[R-sig-hpc] Cannot install Rmpi/pbdMPI_0.1-7.tar.gz in R-3.0.0 on Cray XE6 HERMIT (R-sig-hpc Digest, Vol 56, Issue 7) R-sig-hpc Digest, Vol 56, Issue 11
Martin Ivanov
martin.ivanov at ifg.uni-tuebingen.de
Fri May 17 12:35:39 CEST 2013
Hello, Pragnesh, thank You very much for Your responsivenss.
I followed Your advice and used pbdMPI with aprun, everything was ok.
Now I have a problem with
pbdNCDF4 with the --enable-parallel flag. I suppose it comes from the
fact that netcdf-4.1.1 is no longer supported, and I am forced to use 4.2.
Anyway, I am posting here the output:
This is how I submitted the job for compiling pbdNCDF4:
#!/bin/bash
#PBS -l nodes=1:ppn=1
#PBS -l walltime=00:05:00
#PBS -l pmem=100kb
. /$HOME/.bashrc
module swap PrgEnv-cray PrgEnv-gnu
aprun -n 1 /univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/bin/R CMD
INSTALL
--configure-args="--with-nc-config=/opt/cray/netcdf/4.2.0/bin/nc-config
--enable-parallel"
/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/pbdNCDF4_0.1-1.tar.gz
and this is the output:
ipmiva at eslogin002:/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/test> cat
testNodes.pbs.o608337
user specified nc-config is
/opt/cray/netcdf-hdf5parallel/4.2.0/gnu/47/bin/nc-config
checking for nc-config... yes
Netcdf library version: netCDF 4.2
Netcdf library has version 4 interface present: yes
Netcdf library was compiled with C compiler: cc
configure: creating ./config.status
config.status: creating src/Makevars
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating R/zzz.R
****************** Results of ncdf4 package configure *******************
SPMD_CPPFLAGS = -I/opt/cray/mpt/5.6.4/gni/mpich2-gnu/47/include -DMPI2
-DMPICH2
SPMD_LDFLAGS = -L/opt/cray/mpt/5.6.4/gni/mpich2-gnu/47/lib -lmpich
-lmpl -lopa -lutil -lpthread
NETCDF_HEADER = /opt/cray/netcdf/4.2.0/gnu/46/include/netcdf_par.h
NETCDF_INCLUDE = 0
NETCDF_PAR = TRUE
NETCDF_PAR_OBJS = pncdf4.o
netCDF v4 CPP flags = -I/opt/cray/netcdf/4.2.0/gnu/46/include
-DgFortran -I/opt/cray/netcdf/4.2.0/gnu/46/include
netCDF v4 LD flags = -L/opt/cray/netcdf/4.2.0/gnu/46/lib -lnetcdf
netCDF v4 runtime path =
*************************************************************************
gcc -std=gnu99
-I/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/include -DNDEBUG
-I/opt/cray/netcdf/4.2.0/gnu/46/include -DgFortran
-I/opt/cray/netcdf/4.2.0/gnu/46/include -DNETCDF_INCLUDE=0
-I/opt/cray/mpt/5.6.4/gni/mpich2-gnu/47/include -DMPI2 -DMPICH2
-I/usr/local/include -fpic -g -O2 -c ncdf2.c -o ncdf2.o
gcc -std=gnu99
-I/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/include -DNDEBUG
-I/opt/cray/netcdf/4.2.0/gnu/46/include -DgFortran
-I/opt/cray/netcdf/4.2.0/gnu/46/include -DNETCDF_INCLUDE=0
-I/opt/cray/mpt/5.6.4/gni/mpich2-gnu/47/include -DMPI2 -DMPICH2
-I/usr/local/include -fpic -g -O2 -c ncdf3.c -o ncdf3.o
gcc -std=gnu99
-I/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/include -DNDEBUG
-I/opt/cray/netcdf/4.2.0/gnu/46/include -DgFortran
-I/opt/cray/netcdf/4.2.0/gnu/46/include -DNETCDF_INCLUDE=0
-I/opt/cray/mpt/5.6.4/gni/mpich2-gnu/47/include -DMPI2 -DMPICH2
-I/usr/local/include -fpic -g -O2 -c ncdf.c -o ncdf.o
gcc -std=gnu99
-I/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/include -DNDEBUG
-I/opt/cray/netcdf/4.2.0/gnu/46/include -DgFortran
