Ralph,
Unfortunately I didn't see the ssh output. The output I got was pretty much as
before.
You know, the fact that the error message is not prefixed with a host name
makes me think it could be happening on the host where the job is placed by
PBS. If there is something wrong in the user environment prior to mpirun, that
is not an OpenMPI problem. And yet, in one of the jobs that failed, I have also
printed out the results of 'ldd' on the mpirun executable just prior to
executing the command, and all the shared libraries were resolved:
ldd /release/cfd/openmpi-intel/bin/mpirun
linux-vdso.so.1 => (0x00007fffbbb39000)
libopen-rte.so.0 => /release/cfd/openmpi-intel/lib/libopen-rte.so.0
(0x00002abdf75d2000)
libopen-pal.so.0 => /release/cfd/openmpi-intel/lib/libopen-pal.so.0
(0x00002abdf7887000)
libdl.so.2 => /lib64/libdl.so.2 (0x00002abdf7b39000)
libnsl.so.1 => /lib64/libnsl.so.1 (0x00002abdf7d3d000)
libutil.so.1 => /lib64/libutil.so.1 (0x00002abdf7f56000)
libm.so.6 => /lib64/libm.so.6 (0x00002abdf8159000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00002abdf83af000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00002abdf85c7000)
libc.so.6 => /lib64/libc.so.6 (0x00002abdf87e4000)
libimf.so => /appserv/intel/Compiler/11.1/072/lib/intel64/libimf.so
(0x00002abdf8b42000)
libsvml.so => /appserv/intel/Compiler/11.1/072/lib/intel64/libsvml.so
(0x00002abdf8ed7000)
libintlc.so.5 =>
/appserv/intel/Compiler/11.1/072/lib/intel64/libintlc.so.5 (0x00002abdf90ed000)
/lib64/ld-linux-x86-64.so.2 (0x00002abdf73b1000)
Hence my initial assumption that the shared-library problem was happening with
one of the child processes on a remote node.
So at this point I have more questions than answers. I still don't know if
this message comes from the main mpirun process or one of the child processes,
although it seems that it should not be the main process because of the output
of ldd above.
Any more suggestions are welcomed of course.
Thanks
/release/cfd/openmpi-intel/bin/mpirun --machinefile
/var/spool/PBS/aux/20804.maruhpc4-mgt -np 160 -x LD_LIBRARY_PATH -x
MPI_ENVIRONMENT=1 --mca plm_base_verbose 5 --leave-session-attached
/tmp/fv420804.maruhpc4-mgt/test_jsgl -v -cycles 10000 -ri restart.5000 -ro
/tmp/fv420804.maruhpc4-mgt/restart.5000
[c6n38:16219] mca:base:select:( plm) Querying component [rsh]
[c6n38:16219] mca:base:select:( plm) Query of component [rsh] set priority to
10
[c6n38:16219] mca:base:select:( plm) Selected component [rsh]
Warning: Permanently added 'c6n39' (RSA) to the list of known hosts.^M
Warning: Permanently added 'c6n40' (RSA) to the list of known hosts.^M
Warning: Permanently added 'c6n41' (RSA) to the list of known hosts.^M
Warning: Permanently added 'c6n42' (RSA) to the list of known hosts.^M
Warning: Permanently added 'c5n26' (RSA) to the list of known hosts.^M
Warning: Permanently added 'c3n20' (RSA) to the list of known hosts.^M
Warning: Permanently added 'c4n10' (RSA) to the list of known hosts.^M
Warning: Permanently added 'c4n40' (RSA) to the list of known hosts.^M
/release/cfd/openmpi-intel/bin/orted: error while loading shared libraries:
libimf.so: cannot open shared object file: No such file or directory
--------------------------------------------------------------------------
A daemon (pid 16227) died unexpectedly with status 127 while attempting
to launch so we are aborting.
There may be more information reported by the environment (see above).
This may be because the daemon was unable to find all the needed shared
libraries on the remote node. You may set your LD_LIBRARY_PATH to have the
location of the shared libraries on the remote nodes and this will
automatically be forwarded to the remote nodes.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun noticed that the job aborted, but has no info as to the process
that caused that situation.
--------------------------------------------------------------------------
Warning: Permanently added 'c3n27' (RSA) to the list of known hosts.^M
--------------------------------------------------------------------------
mpirun was unable to cleanly terminate the daemons on the nodes shown
below. Additional manual cleanup may be required - please refer to
the "orte-clean" tool for assistance.
--------------------------------------------------------------------------
c6n39 - daemon did not report back when launched
c6n40 - daemon did not report back when launched
c6n41 - daemon did not report back when launched
c6n42 - daemon did not report back when launched
From: users-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org] On Behalf
Of Ralph Castain
Sent: Friday, December 14, 2012 2:25 PM
To: Open MPI Users
Subject: EXTERNAL: Re: [OMPI users] Problems with shared libraries while
launching jobs
Add -mca plm_base_verbose 5 --leave-session-attached to the cmd line - that
will show the ssh command being used to start each orted.
On Dec 14, 2012, at 12:17 PM, "Blosch, Edwin L"
<edwin.l.blo...@lmco.com<mailto:edwin.l.blo...@lmco.com>> wrote:
I am having a weird problem launching cases with OpenMPI 1.4.3. It is most
likely a problem with a particular node of our cluster, as the jobs will run
fine on some submissions, but not other submissions. It seems to depend on the
node list. I just am having trouble diagnosing which node, and what is the
nature of the problem it has.
One or perhaps more of the orted are indicating they cannot find an Intel Math
library. The error is:
/release/cfd/openmpi-intel/bin/orted: error while loading shared libraries:
libimf.so: cannot open shared object file: No such file or directory
I've checked the environment just before launching mpirun, and LD_LIBRARY_PATH
includes the necessary component to point to where the Intel shared libraries
are located. Furthermore, my mpirun command line says to export the
LD_LIBRARY_PATH variable:
Executing ['/release/cfd/openmpi-intel/bin/mpirun', '--machinefile
/var/spool/PBS/aux/20761.maruhpc4-mgt', '-np 160', '-x LD_LIBRARY_PATH', '-x
MPI_ENVIRONMENT=1', '/tmp/fv420761.maruhpc4-mgt/falconv4_openmpi_jsgl', '-v',
'-cycles', '10000', '-ri', 'restart.1', '-ro',
'/tmp/fv420761.maruhpc4-mgt/restart.1']
My shell-initialization script (.bashrc) does not overwrite LD_LIBRARY_PATH.
OpenMPI is built explicitly --without-torque and should be using ssh to launch
the orted.
What options can I add to get more debugging of problems launching orted?
Thanks,
Ed
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