R devel - Aug 2018 - Get Logical processor count correctly whether NUMA is enabled or disabled

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", 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", 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.kalibera at gmail.com> 
Sent: 21 August 2018 11:50
To: Srinivasan, Arunkumar <Arunkumar.Srinivasan at uk.mlp.com>; r-devel at
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", 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", 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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person. The views expressed in this email are the views of the author

and do not necessarily represent the views of Millennium Capital Partners

LLP (MCP LLP) or any of its affiliates. Outgoing and incoming electronic

communications of MCP LLP and its affiliates, including telephone

communications, may be electronically archived and subject to review

and/or disclosure to someone other than the recipient. MCP LLP is

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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",
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",
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.kalibera at gmail.com>
> Sent: 21 August 2018 11:50
> To: Srinivasan, Arunkumar <Arunkumar.Srinivasan at uk.mlp.com>;
r-devel at 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",
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",
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
>

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.kalibera at gmail.com> 
Sent: 27 August 2018 19:43
To: Srinivasan, Arunkumar <Arunkumar.Srinivasan at uk.mlp.com>; r-devel at
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",
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",
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.kalibera at gmail.com>
> Sent: 21 August 2018 11:50
> To: Srinivasan, Arunkumar <Arunkumar.Srinivasan at uk.mlp.com>; 
> r-devel at 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",
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",
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
>
######################################################################

The information contained in this communication is confidential and

intended only for the individual(s) named above. If you are not a named

addressee, please notify the sender immediately and delete this email

from your system and do not disclose the email or any part of it to any

person. The views expressed in this email are the views of the author

and do not necessarily represent the views of Millennium Capital Partners

LLP (MCP LLP) or any of its affiliates. Outgoing and incoming electronic

communications of MCP LLP and its affiliates, including telephone

communications, may be electronically archived and subject to review

and/or disclosure to someone other than the recipient. MCP LLP is

authorized and regulated by the Financial Conduct Authority. Millennium

Capital Partners LLP is a limited liability partnership registered in

England & Wales with number OC312897 and with its registered office at

50 Berkeley Street, London, W1J 8HD.

######################################################################