cannot install pbdMPI_0.1-7.tar.gz in R-3.0.0 on Cray XE6 HERMIT
Dear all, I am trying to compile pbdMPI_0.1-7.tar.gz on Cray XE6 HERMIT. My environment is this: ipmiva at eslogin003:/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0> module list Currently Loaded Modulefiles: 1) modules/3.2.6.7 13) job/1.5.5-0.1_2.0401.35380.1.10.gem 25) rca/1.0.0-2.0401.38656.2.2.gem 2) xtpe-network-gemini 14) csa/3.0.0-1_2.0401.37452.4.50.gem 26) xe-sysroot/4.1.40 3) xtpe-interlagos 15) dvs/1.8.6_0.9.0-1.0401.1401.1.120 27) atp/1.6.2 4) xt-asyncpe/5.19 16) audit/1.0.0-1.0401.37969.2.32.gem 28) PrgEnv-cray/4.1.40 5) cce/8.1.7 17) ccm/2.2.0-1.0401.37254.2.142 29) cray-mpich2/5.6.4 6) xt-libsci/12.0.01 18) configuration/1.0-1.0401.35391.1.2.gem 30) eswrap/1.0.9 7) udreg/2.3.2-1.0401.5929.3.3.gem 19) hosts/1.0-1.0401.35364.1.115.gem 31) torque/2.5.9 8) ugni/4.0-1.0401.5928.9.5.gem 20) lbcd/2.1-1.0401.35360.1.2.gem 32) moab/6.1.5.s1992 9) pmi/4.0.1-1.0000.9421.73.3.gem 21) nodehealth/5.0-1.0401.38460.12.18.gem 33) system/ws_tools 10) dmapp/3.2.1-1.0401.5983.4.5.gem 22) pdsh/2.26-1.0401.37449.1.1.gem 34) system/hlrs-defaults 11) gni-headers/2.1-1.0401.5675.4.4.gem 23) shared-root/1.0-1.0401.37253.3.50.gem 35) hdf5-parallel/1.8.8 12) xpmem/0.1-2.0401.36790.4.3.gem 24) switch/1.0-1.0401.36779.2.72.gem 36) netcdf-hdf5parallel/4.2.0 And this is my compilation error: ipmiva at eslogin003:/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0> R CMD INSTALL --configure-args="--with-mpi=/opt/cray/mpt/5.6.4/gni/mpich2-cray/74" pbdMPI_0.1-7.tar.gz * installing to library ?/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/lib64/R/library? * installing *source* package ?pbdMPI? ... checking for gcc... gcc -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 gcc -std=gnu99 accepts -g... yes checking for gcc -std=gnu99 option to accept ISO C89... none needed checking for mpirun... F checking for mpiexec... F checking for orterun... F checking for sed... /usr/bin/sed checking for mpicc... F checking for ompi_info... F checking for mpich2version... F Trying to find mpi.h ... Found in /opt/cray/mpt/5.6.4/gni/mpich2-cray/74/include Trying to find libmpi.so or libmpich.a ... Found libmpich in /opt/cray/mpt/5.6.4/gni/mpich2-cray/74/lib checking whether MPICH2 is declared... yes checking whether MPICH2 is declared... (cached) yes checking for openpty in -lutil... yes checking for main in -lpthread... yes >>>> MPI executable is not in PATH ... >>>> Please export or setenv PATH ... ******************* Results of pbdMPI package configure ***************** >> TMP_INC = >> TMP_LIB = >> MPI_ROOT = /opt/cray/mpt/5.6.4/gni/mpich2-cray/74 >> MPITYPE = MPICH2 >> MPI_INCLUDE_PATH = /opt/cray/mpt/5.6.4/gni/mpich2-cray/74/include >> MPI_LIBPATH = /opt/cray/mpt/5.6.4/gni/mpich2-cray/74/lib >> MPI_LIBS = -lutil -lpthread >> MPI_DEFS = -DMPI2 >> MPI_INCL2 = >> PKG_CPPFLAGS = -I/opt/cray/mpt/5.6.4/gni/mpich2-cray/74/include -DMPI2 -DMPICH2 >> PKG_LIBS = -L/opt/cray/mpt/5.6.4/gni/mpich2-cray/74/lib -lmpich -lmpl -lopa -lutil -lpthread ************************************************************************* configure: creating ./config.status config.status: creating src/Makevars configure: creating ./config.status config.status: creating src/Makevars config.status: creating R/zzz.r ** libs gcc -std=gnu99 -I/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/include -DNDEBUG -I/opt/cray/mpt/5.6.4/gni/mpich2-cray/74/include -DMPI2 -DMPICH2 -I/usr/local/include -fpic -g -O2 -c comm_errors.c -o comm_errors.o gcc -std=gnu99 -I/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/include -DNDEBUG -I/opt/cray/mpt/5.6.4/gni/mpich2-cray/74/include -DMPI2 -DMPICH2 -I/usr/local/include -fpic -g -O2 -c comm_sort_double.c -o comm_sort_double.o gcc -std=gnu99 -I/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/include -DNDEBUG -I/opt/cray/mpt/5.6.4/gni/mpich2-cray/74/include -DMPI2 -DMPICH2 -I/usr/local/include -fpic -g -O2 -c comm_sort_integer.c -o comm_sort_integer.o gcc -std=gnu99 -I/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/include -DNDEBUG -I/opt/cray/mpt/5.6.4/gni/mpich2-cray/74/include -DMPI2 -DMPICH2 -I/usr/local/include -fpic -g -O2 -c pkg_dl.c -o pkg_dl.o gcc -std=gnu99 -I/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/include -DNDEBUG -I/opt/cray/mpt/5.6.4/gni/mpich2-cray/74/include -DMPI2 -DMPICH2 -I/usr/local/include -fpic -g -O2 -c pkg_tools.c -o pkg_tools.o gcc -std=gnu99 -I/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/include -DNDEBUG -I/opt/cray/mpt/5.6.4/gni/mpich2-cray/74/include -DMPI2 -DMPICH2 -I/usr/local/include -fpic -g -O2 -c spmd.c -o spmd.o gcc -std=gnu99 -I/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/include -DNDEBUG -I/opt/cray/mpt/5.6.4/gni/mpich2-cray/74/include -DMPI2 -DMPICH2 -I/usr/local/include -fpic -g -O2 -c spmd_allgather.c -o spmd_allgather.o gcc -std=gnu99 -I/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/include -DNDEBUG -I/opt/cray/mpt/5.6.4/gni/mpich2-cray/74/include -DMPI2 -DMPICH2 -I/usr/local/include -fpic -g -O2 -c spmd_allgatherv.c -o spmd_allgatherv.o gcc -std=gnu99 -I/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/include -DNDEBUG -I/opt/cray/mpt/5.6.4/gni/mpich2-cray/74/include -DMPI2 -DMPICH2 -I/usr/local/include -fpic -g -O2 -c spmd_allreduce.c -o spmd_allreduce.o gcc -std=gnu99 -I/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/include -DNDEBUG -I/opt/cray/mpt/5.6.4/gni/mpich2-cray/74/include -DMPI2 -DMPICH2 -I/usr/local/include -fpic -g -O2 -c spmd_bcast.c -o spmd_bcast.o gcc -std=gnu99 -I/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/include -DNDEBUG -I/opt/cray/mpt/5.6.4/gni/mpich2-cray/74/include -DMPI2 -DMPICH2 -I/usr/local/include -fpic -g -O2 -c spmd_communicator.c -o spmd_communicator.o gcc -std=gnu99 -I/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/include -DNDEBUG -I/opt/cray/mpt/5.6.4/gni/mpich2-cray/74/include -DMPI2 -DMPICH2 -I/usr/local/include -fpic -g -O2 -c spmd_gather.c -o spmd_gather.o gcc -std=gnu99 -I/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/include -DNDEBUG -I/opt/cray/mpt/5.6.4/gni/mpich2-cray/74/include -DMPI2 -DMPICH2 -I/usr/local/include -fpic -g -O2 -c spmd_gatherv.c -o spmd_gatherv.o gcc -std=gnu99 -I/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/include -DNDEBUG -I/opt/cray/mpt/5.6.4/gni/mpich2-cray/74/include -DMPI2 -DMPICH2 -I/usr/local/include -fpic -g -O2 -c spmd_info.c -o spmd_info.o gcc -std=gnu99 -I/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/include -DNDEBUG -I/opt/cray/mpt/5.6.4/gni/mpich2-cray/74/include -DMPI2 -DMPICH2 -I/usr/local/include -fpic -g -O2 -c spmd_recv.c -o spmd_recv.o gcc -std=gnu99 -I/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/include -DNDEBUG -I/opt/cray/mpt/5.6.4/gni/mpich2-cray/74/include -DMPI2 -DMPICH2 -I/usr/local/include -fpic -g -O2 -c spmd_reduce.c -o spmd_reduce.o gcc -std=gnu99 -I/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/include -DNDEBUG -I/opt/cray/mpt/5.6.4/gni/mpich2-cray/74/include -DMPI2 -DMPICH2 -I/usr/local/include -fpic -g -O2 -c spmd_scatter.c -o spmd_scatter.o gcc -std=gnu99 -I/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/include -DNDEBUG -I/opt/cray/mpt/5.6.4/gni/mpich2-cray/74/include -DMPI2 -DMPICH2 -I/usr/local/include -fpic -g -O2 -c spmd_scatterv.c -o spmd_scatterv.o gcc -std=gnu99 -I/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/include -DNDEBUG -I/opt/cray/mpt/5.6.4/gni/mpich2-cray/74/include -DMPI2 -DMPICH2 -I/usr/local/include -fpic -g -O2 -c spmd_send.c -o spmd_send.o gcc -std=gnu99 -I/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/include -DNDEBUG -I/opt/cray/mpt/5.6.4/gni/mpich2-cray/74/include -DMPI2 -DMPICH2 -I/usr/local/include -fpic -g -O2 -c spmd_sendrecv.c -o spmd_sendrecv.o gcc -std=gnu99 -I/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/include -DNDEBUG -I/opt/cray/mpt/5.6.4/gni/mpich2-cray/74/include -DMPI2 -DMPICH2 -I/usr/local/include -fpic -g -O2 -c spmd_sendrecv_replace.c -o spmd_sendrecv_replace.o gcc -std=gnu99 -I/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/include -DNDEBUG -I/opt/cray/mpt/5.6.4/gni/mpich2-cray/74/include -DMPI2 -DMPICH2 -I/usr/local/include -fpic -g -O2 -c spmd_tool.c -o spmd_tool.o gcc -std=gnu99 -I/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/include -DNDEBUG -I/opt/cray/mpt/5.6.4/gni/mpich2-cray/74/include -DMPI2 -DMPICH2 -I/usr/local/include -fpic -g -O2 -c spmd_utility.c -o spmd_utility.o gcc -std=gnu99 -I/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/include -DNDEBUG -I/opt/cray/mpt/5.6.4/gni/mpich2-cray/74/include -DMPI2 -DMPICH2 -I/usr/local/include -fpic -g -O2 -c spmd_wait.c -o spmd_wait.o gcc -std=gnu99 -shared -L/usr/local/lib64 -o pbdMPI.so comm_errors.o comm_sort_double.o comm_sort_integer.o pkg_dl.o pkg_tools.o spmd.o spmd_allgather.o spmd_allgatherv.o spmd_allreduce.o spmd_bcast.o spmd_communicator.o spmd_gather.o spmd_gatherv.o spmd_info.o spmd_recv.o spmd_reduce.o spmd_scatter.o spmd_scatterv.o spmd_send.o spmd_sendrecv.o spmd_sendrecv_replace.o spmd_tool.o spmd_utility.o spmd_wait.o -L/opt/cray/mpt/5.6.4/gni/mpich2-cray/74/lib -lmpich -lmpl -lopa -lutil -lpthread -L/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/lib64/R/lib -lR /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../x86_64-suse-linux/bin/ld: /opt/cray/mpt/5.6.4/gni/mpich2-cray/74/lib/libmpich.a(comm_get_attr.o): relocation R_X86_64_32 against `MPIR_ThreadInfo' can not be used when making a shared object; recompile with -fPIC /opt/cray/mpt/5.6.4/gni/mpich2-cray/74/lib/libmpich.a: could not read symbols: Bad value collect2: ld returned 1 exit status make: *** [pbdMPI.so] Error 1 ERROR: compilation failed for package ?pbdMPI? * removing ?/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/lib64/R/library/pbdMPI? Best regards, Martin
Dr. Martin Ivanov Eberhard-Karls-Universit?t T?bingen Mathematisch-Naturwissenschaftliche Fakult?t Fachbereich Geowissenschaften Water & Earth System Science (WESS) H?lderlinstra?e 12, 72074 T?bingen, Deutschland Tel. +4970712974213