[R-sig-hpc] Rmpi installation with openmpi (on local directory)

Rodney Sparapani rsparapa at mcw.edu
Tue Feb 28 18:07:58 CET 2012


Brian Smith wrote:
> Hi,
> 
> I was trying to install the Rmpi package on a cluster (running SGE). I
> first installed the openmpi package in my directory, and then installed the
> Rmpi package (after downloading tarball from cran) by an interactive R
> session.
> 
> If I load Rmpi within an R interactive session everything seems to be fine.
> However, if I try to use the SGE then I get errors:
> 
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>   unable to load shared object
> '/home/bs/R/x86_64-unknown-linux-gnu-library/2.14/Rmpi/libs/Rmpi.so':
>   libmpi.so.0: cannot open shared object file: No such file or directory
> Error: package/namespace load failed for ‘Rmpi’
> Execution halted
> 
> Other details of my attempts at the installation are given below. Any help
> would be greatly appreciated!
> 
> many thanks!
> 
> PS: I have read the previous threads on difficulties in installation of
> Rmpi and have tried to follow the advice/example...
> 
>

Hi Brian et al.:

I'm seeing pretty much the same thing with R 2.14.0 on RHEL 5.7 with GCC 
4.4.4 20100726 (Red Hat 4.4.4-13).  I didn't see a solution in this
thread.  Any ideas?  Thanks in advance.

/opt/local/src/R/Rmpi:$ R CMD INSTALL Rmpi_0.5-9.tar.gz \
--configure-args=--with-mpi=/usr/lib64/openmpi/1.4-gcc

* installing to library '/opt/local/lib64/R/library'
* installing *source* package 'Rmpi' ...
checking for gcc... gcc44 -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 gcc44 -std=gnu99 accepts -g... yes
checking for gcc44 -std=gnu99 option to accept ISO C89... none needed
Trying to find mpi.h ...
Found in /usr/lib64/openmpi/1.4-gcc/include
Trying to find libmpi.so or libmpich.a ...
Found libmpi in /usr/lib64/openmpi/1.4-gcc/lib
checking for openpty in -lutil... yes
checking for main in -lpthread... yes
configure: creating ./config.status
config.status: creating src/Makevars
** Creating default NAMESPACE file
** libs
gcc44 -std=gnu99 -I/opt/local/lib64/R/include -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -I/usr/lib64/openmpi/1.4-gcc/include  -DMPI2
-DOPENMPI -I/usr/local/include    -fpic  -g -c RegQuery.c -o RegQuery.o
gcc44 -std=gnu99 -I/opt/local/lib64/R/include -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -I/usr/lib64/openmpi/1.4-gcc/include  -DMPI2
-DOPENMPI -I/usr/local/include    -fpic  -g -c Rmpi.c -o Rmpi.o
gcc44 -std=gnu99 -I/opt/local/lib64/R/include -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -I/usr/lib64/openmpi/1.4-gcc/include  -DMPI2
-DOPENMPI -I/usr/local/include    -fpic  -g -c conversion.c -o conversion.o
gcc44 -std=gnu99 -I/opt/local/lib64/R/include -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -I/usr/lib64/openmpi/1.4-gcc/include  -DMPI2
-DOPENMPI -I/usr/local/include    -fpic  -g -c internal.c -o internal.o
gcc44 -std=gnu99 -shared -L/usr/local/lib64 -o Rmpi.so RegQuery.o Rmpi.o
conversion.o internal.o -L/usr/lib64/openmpi/1.4-gcc/lib -lmpi -lutil
-lpthread
installing to /opt/local/lib64/R/library/Rmpi/libs
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
   unable to load shared object
'/opt/local/lib64/R/library/Rmpi/libs/Rmpi.so':
   libmpi.so.0: cannot open shared object file: No such file or directory
Error: loading failed
Execution halted
ERROR: loading failed
* removing '/opt/local/lib64/R/library/Rmpi'

/opt/local/src/R/Rmpi:# yum info openmpi openmpi-devel
Loaded plugins: rhnplugin, security
Installed Packages
Name       : openmpi
Arch       : i386
Version    : 1.4
Release    : 4.el5
Size       : 300 k
Repo       : installed
Summary    : Open Message Passing Interface
URL        : http://www.open-mpi.org/
License    : BSD
Description: Open MPI is an open source, freely available implementation 
of both the
            : MPI-1 and MPI-2 standards, combining technologies and 
resources from
            : several other projects (FT-MPI, LA-MPI, LAM/MPI, and 
PACX-MPI) in
            : order to build the best MPI library available.  A 
completely new MPI-2
            : compliant implementation, Open MPI offers advantages for 
system and
            : software vendors, application developers, and computer science
            : researchers. For more information, see 
http://www.open-mpi.org/ .

Name       : openmpi
Arch       : x86_64
Version    : 1.4
Release    : 4.el5
Size       : 316 k
Repo       : installed
Summary    : Open Message Passing Interface
URL        : http://www.open-mpi.org/
License    : BSD
Description: Open MPI is an open source, freely available implementation 
of both the
            : MPI-1 and MPI-2 standards, combining technologies and 
resources from
            : several other projects (FT-MPI, LA-MPI, LAM/MPI, and 
PACX-MPI) in
            : order to build the best MPI library available.  A 
completely new MPI-2
            : compliant implementation, Open MPI offers advantages for 
system and
            : software vendors, application developers, and computer science
            : researchers. For more information, see 
http://www.open-mpi.org/ .

Name       : openmpi-devel
Arch       : i386
Version    : 1.4
Release    : 4.el5
Size       : 3.9 M
Repo       : installed
Summary    : Development files for openmpi
URL        : http://www.open-mpi.org/
License    : BSD
Description: Contains development headers and libraries for openmpi

Name       : openmpi-devel
Arch       : x86_64
Version    : 1.4
Release    : 4.el5
Size       : 3.9 M
Repo       : installed
Summary    : Development files for openmpi
URL        : http://www.open-mpi.org/
License    : BSD
Description: Contains development headers and libraries for openmpi

-- 
Rodney Sparapani, PhD  Center for Patient Care and Outcomes Research
Sr. Biostatistician               http://www.mcw.edu/pcor
4 wheels good, 2 wheels better!   Medical College of Wisconsin (MCW)
WWLD?:  What Would Lombardi Do?   Milwaukee, WI, USA



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