[Python-modules-team] Bug#917652: pywavelets 0.5.1-1.1: FTBFS, alignment problem

[Gianfranco Costamagna]

control: severity -1 serious
control: tags -1 patch pending

Patch uploaded in sid, since the current NMU can't migrate due to this bug


G.

On Sat, 29 Dec 2018 19:23:33 +0000 Steve McIntyre <steve at einval.com> wrote:
> Source: pywavelets
> Version: 0.5.1-1.1
> Severity: important
> User: debian-arm at lists.debian.org
> Usertags: alignment
> 
> Hi!
> 
> I've been doing a full rebuild of the Debian archive, building all
> source packages targeting armel and armhf using arm64 hardware. We are
> planning in future to move all of our 32-bit armel/armhf builds to
> using arm64 machines, so this rebuild is to identify packages that
> might have problems with this configuration.
> 
> A feature of the arm64 kernel is that it does *not* support fixing up
> code with broken alignment, so code that might have built and run OK
> on our older armel/armhf build machines due to kernel fixups will now
> fail.
> 
> When building your package, I've found a bus error (aka alignment
> fault). The full log is online at
> 
>   https://www.einval.com/debian/arm/rebuild-logs/armel/FAIL/pywavelets_0.5.1-1.1_armel.log
> 
> for reference
> 
> I've done a quick bit of debugging to find the source of the
> bug. Here's a gdb stacktrace and variable printout to demonstrate the
> problem.
> 
> (sid-armel)steve at maul:~/debian/build/pywavelets/pywavelets-0.5.1$ gdb /usr/bin/python2.7 core
> ...
> Reading symbols from /usr/bin/python2.7...(no debugging symbols found)...done.
> [New LWP 3291]
> [Thread debugging using libthread_db enabled]
> Using host libthread_db library "/lib/arm-linux-gnueabi/libthread_db.so.1".
> Core was generated by `python2.7 -c import sys ; sys.path.insert(0, '/home/steve/debian/build/pywavele'.
> Program terminated with signal SIGBUS, Bus error.
> #0  double_downcoef_axis (input=0x1011b90, input_info=..., output=0xfe4500, output_info=..., wavelet=0x1161b78, axis=0, coef=COEF_APPROX, dwt_mode=MODE_SYMMETRIC, swt_level=0, 
>     transform=DWT_TRANSFORM) at pywt/_extensions/c/wt.template.c:100
> 100                     temp_input[j] = *(TYPE *)(((char *) input) + input_offset
> (gdb) list  
> 95
> 96              // Copy to temporary input if necessary
> 97              if (make_temp_input)
> 98                  for (j = 0; j < input_info.shape[axis]; ++j)
> 99                      // Offsets are byte offsets, to need to cast to char and back
> 100                     temp_input[j] = *(TYPE *)(((char *) input) + input_offset
> 101                                               + j * input_info.strides[axis]);
> 102
> 103             // Select temporary or direct output and input
> 104             input_row = make_temp_input ? temp_input
> (gdb) p input
> $1 = (const double * const restrict) 0x1011b90
> (gdb) p input_offset 
> $2 = <optimized out>
> (gdb) p j
> $3 = <optimized out>
> 
> This is a classic pattern for alignment problems. You can't just cast
-------------- next part --------------
diff -Nru pywavelets-0.5.1/debian/changelog pywavelets-0.5.1/debian/changelog
--- pywavelets-0.5.1/debian/changelog	2019-12-13 19:37:57.000000000 +0100
+++ pywavelets-0.5.1/debian/changelog	2019-12-18 15:36:45.000000000 +0100
@@ -1,3 +1,11 @@
+pywavelets (0.5.1-1.3) unstable; urgency=medium
+
+  * Non-maintainer upload.
+  * Grab patch from Ubuntu and Balint Reczey to fix an aligment problem on
+    armhf (Closes: #917652)
+
+ -- Gianfranco Costamagna <locutusofborg at debian.org>  Wed, 18 Dec 2019 15:36:45 +0100
+
 pywavelets (0.5.1-1.2) unstable; urgency=medium
 
   * Non-maintainer upload.
diff -Nru pywavelets-0.5.1/debian/patches/03-Explicity-align-data-records-in-test_byte_offset.patch pywavelets-0.5.1/debian/patches/03-Explicity-align-data-records-in-test_byte_offset.patch
--- pywavelets-0.5.1/debian/patches/03-Explicity-align-data-records-in-test_byte_offset.patch	1970-01-01 01:00:00.000000000 +0100
+++ pywavelets-0.5.1/debian/patches/03-Explicity-align-data-records-in-test_byte_offset.patch	2019-12-18 15:36:38.000000000 +0100
@@ -0,0 +1,25 @@
+From a2474a8d81a105c9abe525f5279568322f71a77c Mon Sep 17 00:00:00 2001
+From: Balint Reczey <balint.reczey at canonical.com>
+Date: Fri, 5 May 2017 11:51:14 +0000
+Subject: [PATCH] TST: Explicity align data records in test_byte_offset()
+
+Also use dict for dtype definition because list format
+ignores alignment. See https://github.com/numpy/numpy/issues/663
+---
+ pywt/tests/test_multidim.py | 5 +++--
+ 1 file changed, 3 insertions(+), 2 deletions(-)
+
+--- a/pywt/tests/test_multidim.py
++++ b/pywt/tests/test_multidim.py
+@@ -86,8 +86,9 @@
+ 
+         for mode in pywt.Modes.modes:
+             expected = pywt.dwtn(data, wavelet)
+-            padded = np.ones((3, 6), dtype=np.dtype([('data', data.dtype),
+-                                                     ('pad', 'byte')]))
++            padded = np.ones((3, 6), dtype=np.dtype({'ddata': (data.dtype, 0),
++                                                     'pad': ('byte', data.dtype.itemsize)},
++                                                    align=True))
+             padded[:] = data
+             padded_dwtn = pywt.dwtn(padded['data'], wavelet)
+             for key in expected.keys():
diff -Nru pywavelets-0.5.1/debian/patches/series pywavelets-0.5.1/debian/patches/series
--- pywavelets-0.5.1/debian/patches/series	2015-11-08 20:38:24.000000000 +0100
+++ pywavelets-0.5.1/debian/patches/series	2019-12-18 15:36:38.000000000 +0100
@@ -1,3 +1,4 @@
 01-get_version_from_source.patch
 02-remove_privacy_offenders.patch
+03-Explicity-align-data-records-in-test_byte_offset.patch
 do_not_rewrite_git_revision_on_build.patch