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
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
?/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-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 ?pbdMPI?
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
?pbdMPI-guide.Rnw?
* 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-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