Building Python 3.11.1 on Centos7 with alternative glibc (2.29)

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1

I’d like to build Python 3.11.1 on Centos 7 and glibc 2.29. I can build python3.11 just fine against system glibc, but when I include glibc2.29 in the flags like so:

export LD_LIBRARY_PATH="/usr/local/sqlite3/lib:/usr/local/ssl/lib:/usr/local/zlib-ng/lib:/usr/opt/glibc-2.29/usr/lib64:/usr/lib:/usr/lib64"
export CFLAGS="${CFLAGS} -march=x86-64 -mtune=haswell -Wno-error=format-truncation"
export CPPFLAGS="${CPPFLAGS} -I/usr/local/ssl/include -I/usr/local/zlib-ng/include -I/usr/local/sqlite3/include -I/usr/opt/glibc-2.29/usr/include"
export LDFLAGS="${LDFLAGS} -Wl,-rpath=/usr/local/sqlite3/lib -Wl,-rpath=/usr/local/zlib-ng/lib -Wl,-rpath=/usr/local/ssl/lib -Wl,-rpath=/usr/lib -Wl,-rpath=/usr/opt/glibc-2.29/lib64 -Wl,--dynamic-linker=/usr/opt/glibc-2.29/lib64/ld-linux-x86-64.so.2"
export LD_RUN_PATH="/usr/local/sqlite3/lib:/usr/local/ssl/lib:/usr/local/zlib-ng/lib:/usr/opt/glibc-2.29/lib64"

I get lines like:

