[R-sig-hpc] Error installing Rmpi over OpenMPI: Cannot find orted

[Alejandro Gonzalez]

Hello Eiji, thanks for your reply.

I tried your suggestion, but now when I try to run a simple MPI test on the
master node I get the following:
--------------------------------------------------------------------------
Open RTE was unable to open the hostfile:
    /etc/openmpi/openmpi-default-hostfile
Check to make sure the path and filename are correct.
--------------------------------------------------------------------------
[laicbio:60394] [[40538,0],0] ORTE_ERROR_LOG: Not found in file
base/ras_base_allocate.c at line 248
[laicbio:60394] [[40538,0],0] ORTE_ERROR_LOG: Not found in file
base/plm_base_launch_support.c at line 99
[laicbio:60394] [[40538,0],0] ORTE_ERROR_LOG: Not found in file
plm_rsh_module.c at line 1173

So I guess the new OpenMPI doesn't know about torque. How can I let it know
where torque is? I was guessing that the file /etc/ld.so.conf.d/torque.conf
was meant for that, but it's not working.

What is the file /etc/profile.d/torque.sh for?

Should I follow the same steps you mentioned in the slave nodes of the
cluster?

Kind regards.
Alejandro



2014-11-06 20:30 GMT-06:00 Ei-ji Nakama <nakama at ki.rim.or.jp>:

> 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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> > R-sig-hpc at r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-hpc
>
>
>
> --
> Best Regards,
> --
> Eiji NAKAMA <nakama (a) ki.rim.or.jp>
> "\u4e2d\u9593\u6804\u6cbb"  <nakama (a) ki.rim.or.jp>
>

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