SEGFAULT with auditwheel + patchelf

[magicse]

Describe the bug
SEGFAULT with auditwheel + patchelf
General problem that wheel libs repaired in Qemu Docker image work in Qemu but didn't work in the same image Docker on real ARMv7, and without wheelaudit+patchelf, built packages work well.
GDB show that problem with memory maping in patched /usr/local/lib/python3.10/site-packages/*.libs/libstdc++-ad7c573d.so.6.0.29 .libs/libgcc_s-8c7760c8.so.1

A clear and concise description of what the bug is.
Patched in Qemu docker ARMv7 libraries after that give SEGFAULT on real ARMv7
pypa/auditwheel#414 (comment)

Steps To Reproduce
All steps in this post
home-assistant/core#86589 (comment)

Expected behavior
Worked python wheel
patchelf --version output
patchelf 0.17.2
Additional context
strace of patched lib
home-assistant/core#86589 (comment)

[brenoguim]

Would it be possible to attach de libstdc++ before and after patching? And also the patchelf command that was used? That would help a lot in the investigation.
Attaching the result of readelf -W -a <libname> before and after patching would also help

[magicse]

Would it be possible to attach de libstdc++ before and after patching?

No problem. I'll make this

[magicse]

Here is readelf logs
readelf-aW.zip

Original and patched libs
Libs_original_patched.zip

And also the patchelf command that was used?

I dont know, bacuse this commands make auditwheel python package
pypa/auditwheel#414 (comment)

[brenoguim]

Looks like the alignment of the existing LOAD segments is 0x10000 while patchelf is adding two new load segments with alignment 0x1000. It seems that armv7 requires the former alignment. I don't know for sure if that is the cause, but it's a good guess.
There is code to detect the correct alignment in patchelf, let me see why it didn't kick int.

[magicse]

@brenoguim, this is already a good step towards solving the problem.

[brenoguim]

@magicse would you be able to test the build from #475 ? I don't have an ARMv7 box.

[magicse]

Yes sure

[magicse]

bash-5.1# pip install --force-reinstall cchardet-2.1.7-cp310-cp310-musllinux_1_2_armv7l.whl 
Processing ./cchardet-2.1.7-cp310-cp310-musllinux_1_2_armv7l.whl
Installing collected packages: cchardet
  Attempting uninstall: cchardet
    Found existing installation: cchardet 2.1.7
    Uninstalling cchardet-2.1.7:
      Successfully uninstalled cchardet-2.1.7
Successfully installed cchardet-2.1.7

bash-5.1# python -c "import cchardet"
Segmentation fault

bash-5.1# ldd /usr/local/lib/python3.10/site-packages/cchardet.libs/libstdc++-ad7c573d.so.6.0.29 
        /lib/ld-musl-armhf.so.1 (0x542d0000)
Error loading shared library : Invalid argument (needed by /usr/local/lib/python3.10/site-packages/cchardet.libs/libstdc++-ad7c573d.so.6.0.29)
Error loading shared library error_code: No such file or directory (needed by /usr/local/lib/python3.10/site-packages/cchardet.libs/libstdc++-ad7c573d.so.6.0.29)
Segmentation fault
bash-5.1# 

strace ldd /usr/local/lib/python3.10/site-packages/cchardet.libs/libstdc++-ad7c573d.so.6.0.29

