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Remove superfluous source archive

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This commit is contained in:
Antonio Trande 2023-08-13 13:32:43 +02:00
parent 2c22262810
commit d408b4ba6d
5 changed files with 50 additions and 295 deletions
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66
petsc-3.18.5-fix_make_compatibility.patch
View File

@ -1,66 +0,0 @@
From 5ef50a0f30184c572c1829d0a161b2eb8af8a6a3 Mon Sep 17 00:00:00 2001
From: Satish Balay <balay@mcs.anl.gov>
Date: Fri, 3 Mar 2023 11:10:06 -0600
Subject: [PATCH] GNUMake 4.4.1 requires MAKEFLAGS to be in the correct order.
Prepending -j results in errors when using --print-directory (as it gets
translated to 'w')
Fixed by not modifying MAKEFLAGS
Using MAKE: /home/balay/tmp/make-4.4.1/gmake
Using MAKEFLAGS: -j10 -l18.0 w -- PETSC_DIR=/home/balay/petsc PETSC_ARCH=arch-linux-c-debug
==========================================
gmake[3]: Entering directory '/home/balay/petsc'
/usr/bin/python3 ./config/gmakegen.py --petsc-arch=arch-linux-c-debug
/usr/bin/python3 /home/balay/petsc/config/gmakegentest.py --petsc-dir=/home/balay/petsc --petsc-arch=arch-linux-c-debug --testdir=./arch-linux-c-debug/tests
gmake[3]: *** No rule to make target 'w'. Stop.
---
lib/petsc/conf/rules | 16 +++++++++++++++-
makefile | 4 ++--
2 files changed, 17 insertions(+), 3 deletions(-)
diff --git a/lib/petsc/conf/rules b/lib/petsc/conf/rules
index 7219d0274e7..a24e64130c4 100644
--- a/lib/petsc/conf/rules
+++ b/lib/petsc/conf/rules
@@ -53,7 +53,21 @@ ${PETSC_DIR}/${PETSC_ARCH}/tests/testfiles:
@${MKDIR} -p ${PETSC_DIR}/${PETSC_ARCH}/tests && touch -t 197102020000 ${PETSC_DIR}/${PETSC_ARCH}/tests/testfiles
libs: ${PETSC_DIR}/${PETSC_ARCH}/lib/petsc/conf/files ${PETSC_DIR}/${PETSC_ARCH}/tests/testfiles
- +@cd ${PETSC_DIR} && MAKEFLAGS="-j$(MAKE_NP) -l$(MAKE_LOAD) $(MAKEFLAGS)" ${OMAKE_PRINTDIR} -f gmakefile ${MAKE_PAR_OUT_FLG} V=${V} libs
+ +@r=`echo "${MAKEFLAGS}" | grep ' \-j'`; \
+ if [ "$$?" = 0 ]; then \
+ make_j="";\
+ echo "Skipping adding -jMAKE_NP option as -j option is already specified"; \
+ else \
+ make_j="-j${MAKE_NP}"; \
+ fi; \
+ r=`echo "${MAKEFLAGS}" | grep ' \-l'`; \
+ if [ "$$?" = 0 ]; then \
+ make_l="";\
+ echo "Skipping adding -lMAKE_LOAD option as -l option is already specified"; \
+ else \
+ make_l="-l${MAKE_LOAD}"; \
+ fi; \
+ cd ${PETSC_DIR} && ${OMAKE_PRINTDIR} -f gmakefile $${make_j} $${make_l} ${MAKE_PAR_OUT_FLG} V=${V} libs
# Does nothing; needed for some rules that require actions.
foo:
diff --git a/makefile b/makefile
index a8329057970..8cdd2fc5af1 100644
--- a/makefile
+++ b/makefile
@@ -122,8 +122,8 @@ info:
-@echo "------------------------------------------"
-@echo "Using mpiexec: ${MPIEXEC}"
-@echo "------------------------------------------"
- -@echo "Using MAKE: $(MAKE)"
- -@echo "Using MAKEFLAGS: -j$(MAKE_NP) -l$(MAKE_LOAD) $(MAKEFLAGS)"
+ -@echo "Using MAKE: ${MAKE}"
+ -@echo "Default MAKEFLAGS: MAKE_NP:${MAKE_NP} MAKE_LOAD:${MAKE_LOAD} MAKEFLAGS:${MAKEFLAGS}"
-@echo "=========================================="
#
--
GitLab

