[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)
Martin Ivanov
martin.ivanov at ifg.uni-tuebingen.de
Wed May 15 11:44:42 CEST 2013
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-Universität Tübingen
Mathematisch-Naturwissenschaftliche Fakultät
Fachbereich Geowissenschaften
Water & Earth System Science (WESS)
Hölderlinstraße 12, 72074 Tübingen, Deutschland
Tel. +4970712974213
More information about the R-sig-hpc
mailing list