Tomas, Luke, thank you very much once again for patching both issues swiftly.
This’ll be incredibly valuable to us once we move to 3.6.0.
From: Tomas Kalibera <tomas.kalib...@gmail.com>
Sent: 03 September 2018 13:07
To: r-devel@r-project.org
Cc: Srinivasan, Arunkumar <arunkumar.sriniva...@uk.mlp.com>
Subject: Re: [Rd] Get Logical processor count correctly whether NUMA is enabled
or disabled
A summary for reference: the new detectCores() for Windows in R-devel seems to
be working both for logical and physical cores on systems with >64 logical
processors (thanks to Arun for testing!). If the feature is important for
anyone particularly using an older version of Windows and/or on a system with
>64 logical processors, it would be nice if you could test and report any
possible problem.
As I mentioned earlier, in older versions of R one can as a workaround use
"wmic" to detect the number of processors on systems with >64 logical
processors (with appropriate error handling added as needed):
# detectCores()
out <- system("wmic cpu get numberoflogicalprocessors", intern=TRUE)
sum(as.numeric(gsub("([0-9]+).*", "\\1<file://1>", grep("[0-9]+[ \t]*", out,
value=TRUE))))
#detectCores(logical=FALSE)
out <- system("wmic cpu get numberofcores", intern=TRUE)
sum(as.numeric(gsub("([0-9]+).*", "\\1<file://1>", grep("[0-9]+[ \t]*", out,
value=TRUE))))
The remaining problem with running using >64 processors on Windows turned out
to be due to a bug in sockets communication, debugged and fixed in R-devel by
Luke Tierney.
Tomas
On 08/29/2018 12:42 PM, Srinivasan, Arunkumar wrote:
Dear Tomas, thank you very much. I installed r-devel r75201 and tested.
The machine with 88 cores has NUMA disabled. It therefore has 2 processor
groups with 64 and 24 processors each.
require(parallel)
detectCores()
# [1] 88
This is great!
Then I went on to test with a simple 'foreach()' loop. I started with 64
processors (max limit of 1 processor group). I ran with a simple function of
0.5s sleep.
require(snow)
require(doSNOW)
require(foreach)
cl <- makeCluster(64L, "SOCK")
registerDoSNOW(cl)
system.time(foreach(i=1:64) %dopar% Sys.sleep(0.5))
# user system elapsed
# 0.06 0.00 0.64
system.time(foreach(i=1:65) %dopar% Sys.sleep(0.5))
# user system elapsed
# 0.03 0.01 1.04
stopCluster(cl)
With a cluster of 64 processors and loop running with 64 iterations, it
completed in ~.5s (0.64), and with 65 iterations, it took ~1s as expected.
cl <- makeCluster(65L, "SOCK")
registerDoSNOW(cl)
system.time(foreach(i=1:64) %dopar% Sys.sleep(0.5))
user system elapsed
0.03 0.02 0.61
system.time(foreach(i=1:65) %dopar% Sys.sleep(0.5))
# Timing stopped at: 0.08 0 293
stopCluster(cl)
However, when I increased the cluster to have 65 processors, a loop with 64
iterations seem to complete as expected, but using all 65 processors to loop
over 65 iterations didn't seem to complete. I stopped it after ~5mins. The same
happens with the cluster started with any number between 65 and 88. It seems to
me like we are still not being able to use >64 processors all at the same time
even if detectCores() returns the right count now.
I'd appreciate your thoughts on this.
Best,
Arun.
-----Original Message-----
From: Tomas Kalibera <tomas.kalib...@gmail.com><mailto:tomas.kalib...@gmail.com>
Sent: 27 August 2018 19:43
To: Srinivasan, Arunkumar
<arunkumar.sriniva...@uk.mlp.com><mailto:arunkumar.sriniva...@uk.mlp.com>;
r-devel@r-project.org<mailto:r-devel@r-project.org>
Subject: Re: [Rd] Get Logical processor count correctly whether NUMA is enabled
or disabled
Dear Arun,
thank you for checking the workaround scripts.
I've modified detectCores() to use GetLogicalProcessorInformationEx. It is in
revision 75198 of R-devel, could you please test it on your machines? For a
binary, you can wait until the R-devel snapshot build gets to at least this svn
revision.
Thanks for the link to the processor groups documentation. I don't have a
machine to test this on, but I would hope that snow clusters (e.g.
PSOCK) should work fine on systems with >64 logical processors as they spawn
new processes (not just threads). Note that FORK clusters are not supported on
Windows.
Thanks
Tomas
On 08/21/2018 02:53 PM, Srinivasan, Arunkumar wrote:
Dear Tomas, thank you for looking into this. Here's the output:
# number of logical processors - what detectCores() should return out
<- system("wmic cpu get numberoflogicalprocessors", intern=TRUE)
[1] "NumberOfLogicalProcessors \r" "22 \r" "22
\r"
[4] "20 \r" "22 \r" "\r"
sum(as.numeric(gsub("([0-9]+).*", "\\1<file://1>", grep("[0-9]+[ \t]*", out,
value=TRUE)))) # [1] 86
[I've asked the IT team to understand why one of the values is 20 instead of
22].
