From: Ben Woodcroft <b.woodcroft@uq.edu.au>
To: "Ludovic Courtès" <ludo@gnu.org>
Cc: "guix-devel@gnu.org" <guix-devel@gnu.org>
Subject: Re: [PATCHES] Add vsearch.
Date: Sat, 3 Oct 2015 11:59:33 +1000 [thread overview]
Message-ID: <560F3685.5040102@uq.edu.au> (raw)
In-Reply-To: <87612qof9a.fsf@gnu.org>
[-- Attachment #1: Type: text/plain, Size: 1891 bytes --]
On 02/10/15 00:05, Ludovic Courtès wrote:
> Vsearch fails to build on platforms other than x86_64 (see
> <http://hydra.gnu.org/build/703292/nixlog/2/raw>):
>
> --8<---------------cut here---------------start------------->8---
> In file included from /gnu/store/r0p8d0a3n2zlkj1l5a9xv368yhbgc5bh-gcc-4.9.3-lib/lib/gcc/i686-unknown-linux-gnu/4.9.3/include/xmmintrin.h:1258:0,
> from /gnu/store/r0p8d0a3n2zlkj1l5a9xv368yhbgc5bh-gcc-4.9.3-lib/lib/gcc/i686-unknown-linux-gnu/4.9.3/include/x86intrin.h:31,
> from vsearch.h:69,
> from align_simd.cc:61:
> /gnu/store/r0p8d0a3n2zlkj1l5a9xv368yhbgc5bh-gcc-4.9.3-lib/lib/gcc/i686-unknown-linux-gnu/4.9.3/include/emmintrin.h:686:1: error: inlining failed in call to always_inline ‘__m128i _mm_load_si128(const __m128i*)’: target specific option mismatch
> _mm_load_si128 (__m128i const *__P)
> ^
> align_simd.cc:204:71: error: called from here
> xmm1 = _mm_load_si128((__m128i*)(score_matrix_word + d[1] + i));
> --8<---------------cut here---------------end--------------->8---
>
> My impression is that the code unconditionally uses SSE, meaning that it
> works only on x86_64.
>
> Could you investigate a bit? If that is the case, could you send a
> patch that adds:
>
> (supported-platforms '("x86_64-linux"))
>
> with a comment explaining why?
I think you are right, I have attached the patch.
I also noticed that the license definition was changed from the first
patch applied, removing the public-domain license i.e. from
+ (license (list license:gpl3 license:bsd-2 license:public-domain))))
to
+ (license (list license:gpl3 license:bsd-2))))
Of course you know what you are doing, I just wanted to check because
this changed between the patches I submitted for 1.4.0 and 1.4.1.
Thanks,
ben
[-- Attachment #2: 0001-gnu-vsearch-Restrict-supported-systems-to-x86_64-lin.patch --]
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From 28497af997b07a57ce6006b19c50a467a4f3907f Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Sat, 3 Oct 2015 11:46:22 +1000
Subject: [PATCH] gnu: vsearch: Restrict supported systems to x86_64-linux
* gnu/packages/bioinformatics.scm (vsearch): Restrict supported systems.
---
gnu/packages/bioinformatics.scm | 3 +++
1 file changed, 3 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b04c288..a3619be 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2766,6 +2766,9 @@ vectorization as well as multiple threads to perform accurate alignments at
high speed. VSEARCH uses an optimal global aligner (full dynamic programming
Needleman-Wunsch).")
(home-page "https://github.com/torognes/vsearch")
+ ;; vsearch uses non-portable SSE instrinsics so building fails on other
+ ;; platforms.
+ (supported-systems '("x86_64-linux"))
;; Dual licensed; also includes public domain source.
(license (list license:gpl3 license:bsd-2))))
--
2.4.3
next prev parent reply other threads:[~2015-10-03 1:59 UTC|newest]
Thread overview: 12+ messages / expand[flat|nested] mbox.gz Atom feed top
2015-09-29 22:47 [PATCHES] Add vsearch Ben Woodcroft
2015-10-01 14:05 ` Ludovic Courtès
2015-10-01 19:41 ` Andreas Enge
2015-10-02 11:40 ` Ricardo Wurmus
2015-10-02 18:05 ` Andreas Enge
2015-10-03 1:59 ` Ben Woodcroft [this message]
2015-10-03 12:00 ` Andreas Enge
2015-10-03 20:50 ` Ludovic Courtès
-- strict thread matches above, loose matches on Subject: below --
2015-09-29 12:24 Ben Woodcroft
2015-09-30 2:44 ` Ben Woodcroft
2015-09-30 8:37 ` Ben Woodcroft
2015-10-01 8:55 ` Ludovic Courtès
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