Hi Akshay, You do not have to quit R to run 'top'. You can have, for example, 2 windows, with R running in one and top running in the oher.
Eric On Sat, Jun 10, 2023 at 12:19 AM akshay kulkarni <akshay...@hotmail.com> wrote: > Dear Ivan, > Thanks for the reply. I am pressurised by a fast > approaching deadline and your reply calmed me... > > Take a look at the following code: > > > debug at <tmp>#26: LYG <- mclapply(LYGH, FUN = arfima, mc.cores = 2, > mc.preschedule = FALSE) > Browse[2]> length(LYGH) > [1] 357 > Browse[2]> > ^C > > Browse[2]> LYG <- pbmclapply(LYGH,FUN = arfima,mc.cores = 2,mc.preschedule > = FALSE) > | > > | 0%, ETA NA > > I am debuuging a function FUN wherein the above expressions appear. The > pbmclapply code works well if called inside FUN: > > FUN(arg) > Result.. > > But as you may note, it doesn't work while in debug mode.... > > Also, if I replace pbmclapply by maclapply inside FUN, it hangs.... > > You might be interested in this: > > [ec2-user@ip-172-31-15-116 ~]$ exit > logout > There are stopped jobs. > > THis occurs when I close R and try to exit the shell prompt( I am on an > AWS EC2 RHEL 8 Instance). Can this lead you somewhere? As of now I have > quit R in my machine, so I can't get session info..but please let me know > if you need it necessarily... > > by the by, how do you run top when running R? I think at least in my > machine, you have to quit R to get to the shell prompt... > > I request you TO PLEASE reply to this mail as early as possible. I am > facing an imminent deadline...please excuse my blatant violation of > protocol, but deadlines are deadlines, right? > > THanking you, > Yours sincerely, > AKSHAY M KULKARNI > > > ________________________________ > From: Ivan Krylov <krylov.r...@gmail.com> > Sent: Saturday, June 10, 2023 1:43 AM > To: akshay kulkarni <akshay...@hotmail.com> > Cc: R help Mailing list <r-help@r-project.org> > Subject: Re: [R] inconsistency in mclapply..... > > On Fri, 9 Jun 2023 18:01:44 +0000 > akshay kulkarni <akshay...@hotmail.com> wrote: > > > > LYG <- pbmclapply(LYGH,FUN = arfima,mc.cores = 2,mc.preschedule = > > > FALSE) > > | > > > | > > 0%, ETA NA^ > > > > It just hangs. > > My questions from the last time still stand: > > 0) What is your sessionInfo()? Maybe you're running a parallel BLAS > which doesn't always handle fork() or something. It may be worth > disabling BLAS-level parallelism as long as you're already trying to > use 100% of your processor by other means. > > 1) What does traceback() show after you interrupt pbmclapply? Most > likely, you would be interrupting selectChildren(), but if not, the > problem may lie in a very different place from what I'm expecting. > > 2) While pbmclapply is hung, without interrupting it, take a look at > the state of the system and the processes on it (are you still on RHEL? > use `top` or whatever task manager you're comfortable with). > > a) Is 100% of the CPU being used? 100% of one core? Is system mostly > idle? > > b) Can you find the child processes launched by pbmclapply? > > c) Write down the PID of the child process and attach a debugger to > it (If you're on RHEL, try following this guide: > <https://beej.us/guide/bggdb/#attach>. If GDB asks you to install > additional debug symbols by running debuginfo-install, follow its > guidance and then restart GDB.) and obtain a backtrace. (In GDB, the > command to obtain a backtrace is "backtrace".) Which function is the > child process stuck in? > > -- > Best regards, > Ivan > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@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]] ______________________________________________ R-help@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.
