[R-sig-hpc] Rmpi Setup Troubles

[lists at jdadesign.net]

You are correct -- there is no libmpi.so in that directory, only libmpi.a.

So I need to recompile openMPI to produce shared, rather than a static
libraries?

Jeff

> 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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>>
>
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