[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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