Henrik Bengtsson
2018-Mar-09 05:58 UTC
[Rd] parallel:::newPSOCKnode(): background worker fails immediately if socket on master is not set up in time (BUG?)
A solution is to have parallel:::.slaveRSOCK() attempt to connect
multiple times before failing, e.g.
makeSOCKmaster <- function(master, port, timeout, useXDR, maxTries
= 10L, interval = 1.0) {
port <- as.integer(port)
for (i in seq_len(maxTries)) {
con <- tryCatch({
socketConnection(master, port = port, blocking = TRUE,
open = "a+b", timeout = timeout)
}, error = identity)
if (inherits(con, "connection")) break
Sys.sleep(interval)
}
if (inherits(con, "error")) stop(con)
structure(list(con = con), class = if (useXDR)
"SOCKnode"
else "SOCK0node")
}
One could set 'maxTries' and 'interval' via commandArgs() like
what is
done for the other arguments.
I'm happy to submit an SVN patch if R core thinks this is an
acceptable solution.
/Henrik
On Thu, Mar 8, 2018 at 7:36 PM, Henrik Bengtsson
<henrik.bengtsson at gmail.com> wrote:> I just noticed that parallel:::.slaveRSOCK() passes 'timeout' to
> socketConnection() as a character, i.e. there's a missing timeout <-
> as.integer(timeout), cf. port <- as.integer(port) and useXDR <-
> as.logical(value):
>
>> parallel:::.slaveRSOCK
> function ()
> {
> makeSOCKmaster <- function(master, port, timeout, useXDR) {
> port <- as.integer(port)
> con <- socketConnection(master, port = port, blocking = TRUE,
> open = "a+b", timeout = timeout)
> structure(list(con = con), class = if (useXDR)
> "SOCKnode"
> else "SOCK0node")
> }
> master <- "localhost"
> port <- NA_integer_
> outfile <- Sys.getenv("R_SNOW_OUTFILE")
> methods <- TRUE
> useXDR <- TRUE
> for (a in commandArgs(TRUE)) {
> pos <- regexpr("=", a)
> name <- substr(a, 1L, pos - 1L)
> value <- substr(a, pos + 1L, nchar(a))
> switch(name, MASTER = {
> master <- value
> }, PORT = {
> port <- value
> }, OUT = {
> outfile <- value
> }, TIMEOUT = {
> timeout <- value
> }, XDR = {
> useXDR <- as.logical(value)
> })
> }
> if (is.na(port))
> stop("PORT must be specified")
> sinkWorkerOutput(outfile)
> msg <- sprintf("starting worker pid=%d on %s at %s\n",
Sys.getpid(),
> paste(master, port, sep = ":"), format(Sys.time(),
"%H:%M:%OS3"))
> cat(msg)
> slaveLoop(makeSOCKmaster(master, port, timeout, useXDR))
> }
> <bytecode: 0x4bd4b58>
> <environment: namespace:parallel>
>
> Yet, fix that does *not* seem to change anything.
>
> /Henrik
>
> On Thu, Mar 8, 2018 at 7:05 PM, Henrik Bengtsson
> <henrik.bengtsson at gmail.com> wrote:
>> BACKGROUND:
>>
>> While troubleshooting random, occasionally occurring, errors from
>> parallel::makePSOCKcluster("localhost", port = 11000);
>>
>> Error in socketConnection("localhost", port = port, server =
TRUE,
>> blocking = TRUE, :
>> cannot open the connection
>>
>> I had another look at parallel:::newPSOCKnode(), which is used
>> internally to set up each background worker. It is designed to, first
>> launch the background worker as:
>>
>> system('R --slave --no-restore -e
"parallel:::.slaveRSOCK()" --args
>> MASTER=localhost PORT=11000 OUT=/dev/null TIMEOUT=2592000
XDR=TRUE',
>> wait = FALSE)
>>
>> which immediately tries to connect to a socket on localhost:11000 with
>> timeout. Immediately after the master launched the above (without
>> waiting), it will set up the connection waiting for the connect from
>> the background worker:
>>
>> con <- socketConnection("localhost", port = 11000,
server = TRUE,
>> blocking = TRUE, open = "a+b", timeout = timeout)
>>
>>
>> ISSUE:
>>
>> If we emulate the above process, and remove the OUT=/dev/null such
>> that we can see the output produces by the worker, as:
>>
>> setup <- function(delay = 0) {
>> system('R --slave --no-restore -e
"parallel:::.slaveRSOCK()" --args
>> MASTER=localhost PORT=11000 TIMEOUT=2592000 XDR=TRUE', wait =
FALSE)
>> Sys.sleep(delay)
>> socketConnection("localhost", port = 11000, server = TRUE,
blocking
>> = TRUE, open = "a+b", timeout = 20)
>> }
>>
>> doing:
>>
>>> con <- setup(0)
>> starting worker pid=24983 on localhost:11000 at 18:44:30.087
>>
>> will most likely work, but adding a delay:
>>
>>> con <- setup(5)
>> starting worker pid=25099 on localhost:11000 at 18:45:23.617
>> Warning in socketConnection(master, port = port, blocking = TRUE, open
>> = "a+b", :