-I/opt/cray/netcdf/4.2.0/gnu/46/include -DNETCDF_INCLUDE=0
-I/opt/cray/mpt/5.6.4/gni/mpich2-gnu/47/include -DMPI2 -DMPICH2
-I/usr/local/include -fpic -g -O2 -c src_ncdf4.c -o src_ncdf4.o
gcc -std=gnu99
-I/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/include -DNDEBUG
-I/opt/cray/netcdf/4.2.0/gnu/46/include -DgFortran
-I/opt/cray/netcdf/4.2.0/gnu/46/include -DNETCDF_INCLUDE=0
-I/opt/cray/mpt/5.6.4/gni/mpich2-gnu/47/include -DMPI2 -DMPICH2
-I/usr/local/include -fpic -g -O2 -c pncdf4.c -o pncdf4.o
Application 2281804 exit codes: 1
Application 2281804 resources: utime ~3s, stime ~1s
ipmiva at eslogin002:/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/test> cat
testNodes.pbs.e608228
* installing to library
¿/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/lib64/R/library¿
* installing *source* package ¿pbdNCDF4¿ ...
** libs
pncdf4.c: In function 'R_nc4_open_par':
pncdf4.c:25:2: error: unknown type name 'MPI_Comm'
pncdf4.c:26:2: error: unknown type name 'MPI_Info'
pncdf4.c:40:2: warning: implicit declaration of function 'MPI_Comm_f2c'
[-Wimplicit-function-declaration]
pncdf4.c:43:2: warning: implicit declaration of function 'MPI_Info_f2c'
[-Wimplicit-function-declaration]
pncdf4.c:46:2: warning: implicit declaration of function 'nc_open_par'
[-Wimplicit-function-declaration]
pncdf4.c: In function 'R_nc4_create_par':
pncdf4.c:57:2: error: unknown type name 'MPI_Comm'
pncdf4.c:58:2: error: unknown type name 'MPI_Info'
pncdf4.c:96:2: warning: implicit declaration of function 'nc_create_par'
[-Wimplicit-function-declaration]
make: *** [pncdf4.o] Error 1
ERROR: compilation failed for package ¿pbdNCDF4¿
* removing
¿/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/lib64/R/library/pbdNCDF4¿
* restoring previous
¿/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/lib64/R/library/pbdNCDF4¿
I also tried installing pbdNCDF4 without the option --enable-parallel.
The compilation finished succesfully, but
see what happens when I try to test pbdMPI with the demos:
My PBS script:
#PBS -l nodes=1:ppn=1
#PBS -l walltime=00:05:00
#PBS -l pmem=500kb
. /$HOME/.bashrc
module swap PrgEnv-cray PrgEnv-gnu
cd $PBS_O_WORKDIR
#echo "My machine will have the following nodes:"
#echo "-----------------------------------------"
#cat ${PBS_NODEFILE}
#echo "-----------------------------------------"
aprun -n 1 /univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/bin/Rscript
testNodes.R
The file testNodes.R contains the following:
library(pbdMPI)
source("/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/pbdNCDF4/demo/ncwrite_ser.r")
source("/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/pbdNCDF4/demo/ncread_ser.r")
ipmiva at eslogin002:/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/test> cat
testNodes.pbs.e608281
Loading required package: methods
Loading required package: rlecuyer
High Performance Computing Resource is available via
``http://www.nics.tennessee.edu/getting-an-allocation''.
*** caught segfault ***
address (nil), cause 'memory not mapped'
Traceback:
1: .Call("spmd_comm_rank", as.integer(comm), PACKAGE = "pbdMPI")
2: comm.rank()
3: eval(expr, envir, enclos)
4: eval(ei, envir)
5: withVisible(eval(ei, envir))
6:
source("/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/pbdNCDF4/demo/ncread_ser.r")
aborting ...
