Am 12.03.2014 um 11:39 schrieb Jeff Squyres (jsquyres): > Generally, all you need to ensure that your personal copy of OMPI is used is > to set the PATH and LD_LIBRARY_PATH to point to your new Open MPI > installation. I do this all the time on my development cluster (where I have > something like 6 billion different installations of OMPI available... mmm... > should probably clean that up...) > > export LD_LIBRARY_PATH=path_to_my_ompi/lib:$LD_LIBRARY_PATH > export PATH=path-to-my-ompi/bin:$PATH > > It should be noted that: > > 1. you need to *prefix* your PATH and LD_LIBRARY_PATH with these values > 2. you need to set these values in a way that will be picked up on all > servers that you use in your job. The safest way to do this is in your shell > startup files (e.g., $HOME/.bashrc or whatever is relevant for your shell).
I see "libtorque" in the output below - were these jobs running inside a queuing system? The set paths might be different therein, and need to be set in the job script in this case. -- Reuti > See http://www.open-mpi.org/faq/?category=running#run-prereqs, > http://www.open-mpi.org/faq/?category=running#adding-ompi-to-path, and > http://www.open-mpi.org/faq/?category=running#mpirun-prefix. > > Note the --prefix option that is described in the 3rd FAQ item I cited -- > that can be a bit easier, too. > > > > On Mar 12, 2014, at 2:51 AM, Ross Boylan <r...@biostat.ucsf.edu> wrote: > >> I took the advice here and built a personal copy of the current openmpi, >> to see if the problems I was having with Rmpi were a result of the old >> version on the system. >> >> When I do ldd on the relevant libraries (Rmpi.so is loaded dynamically >> by R) everything looks fine; path references that should be local are. >> But when I run the program and do lsof it shows that both the system and >> personal versions of key libraries are opened. >> >> First, does anyone know which library will actually be used, or how to >> tell which library is actually used, in this situation. I'm running on >> linux (Debian squeeze)? >> >> Second, it there some way to prevent the wrong/old/sytem libraries from >> being loaded? >> >> FWIW I'm still seeing the old misbehavior when I run this way, but, as I >> said, I'm really not sure which libraries are being used. Since Rmpi >> was built against the new/local ones, I think the fact that it doesn't >> crash means I really am using the new ones. >> >> Here are highlights of lsof on the process running R: >> COMMAND PID USER FD TYPE DEVICE SIZE/OFF NODE NAME >> R 17634 ross cwd DIR 254,2 12288 150773764 >> /home/ross/KHC/sunbelt >> R 17634 ross rtd DIR 8,1 4096 2 / >> R 17634 ross txt REG 8,1 5648 3058294 >> /usr/lib/R/bin/exec/R >> R 17634 ross DEL REG 8,1 2416718 >> /tmp/openmpi-sessions-ross@n100_0/60429/1/shared_mem_pool.n100 >> R 17634 ross mem REG 8,1 335240 3105336 >> /usr/lib/openmpi/lib/libopen-pal.so.0.0.0 >> R 17634 ross mem REG 8,1 304576 3105337 >> /usr/lib/openmpi/lib/libopen-rte.so.0.0.0 >> R 17634 ross mem REG 8,1 679992 3105332 >> /usr/lib/openmpi/lib/libmpi.so.0.0.2 >> R 17634 ross mem REG 8,1 93936 2967826 >> /usr/lib/libz.so.1.2.3.4 >> R 17634 ross mem REG 8,1 10648 3187256 >> /lib/libutil-2.11.3.so >> R 17634 ross mem REG 8,1 32320 2359631 >> /usr/lib/libpciaccess.so.0.10.8 >> R 17634 ross mem REG 8,1 33368 2359338 >> /usr/lib/libnuma.so.1 >> R 17634 ross mem REG 254,2 979113 152045740 >> /home/ross/install/lib/libopen-pal.so.6.1.0 >> R 17634 ross mem REG 8,1 183456 2359592 >> /usr/lib/libtorque.so.2.0.0 >> R 17634 ross mem REG 254,2 1058125 152045781 >> /home/ross/install/lib/libopen-rte.so.7.0.0 >> R 17634 ross mem REG 8,1 49936 2359341 >> /usr/lib/libibverbs.so.1.0.0 >> R 17634 ross mem REG 254,2 2802579 152045867 >> /home/ross/install/lib/libmpi.so.1.3.0 >> R 17634 ross mem REG 254,2 106626 152046481 >> /home/ross/Rlib-3.0.1/Rmpi/libs/Rmpi.so >> >> So libmpi, libopen-pal, and libopen-rte all are opened in two versions and >> two locations. >> >> Thanks. >> Ross Boylan >> >> _______________________________________________ >> users mailing list >> us...@open-mpi.org >> http://www.open-mpi.org/mailman/listinfo.cgi/users > > > -- > Jeff Squyres > jsquy...@cisco.com > For corporate legal information go to: > http://www.cisco.com/web/about/doing_business/legal/cri/ > > _______________________________________________ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users
