makeCluster() hangs infinitely

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makeCluster() hangs infinitely

Zhihao Huang
Hi all,

The function makeCluster() of parallel does not work on my laptop. It hangs
infinitely.

*1. Problem Summary:*

> # Loading parallel packages

> library(parallel)

> cl <- makeCluster(2) # It hangs at this line of code.
It hangs at the second line of the code.

*2. Potential Reason*
I also tried to see the details of what it does internally by using the
following code.

> library(future)

> cl <- future::makeClusterPSOCK(1L, verbose = TRUE) # It hangs at this
line of code.
And it returns the following descriptions and hangs.

*Workers: [n = 1] ‘localhost’*

*Base port: 11214*

*Creating node 1 of 1 ...*

*- setting up node*

*Starting worker #1 on ‘localhost’:
'/Library/Frameworks/R.framework/Resources/bin/Rscript'
--default-packages=datasets,utils,grDevices,graphics,stats,methods -e
'parallel:::.slaveRSOCK()' MASTER=localhost PORT=11214 OUT=/dev/null
TIMEOUT=2592000 XDR=TRUE*

*Waiting for worker #1 on ‘localhost’ to connect back*
So the problem is that the "worker #1 on 'local host'" never connects back,
and that's why it hangs forever. I have no idea what causes this.

*3. my sessionInfo():*

R version 3.5.1 (2018-07-02)

Platform: x86_64-apple-darwin15.6.0 (64-bit)

Running under: macOS High Sierra 10.13.6


Matrix products: default

BLAS:
/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib

LAPACK:
/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib


locale:

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8


attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods   base


loaded via a namespace (and not attached):

[1] compiler_3.5.1

I spent hours searching for the solutions but failed. It looks like some
other people met similar problem here
<http://r.789695.n4.nabble.com/makeCluster-hangs-td4748238.html>. Also, I
posted this question online here
<https://stackoverflow.com/questions/52264460/r-parallel-makecluster-hangs-infinitely-on-mac/52284709#52284709>
a
week ago.

Any suggestion would be appreciated. Thanks a lot!

Thanks,
Zhihao
--
Zhihao (Daniel) Huang
Graduate Student
Department of Statistics,
University of Michigan, Ann Arbor
Email: [hidden email]

--
黄 之昊
Zhihao Huang

Graduate Student
Department of Statistics,
University of Michigan, Ann Arbor
Email: [hidden email]

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
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and provide commented, minimal, self-contained, reproducible code.
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Re: makeCluster() hangs infinitely

Henrik Bengtsson-5
Hi,

did you see my answer on StackOverflow? Specifically, if you set
argument 'outfile = NULL' to either of those two functions, you'll get
a little bit more information that *might* provide some clues.

/Henrik


On Sun, Sep 16, 2018 at 5:38 PM Zhihao Huang <[hidden email]> wrote:

