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). 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/
