Error installing Rmpi over OpenMPI: Cannot find orted
hello,
openmpi of ubuntu / debian is built with --with-tm.
openmpi module (mca_plm_tm.so) have a soname(libtorque.so.2) , need
solve the symbol of tm_init, tm_spawn, tm_finalize and tm_poll.
I suggest you do only build torque and maui.
Add /opt/torque/lib to a new file in /etc/ld.so.conf.d/torque.conf and
run ldconfig.
and `apt-get install r-cran-rmpi openmpi-bin'.
I add the following to my cluster for torque,
$ cat torque.profile.sh
# /etc/profile.d/torque.sh
if [ -n "$PBS_ENVIRONMENT" ]; then
if [ "$PBS_ENVIRONMENT" = "PBS_BATCH" ] ; then
cd $PBS_O_WORKDIR
fi
fi
When I appointed plm_rsh_agent in the series of openmpi-1.8, I got
segmentation fault.
most recent version (openmpi1.8.4rc) and I'll be much better off.
2014-11-07 3:21 GMT+09:00 Alejandro Gonzalez <aleco.gt at gmail.com>:
Hello List, this is my first message but I've been using your help for a while, thank you. I have a cluster of Ubuntu 14.04 machines with OpenMPI and I'm not being able to install Rmpi. Here are some more specs of my system: - I installed from sources Torque 4.2.9 and Maui 3.3.1 - OpenMPI version is 1.8.2 (I installed this one from source too) - R version is 3.0.2 (This was installed with apt-get install) When I try to install Rmpi: $ sudo R CMD INSTALL Rmpi_0.6-3.tar.gz --configure-args="--with-mpi=/opt/openmpi" I get the following: --- * installing to library '/usr/local/lib/R/site-library' * installing *source* package 'Rmpi' ... checking for gcc... gcc -std=gnu99 checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc -std=gnu99 accepts -g... yes checking for gcc -std=gnu99 option to accept ISO C89... none needed Trying to find mpi.h ... Found in /opt/openmpi/include Trying to find libmpi.so or libmpich.a ... Found libmpi in /opt/openmpi/lib checking for orted... no configure: error: Cannot find orted. Rmpi needs orted to run. ERROR: configuration failed for package 'Rmpi' * removing '/usr/local/lib/R/site-library/Rmpi' --- I've read the Rmpi news, http://r.789695.n4.nabble.com/Problem-installing-Rmpi-with-Open-MPI-tt4641762.html#none and http://www.open-mpi.org/community/lists/devel/2012/04/10840.php and then tried to install Rmpi using a new build of OpenMPI, that I configured this way: $ ./configure --with-tm=/opt/torque --prefix=/opt/openmpi_disable_dlopen --disable-dlopen But I got the same error (configure: error: Cannot find orted. Rmpi needs orted to run.). Am I doing something wrong? Do you have a clue on how can I install Rmpi? I'd also want to understand more about what does --disable-dlopen mean, why it's necessary for Rmpi and what happens when I run other MPI software when OpenMPI has been configured with --disable-dlopen. May you share me some reading? Thanks in advance. Alejandro [[alternative HTML version deleted]]
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