[R] cannot load pbdMPI package after compilation
Antoine Migeon
antoine.migeon at u-bourgogne.fr
Mon Jun 10 14:15:37 CEST 2013
Thank you, I will try contact the developper.
Antoine Migeon
Université de Bourgogne
Centre de Calcul et Messagerie
Direction des Systèmes d'Information
tel : 03 80 39 52 70
Site du CCUB : http://www.u-bourgogne.fr/dsi-ccub
Le 10/06/2013 08:19, Prof Brian Ripley a écrit :
> On 10/06/2013 03:17, Pascal Oettli wrote:
>> Hello,
>>
>> I am not sure whether it helps you, but I was able to install it.
>>
>> OpenSUSE 12.3
>> R version 3.0.1 Patched (2013-06-09 r62918)
>> pbdMPI version 0.1-6
>> gcc version 4.7.2
>> OpenMPI version 1.6.3
>>
>> I didn't try with the most recent version of ompi (1.6.4).
>
> But the system used to accept that version of pdbMPI for CRAN used it,
> with gcc.
>
> The issue here is likely to be using the Intel compiler with OpenMPI.
> This is a programming matter really off-topic for R-help (see the
> posting guide). The first port of call for help is the package
> maintainer, then if that does not help, the R-devel list. But very
> few R users have access to an Intel compiler, let alone one as recent
> as that, and you will be expected to use a debugger for yourself (see
> 'Writing R Extensions').
>
>>
>> Regards,
>> Pascal
>>
>>
>> On 07/06/13 21:42, Antoine Migeon wrote:
>>> Hello,
>>>
>>> I try to install pbdMPI.
>>> Compilation successful, but load fails with segfault.
>>>
>>> Is anyone can help me?
>>>
>>> R version 3.0.0
>>> pbdMPI version 0.1-6
>>> Intel compiler version 13.1.1
>>> OpenMPI version 1.6.4-1
>>> CPU Intel x86_64
>>>
>>> # R CMD INSTALL pbdMPI_0.1-6.tar.gz
>>> ..
>>> ....
>>> checking for gcc... icc -std=gnu99
>>> checking whether the C compiler works... yes
>>> checking for C compiler default output file name... a.out
>>> checking for suffix of executables...
>>> checking whether we are cross compiling... no
>>> checking for suffix of object files... o
>>> checking whether we are using the GNU C compiler... yes
>>> checking whether icc -std=gnu99 accepts -g... yes
>>> checking for icc -std=gnu99 option to accept ISO C89... none needed
>>> checking for mpirun... mpirun
>>> checking for mpiexec... mpiexec
>>> checking for orterun... orterun
>>> checking for sed... /bin/sed
>>> checking for mpicc... mpicc
>>> checking for ompi_info... ompi_info
>>> checking for mpich2version... F
>>> found sed, mpicc, and ompi_info ...
>>>>> TMP_INC_DIRS = /opt/openmpi/1.6.4-1/intel-13.1.1/include
>>> checking /opt/openmpi/1.6.4-1/intel-13.1.1/include ...
>>> found /opt/openmpi/1.6.4-1/intel-13.1.1/include/mpi.h ...
>>>>> TMP_LIB_DIRS = /opt/openmpi/1.6.4-1/intel-13.1.1/lib64
>>> checking /opt/openmpi/1.6.4-1/intel-13.1.1/lib64 ...
>>> found /opt/openmpi/1.6.4-1/intel-13.1.1/lib64/libmpi.so ...
>>> found mpi.h and libmpi.so ...
>>>>> TMP_INC = /opt/openmpi/1.6.4-1/intel-13.1.1/include
>>>>> TMP_LIB = /opt/openmpi/1.6.4-1/intel-13.1.1/lib64
>>> checking for openpty in -lutil... yes
>>> checking for main in -lpthread... yes
>>>
>>> ******************* Results of pbdMPI package configure
>>> *****************
>>>
>>>>> TMP_INC = /opt/openmpi/1.6.4-1/intel-13.1.1/include
>>>>> TMP_LIB = /opt/openmpi/1.6.4-1/intel-13.1.1/lib64
>>>>> MPI_ROOT =
>>>>> MPITYPE = OPENMPI
>>>>> MPI_INCLUDE_PATH = /opt/openmpi/1.6.4-1/intel-13.1.1/include
>>>>> MPI_LIBPATH = /opt/openmpi/1.6.4-1/intel-13.1.1/lib64
>>>>> MPI_LIBS = -lutil -lpthread
>>>>> MPI_DEFS = -DMPI2
>>>>> MPI_INCL2 =
>>>>> PKG_CPPFLAGS = -I/opt/openmpi/1.6.4-1/intel-13.1.1/include -DMPI2
>>> -DOPENMPI
>>>>> PKG_LIBS = -L/opt/openmpi/1.6.4-1/intel-13.1.1/lib64 -lmpi -lutil
>>> -lpthread
>>> *************************************************************************
>>>
>>> ..
