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Simon Urbanek

2020-Nov-04 01:06 UTC

[Rd] parallel PSOCK connection latency is greater on Linux?

I'm not sure the user would know ;). This is very system-specific issue just
because the Linux network stack behaves so differently from other OSes (for
purely historical reasons). That makes it hard to abstract as a
"feature" for the R sockets that are supposed to be
platform-independent. At least TCP_NODELAY is actually part of POSIX so it is on
better footing, and disabling delayed ACK is practically only useful to work
around the other side having Nagle on, so I would expect it to be rarely used.

This is essentially RFC since we don't have a mechanism for socket options
(well, almost, there is timeout and blocking already...) and I don't think
we want to expose low-level details so perhaps one idea would be to add
something like delay=NA to socketConnection() in order to not touch (NA), enable
(TRUE) or disable (FALSE) TCP_NODELAY. I wonder if there is any other way we
could infer the intention of the user to try to choose the right approach...

Cheers,
Simon

> On Nov 3, 2020, at 02:28, Jeff <jeff at vtkellers.com> wrote:
> 
> Could TCP_NODELAY and TCP_QUICKACK be exposed to the R user so that they
might determine what is best for their potentially latency- or
throughput-sensitive application?
> 
> Best,
> Jeff
> 
> On Mon, Nov 2, 2020 at 14:05, I?aki Ucar <iucar at fedoraproject.org>
wrote:
>> On Mon, 2 Nov 2020 at 02:22, Simon Urbanek <simon.urbanek at
r-project.org> wrote:
>>> It looks like R sockets on Linux could do with TCP_NODELAY --
without (status quo):
>> How many network packets are generated with and without it? If there
>> are many small writes and thus setting TCP_NODELAY causes many small
>> packets to be sent, it might make more sense to set TCP_QUICKACK
>> instead.
>> I?aki
>>> Unit: microseconds
>>>                    expr      min       lq     mean  median       uq
max
>>>  clusterEvalQ(cl, iris) 1449.997 43991.99 43975.21 43997.1 44001.91
48027.83
>>>  neval
>>>   1000
>>> exactly the same machine + R but with TCP_NODELAY enabled in
R_SockConnect():
>>> Unit: microseconds
>>>                    expr     min     lq     mean  median      uq    
max neval
>>>  clusterEvalQ(cl, iris) 156.125 166.41 180.8806 170.247 174.298
5322.234  1000
>>> Cheers,
>>> Simon
>>> > On 2/11/2020, at 3:39 AM, Jeff <jeff at vtkellers.com>
wrote:
>>> >
>>> > I'm exploring latency overhead of parallel PSOCK workers
and noticed that serializing/unserializing data back to the main R session is
significantly slower on Linux than it is on Windows/MacOS with similar hardware.
Is there a reason for this difference and is there a way to avoid the apparent
additional Linux overhead?
>>> >
>>> > I attempted to isolate the behavior with a test that simply
returns an existing object from the worker back to the main R session.
>>> >
>>> > library(parallel)
>>> > library(microbenchmark)
>>> > gcinfo(TRUE)
>>> > cl <- makeCluster(1)
>>> > (x <- microbenchmark(clusterEvalQ(cl, iris), times = 1000,
unit = "us"))
>>> > plot(x$time, ylab = "microseconds")
>>> > head(x$time, n = 10)
>>> >
>>> > On Windows/MacOS, the test runs in 300-500 microseconds
depending on hardware. A few of the 1000 runs are an order of magnitude slower
but this can probably be attributed to garbage collection on the worker.
>>> >
>>> > On Linux, the first 5 or so executions run at comparable
speeds but all subsequent executions are two orders of magnitude slower (~40
milliseconds).
>>> >
>>> > I see this behavior across various platforms and hardware
combinations:
>>> >
>>> > Ubuntu 18.04 (Intel Xeon Platinum 8259CL)
>>> > Linux Mint 19.3 (AMD Ryzen 7 1800X)
>>> > Linux Mint 20 (AMD Ryzen 7 3700X)
>>> > Windows 10 (AMD Ryzen 7 4800H)
>>> > MacOS 10.15.7 (Intel Core i7-8850H)
>>> >
>>> > ______________________________________________
>>> > 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
>> --
>> I?aki ?car
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

Iñaki Ucar

2020-Nov-04 10:41 UTC

head link

[Rd] parallel PSOCK connection latency is greater on Linux?