Best regards,
Martin
On 05/16/2013 07:10 PM, Pragnesh Patel wrote:
> Hi Martin,
>
> Once you submit job, you need to run R using "aprun" command.
>
> e.g aprun -n numberofprocessors Rscript example.R ("aprun -n 2 Rscript
> example.R")
>
>
> Thanks
> Pragnesh
> NICS
>
>
>
> On 5/16/13, Martin Ivanov <martin.ivanov at ifg.uni-tuebingen.de> wrote:
>> Dear Pragnesh,
>>
>> I submitted job in the interactive mode and the same error still
>> appears. This is the exact output:
>>
>>
>> ipmiva at eslogin001:/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/batchJobs> qsub
>> -I -l mppwidth=1,mppnppn=1,mppmem=20M,walltime=00:05:00
>> qsub: waiting for job 607644.sdb to start
>> qsub: job 607644.sdb ready
>>
>> Directory: /zhome/academic/HLRS/ipm/ipmiva
>> Thu May 16 14:45:48 CEST 2013
>> ipmiva at nid03524:~> R
>>
>> R version 3.0.0 (2013-04-03) -- "Masked Marvel"
>> Copyright (C) 2013 The R Foundation for Statistical Computing
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>
>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>> You are welcome to redistribute it under certain conditions.
>> Type 'license()' or 'licence()' for distribution details.
>>
>> Natural language support but running in an English locale
>>
>> R is a collaborative project with many contributors.
>> Type 'contributors()' for more information and
>> 'citation()' on how to cite R or R packages in publications.
>>
>> Type 'demo()' for some demos, 'help()' for on-line help, or
>> 'help.start()' for an HTML browser interface to help.
>> Type 'q()' to quit R.
>>
>> > library(pbdMPI)
>> Loading required package: rlecuyer
>> [Thu May 16 14:46:09 2013] [c1-0c1s2n0] Fatal error in MPI_Init: Other
>> MPI error, error stack:
>> MPIR_Init_thread(428):
>> MPID_Init(184).......: channel initialization failed
>> MPID_Init(538).......: PMI2 init failed: 1
>> ipmiva at nid03524:~>
>>
>>
>> Best regards,
>> Martin
>>
>>
>> On 05/16/2013 02:32 PM, Pragnesh Patel wrote:
>>> Hi Martin,
>>>
>>> Below error make sense, since you are running R on login node. You
>>> need to submit job(using qsub command) from login node and then run R
>>> on compute node. Let me know, if you don't know how to submit job.
>>>
>>> ==============
>>>> > library(pbdMPI)
>>>> Loading required package: rlecuyer
>>>> [Thu May 16 08:58:03 2013] [unknown] Fatal error in MPI_Init: Other MPI
>>>> error, error stack:
>>>> MPIR_Init_thread(428):
>>>> MPID_Init(184).......: channel initialization failed
>>>> MPID_Init(538).......: PMI2 init failed: 1
>>>>
>>> ==============
>>>
>>> Thanks
>>> Pragnesh
>>> NICS
>>>
>>>
>>>
>>> On 5/16/13, Martin Ivanov <martin.ivanov at ifg.uni-tuebingen.de> wrote:
>>>> Hello, Pragnesh,
>>>>
>>>> I did what You suggested, pbdMPI compiles ok, but at loading into R
>>>> there is an errro message. Here is detailed output:
>>>>
>>>> ipmiva at eslogin001:/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/build/source> R
>>>> CMD INSTALL
>>>> --configure-args="--with-mpi=/opt/cray/mpt/5.6.4/gni/mpich2-gnu/47"
>>>> --no-test-load ../../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-gnu/47/include
>>>> Trying to find libmpi.so or libmpich.a ...
