Merge pull request #24 from firedrakeproject/connorjward/merge-upstream

Merge upstream

config/BuildSystem/config/compilerFlags.py

@@ -155,8 +155,10 @@ def outputCompilerMacros(self):
       if out.find('__AVX2__') > -1 and out.find('__FMA__') > -1:
         self.text = self.text + 'Intel instruction sets utilizable by compiler:\n'
         self.text = self.text + '  AVX2\n'
-      if out.find('__AVX512__') > -1:
-        self.text = self.text + '  AVX512\n'
+      if out.find('__AVX512') > -1:
+        self.text = self.text + '  AVX512: '
+        self.text = self.text + ' '.join([i for i in out.split('__') if i.startswith('AVX512')])
+        self.text = self.text + '\n'
     except:
       pass
     for filename in [self.compilerDefines, self.compilerFixes, self.compilerSource, self.compilerObj]:
@@ -176,15 +178,14 @@ def checkIntelHardwareSupport(self):
     try:
       (out, err, ret) = Configure.executeShellCommand('lscpu', log = self.log)
     except:
-      try:
-        (out, err, ret) = Configure.executeShellCommand('sysctl -a', log = self.log)
-        if out.find('hw.optional.avx2_0: 1') > -1 and out.find('hw.optional.fma: 1') > -1:
-          self.text = self.text + 'Intel instruction sets found on CPU:\n'
-          self.text = self.text + '  AVX2\n'
-        if out.find('hw.optional.avx512f: 1') > -1:
-          self.text = self.text + '  AVX512\n'
-      except:
-        pass
+      out = ''
+    if out.find(' avx2 ') > -1 and out.find(' fma ') > -1:
+      self.text = self.text + 'Intel instruction sets found on CPU:\n'
+      self.text = self.text + '  AVX2\n'
+    if out.find(' avx512') > -1:
+      self.text = self.text + '  AVX512: '
+      self.text = self.text + ' '.join([i for i in out.split(' ') if i.startswith('avx512')])
+      self.text = self.text + '\n'
     return
 
   def configure(self):

config/BuildSystem/config/compilerOptions.py

@@ -12,7 +12,7 @@ def getCFlags(self, compiler, bopt, language):
     import config.setCompilers
 
     if language == 'C':
-      if [s for s in ['mpicc','mpiicc'] if os.path.basename(compiler).find(s)>=0]:
+      if [s for s in ['mpicc','mpiicc','mpiicx'] if os.path.basename(compiler).find(s)>=0]:
         try:
           output = self.executeShellCommand(compiler + ' -show', log = self.log)[0]
           self.framework.addMakeMacro('MPICC_SHOW',output.strip().replace('\n','\\\\n').replace('"','\\"'))
@@ -126,7 +126,7 @@ def getCFlags(self, compiler, bopt, language):
   def getCxxFlags(self, compiler, bopt, language):
     import config.setCompilers
 
-    if [s for s in ['mpiCC','mpic++','mpicxx','mpiicxx','mpiicpc'] if os.path.basename(compiler).find(s)>=0]:
+    if [s for s in ['mpiCC','mpic++','mpicxx','mpiicxx','mpiicpc','mpiicpx'] if os.path.basename(compiler).find(s)>=0]:
       try:
         output   = self.executeShellCommand(compiler+' -show', log = self.log)[0]
         self.framework.addMakeMacro('MPICXX_SHOW',output.strip().replace('\n','\\\\n'))
@@ -240,8 +240,7 @@ def getCxxFlags(self, compiler, bopt, language):
     return flags
 
   def getFortranFlags(self, compiler, bopt):
-
-    if [s for s in ['mpif77','mpif90','mpifort','mpiifort'] if os.path.basename(compiler).find(s)>=0]:
+    if [s for s in ['mpif77','mpif90','mpifort','mpiifort','mpiifx'] if os.path.basename(compiler).find(s)>=0]:
       try:
         output   = self.executeShellCommand(compiler+' -show', log = self.log)[0]
         self.framework.addMakeMacro('MPIFC_SHOW',output.strip().replace('\n','\\\\n'))