>
> Hi all,
>
> The function makeCluster() of parallel does not work on my laptop. It hangs
> infinitely.
>
> *1. Problem Summary:*
>
> > # Loading parallel packages
>
> > library(parallel)
>
> > cl <- makeCluster(2) # It hangs at this line of code.
> It hangs at the second line of the code.
>
> *2. Potential Reason*
> I also tried to see the details of what it does internally by using the
> following code.
>
> > library(future)
>
> > cl <- future::makeClusterPSOCK(1L, verbose = TRUE) # It hangs at this
> line of code.
> And it returns the following descriptions and hangs.
>
> *Workers: [n = 1] ‘localhost’*
>
> *Base port: 11214*
>
> *Creating node 1 of 1 ...*
>
> *- setting up node*
>
> *Starting worker #1 on ‘localhost’:
> '/Library/Frameworks/R.framework/Resources/bin/Rscript'
> --default-packages=datasets,utils,grDevices,graphics,stats,methods -e
> 'parallel:::.slaveRSOCK()' MASTER=localhost PORT=11214 OUT=/dev/null
> TIMEOUT=2592000 XDR=TRUE*
>
> *Waiting for worker #1 on ‘localhost’ to connect back*
> So the problem is that the "worker #1 on 'local host'" never connects back,
> and that's why it hangs forever. I have no idea what causes this.
>
> *3. my sessionInfo():*
>
> R version 3.5.1 (2018-07-02)
>
> Platform: x86_64-apple-darwin15.6.0 (64-bit)
>
> Running under: macOS High Sierra 10.13.6
>
>
> Matrix products: default
>
> BLAS:
> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
>
> LAPACK:
> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
>
>
> locale:
>
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
>
> attached base packages:
>
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
>
> loaded via a namespace (and not attached):
>
> [1] compiler_3.5.1
>
> I spent hours searching for the solutions but failed. It looks like some
> other people met similar problem here
> <http://r.789695.n4.nabble.com/makeCluster-hangs-td4748238.html>. Also, I
> posted this question online here
> <https://stackoverflow.com/questions/52264460/r-parallel-makecluster-hangs-infinitely-on-mac/52284709#52284709>
> a
> week ago.
>
> Any suggestion would be appreciated. Thanks a lot!
>
> Thanks,
> Zhihao
> --
> Zhihao (Daniel) Huang
> Graduate Student
> Department of Statistics,
> University of Michigan, Ann Arbor
> Email: [hidden email]
>
> --
> 黄 之昊
> Zhihao Huang
>
> Graduate Student
> Department of Statistics,
> University of Michigan, Ann Arbor
> Email: [hidden email]
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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Re: makeCluster() hangs infinitely

Zhihao Huang
Hi Henrik,

Thanks for the suggestions! I tried your approach, and obtained the
following output, which is pretty similar to the previous ones.

> cl <- future::makeClusterPSOCK(1, outfile = NULL, verbose = TRUE)

*Workers: [n = 1] ‘localhost’*

*Base port: 11214*

*Creating node 1 of 1 ...*

*- setting up node*

*Starting worker #1 on ‘localhost’:
'/Library/Frameworks/R.framework/Resources/bin/Rscript'
--default-packages=datasets,utils,grDevices,graphics,stats,methods -e
'parallel:::.slaveRSOCK()' MASTER=localhost PORT=11214 OUT= TIMEOUT=2592000
XDR=TRUE*

*Waiting for worker #1 on ‘localhost’ to connect back*

starting worker pid=13731 on localhost:11214 at 15:48:41.991
I guess this is a connection problem. I am not sure what these numbers
mean. Do you have any further idea on this? I very much appreciate it!

Thanks,
Zhihao
--
Zhihao (Daniel) Huang
Graduate Student
Department of Statistics,
University of Michigan, Ann Arbor
Email: [hidden email]



On Mon, Sep 17, 2018 at 12:38 AM Henrik Bengtsson <
[hidden email]> wrote:

