[R] Install Rmpi on Linux on a HPC

[Ivan Krylov]

On Thu, 15 Sep 2022 14:39:42 +0900
James Li <jamesli200116 using gmail.com> wrote:

>  *** caught segfault ***
> address 0x1, cause 'memory not mapped'
> 
> Traceback:
>  1: fun(libname, pkgname)
>  2: doTryCatch(return(expr), name, parentenv, handler)
>  3: tryCatchOne(expr, names, parentenv, handlers[[1L]])
>  4: tryCatchList(expr, classes, parentenv, handlers)
>  5: tryCatch(fun(libname, pkgname), error = identity)
>  6: runHook(".onLoad", env, package.lib, package)
>  7: loadNamespace(package, lib.loc)
>  8: doTryCatch(return(expr), name, parentenv, handler)
>  9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
> 10: tryCatchList(expr, classes, parentenv, handlers)
> 11: tryCatch({    attr(package, "LibPath") <- which.lib.loc    ns <-
> loadNamespace(package, lib.loc)    env <- attachNamespace(ns, pos =
> pos, deps, exclude, include.only)}, error = function(e) {    P <- if
> (!is.null(cc <- conditionCall(e)))         paste(" in",
> deparse(cc)[1L]) else ""    msg <- gettextf("package or namespace
> load failed for %s%s:\n %s",         sQuote(package), P,
> conditionMessage(e))    if (logical.return)
> message(paste("Error:", msg), domain = NA)    else stop(msg, call. =
> FALSE, domain = NA)})
> 12: library(Rmpi)

This is a bit useful. The crash is happening in Rmpi:::.onLoad() during
the first line of the script, library(Rmpi), and the reason is that
something takes the number 1 and tries to dereference it as a pointer.

Rmpi's .onLoad does a number of different things [*], and the crash is
happening inside some C code anyway, so we need the debugger.

> Reading symbols from
> /home/exp/R/4.0.5-gcc10.2.0-openmpi-debug/lib64/R/bin/exec/R...done.
> (gdb) quit

In order to get useful information from GDB, you need to type "run" in
the GDB prompt (without the " quotes) and reproduce the crash (for
example, by running library(Rmpi)). Once the R process crashes, you
will return back to the GDB prompt, where you'll need to run "bt full"
(again, without the quotes). After that you can quit.

-- 
Best regards,
Ivan

[*] https://github.com/cran/Rmpi/blob/master/R/zzz.R