[R-sig-hpc] Rmpi Setup Troubles

[Hao Yu]

Hi. Can you check if libmpi.so is installed at /opt/openmpi/tcp-intel//lib/?

This line seems indicating libmpi.a is checked instead of libmpi.so. Hao

/usr/bin/ld: /opt/openmpi/tcp-intel//lib/libmpi.a(comm_init.o): relocation
R_X86_64_32S against `ompi_mpi_comm_null' can not be used when making a
shared object; recompile with -fPIC


lists at jdadesign.net wrote:
> All,
>
> I've been searching around on mailing lists for days but still haven't
> been able to get Rmpi working on my cluster.
>
> Most recently, I've set the mpi paths using configure.args, but still
> can't get the package installed correctly. I'm on RedHat 5 64 bit, trying
> to use OpenMPI. Here's the most recent error I've received:
>
>> install.packages("Rmpi",configure.args=c("--with-mpi=/opt/openmpi/tcp-intel/",
> "--with-mpi-libpath=/opt/openmpi/tcp-intel/lib/",
> "--with-mpi-type=OPENMPI"))
> Installing package(s) into
> ‘/home/jalle6/R/x86_64-redhat-linux-gnu-library/2.12’
> (as ‘lib’ is unspecified)
> trying URL 'http://cran.sixsigmaonline.org/src/contrib/Rmpi_0.5-9.tar.gz'
> Content type 'application/x-gzip' length 87953 bytes (85 Kb)
> opened URL
> ==================================================
> downloaded 85 Kb
>
> * installing *source* package ‘Rmpi’ ...
> checking for gcc... gcc -m64 -std=gnu99
> 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 -m64 -std=gnu99 accepts -g... yes
> checking for gcc -m64 -std=gnu99 option to accept ISO C89... none needed
> Trying to find mpi.h ...
> Found in /opt/openmpi/tcp-intel//include
> Trying 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 -m64 -std=gnu99 -I/usr/include/R -DPACKAGE_NAME=\"\"
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
> -DPACKAGE_BUGREPORT=\"\" -I/opt/openmpi/tcp-intel//include  -DMPI2
> -DOPENMPI -I/usr/local/include    -fpic  -O2 -g -pipe -Wall
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
> --param=ssp-buffer-size=4 -m64 -mtune=generic -c RegQuery.c -o RegQuery.o
> gcc -m64 -std=gnu99 -I/usr/include/R -DPACKAGE_NAME=\"\"
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
> -DPACKAGE_BUGREPORT=\"\" -I/opt/openmpi/tcp-intel//include  -DMPI2
> -DOPENMPI -I/usr/local/include    -fpic  -O2 -g -pipe -Wall
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
> --param=ssp-buffer-size=4 -m64 -mtune=generic -c Rmpi.c -o Rmpi.o
> gcc -m64 -std=gnu99 -I/usr/include/R -DPACKAGE_NAME=\"\"
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
> -DPACKAGE_BUGREPORT=\"\" -I/opt/openmpi/tcp-intel//include  -DMPI2
> -DOPENMPI -I/usr/local/include    -fpic  -O2 -g -pipe -Wall
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
> --param=ssp-buffer-size=4 -m64 -mtune=generic -c conversion.c -o
> conversion.o
> gcc -m64 -std=gnu99 -I/usr/include/R -DPACKAGE_NAME=\"\"
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
> -DPACKAGE_BUGREPORT=\"\" -I/opt/openmpi/tcp-intel//include  -DMPI2
> -DOPENMPI -I/usr/local/include    -fpic  -O2 -g -pipe -Wall
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
> --param=ssp-buffer-size=4 -m64 -mtune=generic -c internal.c -o internal.o
> gcc -m64 -std=gnu99 -shared -L/usr/local/lib64 -o Rmpi.so RegQuery.o
> Rmpi.o conversion.o internal.o -L/opt/openmpi/tcp-intel//lib -lmpi -lutil
> -lpthread -L/usr/lib64/R/lib -lR
> /usr/bin/ld: /opt/openmpi/tcp-intel//lib/libmpi.a(comm_init.o): relocation
> R_X86_64_32S against `ompi_mpi_comm_null' can not be used when making a
> shared object; recompile with -fPIC
> /opt/openmpi/tcp-intel//lib/libmpi.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 ‘/home/jalle6/R/x86_64-redhat-linux-gnu-library/2.12/Rmpi’
>
> The downloaded packages are in
>         ‘/tmp/RtmpbJFYNv/downloaded_packages’
> Warning message:
> In install.packages("Rmpi", configure.args =
> c("--with-mpi=/opt/openmpi/tcp-intel/",  :
>   installation of package 'Rmpi' had non-zero exit status
>>
>
>
> I'll have to confess that I am brand new to MPI, and not much better in
> dealing with compiling/linking C libraries.
>
> Thanks in advance,
> Jeff
>
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