>>>> Found libmpich in /opt/cray/mpt/5.6.4/gni/mpich2-gnu/47/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-gnu/47
>>>> >> MPITYPE = MPICH2
>>>> >> MPI_INCLUDE_PATH = /opt/cray/mpt/5.6.4/gni/mpich2-gnu/47/include
>>>> >> MPI_LIBPATH = /opt/cray/mpt/5.6.4/gni/mpich2-gnu/47/lib
>>>> >> MPI_LIBS = -lutil -lpthread
>>>> >> MPI_DEFS = -DMPI2
>>>> >> MPI_INCL2 =
>>>> >> PKG_CPPFLAGS = -I/opt/cray/mpt/5.6.4/gni/mpich2-gnu/47/include
>>>> -DMPI2 -DMPICH2
>>>> >> PKG_LIBS = -L/opt/cray/mpt/5.6.4/gni/mpich2-gnu/47/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-gnu/47/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-gnu/47/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-gnu/47/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-gnu/47/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-gnu/47/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-gnu/47/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-gnu/47/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-gnu/47/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-gnu/47/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-gnu/47/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-gnu/47/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-gnu/47/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-gnu/47/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-gnu/47/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-gnu/47/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-gnu/47/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-gnu/47/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-gnu/47/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-gnu/47/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-gnu/47/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-gnu/47/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-gnu/47/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-gnu/47/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-gnu/47/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-gnu/47/lib -lmpich -lmpl -lopa -lutil
>>>> -lpthread
>>>> -L/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/lib64/R/lib -lR
>>>> installing via 'install.libs.R' to
>>>> /univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/lib64/R/library/pbdMPI
>>>> ** R
>>>> ** data
>>>> *** moving datasets to lazyload DB
>>>> ** demo
>>>> ** inst
>>>> ** preparing package for lazy loading
>>>> ** help
>>>> *** installing help indices
>>>> converting help for package âpbdMPIâ
>>>> finding HTML links ... done
>>>> 00_pbdMPI-package html
>>>> 11_d.control html
>>>> aa_allgather-method html
>>>> aa_allreduce-method html
>>>> aa_bcast-method html
>>>> aa_gather-method html
>>>> aa_reduce-method html
>>>> aa_scatter-method html
>>>> ab_recv-method html
>>>> ab_send-method html
>>>> ac_irecv-method html
>>>> ac_isend-method html
>>>> ad_sendrecv-method html
>>>> ad_sendrecv.replace-method html
>>>> cc_arrange.mpi.apts html
>>>> cc_comm html
>>>> dd_info html
>>>> dd_prob html
>>>> dd_wait html
>>>> ww_get.jid html
>>>> ww_print_cat html
>>>> ww_seed html
>>>> xx_comm.sort html
>>>> xx_comm_any_all html
>>>> xx_comm_stop_warning html
>>>> yy_api.apply html
>>>> zz_internal html
>>>> zz_spmd.internal html
>>>> ** building package indices
>>>> ** installing vignettes
>>>> âpbdMPI-guide.Rnwâ
>>>> * DONE (pbdMPI)
>>>> Making 'packages.html' ... done
>>>> ipmiva at eslogin001:/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/build/source> R
>>>>
>>>> R version 3.0.0 (2013-04-03) -- "Masked Marvel"
>>>> Copyright (C) 2013 The R Foundation for Statistical Computing
>>>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>>>
>>>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>>>> You are welcome to redistribute it under certain conditions.
>>>> Type 'license()' or 'licence()' for distribution details.
>>>>
>>>> Natural language support but running in an English locale
>>>>
>>>> R is a collaborative project with many contributors.
>>>> Type 'contributors()' for more information and
>>>> 'citation()' on how to cite R or R packages in publications.
>>>>
>>>> Type 'demo()' for some demos, 'help()' for on-line help, or
>>>> 'help.start()' for an HTML browser interface to help.
>>>> Type 'q()' to quit R.
>>>>
>>>> > library(pbdMPI)
>>>> Loading required package: rlecuyer
>>>> [Thu May 16 08:58:03 2013] [unknown] Fatal error in MPI_Init: Other MPI
>>>> error, error stack:
>>>> MPIR_Init_thread(428):
>>>> MPID_Init(184).......: channel initialization failed
>>>> MPID_Init(538).......: PMI2 init failed: 1
>>>>
>>>>
>>>>
>>>> With regard to Your access to HERMIT, it is only possible from my IP and
>>>> I think it is not a good idea.
>>>>
>>>>
>>>> Thank you very much for Your responsiveness.
