[R-sig-hpc] Problems Installing Rmpi on openSUSE 11.1 x86_64
Melwin
win at comets.de
Thu Jul 9 17:20:02 CEST 2009
Thanks, Martin and Hao, for the quick response.
Following Martin's suggestions, I tried
R CMD ldd
/home/francke/R/x86_64-unknown-linux-gnu-library/2.8/Rmpi/libs/Rmpi.so
which yields no apparent problem:
linux-vdso.so.1 => (0x00007fff641fe000)
libmpi.so.0 => /usr/lib64/libmpi.so.0 (0x00007f955bb40000)
libutil.so.1 => /lib64/libutil.so.1 (0x00007f955b93c000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f955b720000)
libR.so => /usr/lib64/R/lib/libR.so (0x00007f955b1e5000)
libc.so.6 => /lib64/libc.so.6 (0x00007f955ae8b000)
/lib64/ld-linux-x86-64.so.2 (0x00007f955c026000)
libRblas.so => /usr/lib64/R/lib/libRblas.so (0x00007f955ac5d000)
libgfortran.so.3 => /usr/lib64/libgfortran.so.3
(0x00007f955a981000)
libm.so.6 => /lib64/libm.so.6 (0x00007f955a72a000)
libreadline.so.5 => /lib64/libreadline.so.5 (0x00007f955a4e8000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007f955a2e4000)
libncurses.so.5 => /lib64/libncurses.so.5 (0x00007f955a09b000)
although "liblam.so.0" is not listed. Is this a problem?
Nevertheless I attempted setting
export LD_LIBRARY_PATH=/usr/lib64
(because thats where "libmpi.so" is) and
export MPI_LIBS="-Lusr/lib64 -lmpi -lam"
(because thats where "liblam.so" is)
Running
ldd /home/francke/R/x86_64-unknown-linux-gnu-library/2.8/Rmpi/libs/Rmpi.so
still gives the same output as above.
Nevertheless, loading Rmpi after starting R still prints the same error.
Please let me know if you've got an idea what else I could do.
gratefully,
Melwin
Am 09.07.2009, 16:44 Uhr, schrieb Hao Yu <hyu at stats.uwo.ca>:
> Sorry. I forgot to say that Rmpi needs liblam.so as well. So use
>> MPI_LIBS="-L${MPI_ROOT}/lib64 -lmpi -lam"
>
> Once compiled, use
>
> ldd path_to_Rmpi.so
>
> to check if all libs are properly set. Again the following line in R
> script
> LD_LIBRARY_PATH=/usr/local/lam/lib
> is useful in case ldd reports libmpi.so.0 or liblam.so.0 are not found.
>
> Hao
>
> Melwin wrote:
>> Thanks to Hao, Brian and Martin (offlist) for their suggestions.
>>
>> I tried them all:
>> - setting LD_LIBRARY_PATH
>> - using "--configure-args=--with-mpi=/path_to_lam"
>> - using mpicc
>> -> all without success when trying to install Rmpi (same error message
>> as
>> before)
>>
>> Since I cannot accept using OpenMPI using 100% CPU power in idle mode, I
>> still need to get LAM working.
>> Martin suggested modifiying "configure.ac":
>>
>> tar xzf Rmpi_0.5-7.tar.gz
>> vim Rmpi/configure.ac
>>
>> I added
>> after line 67: MPITYPE="LAM"
>> after line 128:
>> elif test -f ${MPI_ROOT}/lib64/libmpi.so; then #Till
>> echo "Found libmpi in ${MPI_ROOT}/lib64"
>> MPI_LIBS="-L${MPI_ROOT}/lib64 -lmpi"
>> MPI_INCLUDE="${MPI_INCLUDE} ${MPI_INCLUDE}/64"
>>
>> followed by
>> cd Rmpi && autoconf && cd ..
>> R CMD INSTALL --clean Rmpi
>>
>> compiles without errors (see snippet 1 below).