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                = '2.3.1'
-    self.gitcommit              = 'v'+self.version # main sep-25-2024
+    self.gitcommit              = '1813156fce13718da3ced5aeb2ebbb736a2227bd' # main oct-26-2024
     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/parmmg.py

@@ -11,6 +11,7 @@ def __init__(self, framework):
     self.liblist          = [['libparmmg.a']]
     self.functions        = ['PMMG_Free_all_var']
     self.precisions       = ['double']
+    self.requires32bitint = 1
     return
 
   def setupDependencies(self, framework):

config/BuildSystem/config/packages/petsc4py.py

@@ -123,15 +123,17 @@ def Install(self):
   def configureLibrary(self):
     import sys
     if not self.sharedLibraries.useShared and not self.setCompilers.isCygwin(self.log):
-        raise RuntimeError('petsc4py requires PETSc be built with shared libraries; rerun with --with-shared-libraries')
+      raise RuntimeError('petsc4py requires PETSc be built with shared libraries; rerun with --with-shared-libraries')
+    if sys.version_info < (3, 7):
+      raise RuntimeError('petsc4py requires Python 3.7 at least')
     chkpkgs = ['numpy']
     if sys.version_info >= (3, 12):
       chkpkgs.append('setuptools')
     npkgs  = []
     for pkg in chkpkgs:
       if not getattr(self.python,pkg): npkgs.append(pkg)
     if npkgs:
-      raise RuntimeError('PETSc4py requires Python with "%s" module(s) installed!\n'
+      raise RuntimeError('petsc4py requires Python with "%s" module(s) installed!\n'
                          'Please install using package managers - for ex: "apt" or "dnf" (on linux),\n'
                          'or with "pip" using: %s -m pip install %s' % (" ".join(npkgs), self.python.pyexe, " ".join(npkgs)))
     self.getInstallDir()

config/BuildSystem/config/setCompilers.py

@@ -1491,7 +1491,7 @@ def checkCCompiler(self):
     return
 
   def generateCPreprocessorGuesses(self):
-    '''Determines the C preprocessor from CPP, then --with-cpp, then the C compiler'''
+    '''Determines the C preprocessor from --with-cpp, then CPP, then the C compiler'''
     if 'with-cpp' in self.argDB:
       yield self.argDB['with-cpp']
     elif 'CPP' in self.argDB:

config/install.py

@@ -508,12 +508,13 @@ def copyLib(self, src, dst):
       return
     shutil.copy2(src, dst)
     if self.setCompilers.getCompiler().find('win32fe') < 0 and os.path.splitext(dst)[1] == '.'+self.arLibSuffix:
-      self.executeShellCommand(self.ranlib+' '+dst)
-    if os.path.splitext(dst)[1] == '.dylib' and os.path.isfile('/usr/bin/install_name_tool'):
-      [output,err,flg] = self.executeShellCommand("otool -D "+src)
+      import shlex
+      self.executeShellCommand(shlex.split(self.ranlib) + [dst])
+    if os.path.splitext(dst)[1] == '.dylib' and shutil.which('otool') and shutil.which('install_name_tool'):
+      [output,err,flg] = self.executeShellCommand(['otool', '-D', src])
       oldname = output[output.find("\n")+1:]
       installName = oldname.replace(os.path.realpath(self.archDir), self.installDir)
-      self.executeShellCommand('/usr/bin/install_name_tool -id ' + installName + ' ' + dst)
+      self.executeShellCommand(['install_name_tool', '-id', installName, dst])
     # preserve the original timestamps - so that the .a vs .so time order is preserved
     shutil.copystat(src,dst)
     return

doc/community/index.rst

@@ -4,6 +4,8 @@
 Community
 *********
 
+`Follow PETSc on BlueSky <https://bsky.app/profile/petsc.bsky.social>`__.
+
 PETSc is associated with `NumFOCUS <http://numfocus.org>`__, a 501(c)(3) nonprofit supporting open code and reproducible science, through which you can help support PETSc.
 
