Dear Hao,
after getting some help from Cray directly, Rmpi compiles and works perfectly.
I had to comment out line 3786 in configure, so that there won't be any given parameter.
#PKG_LIBS="-L${MPI_LIBPATH} -lmpich_cray_default64 -lmpl -lopa ${MPI_LIBS}"
Additionally, I had to switch to the gnu-environement and build the C-Code using cc (Cray's own wrapper, cf [1]) instead of gcc. My whole command looks like this:
MAKEFLAGS="CC=cc" R2/bin/R CMD INSTALL Rmpi_0.6-4_cray.tar.gz --configure-args="--with-mpi=$MPICH_DIR --with-Rmpi-type=CRAY" --no-test-load
If you still run into error, you have to build R again using cc, CC and ftn instead of gcc, cpp and gfortran. Nevertheless, my setup worked like this.
Kind regards
Arne
[1] http://docs.cray.com/books/004-2179-001/html-004-2179-001/lymwlrwh.html
Von: Hao Yu <hyu at stats.uwo.ca>
Gesendet: Donnerstag, 17. April 2014 18:44 An: Arne Hendrik Schulz Cc: r-sig-hpc at r-project.org Betreff: Re: [R-sig-hpc] Rmpi: -lopa parameter on compiling needed? Works without Hi Arne, Last year, I was given an access of a Cray cluster to make Rmpi work. After many tries and errors, -lmpich_cray_default64 -lmpl -lopa were used eventually. Whether -lopa is necessary or not for other Cray cluster, I have no answer. But it is good to know that some Cray clusters, -lopa is not necessary. Hao Arne Hendrik Schulz wrote: > Hi all, > I am using the current development version of Rmpi (0.6-4) on a Cray > Cluster. The problem is that it does not compile with the -lopa parameter > as > opa.c/libopa.c is not installed on the cluster (see attachted output > below). > Compiling Rmpi without the -lopa parameter works and using the cluster > with > MPI works, too. Is it really necessary to include libopa? I cannot see any > drawbacks so far. > > Kind regards, > Arne > > P.S.: If anyone would like to test without -lopa, I uploaded a branch of > Rmpi-0.6-4: http://www.ahschulz.de/pub/R/packages/Rmpi_0.6-4_branch.tar.gz > --with-Rmpi-type=CRAY uses the -lopa parameter, > --with-Rmpi-type=CRAY_NOLOPA > dies not. > > Installing Rmpi with -lopa: > R/bin/R CMD INSTALL temp/packages/Rmpi_0.6-4.tar.gz > --configure-args="--with-Rmpi-include=/opt/cray/mpt/6.1.1/gni/mpich2-cray64/ > 81/include > --with-Rmpi-libpath=/opt/cray/mpt/6.1.1/gni/mpich2-cray64/81/lib > --with-Rmpi-type=CRAY" --no-test-load > * installing to library '/gfs1/work/hbmahs32/R/lib64/R/library' > * installing *source* package 'Rmpi' ... > checking for openpty in -lutil... no > checking for main in -lpthread... no > configure: creating ./config.status > config.status: creating src/Makevars > ** libs > (...) > gcc -std=gnu99 -shared -L/usr/local/lib64 -o Rmpi.so RegQuery.o Rmpi.o > conversion.o internal.o -L/opt/cray/mpt/6.1.1/gni/mpich2-cray64/81/lib > -lmpich_cray_default64 -lmpl -lopa > /usr/bin/ld: cannot find -lopa > collect2: error: ld returned 1 exit status > make: *** [Rmpi.so] Error 1 > ERROR: compilation failed for package 'Rmpi' > > > Installing Rmpi without -lopa > R/bin/R CMD INSTALL temp/packages/Rmpi_0.6-4_branch.tar.gz > --configure-args="--with-Rmpi-include=/opt/cray/mpt/6.1.1/gni/mpich2-cray64/ > 81/include > --with-Rmpi-libpath=/opt/cray/mpt/6.1.1/gni/mpich2-cray64/81/lib > --with-Rmpi-type=CRAY_NOLOPA" --no-test-load > * installing to library '/gfs1/work/hbmahs32/R/lib64/R/library' > * installing *source* package 'Rmpi' ... > checking for openpty in -lutil... no > checking for main in -lpthread... no > configure: creating ./config.status > config.status: creating src/Makevars > ** libs > (...) > gcc -std=gnu99 -shared -L/usr/local/lib64 -o Rmpi.so RegQuery.o Rmpi.o > conversion.o internal.o -L/opt/cray/mpt/6.1.1/gni/mpich2-cray64/81/lib > -lmpich_cray_default64 -lmpl > installing to /gfs1/work/hbmahs32/R/lib64/R/library/Rmpi/libs > ** R > ** demo > ** inst > ** preparing package for lazy loading > ** help > *** installing help indices > ** building package indices > * DONE (Rmpi) > > -- > Arne Hendrik Schulz > > ifib: Institute for Information Managment Bremen > Am Fallturm 1 (entrance F) > 28359 Bremen > Germany > > Tel.: +49 (0)421 218 56585 > Fax: +49 (0)421 218 56599 > E-Mail: ahschulz at ifib.de > > Web: www.ifib.de > > > _______________________________________________ > R-sig-hpc mailing list > R-sig-hpc at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-hpc > -- Department of Statistics & Actuarial Sciences Office Phone#:(519)-661-3622 Fax Phone#:(519)-661-3813 The University of Western Ontario London, Ontario N6A 5B7 http://www.stats.uwo.ca/yu