[R-sig-hpc] cannot install Rmpi_0.6-3.tar.gz on Cray XE6 HERMIT

[Martin Ivanov]

Dear all,

I am trying to install Rmpi_0.6-3.tar.gz on Cray XE6 HERMIT. This is my 
environment:

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 the compilation error:

ipmiva at eslogin003:/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0> R CMD INSTALL 
--configure-args="--with-Rmpi-type=MPICH 
--with-mpi=/opt/cray/mpt/5.6.4/gni/mpich2-cray/74 
--with-Rmpi-include=/opt/cray/mpt/5.6.4/gni/mpich2-cray/74/include 
--with-Rmpi-libpath=/opt/cray/mpt/5.6.4/gni/mpich2-cray/74/lib" 
Rmpi_0.6-3.tar.gz
* installing to library 
â/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/lib64/R/libraryâ
* installing *source* package âRmpiâ ...
** package âRmpiâ successfully unpacked and MD5 sums checked
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 
-I/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/include -DNDEBUG 
-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" 
-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" 
-I/opt/cray/mpt/5.6.4/gni/mpich2-cray/74/include   -DMPICH 
-I/usr/local/include    -fpic  -g -O2  -c RegQuery.c -o RegQuery.o
gcc -std=gnu99 
-I/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/include -DNDEBUG 
-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" 
-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" 
-I/opt/cray/mpt/5.6.4/gni/mpich2-cray/74/include   -DMPICH 
-I/usr/local/include    -fpic  -g -O2  -c Rmpi.c -o Rmpi.o
gcc -std=gnu99 
-I/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/include -DNDEBUG 
-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" 
-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" 
-I/opt/cray/mpt/5.6.4/gni/mpich2-cray/74/include   -DMPICH 
-I/usr/local/include    -fpic  -g -O2  -c conversion.c -o conversion.o
gcc -std=gnu99 
-I/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/include -DNDEBUG 
-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" 
-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" 
-I/opt/cray/mpt/5.6.4/gni/mpich2-cray/74/include   -DMPICH 
-I/usr/local/include    -fpic  -g -O2  -c internal.c -o internal.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o Rmpi.so RegQuery.o Rmpi.o 
conversion.o internal.o -L/opt/cray/mpt/5.6.4/gni/mpich2-cray/74/lib 
-lmpich -lmpl -lopa 
-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(allreduce.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: *** [Rmpi.so] Error 1
ERROR: compilation failed for package âRmpiâ
* removing 
â/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/lib64/R/library/Rmpiâ


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