bash-5.1# strace ldd /usr/local/lib/python3.10/site-packages/cchardet.libs/libstdc++-ad7c573d.so.6.0.29 
execve("/usr/bin/ldd", ["ldd", "/usr/local/lib/python3.10/site-p"...], 0x7df67cf4 /* 16 vars */) = 0
set_tls(0x75a9a400)                     = 0
set_tid_address(0x75a997cc)             = 281
brk(NULL)                               = 0x560e0000
brk(0x560f0000)                         = 0x560f0000
mmap2(0x560e0000, 32768, PROT_NONE, MAP_PRIVATE|MAP_FIXED|MAP_ANONYMOUS, -1, 0) = 0x560e0000
getuid32()                              = 0
getpid()                                = 281
rt_sigprocmask(SIG_UNBLOCK, [RT_1 RT_2], NULL, 8) = 0
rt_sigaction(SIGCHLD, {sa_handler=0x54327c11, sa_mask=~[RTMIN RT_1 RT_2], sa_flags=SA_RESTORER, sa_restorer=0x75a501fb}, NULL, 8) = 0
getppid()                               = 278
statx(AT_FDCWD, "/config", AT_STATX_SYNC_AS_STAT, STATX_BASIC_STATS, 0x7dc57698) = -1 ENOSYS (Function not implemented)
stat64("/config", {st_mode=S_IFDIR|0777, st_size=4096, ...}) = 0
statx(AT_FDCWD, ".", AT_STATX_SYNC_AS_STAT, STATX_BASIC_STATS, 0x7dc57698) = -1 ENOSYS (Function not implemented)
stat64(".", {st_mode=S_IFDIR|0777, st_size=4096, ...}) = 0
open("/usr/bin/ldd", O_RDONLY|O_LARGEFILE|O_CLOEXEC) = 3
fcntl64(3, F_SETFD, FD_CLOEXEC)         = 0
fcntl64(3, F_DUPFD_CLOEXEC, 10)         = 10
fcntl64(10, F_SETFD, FD_CLOEXEC)        = 0
close(3)                                = 0
rt_sigaction(SIGINT, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGINT, {sa_handler=0x54327c11, sa_mask=~[RTMIN RT_1 RT_2], sa_flags=SA_RESTORER, sa_restorer=0x75a501fb}, NULL, 8) = 0
rt_sigaction(SIGQUIT, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGQUIT, {sa_handler=SIG_IGN, sa_mask=~[RTMIN RT_1 RT_2], sa_flags=SA_RESTORER, sa_restorer=0x75a501fb}, NULL, 8) = 0
rt_sigaction(SIGTERM, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
read(10, "#!/bin/sh\nexec /lib/ld-musl-armh"..., 2047) = 51
rt_sigaction(SIGQUIT, {sa_handler=SIG_DFL, sa_mask=~[RTMIN RT_1 RT_2], sa_flags=SA_RESTORER, sa_restorer=0x75a501fb}, NULL, 8) = 0
execve("/lib/ld-musl-armhf.so.1", ["/lib/ld-musl-armhf.so.1", "--list", "/usr/local/lib/python3.10/site-p"...], 0x75a98414 /* 16 vars */) = 0
set_tls(0x54802400)                     = 0
set_tid_address(0x548017cc)             = 281
open("/usr/local/lib/python3.10/site-packages/cchardet.libs/libstdc++-ad7c573d.so.6.0.29", O_RDONLY|O_LARGEFILE) = 3
read(3, "\177ELF\1\1\1\0\0\0\0\0\0\0\0\0\3\0(\0\1\0\0\0\0\0\0\0004\0\0\0"..., 936) = 936
mmap2(NULL, 2228224, PROT_READ|PROT_EXEC, MAP_PRIVATE, 3, 0) = 0x75a78000
mmap2(0x75bc8000, 65536, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED, 3, 0x140000) = 0x75bc8000
mmap2(0x75bd0000, 458752, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED, 3, 0x148000) = 0x75bd0000
mmap2(0x75c38000, 393216, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED, 3, 0x1a8000) = 0x75c38000
close(3)                                = 0
writev(1, [{iov_base="\t/lib/ld-musl-armhf.so.1 (0x5477"..., iov_len=38}, {iov_base=NULL, iov_len=0}], 2        /lib/ld-musl-armhf.so.1 (0x54778000)
) = 38
brk(NULL)                               = 0x55000000
brk(0x55010000)                         = 0x55010000
mmap2(0x55000000, 32768, PROT_NONE, MAP_PRIVATE|MAP_FIXED|MAP_ANONYMOUS, -1, 0) = 0x55000000
writev(2, [{iov_base="Error loading shared library : I"..., iov_len=59}, {iov_base="/usr/local/lib/python3.10/site-p"..., iov_len=82}], 2Error loading shared library : Invalid argument (needed by /usr/local/lib/python3.10/site-packages/cchardet.libs/libstdc++-ad7c573d.so.6.0.29) = 141
writev(2, [{iov_base=")", iov_len=1}, {iov_base=NULL, iov_len=0}], 2)) = 1
writev(2, [{iov_base="\n", iov_len=1}, {iov_base=NULL, iov_len=0}], 2
) = 1
open("/etc/ld-musl-armhf.path", O_RDONLY|O_LARGEFILE|O_CLOEXEC) = -1 ENOENT (No such file or directory)
open("/lib/error_code", O_RDONLY|O_LARGEFILE|O_CLOEXEC) = -1 ENOENT (No such file or directory)
open("/usr/local/lib/error_code", O_RDONLY|O_LARGEFILE|O_CLOEXEC) = -1 ENOENT (No such file or directory)
open("/usr/lib/error_code", O_RDONLY|O_LARGEFILE|O_CLOEXEC) = -1 ENOENT (No such file or directory)
writev(2, [{iov_base="Error loading shared library err"..., iov_len=78}, {iov_base="/usr/local/lib/python3.10/site-p"..., iov_len=82}], 2Error loading shared library error_code: No such file or directory (needed by /usr/local/lib/python3.10/site-packages/cchardet.libs/libstdc++-ad7c573d.so.6.0.29) = 160
writev(2, [{iov_base=")", iov_len=1}, {iov_base=NULL, iov_len=0}], 2)) = 1
writev(2, [{iov_base="\n", iov_len=1}, {iov_base=NULL, iov_len=0}], 2
) = 1
--- SIGSEGV {si_signo=SIGSEGV, si_code=SEGV_MAPERR, si_addr=0x76ba40a4} ---
+++ killed by SIGSEGV +++
Segmentation fault
bash-5.1# 

