I am experiencing a 'memory not mapped' error when estimating haplotypes. It is interesting, because it happens only when estimating long haplotypes A~B~C~DRB1~DQB1~DPB1~DQA1. I.e I haven't experienced this error when specifying 6-loci long haplotypes. For environment context, I am using a conda environment with R version 4.3.0, and BIGDAWG 3.0.3 as the only package installed. I am running this environment in a server and giving enough resources I believe. I have increased the requested cores up to 4, thinking it would be a memory issue. I believe enough memory is allocated for the computational task.
Do you have any idea what could be causing the error? I haven't found this in the documentation or any previous issues, and haven't been able to debug myself. Thanks in advance.
Dear developers,
I am experiencing a 'memory not mapped' error when estimating haplotypes. It is interesting, because it happens only when estimating long haplotypes A~B~C~DRB1~DQB1~DPB1~DQA1. I.e I haven't experienced this error when specifying 6-loci long haplotypes. For environment context, I am using a conda environment with R version 4.3.0, and BIGDAWG 3.0.3 as the only package installed. I am running this environment in a server and giving enough resources I believe. I have increased the requested cores up to 4, thinking it would be a memory issue. I believe enough memory is allocated for the computational task.
Hereby the complete error:
caught segfault address 0x30, cause 'memory not mapped'
Traceback: 1: haplo.em.fitter(n.loci, n.subject, weight, geno.vec, n.alleles, max.haps, max.iter = control$max.iter, loci.insert.order, min.posterior = control$min.posterior, tol = control$tol, insert.batch.size = control$insert.batch.size, random.start = 1, iseed1 = iseed1, iseed2 = iseed2, iseed3 = iseed3, verbose = control$verbose) 2: haplo.stats::haplo.em(geno = genos.sub, locus.label = loci.sub) 3: FUN(X[[i]], ...) 4: lapply(X = X, FUN = FUN, ...) 5: parallel::mclapply(HAPsets, H.MC, grp = grp, Strict.Bin = Strict.Bin, Verbose = Verbose, mc.cores = Cores) 6: H.MC.wrapper(SID, Tabsub, loci, loci.ColNames, genos, grp, All.Pairwise, Strict.Bin, Output, Verbose, Cores) 7: BIGDAWG(Data = "path", Results.Dir = path") An irrecoverable exception occurred. R is aborting now ...
Do you have any idea what could be causing the error? I haven't found this in the documentation or any previous issues, and haven't been able to debug myself. Thanks in advance.
Best regards, Daniel Alvarez, Amsterdam UMC