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

Author: connorjward

.gitlab-ci.yml

@@ -421,7 +421,6 @@ gnu-cxx-int64:
 pip-install:
   extends: .test
   stage: stage-2
-  allow_failure: true   # set this after release before the new petsc4py version is uploaded to pypi
   tags:
     - pip, name:jepri
   before_script:
@@ -433,34 +432,45 @@ pip-install:
     - ccache --zero-stats
     - printf "PYTHON:${PYTHON}\n"
   script:
-    - unset PETSC_DIR PETSC_ARCH SLEPC_DIR
     - |
-      if [ $(awk '/define SLEPC_VERSION_RELEASE/{print $3}' include/slepcversion.h) == 1 ]; then
-        pip install --user .;
-        pip install --user src/binding/slepc4py;
-        make -C src/binding/slepc4py/demo;
+      unset PETSC_DIR PETSC_ARCH SLEPC_DIR
+      slepc=$PWD
+      cd ..
+      if [ ! -d petsc ]; then git clone https://gitlab.com/petsc/petsc.git; fi
+      cd petsc
+      git clean ${GIT_CLEAN_FLAGS}
+      git fetch
+      if [ -z ${PETSC_BRANCH+x} ]; then
+        if [ $(awk '/define SLEPC_VERSION_RELEASE/{print $3}' $slepc/include/slepcversion.h) == 1 ]; then
+          git checkout origin/release
+        else
+          git checkout origin/main
+        fi
       else
-        slepc=$PWD;
-        cd ..;
-        if [ ! -d petsc ]; then git clone https://gitlab.com/petsc/petsc.git; fi;
-        cd petsc;
-        petsc=$PWD;
-        git clean ${GIT_CLEAN_FLAGS}
-        git fetch;
-        if [ -z ${PETSC_BRANCH+x} ]; then git checkout origin/main; else git checkout origin/$PETSC_BRANCH; fi;
-        set -eu pipefail;
-        rm -rf /tmp/env;
-        python -m venv /tmp/env;
-        source /tmp/env/bin/activate;
-        set -x;
-        python -m pip install -U pip==23.0.1    # pin version due to issue with pip 23.1
-        pip install numpy;
-        pip install $petsc;
-        pip install $petsc/src/binding/petsc4py;
-        pip install $slepc;
-        pip install $slepc/src/binding/slepc4py;
-        make -C $slepc/src/binding/slepc4py/demo;
+        git checkout origin/$PETSC_BRANCH
       fi
+      petsc=$PWD
+      cd ..
+      set -eu pipefail
+      rm -rf /tmp/venv
+      python -m venv /tmp/venv
+      source /tmp/venv/bin/activate
+      set -x
+      python -m pip install --upgrade pip
+      wheelhouse=$PWD/wheelhouse
+      rm -rf $wheelhouse
+      mkdir -p $wheelhouse
+      export PIP_WHEEL_DIR=$wheelhouse
+      export PIP_FIND_LINKS=$wheelhouse
+      python -m pip wheel $petsc
+      python -m pip wheel $petsc/src/binding/petsc4py
+      python -m pip wheel $slepc
+      python -m pip wheel $slepc/src/binding/slepc4py
+      python -m pip install --pre slepc4py
+      python -m pip list
+      python -m slepc --prefix
+      python -m slepc4py
+      make -C $slepc/src/binding/slepc4py/demo
   after_script:
     - date
 

CHANGELOG.md

@@ -4,9 +4,25 @@
 
 ### Added
 
-- `ST`: new function `STShellSetApplyHermitianTranspose` and other improvements for handling
+- `BV`: new function `BVGetSplitRows()` to split a `BV` row-wise using index sets.
+
+### Changed
+
+- In slepc4py now `EPS.getEigenpair()` and `EPS.getEigenvalue()` will return a real value
+instead of a complex, if the problem is of Hermitian or generalized Hermitian type.
+
+## [3.21] - 2024-03-30
+
+### Added
+
+- `ST`: new function `STShellSetApplyHermitianTranspose()` and other improvements for handling
   the conjugate transpose of the operator.
 
+### Changed
+
+- `SVDGetSignature()` now takes a `Vec` argument instead of `Vec*`. The former interface
+  could not be used from Fortran.
+
 ## [3.20] - 2023-09-29
 
 ### Changed
@@ -454,7 +470,8 @@
 - Classical and modified Gram-Schmidt orthogonalization use iterative refinement, with user options
   for parameter adjustment.
 
