[R-sig-hpc] mpi_comm_spawn error with Rmpi and snow on SGI Altix

[Ei-ji Nakama]

Hi,

Was universe of size specified?

http://www.techpubs.sgi.com/library/tpl/cgi-bin/getdoc.cgi/linux/bks/SGI_Developer/books/MPT_UG/sgi_html/ch03.html#id5188254


2009/2/6 Gad Abraham <gabraham at csse.unimelb.edu.au>:
> Stefan Theussl wrote:
>>
>> Hi Gad,
>>
>> Presumably you have installed an old implementation of MPI. mpi.comm.spawn
>> has been supported since the MPI 1.2 standard as far as I remember. Can you
>> pls tell us which implementation/version of MPI you use? (in case of LAM you
>> may send us the output of 'laminfo')
>
> Hi Stefan & Martin,
>
> I'm merging my offline conversation with Martin.
>
> Details of the system:
> SGI Altix 3700Bx2, SUSE enterprise server 10 SP1
> /usr/lib/libmpi.so comes from the SGI package sgi-mpt-1.21-sgi601r1 which
> according to its release notes supports some MPI2 features like
> MPI_Comm_spawn.
>
> Martin suggested to check if the symbols are in the library, and that
> perhaps Rmpi isn't configuring itself correctly with -DMPI2:
>
>> nm /usr/lib/libmpi.so | grep comm_spawn
> 0000000000099180 W mpi_comm_spawn_
> 0000000000099180 W mpi_comm_spawn__
> 000000000009b390 W mpi_comm_spawn_multiple_
> 000000000009b390 W mpi_comm_spawn_multiple__
> 0000000000164dc0 T MPI_SGI_comm_spawn_request
> 0000000000099180 T pmpi_comm_spawn_
> 0000000000099180 W pmpi_comm_spawn__
> 000000000009b390 T pmpi_comm_spawn_multiple_
> 000000000009b390 W pmpi_comm_spawn_multiple__
>
>
> Here's sample output from R CMD INSTALL Rmpi, -DMPI2 indeed not set:
>
> gcc -std=gnu99 -I/home/gabraham/dmf/Software/R-2.8.1/include
> -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
> -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/include  -DUNKNOWN
> -fPIC -I/usr/local/include    -fpic  -g -O2 -c conversion.c -o conversion.o
>
>
> If I recompile Rmpi with either MPI_DEPS="-DMPI2" R CMD INSTALL Rmpi, or by
> setting MPI_DEPS="-DMPI2" in Rmpi/configure.ac then autoconf then R CMD
> INSTALL, as suggested by Martin, then -DMPI2 is set:
>
> gcc -std=gnu99 -I/home/gabraham/dmf/Software/R-2.8.1/include
> -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
> -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\"  -I/usr/include -DMPI2
> -DUNKNOWN -fPIC -I/usr/local/include    -fpic  -g -O2 -c conversion.c -o
> conversion.o
>
>
> but I get a different error when I run the example code:
>
> Error calling job_getjid(): No such file or directory
> Error in mpi.comm.spawn(slave = mpitask, slavearg = args, nslaves = count,
>  :
>  Error during spawn request
> Calls: makeCluster ... switch -> makeMPIcluster -> mpi.comm.spawn -> .Call
> Execution halted
> MPI: MPI_COMM_WORLD rank 0 has terminated without calling MPI_Finalize()
> MPI: aborting job
>
>
> Thanks,
> Gad
>
> --
> Gad Abraham
> Dept. CSSE and NICTA
> The University of Melbourne
> Parkville 3010, Victoria, Australia
> email: gabraham at csse.unimelb.edu.au
> web: http://www.csse.unimelb.edu.au/~gabraham
>
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>
>
>

-- 
EI-JI Nakama  <nakama (a) ki.rim.or.jp>
"\u4e2d\u9593\u6804\u6cbb"  <nakama (a) ki.rim.or.jp>