Bug 1576671

Summary:	Sagemath does not compile in Fedora 28
Product:	[Fedora] Fedora	Reporter:	artal
Component:	sagemath	Assignee:	Paulo Andrade <paulo.cesar.pereira.de.andrade>
Status:	CLOSED UPSTREAM	QA Contact:	Fedora Extras Quality Assurance <extras-qa>
Severity:	unspecified	Docs Contact:
Priority:	unspecified
Version:	28	CC:	artal, aspronedario, cstratak, paulo.cesar.pereira.de.andrade
Target Milestone:	---
Target Release:	---
Hardware:	x86_64
OS:	Linux
Whiteboard:
Fixed In Version:		Doc Type:	If docs needed, set a value
Doc Text:		Story Points:	---
Clone Of:		Environment:
Last Closed:	2018-08-29 11:53:14 UTC	Type:	Bug
Regression:	---	Mount Type:	---
Documentation:	---	CRM:
Verified Versions:		Category:	---
oVirt Team:	---	RHEL 7.3 requirements from Atomic Host:
Cloudforms Team:	---	Target Upstream Version:
Embargoed:

Description artal 2018-05-10 06:31:35 UTC

Description of problem: Trying to compile sagemath (http://www.sagemath.org) from sources (both 8.2 version and develop git branch) fails. Using fedora gcc-8, there are issues with the packages python2 and python3. It is possible to use gcc-7.2 from sagemath to compile, having success with python2, but the same error with python3


Version-Release number of selected component (if applicable):


How reproducible: Always


Steps to Reproduce:
1. Download sage-8.2.tar.gz from sagemath site
2. Follow the instructions to build it, using their own gcc
3.

Actual results: python3 package fails to build with a dumped core when importing crypt module


Expected results: Success


Additional info: The error is common for an upgraded or a fresh installation of Fedora 28.

Comment 1 artal 2018-05-10 07:45:08 UTC

This is output from gdb:

       Message: Process 28762 (python) of user 1000 dumped core.
                
