[Bioc-devel] BiocParallel on macosx: socketConnection failures with MulticoreParam

[Vincent Carey]

it looks like manager.hostname="127.0.0.1" does the trick.

> options(bphost="127.0.0.1")

> library(BiocParallel)

> register(MulticoreParam(2))

also works.  Many thanks.

On Wed, Nov 22, 2017 at 1:25 PM, Martin Morgan <
martin.morgan at roswellpark.org> wrote:

> Does it help to use the argument manager.hostname="localhost" (or indeed
> the name of your computer) following
>
> https://support.bioconductor.org/p/88307/#88874
>
> ? and can you clarify about how you explored using different ports? See
> also ?SnowParam section 'Global Options'
>
> Martin
>
> On 11/22/2017 12:56 PM, Vincent Carey wrote:
>
>> from example(bplapply), after register(MulticoreParam(2, timeout=5))
>>
>> bplppl> bplapply(1:10, fun)
>>
>> *Error in socketConnection(host, port, TRUE, TRUE, "a+b", timeout =
>> timeout) : *
>>
>> *  cannot open the connection*
>>
>> *In addition: Warning message:*
>>
>> *In socketConnection(host, port, TRUE, TRUE, "a+b", timeout = timeout) :*
>>
>> *  problem in listening on this socket*
>>
>> I have tried turning off firewall, setting an open port, etc., to no
>> avail.
>>
>>
>> options(mc.cores=2); system.time(mclapply(1:10, function(x)Sys.sleep(1)))
>>>
>>
>>     user  system elapsed
>>
>>    0.264   0.114   5.014
>>
>> sessionInfo()
>>>
>>
>> R version 3.4.3 beta (2017-11-20 r73757)
>>
>> Platform: x86_64-apple-darwin15.6.0 (64-bit)
>>
>> Running under: macOS Sierra 10.12.6
>>
>>
>> Matrix products: default
>>
>> BLAS:
>> /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/
>> libRblas.0.dylib
>>
>> LAPACK:
>> /Library/Frameworks/R.framework/Versions/3.4/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] parallel  stats     graphics  grDevices utils     datasets  methods
>>
>> [8] base
>>
>>
>> other attached packages:
>>
>> [1] boot_1.3-20         BiocParallel_1.12.0 rmarkdown_1.8
>>
>>
>> loaded via a namespace (and not attached):
>>
>>   [1] compiler_3.4.3  backports_1.1.1 magrittr_1.5    rprojroot_1.2
>>
>>   [5] tools_3.4.3     htmltools_0.3.6 Rcpp_0.12.13    stringi_1.1.6
>>
>>   [9] knitr_1.17      stringr_1.2.0   digest_0.6.12   evaluate_0.10.1
>>
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>>
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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
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