>> However, when tryinig to load Rmpi in R I get an error:
>>
>>> library("Rmpi")
>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>> kann shared library
>> '/home/francke/R/x86_64-unknown-linux-gnu-library/2.8/Rmpi/libs/Rmpi.so'
>> nicht laden:
>> /usr/lib64/libmpi.so.0: undefined symbol: lam_ssi_cr_did
>> Fehler in library("Rmpi") : .First.lib fehlgeschlagen für 'Rmpi'
>> Error in dyn.unload(file.path(libpath, "libs", paste("Rmpi",
>> .Platform$dynlib.ext, :
>> shared library
>> '/home/francke/R/x86_64-unknown-linux-gnu-library/2.8/Rmpi/libs/Rmpi.so'
>> wurde nicht geladen
>>>
>>
>> Translation:
>>> library("Rmpi")
>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>> could not load shared library
>> '/home/francke/R/x86_64-unknown-linux-gnu-library/2.8/Rmpi/libs/Rmpi.so':
>> /usr/lib64/libmpi.so.0: undefined symbol: lam_ssi_cr_did
>> Error in library("Rmpi") : .First.lib failed for 'Rmpi'
>> Error in dyn.unload(file.path(libpath, "libs", paste("Rmpi",
>> .Platform$dynlib.ext, :
>> shared library
>> '/home/francke/R/x86_64-unknown-linux-gnu-library/2.8/Rmpi/libs/Rmpi.so'
>> not loaded
>>>
>>
>> "Rmpi.so" exists, so I dunno what's wrong. Any help is appreciated,
>>
>> Melwin
>>
>>
>>
>> ####snippet: installation of RMPI
>> * Installing to library
>> '/home/francke/R/x86_64-unknown-linux-gnu-library/2.8'
>> * 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
>> I am here /usr
>> Try to find mpi.h ...
>> Found in /usr/include
>> Try to find libmpi.so or libmpich.a
>> Found libmpi in /usr/lib64
>> Try to find liblam.so ...
>> checking for main in -llam... no
>> liblam not found. Probably not LAM-MPI
>> 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/usr/lib64/R/include -DPACKAGE_NAME=\"\"
>> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
>> -DPACKAGE_BUGREPORT=\"\" -I/usr/include -I/usr/include/64 -DMPI2 -DLAM
>> -fPIC -I/usr/local/include -fpic -fmessage-length=0 -O2 -Wall
>> -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables
>> -fasynchronous-unwind-tables -c conversion.c -o conversion.o
>> gcc -std=gnu99 -I/usr/lib64/R/include -DPACKAGE_NAME=\"\"
>> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
>> -DPACKAGE_BUGREPORT=\"\" -I/usr/include -I/usr/include/64 -DMPI2 -DLAM
>> -fPIC -I/usr/local/include -fpic -fmessage-length=0 -O2 -Wall
>> -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables
>> -fasynchronous-unwind-tables -c internal.c -o internal.o
>> gcc -std=gnu99 -I/usr/lib64/R/include -DPACKAGE_NAME=\"\"
>> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
>> -DPACKAGE_BUGREPORT=\"\" -I/usr/include -I/usr/include/64 -DMPI2 -DLAM
>> -fPIC -I/usr/local/include -fpic -fmessage-length=0 -O2 -Wall
>> -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables
>> -fasynchronous-unwind-tables -c RegQuery.c -o RegQuery.o
>> gcc -std=gnu99 -I/usr/lib64/R/include -DPACKAGE_NAME=\"\"
>> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
>> -DPACKAGE_BUGREPORT=\"\" -I/usr/include -I/usr/include/64 -DMPI2 -DLAM
>> -fPIC -I/usr/local/include -fpic -fmessage-length=0 -O2 -Wall
>> -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables
>> -fasynchronous-unwind-tables -c Rmpi.c -o Rmpi.o
>> gcc -std=gnu99 -shared -L/usr/local/lib64 -o Rmpi.so conversion.o
>> internal.o RegQuery.o Rmpi.o -L/usr/lib64 -lmpi -lutil -lpthread -fPIC
>> -L/usr/lib64/R/lib -lR
>> ** R
>> ** demo
>> ** inst
>> ** preparing package for lazy loading
>> ** help
>> >>> Building/Updating help pages for package 'Rmpi'
>> [...]