> Hi,
>
> did you see my answer on StackOverflow? Specifically, if you set
> argument 'outfile = NULL' to either of those two functions, you'll get
> a little bit more information that *might* provide some clues.
>
> /Henrik
>
>
> On Sun, Sep 16, 2018 at 5:38 PM Zhihao Huang <[hidden email]> wrote:
> >
> > Hi all,
> >
> > The function makeCluster() of parallel does not work on my laptop. It
> hangs
> > infinitely.
> >
> > *1. Problem Summary:*
> >
> > > # Loading parallel packages
> >
> > > library(parallel)
> >
> > > cl <- makeCluster(2) # It hangs at this line of code.
> > It hangs at the second line of the code.
> >
> > *2. Potential Reason*
> > I also tried to see the details of what it does internally by using the
> > following code.
> >
> > > library(future)
> >
> > > cl <- future::makeClusterPSOCK(1L, verbose = TRUE) # It hangs at this
> > line of code.
> > And it returns the following descriptions and hangs.
> >
> > *Workers: [n = 1] ‘localhost’*
> >
> > *Base port: 11214*
> >
> > *Creating node 1 of 1 ...*
> >
> > *- setting up node*
> >
> > *Starting worker #1 on ‘localhost’:
> > '/Library/Frameworks/R.framework/Resources/bin/Rscript'
> > --default-packages=datasets,utils,grDevices,graphics,stats,methods -e
> > 'parallel:::.slaveRSOCK()' MASTER=localhost PORT=11214 OUT=/dev/null
> > TIMEOUT=2592000 XDR=TRUE*
> >
> > *Waiting for worker #1 on ‘localhost’ to connect back*
> > So the problem is that the "worker #1 on 'local host'" never connects
> back,
> > and that's why it hangs forever. I have no idea what causes this.
> >
> > *3. my sessionInfo():*
> >
> > R version 3.5.1 (2018-07-02)
> >
> > Platform: x86_64-apple-darwin15.6.0 (64-bit)
> >
> > Running under: macOS High Sierra 10.13.6
> >
> >
> > Matrix products: default
> >
> > BLAS:
> >
> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
> >
> > LAPACK:
> >
> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
> >
> >
> > locale:
> >
> > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> >
> >
> > attached base packages:
> >
> > [1] stats     graphics  grDevices utils     datasets  methods   base
> >
> >
> > loaded via a namespace (and not attached):
> >
> > [1] compiler_3.5.1
> >
> > I spent hours searching for the solutions but failed. It looks like some
> > other people met similar problem here
> > <http://r.789695.n4.nabble.com/makeCluster-hangs-td4748238.html>. Also,
> I
> > posted this question online here
> > <
> https://stackoverflow.com/questions/52264460/r-parallel-makecluster-hangs-infinitely-on-mac/52284709#52284709
> >
> > a
> > week ago.
> >
> > Any suggestion would be appreciated. Thanks a lot!
> >
> > Thanks,
> > Zhihao
> > --
> > Zhihao (Daniel) Huang
> > Graduate Student
> > Department of Statistics,
> > University of Michigan, Ann Arbor
> > Email: [hidden email]
> >
> > --
> > 黄 之昊
> > Zhihao Huang
> >
> > Graduate Student
> > Department of Statistics,
> > University of Michigan, Ann Arbor
> > Email: [hidden email]
> >
> >         [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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Re: makeCluster() hangs infinitely

Henrik Bengtsson-5
On Mon, Sep 17, 2018 at 12:56 PM Zhihao Huang <[hidden email]> wrote:

>
> Hi Henrik,
>
> Thanks for the suggestions! I tried your approach, and obtained the following output, which is pretty similar to the previous ones.
>
> > cl <- future::makeClusterPSOCK(1, outfile = NULL, verbose = TRUE)
> Workers: [n = 1] ‘localhost’
> Base port: 11214
> Creating node 1 of 1 ...
> - setting up node
> Starting worker #1 on ‘localhost’: '/Library/Frameworks/R.framework/Resources/bin/Rscript' --default-packages=datasets,utils,grDevices,graphics,stats,methods -e 'parallel:::.slaveRSOCK()' MASTER=localhost PORT=11214 OUT= TIMEOUT=2592000 XDR=TRUE
> Waiting for worker #1 on ‘localhost’ to connect back
> starting worker pid=13731 on localhost:11214 at 15:48:41.991
>
> I guess this is a connection problem. I am not sure what these numbers mean. Do you have any further idea on this? I very much appreciate it!

Yes, it looks similar with the important difference of displaying:

"starting worker pid=13731 on localhost:11214 at 15:48:41.991"

That tells us that the background worker (separate R session running
parallel:::.slaveRSOCK()) was successfully launched, which is good.

BTW, you should see something similar with:

    cl <- parallel::makeCluster(1, outfile = NULL)

which helps others help you (in case they say "oh, it might be a
problem with the future package - as the maintainer").

Yes, it looks like a "connection problem" - this could be a firewall
issue or similar.  I'm not on macOS, so I cannot help you there, but
maybe others can pitch in.