-[unreleased]: https://gitlab.com/slepc/slepc/compare/v3.20...main
+[unreleased]: https://gitlab.com/slepc/slepc/compare/v3.21...main
+[3.21]: https://gitlab.com/slepc/slepc/compare/v3.20...v3.21
 [3.20]: https://gitlab.com/slepc/slepc/compare/v3.19...v3.20
 [3.19]: https://gitlab.com/slepc/slepc/compare/v3.18...v3.19
 [3.18]: https://gitlab.com/slepc/slepc/compare/v3.17...v3.18

LICENSE.md

@@ -1,4 +1,4 @@
-Copyright (c) 2002-2023, Universitat Politecnica de Valencia, Spain
+Copyright (c) 2002-2024, Universitat Politecnica de Valencia, Spain
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

config/install.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 from __future__ import print_function
-import os, sys, shutil
+import re, os, sys, shutil
 import subprocess
 
 try:
@@ -302,6 +302,144 @@ def fixConf(self):
     self.fixConfFile(os.path.join(self.destIncludeDir,'slepcconf.h'))
     return
 
+  def fixPythonWheel(self):
+    import glob
+    import shutil
+    #
+    for pattern in (
+        self.destLibDir  + '/*.a',
+        self.destLibDir  + '/*.la',
+        self.destLibDir  + '/pkgconfig',  # TODO: keep?
+        self.destConfDir + '/configure-hash',
+        self.destConfDir + '/uninstall.py',
+        self.destConfDir + '/reconfigure-*.py',
+        self.destConfDir + '/pkg.conf.*',
+        self.destConfDir + '/pkg.git*.*',
+        self.destConfDir + '/modules',  # TODO: keep?
+        self.destShareDir + '/*/examples/src/*',
+        self.destShareDir + '/*/datafiles',
+    ):
+      for pathname in glob.glob(pattern):
+        if os.path.isdir(pathname):
+          shutil.rmtree(pathname)
+        elif os.path.exists(pathname):
+          os.remove(pathname)
+    #
+    for filename in (
+      self.destIncludeDir + '/slepcconf.h',
+      self.destShareDir + '/slepc/examples/gmakefile.test',
+      self.destConfDir + '/slepc_rules_doc.mk',
+      self.destConfDir + '/slepc_rules_util.mk',
+      self.destConfDir + '/slepc_rules',
+      self.destConfDir + '/slepcrules',
+      self.destConfDir + '/slepc_variables',
+      self.destConfDir + '/slepcvariables',
+    ):
+      with open(filename, 'r') as oldFile:
+        contents = oldFile.read()
+      contents = contents.replace(self.installDir, '${SLEPC_DIR}')
+      contents = contents.replace(self.rootDir, '${SLEPC_DIR}')
+      contents = contents.replace(self.petscDir, '${PETSC_DIR}')
+      with open(filename, 'w') as newFile:
+        newFile.write(contents)
+    #
+    def lsdir(dirname, *patterns):
+      return glob.glob(os.path.join(dirname, *patterns))
+    def shell(*args):
+      out  = subprocess.check_output(list(args), universal_newlines=True)
+      return out[:-1] if out[-1:] == '\n' else out
+    plibdir = os.path.join(self.petscDir, 'lib')
+    slibdir = os.path.join(self.installDir, 'lib')
+    if sys.platform == 'linux':
+      libraries = [
+        lib for lib in lsdir(self.destLibDir, 'lib*.so*')
+        if not os.path.islink(lib)
+      ]
+      for shlib in libraries:
+        # fix shared library rpath
+        rpath = shell('patchelf', '--print-rpath', shlib)
+        rpath = rpath.split(os.path.pathsep)
+        if plibdir in rpath:
+          rpath.insert(0, '$ORIGIN/../../petsc/lib')
+          while plibdir in rpath:
+            rpath.remove(plibdir)
+        if slibdir in rpath:
+          rpath.insert(0, '$ORIGIN')
+          while slibdir in rpath:
+            rpath.remove(slibdir)
+        if rpath:
+          rpath = os.path.pathsep.join(rpath)
+          shell('patchelf', '--set-rpath', rpath, shlib)
+        # fix shared library file and symlink
+        basename = os.path.basename(shlib)
+        libname, ext, _ = basename.partition('.so')
+        liblink = libname + ext
+        soname = shell('patchelf', '--print-soname', shlib)
+        for symlink in lsdir(self.destLibDir, liblink + '*'):
+          if os.path.islink(symlink):
+            os.unlink(symlink)
+        curdir = os.getcwd()
+        try:
+          os.chdir(os.path.dirname(shlib))
+          if soname != basename:
+            os.rename(basename, soname)
+          if soname != liblink:
+            os.symlink(soname, liblink)
+        finally:
+          os.chdir(curdir)
+    if sys.platform == 'darwin':
+      def otool(cmd, dylib):
+        pattern = r'''
+          ^\s+ cmd \s %s$\n
+          ^\s+ cmdsize \s \d+$\n
+          ^\s+ (?:name|path) \s (.*) \s \(offset \s \d+\)$
+        ''' % cmd
+        return re.findall(
+          pattern, shell('otool', '-l', dylib),
+          flags=re.VERBOSE | re.MULTILINE,
+        )
+      libraries = [
+        lib for lib in lsdir(self.destLibDir, 'lib*.dylib')
+        if not os.path.islink(lib)
+      ]
+      for dylib in libraries:
+        install_name = otool('LC_ID_DYLIB', dylib)[0]
+        dependencies = otool('LC_LOAD_DYLIB', dylib)
+        runtime_path = otool('LC_RPATH', dylib)
+        # fix shared library install name and rpath
+        install_name = '@rpath/' + os.path.basename(install_name)
+        shell('install_name_tool', '-id', install_name, dylib)
+        for libdir in (plibdir, slibdir):
+          if libdir in runtime_path:
+            shell('install_name_tool', '-delete_rpath', libdir, dylib)
+        for rpath in ('@loader_path', '@loader_path/../../petsc/lib'):
+          if rpath not in runtime_path:
+            shell('install_name_tool', '-add_rpath', rpath, dylib)
+        for dep in dependencies:
+          if os.path.dirname(dep) in (plibdir, slibdir):
+            newid = '@rpath/' + os.path.basename(dep)
+            shell('install_name_tool', '-change', dep, newid, dylib)
+        # fix shared library file and symlink
+        basename = os.path.basename(dylib)
+        libname, ext = os.path.splitext(basename)
+        libname = libname.partition('.')[0]
+        liblink = libname + ext
+        dyname = os.path.basename(install_name)
+        for symlink in lsdir(self.destLibDir, libname + '*' + ext):
+          if os.path.islink(symlink):
+            os.unlink(symlink)
+        curdir = os.getcwd()
+        try:
+          os.chdir(os.path.dirname(dylib))
+          if dyname != basename:
+            os.rename(basename, dyname)
+          if dyname != liblink:
+            os.symlink(dyname, liblink)
+        finally:
+          os.chdir(curdir)
+    #
+    return
+
   def createUninstaller(self):
     uninstallscript = os.path.join(self.destConfDir, 'uninstall.py')
     f = open(uninstallscript, 'w')
@@ -441,14 +579,16 @@ def runcopy(self):
     self.installBin()
     self.installLib()
     self.installShare()
+    self.createUninstaller()
     return
 