>>>>
>>>> Best regards,
>>>> Martin
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On 05/15/2013 08:41 PM, Pragnesh Patel wrote:
>>>>> Hi Martin,
>>>>>
>>>>> Can you try following:
>>>>>
>>>>> ======
>>>>> module swap PrgEnv-cray PrgEnv-gnu
>>>>> echo $LD_LIBRARY_PATH (Please send me output of it)
>>>>> R CMD INSTALL --no-test-load pbdMPI
>>>>> ======
>>>>>
>>>>> This way it will use mpich compiled with gnu compiler.
>>>>> You don't need to do "module swap PrgEnv-cray PrgEnv-gnu" to install
>>>>> other packages.
>>>>>
>>>>>
>>>>> Thanks
>>>>> Pragnesh
>>>>> NICS
>>>>> http://www.nics.tennessee.edu/
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On 5/15/13, r-sig-hpc-request at r-project.org
>>>>> <r-sig-hpc-request at r-project.org> wrote:
>>>>>> Send R-sig-hpc mailing list submissions to
>>>>>> r-sig-hpc at r-project.org
>>>>>>
>>>>>> To subscribe or unsubscribe via the World Wide Web, visit
>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-hpc
>>>>>> or, via email, send a message with subject or body 'help' to
>>>>>> r-sig-hpc-request at r-project.org
>>>>>>
>>>>>> You can reach the person managing the list at
>>>>>> r-sig-hpc-owner at r-project.org
>>>>>>
>>>>>> When replying, please edit your Subject line so it is more specific
>>>>>> than "Re: Contents of R-sig-hpc digest..."
>>>>>>
>>>>>>
>>>>>> Today's Topics:
>>>>>>
>>>>>> 1. Re: cannot install Rmpi/pbdMPI_0.1-7.tar.gz in R-3.0.0 on
>>>>>> Cray XE6 HERMIT (R-sig-hpc Digest, Vol 56, Issue 7) (Martin
>>>>>> Ivanov)
>>>>>>
>>>>>>
>>>>>> ----------------------------------------------------------------------
>>>>>>
>>>>>> Message: 1
>>>>>> Date: Wed, 15 May 2013 11:44:42 +0200
>>>>>> From: Martin Ivanov <martin.ivanov at ifg.uni-tuebingen.de>
>>>>>> To: Pragnesh Patel <pragnesh777 at gmail.com>
>>>>>> Cc: r-sig-hpc at r-project.org
>>>>>> Subject: Re: [R-sig-hpc] cannot install Rmpi/pbdMPI_0.1-7.tar.gz in
>>>>>> R-3.0.0 on Cray XE6 HERMIT (R-sig-hpc Digest, Vol 56, Issue 7)
>>>>>> Message-ID: <5193590A.9090508 at ifg.uni-tuebingen.de>
>>>>>> Content-Type: text/plain; charset=UTF-8; format=flowed
>>>>>>
>>>>>> Dear Pragnesh,
>>>>>>
>>>>>> Thank You very much indeed for Your responsiveness.
>>>>>> I compiled R with the cray compiler. Unfortunately neither Rmpi, nor
>>>>>> pbdMPI
>>>>>> gets compiled on HLRS. I tried both with the gnu and the cray
>>>>>> compilers.
>>>>>> The problem with Rmpi,
>>>>>> actually a very similar one, is posted in this forum as a separate
>>>>>> thread
>>>>>> (https://stat.ethz.ch/pipermail/r-sig-hpc/2013-May/001682.html).
>>>>>> With the gnu compiler things go a little further, actually Rmpi
>>>>>> compiles, but there is an error at loading the package into R.
>>>>>> The admins recommend that everything is compiled with the cray
>>>>>> compiler.
>>>>>> They also do not support netcdf-4.1.1 any more, only the newer
>>>>>> versions.
>>>>>>
>>>>>> Best regards,
>>>>>> Martin
>>>>>>
>>>>>>
>>>>>> On 05/15/2013 01:28 AM, Pragnesh Patel wrote:
>>>>>>> Hi Martin,
>>>>>>>
>>>>>>> Based on following error, it looks like you are using mpich compiled
>>>>>>> with cray compiler. But you use "gcc/gnu" to compile Rmpi and pbdMPI.