 .. image:: /images/community/numfocus.png

doc/community/meetings/2024/index.rst

@@ -15,21 +15,23 @@ Cologne, Germany; May 23-24, 2024
   :alt: PETSc User Meeting 2024 group photo
 
 Scientific committee:
+
 - Dr. Pierre Jolivet            Sorbonne Université, CNRS
 
-- Prof. Dr. Axel Klawonn	University of Cologne
+- Prof. Dr. Axel Klawonn        University of Cologne
 
-- Prof. Dr. Matthew Knepley	University at Buffalo
+- Prof. Dr. Matthew Knepley     University at Buffalo
 
 - Dr. Martin Lanser             University of Cologne
 
-- Prof. Dr. Oliver Rheinbach	TU Bergakademie Freiberg
+- Prof. Dr. Oliver Rheinbach    TU Bergakademie Freiberg
 
 - Dr. Janine Weber              University of Cologne
 
 - Dr. Stefano Zampini           King Abdullah University of Science and Technology
 
 Local Organizing Committee
+
 - Prof. Dr. Axel Klawonn
 
 - Dr. Jascha Knepper

doc/community/meetings/2025/index.rst

@@ -0,0 +1,44 @@
+:orphan:
+
+.. _2025_meeting:
+
+
+2025 PETSc Annual Users Meeting and Tutorial
+********************************************
+
+May 20-21, 2025, University of Buffalo, New York, USA
+
+
+Meeting times
+-------------
+* Monday, May 19 - Tutorial
+* Tuesday, May 20 - Meeting
+* Wednesday, May 21 - Meeting
+
+
+Registration
+------------
+Please `register <https://ti.to/nf-projects/petsc-annual-meeting>`__  to save your seat.
+Fee: $100, for breaks and lunches; free for students.
+
+Submit a presentation
+---------------------
+`Submit an abstract  <https://docs.google.com/forms/d/126KwzajoQvcqU_q7btNsYxFqbe7rJ_vASC-tejZfXDQ>`__ to be included in the schedule.
+We welcome talks from all perspectives, including
+
+* contributions to PETSc
+* use of PETSc in applications or libraries
+* development of libraries and packages `called from PETSc <https://petsc.org/release/install/external_software/>`__
+* just curious about using PETSc in applications
+
+Student Travel Support
+----------------------
+
+We have funding to provide travel support for students attending the meeting without their own funding. To apply, check the
+"Student Funding Support" ticket while registering for the meeting. Early registration will increase your chance of obtaining travel support.
+
+Questions and Meeting Discussion
+--------------------------------
+
+For questions about the meeting contact [email protected].
+Join the discussion about the meeting on the `2025 PETSc Annual Users Meeting Discord channel <https://discord.com/channels/1119324534303109172/1298348560600924200>`__,

doc/community/meetings/meeting.rst

@@ -28,8 +28,8 @@ simulations by scientists and engineers.
 Upcoming Meetings
 =================
 
-- The PETSc Annual User Meeting (PAUM) 2025 will take place in Buffalo, New York, USA on May 19-21, 2025.
-  - `Submit a presentation or poster <https://docs.google.com/forms/d/126KwzajoQvcqU_q7btNsYxFqbe7rJ_vASC-tejZfXDQ>`__
+- The :any:`2025 PETSc annual user meeting<2025_meeting>` will take place May 20-21, 2025 in Buffalo, New York, USA, with
+  tutorials on May 19th.
 
 Previous Meetings
 =================

doc/index.rst

@@ -12,6 +12,14 @@ Immediately jump in and run PETSc code :any:`handson`.
 
 PETSc is developed as :ref:`open-source <doc_license>`, :any:`requests <doc_creepycrawly>` and :any:`contributions <ch_contributing>` are welcome.
 
+.. admonition:: News:
+
+  PETSc is now on `BlueSky <https://bsky.app/profile/petsc.bsky.social>`__.
+
+.. admonition:: News:
+
+  The :any:`2025 PETSc Annual User Meeting<2025_meeting>` will take place May 20-21, 2025 in Buffalo, New York, USA, with tutorials on May 19th.
+
 .. admonition:: News: Mrs Hong Zhang, who has been a PETSc developer for twenty-five years and mentored many students and future PETSc developers, has retired.
 
   .. image:: /images/community/HongZhangDinner.jpg

doc/install/download.rst

@@ -31,16 +31,16 @@ Alternative: Obtain Release Version with Tarball
 
 Tarball which contains only the source. Documentation available `online <https://petsc.org/release>`__.
 
