On Wed, 2014-03-12 at 11:50 +0100, Reuti wrote: > 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
I believe I've already done that. The script the launches everything is (all one line originally) R_PROFILE_USER=~/KHC/sunbelt/Rmpiprofile \ LD_LIBRARY_PATH=/home/ross/install/lib:$LD_LIBRARY_PATH \ PATH=/home/ross/install/bin:$PATH orterun -x R_PROFILE_USER -x LD_LIBRARY_PATH -x PATH -hostfile ~/KHC/sunbelt/hosts \ -np 7 R --no-save -q There is a complication with R; it sticks stuff in front of LD_LIBRARY_PATH. However, the startup script Rmpiprofile fixes that, though I'm not entirely sure that is effective. However, the old libraries that are being loaded are not from any directories R added to LD_LIBRARY_PATH; instead they are from /usr/lib, which is a standard place for the dynamic loader to look. > > 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. > No batch system (see script above for launch mechanism). We threw a lot of stuff MPI configure was looking for onto the system. AFAIK torque isn't even installed. One possible issue is that the Rmpi module for R is not compiled by mpicc; R has its own notions of proper options for the compiler and its own infrastructure for building things. I did pass the location of my local libraries into the build process. This seems more like an issue with the dynamic loader, or with whatever system R is using when it loads Rmpi.so. Ross > -- 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 > > _______________________________________________ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users
