thr3ads.net - R devel - [Rd] SUGGESTION: Proposal to mitigate problem with stray processes left behind by parallel::makeCluster() [Mar 2019]

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Henrik Bengtsson

2019-Mar-18 01:23 UTC

[Rd] SUGGESTION: Proposal to mitigate problem with stray processes left behind by parallel::makeCluster()

(Bcc: CRAN)

This is a proposal helping CRAN and alike as well as individual
developers to avoid stray R processes being left behind that might be
produced when an example or a package test fails to set up a
parallel::makeCluster().


ISSUE

If a package test sets up a PSOCK cluster and then the master process
dies for one reason or the other, the PSOCK worker processes will
remain running for 30 days ('timeout') until they timeout and
terminate that way.  When this happens on CRAN servers, where many
packages are checked all the time, this will result in a lot of stray
R processes.

Here is an example illustrating how R leaves behind stray R processes
if fails to establish a connection to one or more background R
processes launched by 'parallel::makeCluster()'.  First, let's make
sure there are no other R processes running:

  $ ps aux | grep -E "exec[/]R"

Then, lets create a PSOCK cluster for which connection will fail
(because port 80 is reserved):

  $ Rscript -e 'parallel::makeCluster(1L, port=80)'
  Error in socketConnection("localhost", port = port, server = TRUE,
blocking = TRUE,  :
    cannot open the connection
  Calls: <Anonymous> ... makePSOCKcluster -> newPSOCKnode ->
socketConnection
  In addition: Warning message:
  In socketConnection("localhost", port = port, server = TRUE,
blocking = TRUE,  :
    port 80 cannot be opened

The launched R worker is still running:

  $ ps aux | grep -E "exec[/]R"
  hb       20778 37.0  0.4 283092 70624 pts/0    S    17:50   0:00
/usr/lib/R/bin/exec/R --slave --no-restore -e parallel:::.slaveRSOCK()
--args MASTER=localhost PORT=80 OUT=/dev/null SETUPTIMEOUT=120
TIMEOUT=2 592000 XDR=TRUE

This process will keep running for 'TIMEOUT=2592000' seconds (= 30
days).  The reason for this is that it is currently in the state where
it attempts to set up a connection to the main R process:

  > parallel:::.slaveRSOCK
  function ()
  {
      makeSOCKmaster <- function(master, port, setup_timeout, timeout,
          useXDR) {
   ...
          repeat {
              con <- tryCatch({
                  socketConnection(master, port = port, blocking = TRUE,
                    open = "a+b", timeout = timeout)
              }, error = identity)
      ...
  }

In other words, it is stuck in 'socketConnection()' and it won't
time
out until 'timeout' seconds.


SUGGESTION

To mitigate the problem with above stray processes from running 'R CMD
check', we could shorten the 'timeout' which is currently hardcoded
to
30 days (src/library/parallel/R/snow.R).  By making it possible to
control the default via environment variables, e.g.

  setup_timeout = as.numeric(Sys.getenv("R_PARALLEL_SETUP_TIMEOUT", 60
* 2)),      # 2 minutes
  timeout = as.numeric(Sys.getenv("R_PARALLEL_SETUP_TIMEOUT", 60 * 60
* 24 * 30)), # 30 days

it would be straightforward to adjust `R CMD check` to use, say,

  R_PARALLEL_SETUP_TIMEOUT=60

by default.  This would cause any stray processes to time out after 60
seconds (instead of 30 days as now).

/Henrik

Tomas Kalibera

2019-Mar-27 19:52 UTC

head link

[Rd] SUGGESTION: Proposal to mitigate problem with stray processes left behind by parallel::makeCluster()

The problem causing the stray worker processes when the master fails to 
open a server socket to listen to connections from workers is not 
related to timeout in socketConnection(), because socketConnection() 
will fail right away. It is caused by a bug in checking the setup 
timeout (PR 17391).

Fixed in 76275.

