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Subject: [OMPI users] trying to use personal copy of 1.7.4
From: Ross Boylan (ross_at_[hidden])
Date: 2014-03-12 02:51:17


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.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