>> localhost:11000 cannot be opened
>> Error in socketConnection(master, port = port, blocking = TRUE, open =
"a+b", :
>> cannot open the connection
>> Calls: <Anonymous> ... doTryCatch -> recvData ->
makeSOCKmaster ->
>> socketConnection
>>
>> will produce an *instant* error on the worker, and before master opens
>> the server socket. Eventually, master will produce the originally
>> observed error:
>>
>> Error in socketConnection("localhost", port = 11000, server =
TRUE,
>> blocking = TRUE, :
>> cannot open the connection
>>
>> In other words, if the master fails to setup socketConnection()
>> *before* the background workers attempts to connect, it all fails.
>> Such a delay may happen for instance when there is a large CPU load on
>> the test machine.
>>
>> Is this the above bug?
>>
>> /Henrik
>>
>> PS. The background is that I, very occasionally, observe R CMD check
>> error on the above (on CRAN and elsewhere) when testing my future
>> package. The error always go away when retested. This far I've
though
>> this is due to port clashes (since the port is random selected in
>> [11000:11999]) and accepted that it happens. However, after
>> discovering the above, it could be due to the worker launching
"too
>> soon".
>>
>>> sessionInfo()
>> R version 3.4.3 (2017-11-30)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>> Running under: Ubuntu 16.04.4 LTS
>>
>> Matrix products: default
>> BLAS: /usr/lib/atlas-base/atlas/libblas.so.3.0
>> LAPACK: /usr/lib/atlas-base/atlas/liblapack.so.3.0
>>
>> locale:
>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> loaded via a namespace (and not attached):
>> [1] compiler_3.4.3
luke-tierney at uiowa.edu
2018-Mar-09 12:37 UTC
[Rd] parallel:::newPSOCKnode(): background worker fails immediately if socket on master is not set up in time (BUG?)
I'm happy to look at a patch that does this. I'd start with a small interval and increase it by 50%, say, on each try wit a max retry time limit. This isn't eliminating the problem,only reducing the probability, but still worth it. I had considered doing something like this but it didn't seem necessary at the time. You don't want to retry indefinitely since the connection could be failing because the master died, and then you want the workers to die as well. Best, luke On Fri, 9 Mar 2018, Henrik Bengtsson wrote:> A solution is to have parallel:::.slaveRSOCK() attempt to connect > multiple times before failing, e.g. > > makeSOCKmaster <- function(master, port, timeout, useXDR, maxTries > = 10L, interval = 1.0) { > port <- as.integer(port) > for (i in seq_len(maxTries)) { > con <- tryCatch({ > socketConnection(master, port = port, blocking = TRUE, > open = "a+b", timeout = timeout) > }, error = identity) > if (inherits(con, "connection")) break > Sys.sleep(interval) > } > if (inherits(con, "error")) stop(con) > structure(list(con = con), class = if (useXDR) > "SOCKnode" > else "SOCK0node") > } > > One could set 'maxTries' and 'interval' via commandArgs() like what is > done for the other arguments. > > I'm happy to submit an SVN patch if R core thinks this is an > acceptable solution. > > /Henrik > > On Thu, Mar 8, 2018 at 7:36 PM, Henrik Bengtsson > <henrik.bengtsson at gmail.com> wrote: >> I just noticed that parallel:::.slaveRSOCK() passes 'timeout' to >> socketConnection() as a character, i.e. there's a missing timeout <- >> as.integer(timeout), cf. port <- as.integer(port) and useXDR <- >> as.logical(value): >> >>> parallel:::.slaveRSOCK >> function () >> { >> makeSOCKmaster <- function(master, port, timeout, useXDR) { >> port <- as.integer(port) >> con <- socketConnection(master, port = port, blocking = TRUE, >> open = "a+b", timeout = timeout) >> structure(list(con = con), class = if (useXDR) >> "SOCKnode" >> else "SOCK0node") >> } >> master <- "localhost" >> port <- NA_integer_ >> outfile <- Sys.getenv("R_SNOW_OUTFILE") >> methods <- TRUE >> useXDR <- TRUE >> for (a in commandArgs(TRUE)) { >> pos <- regexpr("=", a) >> name <- substr(a, 1L, pos - 1L) >> value <- substr(a, pos + 1L, nchar(a)) >> switch(name, MASTER = { >> master <- value >> }, PORT = { >> port <- value >> }, OUT = { >> outfile <- value >> }, TIMEOUT = { >> timeout <- value >> }, XDR = { >> useXDR <- as.logical(value) >> }) >> } >> if (is.na(port)) >> stop("PORT