Hi,
An update on this:
1) I do have a real user who raised the speed issue doing real analysis
but admitted his script was both unusual and poorly written (aligning
short sequences one at a time).
2) For Bio-Linux users I'm now providing ncbi-blast+-static as an
optional drop-in replacement for
On Fri, Aug 19, 2011 at 10:38:03AM +0200, Steffen M�ller wrote:
> What is special about Debian is not only that there are binary packages.
> We also have the means to let our audience recompile packages in a
> sufficiently easy way.
>
> Now, if you possibly say that getting towards a static varia
On 08/18/2011 04:53 PM, Aaron M. Ucko wrote:
> Olivier Sallou writes:
>
>> I will try to have a look to patch this in the package. However I will
>> go on vacation end of this week. So it will not be done before some time...
>
> No problem, the current packaging ignores test suite errors.
What
Olivier Sallou writes:
> I will try to have a look to patch this in the package. However I will
> go on vacation end of this week. So it will not be done before some time...
No problem, the current packaging ignores test suite errors.
> I am not really fond of providing 2 packages (one dynamic/
On Thu, Aug 18, 2011 at 08:49:49AM +0200, Olivier Sallou wrote:
> I am not really fond of providing 2 packages (one dynamic/ one static).
> Furthermore, static one would be really large, poor debian servers ;-)
I agree with this, specifically because we do not have real life test
comparisons yet
cc'ing the list
Message original
Sujet: Re: BLAST+ speed & build issues
Date : Thu, 18 Aug 2011 08:49:23 +0200
De :Olivier Sallou
Pour : Aaron M. Ucko
Le 8/18/11 6:01 AM, Aaron M. Ucko a écrit :
> [Sorry for the belated reply; I was on vacation when
[Sorry for the belated reply; I was on vacation when this thread started
and have only just caught up to it.]
Tim Booth writes:
> These don't break the build but they should really be disabled. Is
> there an easy way to do this, do you think?
Yes, just comment out the relevant per-project make
On Thu, Aug 04, 2011 at 11:31:34AM +0200, Olivier Sallou wrote:
> I will investigate if there is a way to speedup this. Or if anyone has
> ideas
Please consider forewarding this problem to debian-mentors or
debian-devel - there are more people who might know about things like
this.
Kind regar
Hi,
I quickly build the ncbi-blast+ locally with static build using the
debian build process, and indeed,
static build binaries are much faster (blastx -h) than dynamically
linked ones.
I will investigate if there is a way to speedup this. Or if anyone has
ideas
Olivier
Le 8/3/11 10:48 AM, T
Dear Tim,
Have many thanks for raising this issue. It is weird. But this
is exactly why we have this list IMHO.
On 08/03/2011 10:48 AM, Tim Booth wrote:
> Hi,
>
>> Creating a "static" package would be easy, but would double the size
>> (which is large) for blast+ on servers,
>
> Actually, it m
Hi,
> Creating a "static" package would be easy, but would double the size
> (which is large) for blast+ on servers,
Actually, it makes it about 8x the size, as each binary has its own
copies of every library.
> and it could be confusing for
> the user, no? (selecting between dynamic and static
Hi Tim,
regarding speed, I don't know the reason of the difference between
static and dynamic linking here.
When I created the package I 've chosen the dynamic solution to reduce
the size of the binary, while making the library available for other
software linkage.
Creating a "static" package would
Hi Olivier and Aaron,
I've been playing around with BLAST+, trying to tackle one fairly simple
but unimportant issue and one more complex and problematic issue.
The easy one first:
In the build log (on Launchpad) I see that during the test phase of the
build there are various attempts to connect
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