/opt/rh/devtoolset-11/root/usr/libexec/gcc/x86_64-redhat-linux/11/ld: /tmp/ccaTf9kQ.lto.o: in function `set_inheritable':
/tmp/Python-3.11.1/Python/fileutils.c:1433: undefined reference to `fcntl64'
/opt/rh/devtoolset-11/root/usr/libexec/gcc/x86_64-redhat-linux/11/ld: /tmp/Python-3.11.1/Python/fileutils.c:1452: undefined reference to `fcntl64'
/opt/rh/devtoolset-11/root/usr/libexec/gcc/x86_64-redhat-linux/11/ld: /tmp/Python-3.11.1/Python/fileutils.c:1433: undefined reference to `fcntl64'
/opt/rh/devtoolset-11/root/usr/libexec/gcc/x86_64-redhat-linux/11/ld: /tmp/Python-3.11.1/Python/fileutils.c:1433: undefined reference to `fcntl64'
/opt/rh/devtoolset-11/root/usr/libexec/gcc/x86_64-redhat-linux/11/ld: /tmp/Python-3.11.1/Python/fileutils.c:1307: undefined reference to `fcntl64'
/opt/rh/devtoolset-11/root/usr/libexec/gcc/x86_64-redhat-linux/11/ld: /tmp/ccaTf9kQ.lto.o:/tmp/Python-3.11.1/Python/fileutils.c:1307: more undefined references to `fcntl64' follow
/opt/rh/devtoolset-11/root/usr/libexec/gcc/x86_64-redhat-linux/11/ld: /tmp/ccaTf9kQ.lto.o: in function `os_memfd_create':
/tmp/Python-3.11.1/./Modules/posixmodule.c:13177: undefined reference to `memfd_create'
/opt/rh/devtoolset-11/root/usr/libexec/gcc/x86_64-redhat-linux/11/ld: /tmp/ccaTf9kQ.lto.o: in function `create_stdio.isra.0':
/tmp/Python-3.11.1/Python/pylifecycle.c:2195: undefined reference to `fcntl64'
/opt/rh/devtoolset-11/root/usr/libexec/gcc/x86_64-redhat-linux/11/ld: /tmp/Python-3.11.1/Python/pylifecycle.c:2195: undefined reference to `fcntl64'
/opt/rh/devtoolset-11/root/usr/libexec/gcc/x86_64-redhat-linux/11/ld: /tmp/ccaTf9kQ.lto.o: in function `os_scandir':
/tmp/Python-3.11.1/Python/fileutils.c:2374: undefined reference to `fcntl64'
/opt/rh/devtoolset-11/root/usr/libexec/gcc/x86_64-redhat-linux/11/ld: /tmp/ccaTf9kQ.lto.o: in function `os_listdir':
/tmp/Python-3.11.1/Python/fileutils.c:2374: undefined reference to `fcntl64'
/opt/rh/devtoolset-11/root/usr/libexec/gcc/x86_64-redhat-linux/11/ld: /tmp/ccaTf9kQ.lto.o: in function `signal_set_wakeup_fd':
/tmp/Python-3.11.1/Python/fileutils.c:2416: undefined reference to `fcntl64'
/opt/rh/devtoolset-11/root/usr/libexec/gcc/x86_64-redhat-linux/11/ld: /tmp/ccaTf9kQ.lto.o:/tmp/Python-3.11.1/Python/fileutils.c:2374: more undefined references to `fcntl64' follow
collect2: error: ld returned 1 exit status
make: [Makefile:1196: Programs/_freeze_module] Error 1 (ignored)
./Programs/_freeze_module importlib._bootstrap ./Lib/importlib/_bootstrap.py Python/frozen_modules/importlib._bootstrap.h
make: ./Programs/_freeze_module: No such file or directory
