[gentoo-science] sci-libs/atlas from science overlay - is it multithreaded?

[gentoo-science] sci-libs/atlas from science overlay - is it multithreaded?

[Xavier Fernández i Marín]

Dear all,

After some years with the official blas and lapack libraries from atlas
several weeks ago these packages were discontinued in the official portage
tree, being replaced by the science overlay. I've tried to get the same
functionality than before, but with no luck. 

I used to run sci-mathematics/jags compiled against the atlas-threaded
libraries, and when simulating more than one chain all processors were used
in parallel. But now, with the current sci-libs/atlas libraries this is not
the case anymore.

I have also tried to link jags against openblas, but without luck as well.

I have also tried to compile it against mkl using openmp and even compile
jags without using the official ebuild.

So my questions are:

  - Is there a way to check that atlas is using multithreaded capacities,
    besides checking the libraries towards which it is compiled?

  - What has atlas changed between the last unstable ebuild from the
    official portage tree and the last unstable ebuild from the science
    overlay?

  - Any guess on how I can make use of multithreading in jags in gentoo?


Many thanks.
-- 
-  Xavier  -

Re: [gentoo-science] sci-libs/atlas from science overlay - is it multithreaded?

[justin]

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On 09/04/13 15:40, Xavier Fernández i Marín wrote:
> Dear all,
> 
> After some years with the official blas and lapack libraries from atlas
> several weeks ago these packages were discontinued in the official portage
> tree, being replaced by the science overlay. I've tried to get the same
> functionality than before, but with no luck. 
> 
> I used to run sci-mathematics/jags compiled against the atlas-threaded
> libraries, and when simulating more than one chain all processors were used
> in parallel. But now, with the current sci-libs/atlas libraries this is not
> the case anymore.
> 
> I have also tried to link jags against openblas, but without luck as well.
> 
> I have also tried to compile it against mkl using openmp and even compile
> jags without using the official ebuild.
> 
> So my questions are:
> 
>   - Is there a way to check that atlas is using multithreaded capacities,
>     besides checking the libraries towards which it is compiled?
> 
>   - What has atlas changed between the last unstable ebuild from the
>     official portage tree and the last unstable ebuild from the science
>     overlay?
> 
>   - Any guess on how I can make use of multithreading in jags in gentoo?
> 

Could you provide me a sample script which should run jags in parallel?

Justin


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Re: [gentoo-science] sci-libs/atlas from science overlay - is it multithreaded?

[Xavier Fernández i Marín]

justin vas escriure el dia dt, 09 abr 2013:

> Could you provide me a sample script which should run jags in parallel?

This file generates data and samples (call it desc-000.bug)

-----8<---------------
data {
  Alpha <- 3
  Beta <- 5
  Sigma <- 0.5 
  N <- 500
  for (i in 1:500) {
  epsilon[i] ~ dnorm(0, 1/Sigma^2)
  x[i] ~ dunif(0, 10)
  y[i] <- Alpha + Beta*x[i] + epsilon[i]
  }
}
model {
  for (i in 1:500) {
  y[i] ~ dnorm(mu[i], tau)
  mu[i] <- alpha + beta * x[i]
  }
  alpha ~ dnorm(0, 0.001)
  beta ~ dnorm(0, 0.001)
  tau <- pow(sigma, -2)
  sigma ~ dgamma(0.001, 0.001)
}
-----8<---------------

The sample script with 3 chains (m-000.jmd) that calls the previous file.
-----8<---------------
model in "desc-000.bug"
compile, nchains(3)
initialize
update 10000
monitor alpha
monitor beta
monitor sigma
update 10000
coda *, stem(coda_m-000-)
parameters to "outs-000"
exit
-----8<---------------

HTH,

-- 
-  Xavier  -