(CONFIGDIR)/gmakegentest.py $(TESTDIR)/.DIR | $$(@D)/.DIR
 	$(PYTHON) $(CONFIGDIR)/gmakegentest.py --petsc-dir=$(PETSC_DIR) --petsc-arch=$(PETSC_ARCH) --testdir=$(TESTDIR) --srcdir $(TESTSRCDIR) --pkg-pkgs "$(pkgs)"
 
-ifneq ($(filter-out help docs clean check info gmakeinfo libs all install install-lib checkbadSource checkbadFileChange deletefortranstubs allfortranstubs allfortranstubsinplace alletags clangformat checkclangformat get%,$(MAKECMDGOALS:clean%=clean)),)
+ifneq ($(filter-out help docs clean distclean check info gmakeinfo libs all install install-lib checkbadSource checkbadFileChange deletefortranstubs allfortranstubs allfortranstubsinplace alletags clangformat checkclangformat get%,$(MAKECMDGOALS:clean%=clean)),)
 include $(generatedtest)
 endif
 

include/petscpc.h

@@ -341,6 +341,7 @@ PETSC_EXTERN PetscErrorCode PCGAMGCreateGraph(PC, Mat, Mat *);
 PETSC_EXTERN PetscErrorCode PCGAMGSetAggressiveSquareGraph(PC, PetscBool);
 PETSC_EXTERN PetscErrorCode PCGAMGMISkSetMinDegreeOrdering(PC, PetscBool);
 PETSC_EXTERN PetscErrorCode PCGAMGMISkSetAggressive(PC, PetscInt);
+PETSC_EXTERN PetscErrorCode PCGAMGSetLowMemoryFilter(PC, PetscBool);
 
 PETSC_EXTERN PetscErrorCode PCGAMGClassicalSetType(PC, PCGAMGClassicalType);
 PETSC_EXTERN PetscErrorCode PCGAMGClassicalGetType(PC, PCGAMGClassicalType *);

lib/petsc/conf/rules.doc

@@ -87,7 +87,7 @@ manualpages:
 html:
 	-@export htmlmap_tmp=$$(mktemp) ;\
           petsc_dir=$$(realpath ${PETSC_DIR}); LOCDIR=$$(pwd | sed s"?$${petsc_dir}/??"g)/; \
-          sed -e s?man+manualpages/?man+ROOT/manualpages/? ${HTMLMAP} > $$htmlmap_tmp ;\
+          sed -e s?man+manualpages/?man+HTML_ROOT/manualpages/? ${HTMLMAP} > $$htmlmap_tmp ;\
           cat ${PETSC_DIR}/doc/classic/mpi.www.index >> $$htmlmap_tmp ;\
           ROOT=`echo $${LOCDIR} | sed -e s?/[-a-z_0-9]*?/..?g -e s?src/??g -e s?include/??g` ;\
           loc=`pwd | sed -e s?\$${PETSC_DIR}?$${LOC}/?g -e s?/disks??g`;  \
@@ -112,7 +112,7 @@ html:
               awk '{ sub(/<pre width="80">/,"<pre width=\"80\">\n"); print }' | \
               ${PYTHON} ${PETSC_DIR}/lib/petsc/bin/maint/fixinclude.py $$i $${PETSC_DIR} | \
               grep -E -v '(PetscValid|#if !defined\(__|#define __|#undef __|EXTERN_C )' | \
-              ${MAPNAMES} -map $$htmlmap_tmp -inhtml | sed -e s?ROOT?$${IROOT}?g >> $${loc}/$$i.html ; \
+              ${MAPNAMES} -map $$htmlmap_tmp -inhtml | sed -e s?HTML_ROOT?$${IROOT}?g >> $${loc}/$$i.html ; \
             fi; \
           done ;\
           loc=`pwd | sed -e s?\$${PETSC_DIR}?$${LOC}/?g -e s?/disks??g`; ${RM} $${loc}/index.html; \

makefile

@@ -291,9 +291,12 @@ clean:: allclean
 distclean:
 	@if [ -f ${PETSC_DIR}/${PETSC_ARCH}/lib/petsc/conf/reconfigure-${PETSC_ARCH}.py ]; then \
 	  echo "*** Preserving ${PETSC_DIR}/${PETSC_ARCH}/lib/petsc/conf/reconfigure-${PETSC_ARCH}.py in ${PETSC_DIR} ***"; \
-          mv -f ${PETSC_DIR}/${PETSC_ARCH}/lib/petsc/conf/reconfigure-${PETSC_ARCH}.py ${PETSC_DIR}/; fi
-	@echo "*** Deleting all build files in ${PETSC_DIR}/${PETSC_ARCH} ***"
-	-${RM} -rf ${PETSC_DIR}/${PETSC_ARCH}/
+          mv -f ${PETSC_DIR}/${PETSC_ARCH}/lib/petsc/conf/reconfigure-${PETSC_ARCH}.py ${PETSC_DIR}/; \
+	  echo "*** Deleting all build files in ${PETSC_DIR}/${PETSC_ARCH} ***"; \
+	  ${RM} -rf ${PETSC_DIR}/${PETSC_ARCH}/ ; \
+        else  \
+	  echo "*** Build files in PETSC_ARCH=${PETSC_ARCH} not found. Skipping delete! ***"; \
+        fi
 