157
petsc-3.18.5-fix_python312_compatibility.patch
View File

@ -1,157 +0,0 @@
From f2ed88371e6f236237267476ee72a064ae0cd70f Mon Sep 17 00:00:00 2001
From: "Jose E. Roman" <jroman@dsic.upv.es>
Date: Tue, 20 Jun 2023 17:31:19 +0200
Subject: [PATCH] Fix for python-3.12: 'imp' module has been removed
Fixes #1401
---
config/BuildSystem/script.py | 11 +++---
lib/petsc/bin/petsc_tas_analysis.py | 1 -
.../petsc4py/src/petsc4py/lib/__init__.py | 38 ++++++++++++++-----
3 files changed, 33 insertions(+), 17 deletions(-)
diff --git a/config/BuildSystem/script.py b/config/BuildSystem/script.py
index 5dbf2934fff..f120d335712 100644
--- a/config/BuildSystem/script.py
+++ b/config/BuildSystem/script.py
@@ -132,13 +132,12 @@ class Script(logger.Logger):
@staticmethod
def getModule(root, name):
'''Retrieve a specific module from the directory root, bypassing the usual paths'''
- import imp
+ import importlib.util
- (fp, pathname, description) = imp.find_module(name, [root])
- try:
- return imp.load_module(name, fp, pathname, description)
- finally:
- if fp: fp.close()
+ spec = importlib.util.spec_from_file_location(name, root)
+ module = importlib.util.module_from_spec(spec)
+ sys.modules[name] = module
+ spec.loader.exec_module(module)
@staticmethod
def importModule(moduleName):
diff --git a/lib/petsc/bin/petsc_tas_analysis.py b/lib/petsc/bin/petsc_tas_analysis.py
index 7a74fd06d31..bb1c3e62b55 100755
--- a/lib/petsc/bin/petsc_tas_analysis.py
+++ b/lib/petsc/bin/petsc_tas_analysis.py
@@ -4,7 +4,6 @@ import os
import sys
import importlib
import datetime as date
-import importlib
# Check to ensure that the environmental variable PETSC_DIR has been assigned.
# MPLCONFIGDIR is needed for matplotlib
diff --git a/src/lib/__init__.py b/src/lib/__init__.py
index 85e9daf118e..310334eae21 100644
--- a/src/lib/__init__.py
+++ b/src/lib/__init__.py
@@ -13,7 +13,7 @@
This package is a holds all the available variants of the PETSc
extension module built against specific PETSc configurations. It also
-provides a convenience function using of the builtin ``imp`` module
+provides a convenience function using of the ``importlib`` module
for easily importing any of the available extension modules depending
on the value of a user-provided configuration name, the ``PETSC_ARCH``
environmental variable, or a configuration file.
@@ -45,19 +45,35 @@
Import helper for PETSc-based extension modules.
"""
import sys, os, warnings
- # TODO: use 'importlib' module under Python 3
- with warnings.catch_warnings():
- warnings.filterwarnings("ignore")
+ try:
+ import importlib.machinery
+ import importlib.util
+ except ImportError:
+ importlib = None
import imp
def get_ext_suffix():
- return imp.get_suffixes()[0][0]
+ if importlib:
+ return importlib.machinery.EXTENSION_SUFFIXES[0]
+ else:
+ return imp.get_suffixes()[0][0]
+
def import_module(pkg, name, path, arch):
- fullname = '%s.%s' % (pkg, name)
+ fullname = '{}.{}'.format(pkg, name)
pathlist = [os.path.join(path, arch)]
- f, fn, info = imp.find_module(name, pathlist)
- with f: return imp.load_module(fullname, f, fn, info)
+ if importlib:
+ finder = importlib.machinery.PathFinder()
+ spec = finder.find_spec(fullname, pathlist)
+ module = importlib.util.module_from_spec(spec)
+ sys.modules[fullname] = module
+ spec.loader.exec_module(module)
+ return module
+ else:
+ f, fn, info = imp.find_module(name, pathlist)
+ with f:
+ return imp.load_module(fullname, f, fn, info)
+
# test if extension module was already imported
- module = sys.modules.get('%s.%s' % (pkg, name))
+ module = sys.modules.get('{}.{}'.format(pkg, name))
filename = getattr(module, '__file__', '')
if filename.endswith(get_ext_suffix()):
# if 'arch' is None, do nothing; otherwise this
@@ -66,6 +82,7 @@
if arch is not None and arch != module.__arch__:
raise ImportError("%s already imported" % module)
return module
+
# silence annoying Cython warning
warnings.filterwarnings("ignore", message="numpy.dtype size changed")
warnings.filterwarnings("ignore", message="numpy.ndarray size changed")
From c36e9c688a542448939d85251c93951e001443de Mon Sep 17 00:00:00 2001
From: "Jose E. Roman" <jroman@dsic.upv.es>
Date: Thu, 22 Jun 2023 10:28:53 +0200
Subject: [PATCH 2/2] script.py: improve portability for python < 3.5
---
config/BuildSystem/script.py | 23 +++++++++++++++++------
1 file changed, 17 insertions(+), 6 deletions(-)
diff --git a/config/BuildSystem/script.py b/config/BuildSystem/script.py
index f120d335712..d3305288195 100644
--- a/config/BuildSystem/script.py
+++ b/config/BuildSystem/script.py
@@ -132,12 +132,23 @@ class Script(logger.Logger):
@staticmethod
def getModule(root, name):
'''Retrieve a specific module from the directory root, bypassing the usual paths'''
- import importlib.util
-
- spec = importlib.util.spec_from_file_location(name, root)
- module = importlib.util.module_from_spec(spec)
- sys.modules[name] = module
- spec.loader.exec_module(module)
+ try:
+ import importlib.util
+ except ImportError:
+ importlib = None
+ import imp
+
+ if importlib and sys.version_info > (3,4):
+ spec = importlib.util.spec_from_file_location(name, root)
+ module = importlib.util.module_from_spec(spec) # novermin
+ sys.modules[name] = module
+ spec.loader.exec_module(module)
+ else:
+ (fp, pathname, description) = imp.find_module(name, [root])
+ try:
+ return imp.load_module(name, fp, pathname, description)
+ finally:
+ if fp: fp.close()
@staticmethod
def importModule(moduleName):
--
GitLab

