dear Members,
Thanks for the reply..I do have another
issue; I will be highly obliged if you answer it:
I tried "top" at the bash prompt, but it provides a way to measure CPU
performance of the existing processes. I want to check the CPU usage of the
execution of an R function. So I start R by this
$ R
and at the R prompt I type the function to be executed. But if I type
"top" at the R prompt, it says object "top" not found.
So, should I change to bash prompt after running the R function? If yes, how do
I do it? If not, how to use "top" inside the R prompt?
Again, I think this is an OS isuue....but I could'nt find any answer in the
Internet. I am an independent researcher and I don't have personal access to
experts.......this mail list is the only vent I have.......
Very many thanks for your time and effort...
Yours sincerely,
AKSHAY M KULKARNI
________________________________
From: Jeff Newmiller <jdnewmil at dcn.davis.ca.us>
Sent: Saturday, June 30, 2018 11:46 PM
To: r-help at r-project.org; akshay kulkarni; R help Mailing list
Subject: Re: [R] parallel processing in r...
Use "top" at the bash prompt.
Read about the "mc.cores" parameter to mclapply.
Make a simplified example version of your analysis and post your question in the
context of that example [1][2][3]. You will learn about the issues you are
dealing with in the process of trimming your problem, and will have code you can
share that demonstrates the issue without exposing private information.
Running parallel does not necessarily improve performance because other factors
like task switching overhead and Inter-process-communication (data sharing) can
drag it down. Read about the real benefits and drawbacks of parallelism... there
are many discussions out there out there... you might start with [4].
[1]
http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example
[2] http://adv-r.had.co.nz/Reproducibility.html
[3] https://cran.r-project.org/web/packages/reprex/index.html (read the
vignette)
[4]
https://nceas.github.io/oss-lessons/parallel-computing-in-r/parallel-computing-in-r.html
On June 30, 2018 10:07:49 AM PDT, akshay kulkarni <akshay_e4 at
hotmail.com> wrote:>dear members,
>I am using mclapply to parallelize my code. I am using Red Hat Linux in
>AWS.
>
>When I use mclapply, I see no speed increase. I doubt that the Linux OS
>is allowing fewer than the maximum number of cores to mclapply ( by
>default, mclapply takes all the available cores to it).
>
>How do you check if the number of workers is less than the output given
>by detectCores(), in Linux? Is there any R function for it?
>
>I do acknowledge that help on an OS is not suitable for this mailing
>list, but even Internet could'nt help me. Therefore this mail......
>
>very many thanks for your time and effort...
>yours sincerely,
>AKSHAY M KULKARNI
>
> [[alternative HTML version deleted]]
>
>______________________________________________
>R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide
>http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.
--
Sent from my phone. Please excuse my brevity.
[[alternative HTML version deleted]]
Hello, On Sun, Jul 01, 2018 at 11:31:29AM +0000, akshay kulkarni wrote:> I tried "top" at the bash prompt, but it provides a way to measure > CPU performance of the existing processes. I want to check the CPU > usage of the execution of an R function.Try to open two bash prompts, in one use R and in the other use top to monitor what is going on.> and at the R prompt I type the function to be executed. But if I > type "top" at the R prompt, it says object "top" not found.top is a shell command, no issue with R not knowing about this.> So, should I change to bash prompt after running the R function? If > yes, how do I do it? If not, how to use "top" inside the R prompt?Basically, you can't.> Again, I think this is an OS isuue....but I could'nt find any answer > in the Internet. I am an independent researcher and I don't have > personal access to experts.......this mail list is the only vent I > have.......... (many more dots) Do you think we are experts on your system? Please do your home work and get back to us once it's done. ;-) Cheers, -- Beno?t -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 866 bytes Desc: not available URL: <https://stat.ethz.ch/pipermail/r-help/attachments/20180701/2f010fe0/attachment-0002.sig>
Hi,
On ' how to use "top" inside the R prompt? '
you can use system('top') command.
Thanks,
On Sun, Jul 1, 2018 at 9:53 PM Benoit Vaillant <benoit.vaillant at
no-log.org>
wrote:
> Hello,
>
> On Sun, Jul 01, 2018 at 11:31:29AM +0000, akshay kulkarni wrote:
> > I tried "top" at the bash prompt, but it provides a way to
measure
> > CPU performance of the existing processes. I want to check the CPU
> > usage of the execution of an R function.
>
> Try to open two bash prompts, in one use R and in the other use top to
> monitor what is going on.
>
> > and at the R prompt I type the function to be executed. But if I
> > type "top" at the R prompt, it says object "top"
not found.
>
> top is a shell command, no issue with R not knowing about this.
>
> > So, should I change to bash prompt after running the R function? If
> > yes, how do I do it? If not, how to use "top" inside the R
prompt?
>
> Basically, you can't.
>
> > Again, I think this is an OS isuue....but I could'nt find any
answer
> > in the Internet. I am an independent researcher and I don't have
> > personal access to experts.......this mail list is the only vent I
> > have.......
>
> ... (many more dots) Do you think we are experts on your system?
>
> Please do your home work and get back to us once it's done. ;-)
>
> Cheers,
>
> --
> Beno?t
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
[[alternative HTML version deleted]]
dear Benoit,
Amazing! I did my home work and found out that only two
out of eight processors is being utilized by mclapply.
I am using general purpose t2 instances in AWS, with Linux AMI(Red Hat).
How do I make RHEL utilize all the processors in my linux instance? Should I
use the "configure" command in Linux? Is there any specific command in
AWS linux instances? Or just setting the mc.cores argument of mclapply to
8(there are 8 cores in my linux instance) work?
If the answer is somewhat involved, please refer some online resources....
Very many thanks for your time and effort....
Yours sincerely
AKSHAY M KULKARNI
________________________________
From: Benoit Vaillant <benoit.vaillant at no-log.org>
Sent: Sunday, July 1, 2018 5:52 PM
To: akshay kulkarni
Cc: R help Mailing list
Subject: Re: [R] parallel processing in r...
Hello,
On Sun, Jul 01, 2018 at 11:31:29AM +0000, akshay kulkarni
wrote:> I tried "top" at the bash prompt, but it provides a way to
measure
> CPU performance of the existing processes. I want to check the CPU
> usage of the execution of an R function.
Try to open two bash prompts, in one use R and in the other use top to
monitor what is going on.
> and at the R prompt I type the function to be executed. But if I
> type "top" at the R prompt, it says object "top" not
found.
top is a shell command, no issue with R not knowing about this.
> So, should I change to bash prompt after running the R function? If
> yes, how do I do it? If not, how to use "top" inside the R
prompt?
Basically, you can't.
> Again, I think this is an OS isuue....but I could'nt find any answer
> in the Internet. I am an independent researcher and I don't have
> personal access to experts.......this mail list is the only vent I
> have.......
... (many more dots) Do you think we are experts on your system?
Please do your home work and get back to us once it's done. ;-)
Cheers,
--
Beno?t
[[alternative HTML version deleted]]