>>>>>>> I suggest you to swap your programming environment from "PrgEnv-cray"
>>>>>>> to "PrgEnv-gnu".
>>>>>>>
>>>>>>> That way you would use mpich compiled with gnu compiler (It should be
>>>>>>> somewhere at "/opt/cray/mpt/5.6.4/gni/mpich2-gnu/47/lib" ). You would
>>>>>>> also find "libmpich.so" in
>>>>>>> "/opt/cray/mpt/5.6.4/gni/mpich2-gnu/47/lib".
>>>>>>>
>>>>>>> ========
>>>>>>> "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"
>>>>>>> ========
>>>>>>>
>>>>>>> Let me know, if you still having an issue.
>>>>>>>
>>>>>>> Thanks
>>>>>>> Pragnesh
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On 5/10/13, r-sig-hpc-request at r-project.org
>>>>>>> <r-sig-hpc-request at r-project.org> wrote:
>>>>>>>> Send R-sig-hpc mailing list submissions to
>>>>>>>> r-sig-hpc at r-project.org
>>>>>>>>
>>>>>>>> To subscribe or unsubscribe via the World Wide Web, visit
>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-hpc
>>>>>>>> or, via email, send a message with subject or body 'help' to
>>>>>>>> r-sig-hpc-request at r-project.org
>>>>>>>>
>>>>>>>> You can reach the person managing the list at
>>>>>>>> r-sig-hpc-owner at r-project.org
>>>>>>>>
>>>>>>>> When replying, please edit your Subject line so it is more specific
>>>>>>>> than "Re: Contents of R-sig-hpc digest..."
>>>>>>>>
>>>>>>>>
>>>>>>>> Today's Topics:
>>>>>>>>
>>>>>>>> 1. Re: Fwd: cannot install ncdf4_1.6.1 in R-3.0.0 on Cray XE6
>>>>>>>> HERMIT (R-sig-hpc Digest, Vol 56, Issue 4) (Martin Ivanov)
>>>>>>>> 2. cannot install pbdMPI_0.1-7.tar.gz in R-3.0.0 on Cray XE6
>>>>>>>> HERMIT (Martin Ivanov)
>>>>>>>> 3. cannot install Rmpi_0.6-3.tar.gz on Cray XE6 HERMIT
>>>>>>>> (Martin Ivanov)
>>>>>>>>
>>>>>>>>
>>>>>>>> ----------------------------------------------------------------------
>>>>>>>>
>>>>>>>> Message: 1
>>>>>>>> Date: Fri, 10 May 2013 10:21:00 +0200
>>>>>>>> From: Martin Ivanov <martin.ivanov at ifg.uni-tuebingen.de>
>>>>>>>> To: Pragnesh Patel <pragnesh777 at gmail.com>
>>>>>>>> Cc: r-sig-hpc at r-project.org
>>>>>>>> Subject: Re: [R-sig-hpc] Fwd: cannot install ncdf4_1.6.1 in R-3.0.0
>>>>>>>> on
>>>>>>>> Cray XE6 HERMIT (R-sig-hpc Digest, Vol 56, Issue 4)
>>>>>>>> Message-ID: <518CADEC.5060807 at ifg.uni-tuebingen.de>
>>>>>>>> Content-Type: text/plain; charset=UTF-8; format=flowed
>>>>>>>>
>>>>>>>> Dear Pragnesh,
>>>>>>>> I turned out I had to use the newest versions of the available
>>>>>>>> netcdf
>>>>>>>> libraries to compile ncdf (netcdf-hdf5parallel/4.2.0).
>>>>>>>> With netcdf-4.1.1.0 compilation is never successful. Now I have a
>>>>>>>> problem compiling pbdMPI, which I descripe in a separate thread.
>>>>>>>>
>>>>>>>> Many thanks for Your support.