must be specified") >> sinkWorkerOutput(outfile) >> msg <- sprintf("starting worker pid=%d on %s at %s\n", Sys.getpid(), >> paste(master, port, sep = ":"), format(Sys.time(), "%H:%M:%OS3")) >> cat(msg) >> slaveLoop(makeSOCKmaster(master, port, timeout, useXDR)) >> } >> <bytecode: 0x4bd4b58> >> <environment: namespace:parallel> >> >> Yet, fix that does *not* seem to change anything. >> >> /Henrik >> >> On Thu, Mar 8, 2018 at 7:05 PM, Henrik Bengtsson >> <henrik.bengtsson at gmail.com> wrote: >>> BACKGROUND: >>> >>> While troubleshooting random, occasionally occurring, errors from >>> parallel::makePSOCKcluster("localhost", port = 11000); >>> >>> Error in socketConnection("localhost", port = port, server = TRUE, >>> blocking = TRUE, : >>> cannot open the connection >>> >>> I had another look at parallel:::newPSOCKnode(), which is used >>> internally to set up each background worker. It is designed to, first >>> launch the background worker as: >>> >>> system('R --slave --no-restore -e "parallel:::.slaveRSOCK()" --args >>> MASTER=localhost PORT=11000 OUT=/dev/null TIMEOUT=2592000 XDR=TRUE', >>> wait = FALSE) >>> >>> which immediately tries to connect to a socket on localhost:11000 with >>> timeout. Immediately after the master launched the above (without >>> waiting), it will set up the connection waiting for the connect from >>> the background worker: >>> >>> con <- socketConnection("localhost", port = 11000, server = TRUE, >>> blocking = TRUE, open = "a+b", timeout = timeout) >>> >>> >>> ISSUE: >>> >>> If we emulate the above process, and remove the OUT=/dev/null such >>> that we can see the output produces by the worker, as: >>> >>> setup <- function(delay = 0) { >>> system('R --slave --no-restore -e "parallel:::.slaveRSOCK()" --args >>> MASTER=localhost PORT=11000 TIMEOUT=2592000 XDR=TRUE', wait = FALSE) >>> Sys.sleep(delay) >>> socketConnection("localhost", port = 11000, server = TRUE, blocking >>> = TRUE, open = "a+b", timeout = 20) >>> } >>> >>> doing: >>> >>>> con <- setup(0) >>> starting worker pid=24983 on localhost:11000 at 18:44:30.087 >>> >>> will most likely work, but adding a delay: >>> >>>> con <- setup(5) >>> starting worker pid=25099 on localhost:11000 at 18:45:23.617 >>> Warning in socketConnection(master, port = port, blocking = TRUE, open >>> = "a+b", : >>> localhost:11000 cannot be opened >>> Error in socketConnection(master, port = port, blocking = TRUE, open = "a+b", : >>> cannot open the connection >>> Calls: <Anonymous> ... doTryCatch -> recvData -> makeSOCKmaster -> >>> socketConnection >>> >>> will produce an *instant* error on the worker, and before master opens >>> the server socket. Eventually, master will produce the originally >>> observed error: >>> >>> Error in socketConnection("localhost", port = 11000, server = TRUE, >>> blocking = TRUE, : >>> cannot open the connection >>> >>> In other words, if the master fails to setup socketConnection() >>> *before* the background workers attempts to connect, it all fails. >>> Such a delay may happen for instance when there is a large CPU load on >>> the test machine. >>> >>> Is this the above bug? >>> >>> /Henrik >>> >>> PS. The background is that I, very occasionally, observe R CMD check >>> error on the above (on CRAN and elsewhere) when testing my future >>> package. The error always go away when retested. This far I've though >>> this is due to port clashes (since the port is random selected in >>> [11000:11999]) and accepted that it happens. However, after >>> discovering the above, it could be due to the worker launching "too >>> soon". >>> >>>> sessionInfo() >>> R version 3.4.3 (2017-11-30) >>> Platform: x86_64-pc-linux-gnu (64-bit) >>> Running under: Ubuntu 16.04.4 LTS >>> >>> Matrix products: default >>> BLAS: /usr/lib/atlas-base/atlas/libblas.so.3.0 >>> LAPACK: /usr/lib/atlas-base/atlas/liblapack.so.3.0 >>> >>> locale: >>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> loaded via a namespace (and not attached): >>> [1] compiler_3.4.3 > > ______________________________________________ > 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
Henrik Bengtsson
2018-Mar-10 01:52 UTC
[Rd] parallel:::newPSOCKnode(): background worker fails immediately if socket on master is not set up in time (BUG?)
