[Rd] [External] Re: .Internal(quit(...)): system call failed: Cannot allocate memory

Jan Gorecki j@goreck| @end|ng |rom w|t@edu@p|
Thu Nov 26 11:18:47 CET 2020 

Thank you Luke for looking into it. Your knowledge of gc is definitely
helpful here. I put comments inline below.

Best,
Jan

On Wed, Nov 25, 2020 at 10:38 PM <luke-tierney using uiowa.edu> wrote:
>
> On Tue, 24 Nov 2020, Jan Gorecki wrote:
>
> > As for other calls to system. I avoid calling system. In the past I
> > had some (to get memory stats from OS), but they were failing with
> > exactly the same issue. So yes, if I would add call to system before
> > calling quit, I believe it would fail with the same error.
> > At the same time I think (although I am not sure) that new allocations
> > made in R are working fine. So R seems to reserve some memory and can
> > continue to operate, while external call like system will fail. Maybe
> > it is like this by design, don't know.
>
> Thanks for the report on quit(). We're exploring how to make the
> cleanup on exit more robust to low memory situations like these.
>
> >
> > Aside from this problem that is easy to report due to the warning
> > message, I think that gc() is choking at the same time. I tried to
> > make reproducible example for that, multiple times but couldn't, let
> > me try one more time.
> > It happens to manifest when there is 4e8+ unique characters/factors in
> > an R session. I am able to reproduce it using data.table and dplyr
> > (0.8.4 because 1.0.0+ fails even sooner), but using base R is not easy
> > because of the size. I described briefly problem in:
> > https://github.com/h2oai/db-benchmark/issues/110
>
> Because of the design of R's character vectors, with each element
> allocated separately, R is never going to be great at handling huge
> numbers of distinct strings. But it can do an adequate job given
> enough memory to work with.
>
> When I run your GitHub issue example on a machine with around 500 Gb
> of RAM it seems to run OK; /usr/bin/time reports
>
> 2706.89user 161.89system 37:10.65elapsed 128%CPU (0avgtext+0avgdata 92180796maxresident)k
> 0inputs+103450552outputs (0major+38716351minor)pagefaults 0swaps
>
> So the memory footprint is quite large. Using gc.time() it looks like
> about 1/3 of the time is in GC. Not ideal, and maybe could be improved
> on a bit, but probably not by much. The GC is basically doing an
> adequate job, given enough RAM.

Agree, 1/3 is a lot but still acceptable. So this strictly is not
something that requires intervention.
PS. I wasn't aware of gc.time(), it may be worth linking it from
SeeAlso in gc() manual.

>
> If you run this example on a system without enough RAM, or with other
> programs competing for RAM, you are likely to end up fighting with
> your OS/hardware's virtual memory system. When I try to run it on a
> 16Gb system it churns for an hour or so before getting killed, and
> /usr/bin/time reports a huge number of page faults:
>
> 312523816inputs+0outputs (24761285major+25762068minor)pagefaults 0swaps
>
> You are probably experiencing something similar.

Yes, this is exactly what I am experiencing.
The machine is a bare metal machine of 128GB mem, csv size 50GB,
data.frame size 74GB.
In my case it churns for ~3h before it gets killed with SIGINT from
the parent R process which uses 3h as a timeout for this script.
This is something I would like to be addressed because gc time is far
bigger than actual computation time. This is not really acceptable, I
would prefer to raise an exception instead.

>
> There may be opportunities for more tuning of the GC to better handle
> running this close to memory limits, but I doubt the payoff would be
> worth the effort.

If you don't have plans/time to work on that anytime soon, then I can
fill bugzilla for this problem so it won't get lost in the mailing
list.


