R devel - Nov 2020 - .Internal(quit(...)): system call failed: Cannot allocate memory

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
>
	[[alternative HTML version deleted]]

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?

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

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