Question: BiocParallel 1.4.3: Error following example 4.2.1 - "Error in 0.4 * nx/tasks : non-numeric argument to binary operator"
1
gravatar for lee.tibbert
3.4 years ago by
lee.tibbert20
lee.tibbert20 wrote:

Prompted by Feligernon Bit's recent post on Rbloggers, I tried to check out BiocParallel.

Whilst trying the example in section 4.2.1 ("Ad-hoc clusters of multiple machines,  sockets" of the "Introduction to BiocParallel" (May 6, 2015, December 15, 2015), I am encountering an error: "Error in 0.4 * nx/tasks : non-numeric argument to binary operator".

The only change that I make to the example is to use one "localhost" instead of the three "rhinoN" entries. I get the same failure with one "localhost" & second host "foobar".  I can "ssh localhost" no problem.

The code, error, & systemInfo are below.  I believe that I am using the most up-to-date software, etc.

Seems to me that the issue is probably that "tasks" is zero, causing a divide by zero resulting in a non-numeric Infinity. 

Can some kind soul point out what I am doing wrong?

A big Thank You to the BioConductor & BiocParallel developers.

Thank you,

Lee


> library("BiocParallel", lib.loc="~/R/i686-pc-linux-gnu-library/3.2")
> hosts <- c("localhost")
> param <- SnowParam(workers = hosts, type = "SOCK")
> FUN <- function(i) system("hostname", intern=TRUE)
> bplapply(1:4, FUN, BPPARAM = param)
Error in 0.4 * nx/tasks : non-numeric argument to binary operator

> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: i686-pc-linux-gnu (32-bit)
Running under: Ubuntu 15.10

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocParallel_1.4.3

loaded via a namespace (and not attached):
[1] parallel_3.2.3       futile.logger_1.4.1  tools_3.2.3          lambda.r_1.1.7       futile.options_1.0.0
 


 

biocparallel • 729 views
ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by lee.tibbert20

As a workaround specify workers as a numeric value; SnowParam(workers=1); a fix is in development. Thanks for the report.

ADD REPLYlink written 3.4 years ago by Martin Morgan ♦♦ 23k

Thank you for the timely workaround suggestion.  If I understand correctly SnowParam(workers=1) will put all workers on my local node?  I have been using the workers=numeric (I used 3) & making believe that I was running on remotes to help me learn BiocParallel.  When the fullness of time brings the next version of BiocParallel, I will try again with remote nodes.

Lee

 

ADD REPLYlink written 3.4 years ago by lee.tibbert20

Yep, all the workers on a local node; obviously not particularly satisfactory, but I expect a better solution withing the week.

ADD REPLYlink written 3.4 years ago by Martin Morgan ♦♦ 23k

Thank you. I was testing my understanding.  I have plenty enough right now to help me understand BiocParallel & understand entirely that good fixes take time. I am more than happy to find out that I did not miss something obvious in attempting to duplicate the example.  If the examples where not so good & extensive, I never would have gone down that path ;-)

Lee

ADD REPLYlink written 3.4 years ago by lee.tibbert20
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