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 | e...@debian.org | http://dirk.eddelbuettel.com ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