Please, check a tcpdump session on localhost while running the following script:

library(parallel)
library(tictoc)
cl <- makeCluster(1)
Sys.sleep(1)

for (i in 1:10) {
  tic()
  x <- clusterEvalQ(cl, iris)
  toc()
}

The initialization phase comprises 7 packets. Then, the 1-second sleep
will help you see where the evaluation starts. Each clusterEvalQ
generates 6 packets:

1. main -> worker PSH, ACK 1026 bytes
2. worker -> main ACK 66 bytes
3. worker -> main PSH, ACK 3758 bytes
4. main -> worker ACK 66 bytes
5. worker -> main PSH, ACK 2484 bytes
6. main -> worker ACK 66 bytes

The first two are the command and its ACK, the following are the data
back and their ACKs. In the first 4-5 iterations, I see no delay at
all. Then, in the following iterations, a 40 ms delay starts to happen
between packets 3 and 4, that is: the main process delays the ACK to
the first packet of the incoming result.

So I'd say Nagle is hardly to blame for this. It would be interesting
to see how many packets are generated with TCP_NODELAY on. If there
are still 6 packets, then we are fine. If we suddenly see a gazillion
packets, then TCP_NODELAY does more harm than good. On the other hand,
TCP_QUICKACK would surely solve the issue without any drawback. As
Nagle himself put it once, "set TCP_QUICKACK. If you find a case where
that makes things worse, let me know."

I?aki

On Wed, 4 Nov 2020 at 04:34, Simon Urbanek <simon.urbanek at
r-project.org> wrote:>
> I'm not sure the user would know ;). This is very system-specific issue
just because the Linux network stack behaves so differently from other OSes (for
purely historical reasons). That makes it hard to abstract as a
"feature" for the R sockets that are supposed to be
platform-independent. At least TCP_NODELAY is actually part of POSIX so it is on
better footing, and disabling delayed ACK is practically only useful to work
around the other side having Nagle on, so I would expect it to be rarely used.
>
> This is essentially RFC since we don't have a mechanism for socket
options (well, almost, there is timeout and blocking already...) and I don't
think we want to expose low-level details so perhaps one idea would be to add
something like delay=NA to socketConnection() in order to not touch (NA), enable
(TRUE) or disable (FALSE) TCP_NODELAY. I wonder if there is any other way we
could infer the intention of the user to try to choose the right approach...
>
> Cheers,
> Simon
>
>
> > On Nov 3, 2020, at 02:28, Jeff <jeff at vtkellers.com> wrote:
> >
> > Could TCP_NODELAY and TCP_QUICKACK be exposed to the R user so that
they might determine what is best for their potentially latency- or
throughput-sensitive application?
> >
> > Best,
> > Jeff
> >
> > On Mon, Nov 2, 2020 at 14:05, I?aki Ucar <iucar at
fedoraproject.org> wrote:
> >> On Mon, 2 Nov 2020 at 02:22, Simon Urbanek <simon.urbanek at
r-project.org> wrote:
> >>> It looks like R sockets on Linux could do with TCP_NODELAY --
without (status quo):
> >> How many network packets are generated with and without it? If
there
> >> are many small writes and thus setting TCP_NODELAY causes many
small
> >> packets to be sent, it might make more sense to set TCP_QUICKACK
> >> instead.
> >> I?aki
> >>> Unit: microseconds
> >>>                    expr      min       lq     mean  median    
uq      max
> >>>  clusterEvalQ(cl, iris) 1449.997 43991.99 43975.21 43997.1
44001.91 48027.83
> >>>  neval
> >>>   1000
> >>> exactly the same machine + R but with TCP_NODELAY enabled in
R_SockConnect():
> >>> Unit: microseconds
> >>>                    expr     min     lq     mean  median     
uq      max neval
> >>>  clusterEvalQ(cl, iris) 156.125 166.41 180.8806 170.247
174.298 5322.234  1000
> >>> Cheers,
> >>> Simon
> >>> > On 2/11/2020, at 3:39 AM, Jeff <jeff at
vtkellers.com> wrote:
> >>> >
> >>> > I'm exploring latency overhead of parallel PSOCK
workers and noticed that serializing/unserializing data back to the main R
session is significantly slower on Linux than it is on Windows/MacOS with
similar hardware. Is there a reason for this difference and is there a way to
avoid the apparent additional Linux overhead?
> >>> >
> >>> > I attempted to isolate the behavior with a test that
simply returns an existing object from the worker back to the main R session.
> >>> >
> >>> > library(parallel)
> >>> > library(microbenchmark)
> >>> > gcinfo(TRUE)
> >>> > cl <- makeCluster(1)
> >>> > (x <- microbenchmark(clusterEvalQ(cl, iris), times =
1000, unit = "us"))
> >>> > plot(x$time, ylab = "microseconds")
> >>> > head(x$time, n = 10)
> >>> >
> >>> > On Windows/MacOS, the test runs in 300-500 microseconds
depending on hardware. A few of the 1000 runs are an order of magnitude slower
but this can probably be attributed to garbage collection on the worker.
> >>> >
> >>> > On Linux, the first 5 or so executions run at comparable
speeds but all subsequent executions are two orders of magnitude slower (~40
milliseconds).
> >>> >
> >>> > I see this behavior across various platforms and hardware
combinations:
> >>> >
> >>> > Ubuntu 18.04 (Intel Xeon Platinum 8259CL)
> >>> > Linux Mint 19.3 (AMD Ryzen 7 1800X)
> >>> > Linux Mint 20 (AMD Ryzen 7 3700X)
> >>> > Windows 10 (AMD Ryzen 7 4800H)
> >>> > MacOS 10.15.7 (Intel Core i7-8850H)
> >>> >
> >>> > ______________________________________________
> >>> > 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
> >> --
> >> I?aki ?car
> >
> > ______________________________________________
> > R-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> >
>

