[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
Thu May 16 14:48:17 CEST 2013
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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