[R-sig-hpc] Rmpi Setup Troubles

[lists at jdadesign.net]

Just an update:

I downloaded the most recent OpenMPI RPMs and followed the default
"configure/make install" installation. It properly produced the .so
libraries.

After updating using ldconfig, I was able to get Rmpi working with the
command I had tried previously.

Thanks for your help!


> 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
>>>
>>> _______________________________________________
>>> R-sig-hpc mailing list
>>> R-sig-hpc at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-hpc
>>>
>>
>>
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>>
>
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