-- 
I?aki ?car

Jeff

2020-Nov-10 00:38 UTC

head link

[Rd] parallel PSOCK connection latency is greater on Linux?

I do enjoy free lunch solutions if they exist.

That said, I think the abstraction proposed by Simon is reasonable. 
Whether it should be applied to TCP_NODELAY or TCP_QUICKACK is 
unfortunately beyond my Linux/networking knowledge.

Jeff Keller

On Wed, Nov 4, 2020 at 11:41, I?aki Ucar <iucar at fedoraproject.org> 
wrote:> Please, check a tcpdump session on localhost while running the 
> following script:
> 
> library(parallel)
> library(tictoc)
> cl <- makeCluster(1)
> Sys.sleep(1)
> 
> for (i in 1:10) {
>   tic()
>   x <- clusterEvalQ(cl, iris)
>   toc()
> }
> 
> The initialization phase comprises 7 packets. Then, the 1-second sleep
> will help you see where the evaluation starts. Each clusterEvalQ
> generates 6 packets:
> 
> 1. main -> worker PSH, ACK 1026 bytes
> 2. worker -> main ACK 66 bytes
> 3. worker -> main PSH, ACK 3758 bytes
> 4. main -> worker ACK 66 bytes
> 5. worker -> main PSH, ACK 2484 bytes
> 6. main -> worker ACK 66 bytes
> 
> The first two are the command and its ACK, the following are the data
> back and their ACKs. In the first 4-5 iterations, I see no delay at
> all. Then, in the following iterations, a 40 ms delay starts to happen
> between packets 3 and 4, that is: the main process delays the ACK to
> the first packet of the incoming result.
> 
> So I'd say Nagle is hardly to blame for this. It would be interesting
> to see how many packets are generated with TCP_NODELAY on. If there
> are still 6 packets, then we are fine. If we suddenly see a gazillion
> packets, then TCP_NODELAY does more harm than good. On the other hand,
> TCP_QUICKACK would surely solve the issue without any drawback. As
> Nagle himself put it once, "set TCP_QUICKACK. If you find a case where
> that makes things worse, let me know."
> 
> I?aki
> 
> On Wed, 4 Nov 2020 at 04:34, Simon Urbanek 
> <simon.urbanek at r-project.org <mailto:simon.urbanek at
r-project.org>>
> wrote:
>> 
>>  I'm not sure the user would know ;). This is very system-specific 
>> issue just because the Linux network stack behaves so differently 
>> from other OSes (for purely historical reasons). That makes it hard 
>> to abstract as a "feature" for the R sockets that are
supposed to be
>> platform-independent. At least TCP_NODELAY is actually part of POSIX 
>> so it is on better footing, and disabling delayed ACK is practically 
>> only useful to work around the other side having Nagle on, so I 
>> would expect it to be rarely used.
>> 
>>  This is essentially RFC since we don't have a mechanism for socket
>> options (well, almost, there is timeout and blocking already...) and 
>> I don't think we want to expose low-level details so perhaps one 
>> idea would be to add something like delay=NA to socketConnection() 
>> in order to not touch (NA), enable (TRUE) or disable (FALSE) 
>> TCP_NODELAY. I wonder if there is any other way we could infer the 
>> intention of the user to try to choose the right approach...
>> 
>>  Cheers,
>>  Simon
>> 
>> 
>>  > On Nov 3, 2020, at 02:28, Jeff <jeff at vtkellers.com 
>> <mailto:jeff at vtkellers.com>> wrote:
>>  >
>>  > Could TCP_NODELAY and TCP_QUICKACK be exposed to the R user so 
>> that they might determine what is best for their potentially 
>> latency- or throughput-sensitive application?
>>  >
>>  > Best,
>>  > Jeff
>>  >
>>  > On Mon, Nov 2, 2020 at 14:05, I?aki Ucar 
