Re: Bug#956324: Clustalo bus error on mipsel (Was: Bug#956324: python-biopython: FTBFS on mipsel)
> On Apr 29, 2020, at 09:04, Andreas Tille wrote: > > On Wed, Apr 29, 2020 at 07:14:30AM -0700, Matthew Fernandez wrote: > >> For those on this thread who have access to mipsel hardware or can shell in >> to one of the mipsel build machines, I would suggest running an >> ASan-instrumented test there (`export CFLAGS="-g -fsanitize=address"; export >> CXXFLAGS="-g -fsanitize=address"`) and see what we learn. > > I tried on real hardware. Unfortunately I'm running into > > > > configure:3720: $? = 0 > configure:3709: gcc -v >&5 > Using built-in specs. > COLLECT_GCC=gcc > COLLECT_LTO_WRAPPER=/usr/lib/gcc/mipsel-linux-gnu/9/lto-wrapper > Target: mipsel-linux-gnu > Configured with: ../src/configure -v --with-pkgversion='Debian 9.3.0-10' > --with-bugurl=file:///usr/share/doc/gcc-9/README.Bugs > --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,gm2 --prefix=/usr > --with-gcc-major-version-only --program-suffix=-9 > --program-prefix=mipsel-linux-gnu- --enable-shared --enable-linker-build-id > --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix > --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug > --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new > --enable-gnu-unique-object --disable-libitm --disable-libsanitizer > --disable-libquadmath --disable-libquadmath-support --enable-plugin > --enable-default-pie --with-system-zlib --with-target-system-zlib=auto > --enable-multiarch --disable-werror --enable-multilib --with-arch-32=mips32r2 > --with-fp-32=xx --with-madd4=no --with-lxc1-sxc1=no --enable-targets=all > --with-arch-64=mips64r2 --enable-checking=release --build=mipsel-linux-gnu > --host=mipsel-linux-gnu --target=mipsel-linux-gnu > Thread model: posix > gcc version 9.3.0 (Debian 9.3.0-10) > configure:3720: $? = 0 > configure:3709: gcc -V >&5 > gcc: error: unrecognized command line option '-V' > gcc: fatal error: no input files > compilation terminated. > configure:3720: $? = 1 > configure:3709: gcc -qversion >&5 > gcc: error: unrecognized command line option '-qversion'; did you mean > '--version'? > gcc: fatal error: no input files > compilation terminated. > configure:3720: $? = 1 > configure:3740: checking whether the C compiler works > configure:3762: gcc -g -O2 -fdebug-prefix-map=/home/tille/clustalo=. > -fstack-protector-strong -Wformat -Werror=format-security -fsanitize=address > -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now conftest.c >&5 > /usr/bin/ld: cannot find libasan_preinit.o: No such file or directory > /usr/bin/ld: cannot find -lasan > collect2: error: ld returned 1 exit status > configure:3766: $? = 1 > configure:3804: result: no > configure: failed program was: > > > > I have no idea why libasan_preinit.o and libasan.a are not installed. > The package libgcc-9-dev is installed for sure and on amd64 both files > are included here. It seems the sudo command on eller does not permit > me executing `apt-file update` in a chroot so I have no idea where these > files are on mipsel (if they exist at all). > > Any more help from debian-mipsel is really appreciated. Hm yes, “--disable-libsanitizer” is rather ominous. I guess the mipsel GCC package has been built without ASan support. Surprising that it fails so messily (the front end seems to think -fsanitize=address is an accepted command line option), but libasan does indeed seem not available on mipsel [0]. The other option I suggested was Valgrind, but if you can’t run apt-file you probably can’t install Valgrind either. If anyone spectating has ideas, please chime in. [0]: https://packages.debian.org/search?searchon=contents=libasan.so=exactfilename=sid=mipsel
