Le 19/08/2021 à 17:41, Sokol Serguei a écrit :
Le 19/08/2021 à 17:04, Naeem Khoshnevis a écrit :
Thank you so much, everyone, for responding to this email.
Dirk,
* I didn't think about testing _equality_ of doubles because the
numbers are significantly different (e.g., instead of 0.5,
chooses 1.5). However, that is a valid point, and I should be
aware of that.
* You are right about the serial runs. Whenever I deactivate
OpenMP, the results are correct.
Serguei,
* Thanks for the comments. Yes, I agree. It seems outer is a better
option. We have started with outer. However, outer builds the
entire matrix of differences first, then finds the minimum index.
In our application, it requires 200 GB of memory to build that
matrix.
This problem was hardly foreseeable from examples in hand. But I still
think that a pure R solution can be a runner:
ac=a*sc
bc=b*sc
out=vapply(seq_along(bc), function(i)
which.min(abs(ac-bc[i])+cd[i]), integer(1))
Further optimizing: "+cd[i]" does not change the result of which.min()
so it can be dropped. The same reasoning can be applied to "*sc".
As the problem is reduced to searching the index of the closest value in
'a' to 'b[i]', it can be solved in O(log(n)) time (instead of O(n)) by
binary search if 'a' can be sorted before operations. If 'b' can also be
sorted, then the whole timing can be further reduced. E.g. we can use
findInterval() implementing such optimal searching. However, its result
should be post-processed to find value indexes instead of interval ones
and get back to original indexes instead of sorted ones. Something like:
oa=order(a)
ob=order(b)
ao=a[oa]
bo=b[ob]
i=findInterval(bo, ao) # main work is done here
ii=i+ifelse(i < n & ao[i+1]-bo < bo-ao[i], 1, 0)
out=oa[ii]
out[ob]=out
Serguei.
Best,
Serguei.
* Rcpp does the job with around 10 MB. That is why I switched to
Rcpp. Please let me know your thoughts.
Iñaki,
* Thanks for your suggestion. Yes, the problem is shared values,
and it resolved the issue. I really appreciate it.
Best regards,
Naeem
On Thu, Aug 19, 2021 at 4:56 AM Iñaki Ucar <iu...@fedoraproject.org
<mailto:iu...@fedoraproject.org>> wrote:
On Thu, 19 Aug 2021 at 04:53, Dirk Eddelbuettel <e...@debian.org
<mailto:e...@debian.org>> wrote:
>
>
> Naeem,
>
> I would simplify, simplify, simplify -- as 'Rcpp FAQ 7.31'
reminds us all,
> testing _equality_ of doubles is challenging anyway.
>
> Besides, it may make sense to would ascertain first you get
what you want in
> _purely serial modes_ and then move to OpenMP.
Exactly. Serial execution should be fine. I.e., if you set the number
of threads to 1, then all platforms will return the same result.
However, you have defined a number of variables outside the parallel
region, and then you modify them inside the parallel region. OpenMP
takes those variables as shared by default, which leads to the
unexpected results you are getting. You need to tell OpenMP that
those
variables are threadprivate. Or you could just define them inside the
parallel region, so that OpenMP knows that they are private without
additional hints.
--
Iñaki Úcar
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