Best
Tomas

On 3/18/19 2:23 AM, Henrik Bengtsson wrote:> (Bcc: CRAN)
>
> This is a proposal helping CRAN and alike as well as individual
> developers to avoid stray R processes being left behind that might be
> produced when an example or a package test fails to set up a
> parallel::makeCluster().
>
>
> ISSUE
>
> If a package test sets up a PSOCK cluster and then the master process
> dies for one reason or the other, the PSOCK worker processes will
> remain running for 30 days ('timeout') until they timeout and
> terminate that way.  When this happens on CRAN servers, where many
> packages are checked all the time, this will result in a lot of stray
> R processes.
>
> Here is an example illustrating how R leaves behind stray R processes
> if fails to establish a connection to one or more background R
> processes launched by 'parallel::makeCluster()'.  First, let's
make
> sure there are no other R processes running:
>
>    $ ps aux | grep -E "exec[/]R"
>
> Then, lets create a PSOCK cluster for which connection will fail
> (because port 80 is reserved):
>
>    $ Rscript -e 'parallel::makeCluster(1L, port=80)'
>    Error in socketConnection("localhost", port = port, server =
TRUE,
> blocking = TRUE,  :
>      cannot open the connection
>    Calls: <Anonymous> ... makePSOCKcluster -> newPSOCKnode ->
socketConnection
>    In addition: Warning message:
>    In socketConnection("localhost", port = port, server = TRUE,
> blocking = TRUE,  :
>      port 80 cannot be opened
>
> The launched R worker is still running:
>
>    $ ps aux | grep -E "exec[/]R"
>    hb       20778 37.0  0.4 283092 70624 pts/0    S    17:50   0:00
> /usr/lib/R/bin/exec/R --slave --no-restore -e parallel:::.slaveRSOCK()
> --args MASTER=localhost PORT=80 OUT=/dev/null SETUPTIMEOUT=120
> TIMEOUT=2 592000 XDR=TRUE
>
> This process will keep running for 'TIMEOUT=2592000' seconds (= 30
> days).  The reason for this is that it is currently in the state where
> it attempts to set up a connection to the main R process:
>
>    > parallel:::.slaveRSOCK
>    function ()
>    {
>        makeSOCKmaster <- function(master, port, setup_timeout, timeout,
>            useXDR) {
>     ...
>            repeat {
>                con <- tryCatch({
>                    socketConnection(master, port = port, blocking = TRUE,
>                      open = "a+b", timeout = timeout)
>                }, error = identity)
>        ...
>    }
>
> In other words, it is stuck in 'socketConnection()' and it
won't time
> out until 'timeout' seconds.
>
>
> SUGGESTION
>
> To mitigate the problem with above stray processes from running 'R CMD
> check', we could shorten the 'timeout' which is currently
hardcoded to
> 30 days (src/library/parallel/R/snow.R).  By making it possible to
> control the default via environment variables, e.g.
>
>    setup_timeout =
as.numeric(Sys.getenv("R_PARALLEL_SETUP_TIMEOUT", 60
> * 2)),      # 2 minutes
>    timeout = as.numeric(Sys.getenv("R_PARALLEL_SETUP_TIMEOUT", 60
* 60
> * 24 * 30)), # 30 days
>
> it would be straightforward to adjust `R CMD check` to use, say,
>
>    R_PARALLEL_SETUP_TIMEOUT=60
>
> by default.  This would cause any stray processes to time out after 60
> seconds (instead of 30 days as now).
>
> /Henrik
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

Henrik Bengtsson

2019-Mar-28 04:20 UTC

head link

[Rd] SUGGESTION: Proposal to mitigate problem with stray processes left behind by parallel::makeCluster()

Thank you Tomas.

For the record, I'm confirming that the stray background R worker
process now times out properly after 'setup_timeout' (= 120) seconds:

{0s}$ Rscript -e 'parallel::makeCluster(1L, port=80)'
Error in socketConnection("localhost", port = port, server = TRUE,
blocking = TRUE,  :
  cannot open the connection
Calls: <Anonymous> ... makePSOCKcluster -> newPSOCKnode ->
socketConnection
In addition: Warning message:
In socketConnection("localhost", port = port, server = TRUE, blocking
= TRUE,  :
  port 80 cannot be opened
Execution halted
{1s}$ ps aux | grep -E "exec[/]R"
hb       17645  2.0  0.3 259104 55144 pts/5    S    20:58   0:00
/home/hb/software/R-devel/trunk/lib/R/bin/exec/R --slave --no-restore
-e parallel:::.slaveRSOCK() --args MASTER=localhost PORT=80
OUT=/dev/null SETUPTIMEOUT=120 TIMEOUT=2592000 XDR=TRUE
{2s}$ sleep 120
{122s}$ ps aux | grep -E "exec[/]R"
{122s}$

Good spotting of the bug:

-  if (Sys.time() - t0 > setup_timeout) break
+  if (difftime(Sys.time(), t0, units="secs") > setup_timeout)
break

For those who find this thread, I think what's going on here is that
'setup_timeout = 120' is a numeric that is compared a 'difftime'
than
keeps changing unit as times goes by.  When compared as 'Sys.time() -
t0 > setup_timeout' the LHS would be in units of seconds as long as
less than 60 seconds had passed:
> Sys.time() - t0
Time difference of 59 secs> as.numeric(Sys.time() - t0)[1] 59

However, as soon as more than 60 seconds has passed, the unit turns
into minutes and we're comparing minutes to seconds:
> Sys.time() - t0
Time difference of 1.016667 mins> as.numeric(Sys.time() - t0)[1] 1.016667

which is now compared to 'setup_timeout'.  If the unit remained to be
minutes it would timeout after 120 [minutes]. However, after 120
minutes, the unit of Sys.time() - t0 is in hours, and we're comparing
hours to seconds, and so on.  It would only timeout if we used
'setup_timeout' < 60 seconds.