>>>>>>>>
>>>>>>>> Best regards,
>>>>>>>> Martin
>>>>>>>>
>>>>>>>>
>>>>>>>> On 05/08/2013 09:23 PM, Pragnesh Patel wrote:
>>>>>>>>> ---------- Forwarded message ----------
>>>>>>>>> From: Pragnesh Patel <pragnesh777 at gmail.com>
>>>>>>>>> Date: Wed, 8 May 2013 09:25:13 -0400
>>>>>>>>> Subject: Re: [R-sig-hpc] cannot install ncdf4_1.6.1 in R-3.0.0 on
>>>>>>>>> Cray
>>>>>>>>> XE6 HERMIT (R-sig-hpc Digest, Vol 56, Issue 4)
>>>>>>>>> To: George Ostrouchov <ostrouchovg at ornl.gov>
>>>>>>>>> Cc: Martin Ivanov <martin.ivanov at ifg.uni-tuebingen.de>, Drew
>>>>>>>>> Schmidt
>>>>>>>>> <schmidt at math.utk.edu>
>>>>>>>>>
>>>>>>>>> Hi Martin,
>>>>>>>>>
>>>>>>>>> Please follow below steps for HDF5 installation.
>>>>>>>>>
>>>>>>>>> ============================================
>>>>>>>>>
>>>>>>>>> make distclean
>>>>>>>>>
>>>>>>>>> ./configure --prefix=your home directory \
>>>>>>>>> --with-zlib=/usr \
>>>>>>>>> --with-szlib=$SZIP_DIR \
>>>>>>>>> --enable-fortran \
>>>>>>>>> --enable-cxx \
>>>>>>>>> --enable-parallel \
>>>>>>>>> --enable-shared
>>>>>>>>>
>>>>>>>>> =======================
>>>>>>>>> make all
>>>>>>>>>
>>>>>>>>> # after failing to run newly compiled H5make_libsettings
>>>>>>>>> interactively with aprun. It works fine on backend.
>>>>>>>>> # retry by compiling for frontend and then restart make
>>>>>>>>>
>>>>>>>>> cd src
>>>>>>>>> gcc -o H5make_libsettings H5make_libsettings.c
>>>>>>>>> cd ..
>>>>>>>>>
>>>>>>>>> make all
>>>>>>>>>
>>>>>>>>> # after failing to run newly compiled H5detect
>>>>>>>>> interactively
>>>>>>>>> with
>>>>>>>>> aprun. It works fine on backend.
>>>>>>>>> # retry by compiling for frontend and then restart make
>>>>>>>>>
>>>>>>>>> cd src
>>>>>>>>> gcc -o H5detect H5detect.c
>>>>>>>>> ./H5detect > H5Tinit.c
>>>>>>>>> cd ..
>>>>>>>>>
>>>>>>>>> make all
>>>>>>>>> =======================
>>>>>>>>> make install
>>>>>>>>>
>>>>>>>>> ============================================
>>>>>>>>>
>>>>>>>>> Thanks
>>>>>>>>> Pragnesh
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On 5/7/13, George Ostrouchov <ostrouchovg at ornl.gov> wrote:
>>>>>>>>>> Hi Martin,
>>>>>>>>>>
>>>>>>>>>> Glad that we can help with your configuration. Pragnesh is our CS
>>>>>>>>>> expert
>>>>>>>>>> on the pbdR project.
>>>>>>>>>>
>>>>>>>>>> Let me do a little advertising ...
>>>>>>>>>> If you will be at the UseR! conference this July in Albacete,
>>>>>>>>>> Spain,
>>>>>>>>>> Drew and I are running a pbdR tutorial the day before the
>>>>>>>>>> conference.
>>>>>>>>>> Please consider signing up. We have the most scalable
>>>>>>>>>> infrastructure
>>>>>>>>>> in
>>>>>>>>>> R.
>>>>>>>>>>
>>>>>>>>>> Cheers,
>>>>>>>>>> George
>>>>>>>>>>
>>>>>>>>>> On 5/7/13 1:04 PM, Martin Ivanov wrote:
>>>>>>>>>>> Hello, Pragnesh,
>>>>>>>>>>>
>>>>>>>>>>> Thank You very much for Your responsiveness.
>>>>>>>>>>> Now I am trying to compile hdf5, but unsuccessfully.
