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Issue35713

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Title:Fatal Python error: _PySys_BeginInit: can't initialize sys module
Type:compile errorStage:resolved
Components:BuildVersions:Python 3.7
process
Status:closedResolution:fixed
Dependencies:Superseder:
Assigned To:Nosy List: Tasy, vstinner, xtreak
Priority:normalKeywords:

Created on2019-01-10 22:35 byTasy, last changed2022-04-11 14:59 byadmin. This issue is nowclosed.

Pull Requests
URLStatusLinkedEdit
PR 11647mergedvstinner,2019-01-22 15:51
PR 11647mergedvstinner,2019-01-22 15:51
PR 11647mergedvstinner,2019-01-22 15:51
PR 11650mergedvstinner,2019-01-22 17:43
PR 11650mergedvstinner,2019-01-22 17:43
PR 11650mergedvstinner,2019-01-22 17:43
PR 11658mergedvstinner,2019-01-23 12:30
PR 11658mergedvstinner,2019-01-23 12:30
PR 11658mergedvstinner,2019-01-23 12:30
Messages (14)
msg333423 -(view)Author: (Tasy)Date: 2019-01-10 22:35
..../python -E -S -m sysconfig --generate-posix-vars ;\if test $? -ne 0 ; then \echo "generate-posix-vars failed" ; \rm -f ./pybuilddir.txt ; \exit 1 ; \fiFatal Python error: _PySys_BeginInit: can't initialize sys moduleCurrent thread 0x00002b4e5f9bf400 (most recent call first):Aborted (core dumped)generate-posix-vars failedmake[1]: *** [pybuilddir.txt] Error 1make[1]: Leaving directory `/usr/local/mysoftware/Python-3.7.2/build'make: *** [profile-opt] Error 2
msg333425 -(view)Author: STINNER Victor (vstinner)*(Python committer)Date: 2019-01-10 22:48
> .> .> .Hello. Can you elaborate this part?
msg333427 -(view)Author: (Tasy)Date: 2019-01-10 23:38
Sorry for the confusion. The three dots were for many lines of successful compilation output from make. The rest is the final few lines where the compilation fails.
msg333428 -(view)Author: STINNER Victor (vstinner)*(Python committer)Date: 2019-01-10 23:42
Because it's late, I will say it shortly: if you don't elaborate how you get this error, I will simply close the issue. You have to describe what you are trying to do, your OS, etc.(It works for me!)
msg333429 -(view)Author: Karthikeyan Singaravelan (xtreak)*(Python committer)Date: 2019-01-10 23:45
Please attach the full build log too along with the command executed.
msg333733 -(view)Author: (Tasy)Date: 2019-01-15 22:03
Configuration Options:  ../configure --prefix=$HOME --enable-shared --enable-optimizations --with-system-expat --with-system-ffi --with-ensurepip=yesMake throws the following warning:*** WARNING: renaming "_curses_panel" since importing it failed: No module named '_curses'Python build finished successfully!The necessary bits to build these optional modules were not found:_ssl                  _uuid                                    To find the necessary bits, look in setup.py in detect_modules() for the module's name.The following modules found by detect_modules() in setup.py, have beenbuilt by the Makefile instead, as configured by the Setup files:_abc                  atexit                pwd                time                                                           Failed to build these modules:_curses                                                        Following modules built successfully but were removed because they could not be imported:_curses_panel                                                  Could not build the ssl module!Python requires an OpenSSL 1.0.2 or 1.1 compatible libssl with X509_VERIFY_PARAM_set1_host().LibreSSL 2.6.4 and earlier do not provide the necessary