20
petsc-3.19.4-fix_Cython_requirement.patch
View File

@ -1,20 +0,0 @@
--- a/conf/confpetsc.orig.py 2023-07-31 17:00:55.000000000 +0200
+++ b/conf/confpetsc.py 2023-08-11 12:45:52.386371527 +0200
@@ -100,7 +100,7 @@
return False
REQUIRED = Version(VERSION)
PROVIDED = Version(m.groups()[0])
- if PROVIDED != REQUIRED:
+ if PROVIDED < REQUIRED:
warn("You need Cython == {0} (you have version {1})"
.format(VERSION, CYTHON_VERSION))
return False
@@ -130,7 +130,7 @@
return
finally:
os.chdir(cwd)
- require = 'Cython == %s' % VERSION
+ require = 'Cython == 0.29.36'
if setuptools and not cython_chk(VERSION, verbose=False):
if sys.modules.get('Cython'):
removed = getattr(sys.modules['Cython'], '__version__', '')

101
petsc.spec
View File

@ -290,7 +290,6 @@ Release: %autorelease
License: BSD
URL: https://petsc.org/
Source0: https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-with-docs-%{version}.tar.gz
Source1: https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc4py-%{version}.tar.gz
# These files have been generated by Cython-0.29.36
# PETSC-3.19 is not compatible with Cython-3.0.0 yet
@ -298,20 +297,17 @@ Source1: https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc4py-%{version}
Source2: %{name}-PETSc_cython0.29.36.c
Source3: %{name}-PETSc_cython0.29.36.h
Source4: %{name}-PETSc_api_cython0.29.36.h
Patch9: %{name}-3.19.4-fix_Cython_requirement.patch
## Remove rpath flags
Patch0: %{name}-3.11-no-rpath.patch
## Rename library name for 64-bit integer package
Patch1: %{name}-lib64.patch
Patch2: %{name}-3.18.5-fix_make_compatibility.patch
Patch3: %{name}-3.19.4-fix_mumps_includes.patch
Patch4: %{name}-3.19.4-fix_metis64.patch
Patch5: %{name}-3.15.0-fix_sundials_version.patch
Patch6: %{name}-3.14.1-fix_pkgconfig_file.patch
Patch7: %{name}-3.17.0-avoid_fake_MKL_detection.patch
Patch8: %{name}-3.18.5-fix_python312_compatibility.patch
%if %{with superlu}
BuildRequires: SuperLU-devel >= 5.2.0
@ -460,10 +456,11 @@ BuildRequires: hdf5-openmpi-devel
BuildRequires: scalapack-openmpi-devel
BuildRequires: ptscotch-openmpi-devel
BuildRequires: python3-numpy
%if 0%{?fedora} <= 37
%if 0%{?rhel} || 0%{?fedora} < 39
BuildRequires: python3-Cython
%endif
%else
BuildRequires: python3-pip
%endif
Requires: petsc-openmpi%{?_isa}
Requires: hdf5-openmpi%{?_isa}
Requires: scalapack-openmpi%{?_isa}
@ -492,10 +489,11 @@ BuildRequires: hdf5-mpich-devel
BuildRequires: scalapack-mpich-devel
BuildRequires: ptscotch-mpich-devel
BuildRequires: python3-numpy
%if 0%{?fedora} <= 37
%if 0%{?rhel} || 0%{?fedora} < 39
BuildRequires: python3-Cython
%endif
%else
BuildRequires: python3-pip
%endif
Requires: petsc-mpich%{?_isa}
Requires: hdf5-mpich%{?_isa}
Requires: scalapack-openmpi%{?_isa}
