Hello,
I solved my problem with new version :
- R version 3.0.2
- pbdMPI version 0.2-1
- Intel compiler version 13.1.3
- OpenMPI version 1.6.5
Options for compiling R :
export CC="icc"
export CXX="icpc"
export F77="ifort"
export FC="ifort"
export AR="xiar"
export LD="xild
export IFLAGS="-O3 -fp-model precise -pc 64 -axAVX -fPIC -openmp"
export CFLAGS=$IFLAGS
export CXXFLAGS=$IFLAGS
export CPPFLAGS=$IFLAGS
export FFLAGS=$IFLAGS
export FCFLAGS=$IFLAGS
export MKL="-lmkl_gf_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread"
./configure --with-system-zlib --with-system-bzlib --with-system-pcre \
--with-blas="$MKL"\
--with-lapack \
--with-tcl-config=/usr/lib64/tclConfig.sh \
--with-tk-config=/usr/lib64/tkConfig.sh \
--enable-R-shlib \
--enable-prebuilt-html \
--with-recommended-packages \
--prefix=${MY_INSTALL_DIR} 2>&1 | tee configure.txt
Options for installing Rmpi :
export
LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/usr/local/openmpi/1.6.5/intel/13.1.3/lib/
install.packages("Rmpi",dependencies = TRUE,
configure.args = c(
"--with-Rmpi-include=/usr/local/openmpi/1.6.5/intel/13.1.3/include/",
"--with-Rmpi-libpath=/usr/local/openmpi/1.6.5/intel/13.1.3/lib/",
"--with-Rmpi-type=OPENMPI"
))
No special options for pbdMPI :
install.packages("pbdMPI",dependencies = TRUE)
install.packages("pbdBase",dependencies = TRUE)
Regards
Antoine
Le 10/06/2013 14:15, Antoine Migeon a écrit :
> 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.
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