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Subject: Re: [OMPI users] Possible openmpi bug?
From: Steven Dale (steven_dale_at_[hidden])
Date: 2009-07-17 09:15:54

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_at_[hidden]

Ralph Castain <rhc_at_[hidden]>
Sent by: users-bounces_at_[hidden]
07/17/2009 01:13 AM
Please respond to
Open MPI Users <users_at_[hidden]>

Open MPI Users <users_at_[hidden]>

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

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

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_at_[hidden] /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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