[R-sig-hpc] cannot install pbdMPI_0.1-7.tar.gz in R-3.0.0 on Cray XE6 HERMIT
Martin Ivanov
martin.ivanov at ifg.uni-tuebingen.de
Fri May 10 10:24:50 CEST 2013
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
â/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/lib64/R/libraryâ
* installing *source* package âpbdMPIâ ...
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 âpbdMPIâ
* removing
â/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/lib64/R/library/pbdMPIâ
Best regards,
Martin
--
Dr. Martin Ivanov
Eberhard-Karls-Universität Tübingen
Mathematisch-Naturwissenschaftliche Fakultät
Fachbereich Geowissenschaften
Water & Earth System Science (WESS)
Hölderlinstraße 12, 72074 Tübingen, Deutschland
Tel. +4970712974213
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