Re: Again question about migration to testing
Am 24.04.2020 um 06:21 teilte Sebastiaan Couwenberg mit: > On 4/24/20 12:01 AM, Hilmar Preuße wrote: Hi Sebastiaan, >> I'm quite sure, this regression is not caused by the TL upload, but by >> the Sphinx upload. The last successful autopkgtest was with version >> Sphinx v1.8.5, it fails since v2.4.3. Is there anything I can do to >> clarify the situation? Do I have to file a bug anywhere? > > Start by filing an RC bug against jupyter-sphinx-theme for the failing > autopkgtest [0], testing autoremoval should help get it out of testing > and unblocking migration of packages it blocked. > That worked. The autopkg test works again, and [0] shows that TL 2020 has migrated to testing. Thanks for help! Hilmar [0] https://tracker.debian.org/pkg/texlive-bin -- sigfault #206401 http://counter.li.org signature.asc Description: OpenPGP digital signature
Bug#959143: RFS: libgrokj2k/7.1.0-1 [ITP] -- JPEG 2000 image compression/decompression library
Package: sponsorship-requests Severity: wishlist Dear mentors, I am looking for a sponsor for my package "libgrokj2k". Grok is one of only two actively developed open source JPEG 2000 toolkits on the planet. * Package name: libgrokj2k Version : 7.1.0-1 Upstream Author : boxe...@gmail.com * URL : https://github.com/GrokImageCompression/grok * License : AGPL-3 and BSD-2-clause * Vcs : https://github.com/GrokImageCompression/grok Section : libs It builds those binary packages: libgrokj2k1 - JPEG 2000 image compression/decompression library libgrokj2k1-dev - development files for Grok, a JPEG 2000 image library grokj2k-tools - command-line tools for the Grok JPEG 2000 library To access further information about this package, please visit the following URL: https://mentors.debian.net/package/libgrokj2k Alternatively, one can download the package with dget using this command: dget -x https://mentors.debian.net/debian/pool/main/libg/libgrokj2k/libgrokj2k_7.1.0-1.dsc Changes since the last upload: * Initial release. Closes: #954265 Thank You! -- Aaron Boxer
Bug#956731: Acknowledgement (RFS: check/0.14.0-0.1 [NMU] -- unit test framework for C)
I uploaded a new version, which switches to debhelper compat level 13,
updates the copyright file and disables the auto-test step on ppc architectures.
Changes since the last upload:
* Non-maintainer upload.
* New upstream version 0.14.0
* d/{control,compat}: switch to debhelper compat level 13
* d/control:
- bump std-version to 4.5.0 (no further changes)
- drop dependency fulfilled since jessie
* d/patches: add patch to correct misspelling
* d/rules:
- drop unneeded dh option '--buildsystem=autoconf --with autoreconf'
- break configure lines
- add 'dh_missing --fail-missing'
- disable auto-test for ppc architectures (Closes: #918572, #951667)
* debian: cleanup unnecessary .dirs and .files items
* d/tests: add simple autopkgtest
* d/copyright: update
The unstable version 0.12.0-0.1 is currently prevented from migration
to testing due to #918572 [1].
Also #951667 [2] will be resolved with this new version.
Check 0.11.0 introduces the common check macros 'ck_assert_ptr_null'
and 'ck_assert_ptr_nonnull',
which are e.g. required for SELint [3] which I'd like to package perspectively.