@ -574,30 +572,7 @@ Portable Extensible Toolkit for Scientific Computation (developer files).
%setup -qc
%if %{with python}
%setup -q -T -D -a 1
cp -a petsc4py-%{version}/* %{name}-%{version}/
rm -rf %{name}-%{version}/*.egg-info
rm -rf %{name}-%{version}/src/binding/petsc4py/src/petsc4py.egg-info
rm -rf petsc4py-%{version}
# Use pre-generated Cython files
%if 0%{?fedora} > 38
rm -f %{name}-%{version}/src/binding/petsc4py/src/PETSc.c
install -pm 644 %{SOURCE2} %{name}-%{version}/src/binding/petsc4py/src/PETSc.c
install -pm 644 %{SOURCE2} %{name}-%{version}/src/binding/petsc4py/src/petsc4py/PETSc.c
rm -f %{name}-%{version}/src/binding/petsc4py/src/PETSc.h
install -pm 644 %{SOURCE3} %{name}-%{version}/src/binding/petsc4py/src/PETSc.h
install -pm 644 %{SOURCE3} %{name}-%{version}/src/binding/petsc4py/src/petsc4py/PETSc.h
rm -f %{name}-%{version}/src/binding/petsc4py/src/PETSc_api.h
install -pm 644 %{SOURCE4} %{name}-%{version}/src/binding/petsc4py/src/PETSc_api.h
install -pm 644 %{SOURCE4} %{name}-%{version}/src/binding/petsc4py/src/petsc4py/PETSc_api.h
pushd %{name}-%{version}
%patch -P 9 -p1 -b .backup
popd
%endif
# Remove pre-generated Cython files
#rm $(grep -rl '/\* Generated by Cython')
rm -rf %{name}-%{version}/src/binding/petsc4py/src/*.egg-info
%if 0%{?fedora}
for i in `find . -name 'setup.py' -o -name 'configure' -o -name '*.py'`; do
@ -607,12 +582,12 @@ done
%endif
pushd %{name}-%{version}
#patch -P 2 -p1 -b .backup
%patch -P 7 -p1 -b .backup
popd
%if 0%{?python3_version_nodots} >= 312
#patch -P 8 -p1 -b .backup
%endif
# Remove pregenerated Cython C sources
pushd %{name}-%{version}
#rm $(grep -rl '/\* Generated by Cython')
popd
%if %{with arch64}
@ -633,9 +608,20 @@ popd
%if %{with openmpi}
cp -a %{name}-%{version} buildopenmpi_dir
%if 0%{?fedora} > 38
cp %{SOURCE2} buildopenmpi_dir/src/binding/petsc4py/src/petsc4py/PETSc.c
cp %{SOURCE3} buildopenmpi_dir/src/binding/petsc4py/src/petsc4py/PETSc.h
cp %{SOURCE4} buildopenmpi_dir/src/binding/petsc4py/src/petsc4py/PETSc_api.h
%endif
%endif
%if %{with mpich}
cp -a %{name}-%{version} buildmpich_dir
%if 0%{?fedora} > 38
cp %{SOURCE2} buildmpich_dir/src/binding/petsc4py/src/petsc4py/PETSc.c
cp %{SOURCE3} buildmpich_dir/src/binding/petsc4py/src/petsc4py/PETSc.h
cp %{SOURCE4} buildmpich_dir/src/binding/petsc4py/src/petsc4py/PETSc_api.h
%endif
%endif
# Do NOT move up this patch
@ -709,7 +695,7 @@ popd
%endif
%if %{with openmpi}
pushd buildopenmpi_dir
cd buildopenmpi_dir
%{_openmpi_load}
export CC=mpicc
@ -740,19 +726,21 @@ make \
V=1 MAKE_NP=$RPM_BUILD_NCPUS PETSC_DIR=%{_builddir}/%{name}-%{version}/buildopenmpi_dir PETSC_ARCH=%{_arch} all
%if %{with python}
pushd src/binding/petsc4py
export PETSC_ARCH=%{_arch}