   def runfix(self):
     self.fixConf()
+    if os.environ.get('PEP517_BUILD_BACKEND'):
+      self.fixPythonWheel()
     return
 
   def rundone(self):
-    self.createUninstaller()
     if self.destDir == self.installDir:
       self.outputInstallDone()
     else:

config/packages/elpa.py

@@ -18,7 +18,7 @@ def __init__(self,argdb,log):
     self.packagetype    = 'gnu'
     self.installable    = True
     self.downloadable   = True
-    self.version        = '2023.11.001'
+    self.version        = '2024.03.001'
     self.archive        = 'elpa-'+self.version+'.tar.gz'
     self.url            = 'https://elpa.mpcdf.mpg.de/software/tarball-archive/Releases/'+self.version+'/'+self.archive
     self.supportssingle = True

config/packages/hpddm.py

@@ -17,8 +17,8 @@ def __init__(self,argdb,log):
     package.Package.__init__(self,argdb,log)
     self.packagename    = 'hpddm'
     self.downloadable   = True
-    # self.gitcommit      = 'a789a193f3c9c7c3c2674eb8d1f8db95cd1ae48c'
-    self.version        = '2.2.5'
+    self.gitcommit      = '28add19c6968c41497468f4f4ac156196b051ea9'
+    # 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'
     self.archive        = 'hpddm-'+obj+'.tar.gz'