[1]: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=918572
[2]: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=951667
[3]: https://github.com/TresysTechnology/selint
p.s.: due to timeout tests the build can take up to 15 minutes, see
https://salsa.debian.org/cgzones/check/-/jobs/705379
Re: Bug#956324: Clustalo bus error on mipsel (Was: Bug#956324: python-biopython: FTBFS on mipsel)
Hi Matthew, On Wed, Apr 29, 2020 at 07:14:30AM -0700, Matthew Fernandez wrote: > > To add another data point to this discussion, one other (fruitless) thing I > tried previously was cross-compiling Clustal Omega. From an amd64 host, it’s > possible to target mipsel using the GCC cross-compilers in the standard > Debian repositories. You can then run the resulting binary using Qemu’s user > mode. Using this technique, the f002 test runs to completion with no bus > error. This is not really surprising as AFAIK unaligned accesses that would > trigger a bus error on mipsel hardware would be silently allowed in this > configuration (Qemu doesn’t faithfully emulate this hardware behaviour and > amd64 allows unaligned access). > > Unfortunately the repositories’ cross-compilers have been built without ASan > enabled and you can’t attach to an emulated mipsel process with a native > Valgrind. So debugging memory safety issues is not straightforward. To go > further with this approach, you would have to build a mipsel-targeting > cross-compiler with ASan enabled or cross-compile Valgrind to mipsel. For a > true masochist, it may be possible to attach to the process with GDB or rr > and reverse-step from the location Andreas has quoted, but I wouldn’t trust > the debugger not to crash in this configuration. Even then the issue may not > be reproducible because it may be dependent on transformations/optimizations > only performed by the particular version of the native mipsel compiler called > during packaging. Thanks a lot for your effort. > For those on this thread who have access to mipsel hardware or can shell in > to one of the mipsel build machines, I would suggest running an > ASan-instrumented test there (`export CFLAGS="-g -fsanitize=address"; export > CXXFLAGS="-g -fsanitize=address"`) and see what we learn. I tried on real hardware. Unfortunately I'm running into configure:3720: $? = 0 configure:3709: gcc -v >&5 Using built-in specs. COLLECT_GCC=gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/mipsel-linux-gnu/9/lto-wrapper Target: mipsel-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 9.3.0-10' --with-bugurl=file:///usr/share/doc/gcc-9/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,gm2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-9 --program-prefix=mipsel-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libsanitizer --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --with-target-system-zlib=auto --enable-multiarch --disable-werror --enable-multilib --with-arch-32=mips32r2 --with-fp-32=xx --with-madd4=no --with-lxc1-sxc1=no --enable-targets=all --with-arch-64=mips64r2 --enable-checking=release --build=mipsel-linux-gnu --host=mipsel-linux-gnu --target=mipsel-linux-gnu Thread model: posix gcc version 9.3.0 (Debian 9.3.0-10) configure:3720: $? = 0 configure:3709: gcc -V >&5 gcc: error: unrecognized command line option '-V' gcc: fatal error: no input files compilation terminated. configure:3720: $? = 1 configure:3709: gcc -qversion >&5 gcc: error: unrecognized command line option '-qversion'; did you mean '--version'? gcc: fatal error: no input files compilation terminated. configure:3720: $? = 1 configure:3740: checking whether the C compiler works configure:3762: gcc -g -O2 -fdebug-prefix-map=/home/tille/clustalo=. -fstack-protector-strong -Wformat -Werror=format-security -fsanitize=address -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now conftest.c >&5 /usr/bin/ld: cannot find libasan_preinit.o: No such file or directory /usr/bin/ld: cannot find -lasan collect2: error: ld returned 1 exit status configure:3766: $? = 1 configure:3804: result: no configure: failed program was: I have no idea why libasan_preinit.o and libasan.a are not installed. The package libgcc-9-dev is installed for sure and on amd64 both files are included here. It seems the sudo command on eller does not permit me executing `apt-file update` in a chroot so I have no idea where these files are on mipsel (if they exist at all). Any more help from debian-mipsel is really appreciated. Kind regards Andreas. -- http://fam-tille.de
Re: Bug#956324: Clustalo bus error on mipsel (Was: Bug#956324: python-biopython: FTBFS on mipsel)