make: [Makefile:1205: Python/frozen_modules/importlib._bootstrap.h] Error 127 (ignored)
./Programs/_freeze_module importlib._bootstrap_external ./Lib/importlib/_bootstrap_external.py Python/frozen_modules/importlib._bootstrap_external.h
make: ./Programs/_freeze_module: No such file or directory
make: [Makefile:1208: Python/frozen_modules/importlib._bootstrap_external.h] Error 127 (ignored)
gcc -pthread -c  -DNDEBUG -g -fwrapv -O3 -Wall -march=x86-64 -mtune=haswell -Wno-error=format-truncation  -march=x86-64 -mtune=haswell -Wno-error=format-truncation  -fno-semantic-interposition -flto -fuse-linker-plugin -ffat-lto-objects -flto-partition=none -g -std=c11 -Werror=implicit-function-declaration -fvisibility=hidden  -I./Include/internal  -I. -I./Include -I/usr/local/ssl/include -I/usr/local/zlib-ng/include -I/usr/local/sqlite3/include -I/usr/opt/glibc-2.29/usr/include  -I/usr/local/ssl/include -I/usr/local/zlib-ng/include -I/usr/local/sqlite3/include -I/usr/opt/glibc-2.29/usr/include  -DPy_BUILD_CORE -o Programs/_bootstrap_python.o Programs/_bootstrap_python.c
Programs/_bootstrap_python.c:13:10: fatal error: Python/frozen_modules/importlib._bootstrap.h: No such file or directory
   13 | #include "Python/frozen_modules/importlib._bootstrap.h"
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make: [Makefile:2460: Programs/_bootstrap_python.o] Error 1 (ignored)
./Programs/_freeze_module getpath ./Modules/getpath.py Python/frozen_modules/getpath.h
make: ./Programs/_freeze_module: No such file or directory
make: [Makefile:1200: Python/frozen_modules/getpath.h] Error 127 (ignored)
gcc -pthread -c  -DNDEBUG -g -fwrapv -O3 -Wall -march=x86-64 -mtune=haswell -Wno-error=format-truncation  -march=x86-64 -mtune=haswell -Wno-error=format-truncation  -fno-semantic-interposition -flto -fuse-linker-plugin -ffat-lto-objects -flto-partition=none -g -std=c11 -Werror=implicit-function-declaration -fvisibility=hidden  -I./Include/internal  -I. -I./Include -I/usr/local/ssl/include -I/usr/local/zlib-ng/include -I/usr/local/sqlite3/include -I/usr/opt/glibc-2.29/usr/include  -I/usr/local/ssl/include -I/usr/local/zlib-ng/include -I/usr/local/sqlite3/include -I/usr/opt/glibc-2.29/usr/include  -DPy_BUILD_CORE -DPYTHONPATH='""' \
	-DPREFIX='"/usr"' \
	-DEXEC_PREFIX='"/usr"' \
	-DVERSION='"3.11"' \
	-DVPATH='""' \
	-DPLATLIBDIR='"lib"' \
	-DPYTHONFRAMEWORK='""' \
	-o Modules/getpath.o ./Modules/getpath.c
./Modules/getpath.c:22:10: fatal error: ../Python/frozen_modules/getpath.h: No such file or directory
   22 | #include "../Python/frozen_modules/getpath.h"
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.

