R:scheduled cores 1, 5 did not deliver results

Question

[wangjincheng]

hi, I'm using R package which using multi-cores, but it always show the error below:

In mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed,  :
  scheduled cores 1, 5 did not deliver results, all values of the jobs will be affected

Do you have any suggestions to avoid this error?

[MatthewP]

You should use lapply to test your code works fine before you use mclapply. If your code has some problems mclapply may not report origin error messages, so you can not debug, but lapply will.

[wangjincheng]

My code was:

library(GeneImp)

nchr = NCHR
wsize = WSIZE
nthread = NTHREAD
vcf = paste("test.", nchr, ".PLs.vcf.gz", sep="")
ref.vcf = paste("/ALL.chr", nchr, ".genotypes.vcf.gz", sep="")

imputevcf(vcfname=vcf, ref.vcfname=ref.vcf, klthresh=wsize, flanksize=0.5,
          filtermethod=c("pairrand"), numfilterhaps=200,
          maxjobs=nthread, write.dir=NULL, temp.dir=NULL,
          verbose=0, diagnostics=FALSE)

And the error was:

[E::hts_open_format] Failed to open file XXX:No such file or directory
tbx_index_build failed:XXX
Warning message:
In mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed,  :
  scheduled cores 1, 4, 5 did not deliver results, all values of the jobs will be affected

I am confused about lapply, cause multiple-core was used inside the package GeneImp function.... , should I define how to use multi-core additionally?

Thanks for your reply!

[ATpoint]

Please add a reproducible example. It just means an error happened in a subset of the data. Cannot help without details. Debug as suggested with lapply.

[wangjincheng]

I submit several bash scripts into different nodes, output shows error which I mentioned before. But when I run the script one by one, it seems less error occurred.