Fwd: Re: BLAST+ speed & build issues

2011-08-04 Thread Olivier Sallou
Hi, we have a package on DebianMed which has performance issue regarding static build vs dynamic link build (latest gcc) Has only impacted compile option is the static vs dynamic choice, has anyone an idea on where we could investigate or how we could speedup this? For info, executable is quite la

Re: Fwd: Re: BLAST+ speed & build issues

2011-08-04 Thread Julian Taylor
On 08/04/2011 12:02 PM, Olivier Sallou wrote: > Hi, > we have a package on DebianMed which has performance issue regarding > static build vs dynamic link build (latest gcc) > Has only impacted compile option is the static vs dynamic choice, has > anyone an idea on where we could investigate or how

Re: Fwd: Re: BLAST+ speed & build issues

2011-08-04 Thread Samuel Thibault
Julian Taylor, le Thu 04 Aug 2011 12:32:27 +0200, a écrit : > You might be able to reduce startup time by only linking against the > libraries you need or lazyly dynamically loading them. Or use prelink. Samuel -- To UNSUBSCRIBE, email to debian-devel-requ...@lists.debian.org with a subject of

Re: Fwd: Re: BLAST+ speed & build issues

2011-08-04 Thread Yves-Alexis Perez
On jeu., 2011-08-04 at 13:27 +0200, Samuel Thibault wrote: > Julian Taylor, le Thu 04 Aug 2011 12:32:27 +0200, a écrit : > > You might be able to reduce startup time by only linking against the > > libraries you need or lazyly dynamically loading them. > > Or use prelink. Which as issues especia

Re: Fwd: Re: BLAST+ speed & build issues

2011-08-04 Thread Mike Hommey
On Thu, Aug 04, 2011 at 01:50:01PM +0200, Yves-Alexis Perez wrote: > On jeu., 2011-08-04 at 13:27 +0200, Samuel Thibault wrote: > > Julian Taylor, le Thu 04 Aug 2011 12:32:27 +0200, a écrit : > > > You might be able to reduce startup time by only linking against the > > > libraries you need or lazy

Re: Fwd: Re: BLAST+ speed & build issues

2011-08-04 Thread olivier sallou
Linking against "needed" lib is quite difficult (would need to be done on upstream), package is rather complex regarding compilation. And each solution has its pros and cons I think we will have to discuss on validity to provide static builds ( takes a lot of space on package vs perf loss) Th

Re: Fwd: Re: BLAST+ speed & build issues

2011-08-04 Thread Stephen Frost
Olivier, Because "-h is slow" hardly seems like a good justification for having static packages. Last I checked (which wasn't long ago..), BLAST is typically a long-running process (at least on the stuff we're doing..). Also, are subsequent calls (even '-h' ones) faster? I'd expect them to be, o

Re: Fwd: Re: BLAST+ speed & build issues

2011-08-06 Thread Kurt Roeckx
On Thu, Aug 04, 2011 at 12:02:25PM +0200, Olivier Sallou wrote: > For info, executable is quite large 11MB (static) vs 2M (dynamic). The 11MB probably contains a whole bunch of libraries instead, making it larger. I don't see how this is relavant. > Dynamic build exe is linked against: > osallou