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.

LD_LIBRARY_PATH=/usr/local/lib.

Configuration done with defaults.

Any ideas are welcome.




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Steve Dale
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