APIs,https://github.com/libressl-portable/portable/issues/381There ther is a following error...0:06:18 load avg: 0.55 [171/416] test_hashlib*** Error in `./python': corrupted size vs. prev_size: 0x000000000276b7a0 ***Fatal Python error: AbortedCurrent thread 0x00002ba4468c7bc0 (most recent call first):  File "/usr/local/data/mySoftware/Python-3.7.2/Lib/test/test_hashlib.py", line 904 in _test_pbkdf2_hmac  File "/usr/local/data/mySoftware/Python-3.7.2/Lib/test/test_hashlib.py", line 935 in test_pbkdf2_hmac_c  File "/usr/local/data/mySoftware/Python-3.7.2/Lib/unittest/case.py", line 615 in run  File "/usr/local/data/mySoftware/Python-3.7.2/Lib/unittest/case.py", line 663 in __call__  File "/usr/local/data/mySoftware/Python-3.7.2/Lib/unittest/suite.py", line 122 in run  File "/usr/local/data/mySoftware/Python-3.7.2/Lib/unittest/suite.py", line 84 in __call__  File "/usr/local/data/mySoftware/Python-3.7.2/Lib/unittest/suite.py", line 122 in run  File "/usr/local/data/mySoftware/Python-3.7.2/Lib/unittest/suite.py", line 84 in __call__  File "/usr/local/data/mySoftware/Python-3.7.2/Lib/unittest/suite.py", line 122 in run  File "/usr/local/data/mySoftware/Python-3.7.2/Lib/unittest/suite.py", line 84 in __call__  File "/usr/local/data/mySoftware/Python-3.7.2/Lib/test/support/testresult.py", line 162 in run  File "/usr/local/data/mySoftware/Python-3.7.2/Lib/test/support/__init__.py", line 1895 in _run_suite  File "/usr/local/data/mySoftware/Python-3.7.2/Lib/test/support/__init__.py", line 1991 in run_unittest  File "/usr/local/data/mySoftware/Python-3.7.2/Lib/test/libregrtest/runtest.py", line 178 in test_runner  File "/usr/local/data/mySoftware/Python-3.7.2/Lib/test/libregrtest/runtest.py", line 182 in runtest_inner  File "/usr/local/data/mySoftware/Python-3.7.2/Lib/test/libregrtest/runtest.py", line 137 in runtest  File "/usr/local/data/mySoftware/Python-3.7.2/Lib/test/libregrtest/main.py", line 407 in run_tests_sequential  File "/usr/local/data/mySoftware/Python-3.7.2/Lib/test/libregrtest/main.py", line 514 in run_tests  File "/usr/local/data/mySoftware/Python-3.7.2/Lib/test/libregrtest/main.py", line 615 in _main  File "/usr/local/data/mySoftware/Python-3.7.2/Lib/test/libregrtest/main.py", line 582 in main  File "/usr/local/data/mySoftware/Python-3.7.2/Lib/test/libregrtest/main.py", line 636 in main  File "/usr/local/data/mySoftware/Python-3.7.2/Lib/test/regrtest.py", line 46 in _main  File "/usr/local/data/mySoftware/Python-3.7.2/Lib/test/regrtest.py", line 50 in <module>  File "/usr/local/data/mySoftware/Python-3.7.2/Lib/runpy.py", line 85 in _run_code  File "/usr/local/data/mySoftware/Python-3.7.2/Lib/runpy.py", line 193 in _run_module_as_mainAborted (core dumped)make[1]: Leaving directory `/usr/local/data/mySoftware/Python-3.7.2/build'make build_all_merge_profilemake[1]: Entering directory `/usr/local/data/mySoftware/Python-3.7.2/build'truemake[1]: Leaving directory `/usr/local/data/mySoftware/Python-3.7.2/build'# Remove profile generation binary since we are done with it.make cleanmake[1]: Entering directory `/usr/local/data/mySoftware/Python-3.7.2/build'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 build -name 'fficonfig.h' -exec rm -f {} ';' || truefind build -name '*.py' -exec rm -f {} ';' || truefind build -name '*.py[co]' -exec rm -f {} ';' || truerm -f pybuilddir.txtrm -fLib/lib2to3/*Grammar*.picklerm -fPrograms/_testembedPrograms/_freeze_importlibfind build -type f -a ! -name '*.gc??' -exec rm -f {} ';'rm -fInclude/pydtrace_probes.hrm -f profile-gen-stampmake[1]: Leaving directory `/usr/local/data/mySoftware/Python-3.7.2/build'# This is an expensive target to build and it does not have proper# makefile dependency information.  