>> <iucar at fedoraproject.org <mailto:iucar at
fedoraproject.org>> wrote:
>>  >> On Mon, 2 Nov 2020 at 02:22, Simon Urbanek 
>> <simon.urbanek at r-project.org <mailto:simon.urbanek at
r-project.org>>
>> wrote:
>>  >>> It looks like R sockets on Linux could do with
TCP_NODELAY --
>> without (status quo):
>>  >> How many network packets are generated with and without it?
If
>> there
>>  >> are many small writes and thus setting TCP_NODELAY causes
many
>> small
>>  >> packets to be sent, it might make more sense to set
TCP_QUICKACK
>>  >> instead.
>>  >> I?aki
>>  >>> Unit: microseconds
>>  >>>                    expr      min       lq     mean 
median
>>  uq      max
>>  >>>  clusterEvalQ(cl, iris) 1449.997 43991.99 43975.21
43997.1
>> 44001.91 48027.83
>>  >>>  neval
>>  >>>   1000
>>  >>> exactly the same machine + R but with TCP_NODELAY enabled
in
>> R_SockConnect():
>>  >>> Unit: microseconds
>>  >>>                    expr     min     lq     mean  median  
uq
>>      max neval
>>  >>>  clusterEvalQ(cl, iris) 156.125 166.41 180.8806 170.247
174.298
>> 5322.234  1000
>>  >>> Cheers,
>>  >>> Simon
>>  >>> > On 2/11/2020, at 3:39 AM, Jeff <jeff at
vtkellers.com
>> <mailto:jeff at vtkellers.com>> wrote:
>>  >>> >
>>  >>> > I'm exploring latency overhead of parallel PSOCK
workers and
>> noticed that serializing/unserializing data back to the main R 
>> session is significantly slower on Linux than it is on Windows/MacOS 
>> with similar hardware. Is there a reason for this difference and is 
>> there a way to avoid the apparent additional Linux overhead?
>>  >>> >
>>  >>> > I attempted to isolate the behavior with a test that
simply
>> returns an existing object from the worker back to the main R 
>> session.
>>  >>> >
>>  >>> > library(parallel)
>>  >>> > library(microbenchmark)
>>  >>> > gcinfo(TRUE)
>>  >>> > cl <- makeCluster(1)
>>  >>> > (x <- microbenchmark(clusterEvalQ(cl, iris),
times = 1000,
>> unit = "us"))
>>  >>> > plot(x$time, ylab = "microseconds")
>>  >>> > head(x$time, n = 10)
>>  >>> >
>>  >>> > On Windows/MacOS, the test runs in 300-500
microseconds
>> depending on hardware. A few of the 1000 runs are an order of 
>> magnitude slower but this can probably be attributed to garbage 
>> collection on the worker.
>>  >>> >
>>  >>> > On Linux, the first 5 or so executions run at
comparable
>> speeds but all subsequent executions are two orders of magnitude 
>> slower (~40 milliseconds).
>>  >>> >
>>  >>> > I see this behavior across various platforms and
hardware
>> combinations:
>>  >>> >
>>  >>> > Ubuntu 18.04 (Intel Xeon Platinum 8259CL)
>>  >>> > Linux Mint 19.3 (AMD Ryzen 7 1800X)
>>  >>> > Linux Mint 20 (AMD Ryzen 7 3700X)
>>  >>> > Windows 10 (AMD Ryzen 7 4800H)
>>  >>> > MacOS 10.15.7 (Intel Core i7-8850H)
>>  >>> >
>>  >>> > ______________________________________________
>>  >>> > R-devel at r-project.org <mailto:R-devel at
r-project.org> mailing
>> list
>>  >>> >
<https://stat.ethz.ch/mailman/listinfo/r-devel>
>>  >>> >
>>  >>> ______________________________________________
>>  >>> R-devel at r-project.org <mailto:R-devel at
r-project.org> mailing
>> list
>>  >>> <https://stat.ethz.ch/mailman/listinfo/r-devel>
>>  >> --
>>  >> I?aki ?car
>>  >
>>  > ______________________________________________
>>  > R-devel at r-project.org <mailto:R-devel at r-project.org>
mailing list
>>  > <https://stat.ethz.ch/mailman/listinfo/r-devel>
>>  >
>> 
> 
> 
> --
> I?aki ?car

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