/Henrik

>
> Thanks,
> Zhihao
> --
> Zhihao (Daniel) Huang
> Graduate Student
> Department of Statistics,
> University of Michigan, Ann Arbor
> Email: [hidden email]
>
>
>
> On Mon, Sep 17, 2018 at 12:38 AM Henrik Bengtsson <[hidden email]> wrote:
>>
>> Hi,
>>
>> did you see my answer on StackOverflow? Specifically, if you set
>> argument 'outfile = NULL' to either of those two functions, you'll get
>> a little bit more information that *might* provide some clues.
>>
>> /Henrik
>>
>>
>> On Sun, Sep 16, 2018 at 5:38 PM Zhihao Huang <[hidden email]> wrote:
>> >
>> > Hi all,
>> >
>> > The function makeCluster() of parallel does not work on my laptop. It hangs
>> > infinitely.
>> >
>> > *1. Problem Summary:*
>> >
>> > > # Loading parallel packages
>> >
>> > > library(parallel)
>> >
>> > > cl <- makeCluster(2) # It hangs at this line of code.
>> > It hangs at the second line of the code.
>> >
>> > *2. Potential Reason*
>> > I also tried to see the details of what it does internally by using the
>> > following code.
>> >
>> > > library(future)
>> >
>> > > cl <- future::makeClusterPSOCK(1L, verbose = TRUE) # It hangs at this
>> > line of code.
>> > And it returns the following descriptions and hangs.
>> >
>> > *Workers: [n = 1] ‘localhost’*
>> >
>> > *Base port: 11214*
>> >
>> > *Creating node 1 of 1 ...*
>> >
>> > *- setting up node*
>> >
>> > *Starting worker #1 on ‘localhost’:
>> > '/Library/Frameworks/R.framework/Resources/bin/Rscript'
>> > --default-packages=datasets,utils,grDevices,graphics,stats,methods -e
>> > 'parallel:::.slaveRSOCK()' MASTER=localhost PORT=11214 OUT=/dev/null
>> > TIMEOUT=2592000 XDR=TRUE*
>> >
>> > *Waiting for worker #1 on ‘localhost’ to connect back*
>> > So the problem is that the "worker #1 on 'local host'" never connects back,
>> > and that's why it hangs forever. I have no idea what causes this.
>> >
>> > *3. my sessionInfo():*
>> >
>> > R version 3.5.1 (2018-07-02)
>> >
>> > Platform: x86_64-apple-darwin15.6.0 (64-bit)
>> >
>> > Running under: macOS High Sierra 10.13.6
>> >
>> >
>> > Matrix products: default
>> >
>> > BLAS:
>> > /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
>> >
>> > LAPACK:
>> > /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
>> >
>> >
>> > locale:
>> >
>> > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>> >
>> >
>> > attached base packages:
>> >
>> > [1] stats     graphics  grDevices utils     datasets  methods   base
>> >
>> >
>> > loaded via a namespace (and not attached):
>> >
>> > [1] compiler_3.5.1
>> >
>> > I spent hours searching for the solutions but failed. It looks like some
>> > other people met similar problem here
>> > <http://r.789695.n4.nabble.com/makeCluster-hangs-td4748238.html>. Also, I
>> > posted this question online here
>> > <https://stackoverflow.com/questions/52264460/r-parallel-makecluster-hangs-infinitely-on-mac/52284709#52284709>
>> > a
>> > week ago.
>> >
>> > Any suggestion would be appreciated. Thanks a lot!
>> >
>> > Thanks,
>> > Zhihao
>> > --
>> > Zhihao (Daniel) Huang
>> > Graduate Student
>> > Department of Statistics,
>> > University of Michigan, Ann Arbor
>> > Email: [hidden email]
>> >
>> > --
>> > 黄 之昊
>> > Zhihao Huang
>> >
>> > Graduate Student
>> > Department of Statistics,
>> > University of Michigan, Ann Arbor
>> > Email: [hidden email]
>> >
>> >         [[alternative HTML version deleted]]
>> >
>> > ______________________________________________
>> > [hidden email] mailing list -- To UNSUBSCRIBE and more, see
>> > https://stat.ethz.ch/mailman/listinfo/r-help
>> > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> > and provide commented, minimal, self-contained, reproducible code.

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.