/Henrik

On Wed, Mar 27, 2019 at 12:52 PM Tomas Kalibera
<tomas.kalibera at gmail.com> wrote:>
>
> The problem causing the stray worker processes when the master fails to
> open a server socket to listen to connections from workers is not
> related to timeout in socketConnection(), because socketConnection()
> will fail right away. It is caused by a bug in checking the setup
> timeout (PR 17391).
>
> Fixed in 76275.
>
> Best
> Tomas
>
> On 3/18/19 2:23 AM, Henrik Bengtsson wrote:
> > (Bcc: CRAN)
> >
> > This is a proposal helping CRAN and alike as well as individual
> > developers to avoid stray R processes being left behind that might be
> > produced when an example or a package test fails to set up a
> > parallel::makeCluster().
> >
> >
> > ISSUE
> >
> > If a package test sets up a PSOCK cluster and then the master process
> > dies for one reason or the other, the PSOCK worker processes will
> > remain running for 30 days ('timeout') until they timeout and
> > terminate that way.  When this happens on CRAN servers, where many
> > packages are checked all the time, this will result in a lot of stray
> > R processes.
> >
> > Here is an example illustrating how R leaves behind stray R processes
> > if fails to establish a connection to one or more background R
> > processes launched by 'parallel::makeCluster()'.  First,
let's make
> > sure there are no other R processes running:
> >
> >    $ ps aux | grep -E "exec[/]R"
> >
> > Then, lets create a PSOCK cluster for which connection will fail
> > (because port 80 is reserved):
> >
> >    $ Rscript -e 'parallel::makeCluster(1L, port=80)'
> >    Error in socketConnection("localhost", port = port,
server = TRUE,
> > blocking = TRUE,  :
> >      cannot open the connection
> >    Calls: <Anonymous> ... makePSOCKcluster -> newPSOCKnode
-> socketConnection
> >    In addition: Warning message:
> >    In socketConnection("localhost", port = port, server =
TRUE,
> > blocking = TRUE,  :
> >      port 80 cannot be opened
> >
> > The launched R worker is still running:
> >
> >    $ ps aux | grep -E "exec[/]R"
> >    hb       20778 37.0  0.4 283092 70624 pts/0    S    17:50   0:00
> > /usr/lib/R/bin/exec/R --slave --no-restore -e parallel:::.slaveRSOCK()
> > --args MASTER=localhost PORT=80 OUT=/dev/null SETUPTIMEOUT=120
> > TIMEOUT=2 592000 XDR=TRUE
> >
> > This process will keep running for 'TIMEOUT=2592000' seconds
(= 30
> > days).  The reason for this is that it is currently in the state where
> > it attempts to set up a connection to the main R process:
> >
> >    > parallel:::.slaveRSOCK
> >    function ()
> >    {
> >        makeSOCKmaster <- function(master, port, setup_timeout,
timeout,
> >            useXDR) {
> >     ...
> >            repeat {
> >                con <- tryCatch({
> >                    socketConnection(master, port = port, blocking =
TRUE,
> >                      open = "a+b", timeout = timeout)
> >                }, error = identity)
> >        ...
> >    }
> >
> > In other words, it is stuck in 'socketConnection()' and it
won't time
> > out until 'timeout' seconds.
> >
> >
> > SUGGESTION
> >
> > To mitigate the problem with above stray processes from running 'R
CMD
> > check', we could shorten the 'timeout' which is currently
hardcoded to
> > 30 days (src/library/parallel/R/snow.R).  By making it possible to
> > control the default via environment variables, e.g.
> >
> >    setup_timeout =
as.numeric(Sys.getenv("R_PARALLEL_SETUP_TIMEOUT", 60
> > * 2)),      # 2 minutes
> >    timeout =
as.numeric(Sys.getenv("R_PARALLEL_SETUP_TIMEOUT", 60 * 60
> > * 24 * 30)), # 30 days
> >
> > it would be straightforward to adjust `R CMD check` to use, say,
> >
> >    R_PARALLEL_SETUP_TIMEOUT=60
> >
> > by default.  This would cause any stray processes to time out after 60
> > seconds (instead of 30 days as now).
> >
> > /Henrik
> >
> > ______________________________________________
> > R-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
>
>

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