<snip>

/opt/rh/devtoolset-11/root/usr/libexec/gcc/x86_64-redhat-linux/11/ld: cannot find Programs/_bootstrap_python.o: No such file or directory
/opt/rh/devtoolset-11/root/usr/libexec/gcc/x86_64-redhat-linux/11/ld: cannot find Modules/getpath.o: No such file or directory
collect2: error: ld returned 1 exit status
make: [Makefile:1108: _bootstrap_python] Error 1 (ignored)
./Programs/_freeze_module zipimport ./Lib/zipimport.py Python/frozen_modules/zipimport.h
make: ./Programs/_freeze_module: No such file or directory
make: [Makefile:1211: Python/frozen_modules/zipimport.h] Error 127 (ignored)
./_bootstrap_python ./Programs/_freeze_module.py abc ./Lib/abc.py Python/frozen_modules/abc.h
make: ./_bootstrap_python: No such file or directory
make: [Makefile:1214: Python/frozen_modules/abc.h] Error 127 (ignored)
./_bootstrap_python ./Programs/_freeze_module.py codecs ./Lib/codecs.py Python/frozen_modules/codecs.h
make: ./_bootstrap_python: No such file or directory
make: [Makefile:1217: Python/frozen_modules/codecs.h] Error 127 (ignored)
./_bootstrap_python ./Programs/_freeze_module.py io ./Lib/io.py Python/frozen_modules/io.h
make: ./_bootstrap_python: No such file or directory
make: [Makefile:1220: Python/frozen_modules/io.h] Error 127 (ignored)
./_bootstrap_python ./Programs/_freeze_module.py _collections_abc ./Lib/_collections_abc.py Python/frozen_modules/_collections_abc.h
make: ./_bootstrap_python: No such file or directory
make: [Makefile:1223: Python/frozen_modules/_collections_abc.h] Error 127 (ignored)
./_bootstrap_python ./Programs/_freeze_module.py _sitebuiltins ./Lib/_sitebuiltins.py Python/frozen_modules/_sitebuiltins.h
make: ./_bootstrap_python: No such file or directory
make: [Makefile:1226: Python/frozen_modules/_sitebuiltins.h] Error 127 (ignored)
./_bootstrap_python ./Programs/_freeze_module.py genericpath ./Lib/genericpath.py Python/frozen_modules/genericpath.h
make: ./_bootstrap_python: No such file or directory
make: [Makefile:1229: Python/frozen_modules/genericpath.h] Error 127 (ignored)
./_bootstrap_python ./Programs/_freeze_module.py ntpath ./Lib/ntpath.py Python/frozen_modules/ntpath.h
make: ./_bootstrap_python: No such file or directory
make: [Makefile:1232: Python/frozen_modules/ntpath.h] Error 127 (ignored)
./_bootstrap_python ./Programs/_freeze_module.py posixpath ./Lib/posixpath.py Python/frozen_modules/posixpath.h
make: ./_bootstrap_python: No such file or directory
make: [Makefile:1235: Python/frozen_modules/posixpath.h] Error 127 (ignored)
./_bootstrap_python ./Programs/_freeze_module.py os ./Lib/os.py Python/frozen_modules/os.h
make: ./_bootstrap_python: No such file or directory
make: [Makefile:1238: Python/frozen_modules/os.h] Error 127 (ignored)
./_bootstrap_python ./Programs/_freeze_module.py site ./Lib/site.py Python/frozen_modules/site.h
make: ./_bootstrap_python: No such file or directory
make: [Makefile:1241: Python/frozen_modules/site.h] Error 127 (ignored)
./_bootstrap_python ./Programs/_freeze_module.py stat ./Lib/stat.py Python/frozen_modules/stat.h
make: ./_bootstrap_python: No such file or directory
make: [Makefile:1244: Python/frozen_modules/stat.h] Error 127 (ignored)
./_bootstrap_python ./Programs/_freeze_module.py importlib.util ./Lib/importlib/util.py Python/frozen_modules/importlib.util.h
make: ./_bootstrap_python: No such file or directory
make: [Makefile:1247: Python/frozen_modules/importlib.util.h] Error 127 (ignored)
./_bootstrap_python ./Programs/_freeze_module.py importlib.machinery ./Lib/importlib/machinery.py Python/frozen_modules/importlib.machinery.h
make: ./_bootstrap_python: No such file or directory
make: [Makefile:1250: Python/frozen_modules/importlib.machinery.h] Error 127 (ignored)
./_bootstrap_python ./Programs/_freeze_module.py runpy ./Lib/runpy.py Python/frozen_modules/runpy.h
make: ./_bootstrap_python: No such file or directory