>>>>>>>>>>> Here is my setting:
>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>> 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
>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> R-sig-hpc mailing list
>>>>>>>>>>> R-sig-hpc at r-project.org
>>>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-hpc
>>>>>>>>>> --
>>>>>>>>>> George Ostrouchov, Ph.D.
>>>>>>>>>> Scientific Data Group
>>>>>>>>>> Computer Science and Mathematics Division
>>>>>>>>>> Oak Ridge National Laboratory
>>>>>>>>>> (865) 574-3137 http://www.csm.ornl.gov/~ost
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>> --
>>>>>>>> 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
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ------------------------------
>>>>>>>>
>>>>>>>> Message: 2
>>>>>>>> Date: Fri, 10 May 2013 10:24:50 +0200
>>>>>>>> From: Martin Ivanov <martin.ivanov at ifg.uni-tuebingen.de>
>>>>>>>> To: "R-sig-hpc at r-project.org" <r-sig-hpc at r-project.org>
>>>>>>>> Subject: [R-sig-hpc] cannot install pbdMPI_0.1-7.tar.gz in R-3.0.0
>>>>>>>> on
>>>>>>>> Cray XE6 HERMIT
>>>>>>>> Message-ID: <518CAED2.5090305 at ifg.uni-tuebingen.de>
>>>>>>>> Content-Type: text/plain; charset=UTF-8; format=flowed
>>>>>>>>
>>>>>>>> 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
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ------------------------------
>>>>>>>>
>>>>>>>> Message: 3
>>>>>>>> Date: Fri, 10 May 2013 10:30:42 +0200
>>>>>>>> From: Martin Ivanov <martin.ivanov at ifg.uni-tuebingen.de>
>>>>>>>> To: "R-sig-hpc at r-project.org" <r-sig-hpc at r-project.org>
>>>>>>>> Subject: [R-sig-hpc] cannot install Rmpi_0.6-3.tar.gz on Cray XE6
>>>>>>>> HERMIT
>>>>>>>> Message-ID: <518CB032.8070803 at ifg.uni-tuebingen.de>
>>>>>>>> Content-Type: text/plain; charset=UTF-8; format=flowed
>>>>>>>>
>>>>>>>> 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
>>>>>>>> ?/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/lib64/R/library?
>>>>>>>> * installing *source* package ?Rmpi? ...
>>>>>>>> ** package ?Rmpi? 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 ?Rmpi?
>>>>>>>> * removing
>>>>>>>> ?/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/lib64/R/library/Rmpi?
>>>>>>>>
>>>>>>>>
>>>>>>>> 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
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ------------------------------
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> R-sig-hpc mailing list
>>>>>>>> R-sig-hpc at r-project.org
>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-hpc
>>>>>>>>
>>>>>>>>
>>>>>>>> End of R-sig-hpc Digest, Vol 56, Issue 7
>>>>>>>> ****************************************
>>>>>>>>
>>>>>> --
>>>>>> 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
>>>>>>
>>>>>>
>>>>>>
>>>>>> ------------------------------
>>>>>>
>>>>>> _______________________________________________
>>>>>> R-sig-hpc mailing list
>>>>>> R-sig-hpc at r-project.org
>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-hpc
>>>>>>
>>>>>>
>>>>>> End of R-sig-hpc Digest, Vol 56, Issue 11
>>>>>> *****************************************
>>>>>>
>>>> --
>>>> Dr. Martin Ivanov
>>>> Eberhard-Karls-Universität Tübingen
>>>> Mathematisch-Naturwissenschaftliche Fakultät
>>>> Fachbereich Geowissenschaften
>>>> Water & Earth System Science (WESS)
>>>> Hölderlinstraße 12, 72074 Tübingen, Deutschland
>>>> Tel. +4970712974213
>>>>
>>>>
>>
>> --
>> Dr. Martin Ivanov
>> Eberhard-Karls-Universität Tübingen
>> Mathematisch-Naturwissenschaftliche Fakultät
>> Fachbereich Geowissenschaften
>> Water & Earth System Science (WESS)
>> Hölderlinstraße 12, 72074 Tübingen, Deutschland
>> Tel. +4970712974213
>>
>>
--
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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