[R] Problem installing Rmpi with Open MPI

[Dirk Eddelbuettel]

On 31 August 2012 at 07:14, Linh Tran wrote:
| I took some time to think about it and don't know that it was the case 
| for me. If the openmpi-bin package was missing, I wouldn't have been 
| able to even use openmpi and during my trouble, I would check the mpi 
| software each time I installed it to verify that it worked (using some 
| simple example commands). Furthermore, I checked the parent folder after 
| each installation and saw non-empty bin folders in them each time. Did 
| the error code somehow point to that? It could have been that the 
| open-mpi bin package somehow installed itself during my troubleshooting.

Hao and I both arrived the conclusion that _loading_ Rmpi fails if
openmpi-bin is not installed. I attributed that to orterun, it is actually
orted which is used.  Which makes complete sense.

So to recap out experience: yes, one may manage to compile and link Rmpi, but
it will not run with orted.
 
| I also don't know whether it was the "enable-shared" option, the 
| "disable-dlopen" option, or both that helped me finally get Rmpi to 
| work. I could go back and uninstall everything to start over and 
| pinpoint it, though I don't think I can go through the frustration 
| again. Regardless, I hope that this information helps other users.

For Hao and myself, Rmpi works with stock Open MPI packages from Debian /
Ubuntu, which appears to contradict Brian Ripley's assertion that
disable-dlopen is a must. 
 
| Thank you very much Dirk and Brian for your help. And thank you Hao for 
| such a great job with the Rmpi package. As always, guys like you are 
| what make R so successful.

Seconded -- the Open MPI folks provide a great tool and it has been a
pleasure to support Rmpi in Debian/Ubuntu as Hao is a very responsive
upstream author who has written a tremendously useful package.

Dirk


| 
| 
| On 08/30/2012 11:02 AM, Dirk Eddelbuettel wrote:
| > On 29 August 2012 at 20:07, Linh Tran wrote:
| > | Thank you for the advice. I tried using the command, and it still
| > | wouldn't load.
| > |
| > | I tried uninstalling all of the MPI interfaces, reinstalled openmpi
| > | using the "--enabled-shared --disable-dlopen" command, and Rmpi was able
| > | to install sucessfully inside R.
| >
| > I just spent some time going over this, along with Prof Hao, the author of
| > Rmpi.  You may simply have been missing the openmpi-bin package which
| > provides tools like orterun -- Open MPI now needs this at startup.  This may
| > get added to configure tests in the future to alert users.
| >
| > With this openmpi-bin package installed, I could easily install Rmpi on
| > Debian and Ubuntu using the distro's Open MPI packages. No need for local
| > Open MPI builds.  Also note this post on the Open MPI list:
| >
| >     http://www.open-mpi.org/community/lists/devel/2012/04/10840.php
| >
| > Static builds may lead to loss of resources at runtime as you may have
| > multiple copies running.
| >   
| > | Thank you to Prof Ripley for pointing that out! I think it was shared
| > | and dlopen options that kept preventing me from succeeding.
| >
| > I believe this advise to be incorrect. We have been using dynamically linked
| > builds of Open MPI for several years on Debian with good success. I was
| > involved in an overhaul of Debian's Open MPI packages around 2006/2007; the
| > package has since been very well maintained by others.
| >
| > Dirk
| >   
| > | On 08/29/2012 01:40 PM, Dirk Eddelbuettel wrote:
| > | > On 29 August 2012 at 11:37, Linh Tran wrote:
| > | > | I've spent a few days trying to install Rmpi with no luck. I originally
| > | > | tried using mpich, moved on to mpich2, and then to openmpi. I've gotten
| > | > | the furthest with openmpi, though am still running into this problem and
| > | > | can't figure it out. Can someone help!? Thanks so much in advanced.
| > | > |
| > | > | I'm using an HP Envy laptop with Ubuntu 12.04. Output is below, with the
| > | > | error at the bottom.
| > | >
| > | > I suggest you do
| > | >
| > | >     sudo apt-get install r-cran-rmpi
| > | >
| > | > which installs the prebuild Rmpi as well as the Open MPI libary it depends upon.
| > | >
| > | > Dirk
| > | >
| > |
| >
| 

-- 
Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com