Perhaps there's an RPATH issue here? I don't fully understand the structure of Rmpi, but is there both an app and a library (or two separate libraries) that are linking against MPI?
I.e., what we want is:
app -----------------> ~ross/OMPI
--> library --
But what we're getting is:
app ---> /usr/OMPI
--> library ---> ~ross/OMPI
If one of them was first linked against the /usr/OMPI and managed to get an RPATH then it could override your LD_LIBRARY_PATH.
On Mar 12, 2014, at 5:39 AM, Jeff Squyres (jsquyres) <jsquyres_at_[hidden]> wrote:
> 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 <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
>> users mailing list
> Jeff Squyres
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