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 ... >>> >>> >> >> ______________________________________________ >> R-help@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide >> http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. > > ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