make: [Makefile:1253: Python/frozen_modules/runpy.h] Error 127 (ignored)
./_bootstrap_python ./Programs/_freeze_module.py __hello__ ./Lib/__hello__.py Python/frozen_modules/__hello__.h
make: ./_bootstrap_python: No such file or directory
make: [Makefile:1256: Python/frozen_modules/__hello__.h] Error 127 (ignored)
./_bootstrap_python ./Programs/_freeze_module.py __phello__ ./Lib/__phello__/__init__.py Python/frozen_modules/__phello__.h
make: ./_bootstrap_python: No such file or directory
make: [Makefile:1259: Python/frozen_modules/__phello__.h] Error 127 (ignored)
./_bootstrap_python ./Programs/_freeze_module.py __phello__.ham ./Lib/__phello__/ham/__init__.py Python/frozen_modules/__phello__.ham.h
make: ./_bootstrap_python: No such file or directory
make: [Makefile:1262: Python/frozen_modules/__phello__.ham.h] Error 127 (ignored)
./_bootstrap_python ./Programs/_freeze_module.py __phello__.ham.eggs ./Lib/__phello__/ham/eggs.py Python/frozen_modules/__phello__.ham.eggs.h
make: ./_bootstrap_python: No such file or directory
make: [Makefile:1265: Python/frozen_modules/__phello__.ham.eggs.h] Error 127 (ignored)
./_bootstrap_python ./Programs/_freeze_module.py __phello__.spam ./Lib/__phello__/spam.py Python/frozen_modules/__phello__.spam.h
make: ./_bootstrap_python: No such file or directory
make: [Makefile:1268: Python/frozen_modules/__phello__.spam.h] Error 127 (ignored)
./_bootstrap_python ./Programs/_freeze_module.py frozen_only ./Tools/freeze/flag.py Python/frozen_modules/frozen_only.h
make: ./_bootstrap_python: No such file or directory
make: [Makefile:1271: Python/frozen_modules/frozen_only.h] Error 127 (ignored)
./_bootstrap_python ./Tools/scripts/deepfreeze.py \
Python/frozen_modules/importlib._bootstrap.h:importlib._bootstrap \
Python/frozen_modules/importlib._bootstrap_external.h:importlib._bootstrap_external \
Python/frozen_modules/zipimport.h:zipimport \
Python/frozen_modules/abc.h:abc \
Python/frozen_modules/codecs.h:codecs \
Python/frozen_modules/io.h:io \
Python/frozen_modules/_collections_abc.h:_collections_abc \
Python/frozen_modules/_sitebuiltins.h:_sitebuiltins \
Python/frozen_modules/genericpath.h:genericpath \
Python/frozen_modules/ntpath.h:ntpath \
Python/frozen_modules/posixpath.h:posixpath \
Python/frozen_modules/os.h:os \
Python/frozen_modules/site.h:site \
Python/frozen_modules/stat.h:stat \
Python/frozen_modules/importlib.util.h:importlib.util \
Python/frozen_modules/importlib.machinery.h:importlib.machinery \
Python/frozen_modules/runpy.h:runpy \
Python/frozen_modules/__hello__.h:__hello__ \
Python/frozen_modules/__phello__.h:__phello__ \
Python/frozen_modules/__phello__.ham.h:__phello__.ham \
Python/frozen_modules/__phello__.ham.eggs.h:__phello__.ham.eggs \
Python/frozen_modules/__phello__.spam.h:__phello__.spam \
Python/frozen_modules/frozen_only.h:frozen_only \
-o Python/deepfreeze/deepfreeze.c
make: ./_bootstrap_python: No such file or directory
make: [Makefile:1292: Python/deepfreeze/deepfreeze.c] Error 127 (ignored)
Note: Deepfreeze may have added some global objects,
      so run 'make regen-global-objects' if necessary.
gcc -pthread -c  -DNDEBUG -g -fwrapv -O3 -Wall -march=x86-64 -mtune=haswell -Wno-error=format-truncation  -march=x86-64 -mtune=haswell -Wno-error=format-truncation  -fno-semantic-interposition -flto -fuse-linker-plugin -ffat-lto-objects -flto-partition=none -g -std=c11 -Werror=implicit-function-declaration -fvisibility=hidden  -I./Include/internal  -I. -I./Include -I/usr/local/ssl/include -I/usr/local/zlib-ng/include -I/usr/local/sqlite3/include -I/usr/opt/glibc-2.29/usr/include  -I/usr/local/ssl/include -I/usr/local/zlib-ng/include -I/usr/local/sqlite3/include -I/usr/opt/glibc-2.29/usr/include  -DPy_BUILD_CORE -o Python/deepfreeze/deepfreeze.o Python/deepfreeze/deepfreeze.c
cc1: fatal error: Python/deepfreeze/deepfreeze.c: No such file or directory
compilation terminated.