                Stack trace of thread 28762:
                #0  0x00007fcabcc2cc81 __strlen_avx2 (libc.so.6)
                #1  0x00007fcabd9dd158 do_mkvalue (/usr/local/sagegit/local/var/tmp/sage/build/python3-3.6.1.p1/src/libpython3.6m.so.1.0)
                #2  0x00007fcabd9dda2e va_build_value (/usr/local/sagegit/local/var/tmp/sage/build/python3-3.6.1.p1/src/libpython3.6m.so.1.0)
                #3  0x00007fcabd9ddaee Py_BuildValue (/usr/local/sagegit/local/var/tmp/sage/build/python3-3.6.1.p1/src/libpython3.6m.so.1.0)
                #4  0x00007fcab5e0a801 crypt_crypt_impl (_crypt.cpython-36m-x86_64-linux-gnu.so)
                #5  0x00007fcabd925ed5 _PyCFunction_FastCallDict (/usr/local/sagegit/local/var/tmp/sage/build/python3-3.6.1.p1/src/libpython3.6m.so.1.0)
                #6  0x00007fcabd9b1f3f call_function (/usr/local/sagegit/local/var/tmp/sage/build/python3-3.6.1.p1/src/libpython3.6m.so.1.0)
                #7  0x00007fcabd9b564f _PyEval_EvalFrameDefault (/usr/local/sagegit/local/var/tmp/sage/build/python3-3.6.1.p1/src/libpython3.6m.so.1.0)
                #8  0x00007fcabd9b1b3a _PyEval_EvalCodeWithName (/usr/local/sagegit/local/var/tmp/sage/build/python3-3.6.1.p1/src/libpython3.6m.so.1.0)
                #9  0x00007fcabd9b1dd2 fast_function (/usr/local/sagegit/local/var/tmp/sage/build/python3-3.6.1.p1/src/libpython3.6m.so.1.0)
                #10 0x00007fcabd9b564f _PyEval_EvalFrameDefault (/usr/local/sagegit/local/var/tmp/sage/build/python3-3.6.1.p1/src/libpython3.6m.so.1.0)
                #11 0x00007fcabd9b1b3a _PyEval_EvalCodeWithName (/usr/local/sagegit/local/var/tmp/sage/build/python3-3.6.1.p1/src/libpython3.6m.so.1.0)
                #12 0x00007fcabd9b218f PyEval_EvalCodeEx (/usr/local/sagegit/local/var/tmp/sage/build/python3-3.6.1.p1/src/libpython3.6m.so.1.0)
                #13 0x00007fcabd9b21bb PyEval_EvalCode (/usr/local/sagegit/local/var/tmp/sage/build/python3-3.6.1.p1/src/libpython3.6m.so.1.0)
                #14 0x00007fcabd9af19d builtin_exec_impl (/usr/local/sagegit/local/var/tmp/sage/build/python3-3.6.1.p1/src/libpython3.6m.so.1.0)
                #15 0x00007fcabd926085 PyCFunction_Call (/usr/local/sagegit/local/var/tmp/sage/build/python3-3.6.1.p1/src/libpython3.6m.so.1.0)
                #16 0x00007fcabd9b9098 do_call_core (/usr/local/sagegit/local/var/tmp/sage/build/python3-3.6.1.p1/src/libpython3.6m.so.1.0)
                #17 0x00007fcabd9b1b3a _PyEval_EvalCodeWithName (/usr/local/sagegit/local/var/tmp/sage/build/python3-3.6.1.p1/src/libpython3.6m.so.1.0)
                #18 0x00007fcabd9b1dd2 fast_function (/usr/local/sagegit/local/var/tmp/sage/build/python3-3.6.1.p1/src/libpython3.6m.so.1.0)
                #19 0x00007fcabd9b564f _PyEval_EvalFrameDefault (/usr/local/sagegit/local/var/tmp/sage/build/python3-3.6.1.p1/src/libpython3.6m.so.1.0)
                #20 0x00007fcabd9b2139 _PyFunction_FastCall (/usr/local/sagegit/local/var/tmp/sage/build/python3-3.6.1.p1/src/libpython3.6m.so.1.0)
                #21 0x00007fcabd9b564f _PyEval_EvalFrameDefault (/usr/local/sagegit/local/var/tmp/sage/build/python3-3.6.1.p1/src/libpython3.6m.so.1.0)
                #22 0x00007fcabd9b2139 _PyFunction_FastCall (/usr/local/sagegit/local/var/tmp/sage/build/python3-3.6.1.p1/src/libpython3.6m.so.1.0)
                #23 0x00007fcabd9b564f _PyEval_EvalFrameDefault (/usr/local/sagegit/local/var/tmp/sage/build/python3-3.6.1.p1/src/libpython3.6m.so.1.0)
                #24 0x00007fcabd9b2139 _PyFunction_FastCall (/usr/local/sagegit/local/var/tmp/sage/build/python3-3.6.1.p1/src/libpython3.6m.so.1.0)
                #25 0x00007fcabd9b564f _PyEval_EvalFrameDefault (/usr/local/sagegit/local/var/tmp/sage/build/python3-3.6.1.p1/src/libpython3.6m.so.1.0)
                #26 0x00007fcabd9ba77f _PyFunction_FastCall (/usr/local/sagegit/local/var/tmp/sage/build/python3-3.6.1.p1/src/libpython3.6m.so.1.0)
                #27 0x00007fcabd8be76e _PyObject_FastCallDict (/usr/local/sagegit/local/var/tmp/sage/build/python3-3.6.1.p1/src/libpython3.6m.so.1.0)
                #28 0x00007fcabd8bf844 _PyObject_CallMethodIdObjArgs (/usr/local/sagegit/local/var/tmp/sage/build/python3-3.6.1.p1/src/libpython3.6m.so.1.0)
                #29 0x00007fcabd9d4781 PyImport_ImportModuleLevelObject (/usr/local/sagegit/local/var/tmp/sage/build/python3-3.6.1.p1/src/libpython3.6m.so.1.0)
                #30 0x00007fcabd9b9515 import_name (/usr/local/sagegit/local/var/tmp/sage/build/python3-3.6.1.p1/src/libpython3.6m.so.1.0)
                #31 0x00007fcabd9b1b3a _PyEval_EvalCodeWithName (/usr/local/sagegit/local/var/tmp/sage/build/python3-3.6.1.p1/src/libpython3.6m.so.1.0)
                #32 0x00007fcabd9b218f PyEval_EvalCodeEx (/usr/local/sagegit/local/var/tmp/sage/build/python3-3.6.1.p1/src/libpython3.6m.so.1.0)
                #33 0x00007fcabd9b21bb PyEval_EvalCode (/usr/local/sagegit/local/var/tmp/sage/build/python3-3.6.1.p1/src/libpython3.6m.so.1.0)
                #34 0x00007fcabd9e572f run_mod (/usr/local/sagegit/local/var/tmp/sage/build/python3-3.6.1.p1/src/libpython3.6m.so.1.0)
                #35 0x00007fcabd9e57ab PyRun_SimpleStringFlags (/usr/local/sagegit/local/var/tmp/sage/build/python3-3.6.1.p1/src/libpython3.6m.so.1.0)
                #36 0x00007fcabda03e06 run_command (/usr/local/sagegit/local/var/tmp/sage/build/python3-3.6.1.p1/src/libpython3.6m.so.1.0)
                #37 0x0000000000400a8e main (python)
                #38 0x00007fcabcaf31bb __libc_start_main (libc.so.6)
                #39 0x0000000000400b4a _start (python)

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Reading symbols from /usr/local/sagegit/local/var/tmp/sage/build/python3-3.6.1.p1/src/python...done.
[New LWP 28762]

warning: .dynamic section for "/usr/lib64/libpython3.6m.so.1.0" is not at the expected address (wrong library or version mismatch?)
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib64/libthread_db.so.1".
Core was generated by `./python -c import crypt'.
Program terminated with signal SIGSEGV, Segmentation fault.
#0  __strlen_avx2 () at ../sysdeps/x86_64/multiarch/strlen-avx2.S:62
62              VPCMPEQ (%rdi), %ymm0, %ymm1

Comment 2 Dario Asprone 2018-05-18 05:16:30 UTC

The only problem in any way attributable to Fedora 28 is the python 3.6.1 error, the python 2 one and the linbox one (which you encounter once the python 3 error is fixed) are due to the new gcc 8 compiler, and are SageMath bugs.
See https://trac.sagemath.org/ticket/25391 for a complete fix (albeit the python 3 fix is more of a workaround).

Comment 3 artal 2018-05-18 16:36:19 UTC

(In reply to Dario Asprone from comment #2)
> The only problem in any way attributable to Fedora 28 is the python 3.6.1
> error, the python 2 one and the linbox one (which you encounter once the
> python 3 error is fixed) are due to the new gcc 8 compiler, and are SageMath
> bugs.
> See https://trac.sagemath.org/ticket/25391 for a complete fix (albeit the
> python 3 fix is more of a workaround).

Applying your patches, everything is OK.

Comment 4 Charalampos Stratakis 2018-08-28 18:19:21 UTC

Downloading sagemath 8.3 tarball which includes the aforementioned fixes on a F28 machine now and invoking 'make python2' or 'make python3', it compiles successfully.

Could you verify it so the bug can be closed?

Comment 5 artal 2018-08-29 07:54:33 UTC

Even the beta versions compile perfectly now with 'make build'. For me, it can be closed.