> On Apr 29, 2020, at 02:12, Andreas Tille wrote: > > Hi, > > On Wed, Apr 29, 2020 at 10:30:35AM +0800, 黄佳文 wrote: >> I am a developer from Loongson company (R & D CPU/mip64el), I've been >> looking at this recently. > > Very nice to see mips developers to care for biological software. :-) > >> I did two experiments, and I found that when I used Python 3,7 to compile >> python-biopython, Build successfully. >> In the same environment, I just upgrade Python 3.7 to Python 3.8, and then >> compile python-biopytho, Build fails, but not bus error. >> I found through online query that some symbol tables were added and deleted >> in upgrading Python 3.7 to 3.8. The following are symbol tables: > > Sorry to insist here - I do not think that it is a Python version problem > at all. The issue can be reproduced in clustalo only which is pure C code. > May be you have a look at > > https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=956324#59 > > and the following discussion. Despite Matthew has found some issues inside > the C code it did not helped to prevent: > > > Starting program: /home/tille/clustalo/src/clustalo -i > debian/tests/biopython_testdata/f002 --guidetree-out temp_test.dnd -o > temp_test.aln --outfmt clustal --force > [Thread debugging using libthread_db enabled] > Using host libthread_db library "/lib/mipsel-linux-gnu/libthread_db.so.1". > > Program received signal SIGBUS, Bus error. > 0x5556a1b8 in PairDistances (distmat=0x7fff278c, mseq=0x55692a30, > pairdist_type=, bPercID=, istart=0, iend=3, > jstart=0, jend=3, fdist_in=0x0, >fdist_out=0x0) at pair_dist.c:346 > 346 NewProgress(, LogGetFP(, LOG_INFO), > > > That's the issue we need to care about here. To add another data point to this discussion, one other (fruitless) thing I tried previously was cross-compiling Clustal Omega. From an amd64 host, it’s possible to target mipsel using the GCC cross-compilers in the standard Debian repositories. You can then run the resulting binary using Qemu’s user mode. Using this technique, the f002 test runs to completion with no bus error. This is not really surprising as AFAIK unaligned accesses that would trigger a bus error on mipsel hardware would be silently allowed in this configuration (Qemu doesn’t faithfully emulate this hardware behaviour and amd64 allows unaligned access). Unfortunately the repositories’ cross-compilers have been built without ASan enabled and you can’t attach to an emulated mipsel process with a native Valgrind. So debugging memory safety issues is not straightforward. To go further with this approach, you would have to build a mipsel-targeting cross-compiler with ASan enabled or cross-compile Valgrind to mipsel. For a true masochist, it may be possible to attach to the process with GDB or rr and reverse-step from the location Andreas has quoted, but I wouldn’t trust the debugger not to crash in this configuration. Even then the issue may not be reproducible because it may be dependent on transformations/optimizations only performed by the particular version of the native mipsel compiler called during packaging. For those on this thread who have access to mipsel hardware or can shell in to one of the mipsel build machines, I would suggest running an ASan-instrumented test there (`export CFLAGS="-g -fsanitize=address"; export CXXFLAGS="-g -fsanitize=address"`) and see what we learn.
Re: Bug#956324: Clustalo bus error on mipsel (Was: Bug#956324: python-biopython: FTBFS on mipsel)
Hi, On Wed, Apr 29, 2020 at 10:30:35AM +0800, 黄佳文 wrote: > I am a developer from Loongson company (R & D CPU/mip64el), I've been > looking at this recently. Very nice to see mips developers to care for biological software. :-) > I did two experiments, and I found that when I used Python 3,7 to compile > python-biopython, Build successfully. > In the same environment, I just upgrade Python 3.7 to Python 3.8, and then > compile python-biopytho, Build fails, but not bus error. > I found through online query that some symbol tables were added and deleted > in upgrading Python 3.7 to 3.8. The following are symbol tables: Sorry to insist here - I do not think that it is a Python version problem at all. The issue can be reproduced in clustalo only which is pure C code. May be you have a look at https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=956324#59 and the following discussion. Despite Matthew has found some issues inside the C code it did not helped to prevent: Starting program: /home/tille/clustalo/src/clustalo -i debian/tests/biopython_testdata/f002 --guidetree-out temp_test.dnd -o temp_test.aln --outfmt clustal --force [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib/mipsel-linux-gnu/libthread_db.so.1". Program received signal SIGBUS, Bus error. 0x5556a1b8 in PairDistances (distmat=0x7fff278c, mseq=0x55692a30, pairdist_type=, bPercID=, istart=0, iend=3, jstart=0, jend=3, fdist_in=0x0, fdist_out=0x0) at pair_dist.c:346 346 NewProgress(, LogGetFP(, LOG_INFO), That's the issue we need to care about here. Kind regards and thanks a lot for the attempt to help Andreas.