<snip>

/opt/rh/devtoolset-11/root/usr/libexec/gcc/x86_64-redhat-linux/11/ld: cannot find Python/deepfreeze/deepfreeze.o: No such file or directory
/opt/rh/devtoolset-11/root/usr/libexec/gcc/x86_64-redhat-linux/11/ld: cannot find Modules/getpath.o: No such file or directory
collect2: error: ld returned 1 exit status
make: [Makefile:836: python] Error 1 (ignored)
Creating directory /usr/bin
Creating directory /usr/lib
if test "no-framework" = "no-framework" ; then \
	/usr/bin/install -c python /tmp/python-3.11.1-rpmbuild/usr/bin/python3.11; \
else \
	/usr/bin/install -c -s Mac/pythonw /tmp/python-3.11.1-rpmbuild/usr/bin/python3.11; \
fi
/usr/bin/install: cannot stat ‘python’: No such file or directory
make: [Makefile:1926: altbininstall] Error 1 (ignored)
if test "3.11" != "3.11"; then \
	if test -f /tmp/python-3.11.1-rpmbuild/usr/bin/python3.11 -o -h /tmp/python-3.11.1-rpmbuild/usr/bin/python3.11; \
	then rm -f /tmp/python-3.11.1-rpmbuild/usr/bin/python3.11; \
	fi; \
	(cd /tmp/python-3.11.1-rpmbuild/usr/bin; ln python3.11 python3.11); \
fi
if test "x" != "x" ; then \
	rm -f /tmp/python-3.11.1-rpmbuild/usr/bin/python3.11-32; \
	lipo  \
		-output /tmp/python-3.11.1-rpmbuild/usr/bin/python3.11-32 \
		/tmp/python-3.11.1-rpmbuild/usr/bin/python3.11; \
fi
if test "x" != "x" ; then \
	rm -f /tmp/python-3.11.1-rpmbuild/usr/bin/python3.11-intel64; \
	lipo  \
		-output /tmp/python-3.11.1-rpmbuild/usr/bin/python3.11-intel64 \
		/tmp/python-3.11.1-rpmbuild/usr/bin/python3.11; \
fi
Running code to generate profile data (this can take a while):
# First, we need to create a clean build with profile generation
# enabled.
make profile-gen-stamp
make[1]: Entering directory '/tmp/Python-3.11.1'
make clean
make[2]: Entering directory '/tmp/Python-3.11.1'
find . -depth -name '__pycache__' -exec rm -rf {} ';'
find . -name '*.py[co]' -exec rm -f {} ';'
find . -name '*.[oa]' -exec rm -f {} ';'
find . -name '*.s[ol]' -exec rm -f {} ';'
find . -name '*.so.[0-9]*.[0-9]*' -exec rm -f {} ';'
find . -name '*.wasm' -exec rm -f {} ';'
find . -name '*.lst' -exec rm -f {} ';'
find build -name 'fficonfig.h' -exec rm -f {} ';' || true
find build -name '*.py' -exec rm -f {} ';' || true
find build -name '*.py[co]' -exec rm -f {} ';' || true
rm -f pybuilddir.txt
rm -f Lib/lib2to3/*Grammar*.pickle
rm -f _bootstrap_python
rm -f python.html python*.js python.data python*.symbols python*.map
rm -f ./usr/lib/python3.11/os.py
rm -f Programs/_testembed Programs/_freeze_module
rm -f Python/deepfreeze/*.[co]
rm -f Python/frozen_modules/*.h
rm -f Python/frozen_modules/MANIFEST
find build -type f -a ! -name '*.gc??' -exec rm -f {} ';'
rm -f Include/pydtrace_probes.h
rm -f profile-gen-stamp
make[3]: Entering directory '/tmp/Python-3.11.1'
find . -name '*.gc??' -exec rm -f {} ';'
find . -name '*.profclang?' -exec rm -f {} ';'
find . -name '*.dyn' -exec rm -f {} ';'
rm -f /tmp/Python-3.11.1/coverage.info
rm -rf /tmp/Python-3.11.1/lcov-report
rm -f profile-run-stamp
make[3]: Leaving directory '/tmp/Python-3.11.1'
make[2]: Leaving directory '/tmp/Python-3.11.1'
touch profile-clean-stamp
Building with support for profile generation:
make build_all_generate_profile
make[2]: Entering directory '/tmp/Python-3.11.1'
make build_all CFLAGS_NODIST=" -fprofile-generate" LDFLAGS_NODIST=" -fprofile-generate" LIBS="-lpthread -ldl  -lutil"
make[3]: Entering directory '/tmp/Python-3.11.1'
gcc -pthread -c  -DNDEBUG -g -fwrapv -O3 -Wall -march=x86-64 -mtune=haswell -Wno-error=format-truncation  -march=x86-64 -mtune=haswell -Wno-error=format-truncation  -fno-semantic-interposition -flto -fuse-linker-plugin -ffat-lto-objects -flto-partition=none -g -std=c11 -Werror=implicit-function-declaration -fvisibility=hidden -fprofile-generate -I./Include/internal  -I. -I./Include -I/usr/local/ssl/include -I/usr/local/zlib-ng/include -I/usr/local/sqlite3/include -I/usr/opt/glibc-2.29/usr/include  -I/usr/local/ssl/include -I/usr/local/zlib-ng/include -I/usr/local/sqlite3/include -I/usr/opt/glibc-2.29/usr/include  -DPy_BUILD_CORE -o Programs/python.o ./Programs/python.c

Any thoughts on how to resolve this?

2

Is the linux kernel too old to support 64 bit time?

3

Is the linux kernel too old…

I’m able to build successfully when I don’t specify glibc2.29, so it can’t be the linux kernel. I’ve also built 3.11.1 on Centos6, for that matter (though not specifying any custom glibc).

4

I wonder if you need this option when you build glibc?
What I am guessing is that the 64 time API is only present if the kernel headers show its supported in the kernel.
But that just a guess on my part.

Why can’t you use the Centos 7 glibc?

'--enable-kernel=VERSION'
     This option is currently only useful on GNU/Linux systems.  The
     VERSION parameter should have the form X.Y.Z and describes the
     smallest version of the Linux kernel the generated library is
     expected to support.  The higher the VERSION number is, the less
     compatibility code is added, and the faster the code gets.