-- `petsc-3.22.1.tar.gz <https://web.cels.anl.gov/projects/petsc/download/release-snapshots/petsc-3.22.1.tar.gz>`__
+- `petsc-3.22.2.tar.gz <https://web.cels.anl.gov/projects/petsc/download/release-snapshots/petsc-3.22.2.tar.gz>`__
 
 Tarball which includes all documentation, recommended for offline use.
 
-- `petsc-with-docs-3.22.1.tar.gz <https://web.cels.anl.gov/projects/petsc/download/release-snapshots/petsc-with-docs-3.22.1.tar.gz>`__
+- `petsc-with-docs-3.22.2.tar.gz <https://web.cels.anl.gov/projects/petsc/download/release-snapshots/petsc-with-docs-3.22.2.tar.gz>`__
 
 
 Tarball to enable a separate installation of petsc4py.
 
-- `petsc4py-3.22.1.tar.gz  <https://web.cels.anl.gov/projects/petsc/download/release-snapshots/petsc4py-3.22.1.tar.gz>`__
+- `petsc4py-3.22.2.tar.gz  <https://web.cels.anl.gov/projects/petsc/download/release-snapshots/petsc4py-3.22.2.tar.gz>`__
 
 To extract the sources use:
 
@@ -117,6 +117,9 @@ PETSc does not follow  **Semantic Versioning**, :cite:`semver-webpage`, rather i
 - MINOR version, with new functionality and likely small API changes; most changes are backward compatible with deprecation. On a 6 month cycle.
 - PATCH version, with bug fixes - and minor functionality updates preserving the current API. On a monthly cycle.
 
+PETSc provides tools to allow you to stipulate what versions of PETSc it works with at configure time, compile time, or runtime of your package, see
+:any:`ch_versionchecking`.
+
 .. rubric:: References
 
 .. bibliography:: /petsc.bib

doc/install/install.rst

@@ -682,8 +682,8 @@ Note that using OpenMP within MPI code must be done carefully to prevent too man
    An NVIDIA GPU is **required** to use `CUDA`_-accelerated code. Check that your machine
    has a `CUDA`_ enabled GPU by consulting https://developer.nvidia.com/cuda-gpus.
 
-On Linux - make sure you have compatible `NVIDIA driver
-<https://developer.nvidia.com/cuda-downloads>`__ installed.
+On Linux - verify [#]_ that CUDA compatible `NVIDIA driver
+<https://www.nvidia.com/en-us/drivers>`__ is installed.
 
 On Microsoft Windows - Use either `Cygwin`_ or `WSL`_ the latter of which is entirely untested right
 now. If you have experience with `WSL`_ and/or have successfully built PETSc on Microsoft Windows
@@ -695,7 +695,7 @@ In most cases you need only pass the configure option ``--with-cuda``; check
 
 CUDA build of PETSc currently works on Mac OS X, Linux, Microsoft Windows with `Cygwin`_.
 
-Examples that use CUDA have the suffix .cu; see ``$PETSC_DIR/src/snes/tutorials/ex47.cu``
+Examples that use CUDA have the suffix .cu; see ``$PETSC_DIR/src/snes/tutorials/ex47cu.cu``
 
 .. _doc_config_accel_kokkos:
 
@@ -790,3 +790,4 @@ systems.  Also note the configuration examples in ``config/examples``.
 .. [#] The two packages provide slightly different (though largely overlapping) functionality which can only be fully used if both packages are installed.
 .. [#] Apple provides customized ``clang`` and ``clang++`` for its system. To use the unmodified LLVM project ``clang`` and ``clang++``
        install them with brew.
+.. [#] To verify CUDA compatible Nvidia driver on Linux - run the utility ``nvidia-smi`` - it should provide the version of the Nvidia driver currently installed, and the maximum CUDA version it supports.