export PETSC_DIR=./
export PETSC_DIR=../../../
%py3_build
unset PETSC_ARCH
unset PETSC_DIR
%endif
%{_openmpi_unload}
popd
%endif
%{_openmpi_unload}
cd ..
%endif
%if %{with mpich}
pushd buildmpich_dir
cd buildmpich_dir
%{_mpich_load}
export CC=mpicc
@ -783,15 +771,17 @@ make \
V=1 MAKE_NP=$RPM_BUILD_NCPUS PETSC_DIR=%{_builddir}/%{name}-%{version}/buildmpich_dir PETSC_ARCH=%{_arch} all
%if %{with python}
pushd src/binding/petsc4py
export PETSC_ARCH=%{_arch}
export PETSC_DIR=./
export PETSC_DIR=../../../
%py3_build
unset PETSC_ARCH
unset PETSC_DIR
popd
%endif
%{_mpich_unload}
popd
cd ..
%endif
%install
@ -901,9 +891,13 @@ sed -e 's|${PETSC_DIR}|%{_prefix}|g' -i %{buildroot}$MPI_LIB/%{name}/conf/petscr
sed -e 's|${PETSC_DIR}|%{_prefix}|g' -i %{buildroot}$MPI_LIB/%{name}/conf/petscvariables
%if %{with python}
pushd src/binding/petsc4py
export PETSC_ARCH=%{_arch}
export PETSC_DIR=./
%py3_install
export PETSC_DIR=../../../
%py3_install -- --verbose
unset PETSC_ARCH
unset PETSC_DIR
popd
# Install petsc4py files into MPI directories
%if 0%{?rhel}
@ -919,11 +913,11 @@ rm -rf %{buildroot}%{python3_sitearch}/%{pymodule_name}-%{pymodule_version}-py%{
chrpath -r %{_libdir}/openmpi/lib %{buildroot}$MPI_PYTHON3_SITEARCH/%{pymodule_name}/lib/%{_arch}/*.so
%endif
%{_openmpi_unload}
popd
cd ..
%endif
%if %{with mpich}
pushd buildmpich_dir
cd buildmpich_dir
%{_mpich_load}
mkdir -p %{buildroot}$MPI_LIB %{buildroot}$MPI_INCLUDE/%{name}
mkdir -p %{buildroot}$MPI_FORTRAN_MOD_DIR/%{name}
@ -960,9 +954,13 @@ sed -e 's|${PETSC_DIR}|%{_prefix}|g' -i %{buildroot}$MPI_LIB/%{name}/conf/petscr
sed -e 's|${PETSC_DIR}|%{_prefix}|g' -i %{buildroot}$MPI_LIB/%{name}/conf/petscvariables
%if %{with python}
pushd src/binding/petsc4py
export PETSC_ARCH=%{_arch}
export PETSC_DIR=./
%py3_install
export PETSC_DIR=../../../
%py3_install -- --verbose
unset PETSC_ARCH
unset PETSC_DIR
popd
# Install petsc4py files into MPI directories
%if 0%{?rhel}
@ -978,7 +976,7 @@ rm -rf %{buildroot}%{python3_sitearch}/%{pymodule_name}-%{pymodule_version}-py%{
chrpath -r %{_libdir}/mpich/lib %{buildroot}$MPI_PYTHON3_SITEARCH/%{pymodule_name}/lib/%{_arch}/*.so
%endif
%{_mpich_unload}
popd
cd ..
%endif
# Move html documentation in _pkgdocdir
@ -1199,3 +1197,4 @@ xvfb-run -a make MAKE_NP=$RPM_BUILD_NCPUS all test -C build64 V=1 MPIEXEC='%{_bu
%changelog
%autochangelog

1
sources
View File

@ -1,2 +1 @@
SHA512 (petsc-with-docs-3.19.4.tar.gz) = 34011695e33594541132957afffc4f8c94ce3ff71e6322c76630a8afd39a2e91c8ac36c33bd1d749792a0167ee18a742d205b54269eceec2f5cbf01e5ae12809
SHA512 (petsc4py-3.19.4.tar.gz) = f6ffd84fff1124636b362cdf304137b37f2227a1a188206d70c78ba2bb90032088f0275a5be68c6e6b603e38cb27965fc08bf3f2cf001d63f29675cc984f9d1c