[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 14:32:33 CEST 2013
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
>
>
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