>
> Best,
>
> luke
>
> > It would help if gcinfo() could take FALSE/TRUE/2L where 2L will print
> > even more information about gc, like how much time the each gc()
> > process took, how many objects it has to check on each level.
> >
> > Best regards,
> > Jan
> >
> >
> >
> > On Tue, Nov 24, 2020 at 1:05 PM Tomas Kalibera <tomas.kalibera using gmail.com> wrote:
> >>
> >> On 11/24/20 11:27 AM, Jan Gorecki wrote:
> >>> Thanks Bill for checking that.
> >>> It was my impression that warnings are raised from some internal
> >>> system calls made when quitting R. At that point I don't have much
> >>> control over checking the return status of those.
> >>> Your suggestion looks good to me.
> >>>
> >>> Tomas, do you think this could help? could this be implemented?
> >>
> >> I think this is a good suggestion. Deleting files on Unix was changed
> >> from system("rm") to doing that in C, and deleting the session directory
> >> should follow.
> >>
> >> It might also help diagnosing your problem, but I don't think it would
> >> solve it. If the diagnostics in R works fine and the OS was so
> >> hopelessly out of memory that it couldn't run any more external
> >> processes, then really this is not a problem of R, but of having
> >> exhausted the resources. And it would be a coincidence that just this
> >> particular call to "system" at the end of the session did not work.
> >> Anything else could break as well close to the end of the script. This
> >> seems the most likely explanation to me.
> >>
> >> Do you get this warning repeatedly, reproducibly at least in slightly
> >> different scripts at the very end, with this warning always from quit()?
> >> So that the "call" part of the warning message has .Internal(quit) like
> >> in the case you posted? Would adding another call to "system" before the
> >> call to "q()" work - with checking the return value? If it is always
> >> only the last call to "system" in "q()", then it is suspicious, perhaps
> >> an indication that some diagnostics in R is not correct. In that case, a
> >> reproducible example would be the key - so either if you could diagnose
> >> on your end what is the problem, or create a reproducible example that
> >> someone else can use to reproduce and debug.
> >>
> >> Best
> >> Tomas
> >>
> >>>
> >>> On Mon, Nov 23, 2020 at 7:10 PM Bill Dunlap <williamwdunlap using gmail.com> wrote:
> >>>> The call to system() probably is an internal call used to delete the session's tempdir().  This sort of failure means that a potentially large amount of disk space is not being recovered when R is done.  Perhaps R_CleanTempDir() could call R_unlink() instead of having a subprocess call 'rm -rf ...'.  Then it could also issue a specific warning if it was impossible to delete all of tempdir().  (That should be very rare.)
> >>>>
> >>>>> q("no")
> >>>> Breakpoint 1, R_system (command=command using entry=0x7fffffffa1e0 "rm -Rf /tmp/RtmppoKPXb") at sysutils.c:311
> >>>> 311     {
> >>>> (gdb) where
> >>>> #0  R_system (command=command using entry=0x7fffffffa1e0 "rm -Rf /tmp/RtmppoKPXb") at sysutils.c:311
> >>>> #1  0x00005555557c30ec in R_CleanTempDir () at sys-std.c:1178
> >>>> #2  0x00005555557c31d7 in Rstd_CleanUp (saveact=<optimized out>, status=0, runLast=<optimized out>) at sys-std.c:1243
> >>>> #3  0x00005555557c593d in R_CleanUp (saveact=saveact using entry=SA_NOSAVE, status=status using entry=0, runLast=<optimized out>) at system.c:87
> >>>> #4  0x00005555556cc85e in do_quit (call=<optimized out>, op=<optimized out>, args=0x555557813f90, rho=<optimized out>) at main.c:1393
> >>>>
> >>>> -Bill
> >>>>
> >>>> On Mon, Nov 23, 2020 at 3:15 AM Tomas Kalibera <tomas.kalibera using gmail.com> wrote:
> >>>>> On 11/21/20 6:51 PM, Jan Gorecki wrote:
> >>>>>> Dear R-developers,
> >>>>>>
> >>>>>> Some of the more fat scripts (50+ GB mem used by R) that I am running,
> >>>>>> when they finish they do quit with q("no", status=0)
> >>>>>> Quite often it happens that there is an extra stderr output produced
> >>>>>> at the very end which looks like this:
> >>>>>>
> >>>>>> Warning message:
> >>>>>> In .Internal(quit(save, status, runLast)) :
> >>>>>>     system call failed: Cannot allocate memory
> >>>>>>
> >>>>>> Is there any way to avoid this kind of warnings? I am using stderr
> >>>>>> output for detecting failures in scripts and this warning is a false
> >>>>>> positive of a failure.
> >>>>>>
> >>>>>> Maybe quit function could wait little bit longer trying to allocate
> >>>>>> before it raises this warning?
> >>>>> If you see this warning, some call to system() or system2() or similar,
> >>>>> which executes an external program, failed to even run a shell to run
> >>>>> that external program, because there was not enough memory. You should
> >>>>> be able to find out where it happens by checking the exit status of
> >>>>> system().
> >>>>>
> >>>>> Tomas
> >>>>>
> >>>>>
> >>>>>> Best regards,
> >>>>>> Jan Gorecki
> >>>>>>
> >>>>>> ______________________________________________
> >>>>>> R-devel using r-project.org mailing list
> >>>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
> >>>>> ______________________________________________
> >>>>> R-devel using r-project.org mailing list
> >>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
> >>
> >>
> >
> > ______________________________________________
> > R-devel using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> >
>
> --
> Luke Tierney
> Ralph E. Wareham Professor of Mathematical Sciences
> University of Iowa                  Phone:             319-335-3386
> Department of Statistics and        Fax:               319-335-3017
>     Actuarial Science
> 241 Schaeffer Hall                  email:   luke-tierney using uiowa.edu
> Iowa City, IA 52242                 WWW:  http://www.stat.uiowa.edu

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