Great. For the record of this thread, I've submitted patch PR17391 (https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=17391). I've patched it against the latest R-devel on the SVN, passes 'make check-all', and I've verified it works with the above tests. /Henrik On Fri, Mar 9, 2018 at 4:37 AM, <luke-tierney at uiowa.edu> wrote:> I'm happy to look at a patch that does this. I'd start with a small > interval and increase it by 50%, say, on each try wit a max retry time > limit. This isn't eliminating the problem,only reducing the > probability, but still worth it. I had considered doing something like > this but it didn't seem necessary at the time. You don't want to retry > indefinitely since the connection could be failing because the master > died, and then you want the workers to die as well. > > Best, > > luke > > > On Fri, 9 Mar 2018, Henrik Bengtsson wrote: > >> A solution is to have parallel:::.slaveRSOCK() attempt to connect >> multiple times before failing, e.g. >> >> makeSOCKmaster <- function(master, port, timeout, useXDR, maxTries >> = 10L, interval = 1.0) { >> port <- as.integer(port) >> for (i in seq_len(maxTries)) { >> con <- tryCatch({ >> socketConnection(master, port = port, blocking = TRUE, >> open = "a+b", timeout = timeout) >> }, error = identity) >> if (inherits(con, "connection")) break >> Sys.sleep(interval) >> } >> if (inherits(con, "error")) stop(con) >> structure(list(con = con), class = if (useXDR) >> "SOCKnode" >> else "SOCK0node") >> } >> >> One could set 'maxTries' and 'interval' via commandArgs() like what is >> done for the other arguments. >> >> I'm happy to submit an SVN patch if R core thinks this is an >> acceptable solution. >> >> /Henrik >> >> On Thu, Mar 8, 2018 at 7:36 PM, Henrik Bengtsson >> <henrik.bengtsson at gmail.com> wrote: >>> >>> I just noticed that parallel:::.slaveRSOCK() passes 'timeout' to >>> socketConnection() as a character, i.e. there's a missing timeout <- >>> as.integer(timeout), cf. port <- as.integer(port) and useXDR <- >>> as.logical(value): >>> >>>> parallel:::.slaveRSOCK >>> >>> function () >>> { >>> makeSOCKmaster <- function(master, port, timeout, useXDR) { >>> port <- as.integer(port) >>> con <- socketConnection(master, port = port, blocking = TRUE, >>> open = "a+b", timeout = timeout) >>> structure(list(con = con), class = if (useXDR) >>> "SOCKnode" >>> else "SOCK0node") >>> } >>> master <- "localhost" >>> port <- NA_integer_ >>> outfile <- Sys.getenv("R_SNOW_OUTFILE") >>> methods <- TRUE >>> useXDR <- TRUE >>> for (a in commandArgs(TRUE)) { >>> pos <- regexpr("=", a) >>> name <- substr(a, 1L, pos - 1L) >>> value <- substr(a, pos + 1L, nchar(a)) >>> switch(name, MASTER = { >>> master <- value >>> }, PORT = { >>> port <- value >>> }, OUT = { >>> outfile <- value >>> }, TIMEOUT = { >>> timeout <- value >>> }, XDR = { >>> useXDR <- as.logical(value) >>> }) >>> } >>> if (is.na(port)) >>> stop("PORT must be specified") >>> sinkWorkerOutput(outfile) >>> msg <- sprintf("starting worker pid=%d on %s at %s\n", Sys.getpid(), >>> paste(master, port, sep = ":"), format(Sys.time(), "%H:%M:%OS3")) >>> cat(msg) >>> slaveLoop(makeSOCKmaster(master, port, timeout, useXDR)) >>> } >>> <bytecode: 0x4bd4b58> >>> <environment: namespace:parallel> >>> >>> Yet, fix that does *not* seem to change anything. >>> >>> /Henrik >>> >>> On Thu, Mar 8, 2018 at 7:05 PM, Henrik Bengtsson >>> <henrik.bengtsson at gmail.com> wrote: >>>> >>>> BACKGROUND: >>>> >>>> While troubleshooting random, occasionally occurring, errors from >>>> parallel::makePSOCKcluster("localhost", port = 11000); >>>> >>>> Error in socketConnection("localhost", port = port, server = TRUE, >>>> blocking = TRUE, : >>>> cannot