HPC submission issues.

[sunabcun]

Hi, I tried to run RnBeads in HPC and consistently having an issue. I thought that it is related to the memory issues and I changed the rnb.cr as mem="32G" to mem.size="32G" and it seems to work longer but it causes the issues again. I'm not sure what I can do more about this. Thanks!

in R

library(RnBeads) 
xml.file <- "submit.xml"
arch <- new("ClusterArchitectureSLURM")
rnb.cr <- new("RnBClusterRun",arch)
rnb.cr <- setModuleResourceRequirements(rnb.cr,c(mem.size="32G"),"all")
rnb.cr <- setModuleNumCores(rnb.cr,4L,"all")
rnb.cr <- setModuleNumCores(rnb.cr,2L,"exploratory")
run(rnb.cr, "rnbeads_analysis", xml.file) 

2021-05-26 12:17:58     1.6  STATUS         COMPLETED Automatically parsing the provided sample annotation file
2021-05-26 12:17:58     1.6    INFO         Reading BED file: data/Methylation_cov/dataset/coverage/HDF1_1_bismark.cov
2021-05-26 12:26:25     2.4    INFO         Reading BED file: data/Methylation_cov/dataset/coverage/HDF1_2_bismark.cov
2021-05-26 12:33:59     2.9    INFO         Reading BED file: data/Methylation_cov/dataset/coverage/HDF2_1_bismark.cov
2021-05-26 12:42:48     3.0    INFO         Reading BED file: data/Methylation_cov/dataset/coverage/HDF2_2_bismark.cov
2021-05-26 12:49:06     2.8    INFO         Reading BED file: data/Methylation_cov/dataset/coverage/HDF3_1_bismark.cov
2021-05-26 12:58:07     3.0    INFO         Reading BED file: data/Methylation_cov/dataset/coverage/HDF3_2_bismark.cov
2021-05-26 13:06:58     3.0    INFO         Reading BED file: data/Methylation_cov/dataset/coverage/HDFPA_1_bismark.cov
2021-05-26 13:15:57     3.0    INFO         Reading BED file: data/Methylation_cov/dataset/coverage/HDFPA_2_bismark.cov
2021-05-26 13:24:12     3.0    INFO         Reading BED file: data/Methylation_cov/dataset/coverage/KPA_1_bismark.cov
2021-05-26 13:33:03     3.0    INFO         Reading BED file: data/Methylation_cov/dataset/coverage/KPA_2_bismark.cov
2021-05-26 13:41:11     2.9    INFO         Reading BED file: data/Methylation_cov/dataset/coverage/P5_1_bismark.cov
2021-05-26 13:50:12     3.0    INFO         Reading BED file: data/Methylation_cov/dataset/coverage/P5_2_bismark.cov
2021-05-26 13:58:57     3.0    INFO         Reading BED file: data/Methylation_cov/dataset/coverage/P16_1_bismark.cov
2021-05-26 14:07:30     3.0    INFO         Reading BED file: data/Methylation_cov/dataset/coverage/P16_2_bismark.cov
2021-05-26 14:16:13     3.0    INFO         Reading BED file: data/Methylation_cov/dataset/coverage/P17_1_bismark.cov
2021-05-26 14:24:47     2.9    INFO         Reading BED file: data/Methylation_cov/dataset/coverage/P17_2_bismark.cov

 *** caught bus error ***
address 0x2b856937c000, cause 'non-existent physical address'

Traceback:
 1: `[<-.ff`(`*tmp*`, i2, value = c(0, 0, 0, 0, 25, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0$
 2: `[<-`(`*tmp*`, i2, value = c(0, 0, 0, 0, 25, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0$
 3: `[<-.ffdf`(`*tmp*`, i, , value = list(V1 = c(177L, 177L, 177L, 177L, 177L, 177L, 177L, 177L, 177L, 177L, 177L, 177L, 177L, 177L, 177L, 177L, 177L$
 4: `[<-`(`*tmp*`, i, , value = list(V1 = c(177L, 177L, 177L, 177L, 177L, 177L, 177L, 177L, 177L, 177L, 177L, 177L, 177L, 177L, 177L, 177L, 177L, 177$
 5: read.table.ffdf(FUN = "read.delim", ...)
 6: read.delim.ffdf(x = NULL, file = file, next.rows = 10000L, ...,     colClasses = columnClasses, header = FALSE)
 7: FUN(X[[i]], ...)
 8: lapply(file.names, read.single.bed, context = "cg", ..., skip = skip.lines,     ffread = useff)
 9: lapply(file.names, read.single.bed, context = "cg", ..., skip = skip.lines,     ffread = useff)
10: read.bed.files(base.dir = data.source[[1]], sample.sheet = data.source[[2]],     file.names.col = filename.column, verbose = verbose, skip.lines $
11: rnb.execute.import(data.source, data.type)
12: rnb.step.import(data.source, data.type, report)
13: rnb.run.import(data.source, data.type, report.dir)
An irrecoverable exception occurred. R is aborting now ...
/var/spool/slurmd/job1764089/slurm_script: line 4: 24168 Bus error               Rscript /gpfs/home/ys16b/R/x86_64-redhat-linux-gnu-library/4.0/RnBea$

[demuellae]

Does the analysis work when you don't use cluster submission?

[sunabcun]

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