# number of cores - what detectCores(FALSE) should return out <-
system("wmic cpu get numberofcores", intern=TRUE)
[1] "NumberOfCores \r" "22 \r" "22 \r" "20
\r" "22 \r"
[6] "\r"
sum(as.numeric(gsub("([0-9]+).*", "\\1<file://1>", grep("[0-9]+[ \t]*", out,
value=TRUE)))) # [1] 86
[Currently hyperthreading is disabled. So this output being identical to the
previous output makes sense].
system("wmic computersystem get numberofprocessors")
NumberOfProcessors
4
In addition, I'd also bring to your attention this documentation:
https://docs.microsoft.com/en-us/windows/desktop/ProcThread/processor-groups on
processor groups which explain how one should go about running a process ro run
on multiple groups (which seems to be different to NUMA). All this seems overly
complicated to allow a process to use all cores by default TBH.
Here's a project on Github 'fio' where the issue of running a process on more
than 1 processor group has come up - https://github.com/axboe/fio/issues/527
and is addressed -
https://github.com/axboe/fio/blob/c479640d6208236744f0562b1e79535eec290e2b/os/os-windows-7.h
. I am not sure though if this is entirely relevant since we would be forking
new processes in R instead of allowing a single process to use all cores.
Apologies if this is utterly irrelevant.
Thank you,
Arun.
From: Tomas Kalibera <tomas.kalib...@gmail.com><mailto:tomas.kalib...@gmail.com>
Sent: 21 August 2018 11:50
To: Srinivasan, Arunkumar
<arunkumar.sriniva...@uk.mlp.com><mailto:arunkumar.sriniva...@uk.mlp.com>;
r-devel@r-project.org<mailto:r-devel@r-project.org>
Subject: Re: [Rd] Get Logical processor count correctly whether NUMA
is enabled or disabled
Dear Arun,
thank you for the report. I agree with the analysis, detectCores() will only
report logical processors in the NUMA group in which R is running. I don't have
a system to test on, could you please check these workarounds for me on your
systems?
# number of logical processors - what detectCores() should return out
<- system("wmic cpu get numberoflogicalprocessors", intern=TRUE)
sum(as.numeric(gsub("([0-9]+).*", "\\1<file://1>", grep("[0-9]+[ \t]*", out,
value=TRUE))))
# number of cores - what detectCores(FALSE) should return out <-
system("wmic cpu get numberofcores", intern=TRUE)
sum(as.numeric(gsub("([0-9]+).*", "\\1<file://1>", grep("[0-9]+[ \t]*", out,
value=TRUE))))
# number of physical processors - as a sanity check
system("wmic computersystem get numberofprocessors")
Thanks,
Tomas
On 08/17/2018 05:11 PM, Srinivasan, Arunkumar wrote:
Dear R-devel list,
R's detectCores() function internally calls "ncpus" function to get the total
number of logical processors. However, this doesnot seem to take NUMA into
account on Windows machines.
On a machine having 48 processors (24 cores) in total and windows server 2012
installed, if NUMA is enabled and has 2 nodes (node 0 and node 1 each having 24
CPUs), then R's detectCores() only detects 24 instead of the total 48. If NUMA
is disabled, detectCores() returns 48.
Similarly, on a machine with 88 cores (176 processors) and windows server 2012,
detectCores() with NUMA disabled only returns the maximum value of 64. If NUMA
is enabled with 4 nodes (44 processors each), then detectCores() will only
return 44. This is particularly limiting since we cannot get to use all
processors by enabling/disabling NUMA in this case.
We think this is because R's ncpus.c file uses
"PSYSTEM_LOGICAL_PROCESSOR_INFORMATION"
(https://msdn.microsoft.com/en-us/library/windows/desktop/ms683194(v=vs.85).aspx)
instead of "PSYSTEM_LOGICAL_PROCESSOR_INFORMATION_EX"
(https://msdn.microsoft.com/en-us/library/windows/desktop/dd405488(v=vs.85).aspx).
Specifically, quoting from the first link:
"On systems with more than 64 logical processors, the
GetLogicalProcessorInformation function retrieves logical processor information
about processors in the
https://msdn.microsoft.com/en-us/library/windows/desktop/dd405503(v=vs.85).aspx
to which the calling thread is currently assigned. Use the
https://msdn.microsoft.com/en-us/library/windows/desktop/dd405488(v=vs.85).aspx
function to retrieve information about processors in all processor groups on
the system."
Therefore, it might be possible to get the right count of total processors even
with NUMA enabled by using "GetLogicalProcessorInformationEX". It'd be nice to
know what you think.
Thank you very much,
Arun.
--
Arun Srinivasan
Analyst, Millennium Management LLC
50 Berkeley Street | London, W1J 8HD
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