[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
Pragnesh Patel
pragnesh777 at gmail.com
Thu May 16 19:10:55 CEST 2013
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
>
>
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