[R] Rmpi installation error

[Martin Morgan]

Sunitha -- I think Rmpi finds an MPICH1 installation, rather than
MPICH2. Martin

"Sunithak" <sunithak at cdac.in> writes:

> Hello everybody,
> I am trying to install Rmpi on 64-bit HP-Proliant server. I am facing the
> following error:
>
>
> * Installing *source* package 'Rmpi' ...
> Try to find mpi.h ...
> Found in /usr/local/mpich-1.2.7p1/include
> Try to find libmpi or libmpich ...
> Found libmpich in /usr/local/mpich-1.2.7p1/lib
> Try to find liblam ...
> checking for main in -llam... no
> liblam not found. Probably not LAM-MPI
> checking for openpty in -lutil... no
> checking for main in -lpthread... no
> configure: creating ./config.status
> config.status: creating src/Makevars
> ** libs
> gcc -I/usr/local/lib64/R/include -I/usr/local/lib64/R/include -DPACKAGE_NAME
> =\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -D
> PACKAGE_BUGREPORT=\"\"  -I/usr/local/mpich-1.2.7p1/include -DMPI2 -I/usr/loc
> al/include   -fpic  -g -O2 -std=gnu99 -c conversion.c -o conversion.o
> gcc -I/usr/local/lib64/R/include -I/usr/local/lib64/R/include -DPACKAGE_NAME
> =\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -D
> PACKAGE_BUGREPORT=\"\"  -I/usr/local/mpich-1.2.7p1/include -DMPI2 -I/usr/loc
> al/include   -fpic  -g -O2 -std=gnu99 -c internal.c -o internal.o
> gcc -I/usr/local/lib64/R/include -I/usr/local/lib64/R/include -DPACKAGE_NAME
> =\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -D
> PACKAGE_BUGREPORT=\"\"  -I/usr/local/mpich-1.2.7p1/include -DMPI2 -I/usr/loc
> al/include   -fpic  -g -O2 -std=gnu99 -c RegQuery.c -o RegQuery.o
> gcc -I/usr/local/lib64/R/include -I/usr/local/lib64/R/include -DPACKAGE_NAME
> =\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -D
> PACKAGE_BUGREPORT=\"\"  -I/usr/local/mpich-1.2.7p1/include -DMPI2 -I/usr/loc
> al/include   -fpic  -g -O2 -std=gnu99 -c Rmpi.c -o Rmpi.o
> Rmpi.c: In function `mpi_universe_size':
> Rmpi.c:84: warning: implicit declaration of function `MPI_Comm_get_attr'
> Rmpi.c:84: error: `MPI_UNIVERSE_SIZE' undeclared (first use in this
> function)
> Rmpi.c:84: error: (Each undeclared identifier is reported only once
> Rmpi.c:84: error: for each function it appears in.)
> Rmpi.c: In function `mpi_comm_spawn':
> Rmpi.c:873: warning: implicit declaration of function `MPI_Comm_spawn'
> Rmpi.c:873: error: `MPI_ARGV_NULL' undeclared (first use in this function)
> Rmpi.c: In function `mpi_comm_get_parent':
> Rmpi.c:897: warning: implicit declaration of function `MPI_Comm_get_parent'
> Rmpi.c: In function `mpi_comm_disconnect':
> Rmpi.c:910: warning: implicit declaration of function `MPI_Comm_disconnect'
> make: *** [Rmpi.o] Error 1
> chmod: cannot access `/usr/local/lib64/R/library/Rmpi/libs/*': No such file
> or directory
> ERROR: compilation failed for package 'Rmpi'
> ** Removing '/usr/local/lib64/R/library/Rmpi'
>
>
> can any of you please suggest as to what needs to be done?
>
> Thanks for your time
> regards
> Sunitha Manjari
> Bioinformatics Team
> C-DAC, Pune-411007
> Maharashtra
> INDIA
>
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-- 
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org