Hi!

First seen on the build arm-arm-01 which is an arm64 machine
configured to build for armhf, build log at

https://buildd.debian.org/status/fetch.php?pkg=python-fitsio&arch=armhf&ver=0.9.11%2Bdfsg-1%2Bb2&stamp=1530604224&raw=0

I can similarly reproduce this on other arm64 hardware. Backtrace
shows:

(gdb) bt
#0  ffi8fi8 (input=input@entry=0x16568df, ntodo=ntodo@entry=1, scale=1, zero=0, output=output@entry=0xfff3d1a0, status=status@entry=0xfff44384) at putcolj.c:1871
#1  0xf6cc5a8a in ffpcljj (fptr=0x15d3660, colnum=8, firstrow=<optimized out>, firstelem=1, nelem=1, array=0x16568df, status=0xfff44384) at putcolj.c:1428
#2  0xf6cc5c3c in ffpcljj (fptr=<optimized out>, colnum=<optimized out>, firstrow=<optimized out>, firstelem=firstelem@entry=1, nelem=nelem@entry=1, array=array@entry=0x16568df,
    status=status@entry=0xfff44384) at putcolj.c:1538
#3  0xf6cbc2b4 in ffpcl (fptr=<optimized out>, datatype=<optimized out>, colnum=<optimized out>, firstrow=1, firstelem=1, nelem=1, array=0x16568df, status=0xfff44384) at putcol.c:701
#4  0xf6e02a26 in ?? ()
Backtrace stopped: previous frame identical to this frame (corrupt stack?)
(gdb) p input
$2 = (LONGLONG *) 0x16568df

Disassembly of the problem area gives:

   0xf6cc54ce <+206>:   ldr.w   r0, [r10]
   0xf6cc54d2 <+210>:   ldmia.w sp!, {r4, r5, r6, r7, r8, r10, r11, pc}
   0xf6cc54d6 <+214>:   cmp     r1, #0
   0xf6cc54d8 <+216>:   ble.n   0xf6cc54ca <ffi8fi8+202>
   0xf6cc54da <+218>:   subs    r2, #8
   0xf6cc54dc <+220>:   add.w   r1, r0, r1, lsl #3
=> 0xf6cc54e0 <+224>:   ldrd    r4, r5, [r0], #8
   0xf6cc54e4 <+228>:   cmp     r1, r0
   0xf6cc54e6 <+230>:   strd    r4, r5, [r2, #8]!
   0xf6cc54ea <+234>:   bne.n   0xf6cc54e0 <ffi8fi8+224>
   0xf6cc54ec <+236>:   vpop    {d8-d12}
   0xf6cc54f0 <+240>:   ldr.w   r0, [r10]

The offending ldrd instruction here clearly matches up with the
source, which is the simple-case loop in ffi8fi8():

    if (scale == 1. && zero == 0.)
    {
        for (ii = 0; ii < ntodo; ii++)
                output[ii] = input[ii];
    }

The ldrd instruction will be the read from input[ii]. That's clearly
unaligned, given the LONGLONG *input which starts at 0x16568df.

This doesn't look like an issue with the compiler coalescing unrelated
values (which was an initial guess at the problem when discussing it
in #debian-buildd). It's simply reading an unaligned 64-bit value and
that's failing.

...
as we have (slow) alignment fixups enabled in the kernel. Disabling
that briefly and rebuilding, I see exactly the same build failure:

...
I: pybuild base:217: cd /home/93sam/build/python-fitsio/python-fitsio-0.9.11+dfsg/.pybuild/cpython2_2.7_fitsio/build; python2.7 -m unittest discover -v
testAsciiTableWriteRead (fitsio.test.TestReadWrite) ... ok
testBz2Read (fitsio.test.TestReadWrite) ... skipped 'bzip2 is not supported with debian cfitsio package'
testChecksum (fitsio.test.TestReadWrite) ... Bus error
E: pybuild pybuild:336: test: plugin distutils failed with: exit code=135: cd /home/93sam/build/python-fitsio/python-fitsio-0.9.11+dfsg/.pybuild/cpython2_2.7_fitsio/build; python2.7 -m unittest discover -v
dh_auto_test: pybuild --test -i python{version} -p 2.7 returned exit code 13
debian/rules:10: recipe for target 'build' failed
make: *** [build] Error 25
dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2

control: forwarded -1 https://github.com/esheldon/fitsio/issues/86

This is upstream issue #86. Marking the bug as forwarded.

We believe that the bug you reported is fixed in the latest version of
python-fitsio, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 902990@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Ole Streicher <olebole@debian.org> (supplier of updated python-fitsio package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@ftp-master.debian.org)
Format: 1.8
Date: Thu, 05 Jul 2018 11:09:18 +0200
Source: python-fitsio
Binary: python-fitsio python3-fitsio
Architecture: source
Version: 0.9.11+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Astronomy Team <debian-astro-maintainers@lists.alioth.debian.org>
Changed-By: Ole Streicher <olebole@debian.org>
Description:
 python-fitsio - Python 2 library to read from and write to FITS files
 python3-fitsio - Python 3 library to read from and write to FITS files
Closes: 902990
Changes:
 python-fitsio (0.9.11+dfsg-2) unstable; urgency=medium
 .
   * Update VCS fields to use salsa.d.o
   * Push compat to 11
   * Push Standards-Version to 4.1.5. Change copyright format URL to https
   * Fix aligned read (Closes: #902990)
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Hi,

I still don't have a final solution here, and upstreams proposed
solution does not work. Therefore, I adopted Ubuntus approach disabling
the tests for armhf until a solution is found. This makes the package
still usable on armhf (with the danger of running into an alignment
problem), but allows to lower the severity to important.

Cheers

Ole

The original bug is resolved by disabling build time tests on armhf. The
new one (with severity "important") is however kept open until the
problem is resolved upstream.

Cheers

Ole

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