So, we create a "stamp" file# to record its completion and avoid re-running it.touch profile-run-stampRebuilding with profile guided optimizations:rm -f profile-clean-stampmake build_all CFLAGS_NODIST=" -fprofile-use -fprofile-correction" LDFLAGS_NODIST=""make[1]: Entering directory `/usr/local/data/mySoftware/Python-3.7.2/build'And then finally :Modules/_localemodule.oModules/_iomodule.oModules/iobase.oModules/fileio.oModules/bytesio.oModules/bufferedio.oModules/textio.oModules/stringio.oModules/zipimport.oModules/faulthandler.oModules/_tracemalloc.oModules/hashtable.oModules/symtablemodule.oModules/xxsubtype.oPython/frozen.ogcc -pthread -shared     -Wl,--no-as-needed -o libpython3.so -Wl,-hlibpython3.so libpython3.7m.sogcc -pthread     -Xlinker -export-dynamic -o pythonPrograms/python.o -L. -lpython3.7m -lpthread -ldl  -lutil   -lm  gcc -pthread     -Xlinker -export-dynamic -oPrograms/_testembedPrograms/_testembed.o -L. -lpython3.7m -lpthread -ldl  -lutil   -lm  LD_LIBRARY_PATH=/usr/local/data/mySoftware/Python-3.7.2/build:$HOME/lib:/usr/local/cuda/lib64:$HOME/lib/cuda/lib64:$HOME/lib/cuda/extras/CUPTI/lib64:/usr/local/data/lib:/usr/local/lib/:/usr/lib/ ./python -E -S -m sysconfig --generate-posix-vars ;\if test $? -ne 0 ; then \echo "generate-posix-vars failed" ; \rm -f ./pybuilddir.txt ; \exit 1 ; \fiFatal Python error: _PySys_BeginInit: can't initialize sys moduleCurrent thread 0x00002adc936069c0 (most recent call first):Aborted (core dumped)generate-posix-vars failedmake[1]: *** [pybuilddir.txt] Error 1make[1]: Leaving directory `/usr/local/data/mySoftware/Python-3.7.2/build'make: *** [profile-opt] Error 2
msg333853 -(view)Author: STINNER Victor (vstinner)*(Python committer)Date: 2019-01-17 12:12
What is your OS (name and version)?What is your compiler (name and version)?> Fatal Python error: _PySys_BeginInit: can't initialize sys moduleI have no idea why you get this error. You should try to run this function in a debugger like gdb and run the code step by step to see what happens."""0:06:18 load avg: 0.55 [171/416] test_hashlib*** Error in `./python': corrupted size vs. prev_size: 0x000000000276b7a0 ***Fatal Python error: AbortedCurrent thread 0x00002ba4468c7bc0 (most recent call first):  File "/usr/local/data/mySoftware/Python-3.7.2/Lib/test/test_hashlib.py", line 904 in _test_pbkdf2_hmac"""That's maybe unrelated, but _test_pbkdf2_hmac() is not supposed to crash.
msg333984 -(view)Author: (Tasy)Date: 2019-01-18 15:51
Compiler:$ gcc --versiongcc (Ubuntu 4.8.4-2ubuntu1~14.04.4) 4.8.4OS:$ uname -aLinux machine 4.4.0-141-generic #167~14.04.1-Ubuntu SMP Mon Dec 10 13:20:24 UTC 2018 x86_64 x86_64 x86_64 GNU/LinuxHome directory is of type nfs in case that is relevant.I'll try to do the gdb thing over the weekend.
msg333992 -(view)Author: STINNER Victor (vstinner)*(Python committer)Date: 2019-01-18 16:55
Hum. Are you aware that PGO with GCC is broken on such old and unsupported Ubuntu version?My old note about that:"PGO is broken on Ubuntu 14.04 LTS with GCC 4.8.4-2ubuntu1~14.04:Modules/socketmodule.c:7743:1: internal compiler error: in edge_badness, at ipa-inline.c:895"https://pyperformance.readthedocs.io/usage.html#compileSee alsohttps://bugs.python.org/issue31963I suggest you to not use PGO compilation on old Ubuntu. Maybe upgrade to latest Ubuntu LTS?