>> ** building package indices ...
>> * DONE (Rmpi)
>> ####end snippet
>>
>>
>>
>>
>>
>>
>> 2009/6/26 Hao Yu <hyu at stats.uwo.ca>:
>>> Hi Melwin,
>>>
>>> Did you try
>>>
>>> R CMD INSTALL Rmpi_0.5-7.tar.gz
>>> --configure-args=--with-mpi=/path_to_lam
>>>
>>> Your system may have several mpi and Rmpi did not find a right mpi.
>>>
>>> BTW, when you are installing lam, make sure to turn dynamic lib on. The
>>> default one is static one and Rmpi needs libmpi.so to work.
>>>
>>> Hao
>>>
>>> Melwin wrote:
>>>> Thanks for the reply.
>>>>
>>>> 2009/6/24 Rowe, Brian Lee Yung (Portfolio Analytics) <B_Rowe at ml.com>:
>>>>> Did you confirm that your MPI installation is working? That is the
>>>>> probably the first step.
>>>> LAM seems to work ok:
>>>> johnson at linuxmodel:~> lamboot -v
>>>>
>>>> LAM 7.1.4/MPI 2 C++/ROMIO - Indiana University
>>>>
>>>> n-1<4165> ssi:boot:base:linear: booting n0 (localhost)
>>>> n-1<4165> ssi:boot:base:linear: finished
>>>> johnson at linuxmodel:~> lamexec C hostname
>>>> linuxmodel
>>>>
>>>>
>>>>> Regarding LD_LIBRARY_PATH, since I don't know what your configuration
>>>>> is, make sure you export it to your environment and also don't
>>>>> overwrite
>>>>> any existing values.
>>>>> i.e. This is better:
>>>>> $ export LD_LIBRARY_PATH=/usr/lib64:$LD_LIBRARY_PATH
>>>>> since it looks like you're on a 64 bit platform.
>>>>
>>>> Tried that. Same results as before:
>>>> johnson at linuxmodel:~> R CMD INSTALL Rmpi_0.5-7.tar.gz
>>>> * Installing to library
>>>> '/home/johnson/R/x86_64-unknown-linux-gnu-library/2.8'
>>>> * 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
>>>> I am here /usr
>>>> Try to find mpi.h ...
>>>> Found in /usr/include
>>>> Try to find libmpi.so or libmpich.a
>>>> checking for main in -lmpi... no
>>>> libmpi not found. exiting...
>>>> ERROR: configuration failed for package 'Rmpi'
>>>> ** Removing
>>>> '/home/johnson/R/x86_64-unknown-linux-gnu-library/2.8/Rmpi'
>>>>
>>>>> I use OpenMPI and it include an mpi-based compiler which I found to
>>>>> work
>>>>> better than gcc directly. You might try that. Just make sure you
>>>>> export
>>>>> your MPI_ROOT.
>>>> I would love to use OpenMPI, but I gather the slave spawning from
>>>> within R
>>>> is not yet possible - which is what I need in interactive mode
>>>> (https://stat.ethz.ch/pipermail/r-sig-hpc/2009-February/000104.html).
>>>> I'd
>>>> love to hear that this has changed.
>>>>
>>>>> It would also probably help to include a bit more output
>>>>> from the compilation process.
>>>> The dump above contains the entire output, I hope that helps.
>>>>
>>>> thanks again,
>>>> Melwin
>>>>
>>>> _______________________________________________
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>>>> R-sig-hpc at r-project.org
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>>>>
>>>
>>>
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>>
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