From iuke-tier@ey m@iii@g oii uiow@@edu  Tue Dec  1 17:54:32 2020
From: iuke-tier@ey m@iii@g oii uiow@@edu (iuke-tier@ey m@iii@g oii uiow@@edu)
Date: Tue, 1 Dec 2020 10:54:32 -0600 (CST)
Subject: [Rd] [External] Re: .Internal(quit(...)): system call failed:
 Cannot allocate memory
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The fact that your max resident size isn't affected looks odd.  Are
you setting the environment variable outside R? When I run

     env R_MAX_VSIZE=16Gb /usr/bin/time bin/Rscript jg.R 1e9 2e0 0 0

(your code in jg.R). I get a quick failure with 11785524maxresident)k

Best,

luke

On Tue, 1 Dec 2020, Jan Gorecki wrote:

> 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 at 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 at 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 at 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 at 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 at entry=0x7fffffffa1e0 "rm -Rf /tmp/RtmppoKPXb") at sysutils.c:311
>>>>>>>> 311     {
>>>>>>>> (gdb) where
>>>>>>>> #0  R_system (command=command at 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 at entry=SA_NOSAVE, status=status at 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 at 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 at r-project.org mailing list
>>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>>>>>>> ______________________________________________
>>>>>>>>> R-devel at r-project.org mailing list
>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>>>>
>>>>>>
>>>>>
>>>>> ______________________________________________
>>>>> R-devel at 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 at 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 at 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 at uiowa.edu
Iowa City, IA 52242                 WWW:  http://www.stat.uiowa.edu



[Rd] [External] Re: .Internal(quit(...)): system call failed: Cannot allocate memory
iuke-tier@ey m@iii@g oii uiow@@edu