open the connection >>>> >>>> I had another look at parallel:::newPSOCKnode(), which is used >>>> internally to set up each background worker. It is designed to, first >>>> launch the background worker as: >>>> >>>> system('R --slave --no-restore -e "parallel:::.slaveRSOCK()" --args >>>> MASTER=localhost PORT=11000 OUT=/dev/null TIMEOUT=2592000 XDR=TRUE', >>>> wait = FALSE) >>>> >>>> which immediately tries to connect to a socket on localhost:11000 with >>>> timeout. Immediately after the master launched the above (without >>>> waiting), it will set up the connection waiting for the connect from >>>> the background worker: >>>> >>>> con <- socketConnection("localhost", port = 11000, server = TRUE, >>>> blocking = TRUE, open = "a+b", timeout = timeout) >>>> >>>> >>>> ISSUE: >>>> >>>> If we emulate the above process, and remove the OUT=/dev/null such >>>> that we can see the output produces by the worker, as: >>>> >>>> setup <- function(delay = 0) { >>>> system('R --slave --no-restore -e "parallel:::.slaveRSOCK()" --args >>>> MASTER=localhost PORT=11000 TIMEOUT=2592000 XDR=TRUE', wait = FALSE) >>>> Sys.sleep(delay) >>>> socketConnection("localhost", port = 11000, server = TRUE, blocking >>>> = TRUE, open = "a+b", timeout = 20) >>>> } >>>> >>>> doing: >>>> >>>>> con <- setup(0) >>>> >>>> starting worker pid=24983 on localhost:11000 at 18:44:30.087 >>>> >>>> will most likely work, but adding a delay: >>>> >>>>> con <- setup(5) >>>> >>>> starting worker pid=25099 on localhost:11000 at 18:45:23.617 >>>> Warning in socketConnection(master, port = port, blocking = TRUE, open >>>> = "a+b", : >>>> localhost:11000 cannot be opened >>>> Error in socketConnection(master, port = port, blocking = TRUE, open >>>> "a+b", : >>>> cannot open the connection >>>> Calls: <Anonymous> ... doTryCatch -> recvData -> makeSOCKmaster -> >>>> socketConnection >>>> >>>> will produce an *instant* error on the worker, and before master opens >>>> the server socket. Eventually, master will produce the originally >>>> observed error: >>>> >>>> Error in socketConnection("localhost", port = 11000, server = TRUE, >>>> blocking = TRUE, : >>>> cannot open the connection >>>> >>>> In other words, if the master fails to setup socketConnection() >>>> *before* the background workers attempts to connect, it all fails. >>>> Such a delay may happen for instance when there is a large CPU load on >>>> the test machine. >>>> >>>> Is this the above bug? >>>> >>>> /Henrik >>>> >>>> PS. The background is that I, very occasionally, observe R CMD check >>>> error on the above (on CRAN and elsewhere) when testing my future >>>> package. The error always go away when retested. This far I've though >>>> this is due to port clashes (since the port is random selected in >>>> [11000:11999]) and accepted that it happens. However, after >>>> discovering the above, it could be due to the worker launching "too >>>> soon". >>>> >>>>> sessionInfo() >>>> >>>> R version 3.4.3 (2017-11-30) >>>> Platform: x86_64-pc-linux-gnu (64-bit) >>>> Running under: Ubuntu 16.04.4 LTS >>>> >>>> Matrix products: default >>>> BLAS: /usr/lib/atlas-base/atlas/libblas.so.3.0 >>>> LAPACK: /usr/lib/atlas-base/atlas/liblapack.so.3.0 >>>> >>>> locale: >>>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>>> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >>>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >>>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets methods base >>>> >>>> loaded via a namespace (and not attached): >>>> [1] compiler_3.4.3 >> >> >> ______________________________________________ >> 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
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