I remember having a conversation with someone from R at Supercomputing last year, and this was one of the issues we discussed. The problem is that you have to ensure that R is built against the OMPI you are going to use, and it is usually better to have configured OMPI --disable-dlopen --enable-static to avoid library confusion when you later run R.

I'd give that a try and see if it solves your problems. The "recipe" given by Bennet looked right to me.


On Mar 12, 2014, at 12:32 PM, Ross Boylan <ross@biostat.ucsf.edu> wrote:

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 <ross@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

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Jeff Squyres
jsquyres@cisco.com
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