Hi,
you have to make sure that all nodes have all packages loaded and
access to all of the objects (and data files).
/Henrik
On Tue, Nov 15, 2011 at 12:19 PM, Qian <littleduc...@gmail.com> wrote:
> Dear all,
>
> I am working the parameter tuning for CbsModel. Every time I re-run
> segmentation it takes long time and I am working on 50 snp6.0 array. I
> checked the CPU usage, 4 CPU are parked. I would like to use all the 8
> cpus on my computer. I am not sure how to write the wrapper function
> since function "fit" will write results to harddrive, I got the
> following error message when I try to use snowfall package. My
> question is how to run the program using all the cpus?
>
> Thanks,
> Qian
>
> library(snowfall)
> sfInit(parallel=TRUE, cpus=8)
>
> wrapper <- function(a) {
> sm =CbsModel(a,ceR)
> fit(sm,chromosomes=1:22,verbose=-10)
> # return(sm)
> }
>
> result <- sfLapply(cesN, wrapper)
>
> Error in checkForRemoteErrors(val) :
> 8 nodes produced errors; first error: could not find function
> "CbsModel"
>
>
> sfStop()
>
>> sessionInfo()
> R version 2.14.0 (2011-10-31)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
> States.1252
> [3] LC_MONETARY=English_United States.1252
> LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] splines stats graphics grDevices datasets utils
> methods base
>
> other attached packages:
> [1] cmprsk_2.2-2 survival_2.36-10
> mvna_1.2-1
> [4] lattice_0.20-0 snowfall_1.84
> snow_0.3-7
> [7] RColorBrewer_1.0-5 DNAcopy_1.28.0
> gcrma_2.26.0
> [10] Biobase_2.14.0 preprocessCore_1.16.0
> aroma.affymetrix_2.3.0
> [13] affxparser_1.26.1 aroma.apd_0.2.0
> R.huge_0.3.0
> [16] aroma.core_2.3.1 aroma.light_1.22.0
> matrixStats_0.4.0
> [19] R.rsp_0.6.7 R.filesets_1.1.3
> digest_0.5.1
> [22] R.cache_0.5.2 BiocInstaller_1.2.1
> R.utils_1.9.3
> [25] R.oo_1.8.3 affy_1.32.0
> R.methodsS3_1.2.1
>
> loaded via a namespace (and not attached):
> [1] affyio_1.22.0 Biostrings_2.22.0 grid_2.14.0
> IRanges_1.12.1
> [5] tools_2.14.0 zlibbioc_1.0.0
>
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
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>
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group with website http://www.aroma-project.org/.
To post to this group, send email to aroma-affymetrix@googlegroups.com
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