[brenoguim]

Ouch! I'll take a look at it later on tonight.

[magicse]

Hi @brenoguim, thank you very much for helping ..... It's very kind of you.

[magicse]

Colorfull comparison of differences of readelf log of original and patched files

[brenoguim]

The new loads (second image) are still using alignment 0x1000 instead. Could you double check you used the patchelf with my fix?

[magicse]

ok no problem. Also colorful logs are first logs not actual.
It this archive https://github.com/NixOS/patchelf/suites/11359838081/artifacts/584162670 ? Am i correct ?

[magicse]

Also here grep of wheelaudit for patchelf

bash-5.1# grep -r "patchelf" /usr/local/lib/python3.10/site-packages/auditwheel/*
grep: /usr/local/lib/python3.10/site-packages/auditwheel/__pycache__/patcher.cpython-310.pyc: binary file matches
/usr/local/lib/python3.10/site-packages/auditwheel/patcher.py:def _verify_patchelf() -> None:
/usr/local/lib/python3.10/site-packages/auditwheel/patcher.py:    """This function looks for the ``patchelf`` external binary in the PATH,
/usr/local/lib/python3.10/site-packages/auditwheel/patcher.py:    if not find_executable("patchelf"):
/usr/local/lib/python3.10/site-packages/auditwheel/patcher.py:        raise ValueError("Cannot find required utility `patchelf` in PATH")
/usr/local/lib/python3.10/site-packages/auditwheel/patcher.py:        version = check_output(["patchelf", "--version"]).decode("utf-8")
/usr/local/lib/python3.10/site-packages/auditwheel/patcher.py:        raise ValueError("Could not call `patchelf` binary")
/usr/local/lib/python3.10/site-packages/auditwheel/patcher.py:    m = re.match(r"patchelf\s+(\d+(.\d+)?)", version)
/usr/local/lib/python3.10/site-packages/auditwheel/patcher.py:        f"patchelf {version} found. auditwheel repair requires " "patchelf >= 0.14."
/usr/local/lib/python3.10/site-packages/auditwheel/patcher.py:        _verify_patchelf()
/usr/local/lib/python3.10/site-packages/auditwheel/patcher.py:                "patchelf",
/usr/local/lib/python3.10/site-packages/auditwheel/patcher.py:        check_call(["patchelf", "--set-soname", new_so_name, file_name])
/usr/local/lib/python3.10/site-packages/auditwheel/patcher.py:        check_call(["patchelf", "--remove-rpath", file_name])
/usr/local/lib/python3.10/site-packages/auditwheel/patcher.py:        check_call(["patchelf", "--force-rpath", "--set-rpath", rpath, file_name])
/usr/local/lib/python3.10/site-packages/auditwheel/patcher.py:            check_output(["patchelf", "--print-rpath", file_name])
bash-5.1#