Re: Bug#889147: abyss: PairedDBG_LoadAlgorithm test fails on sparc64 due to strict alignment violation
James Clarke <jrtc27@debian.org> writes:
> user debian-sparc@lists.debian.org
> usertags sparc64
> thanks
>
> (You missed the User: pseudoheader)
>
>> On 2 Feb 2018, at 14:46, David Matthew Mattli <dmm@mattli.us> wrote:
>>
>> Package: abyss
>> Severity: normal
>> Tags: patch upstream
>> Usertags: sparc64
>>
>> Dear Maintainer,
>>
>> This package currently FTBFS on sparc64 due to the
>> PairedDBG_LoadAlgorithm test failing with a SIGBUS. The Kmer.load and
>> Kmer.storeReverse methods in the Common/Kmer.cpp file cast a uint8_t*
>> to a size_t* without ensuring the pointer value has the proper
>> alignment.
>>
>> To fix this I added an aligned stack allocated buffer and memcpy to
>> that. Stack allocated is appropriate because the buffer size is
>> small(32 bytes) and known at compile time.
>
> Hi,
> As a sparc64 porter, thanks for fixing packages! Just a couple of
> comments on the patch.
>
>> --- a/Common/Kmer.cpp
>> +++ b/Common/Kmer.cpp
>> @@ -188,9 +188,10 @@
>> Seq seq;
>> #if MAX_KMER > 96
>> # if WORDS_BIGENDIAN
>> - const size_t *s = reinterpret_cast<const size_t*>(src);
>> + size_t buf[Kmer::NUM_BYTES];
>
> Should be divided by sizeof(size_t). Also, why not call it s? That should
> reduce the number of changes.
>
>> + memcpy(buf, src, Kmer::NUM_BYTES);
>> size_t *d = reinterpret_cast<size_t*>(&seq + 1);
>> - copy(s, s + Kmer::NUM_BYTES/sizeof(size_t), reverse_iterator<size_t*>(d));
>> + copy(buf, buf + Kmer::NUM_BYTES/sizeof(size_t), reverse_iterator<size_t*>(d));
>> # else
>> uint8_t *d = reinterpret_cast<uint8_t*>(&seq);
>> memcpy(d, src, sizeof seq);
>> @@ -235,9 +236,10 @@
>> #if MAX_KMER > 96
>> # if WORDS_BIGENDIAN
>> const size_t *s = reinterpret_cast<const size_t*>(&seq);
>> - size_t *d = reinterpret_cast<size_t*>(dest);
>> + size_t d[Kmer::NUM_BYTES];
>
> Ditto for the size (this time you used the same name as before).
>
>> copy(s, s + Kmer::NUM_BYTES/sizeof(size_t),
>> reverse_iterator<size_t*>(d + Kmer::NUM_BYTES/sizeof(size_t)));
>> + memcpy(dest, d, Kmer::NUM_BYTES);
>> reverse(dest, dest + Kmer::NUM_BYTES);
>> # else
>> memcpy(dest, &seq, Kmer::NUM_BYTES);
>
> Regards,
> James
Thanks for the quick feedback! How does this revised patch look?
Thanks,
David
--- a/Common/Kmer.cpp
+++ b/Common/Kmer.cpp
@@ -188,7 +188,8 @@
Seq seq;
#if MAX_KMER > 96
# if WORDS_BIGENDIAN
- const size_t *s = reinterpret_cast<const size_t*>(src);
+ size_t s[Kmer::NUM_BYTES/sizeof(size_t)];
+ memcpy(s, src, Kmer::NUM_BYTES);
size_t *d = reinterpret_cast<size_t*>(&seq + 1);
copy(s, s + Kmer::NUM_BYTES/sizeof(size_t), reverse_iterator<size_t*>(d));
# else
@@ -235,9 +236,10 @@
#if MAX_KMER > 96
# if WORDS_BIGENDIAN
const size_t *s = reinterpret_cast<const size_t*>(&seq);
- size_t *d = reinterpret_cast<size_t*>(dest);
+ size_t d[Kmer::NUM_BYTES/sizeof(size_t)];
copy(s, s + Kmer::NUM_BYTES/sizeof(size_t),
reverse_iterator<size_t*>(d + Kmer::NUM_BYTES/sizeof(size_t)));
+ memcpy(dest, d, Kmer::NUM_BYTES);
reverse(dest, dest + Kmer::NUM_BYTES);
# else
memcpy(dest, &seq, Kmer::NUM_BYTES);
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