readChangeoDb failed in sbatch mode on Farnam

Issue #51 resolved
Julian Zhou created an issue
 *** caught illegal operation ***
address 0x2ac521618728, cause 'illegal operand'

 1: .Call("readr_guess_header_", PACKAGE = "readr", sourceSpec, tokenizerSpec,     locale_)
 2: guess_header_(datasource, tokenizer, locale)
 3: guess_header(ds_header, tokenizer, locale)
 4: col_spec_standardise(data, skip = skip, comment = comment, guess_max = guess_max,     col_names = col_names, col_types = col_types, tokenizer = tokenizer,     locale = locale)
 5: read_delimited(file, tokenizer, col_names = col_names, col_types = col_types,     locale = locale, skip = skip, comment = comment, n_max = n_max,     guess_max = guess_max, progress = progress)
 6: readr::read_tsv(file, na = c("", "NA", "None"))
 7: withCallingHandlers(expr, message = function(c) invokeRestart("muffleMessage"))
 8: suppressMessages(readr::read_tsv(file, na = c("", "NA", "None")))
 9: readChangeoDb(paste0("d", d, ""))
An irrecoverable exception occurred. R is aborting now ...
/var/spool/slurmd/job1509736/slurm_script: line 14: 39668 Illegal instruction

Solution: use base R

read.table("", sep="\t", header=T, stringsAsFactors=F)

Comments (6)

  1. Jason Vander Heiden

    So... We can't switch to base R for performance reasons (see #39). Hrm. I wonder if this is GCC related?

  2. Julian Zhou reporter

    Welp, remember that one time we tried numerous things including changing GCC versions on Farnam and nothing worked? That was for mutate_at/each from dplyr, but I suspect the same thing won't for readr either..

  3. Jason Vander Heiden

    Yeah, I'm sure you're right. It stands to reason we'll have this problem with dplyr in general using sbatch.

  4. Julian Zhou reporter

    Ergh last time I was able to work around to the problem by running interactive instead of sbatch, but now it fails in interactive mode too :/


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