>>> icc -std=gnu99 -I/usr/local/R/3.0.0/intel13/lib64/R/include -DNDEBUG
>>> -I/opt/openmpi/1.6.4-1/intel-13.1.1/include -DMPI2 -DOPENMPI -O3
>>> -fp-model precise -pc 64 -axAVX -fpic -O3 -fp-model precise -pc 64
>>> -axAVX -c comm_errors.c -o comm_errors.o
>>> icc -std=gnu99 -I/usr/local/R/3.0.0/intel13/lib64/R/include -DNDEBUG
>>> -I/opt/openmpi/1.6.4-1/intel-13.1.1/include -DMPI2 -DOPENMPI -O3
>>> -fp-model precise -pc 64 -axAVX -fpic -O3 -fp-model precise -pc 64
>>> -axAVX -c comm_sort_double.c -o comm_sort_double.o
>>> .
>>> ..
>>> ....
>>> ** testing if installed package can be loaded
>>> sh: line 1: 2905 Segmentation fault
>>> '/usr/local/R/3.0.0/intel13/lib64/R/bin/R' --no-save --slave 2>&1 <
>>> /tmp/RtmpGkncGK/file1e541c57190
>>> ERROR: loading failed
>>>
>>> *** caught segfault ***
>>> address (nil), cause 'unknown'
>>>
>>> Traceback:
>>> 1: .Call("spmd_initialize", PACKAGE = "pbdMPI")
>>> 2: fun(libname, pkgname)
>>> 3: doTryCatch(return(expr), name, parentenv, handler)
>>> 4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
>>> 5: tryCatchList(expr, classes, parentenv, handlers)
>>> 6: tryCatch(fun(libname, pkgname), error = identity)
>>> 7: runHook(".onLoad", env, package.lib, package)
>>> 8: loadNamespace(package, c(which.lib.loc, lib.loc))
>>> 9: doTryCatch(return(expr), name, parentenv, handler)
>>> 10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
>>> 11: tryCatchList(expr, classes, parentenv, handlers)
>>> 12: tryCatch(expr, error = function(e) { call <- conditionCall(e)
>>> if (!is.null(call)) { if (identical(call[[1L]],
>>> quote(doTryCatch))) call <- sys.call(-4L) dcall <-
>>> deparse(call)[1L] prefix <- paste("Error in", dcall, ": ")
>>> LONG <- 75L msg <- conditionMessage(e) sm <-
>>> strsplit(msg,
>>> "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L],
>>> type = "w") if (is.na(w)) w <- 14L + nchar(dcall,
>>> type = "b") + nchar(sm[1L], type = "b") if (w >
>>> LONG) prefix <- paste0(prefix, "\n ") } else prefix
>>> <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n")
>>> .Internal(seterrmessage(msg[1L])) if (!silent &&
>>> identical(getOption("show.error.messages"), TRUE)) {
>>> cat(msg, file = stderr()) .Internal(printDeferredWarnings())
>>> } invisible(structure(msg, class = "try-error", condition = e))})
>>> 13: try({ ns <- loadNamespace(package, c(which.lib.loc, lib.loc))
>>> env <- attachNamespace(ns, pos = pos, deps)})
>>> 14: library(pkg_name, lib.loc = lib, character.only = TRUE,
>>> logical.return = TRUE)
>>> 15: withCallingHandlers(expr, packageStartupMessage = function(c)
>>> invokeRestart("muffleMessage"))
>>> 16: suppressPackageStartupMessages(library(pkg_name, lib.loc = lib,
>>> character.only = TRUE, logical.return = TRUE))
>>> 17: doTryCatch(return(expr), name, parentenv, handler)
>>> 18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
>>> 19: tryCatchList(expr, classes, parentenv, handlers)
>>> 20: tryCatch(expr, error = function(e) { call <- conditionCall(e)
>>> if (!is.null(call)) { if (identical(call[[1L]],
>>> quote(doTryCatch))) call <- sys.call(-4L) dcall <-
>>> deparse(call)[1L] prefix <- paste("Error in", dcall, ": ")
>>> LONG <- 75L msg <- conditionMessage(e) sm <-
>>> strsplit(msg,
>>> "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L],
>>> type = "w") if (is.na(w)) w <- 14L + nchar(dcall,
>>> type = "b") + nchar(sm[1L], type = "b") if (w >
>>> LONG) prefix <- paste0(prefix, "\n ") } else prefix
>>> <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n")
>>> .Internal(seterrmessage(msg[1L])) if (!silent &&
>>> identical(getOption("show.error.messages"), TRUE)) {
>>> cat(msg, file = stderr()) .Internal(printDeferredWarnings())
>>> } invisible(structure(msg, class = "try-error", condition = e))})
>>> 21: try(suppressPackageStartupMessages(library(pkg_name, lib.loc =
>>> lib, character.only = TRUE, logical.return = TRUE)))
>>> 22: tools:::.test_load_package("pbdMPI",
>>> "/usr/local/R/3.0.0/intel13/lib64/R/library")
>>> aborting ...
>>>
>>>
>>
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>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
>
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