[R-sig-hpc] installing Rmpi

[Markus Schmidberger]

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