Okay, just checking the obvious. :-)

We regularly run with the exact same configuration here (i.e., slurm + 16cpus/node) without problem on jobs that are both short and long, so it seems doubtful that it would be an OMPI bug. However, it is possible as the difference could be due to configuration and/or parameter settings. We have seen some site-specific problems that are easily resolved with parameter changes.

You might take a look at our (LANL's) platform files for our slurm-based system and see if they help. You will find them in the tarball at


Specifically, since you probably aren't running panasas (?), look at the optimized-nopanasas and optimized-nopanasas.conf (they are a pair) files to see how we configure the system for build, and the mca params we use to execute applications. If you can, I would suggest giving them a try (adjusting as required for your setup - e.g., you may want not want the -m64 flags) and see if it resolves the problem.


On Jul 17, 2009, at 7:15 AM, Steven Dale wrote:

I think it unlikely that its a time limit thing. Firstly, slurm is set up with no time limit on jobs, and we get the same behaviour whether or not slurm is in the picture.
In addition, we've run several other much larger jobs with a greater number of permutations and they complete fine.

This job takes about 5-10 minutes to run. We've run jobs that take a week or more and the indivdual R process can be seen to run for days at a time and they run fine.

In addition, I'd find it hard to believe (although I concede the possibility) that jobs entirely self-contained within the same box run slower that jobs which span 2 boxes over the network. (14 cpus vs 17 cpus for example).

Steve Dale
Senior Platform Analyst
Health Canada
Phone: (613)-948-4910
E-mail: steven_dale@hc-sc.gc.ca

Ralph Castain <rhc@open-mpi.org>
Sent by: users-bounces@open-mpi.org

07/17/2009 01:13 AM
Please respond to
Open MPI Users <users@open-mpi.org>

Open MPI Users <users@open-mpi.org>
Re: [OMPI users] Possible openmpi bug?

From what I can see, it looks like your job is being terminated - something is killing mpirun. Is it possible that the job runs slowly enough on 14 or less cpus that it simply isn't completing within your specified time limit?

The lifeline message simply indicates that a process self-aborted because it lost contact with its local daemon - in this case, mpirun (as that is always daemon 0) - which means that the daemon was terminated for some reason.

On Jul 16, 2009, at 11:15 AM, Steven Dale wrote:

Here is my situation:

2 Dell R900's with 16 cpus each and 64 GB RAM

OS: SuSE SLES 10 SP2 patched up to date

R version 2.9.1

Rmpi version 0.5-7

snow version 0.3-3

maanova library version 1.14.0

openmpi version 1.3.3

slurm version 2.0.3

With a given set of R code, we get abnormal exits when using 14 or less cpus. When using 15 or more, the job completes normally.
error is a variation on:

[pdp-dev-r01:22618] [[15549,1],0] routed:binomial: Connection to lifeline [[15549,0],0] lost

during the array permutations.

Increasing the number of permutations above 200 also produces similar results.

The R code is executed with a typical command line for 14 cpus being:

sbatch -n 14 -i ./Rtest.txt --mail-type=ALL
--mail-user=steven_dale@hc-sc.gc.ca /usr/local/bin/R --no-save

Config.log, ompi_info, Rscript.txt and slurm outputs are attached. Network is GB Ethernet copper tcp/ip.

I think this to be an openmpi error/bug due to the routed:binomial message. This also had the same results with openmpi-1.3.2, R 2.9.0, maanova 1.12 and slurm 2.0.1.

No non-default MCA parameters are set.


Configuration done with defaults.

Any ideas are welcome.

Steve Dale

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