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...)
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 <ross_at_[hidden]> 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_at_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.18.104.22.168
> 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.
> Ross Boylan
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