doc/manual/additional.rst

@@ -7,6 +7,7 @@ Additional Information
    :maxdepth: 2
 
    fortran
+   versionchecking
    matlab
    profiling
    performance

doc/manual/versionchecking.rst

@@ -0,0 +1,72 @@
+.. _ch_versionchecking:
+
+Checking the PETSc version
+--------------------------
+The PETSc version
+is defined in ``$PETSC_DIR/include/petscversion.h`` with the three macros
+``PETSC_VERSION_MAJOR``, ``PETSC_VERSION_MINOR``, and ``PETSC_VERSION_SUBMINOR``.
+
+The shell commands ``make getversion`` or ``$PETSC_DIR/lib/petsc/bin/petscversion`` prints out the PETSc version.
+The command 
+
+   .. code-block:: console
+
+      $ $PETSC_DIR/lib/petsc/bin/petscversion <eq,gt,lt,ge,le> major.minor<.subminor>
+
+allows one to add tests to make files, CMake files, configure scripts etc, to ensure the PETSc version is compatible with your applications. For example,
+
+   .. code-block:: console
+
+      $ $PETSC_DIR/lib/petsc/bin/petscversion eq 3.22
+
+returns 1 if the PETSc version is 3.22 (any subminor version is allowed). While 
+
+   .. code-block:: console
+
+      $ $PETSC_DIR/lib/petsc/bin/petscversion ge 3.21
+
+returns 1 if the PETSc version is 3.21 or higher.
+
+
+Though we try to avoid making changes to the PETSc API, they are inevitable; thus we
+provide tools to help manage one's application to be robust to such changes.
+
+During configure/make time
+~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The command
+
+.. code-block:: console
+
+   $ $PETSC_DIR/lib/petsc/bin/petscversion eq xxx.yyy[.zzz]
+
+prints out 1 if the PETSc version matches ``xxx.yyy[.zzz]`` and 0 otherwise. The command works in a similar
+way for ``lt``, ``le``, ``gt``, and ``ge``. This allows your application configure script, or ``makefile`` or ``CMake`` file
+to check if the PETSc version is compatible with application even before beginning to compile your code.
+
+
+During compile time
+~~~~~~~~~~~~~~~~~~~
+
+The CPP macros
+
+- ``PETSC_VERSION_EQ(MAJOR,MINOR,SUBMINOR)``
+- ``PETSC_VERSION_LT(MAJOR,MINOR,SUBMINOR)``
+- ``PETSC_VERSION_LE(MAJOR,MINOR,SUBMINOR)``
+- ``PETSC_VERSION_GT(MAJOR,MINOR,SUBMINOR)``
+- ``PETSC_VERSION_GE(MAJOR,MINOR,SUBMINOR)``
+
+may be used in the source code to choose different code paths or error out depending on the PETSc version.
+
+At Runtime
+~~~~~~~~~~
+
+
+The command
+
+.. code-block:: C
+
+   char  version(lengthofversion);
+   PetscErrorCode PetscGetVersion(char version[], size_t lengthofversion)
+
+gives access to the version at runtime.

doc/public/_redirects

@@ -4,3 +4,5 @@
 /main/download /main/install/download 302
 /release/docs/* /release/:splat 301
 /main/docs/* /main/:splat 301
+/community/* /release/community/:splat 301
+/manualpages/* /release/manualpages/:splat 301

gmakefile.test

@@ -455,6 +455,7 @@ help-nontest:
 	-@echo "   libs - build (update) the PETSc and related libraries"
 	-@echo "   check - run a basic check that the libraries are built correctly and can be used"
 	-@echo "   "
+	-@echo "   getversion - print the PETSc version, or $PETSC_DIR/lib/petsc/bin/petscversion"
 	-@echo "   getmpiexec - print the mpiexec to use to run PETSc programs"
 	-@echo "   getlinklibs - print the libraries that a PETSc application must link against"
 	-@echo "   getincludedirs - print the include directories that a PETSc application must be compiled against"

include/petsc/private/viewercgnsimpl.h

@@ -20,8 +20,9 @@ typedef struct {
   PetscInt       batch_size;
 
   // Solution reading information
-  PetscInt solution_index;      // User set solution index
-  int      solution_file_index; // CGNS file solution index for direct access
+  PetscInt solution_index;              // User set solution index
+  int      solution_file_index;         // CGNS file solution index for direct access
+  int      solution_file_pointer_index; // CGNS file solution index for FlowSolutionPointers (and other related arrays), index by 1
   char    *solution_name;
 } PetscViewer_CGNS;