search for: mpicc

...#39;ve noted I working on a linux machine, and it's running RHEL 4.0. I've build the lam package (we're very familiar with all the mpi libraries and so that is not an issue), and then I attempted to install taskPR... A). I added the lam binaries to my command search PATH B). Defined CC=mpicc C). Started R, and tried the install using install.packages(c("taskPR_0.2.7.tar.gz"), repos=NULL, configure.args= c(taskPR="--with-mpi='/usr/local/lam-7.1.4'")) The configure/install fails, and I've appended the output below. I can understand why it's failing, h...

.../lib/Linux_HAMMER64SSE2_4 -lptf77blas -lpthread -latlas" ### Lam-MPI 7.1.2 Configure: ./configure --prefix=$prefix --enable-shared --disable-static --without-romio --with-rsh="ssh -xq" ### Rmpi INSTALL R CMD INSTALL Rmpi --configure-args="--with-mpi=$prefix --prefix=$prefix CC=mpicc" -l $R_LIBS * Installing *source* package 'Rmpi' ... Try to find mpi.h ... Found in /gcm/home/a347549/local64/include Try to find libmpi or libmpich ... checking for main in -lmpi... yes Try to find liblam ... checking for main in -llam... yes checking for openpty in -lutil... yes che...

I am running into the following issue that has been previously reported on the R-devel mailing list. The short version is that I'm writing a package for MPI, and I'd like to change CC and SHLIB_LD to "mpicc". Trying to change them in Makevars.in has no effect, because the values are clobbered by /etc/R/Makeconf. Will the following changes to Makeconf.in introduce any problems? --Michael Subject: [Rd] R CMD INSTALL configure.args and CC customization From: Paul Johnson (paul... at gmail.com) D...

One way to deal with this is to install R itself with mpicc. Then all packages are installed with mpicc and get the required MPI libraries and includes by default. I have done this with R-2.13.0 on an Opteron cluster running CentOS-5 a while ago and so far it has worked out great. I crosspost to r-sig-hpc and welcome others to comment if there are pote...

...MD INSTALL wants a dash, as in "--configure-args=". The "period" versus the "hyphen" was killing me all morning! When building Rmpi, I had to specify configure options to let R know which MPI library to use. I *tried* to avoid that by forcing the compiler to be "mpicc", not "gcc". I believe that if one uses mpicc, then the compiler really is gcc, but it is initiated with the INC and LIB dirs set so that the configure can find what it needs. But gcc seems to be deeply glued to R installation of packages. I find various posts in the r-help list...

Dear R Debian Users: I wrote a quick C program (eventually to become R code) and compiled it as: mpicc -o greet greet.c So far so good. Now when I run mpirun, this happens: erin at erin-laptop:~$ mpirun -np 2 greet ----------------------------------------------------------------------------- It seems that there is no lamd running on the host erin-laptop. This indicates that the LAM/MPI runtime...

...hether 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 ... >&gt...

...th LAM/MPI (or maybe I am just confused because I also look at LLNL's slurm for use with Open MPI ?) Has anybody gotten Open MPI and Rmpi to work on simple demos? Similarly, is anybody using snow with Rmpi and Open MPI yet? Also, the Open MPI FAQ is pretty clear on their preference for using mpicc for compiling/linking to keep control of the compiler and linker options and switches. Note that e.g. on my Debian system edd at ron:~> mpicc --showme:link -pthread -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl whereas Rmpi built with just the default from R CMD:...

...39;t seem to work since it generates debug info for the C code, not the IR. I really need GDB (lli doesn't solve my problems) in order to debug multi-threaded and multi-process MPI code. More clearly, if I have a file hello.ll and I execute: $> llc hello.ll -march=x86-64 -o hello.s $> mpicc -O0 hello.s -o hello Can I debug "hello" with GDB at the IR level? If so, how? If not, would it be possible to add debug info generation at the IR level (and how much effort required)? I read something about DwarfDebug but it's not clear to me how to use it or even if it does what...

...hether we are using the GNU C compiler... yes checking whether gcc -std=gnu99 accepts -g... yes checking for gcc -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... mpich2version found sed, mpicc, and ompi_info ... gcc: error: unrecognized option '--showme:incdirs'>> TMP_INC_DIRS = gcc: error: unrecognized option '--showme:libdirs'>> TMP_LIB_DIRS = I am here...