msg333999 -(view)Author: (Tasy)Date: 2019-01-18 17:52
compiling without optimizations worked.
msg334219 -(view)Author: STINNER Victor (vstinner)*(Python committer)Date: 2019-01-22 16:39
New changesetbf4ac2d2fd520c61306b2676db488adab9b5d8c5 by Victor Stinner in branch 'master':bpo-35713: Rework Python initialization (GH-11647)https://github.com/python/cpython/commit/bf4ac2d2fd520c61306b2676db488adab9b5d8c5
msg334233 -(view)Author: STINNER Victor (vstinner)*(Python committer)Date: 2019-01-22 20:18
New changeset6d43f6f081023b680d9db4542d19b9e382149f0a by Victor Stinner in branch 'master':bpo-35713: Split _Py_InitializeCore into subfunctions (GH-11650)https://github.com/python/cpython/commit/6d43f6f081023b680d9db4542d19b9e382149f0a
msg334258 -(view)Author: STINNER Victor (vstinner)*(Python committer)Date: 2019-01-23 14:04
New changesetab67281e95de1a88c4379a75a547f19a8ba5ec30 by Victor Stinner in branch 'master':bpo-35713: Reorganize sys module initialization (GH-11658)https://github.com/python/cpython/commit/ab67281e95de1a88c4379a75a547f19a8ba5ec30
msg334259 -(view)Author: STINNER Victor (vstinner)*(Python committer)Date: 2019-01-23 14:06
"""> Fatal Python error: _PySys_BeginInit: can't initialize sys moduleI have no idea why you get this error. You should try to run this function in a debugger like gdb and run the code step by step to see what happens."""I pushed 3 changes to get working exceptions and working sys.stderr earlier during Python initialization. It should help to display the current exceptions when Py_FatalError() is called during early stage of the Python initialization.
History
DateUserActionArgs
2022-04-11 14:59:10adminsetgithub: 79894
2019-01-23 14:06:29vstinnersetmessages: +msg334259
2019-01-23 14:04:42vstinnersetmessages: +msg334258
2019-01-23 12:30:30vstinnersetpull_requests: +pull_request11456
2019-01-23 12:30:24vstinnersetpull_requests: +pull_request11455
2019-01-23 12:30:17vstinnersetpull_requests: +pull_request11454
2019-01-22 20:18:20vstinnersetmessages: +msg334233
2019-01-22 17:44:00vstinnersetpull_requests: +pull_request11437
2019-01-22 17:43:52vstinnersetpull_requests: +pull_request11436
2019-01-22 17:43:44vstinnersetpull_requests: +pull_request11435
2019-01-22 16:39:06vstinnersetmessages: +msg334219
2019-01-22 15:52:05vstinnersetpull_requests: +pull_request11432
2019-01-22 15:51:59vstinnersetpull_requests: +pull_request11431
2019-01-22 15:51:52vstinnersetpull_requests: +pull_request11430
2019-01-18 17:52:46Tasysetstatus: open -> closed
resolution: fixed
messages: +msg333999

stage: resolved
2019-01-18 16:55:55vstinnersetmessages: +msg333992
2019-01-18 15:51:09Tasysetmessages: +msg333984
2019-01-17 12:12:50vstinnersetmessages: +msg333853
2019-01-15 22:03:41Tasysetmessages: +msg333733
2019-01-10 23:45:02xtreaksetnosy: +xtreak
messages: +msg333429
2019-01-10 23:42:00vstinnersetmessages: +msg333428
2019-01-10 23:38:41Tasysetmessages: +msg333427
2019-01-10 22:48:50vstinnersetnosy: +vstinner
messages: +msg333425
2019-01-10 22:35:31Tasycreate
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