[Rd] [External] Re: .Internal(quit(...)): system call failed: Cannot allocate memory
Jan Gorecki
j@goreck| @end|ng |rom w|t@edu@p|
Tue Dec 1 17:16:51 CET 2020
Thank you Luke,
I tried your suggestion about R_MAX_VSIZE but I am not able to get the
error you are getting.
I tried recent R devel as I have seen you made a change to GC there.
My machine is 128GB, free -h reports 125GB available. I tried to set
128, 125 and 100. In all cases the result is "Command terminated by
signal 9". Each took around 6-6.5h.
Details below, if it tells you anything how could I optimize it (or
raise an exception early) please do let me know.
R 4.0.3
unset R_MAX_VSIZE
User time (seconds): 40447.92
System time (seconds): 4034.37
Percent of CPU this job got: 201%
Elapsed (wall clock) time (h:mm:ss or m:ss): 6:07:59
Maximum resident set size (kbytes): 127261184
Major (requiring I/O) page faults: 72441
Minor (reclaiming a frame) page faults: 3315491751
Voluntary context switches: 381446
Involuntary context switches: 529554
File system inputs: 108339200
File system outputs: 120
R-devel 2020-11-27 r79522
unset R_MAX_VSIZE
User time (seconds): 40713.52
System time (seconds): 4039.52
Percent of CPU this job got: 198%
Elapsed (wall clock) time (h:mm:ss or m:ss): 6:15:52
Maximum resident set size (kbytes): 127254796
Major (requiring I/O) page faults: 72810
Minor (reclaiming a frame) page faults: 3433589848
Voluntary context switches: 384363
Involuntary context switches: 609024
File system inputs: 108467064
File system outputs: 112
R_MAX_VSIZE=128Gb
User time (seconds): 40411.13
System time (seconds): 4227.99
Percent of CPU this job got: 198%
Elapsed (wall clock) time (h:mm:ss or m:ss): 6:14:01
Maximum resident set size (kbytes): 127249316
Major (requiring I/O) page faults: 88500
Minor (reclaiming a frame) page faults: 3544520527
Voluntary context switches: 384117
Involuntary context switches: 545397
File system inputs: 111675896
File system outputs: 120
R_MAX_VSIZE=125Gb
User time (seconds): 40246.83
System time (seconds): 4042.76
Percent of CPU this job got: 201%
Elapsed (wall clock) time (h:mm:ss or m:ss): 6:06:56
Maximum resident set size (kbytes): 127254200
Major (requiring I/O) page faults: 63867
Minor (reclaiming a frame) page faults: 3449493803
Voluntary context switches: 370753
Involuntary context switches: 614607
File system inputs: 106322880
File system outputs: 112
R_MAX_VSIZE=100Gb
User time (seconds): 41837.10
System time (seconds): 3979.57
Percent of CPU this job got: 192%
Elapsed (wall clock) time (h:mm:ss or m:ss): 6:36:34
Maximum resident set size (kbytes): 127256940
Major (requiring I/O) page faults: 66829
Minor (reclaiming a frame) page faults: 3357778594
Voluntary context switches: 391149
Involuntary context switches: 646410
File system inputs: 106605648
File system outputs: 120
On Fri, Nov 27, 2020 at 10:18 PM <luke-tierney using uiowa.edu> wrote:
>
> On Thu, 26 Nov 2020, Jan Gorecki wrote:
>
> > 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.
>
> I'm not convinced anything useful can be done that would work well for
> your application without working badly for others.
>
> If you want to drive this close to your memory limits you are probably
> going to have to take responsibility for some tuning at your end. One
> option in ?Memory you might try is the R_MAX_VSIZE environment
> variable. On my 16Gb machine with R_MAX_VSIZE=16Gb your example fails
> very quickly with
>
> Error: vector memory exhausted (limit reached?)
>
> rather than churning for an hour trying to make things work. Setting
> memory and/or virtual memory limits in your shell is another option.
>
> Best,
>
> luke
>
> >
> >
> >>
> >> 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
> >
>
> --
> 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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