config/packages/slicot.py

@@ -17,8 +17,8 @@ def __init__(self,argdb,log):
     self.packagename    = 'slicot'
     self.installable    = True
     self.downloadable   = True
-    self.gitcommit      = '401037e4992827cd7476baae615be6fe818b71d4'
-    #self.version        = '5.8'
+    #self.gitcommit      = 'a037f7eb76134d45e7d222b7f017d5cbd16eb731'
+    self.version        = '5.9'
     obj = self.version if hasattr(self,'version') else self.gitcommit
     self.url            = 'https://github.com/SLICOT/SLICOT-Reference/archive/'+('v'+obj if hasattr(self,'version') else obj)+'.tar.gz'
     self.archive        = 'slicot-'+obj+'.tar.gz'
@@ -56,20 +56,6 @@ def DownloadAndInstall(self,slepcconf,slepcvars,slepc,petsc,archdir,prefixdir):
     cont += 'LPKAUXLIB = ../'+libname+'\n'  # TODO: use a separate library for this
     self.WriteMakefile('make_Unix.inc',builddir,cont)
 
-    # Patch top level makefile_Unix
-    (result,output) = self.RunCommand('cd '+builddir+' && '+petsc.sedinplace+' -e "s?MAKE.?MAKE) -f makefile_Unix?" makefile_Unix')
-    if result:
-      self.log.Exit('Problem when patching file makefile_Unix')
-
-    # Patch makefile_Unix in src
-    sedargs = ' -e "s?make.inc?make_Unix.inc?"'
-    remfiles = ['MB04RD', 'MB04RS', 'MB04RT', 'MB04RV', 'MB04RW', 'MB04RZ', 'zelctg']
-    for f in remfiles:
-      sedargs = sedargs + ' -e "s?'+f+'.o??"'
-    (result,output) = self.RunCommand('cd '+os.path.join(builddir,'src')+' && '+petsc.sedinplace+' '+sedargs+' makefile_Unix')
-    if result:
-      self.log.Exit('Problem when patching file makefile_Unix in src')
-
     # Build package
     target = 'lib'
     (result,output) = self.RunCommand('cd '+builddir+' && '+petsc.make+' -f makefile_Unix cleanlib && '+petsc.make+' -f makefile_Unix -j'+petsc.make_np+' '+target)

config/packages/sowing.py

@@ -18,8 +18,8 @@ def __init__(self,argdb,log):
     self.packagename  = 'sowing'
     self.downloadable = True
     self.inplace      = False
-    #self.gitcommit    = '7e1bbd0d8427274768a13849372ce0ee911f4ac5'
-    self.version      = '1.1.26-p7'
+    #self.gitcommit    = '2fe1f1f12257b274cbb0b4425f2994965bcc9bde'
+    self.version      = '1.1.26.9'
     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'

docs/changes.html

@@ -210,6 +210,11 @@
     <td> 3.20 </td>
     <td> Sep 2023 </td>
   </tr>
+  <tr>
+    <td> 3.21 </td>
+    <td> 3.21 </td>
+    <td> Mar 2024 </td>
+  </tr>
 </table>
 
 <font face="Arial, Helvetica, sans-serif" size="2">A changelog of the different versions can be found <a href="https://gitlab.com/slepc/slepc/-/blob/main/CHANGELOG.md" target=_blank>here</a>.</font>

docs/instal.html

@@ -32,14 +32,14 @@
         The main steps for the installation are:</p>
       <ol>
         <li style="padding-top: 0.5em">
-          Unbundle the distribution file <strong>slepc-3.20.0.tar.gz</strong> with a usual
-    command such as <code>tar xzf slepc-3.20.0.tar.gz</code>.
+          Unbundle the distribution file <strong>slepc-3.21.0.tar.gz</strong> with a usual
+    command such as <code>tar xzf slepc-3.21.0.tar.gz</code>.
     This will create a directory and unpack the software there.<br>
           </li>
         <li style="padding-top: 0.5em">Set the environment variable <code>SLEPC_DIR</code>
     to the full path of the SLEPc home directory, for example,<br>
     <div style="padding-top: 0.4em; padding-bottom: 0.4em;">
-      <code style="margin-left: 1cm">export SLEPC_DIR=/home/username/slepc-3.20.0</code><br>
+      <code style="margin-left: 1cm">export SLEPC_DIR=/home/username/slepc-3.21.0</code><br>
     </div>
     In addition to this variable, <code>PETSC_DIR</code>
     and <code>PETSC_ARCH</code> must also be set appropriately.<br>