 info:
 	+@${OMAKE} -f gmakefile gmakeinfo

src/binding/petsc4py/src/lib-petsc/custom.h

@@ -359,6 +359,67 @@ PetscErrorCode KSPConverged(KSP ksp,PetscInt iter,PetscReal rnorm,KSPConvergedRe
   PetscFunctionReturn(PETSC_SUCCESS);
 }
 
+typedef struct {
+  PetscBool prepend_custom;
+  PetscErrorCode (*convtest)(KSP, PetscInt, PetscReal, KSPConvergedReason *, void *);
+  PetscErrorCode (*convdestroy)(void *);
+  PetscErrorCode (*convtestcustom)(KSP, PetscInt, PetscReal, KSPConvergedReason *, void *);
+  void *convctx;
+} KSPConvergedNativeCtx;
+
+static
+PetscErrorCode KSPConvergedNative_Private(KSP ksp, PetscInt n, PetscReal rnorm, KSPConvergedReason *reason, void *cctx)
+{
+  KSPConvergedNativeCtx *ctx = (KSPConvergedNativeCtx *)cctx;
+
+  PetscFunctionBegin;
+  *reason = KSP_CONVERGED_ITERATING;
+  if (ctx->prepend_custom) {
+    PetscCall((*ctx->convtestcustom)(ksp, n, rnorm, reason, NULL));
+    if (*reason) {
+      PetscCall(PetscInfo(ksp, "User provided prepended Python convergence test reason %s KSP iterations=%" PetscInt_FMT ", rnorm=%g\n", KSPConvergedReasons[*reason], n, (double)rnorm));
+      PetscFunctionReturn(PETSC_SUCCESS);
+    }
+  }
+  PetscCall((*ctx->convtest)(ksp, n, rnorm, reason, ctx->convctx));
+  if (*reason) {
+    PetscCall(PetscInfo(ksp, "Default convergence test reason %s KSP iterations=%" PetscInt_FMT ", rnorm=%g\n", KSPConvergedReasons[*reason], n, (double)rnorm));
+    PetscFunctionReturn(PETSC_SUCCESS);
+  }
+  if (!ctx->prepend_custom) {
+    PetscCall((*ctx->convtestcustom)(ksp, n, rnorm, reason, NULL));
+    if (*reason) PetscCall(PetscInfo(ksp, "User provide appended Python convergence test reason %s KSP iterations=%" PetscInt_FMT ", rnorm=%g\n", KSPConvergedReasons[*reason], n, (double)rnorm));
+  }
+  PetscFunctionReturn(PETSC_SUCCESS);
+}
+
+static PetscErrorCode KSPConvergedNative_Destroy(void *cctx)
+{
+  KSPConvergedNativeCtx *ctx = (KSPConvergedNativeCtx *)cctx;
+
+  PetscFunctionBegin;
+  PetscCheck(ctx, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Missing context");
+  if (ctx->convdestroy) PetscCall((*ctx->convdestroy)(ctx->convctx));
+  PetscCall(PetscFree(ctx));
+  PetscFunctionReturn(PETSC_SUCCESS);
+}
+
+static
+PetscErrorCode KSPAddConvergenceTest(KSP ksp, PetscErrorCode (*custom)(KSP, PetscInt, PetscReal, KSPConvergedReason *, void *), PetscBool prepend)
+{
+  KSPConvergedNativeCtx *ctx;
+
+  PetscFunctionBegin;
+  PetscValidHeaderSpecific(ksp,KSP_CLASSID,1);
+  PetscValidLogicalCollectiveBool(ksp,prepend,3);
+  PetscCall(PetscNew(&ctx));
+  ctx->convtestcustom = custom;
+  ctx->prepend_custom = prepend;
+  PetscCall(KSPGetAndClearConvergenceTest(ksp, &ctx->convtest, &ctx->convctx, &ctx->convdestroy));
+  PetscCall(KSPSetConvergenceTest(ksp, KSPConvergedNative_Private, ctx, KSPConvergedNative_Destroy));
+  PetscFunctionReturn(PETSC_SUCCESS);
+}
+
 static
 PetscErrorCode KSPLogHistory(KSP ksp,PetscReal rnorm)
 {