Hello Caml-community--
First of all, big thanks to Will Farr, Mike Lin, Martin Jambon, and Markus
Mottl.
So far, I rewrote things in a non-functional way to avoid unecessary memory
allocation, and then used the float operations directly. This resulted in a 4
fold increase in speed. Second, I mov
These are good points. I tend to compulsively eliminate any kind of memory
allocation from my numerical loops -- it's true the OCaml allocator is a lot
faster than malloc, but you could end up repaying a lot of that back to the
GC later!
The silly library I sent out does operate on OCaml float arra
Unless you want to interface C-calls into BLAS/LAPACK directly without
bounds checking, releasing the OCaml-lock, and other "fru-fru", it
seems unlikely that you will get much of an advantage using those
libraries given the small size of your matrices. E.g. Lacaml is
optimized for larger matrices
Mike and Erick,
In some of my work, I've got code which is constantly creating and
multiplying 4x4 matrices (Lorentz transforms). I usually write in a
functional style, so I do not generally overwrite old matrices with
the multiplication results. I have discovered that, at these sizes,
it's abou
Erick, we should compare notes sometime. I have a lot of code for doing this
kind of stuff (I am working on empirical codon models with 61x61 rate
matrices). The right way to speed up matrix-vector operations is to use BLAS
via either Lacaml or ocamlgsl. But if, like me, you like to
counterproducti
Erick Matsen wrote:
> Wow, once again I am amazed by the vitality of this list. Thank you
> for your suggestions.
>
> Here is the context: we are interested in calculating the likelihood
> of taxonomic placement of short "metagenomics" sequence fragments from
> unknown organisms in the ocean. We s
Erick,
Sorry about the long email, but here is an explanation of what
"boxing" means, how it slows you down in this case, and how you can
(eventually) figure out whether it will slow you down in general. I'm
not an expert, so I've probably made mistakes in the following, but I
think the broad out
Wow, once again I am amazed by the vitality of this list. Thank you
for your suggestions.
Here is the context: we are interested in calculating the likelihood
of taxonomic placement of short "metagenomics" sequence fragments from
unknown organisms in the ocean. We start by assuming a model of
sequ
> I'm working on speeding up some code, and I wanted to check with
> someone before implementation.
>
> As you can see below, the code primarily spends its time multiplying
> relatively small matrices. Precision is of course important but not
> an incredibly crucial issue, as the most important th
On Friday 20 February 2009 15:40:00 Erick Matsen wrote:
> Hello Ocaml community---
>
> I'm working on speeding up some code, and I wanted to check with
> someone before implementation.
>
> As you can see below, the code primarily spends its time multiplying
> relatively small matrices. Precision is
this helps
Rabih
-Message d'origine-
De : caml-list-boun...@yquem.inria.fr [mailto:caml-list-boun...@yquem.inria.fr]
De la part de Erick Matsen
Envoyé : vendredi 20 février 2009 16:40
À : caml-l...@inria.fr
Objet : [Caml-list] speeding up matrix multiplication (newbie question)
H
Hello Ocaml community---
I'm working on speeding up some code, and I wanted to check with
someone before implementation.
As you can see below, the code primarily spends its time multiplying relatively
small matrices. Precision is of course important but not an incredibly crucial
issue, as the mo
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