[R-sig-hpc] installing Rmpi

[Hao Yu]

Markus,

This may be library link issue. Try
R CMD ldd path_to_Rmpi.so
to see if Rmpi finds needed libraries. Otherwise you may modify R script
to include (very beginning)
LD_LIBRARY_PATH=/path_to_mpi_lib

Hao

Markus Schmidberger wrote:
> Dear Hao,
>
> thanks for the tip, this works. Now I can install Rmpi.
> But after loading Rmpi it fails:
>
> library(Rmpi)
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>   unable to load shared library
> '/home/hlrb2/pr32di/lu57waf2/ia64/Rlibrary/Rmpi/libs/Rmpi.so':
>   /home/hlrb2/pr32di/lu57waf2/ia64/Rlibrary/Rmpi/libs/Rmpi.so: undefined
> symbol: MPI_Test_cancelled
> Error in library(Rmpi) : .First.lib failed for 'Rmpi'
> Error in dyn.unload(file.path(libpath, "libs", paste("Rmpi",
> .Platform$dynlib.ext,  :
>   dynamic/shared library
> '/home/hlrb2/pr32di/lu57waf2/ia64/Rlibrary/Rmpi/libs/Rmpi.so' was not
> loaded
>
> we are using openmpi 1.3.0
>
> Best
> Markus
>
>
> Hao Yu schrieb:
>> Markus,
>>
>> Can you try to take -fPIC flag out in Rmpi (comment out the line
>> PKG_LIBS="${MPI_LIBS} -fPIC" in configure.ac)? The flag -fPIC was added
>> due to the same reason.
>>
>> Hao
>>
>> Markus Schmidberger wrote:
>>
>>> Hi,
>>>
>>> I have R 2.9.2 compiled with gcc.
>>> Now I try to INSTALL Rmpi, linked to the correct header files. The
>>> configure-file finds everything correct, but than fails.
>>>
>>> Any idea?
>>>
>>>  R CMD INSTALL Rmpi_0.5-7.tar.gz
>>> --configure-args=--with-mpi=/lrz/sys/parallel/openmpi/1.3.0/altix_shm
>>> * Installing to library '/home/hlrb2/pr32di/lu57waf2/ia64/Rlibrary'
>>> * Installing *source* package 'Rmpi' ...
>>> checking for gcc... gcc
>>> checking for C compiler default output file name... a.out
>>> checking whether the C compiler works... yes
>>> checking whether we are cross compiling... no
>>> checking for suffix of executables...
>>> checking for suffix of object files... o
>>> checking whether we are using the GNU C compiler... yes
>>> checking whether gcc accepts -g... yes
>>> checking for gcc option to accept ISO C89... none needed
>>> Try to find mpi.h ...
>>> Found in /lrz/sys/parallel/openmpi/1.3.0/altix_shm/include
>>> Try to find libmpi.so or libmpich.a
>>> checking for main in -lmpi... yes
>>> checking for openpty in -lutil... yes
>>> checking for main in -lpthread... yes
>>> configure: creating ./config.status
>>> config.status: creating src/Makevars
>>> ** libs
>>> gcc -std=gnu99 -I/lrz/sys/applications/R/2.8.1gccO3//lib/R/include
>>> -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DP
>>> ACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\"
>>> -I/lrz/sys/parallel/openmpi/1.3.0/altix_shm/in                   clude
>>> -DMPI2 -DOPENMPI -fPIC -I/usr/local/include    -fPIC  -O3 -c
>>> conversion.c -o conversion.o
>>> gcc -std=gnu99 -I/lrz/sys/applications/R/2.8.1gccO3//lib/R/include
>>> -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DP
>>> ACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\"
>>> -I/lrz/sys/parallel/openmpi/1.3.0/altix_shm/in                   clude
>>> -DMPI2 -DOPENMPI -fPIC -I/usr/local/include    -fPIC  -O3 -c internal.c
>>> -o internal.o
>>> gcc -std=gnu99 -I/lrz/sys/applications/R/2.8.1gccO3//lib/R/include
>>> -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DP
>>> ACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\"
>>> -I/lrz/sys/parallel/openmpi/1.3.0/altix_shm/in                   clude
>>> -DMPI2 -DOPENMPI -fPIC -I/usr/local/include    -fPIC  -O3 -c RegQuery.c
>>> -o RegQuery.o
>>> gcc -std=gnu99 -I/lrz/sys/applications/R/2.8.1gccO3//lib/R/include
>>> -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DP
>>> ACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\"
>>> -I/lrz/sys/parallel/openmpi/1.3.0/altix_shm/in                   clude
>>> -DMPI2 -DOPENMPI -fPIC -I/usr/local/include    -fPIC  -O3 -c Rmpi.c -o
>>> Rmpi.o
>>> gcc -std=gnu99 -shared  -o Rmpi.so conversion.o internal.o RegQuery.o
>>> Rmpi.o -L/lrz/sys/parallel/openmpi/1.3.0/al
>>> tix_shm/lib -lmpi -lutil -lpthread -fPIC
>>> -L/lrz/sys/applications/R/2.8.1gccO3//lib/R/lib -lR
>>> /usr/lib/gcc/ia64-suse-linux/4.1.2/../../../../ia64-suse-linux/bin/ld:
>>> /lrz/sys/parallel/openmpi/1.3.0/altix_shm/
>>> lib/libmpi.a(ad_init.o): @gprel relocation against dynamic symbol
>>> ADIOI_Flatlist
>>> /usr/lib/gcc/ia64-suse-linux/4.1.2/../../../../ia64-suse-linux/bin/ld:
>>> final link failed: Nonrepresentable sectio                   n on
>>> output
>>> collect2: ld returned 1 exit status
>>> make: *** [Rmpi.so] Error 1
>>> chmod: cannot access
>>> `/home/hlrb2/pr32di/lu57waf2/ia64/Rlibrary/Rmpi/libs/*': No such file
>>> or
>>> directory
>>> ERROR: compilation failed for package 'Rmpi'
>>> ** Removing '/home/hlrb2/pr32di/lu57waf2/ia64/Rlibrary/Rmpi'
>>> ** Restoring previous '/home/hlrb2/pr32di/lu57waf2/ia64/Rlibrary/Rmpi'
>>>
>>> Thanks
>>> Markus
>>>
>>>
>>> --
>>> Dipl.-Tech. Math. Markus Schmidberger
>>>
>>> Ludwig-Maximilians-Universität München
>>> IBE - Institut für medizinische Informationsverarbeitung,
>>> Biometrie und Epidemiologie
>>> Marchioninistr. 15, D-81377 Muenchen
>>> URL: http://www.ibe.med.uni-muenchen.de
>>> Mail: Markus.Schmidberger [at] ibe.med.uni-muenchen.de
>>> Tel: +49 (089) 7095 - 4497
>>>
>>>
>>
>>
>>
>
>
> --
> Dipl.-Tech. Math. Markus Schmidberger
>
> Ludwig-Maximilians-Universität München
> IBE - Institut für medizinische Informationsverarbeitung,
> Biometrie und Epidemiologie
> Marchioninistr. 15, D-81377 Muenchen
> URL: http://www.ibe.med.uni-muenchen.de
> Mail: Markus.Schmidberger [at] ibe.med.uni-muenchen.de
> Tel: +49 (089) 7095 - 4497
>


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