...receive the following dump during installation of the Matrix package: * installing *source* package 'Matrix' ... ** package 'Matrix' successfully unpacked and MD5 sums checked ** libs make[3]: Entering directory `/state/partition1/tmp/RtmpCw7v7G/R.INSTALL3227fa892a3/Matrix/src' mpicc -I/home/tbarik/src/R-3.1.1/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/incl ude -fpic -I/home/tbarik/include -c CHMfactor.c -o CHMfactor.o In file included from CHMfactor.h:4, from CHMfactor.c:2: Mutils.h: In function 'inv_permutation': Mutils....

Dear R People: I am having some trouble with the snow package. It requires MPICH2 and Rmpi. Rmpi is fine. However, I downloaded the MPICH2 package, and installed. There is no mpicc, mpirun, etc. Does anyone have any suggestions, please? Thanks in advance! Sincerely, Erin Hodgess Associate Professor Department of Computer and Mathematical Sciences University of Houston - Downtown mailto: hodgess at gator.uhd.edu

...load(file.path(libpath, "libs", paste("Rmpi", .Platform$dynlib.ext, : dynamic/shared library '/home/<username>/.Rlib/Rmpi/libs/Rmpi.so' was not loaded > The undefined symbol is for the PGI debugger. It doesn't matter if the $CC variable is gcc, pgcc, or mpicc, and all three do show up in the make output during the configure process. Thanks for your help, Joshua

...rates debug info for the C code, not the IR. I really need GDB > (lli doesn't solve my problems) in order to debug multi-threaded and > multi-process MPI code. > > More clearly, if I have a file hello.ll and I execute: > > $> llc hello.ll -march=x86-64 -o hello.s > $> mpicc -O0 hello.s -o hello > > Can I debug "hello" with GDB at the IR level? If so, how? If not, would it be > possible to add debug info generation at the IR level (and how much effort > required)? I read something about DwarfDebug but it's not clear to me how to use > it or...

...rates debug info for the C code, not the IR. I > really need GDB (lli doesn't solve my problems) in order to debug > multi-threaded and multi-process MPI code. > > More clearly, if I have a file hello.ll and I execute: > > $> llc hello.ll -march=x86-64 -o hello.s > $> mpicc -O0 hello.s -o hello > > Can I debug "hello" with GDB at the IR level? If so, how? If not, would it > be possible to add debug info generation at the IR level (and how much > effort required)? I read something about DwarfDebug but it's not clear to > me how to use it or...

Dear R Gurus: Is there a problem with Rmpi on x86 with SUSE 10.1, please? I've tried everything and it still won't load. Has anyone else dealt with this please? Thanks, Edna Bell

Hi folks, In our scientific simulation tool, we set up our build system to link against LLVMSupport to print stack traces for debugging purposes, also from other compilers. This works very well on most hosts, but we fail to make it work with gcc on a Cray XC 40 cluster. They have a very restrictive toolchain setup (everything is controlled by the “module” command; you never get to see any real

When I install openmpi, openmpi-libs and openmpi-devel (using yum) for CentOS 5, I'm not getting anything set in alternatives for mpi- run and mpicc, etc. Is it supposed to? Cheers, Tony Schreiner Boston College

...ne=yes (default) and headers/libs are not available As you can see, the R configure script finds the header files, but something happens with the rl_callback_read_char. Here is more info on this from the config.log: configure:22995: checking for rl_callback_read_char in -lreadline configure:23020: mpicc -g -o conftest -O2 -fPIC -I/home/giessen/ivanov/build/packages/usr/include -I/home/giessen/ivanov/build/packages/usr/include/readline -I/home/giessen/ivanov/build/packages/usr/include -I/home/giessen/ivanov/build/packages/usr/include/readline -L/home/giessen/ivanov/build/packages/usr/lib64 -L/home/...

...t the IR. I really need GDB > > (lli doesn't solve my problems) in order to debug multi-threaded and > > multi-process MPI code. > > > > More clearly, if I have a file hello.ll and I execute: > > > > $> llc hello.ll -march=x86-64 -o hello.s > > $> mpicc -O0 hello.s -o hello > > > > Can I debug "hello" with GDB at the IR level? If so, how? If not, would it be > > possible to add debug info generation at the IR level (and how much effort > > required)? I read something about DwarfDebug but it's not clear to me h...